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A large number of chemicals are constantly introduced to surface water from anthropogenic and natural sources. Although substantial efforts have been made to identify these chemicals (e.g potentially anthropogenic contaminants) in surface waters using liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS), a large number of LC-HRMS chemical signals often with high peak intensity are left unidentified. In addition to synthetic chemicals and transformation products, these signals may also represent plant secondary metabolites (PSMs) released from vegetation through various pathways such as leaching, surface run-off and rain sewers or input of litter from vegetation. While this may be considered as a confounding factor in screening of water contaminants, it could also contribute to the cumulative toxic risk of water contamination. However, it is hardly known to what extent these metabolites contribute to the chemical mixture of surface waters. Thus, reducing the number of unknowns in water samples by identifying also PSMs in significant concentrations in surface waters will help to improve monitoring and assessment of water quality potentially impacted by complex mixtures of natural and synthetic compounds. Therefore, the main focus of the present study was to identify the occurrence of PSMs in river waters and explore the link between the presence of vegetation along rivers and detection of their corresponding PSMs in river
water.
In order to achieve the goals of the present thesis, two chemical screening approaches, namely, non-target and target screening using LC-HRMS were implemented. (1) Non-target analysis involving a novel approach has been applied to associate unknown peaks of high intensity in LC-HRMS to PSMs from surrounding vegetation by focusing on peaks overlapping between river water and aqueous plant extracts (Annex A1). (2) LC–HRMS target screening in river waters were performed for about 160 PSMs, which were selected from a large phytotoxin database (Annex A2 and A3) considering their expected abundance in the vegetation, their potential mobility, persistence and toxicity in the water cycle and commercial availability of standards.
In non-target screening (Annex A1), a high number of overlapping peaks has been found in between aqueous plant extracts and water from adjacent location, suggesting a significant impact of vegetation on chemical mixtures detectable in river waters. The chemical structures were assigned for 12 pairs of peaks while several pairs of peaks
whose MS/MS spectra matched but no structure suggestion were made by the implemented software tools for retrieving possible chemical structure. Nevertheless, the pairs of peaks with matching spectra represented the same chemical structure. The identified compound belonged to different compound classes such as coumarins, flavonoids besides others. For the identified PSMs individual concentration up to 5 µg/L were measured. The concentration and the number of detected PSMs per sample were correlated with the rain event and vegetation coverage.
Target screening unraveled the occurrence of 33 out of 160 target compounds in river waters (Annex A2 and A3). The identified compounds belonged to different classes such as alkaloids, coumarins, flavonoids, and other compounds. Individual compound concentrations were up to several thousand ng/L with the toxic alkaloids narciclasine and
lycorine recording highest maximum concentrations. The neurotoxic alkaloid coniine from poison hemlock was detected at concentrations up to 0.4 µg/L while simple coumarins
esculetin and fraxidin occurred at concentrations above 1 µg/L. The occurrence of some PSMs in river water were correlated to the specific vegetation growing along the rivers while the others were linked to a wide range of vegetation. As an example, narciclasine and lycorine was emitted by the dominant plant species from Amaryllidaceae family (e.g. Galanthus nivalis (snow drop), Leucojum vernum and Anemone nemorosa) while intermedine and echimidine were from Symphytum officinale. The ubiquitous occurrence of simple coumarins fraxidin, scopoletin and aesculetin could be linked to their presence in a wide range of vegetation.
Due to lack of aquatic toxicity data for the identified PSMs (in both target and non-target) and extremely scarce exposure data, no reliable risk assessment was possible.
Alternatively, risk estimation was performed using the threshold for toxicological concern (TTC) concept developed for drinking water contaminants. Many of the identified PSMs
exceeded the TTC value (0.1 µg/L) thus caution should be taken when using such surface waters for drinking water abstraction or recreational use.
This thesis provides an overview of the occurrence of PSMs in river water impacted by the massive presence of vegetation. Concentration for many of the identified PSMs are well within the range of those of synthetic environmental contaminants. Thus, this study adds to a series of recent results suggesting that possibly toxic PSMs occur in relevant concentrations in European surface waters and should be considered in monitoring and risk assessment of water resources. Aquatic toxicity data for PSMs are extensively lacking but are required to include these compounds in the assessment of risks to aquatic organisms and for eliminating risks to human health during drinking water production.
This thesis is concerned with protein structures determined by nuclear magnetic resonance (NMR), and the text focuses on their analysis in terms of accuracy, gauged by the correspondence between the structural model and the experimental data it was calculated from, and in terms of precision, i.e. the degree of uncertainty of the atomic positions. Additionally, two protein structure calculation projects are described...
Movement of the Rieske domain of the iron–sulfur protein is essential for intramolecular electron transfer within complex III2 (CIII2) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII2 from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII2 with a reduced high-potential chain increased the occupancy of the Qo site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c1 subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c1 than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd1-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
The yeast fatty acid synthase (FAS) is a barrel-shaped 2.6 MDa complex. Upon barrel-formation, two multidomain subunits, each more than 200 kDa large, intertwine to form a heterododecameric complex that buries 170,000 Å2 of protein surface. In spite of the rich knowledge about yeast FAS in structure and function, its assembly remained elusive until recently, when co-translational interaction of the β-subunit with the nascent α-subunit was found to initiate assembly. Here, we characterize the co-translational assembly of yeast FAS at a molecular level. We show that the co-translationally formed interface is sensitive to subtle perturbations, so that the exchange of two amino acids located in the emerging interface can prevent assembly. On the other hand, assembly can also be initiated via the co-translational interaction of the subunits at other sites, which implies that this process is not strictly site or sequence specific. We further highlight additional steps in the biogenesis of yeast FAS, as the formation of a dimeric subunit that orchestrates complex formation and acts as platform for post-translational phosphopantetheinylation. The presented data supports the understanding of the recently discovered prevalence of eukaryotic complexes for co-translational assembly, and is valuable for further harnessing FAS in the biotechnological production of aliphatic compounds.
Due to recent technical developments, it became evident that the mammalian transcriptome is much more complex than originally expected. Alternative splicing(AS) and the transcription of long non-coding RNAs (lncRNAs) are two phenomenas which have been greatly underestimated in their frequency. Nowadays it is accepted that almost every gene has at least one alternative isoform and the number of lncRNAs exceeds the one of protein-coding genes.
We built user-friendly web interfaces which can process Affymetrix GeneChip Exon 1.0 ST Arrays (exon arrays) and GeneChip Gene 1.0 ST Arrays (gene arrays)for the analysis of alternative splicing events. Results are presented with detailed annotation information and graphics to identify splice events and to facilitate biological validations. Based on two studies using exon arrays, we show how our tools were used to profile genome-wide splicing changes under silencing of Jmjd6 and under hypoxic conditions. Since gene arrays are not intended for AS analysis originally, we demonstrated their applicability by profiling alternative splicing events during embryonic heart development.
To measure lncRNAs expressions with exon arrays, we completely re-annotation all probes and built a lncRNA specific annotation. To demonstrate the applicability of exon arrays in combination with our annotation, we profiled the expression of tens of thousands of lncRNAs. Further, our custom annotation allows for a detailed inspection of lncRNAs and to distinguish between isoforms, as we validated by RTPCR.
To allow for a general usage to the research community, we integrated the annotation in an easy-to-use web interface, which provides various helpful features for the analysis of lncRNAs.
RNA modifications are widespread in the RNA world. Nevertheless, their functions remain enigmatic. Recent analysis in tRNAs, mRNAs and rRNAs have revealed that apart from enriching their topological potential, these chemical modifications provide an added significant regulatory level to gene expression...
5‐Lipoxygenase (5‐LO) is the initial enzyme in the biosynthesis of leukotrienes, which are mediators involved in pathophysiological conditions such as asthma and certain cancer types. Knowledge of proteins involved in 5‐LO pathway regulation, including gene regulatory proteins, is needed to evaluate all options for therapeutic intervention in these diseases. Here, we present a mass spectrometric screening of ALOX5 promoter‐interacting proteins, obtained by DNA pulldown and label‐free quantitative mass spectrometry. Protein preparations from myeloid and B‐lymphocytic cell lines were screened for promoter DNA interactors. Through statistical analysis, 66 proteins were identified as specific ALOX5 promotor binding proteins. Among those, the 15 most likely candidates for a prominent role in ALOX5 gene regulation are the known ALOX5 interactors Sp1 and Sp3, the related factor Sp2, two Krüppel‐like factors (KLF13 and KLF16) and six other zinc finger proteins (MAZ, PRDM10, VEZF1, ZBTB7A, ZNF281 and ZNF579). Intriguingly, we also identified two helicases (BLM and DHX36) and the proteins hnRNPD and hnRNPK, which are, together with the protein MAZ, known to interact with DNA G‐quadruplex structures. As G‐quadruplexes are implicated in gene regulation, spectroscopic and antibody‐based methods were used to confirm their presence within the GC‐rich sequence of the ALOX5 promoter. In summary, we have systematically characterized the interactome of the ALOX5 promoter, identifying several zinc finger proteins as novel potential ALOX5 gene regulators. Further, we have shown that the ALOX5 promoter can form DNA G‐quadruplex structures, which may play a functional role in ALOX5 gene regulation.
Analysis of coding principles in the olfactory system and their application in cheminformatics
(2007)
Unser Geruchssinn vermittelt uns die Wahrnehmung der chemischen Welt. Im Laufe der Evolution haben sich in unserem olfaktorischen System Mechanismen entwickelt, die wahrscheinlich optimal auf die Erfüllung dieser Aufgabe angepasst sind. Die Analyse dieser Verarbeitungsstrategien verspricht Einblicke in effiziente Algorithmen für die Kodierung und Verarbeitung chemischer Information, deren Entwicklung und Anwendung dem Kern der Chemieinformatik entspricht. In dieser Arbeit nähern wir uns der Entschlüsselung dieser Mechanismen durch die rechnerische Modellierung von funktionellen Einheiten des olfaktorischen Systems. Hierbei verfolgten wir einen interdisziplinären Ansatz, der die Gebiete der Chemie, der Neurobiologie und des maschinellen Lernens mit einbezieht.
The TATA Box Binding Protein (TBP) is a 20 kD protein that is essential and universally conserved in eucarya and archaea. Especially among archaea, organisms can be found that live below 0°C as well as organisms that grow above 100°C. The archaeal TBPs show a high sequence identity and a similar structure consisting of α-helices and β-sheets that are arranged in a saddle-shape 2-symmetric fold. In previous studies, we have characterized the thermal stability of thermophilic and mesophilic archaeal TBPs by infrared spectroscopy and showed the correlation between the transition temperature (Tm) and the optimal growth temperature (OGT) of the respective donor organism. In this study, a “new” mutant TBP has been constructed, produced, purified and analyzed for a deeper understanding of the molecular mechanisms of thermoadaptation. The β-sheet part of the mutant consists of the TBP from Methanothermobacter thermoautotrophicus (OGT 65°C, MtTBP65) whose α-helices have been exchanged by those of Methanosarcina mazei (OGT 37°C, MmTBP37). The Hybrid-TBP irreversibly aggregates after thermal unfolding just like MmTBP37 and MtTBP65, but the Tm lies between that of MmTBP37 and MtTBP65 indicating that the interaction between the α-helical and β-sheet part of the TBP is crucial for the thermal stability. The temperature stability is probably encoded in the variable α-helices that interact with the highly conserved and DNA binding β-sheets.
Fas Ligand (FasL; CD95L; CD178; TNSF6) is a 40 kDa glycosylated type II transmembrane protein with 279 aa in mice and 281 aa in humans that belongs to the tumor necrosis factor (TNF) family. The extracellular domain (ECD) harbors a TNF homology domain, the receptor binding site, a motif for self assembly and trimerization, and several putative N-glycosylation and a metalloprotease cleavage site/s. The cytoplasmic tail of FasL is the longest of all TNFL family members and contains several conserved signaling motifs, such as a putative tandem Casein kinase I phosphorylation site, a unique proline-rich domain (PRD) and phosphorylatable tyrosine residues (Y7 in mice; Y7, Y9, Y13 in human). The FasL/Fas system is renowned for the potent induction of apoptosis in the receptor-bearing cell and is especially important for immune system functions. It is involved in the killing of target cells by natural killer (NK) and cytotoxic T cells, in the (self) elimination of effector cells following the proliferative phase of an immune response (activation-induced cell death; AICD), in the maintenance of immuneprivileged sites and in the induction and maintenance of peripheral tolerance. Owing to its potent pro-apoptotic signaling capacity and important functions, FasL expression and activity are tightly regulated at transcriptional and posttranscriptional levels and restricted to few cell types, such as immune effector cells and cells of immune-privileged sites. In contrast, Fas is expressed in a variety of tissues including lymphoid tissues, liver, heart, kidney, pancreas, brain and ovary. In addition to its pro-apoptotic function, the FasL/Fas system can also elicit nonapoptotic signals in the receptor-expressing cell. Among others, Fas-signaling exerts co-stimulatory functions in the immune system, e.g. by promoting survival, activation and proliferation of T cells. Besides the capacity to deliver a signal into receptor-bearing cells (‘forward signal’), FasL can receive and transmit signals into the ligand-expressing cell. This phenomenon has been described for several TNF family ligands and is known as ‘reverse signaling’. The first evidence for the existence of reverse signaling into FasL-bearing cells stems from two studies that demonstrated either co-stimulation of murine CD8+ T cell lines by FasL cross-linking or inhibition of activation-induced proliferation of murine CD4+ T cells. In both cases, the observed changes of proliferative behaviour critically depended on the presence of a signaling-competent FasL. Almost certainly, the FasL ICD is functionally involved in signal-transmission: (i) The ICD is highly conserved across species and harbors several signaling motifs, most notably a unique PRD. (ii) Numerous proteins have been identified which interact with the FasL PRD via their SH3 or WW domains and regulate various aspects of FasL biology, such as FasL sorting, storage, cell surface expression and the linkage of FasL to intracellular signaling pathways. (iii) Post-translational modifications of the ICD have been implicated in the sorting of FasL to vesicles and the FasL-dependent activation of Nuclear factor of activated T cells (NFAT). (iv) Proteolytic processing of FasL liberates the ICD and allows its translocation into the nucleus where it might influence gene transcription. (v) It could be shown that overexpression of the FasL ICD is sufficient to initiate reverse signaling upon concomitant T cell receptor (TCR) stimulation and ICD cross-linking. Conflicting data on the consequences of FasL reverse signaling exist, and costimulatory as well as inhibitory functions have been reported. These discrepancies probably reflect the use of artificial experimental systems. Neither the precise molecular mechanism underlying FasL reverse signaling, nor its physiological relevance have been addressed at the endogenous protein level in vivo. Therefore, a ‘knockout/knockin’ mouse model in which wildtype FasL was replaced with a deletion mutant lacking the intracellular portion (FasL Delta Intra) was established in the group of PD Dr. Martin Zörnig. In the present study, FasL Delta Intra mice were phenotypically characterized and were employed to investigate the physiological consequences of FasL reverse signaling at the molecular and cellular level. To ensure that FasL Delta Intra mice represent a suitable model to study the consequences of FasL reverse signaling, we demonstrated that activated lymphocytes from homozygous FasL Delta Intra or wildtype mice express comparable amounts of (truncated) FasL at the cell surface. The truncated protein retains the capacity to induce apoptosis in Fas receptor-positive target cells, as co-culture assays with FasL-expressing activated lymphocytes and Fas-sensitive target cells showed. Additionally, systematic screening of unchallenged mice did not reveal any phenotypic abnormalities. Notably, signs of a lymphoproliferative autoimmune disease associated with FasL-deficiency could not be detected. As several reports have implicated FasL reverse signaling in the regulation of T cell expansion and activation, proliferation of lymphocytes isolated from FasL Delta Intra and wildtype mice in response to antigen receptor stimulation was investigated. Using CFSE dilution assays it could be demonstrated that the proliferative response of CD4+ T cells, CD8+ T cells and of B cells was enhanced in the absence of the FasL ICD. Interestingly, this effect was most pronounced in B cells and could only be detected in CD4+ T cells after depletion of CD4+CD25+ regulatory T cells. To our Summary knowledge, this is the first time that FasL reverse signaling has been demonstrated in B cells. In a series of experiments, the activation of several pathways that are known to play important roles in signal-transmission initiated upon antigen receptor triggering was assessed. As a molecular correlate for the observed enhancement of activation-induced proliferation, Extracellular signal regulated kinase (ERK1/2) phosphorylation was significantly increased in FasL Delta Intra mice following antigen receptor crosslinking. Surprisingly, B cell stimulation lead to a comparable extent of activating phosphorylations on S38 in c-Raf and S218/S222 in MEK1/2 in cells isolated from wildtype and FasL Delta Intra mice, indicating that Mitogen activated protein kinases (MAPKs) upstream of ERK1/2 (Raf-1 and MEK1/2) apparently do not contribute to the differential regulation of ERK1/2. Experiments in which activation-induced Akt phosphorylation (S473) was quantified also did not suggest a participation of Phosphoinositol specific kinase 3 (PI3K)/Akt signals in this process. Instead, further characterization of the upstream pathway revealed an involvement of Phospholipase C gamma (PLC gamma) and Protein kinase C (PKC) signals in FasL-dependent ERK1/2- regulation. Previous studies in our group revealed a Notch-like processing of FasL, resulting in the transcriptional regulation of a reporter gene. Furthermore, an interaction of the FasL ICD with the transcription factor Lymphoid-enhancer binding factor-1 (Lef-1) that affected Lef-1-dependent reporter gene transcription could be demonstrated. Therefore, a molecular analysis of activated lymphocytes was performed to identify FasL reverse signaling target genes. The differential expression of promising candidates was verified by quantitative real-time PCR (qRT-PCR), which showed that the transcription of genes associated with lymphocyte proliferation and activation was increased in FasL Delta Intra mice compared to wildtype mice. Interestingly, an extensive regulation of Lef-1-dependent Wnt/beta-Catenin signalingrelated genes was found. Lef-1 mRNA (RT-PCR) and protein (intracellular FACS staining) could be detected in mature B cells, suggesting the possibility of FasL ICD-mediated inhibition of Lef-1-dependent gene expression in these cells, initiated by Notch-like processing of FasL. To investigate the consequences of FasL reverse signaling in vivo, a potential participation of the FasL ICD in the regulation of immune responses upon various challenges was analyzed. In experiments in which thymocyte proliferation or the expansion of antigen-specific T cells following a challenge with the superantigen Staphylococcus enterotoxin B (SEB), with Lymphocytic choriomeningitis virus (LCMV) or with Listeria monocytogenes were investigated, comparable results were obtained with wildtype and FasL Delta Intra mice. Likewise, the recruitment of neutrophils in a thioglycollate-induced model of peritonitis was not affected by deletion of the FasL ICD. These findings might reflect regulatory mechanisms operating in vivo, such as control exerted by regulatory T cells. Along these lines, proliferative differences in CD4+ T cells could only be detected ex vivo after depletion of CD4+CD25+ regulatory T cells. Furthermore, several in vitro studies indicate that retrograde FasL signals can be observed under conditions of suboptimal lymphocyte stimulation, but not when the TCR is optimally stimulated. Therefore, the potent initiation of antigen receptor signaling by stimuli like SEB or LCMV might have masked inhibitory FasL reverse signaling in these experiments. In agreement with the observed hyperactivation of lymphocytes in the absence of the ICD ex vivo, the increase in germinal center B cells (GCs) following immunization with the hapten 3-hydroxy 4-nitrophenylacetyl (NP) and the number of antibody-secreting PCs was significantly higher in FasL Delta Intra mice. The larger quantity of PCs correlated with increased titers of NP-binding, i.e. antigen-specific, IgM and IgG1 antibodies in the serum of FasL Delta Intra mice after immunization. These data suggest that FasL reverse signaling exerts immunmodulatory functions. Supporting this notion, a model of Ovalbumin-induced allergic airway inflammation revealed an involvement of retrograde FasL-signals in the recruitment of immune effector cells into the lung and in the activation of T cells following exposure of mice to Ovalbumin. Together, our ex vivo and in vivo findings based on endogenous FasL protein levels demonstrate that FasL ICD-mediated reverse signaling is a negative modulator of certain immune responses. It is tempting to speculate that FasL reverse signaling might be a fine-tuning mechanism to prevent autoimmune diseases, a theory which will be tested in adequate mouse models in the future.
Ribosome biogenesis is best understood in the yeast Saccharomyces cerevisiae. In human or mammalian ribosome biogenesis, it has been shown that basic principles are conserved to yeast, but additional features have been reported. Our understanding about the interplay between proteins and RNA in human ribosome biogenesis is far from complete.
The present study focused on the analysis of the human ribosome biogenesis co-factors PWP2, EMG1 and Exportin 5 (XPO5) to understand the degree of conservation of ribosome biogenesis. The proteins were characterized in respect to their localization and interaction partners. For the early 90S co-factor, PWP2, it was possible to pull down and identify the human UTP-B complex with MALDI mass spectrometry. Besides the orthologues of the members of this complex known in yeast (TBL3, WDR3, WDR36, UTP6, UTP18), the human UTP-B complex is not only conserved from yeast to humans, but contains also additional components, like the DEAD-box RNA helicase DDX21, which lacks a yeast orthologue. DDX21 was localized to the nucleus, assembled to the native UTP-B complex and co-precipitated also with other UTP-B complex members, presumably extending the functions of this complex in ribosome biogenesis.
This phenomenon was also observed for the 90S co-factor EMG1, an RNA methyltransferase, whose mutant form causes the Bowen-Conradi syndrome, if aspartic acid is mutated to glycine at position 86. This study revealed that the mutant, EMG1-D86G, clearly lost its nucleolar localization and co-precipitated to histones for unknown reasons.
A participation of the nuclear export receptor XPO5 in human ribosome biogenesis was shown in this study. Pulldown analysis, sucrose density gradients and UV crosslinking and analysis of cDNAs of XPO5 revealed the involvement of XPO5 in pre-60S subunit maturation. Moreover, besides the known pre-miRNAs and tRNAs as substrates for nuclear export, XPO5 crosslinked to snoRNAs. XPO5 was further demonstrated to interact with the miRNA Let-7a, which has an important regulatory function for MYC, a transcription factor required for ribosome biogenesis.
All results support a role of these proteins in human ribosome biogenesis and therefore it seems that the biogenesis of ribosomes in human cells requires additional components, like DDX21 and XPO5.
Fossils are often anatomically and functionally compared to extant model taxa such as Pan, Gorilla, Pongo and modern Homo sapiens to put the respective fossils into the (taxonomical) context of human evolution. Therefore, knowledge of extant hominid anatomy is necessary as well as knowledge of which traits differ between sexes, populations, (sub-)species and taxa, and whether these differences are pronounced enough to separate respective groups. Dental and mandibular structures have been of particular interest in many paleoanthropological studies, simply due to the fact that these morphological structures are most abundant in the human fossil record.
Various studies have addressed questions regarding taxonomy, variation and sexual dimorphism of hominid taxa with regard to dental and mandibular size. Tooth size, however, has almost exclusively referred to crown size, with little focus on root size. The focus on tooth crowns is partly due to roots being embedded in mandibular bone which makes access difficult. With the help of micro-computed tomography (μCT) it is now possible to render virtual 3D models of dental roots and measure these models without harming the original specimens. In addition, measurements are much more precise using μCT data than previous techniques such as 2D x-rays. The present study used 3D models of 231 (first, second and third) molars and 80 mandibles of 53 Pan troglodytes verus (consisting of individuals form the Tai and Liberia populations), 14 Gorilla sp. and 13 Pongo sp. individuals to investigate molar and mandibular sizes within, and between, taxa and populations with regard to sexual dimorphism, variability and taxonomical value. Molar root size was assessed by applying 7 measurements to each molar. Mandibular size was investigated using three different measurements: overall mandibular size, mandibular robusticity (at each molar position) and 15 linear measurements. Overall mandibular size and root measurements were used to investigate the dental and mandibular size relationship. Furthermore, based on data acquired from great apes, how well fossil mandibles (including their dentition) of Australopithecus africanus, Paranthropus sp. and Homo sp. match one or multiple extant hominid taxa was examined Overall, molar root and mandibular metrics are suitable to differentiate between sexes, populations and taxa. Investigation of 40 (21 molar and 19 mandibular) different measure ments resulted in five common characteristics among Pan, Gorilla and Pongo only: firstly, molar root size sequence in root volume and root surface area (M3 < M1 < M2). Secondly, M2 as the molar with the largest cervical area, root volume, root surface area and mesial root lengths and thirdly, mandibular robusticity is larger in females than in males, yet the difference is not signifficant. Fourthly, mandibular length and premolar width are sexually dimorphic and fifthly, the best factors to discriminate between taxa are bicondyle width and molar root length. There is no generalized answer to the question which molar and/or measurement (dental or mandibular) is best to discriminate between sex or taxa in extant hominids. Moreover, size relationships differ among taxa, depending on the measurement. The overall trend, however, is that Pan is the taxa with the smallest, and Gorilla the largest, mean values. Among Pan populations, Liberian chimpanzees tend to have larger average values compared to Tai chimpanzees, with the exception of mandibular robusticity. The highest percentage of sexual dimorphic measurements is found in Pongo, yet only half of the measurements are statistically different between sexes. African apes are less sexually dimorphic compared to Pongo, and surprisingly, Gorilla is only slightly more dimorphic than Pan. The study also shows that statements and conclusions relating to \mandibular size" should not be generalized: whereas male and female Pongo do not differ significantly in overall mandibular size, they do differ in linear mandibular measurements. Moreover, Gorilla has the overall largest mandible, yet robusticity is higher in Pan, as are some linear measurements. Sexual dimorphism in overall mandibular size does not seem to reflect body mass dimorphism, whereas mandibular size appears to be related to body mass. The same was previously proposed for mandibular robusticity, yet Pan, the smallest taxa, has the most robust mandibular corpus (> Gorilla > Pongo). A substantial amount of molar measurements that positively correlate with (overall) mandibular size was found, but in African apes only. This contrasts with former studies which found no, or weak, correlations between dental and mandibular sizes. Given that the percentage of correlation is highest in Pan, and not present in Pongo, it is proposed that small jaws feature small teeth, rather than large jaws feature large teeth. This proposition assumes a size-threshold from which, when reached, dental and mandibular sizes no longer correlate, as has been previously proposed for the relationship between canine size and mandibular breadth. This assumption is further supported by the fact that the smaller and more robust Tai population shows more significant correlation compared to the less robust and larger Liberia population. Results show that fossil metrics are similar to one or multiple extant hominid taxa, depending on the measurement (dental or mandibular) used for comparison. Subsequently, the assignment to a specific sex depends on the earlier selected extant model taxa. Therefore the study questions whether choosing one model taxa for one fossil, or taxonomical group, is advisable. This study is the first to extensively investigate molar root size in extant hominids and to broadly describe differences in molar root sizes among and between taxa and therefore provides a solid database for future studies. The same applies to mandibular robusticity which has not been investigated as systematically or to such a great extent as in this work. The study specifically shows how complex the search for taxa or sex differentiating molar root and/or mandibular measurements is. Subsequently it shows that generalizations in relation to taxonomical values and statements about sexual dimorphism can be misleading.
In addition, the study contributes to the understanding of intra- and inter-population differences within Pan torglodytes verus. Furthermore, it could be demonstrated that results of a subspecies sample very likely depend on the sample composition, i.e. whether the sample consists of individuals from one or more populations. This study serves as a database for further studies investigating molar root sizes in great apes, whether these studies are investigating various relationships between taxa, population or sex, or as database to investigate functional adaptations or to examine mandibular robusticity and molar root relationships.
Aphids annually infest winter wheat, Triticum aestivum L., in late spring and early summer in Central Europe, but densities leading to strong yield losses are reached only occasionally (Basedow et al., 1994). Three aphid species, Sitobion avenae Fabr., Metopolophium dirhodum Walk. and R. padi L., usually occur in cereal crops with increasing densities from late spring onwards (Basedow et al., 1994). Modelling population levels of cereal aphids is a key tool in integrated pest management for winter wheat. Over the last 30 years, considerable efforts have been made to investigate the population dynamics of aphids (DeWit and Rabbinge, 1979; Entwistle and Dixon, 1987). In Central Europe to date, two models have attained greater importance in late spring: LAUS (Friesland, 1986) and GETLAUS01 (Gosselke et al., 2001). The first one estimates the population level of S. avenae in spring in winter wheat fields and has obtained regional significance in practical plant protection. In contrast, the model GETLAUS01 is a scientific model, not designed for practical plant protection. It describes in great detail the population dynamics of S. avenae, R. padi and M. dirhodum. Both models have been improved over time and extended with several factors, e.g. by including the effects of antagonists, fertilisation, crop density, plant protection agents and meteorological parameters on population development. The objective of this study was to analyse the following three factors in terms of their impact on population and migration characteristics: cultivar, proximity between winter and summer hosts and migration (according to meteorological parameters).
Rhythmic changes in environmental lighting conditions have ever been the most reliable environmental cue for life on earth. Nature has therefore selected a genetically encrypted endogenous clock very early in evolution, as it provided cells and subsequently organisms with the ability to anticipate persevering periods of light and darkness. Rhythm generation within the mammalian circadian system is achieved by clock genes and their protein products. The mammalian endogenous master clock, which synchronizes the body to environmental time, is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. As an integral part of the time-coding system, the pineal gland serves the need to tune the body to the temporal environment by the rhythmic nocturnal synthesis and immediate release of the hormone melatonin. In contrast to the transcriptional regulation of melatonin synthesis in rodents, a post-translational shaping is indicated in the human pineal gland. Another important mediator of circadian time and seasonality to the body is the pituitary gland. The aim of this work was to elucidate regulation of melatonin synthesis in the human pineal gland. Furthermore, presence and regulation of clock genes in the human pineal and pituitary gland, and in the SCN were analyzed. Therefore, human tissue, taken from regular autopsies, was analyzed simultaneously for different parameters involved in melatonin biosynthesis and circadian rhythm generation. Presented data demonstrate that post-mortem brain tissue can be used to detect the remnant profile of pre-mortem adaptive changes in neuronal activity. In particular, our results give strong experimental support for the idea that transcriptional mechanisms are not dominant for the generation of rhythmic melatonin synthesis in the human pineal gland. Together with data obtained for clock genes and their protein products in the pituitary, data presented here offer 1) a new working hypothesis for post-translational regulation of melatonin biosynthesis in the human pineal gland, and 2) a novel twist in the molecular competence of clock gene proteins, achieved by nucleo-cytoplasmic shuttling in neuronal and neuroendocrine human tissue. Furthermore, in this study, oscillations in abundance of clock gene proteins were demonstrated for the first time in the human SCN.
Mutants of Anacystis R2 with different amino acid exchanges in positions 255 and/or 264 in copy I of the psbA gene, leading to different tolerances to DCMU-type herbicides, are com- pared with the respective wild type concerning pigmentation and incorporation of 35S into the D1 protein upon growth in the presence of [35S]methionine. All mutants have shade-type appearance compared to the wild type, although to different extents depending on site and mode of the amino acid exchange in the D1 protein. Except for 3 mutants, there is no correlation between shade-type appearance on one hand and resistance towards a certain inhibitor on the other hand.
Not only the molar ratio of phycocyanin (PC) to chlorophyll (Chi) is higher in all mutants compared to the respective wild type, but also the rate of synthesis of the D1 protein. On the background of different levels of total 35S incorporation within 18 min, D1 synthesis can be related to shade adaptation. Degradation of the D1 protein remains to be thoroughly studied in this context.
No reproducible differences in whole chain electron transport were observed between mutants and wild type.
Background The EGF receptor has been shown to internalize via clathrin-independent endocytosis (CIE) in a ligand concentration dependent manner. From a modeling point of view, this resembles an ultrasensitive response, which is the ability of signaling networks to suppress a response for low input values and to increase to a pre-defined level for inputs exceeding a certain threshold. Several mechanisms to generate this behaviour have been described theoretically, the underlying assumptions of which, however, have not been experimentally demonstrated for the EGF receptor internalization network. Results Here, we present a mathematical model of receptor sorting into alternative pathways that explains the EGF-concentration dependent response of CIE. The described mechanism involves a saturation effect of the dominant clathrin-dependent endocytosis pathway and implies distinct steady-states into which the system is forced for low vs high EGF stimulations. The model is minimal since no experimentally unjustified reactions or parameter assumptions are imposed. We demonstrate the robustness of the sorting effect for large parameter variations and give an analytic derivation for alternative steady-states that are reached. Further, we describe extensibility of the model to more than two pathways which might play a role in contexts other than receptor internalization. Conclusions Our main result is that a scenario where different endocytosis routes consume the same form of receptor corroborates the observation of a clear-cut, stimulus dependent sorting. This is especially important since a receptor modification discriminating between the pathways has not been found. The model is not restricted to EGF receptor internalization and might account for ultrasensitivity in other cellular contexts.
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited disturbance of the heart rhythm (arrhythmia) that is induced by stress or that occurs during exercise. Most mutations that have been linked to CPVT are found in two genes, i.e., ryanodine receptor 2 (RyR2) and calsequestrin 2 (CASQ2), two proteins fundamentally involved in the regulation of intracellular Ca2+ in cardiac myocytes. We inserted six CPVT-causing mutations via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 into unc-68 and csq-1, the Caenorhabditis elegans homologs of RyR and CASQ, respectively. We characterized those mutations via video-microscopy, electrophysiology, and calcium imaging in our previously established optogenetic arrhythmia model. In this study, we additionally enabled high(er) throughput recordings of intact animals by combining optogenetic stimulation with a microfluidic chip system. Whereas only minor/no pump deficiency of the pharynx was observed at baseline, three mutations of UNC-68 (S2378L, P2460S, Q4623R; RyR2-S2246L, -P2328S, -Q4201R) reduced the ability of the organ to follow 4 Hz optogenetic stimulation. One mutation (Q4623R) was accompanied by a strong reduction of maximal pump rate. In addition, S2378L and Q4623R evoked an altered calcium handling during optogenetic stimulation. The 1,4-benzothiazepine S107, which is suggested to stabilize RyR2 channels by enhancing the binding of calstabin2, reversed the reduction of pumping ability in a mutation-specific fashion. However, this depends on the presence of FKB-2, a C. elegans calstabin2 homolog, indicating the involvement of calstabin2 in the disease-causing mechanisms of the respective mutations. In conclusion, we showed for three CPVT-like mutations in C. elegans RyR a reduced pumping ability upon light stimulation, i.e., an arrhythmia-like phenotype, that can be reversed in two cases by the benzothiazepine S107 and that depends on stabilization via FKB-2. The genetically amenable nematode in combination with optogenetics and high(er) throughput recordings is a promising straightforward system for the investigation of RyR mutations and the selection of mutation-specific drugs.
Signal transducer and activator of transcription 6 (STAT6) regulates transcriptional activation in response to interleukin-4 (IL-4)-induced tyrosine phosphorylation by direct interaction with coactivators. The CREB-binding protein and the nuclear coactivator 1 (NCoA-1), a member of the p160/steroid receptor coactivator family, bind independently to specific regions of STAT6 and act as coactivators. In this study we show that an LXXLL motif in the STAT6 transactivation domain mediates the interaction with NCoA-1. Peptides representing this motif as well as antibodies generated against this motif inhibited STAT6/NCoA-1 interaction in glutathione S-transferase pulldown assays. Peptides derived from the STAT6 transactivation domain adjacent to the LXXLL motif as well as antibodies against these peptides showed no inhibitory effect. Mutagenesis of the LXXLL motif eliminated the STAT6/NCoA-1 interaction in vitro and in vivo, supporting the specific role of this motif in NCoA-1 binding. Importantly, mutagenesis of the STAT-LXXLL motif strongly diminished the IL-4-regulated activation of the endogenous STAT6 target gene eotaxin-3. Taken together, these results indicate that the STAT6-LXXLL-binding motif mediates the interaction with NCoA-1 in transcriptional activation and represents a new potential drug target for the inhibition of the STAT6 transactivation function in allergic diseases.
BACKGROUND:
Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes.
RESULTS:
Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates.
CONCLUSIONS:
The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 108 cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.
ABC transporters fulfill diverse physiological functions in different cellularlocalizations ranging from the plasma membrane to intracellular membranouscompartments. Several ABC transporters have been spotted in the endolyso-somal system, which consists of endosomes, autophagosomes, lysosomes, andlysosome-related organelles. In this review, we present an overview of lysoso-mal ABC transporters including ABCA2, ABCA3, ABCA5, ABCB6,ABCB9, and ABCD4, discussing their trafficking routes, putative substrates,potential physiological functions, and associated diseases. In addition, weoffer a critical evaluation of the literature linking ABC transporters to lyso-somal drug sequestration, examining pitfalls associated with in vitro modelsof drug resistance.
Invasive alien species (IAS) are a major global challenge requiring urgent action, and the Strategic Plan for Biodiversity (2011–2020) of the Convention on Biological Diversity (CBD) includes a target on the issue. Meeting the target requires an understanding of invasion patterns. However, national or regional analyses of invasions are limited to developed countries. We identified 488 IAS in China’s terrestrial habitats, inland waters and marine ecosystems based on available literature and field work, including 171 animals, 265 plants, 26 fungi, 3 protists, 11 procaryots, and 12 viruses. Terrestrial plants account for 51.6% of the total number of IAS, and terrestrial invertebrates (104 species) for 21.3%. Of the total numbers, 67.9% of plant IAS and 34.8% of animal IAS were introduced intentionally. All other taxa were introduced unintentionally despite very few animal and plant species that invaded naturally. In terms of habitats, 64.3% of IAS occur on farmlands, 13.9% in forests, 8.4% in marine ecosystems, 7.3% in inland waters, and 6.1% in residential areas. Half of all IAS (51.1%) originate from North and South America, 18.3% from Europe, 17.3% from Asia not including China, 7.2% from Africa, 1.8% from Oceania, and the origin of the remaining 4.3% IAS is unknown. The distribution of IAS can be divided into three zones. Most IAS are distributed in coastal provinces and the Yunnan province; provinces in Middle China have fewer IAS, and most provinces in West China have the least number of IAS. Sites where IAS were first detected are mainly distributed in the coastal region, the Yunnan Province and the Xinjiang Uyghur Autonomous Region. The number of newly emerged IAS has been increasing since 1850. The cumulative number of firstly detected IAS grew exponentially.
The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop—a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect. We then use NMR spectroscopy to confirm the existence of this cation-binding site and to demonstrate its effects on RNA stability. Lastly, using quantum chemical calculations, we show that the cation-binding site is altering the electronic environment of the wild-type U-turn so that it is more similar to the cytosine mutant. The study reveals an amazingly complex and delicate interplay between various energy contributions shaping up the 3D structure and evolution of nucleic acids.
Targeted protein degradation is a drug modality represented by compounds that recruit a target to an E3 ubiquitin ligase to promote target ubiquitination and proteasomal degradation. Historically, the field distinguishes monovalent degraders from bifunctional degraders (PROTACs) that connect target and ligase via separate binding ligands joined via a linker1–4. Here, we elucidate the mechanism of action of a PROTAC-like degrader of the transcriptional coactivator BRD4, composed of a BRD4 ligand linked to a ligand for the E3 ligase CRL4DCAF15. Using orthogonal CRISPR/Cas9 screens we identify the degrader activity is independent of DCAF15, and relies on a different CRL4 substrate receptor, DCAF16. We demonstrate an intrinsic affinity between BRD4 and DCAF16, which is dependent on the tandem bromodomains of BRD4 and further increased by the degrader without physically engaging DCAF16 in isolation. Structural characterization of the resulting ternary complex reveals both BRD4 bromodomains are bivalently engaged in cis by the degrader and are bound to DCAF16 through several interfacial BRD4-DCAF16 and degrader-DCAF16 contacts. Our findings demonstrate that intramolecularly bridging domains can confer glue-type stabilization of intrinsic target-E3 interactions, and we propose this as a general strategy to modulate the surface topology of target proteins to nucleate co-opting of E3 ligases or other cellular effector proteins for effective proximity-based pharmacology.
Many naturally occurring or artificially created RNAs are capable of binding to guanine or guanine derivatives with high affinity and selectivity. They bind their ligands using very different recognition modes involving a diverse set of hydrogen bonding and stacking interactions. Apparently, the potential structural diversity for guanine, guanosine, and guanine nucleotide binding motifs is far from being fully explored. Szostak and coworkers have derived a large set of different GTP-binding aptamer families differing widely in sequence, secondary structure, and ligand specificity. The so-called class V–GTP aptamer from this set binds GTP with very high affinity and has a complex secondary structure. Here we use solution NMR spectroscopy to demonstrate that the class V aptamer binds GTP through the formation of an intermolecular two-layered G-quadruplex structure that directly incorporates the ligand and folds only upon ligand addition. Ligand binding and G-quadruplex formation depend strongly on the identity of monovalent cations present with a clear preference for potassium ions. GTP binding through direct insertion into an intermolecular G-quadruplex is a previously unobserved structural variation for ligand-binding RNA motifs and rationalizes the previously observed specificity pattern of the class V aptamer for GTP analogs.
Additive manufacturing or 3D printing as an umbrella term for various materials processing methods has distinct advantages over many other processing methods, including the ability to generate highly complex shapes and designs. However, the performance of any produced part not only depends on the material used and its shape, but is also critically dependent on its surface properties. Important features, such as wetting or fouling, critically depend mainly on the immediate surface energy. To gain control over the surface chemistry post-processing modifications are generally necessary, since it′s not a feature of additive manufacturing. Here, we report on the use of initiator and catalyst-free photografting and photopolymerization for the hydrophilic modification of microfiber scaffolds obtained from hydrophobic medical-grade poly(ε-caprolactone) via melt-electrowriting. Contact angle measurements and Raman spectroscopy confirms the formation of a more hydrophilic coating of poly(2-hydroxyethyl methacrylate). Apart from surface modification, we also observe bulk polymerization, which is expected for this method, and currently limits the controllability of this procedure.
Hundreds of genes have been associated with respiratory chain disease (RCD), the most common inborn error of metabolism so far. Elimination of the respiratory electron chain by depleting the entire mitochondrial DNA (mtDNA, ρ0 cells) has therefore one of the most severe impacts on the energy metabolism in eukaryotic cells. In this study, proteomic data sets including the post-translational modifications (PTMs) phosphorylation and ubiquitination were integrated with metabolomic data sets and selected enzyme activities in the osteosarcoma cell line 143B.TK−. A shotgun based SILAC LC-MS proteomics and a targeted metabolomics approach was applied to elucidate the consequences of the ρ0 state. Pathway and protein–protein interaction (PPI) network analyses revealed a nonuniform down-regulation of the respiratory electron chain, the tricarboxylic acid (TCA) cycle, and the pyruvate metabolism in ρ0 cells. Metabolites of the TCA cycle were dysregulated, such as a reduction of citric acid and cis-aconitic acid (six and 2.5-fold), and an increase of lactic acid, oxalacetic acid (both twofold), and succinic acid (fivefold) in ρ0 cells. Signaling pathways such as GPCR, EGFR, G12/13 alpha, and Rho GTPases were up-regulated in ρ0 cells, which could be indicative for the mitochondrial retrograde response, a pathway of communication from mitochondria to the nucleus. This was supported by our phosphoproteome data, which revealed two main processes, GTPase-related signal transduction and cytoskeleton organization. Furthermore, a general de-ubiquitination in ρ0 cells was observed, for example, 80S ribosomal proteins were in average threefold and SLC amino acid transporters fivefold de-ubiquitinated. The latter might cause the observed significant increase of amino acid levels in ρ0 cells. We conclude that an elimination of the respiratory electron chain, e.g. mtDNA depletion, not only leads to an uneven down-regulation of mitochondrial energy pathways, but also triggers the retrograde response.
High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
We present a dataset of free-viewing eye-movement recordings that contains more than 2.7 million fixation locations from 949 observers on more than 1000 images from different categories. This dataset aggregates and harmonizes data from 23 different studies conducted at the Institute of Cognitive Science at Osnabrück University and the University Medical Center in Hamburg-Eppendorf. Trained personnel recorded all studies under standard conditions with homogeneous equipment and parameter settings. All studies allowed for free eye-movements, and differed in the age range of participants (~7–80 years), stimulus sizes, stimulus modifications (phase scrambled, spatial filtering, mirrored), and stimuli categories (natural and urban scenes, web sites, fractal, pink-noise, and ambiguous artistic figures). The size and variability of viewing behavior within this dataset presents a strong opportunity for evaluating and comparing computational models of overt attention, and furthermore, for thoroughly quantifying strategies of viewing behavior. This also makes the dataset a good starting point for investigating whether viewing strategies change in patient groups.
An exciting in vivo function of ATP-sensitive potassium channels in substantia nigra dopamine neurons Ð Implications for burst firing and novelty coding ÐPhasic burst activity is a key feature of dopamine (DA) midbrain neurons. This particular pattern of excitation of DA neurons occurs via a synaptically triggered transition from low-frequency background spiking to transient high-frequency discharges. Burst-firing mediated phasic DA release is critical for flexible switching of behavioural strategies in response to unexpected rewards, novelty and other salient stimuli. However, the cellular and molecular bases of burst signalling in distinct DA subpopulations of the substantia nigra (SN) or the ventral tegmental area (VTA) are unknown.
DA neuron excitability is controlled by synaptic network inputs, neurotransmitter receptors and ion channels, which generate action potentials and determine frequency and pattern of electrical activity in a complex interplay. ATP-sensitive potassium (K-ATP) channels are widely expressed throughout the brain, where in most cases they are believed to act as metabolically-controlled 'excitation brakes' by matching excitability to cellular energy states. However, their precise physiological in vivo function in DA neurons remains elusive.
To study burst firing and the underlying ionic mechanisms with single cell resolution, in vivo single-unit recordings were combined with juxtacellular neurobiotin labelling as well as immunohistochemical and anatomical identification of individual DA neurons. In vivo recordings were performed in adult isoflurane-anaesthetised wildtype (WT) and global K-ATP channel knockout mice, lacking the pore forming Kir6.2 subunit (Kir6.2-/-). In addition, DA cell-selective functional silencing of K-ATP channel activity in vivo was established using virus-mediated expression of dominant-negative Kir6.2 subunits. Careful control experiments ruled out any significant contributions from nonDA neurons as transduction was effectively limited to SN DA neurons rather than affecting those cells that innervate them. Virus-based K-ATP channel silencing in combination with juxtacellular recording and labelling was achieved to define the electrophysiological phenotype of individually identified, virally-transduced DA neurons in vivo.
Single-unit recordings revealed that K-ATP channels Ð in contrast to their conventional hyperpolarising role Ð in a subpopulation of DA neurons located in the medial SN (m-SN) act as cell-type selective gates for excitatory burst firing in vivo. The percentage of spikes in bursts was threefold reduced in Kir6.2-/- compared to WT mice. Classification of firing patterns based on visual inspection of autocorrelation histograms and on a newly developed spike-train-model confirmed the dramatic shift from phasic burst to tonic single-spike oscillatory firing in Kir6.2-/-. This significant decrease of burstiness was selective for m-SN DA neurons and was not exhibited by DA cells in the lateral SN or VTA. Virus-based K-ATP channel silencing in vivo unequivocally demonstrated that the activity of postsynaptic K-ATP channels was sufficient to disrupt bursting in m-SN DA neuron subtypes. Patch-clamp recordings in brain slices indicated an essential role of K-ATP channels for NMDA-mediated in vitro bursting. In accordance with previous studies in DA midbrain neurons, NMDA receptor stimulation triggered burst-like firing in m-SN DA cells in vitro, but only when K-ATP channels were co-activated in these neurons.
K-ATP channel-gated burst firing in m-SN DA neurons might be functionally relevant in awake, freely moving mice. To explore the behavioural consequences of SN DA neuron subtype-selective K-ATP channel suppression, spontaneous open field (OF) behaviour of mice with bilateral K-ATP silencing across the whole SN (medial + lateral) or in only the lateral SN was tested. Analysis of WT and global Kir6.2-/- mice showed reduced exploratory locomotor activity of Kir6.2-/- in a novel OF environment. Remarkably, K-ATP channel silencing in m-SN DA neurons phenocopied this novelty-exploration deficit, indicating that K-ATP channel-gated burst firing in medial but not lateral SN DA neurons is crucial for WT-like novelty-dependent exploratory behaviour.
In summary, a novel role of K-ATP channels in promoting the excitatory switch from tonic to phasic firing in vivo in a cell-type specific manner was discovered. The present PhD thesis provides several important insights into the pivotal function of K-ATP channels in medial SN DA cells, which project to the dorsomedial striatum, for burst firing and its important consequences for context-dependent exploratory behaviour.
In collaboration with two other research groups transcriptional up-regulation of K-ATP channel and NMDA receptor subunits and high levels of in vivo burst firing were detected in surviving SN DA neurons from Parkinson's disease (PD) patients Ð providing a potential link of K-ATP channel activity to neurodegenerative pathomechanisms of PD. Using high-resolution fMRI imaging another study in humans has recently identified distinct DA midbrain regions that are preferentially activated by either reward or novelty. Taken together, these human data and the results of the present PhD thesis suggest that burst-gating K-ATP channel function in SN DA neurons impacts on phenotypes in disease as well as in health.
1. Halobacillus halophilus akkumuliert zum Ausgleich geringer, extrazellulärer Wasserpotentiale kompatible Solute. Bei Anzuchten in Gegenwart von 0,4 – 1,5 M NaCl wurden Glutamin und Glutamat als die dominierenden kompatiblen Solute identifiziert, während zwischen 2,0 und 3,0 M NaCl Prolin das dominierende Solut darstellt. Außerdem wurde Ectoin als zweites kompatibles Solut gefunden, das spezifisch bei hohen Salzgehalten akumuliert wird. Die Konzentrationen während der exponentiellen Wachstumsphase war jedoch um den Faktor 6 – 7 geringer im Vergleich zu Prolin. 2. Aus Wachstumsexperimenten in Gegenwart unterschiedlicher Anionen war bekannt, dass Glutamat, im Gegensatz zu Gluconat und Nitrat, in der Lage ist, das Wachstum von H. halophilus auch in Abwesenheit von Chlorid zu ermöglichen. Um der Frage nachzugehen, ob die wachstumsfördernde Wirkung von unphysiologisch hohen Glutamat-Konzentrationen im Medium auf die Verwendung von Glutamat als kompatiblem Solut in den Zellen zurückzuführen ist, wurden Gesamtsolutepools von Chlorid-, Nitrat-, Gluconat- und Glutamat-gezogenen Zellen gemessen. In NaCl-gezogenen Zellen zeigte sich Glutamat als dominantes Solut, während Prolin und Glutamin einen geringeren Teil am Gesamtpool ausmachten. In Nitrat-gezogenen Zellen betrug der Gesamtpool nur noch 83% und in Gluconat-gezogenen Zellen nur noch 27% im Vergleich zu Chlorid-gezogenen Zellen. Zellen, die mit Glutamat gezogen wurden, zeigten jedoch eine Gesamtkonzentration an Soluten, die ca. 100% über dem Vergleichswert aus Chlorid-gezogenen Zellen lag. Die Konzentration an Glutamin in den Zellen stieg dabei um 168%, die Konzentration an Glutamat sogar um 299%. Die Prolinkonzentration verringerte sich um 32%. Diese Daten belegen, dass der wachstumsstimulierende Effekt von Glutamat auf die Verwendung als kompatibles Solut zurückzuführen ist. 3. Zur Untersuchung der molekularen Grundlage der Salzadaptation sowie der Abhängigkeit von Chlorid in H. halophilus wurde in Zusammenarbeit mit der Gruppe von Prof. D. Oesterhelt (MPI für Biochemie, Martinsried) die Sequenzierung des Genoms begonnen. Das Projekt ist zur Zeit noch nicht abgeschlossen und befindet sich in der „Lückenschluß-Phase“. Die bisherigen Sequenzdaten konnten dennoch für die in dieser Arbeit beschriebenen Untersuchungen herangezogen werden. Das Genom besitzt eine Größe von ca. 4,1 Mbp mit einem ungefähren GC-Gehalt von 40%. Außerdem wurden 2 Plasmide identifiziert mit einer Größe von 16047 und 3329 bp. 4. Die Schlüsselgene bekannter Biosynthesewege für Glutamin und Glutamat konnten identifiziert werden. Darunter befinden sich zwei Isogene für eine Glutamatdehydrogenase (gdh1 und gdh2), ein Gen für die große Untereinheit einer Glutamatsynthase (gltA), zwei Gene für die kleine Untereinheit einer Glutamat-Synthase (gltB1 und gltB2) und zwei Isogene für eine Glutaminsynthetase (glnA1 und glnA2). glnA1 befindet sich in einem Cluster zusammen mit einem Gen, das für einen Regulator kodiert (glnR), wie er auch aus B. subtilis bekannt ist. Über reverse Transkription von mRNA und anschließender PCR-Analyse konnte gezeigt werden, dass sowohl gltA/gltB1 als auch glnA1/glnR in einem Operon organisiert sind. 5. Wurde die Transkriptmenge der in Punkt 4 erwähnten Biosynthesegene in Zellen quantifiziert, die in Gegenwart unterschiedlicher Salzkonzentrationen (0,4 – 3,0 M NaCl) gezogen wurden, so zeigte sich keine Abhängigkeit von der Salzkonzentration für die Gene gltA, glnA1 und gdh1. Über die Transkriptmengen von gdh2 ließ sich keine abschließende Aussage treffen, da die gefundenen Transkriptmengen sehr gering waren und daher zu sehr großen Varianzen bei der Quantifizierung führten. Eine klare Abhängigkeit der Transkriptmenge von der im Medium zugesetzten Salzkonzentration konnte für glnA2 gezeigt werden. Die glnA2 mRNA-Menge stieg dabei mit steigender Salzkonzentration an und erreichte bei 1,5 – 2.0 M NaCl ein Maximum. Bei diesen Salzkonzentrationen war die Menge an mRNA ca. 4 mal höher als der Vergleichswert bei 0,4 M NaCl. Bei höhern Salzkonzentrationen sank die Menge an Transkript wieder leicht und war dann ca. nur noch 3 mal so hoch wie bei 0,4 M NaCl. 6. Die zelluläre Konzentration der glnA2-Transkripte in Abhängigkeit unterschiedlicher Anionen im Anzuchtmedium wurde untersucht. Die Quantifizierung der glnA2–mRNA ergab eine 2 mal höhere Transkriptmenge in Gegenwart von Chlorid verglichen mit Nitrat oder Gluconat. 7. Es wurde nach Enzymaktivitäten der bekannten Schlüsselenzyme im Glutamat und Glutamin-Biosyntheseweg gesucht. Eine Glutamatdehydrogenase und eine Glutamatsynthase – Aktivität konnte nicht oder nur in vernachlässigbarem Maße nachgewiesen werden. Im Gegensatz dazu konnt eine Glutaminsynthetase – Aktivität eindeutig belegt werden. Diese Aktivität erwies sich abhängig von der Art und der Konzentration des angebotenen Anions im Medium. Maximale Aktivitäten wurden mit NaCl in einer Konzentration von 2,5 – 3,0 M erreicht. Interessanterweise erwies sich die Glutaminsynthetase – Aktivität auch abhängig von der Art des im Testpuffers verwendeten Anions. Hier zeigte sich eine deutliche Stimulierung der Aktivität durch das Anion Chlorid. [Die für diesen Punkt zugrunde liegenden Daten wurden im Rahmen einer von mir mitbetreuten Diplomarbeit von Jasmin F. Sydow erhoben und sind aus Gründen der vollständigen Darstellung des Projektverlaufes mitaufgeführt!] 8. Wie im Punkt 1 dargelegt, wird Prolin vor allem bei hohen Salzkonzentrationen in H. halophilus - Zellen akkumuliert. Neben der Abhängigkeit von der Salzkonzentration wurde außerdem die Abhängigkeit von der Wachstumsphase untersucht. Die Analyse der Prolinkonzentrationen während verschiedener Wachstumsphasen in Kulturen, die bei 1,0 bzw. 2,5 M NaCl angezogen wurden, zeigte, (i) dass die Prolinkonzentration während der frühen exponentiellen Phase ca. 2,5-fach erhöht war im Vergleich zu Niedrigsalz-Zellen, (ii) dass die Prolinkonzentration beim Übergang von der frühen in die späte exponentielle Phase dramatisch abnahm (um 64% bei 2,5 M NaCl) und dass (iii) in der stationären Phase Prolin praktisch nicht mehr nachzuweisen war. 9. Die Biosynthesegene für die Herstellung von Prolin aus Glutamat konnten im Genom von H. halophilus identifiziert werden. Es handelt sich dabei um ein Cluster von 3 Genen, die für eine putative Pyrrolin-5-carboxylatreductase (proH), eine Glutamat-5-kinase (proJ), und eine Glutamat-5-semialdehyd-dehydrogenase (proA) kodieren. Mittels reverser Transkription von mRNA und anschließenden PCR-Analysen konnte gezeigt werden, dass die drei Gene ein Operon bilden. 10. Eine Quantifizierung der Transkriptmengen der Biosynthesegene proH, proJ und proA mittels quantitativer PCR in Zellen, die bei unterschiedlichen NaCl-Konzentrationen gezogen wurden, zeigte einen deutlichen Zusammenhang zwischen der Salinität des Mediums und der Menge an Transkript. Diese war umso höher, je höher die Salinität des Mediums war. Die maximale Transkriptmenge (6-fach) wurde bei einer Salzkonzentration von 2,5 M NaCl erreicht. Bei noch höherer Salzkonzentration sank die Transkriptmenge auf die ca. 5-fache Menge des Kontrollwertes ab. 11. Um die Regulation und Dynamik der Osmoregulation unabhängig vom Wachstum untersuchen zu können, wurde ein Zellsuspensions-System für H. halophilus etabliert, bei dem eine konzentrierte Zellsuspension direkt von geringen auf hohe Salzkonzentrationen überführt wurde und bei dem die Prozesse der Transkription, Translation und Solut-Biosynthese erhalten blieben. Beispielhaft wurde dieses System an der Produktion von Prolin nach einem Salzschock von 0,8 auf 2,0 M NaCl getestet. Es zeigte sich bei der Analyse, dass sich die Transkriptmengen unmittelbar nach dem Salzschock deutlich erhöhten und bereits nach 1,5 Stunden ein Maximum erreicht wurde. Verglichen mit dem Wert zu Beginn des Versuches waren die Transkriptmengen ca. 13-fach erhöht, sanken im weiteren Verlauf jedoch wieder ab und blieben bei einer 4-fachen Transkriptmenge konstant. Mit der Erhöhung der Transkriptmenge ging auch eine Erhöhung der Prolinkonzentration einher, die ein Maximum von ca. 6 μmol/mg Protein nach 6 Stunden erreichte. Auch diese Konzentration verringerte sich im weiteren Verlauf wieder und erreichte nach 20 Stunden den Ausgangswert. 12. Um den Einfluß diverser Anionen bzw. Osmolyte im Medium auf die Produktion von Prolin zu untersuchen, wurden Zellsuspensionen von H. halophilus einer Erhöhung der Osmolarität von 0,8 M auf 2,0 M unterzogen. Es zeigte sich dabei, dass die maximale Akkumulation von Prolin in Anwesenheit von Chlorid am höchsten war. Nitrat und Glutamat führten zu ähnlichen, aber leicht geringeren maximalen Konzentrationen (92 bzw. 83% des Chloridwertes). Gluconat führte noch zu einer Akkumulation von ca. 51%, während die anderen Osmolyte zu keiner Akkumulation führten. Eine Analyse der Transkriptmengen zeigte jedoch ein völlig anderes Bild. Während Chlorid, Nitrat und Gluconat zu vergleichbaren Anstiegen der Transkripmengen führten, war die maximale Transkriptmenge der Glutamatinkubierten Zellen 3-9 mal höher als in Vergleichszellen mit Chlorid. In anschließenden Titrationsexperimenten mit verschiedenen Glutamatkonzentrationen konnte gezeigt werden, dass eine minimale Konzentration von 0,2 M Glutamat ausreichend ist, um eine 90-fache Steigerung der Transkriptmenge herbeizuführen. 13. Als Antwort auf Hochsalz-Bedingungen akkumuliert H. halophilus neben Prolin auch Ectoin. Die Ectoinkonzentration bei 2,5 M NaCl war ca. 2-3 mal höher als in Zellen, die bei 1,0 M gezogen wurden. Die Bestimmung der intrazellulären Ectoin-Konzentrationen während des Wachstums zeigte außerdem, dass die Produktion von Ectoin wachstumsphasenabhängig ist. Die Konzentration in der stationären Phase war ca. 5-fach höher als in der exponentiellen Phase. Die Entwicklung der Ectoin- Konzentration verhielt sich somit reziprok zur Entwicklung der Prolin-Konzentration während des Wachstums. 14. Es wurde ein Cluster von drei Genen im Genom von H. halophilus identifiziert, deren Genprodukte die Biosynthese von Ectoin aus Aspartatsemialdehyd katalysieren. ectA kodiert dabei für eine putative Diaminobutyrat-Acetyltransferase, ectB für eine putative Diaminobutyrat-2-oxoglutarat-Transaminase und ectC für eine putative Ectoin-Synthase. Mittels reverser Transkription von mRNA und anschließenden PCR-Analysen konnte gezeigt werden, dass die drei Gene ein Operon bilden. 15. Die Transkription der ect-Gene war abhängig von der Salinität des Mediums. Ab 2,0 M stieg die Menge an RNA um das 10-fache an und erreichte bei 3,0 M ein Maximum mit der 23,5-fachen Menge. 16. Nach einem osmotischen Schock stieg die Konzentration an ect-mRNA signifikant und erreichte ein Maximum nach 3 - 4 Stunden. Das Maximum wurde somit 1,5 – 2,5 Stunden später erreicht als bei anderen Genen der Solute-Biosynthese wie etwa gdh1, das für eine Glutamatdehydrogenase, glnA2, das für eine Glutamin-Synthetase oder proH, das für eine Pyrrolin-5-Carboxylase kodiert. Die maximal erreichten Wert lagen 13-fach (ectA), 6,5-fach (ectB) und 3-fach (ectC) über dem Wert vor dem Salzschock. Gegen EctC wurden polyklonale Antikörper generiert. Western-Blot Analysen mit diesem Antikörper zeigten, dass die EctC-Menge nach 4 Stunden um das 2,5-fache stieg, dann aber wieder abfiel auf das 1,6 – 1,7-fache des Ausgangswertes. Der Rückgang an EctC fand keine Entsprechung in der gemessenen Ectoin-Konzentration, welche über einen Zeitraum von 18 Stunden kontinuierlich anstieg. Die maximale Konzentration nach 18 Stunden betrug das ca. 6,3-fache des Ausgangswertes. 17. Wurden H. halophilus Zellen mit anderen Osmolyten außer NaCl geschockt, so ergab sich folgendes Bild der Regulation der Ectoin-Biosynthese: (i) die Transkription der ect-Gene zeigte keine Chlorid-abhängige Regulation. Die maximale Transkriptmenge wurde in Gegenwart von Nitrat erreicht, wohingegen Gluconat zu vergleichbachen mRNA-Mengen führte wie Chlorid. Glutamat führte nur zu schwacher Stimulierung der Transkription. (ii) auf Ebene der Proteinmenge war zu sehen, dass die Menge an EctC nach osmotischem Schock vergleichbar war in Zellen, die mit Chlorid oder Nitrat inkubiert wurden. Gluconat führte nur zu einer 40%-igen Zunahme während andere Osmolyte nahezu wirkungslos auf die Menge an EctC blieben. (iii) die höchste Akkumulation an Ectoin nach einer plötzlichen Erhöhung der Osmolarität wurde erreicht mit Chlorid (6-fache Zunahme) gefolgt von Nitrat (5,6-fache Zunahme). Gluconat führte lediglich zu einer 3,3-fachen und Glutamat nur noch zu einer 2-fachen Steigerung der Ectoinkonzentration. Glutamat hat somit ähnliche Effekte wie Tartrat, Saccharose oder Sulfat. Succinat führte zu keiner Akkumulation und Glycin sogar zu einer deutlichen Abnahme. Die Produktion von Ectoin ist somit hauptsächlich abhängig vom Anion/Osmolyt und nur untergeordnet von der Osmolarität.
Targeting self-renewal and tumorigenicity has been proposed as a potential strategy against cancer stem cells (CSCs). Epigenetic proteins are key modulators of gene expression and cancer development contributing to regulation and maintenance of self-renewal and tumorigenicity. Here, we have screened a small-molecule epigenetic inhibitor library using 3D in vitro models in order to determine potential epigenetic targets associated with self-renewal and tumorigenicity in Canine Mammary Cancer (CMC) cells. We identified inhibition of BET proteins as a promising strategy to inhibit CMC colonies and tumorspheres formation. Low doses of (+)-JQ1 were able to downregulate important genes associated to self-renewal pathways such as WNT, NOTCH, Hedgehog, PI3K/AKT/mTOR, EGF receptor and FGF receptor in CMC tumorspheres. In addition, we observed downregulation of ZEB2, a transcription factor important for the maintenance of self-renewal in canine mammary cancer cells. Furthermore, low doses of (+)-JQ1 were not cytotoxic in CMC cells cultured in 2D in vitro models but induced G2/M cell cycle arrest accompanied by upregulation of G2/M checkpoint-associated genes including BTG2 and CCNG2. Our work indicates the BET inhibition as a new strategy for canine mammary cancers by modulating the self-renewal phenotype in tumorigenic cells such as CSCs.
Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non-native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non-native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non-native species.
Background: The ideal biofuel should not only be a regenerative fuel from renewable feedstocks, but should also be compatible with the existing fuel distribution infrastructure and with normal car engines. As the so-called drop-in biofuel, the fatty alcohol 1-octanol has been described as a valuable substitute for diesel and jet fuels and has already been produced fermentatively from sugars in small amounts with engineered bacteria via reduction of thioesterase-mediated premature release of octanoic acid from fatty acid synthase or via a reversal of the β-oxidation pathway.
Results: The previously engineered short-chain acyl-CoA producing yeast Fas1R1834K/Fas2 fatty acid synthase variant was expressed together with carboxylic acid reductase from Mycobacterium marinum and phosphopantetheinyl transferase Sfp from Bacillus subtilis in a Saccharomyces cerevisiae Δfas1 Δfas2 Δfaa2 mutant strain. With the involvement of endogenous thioesterases, alcohol dehydrogenases, and aldehyde reductases, the synthesized octanoyl-CoA was converted to 1-octanol up to a titer of 26.0 mg L−1 in a 72-h fermentation. The additional accumulation of 90 mg L−1 octanoic acid in the medium indicated a bottleneck in 1-octanol production. When octanoic acid was supplied externally to the yeast cells, it could be efficiently converted to 1-octanol indicating that re-uptake of octanoic acid across the plasma membrane is not limiting. Additional overexpression of aldehyde reductase Ahr from Escherichia coli nearly completely prevented accumulation of octanoic acid and increased 1-octanol titers up to 49.5 mg L−1. However, in growth tests concentrations even lower than 50.0 mg L−1 turned out to be inhibitory to yeast growth. In situ extraction in a two-phase fermentation with dodecane as second phase did not improve growth, indicating that 1-octanol acts inhibitive before secretion. Furthermore, 1-octanol production was even reduced, which results from extraction of the intermediate octanoic acid to the organic phase, preventing its re-uptake.
Conclusions: By providing chain length control via an engineered octanoyl-CoA producing fatty acid synthase, we were able to specifically produce 1-octanol with S. cerevisiae. Before metabolic engineering can be used to further increase product titers and yields, strategies must be developed that cope with the toxic effects of 1-octanol on the yeast cells.
A low potential electron carrier ferredoxin (E0′ ≈ −500 mV) is used to fuel the only bioenergetic coupling site, a sodium-motive ferredoxin:NAD+ oxidoreductase (Rnf) in the acetogenic bacterium Acetobacterium woodii. Because ferredoxin reduction with physiological electron donors is highly endergonic, it must be coupled to an exergonic reaction. One candidate is NADH-dependent caffeyl-CoA reduction. We have purified a complex from A. woodii that contains a caffeyl-CoA reductase and an electron transfer flavoprotein. The enzyme contains three subunits encoded by the carCDE genes and is predicted to have, in addition to FAD, two [4Fe-4S] clusters as cofactor, which is consistent with the experimental determination of 4 mol of FAD, 9 mol of iron, and 9 mol of acid-labile sulfur. The enzyme complex catalyzed caffeyl-CoA-dependent oxidation of reduced methyl viologen. With NADH as donor, it catalyzed caffeyl-CoA reduction, but this reaction was highly stimulated by the addition of ferredoxin. Spectroscopic analyses revealed that ferredoxin and caffeyl-CoA were reduced simultaneously, and a stoichiometry of 1.3:1 was determined. Apparently, the caffeyl-CoA reductase-Etf complex of A. woodii uses the novel mechanism of flavin-dependent electron bifurcation to drive the endergonic ferredoxin reduction with NADH as reductant by coupling it to the exergonic NADH-dependent reduction of caffeyl-CoA.
NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.
Alien plants were first recorded in 1937 in the 2 million ha Kruger National Park (KNP, a savanna protected area in South Africa), and attempts to control them began in the mid-1950s. The invasive alien plant control program expanded substantially in the late 1990s, but its overall efficacy has not been determined. We present an assessment of invasive alien plant control operations over several decades in KNP. We based our assessment on available information from a range of control programs funded from various sources, including national public works programs, KNP operational funds, and foreign donor funds. Over ZAR 350 million (~ US$ 27 million) has been spent on control interventions between 1997 and 2016. We found evidence of good progress with the control of several species, notably Opuntia stricta, Sesbania punicea, Lantana camara and several aquatic weeds, often because of effective biological control. On the other hand, we found that over one third (40%) of the funding was spent on species that have subsequently been recognised as being of lower priority, most of which were alien annual weeds. The allocation of funds to non-priority species was sometimes driven by the need to meet additional objectives (such as employment creation), or by perceptions about relative impact in the absence of documented evidence. We also found that management goals were limited to inputs (funds disbursed, employment created, and area treated) rather than to ecological outcomes, and progress was consequently not adequately monitored. At a species level, four out of 36 species were considered to be under complete control, and a further five were under substantial control. Attempts to control five annual species were all considered to be ineffective. On the basis of our findings, we recommend that more studies be done to determine impacts associated with individual invasive alien species; that the criteria used to prioritise invasive alien species be documented based on such assessments, so that management can justify a focus on priority species; and that funding be re-directed to those species that clearly pose greater threats, and for which other solutions (such as biological control) are not an option.
The banana leaf spotting disease yellow Sigatoka is established and actively controlled in Australia through intensive chemical treatments and diseased leaf removal. In the State of Queensland, the State government imposes standards for de-leafing to minimise the risk of the disease spreading in 6 banana pest quarantine areas. Of these, the Northern Banana Pest Quarantine Area is the most significant in terms of banana production. Previous regulations imposed obligations on owners of banana plants within this area to remove leaves from plants with visible spotting on more than 15 per cent of any leaf during the wet season. Recently, this leaf disease threshold has been lowered to 5 per cent. In this paper we examine the likely impact this more-costly regulation will have on the spread of the disease. We estimate that the average net benefit of reducing the diseased leaf threshold is only likely to be $1.4 million per year over the next 30 years, expressed as the annualised present value of tightened regulation. This result varies substantially when the timeframe of the analysis is changed, with shorter time frames indicating poorer net returns from the change in protocols. Overall, the benefit of the regulation change is likely to be minor.
The National Collection of Arachnids, Instituto de Biología, Universidad Nacional Autónoma de México (México City) houses 476 chilopod samples, of which 197 are determined to genus and/or species. These are documented here and represent several new state records. Topotypes of eight species of centipedes described by R. V. Chamberlin also documented.
Synthesis of acetate from carbon dioxide and molecular hydrogen is considered to be the first carbon assimilation pathway on earth. It combines carbon dioxide fixation into acetyl-CoA with the production of ATP via an energized cell membrane. How the pathway is coupled with the net synthesis of ATP has been an enigma. The anaerobic, acetogenic bacterium Acetobacterium woodii uses an ancient version of this pathway without cytochromes and quinones. It generates a sodium ion potential across the cell membrane by the sodium-motive ferredoxin:NAD oxidoreductase (Rnf). The genome sequence of A. woodii solves the enigma: it uncovers Rnf as the only ion-motive enzyme coupled to the pathway and unravels a metabolism designed to produce reduced ferredoxin and overcome energetic barriers by virtue of electron-bifurcating, soluble enzymes.
The genetic control of anterior brain development is highly conserved throughout animals. For instance, a conserved anterior gene regulatory network specifies the ancestral neuroendocrine center of animals and the apical organ of marine organisms. However, its contribution to the brain in non-marine animals has remained elusive. Here, we study the function of the Tc-foxQ2 forkhead transcription factor, a key regulator of the anterior gene regulatory network of insects. We characterized four distinct types of Tc-foxQ2 positive neural progenitor cells based on differential co-expression with Tc-six3/optix, Tc-six4, Tc-chx/vsx, Tc-nkx2.1/scro, Tcey, Tc-rx and Tc-fez1. An enhancer trap line built by genome editing marked Tc-foxQ2 positive neurons, which projected through the primary brain commissure and later through a subset of commissural fascicles. Eventually, they contributed to the central complex. Strikingly, in Tc-foxQ2 RNAi knock-down embryos the primary brain commissure did not split and subsequent development of midline brain structures stalled. Our work establishes foxQ2 as a key regulator of brain midline structures, which distinguish the protocerebrum from segmental ganglia. Unexpectedly, our data suggest that the central complex evolved by integrating neural cells from an ancestral anterior neuroendocrine center.
The adaptive immune system protects against daily infections and malignant transformation. In this, the translocation of antigenic peptides by the transporter associated with antigen processing (TAP) into the ER lumen is an essential step in the antigen presentation by MHC I molecules. The heterodimeric ATP-binding cassette transporter (ABC) TAP consist of the two halftransporters TAP1 and TAP2. Each monomer contains an N-terminal transmembrane domain (TMD) and a conserved C-terminal nucleotide-binding domain (NBD). Together, the TMDs build the translocation core and the NBDs bind and hydrolyze ATP, energizing the peptide transport. TAP features an asymmetry in the two ATP-binding sites that are built of several conserved motifs. One motif is the D-loop with the consensus sequence SALD. The highly conserved aspartate of the D-loop of TAP1 reaches into the canonic ATP-binding site and contacts the Walker A motif and the H-loop of the opposite NBD, while the Asp of D-loop of TAP2 is part of the non-canonic ATP-binding site.
To examine this ABC transport complex in mechanistic detail, a purification and reconstitution procedure was established with the function of TAP being preserved. The heterodimeric TAP complex was purified via a His10-tag at TAP1 in a 1:1 ratio of the subunits. Nucleotide binding to the purified transporter was elucidated by tryptophan quenching assays and the affinity constants for MgADP and MgATP were determined to be 1.0 μM and 0.7 μM, respectevely. In addition, the TAP complex shows strict coupling between peptide binding and ATP hydrolysis, revealing no basal ATPase activity in the absence of peptides. Furthermore, TAP was reconstituted into proteoliposomes and the activity was tested by peptide transport and ATP hydrolysis. Interestingly, the kinetic parameters of the transporter in the reconstituted state are comparable to the data gained for TAP in microsomes.
To characterize the functional importance of the D-loop, D-loop mutants of either TAP1 or TAP2 were analyzed. Strikingly, TAP containing a mutated D-loop in TAP1 (D674A) shows an ATP-hydrolysis independent peptide translocation. Accordingly, the MHC I surface expression is similar to the wildtype situation. However, the same mutation in TAP2 (D638A) results in an ATPase dependent peptide transport similar to wildtype, whereas TAP containing mutations in both subunits leads to an inactive transporter. Although all D-loop mutants showed no altered peptide binding activity, the TAP1 mutant is inactive in peptide-stimulated ATPase activity. Strikingly, ATP or ADP binding is strictly required for the peptide translocation. Experiments carried out in proteoliposomes demonstrate that wildtype TAP can export peptides against their gradient when low peptide concentrations are offered. In contrast, the D674A mutant can facilitate peptide translocation along their concentration gradient in the two directions. At high peptide concentrations, TAP is trapped in a transport incompetent state induced by trans-inhibition. In conclusion, a TAP mutant that uncouples solute translocation from ATP hydrolysis was created. Since this passive substrate movement is strictly dependent on binding of ATP or ADP, an active transporter was turned into a “nucleotide-gated facilitator”.
In a cysteine cross-linking approach the conformational changes of TAP during peptide transport and the flexibility of the nucleotide binding domains were examined. Single cysteines were introduced in the D-loops of TAP1 and TAP2. Cross-linking by copper-phenantroline (CuPhe) was possible for all combinations. However, by adding ATP, ADP or peptide to the TAP complex no differences in the cross-linking efficiency were detected. By CuPhe cross-linking TAP was trapped in a conformation, in which the peptide binding site was not accessible. To complete a transport cycle, a flexibility of at least 17.8 Å of the NBDs is needed, since TAP cross-linked by CuPhe (2.0 Å) or bismaleimidoethane (BMOE, 8.0 Å) was transport inactive but when TAP was cross-linked by 1,11-bismaleimido-triethyleneglycol (BM[PEG]3, 17.8 Å) transport activity was preserved.
Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologues of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely abolish growth on arginine as nitrogen source. Growth rate of the deletion mutant strongly increased during serial transfer in shake-flask cultures. A combination of RNAseq-based transcriptome analysis and 13C-15N-based flux analysis was used to elucidate the arginase-independent pathway. Isotopic 13C15N-enrichment in γ-aminobutyrate revealed succinate as the entry point in the TCA cycle of the alternative pathway. Transcript analysis combined with enzyme activity measurements indicated increased expression in the Klcar1Δ mutant of a guanidinobutyrase (EC.3.5.3.7), a key enzyme in a new pathway for arginine degradation. Expression of the K. lactis KLLA0F27995g (renamed KlGBU1) encoding guanidinobutyrase enabled S. cerevisiae to use guanidinobutyrate as sole nitrogen source and its deletion in K. lactis almost completely abolish growth on this nitrogen source. Phylogenetic analysis suggests that this enzyme activity is widespread in fungi.
Tree-related microhabitats (TreMs) describe the microhabitats that a tree can provide for a multitude of other taxonomic groups and have been proposed as an important indicator for forest biodiversity (Asbeck et al., 2021). So far, the focus of TreM studies has been on temperate forests, although many trees in the tropics harbour exceptionally high numbers of TreMs. In this study, TreMs in the lowland tropical forests of the Choco (Ecuador) and in the mountain tropical forests of Mount Kilimanjaro (Tanzania) were surveyed. Our results extend the existing typology of TreMs of Larrieu et al. (2018) to include tropical forests and enabled a comparison of the relative recordings and diversity of TreMs between tropical and temperate forests. A new TreM form, Root formations, and three new TreM groups, concavities build by fruits or leaves, dendrotelms, and root formations, were established. In total, 15 new TreM types in five different TreM groups were specified. The relative recordings of most TreMs were similar between tropical and temperate forests. However, ivy and lianas, and ferns were more common in the lowland rainforest than in temperate forests, and bark microsoil, limb breakage, and foliose and fruticose lichens in tropical montane forest than in lowland rainforest. Mountain tropical forests hosted the highest diversity for common and dominant TreM types, and lowland tropical forest the highest diversity for rare TreMs. Our extended typology of tree-related microhabitats can support studies of forest-dwelling biodiversity in tropical forests. Specifically, given the ongoing threat to tropical forests, TreMs can serve as an additional tool allowing rapid assessments of biodiversity in these hyperdiverse ecosystems.
Alzheimer’s Disease (AD) is a progressive and irreversible neurodegenerative disorder, characterized by the accumulation of abeta-amyloid aggregates, which triggers tau hyperphosphorylation and neuronal loss. While the precise mechanisms underlying neurodegeneration in AD are not entirely understood, it is known that loss of proteostasis is implicated in this process. Maintaining neuronal proteostasis requires proper transfer RNA (tRNA) modifications, which are crucial for optimal translation. However, research into tRNA epitranscriptome in AD is limited, and it is not yet clear how alterations in tRNA modifying enzymes and tRNA modifications might contribute to disease progression. Here, we report that expression of the tRNA modifying enzyme ELP3 is reduced in the brain of AD patients and amyloid AD mouse models, suggesting ELP3 is implicated in proteostasis dysregulation observed in AD. To investigate the role of ELP3 specifically in neuronal proteostasis impairments in the context of amyloid pathology, we analyzed SH-SY5Y neuronal cells carrying the amyloidogenic Swedish familial AD mutation in the APP gene (SH-SWE) or the wild-type gene (SH-WT). Similarly to the amyloid mouse models, SH-SWE exhibited reduced levels of ELP3 which was associated with tRNA hypomodifications and reduced abundance, as well as proteostasis impairments. Furthermore, the knock-down of ELP3 in SH-WT recapitulated the proteostasis impairments observed in SH-SWE cells. Importantly, the correction of tRNA deficits due to ELP3 reduction rescued and reverted proteostasis impairments of SH-SWE and SH-WT knock-down for ELP3, respectively. Additionally, SH-WT exposed to the secretome of SH-SWE or synthetic amyloid aggregates recapitulate the SH-SWE phenotype, characterized by reduced ELP3 expression, tRNA hypomodification and increased protein aggregation. Taken together, our data suggest that amyloid pathology dysregulates neuronal proteostasis through the reduction of ELP3 and tRNA modifications. This study highlights the modulation of tRNA modifications as a potential therapeutic avenue to restore neuronal proteostasis in AD and preserve neuronal function.
In humans, screams have strong amplitude modulations (AM) at 30 to 150 Hz. These AM correspond to the acoustic correlate of perceptual roughness. In bats, distress calls can carry AMs, which elicit heart rate increases in playback experiments. Whether amplitude modulation occurs in fearful vocalisations of other animal species beyond humans and bats remains unknown. Here we analysed the AM pattern of rats’ 22-kHz ultrasonic vocalisations emitted in a fear conditioning task. We found that the number of vocalisations decreases during the presentation of conditioned stimuli. We also observed that AMs do occur in rat 22-kHz vocalisations. AMs are stronger during the presentation of conditioned stimuli, and during escape behaviour compared to freezing. Our results suggest that the presence of AMs in vocalisations emitted could reflect the animal’s internal state of fear related to avoidance behaviour.
Fungi and prokaryotes are dominant colonizers of wood and mediate its decomposition. Much progress has been achieved to unravel these communities and link them to specific wood properties. However, comparative studies considering both groups of organisms and assessing their relationships to wood resources are largely missing. Bipartite interaction networks provide an opportunity to investigate this colonizer-resource relationship more in detail and aim to directly compare results between different biotic groups. The main questions were as follows. Are network structures reflecting the trophic relationship between fungal and prokaryotic colonizers and their resources? If so, do they reflect the critical role of these groups, especially that of fungi, during decomposition? We used amplicon sequencing data to analyze fungal and prokaryotic interaction networks from deadwood of 13 temperate tree species at an early to middle stage of decomposition. Several diversity- and specialization-related indices were determined and the observed network structures were related to intrinsic wood traits. We hypothesized nonrandom bipartite networks for both groups and a higher degree of specialization for fungi, as they are the key players in wood decomposition. The results reveal highly modular and specialized interaction networks for both groups of organisms, demonstrating that many fungi and prokaryotes are resource-specific colonizers. However, as the level of specialization of fungi significantly surpassed that of prokaryotes, our findings reflect the strong association between fungi and their host. Our novel approach shows that the application of bipartite interaction networks is a useful tool to explore, quantify, and compare the deadwood-colonizers relationship based on sequencing data.
IMPORTANCE Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling. The aim of this study was to explore and quantify the relationship between these two main wood-inhabiting organism groups and their corresponding host trees. Two independent DNA-based amplicon sequencing data sets (fungi and prokaryotes) were analyzed via bipartite interaction networks. The links in the networks represent the interactions between the deadwood colonizers and their deadwood hosts. The networks allowed us to analyze whether many colonizing species interact mostly with a restricted number of deadwood tree species, so-called specialization. Our results demonstrate that many prokaryotes and fungi are resource-specific colonizers. The direct comparison between both groups revealed significantly higher specialization values for fungi, emphasizing their strong association to respective host trees, which reflects their dominant role in exploiting this resource.
Macrophages respond to the Th2 cytokine IL-4 with elevated expression of arachidonate 15-lipoxygenase (ALOX15). Although IL-4 signaling elicits anti-inflammatory responses, 15-lipoxygenase may either support or inhibit inflammatory processes in a context-dependent manner. AMP-activated protein kinase (AMPK) is a metabolic sensor/regulator that supports an anti-inflammatory macrophage phenotype. How AMPK activation is linked to IL-4-elicited gene signatures remains unexplored. Using primary human macrophages stimulated with IL-4, we observed elevated ALOX15 mRNA and protein expression, which was attenuated by AMPK activation. AMPK activators, e.g. phenformin and aminoimidazole-4-carboxamide 1-β-d-ribofuranoside inhibited IL-4-evoked activation of STAT3 while leaving activation of STAT6 and induction of typical IL-4-responsive genes intact. In addition, phenformin prevented IL-4-induced association of STAT6 and Lys-9 acetylation of histone H3 at the ALOX15 promoter. Activating AMPK abolished cellular production of 15-lipoxygenase arachidonic acid metabolites in IL-4-stimulated macrophages, which was mimicked by ALOX15 knockdown. Finally, pretreatment of macrophages with IL-4 for 48 h increased the mRNA expression of the proinflammatory cytokines IL-6, IL-12, CXCL9, and CXCL10 induced by subsequent stimulation with lipopolysaccharide. This response was attenuated by inhibition of ALOX15 or activation of AMPK during incubation with IL-4. In conclusion, limiting ALOX15 expression by AMPK may promote an anti-inflammatory phenotype of IL-4-stimulated human macrophages.
Amino acids can induce yeast cell adhesion but how amino acids are sensed and signal the modulation of the FLO adhesion genes is not clear. We discovered that the budding yeast Saccharomyces cerevisiae CEN.PK evolved invasive growth ability under prolonged nitrogen limitation. Such invasive mutants were used to identify amino acid transporters as regulators of FLO11 and invasive growth. One invasive mutant had elevated levels of FLO11 mRNA and a Q320STOP mutation in the SFL1 gene that encodes a protein kinase A pathway regulated repressor of FLO11. Glutamine-transporter genes DIP5 and GNP1 were essential for FLO11 expression, invasive growth and biofilm formation in this mutant. Invasive growth relied on known regulators of FLO11 and the Ssy1-Ptr3-Ssy5 complex that controls DIP5 and GNP1, suggesting that Dip5 and Gnp1 operates downstream of the Ssy1-Ptr3-Ssy5 complex for regulation of FLO11 expression in a protein kinase A dependent manner. The role of Dip5 and Gnp1 appears to be conserved in the S. cerevisiae strain ∑1278b since the dip5 gnp1 ∑1278b mutant showed no invasive phenotype.
Secondly, the amino acid transporter gene GAP1 was found to influence invasive growth through FLO11 as well as other FLO genes. Cells carrying a dominant loss-of-function PTR3647::CWNKNPLSSIN allele had increased transcription of the adhesion genes FLO1, 5, 9, 10, 11 and the amino acid transporter gene GAP1. Deletion of GAP1 caused loss of FLO11 expression and invasive growth. However, deletions of FLO11 and genes encoding components of the mitogen-activated protein kinase pathway or the protein kinase A pathway were not sufficient to abolish invasive growth, suggesting involvement of other FLO genes and alternative pathways. Increased intracellular amino acid pools in the PTR3647::CWNKNPLSSIN-containing strain opens the possibility that Gap1 regulates the FLO genes through alteration of the amino acid pool sizes.
Autophagy is the highly conserved catabolic process, which enables the survival of a cell under unfavorable environmental conditions. In a constantly changing environment, cells must be capable of dynamically oscillating between anabolism and catabolism in order to maintain cellular homeostasis. In this context, the activity of the mechanistic Target Of Rapamycin Complex 1 (mTORC1) is of major importance. As a central signaling node, it directly controls the process of macroautophagy and thus cellular metabolism. Thereby, the control of mTORC1 is equally crucial as the regulation of cellular homeostasis itself, whereby particular importance is attributed to amino acid sensory proteins. In this review, we describe the recent findings of macroautophagy and mTORC1 regulation by upstream amino acid stimuli in different subcellular localizations. We highlight in detail which proteins of the sensor complexes play a specific role in this regulation and point out additional non-canonical functions, e.g. in the regulation of macroautophagy, which have received little attention so far.
Ambrosia artemisiifolia (common ragweed) is an invasive species native to North America and was accidentally introduced to Europe in the 19th century. Widespread in disturbed habitats, it is a major weed in spring-sown crops and it causes serious allergic rhinitis and asthma due to its allergenic pollen. The aim of this research was to analyse the effects of both competitive vegetation and herbivory by Ophraella communa to control A. artemisiifolia in an agricultural area of north-western Italy. Hayseed mixtures, both over-seeded over the resident plant community or after ploughing, when seeded before the winter season, were able to suppress the establishment of A. artemisiifolia as well as to reduce its growth in terms of plant height and inflorescence size. Defoliation of A. artemisiifolia by O. communa at the end of the growing season was conspicuous but most of the plants still produced flowers and seeds. However, significant O. communa attack was recorded for reproductive structures. As for non-target species, O. communa was mainly recorded on Asteraceae, with low density and low degree of damage. Reduction of inflorescence size due to competitive vegetation and damage to male flowers by O. communa may diminish the amount of available pollen. The results of this study may be useful for the implementation of management measures to control A. artemisiifolia in agricultural areas using mixtures of native species.
Many cases of early-onset inherited Alzheimer's disease (AD) are caused by mutations in the presenilin-1 (PS1) gene. Expression of PS1 mutations in cell culture systems and in primary neurons from transgenic mice increases their vulnerability to cell death. Interestingly, enhanced vulnerability to cell death has also been demonstrated for peripheral lymphocytes from AD patients. We now report that lymphocytes from PS1 mutant transgenic mice show a similar hypersensitivity to cell death as do peripheral cells from AD patients and several cell culture systems expressing PS1 mutations. The cell death-enhancing action of mutant PS1 was associated with increased production of reactive oxygen species and altered calcium regulation, but not with changes of mitochondrial cytochrome c. Our study further emphasizes the pathogenic role of mutant PS1 and may provide the fundamental basis for new efforts to close the gap between studies using neuronal cell lines transfected with mutant PS1, neurons from transgenic animals, and peripheral cells from AD patients. Copyright 2001 Academic Press.
Mountains, with their isolated position and altitudinal belts, are hotspots of biodiversity. Their flora and fauna have been observed worldwide since the days of Alexander von Humboldt, which has led to basic knowledge and understanding of species composition and the most important driving forces of ecosystem differentiation in such altitudinal gradients. Systematically designed analyses of changes in species composition with increasing elevation have been increasingly implemented since the 1990s. Since global climate change is one of the most important problems facing the world this century, a focus on such ecosystem studies is urgently needed. To identify the main future needs of such research we analyze the studies dealing with species changes of diverse taxonomical groups along altitudinal gradients (0 to 6,400 m a.s. l.) on all continents, published during the past one to two decades. From our study we can conclude that although mountains are powerful for climate change research most studies have to face the challenge of separating confounding effects driving species assemblages along altitudinal gradients. Our study therefore supports the view of the need of a global altitudinal concept including that (1) not only one or a few taxonomical groups should be analyzed, but rather different taxonomical groups covering all ecosystem functions simultaneously; (2) relevant site conditions should be registered to reveal direct environmental variables responsible for species distribution patterns and to resolve inconsistent effects along the altitudinal gradients; (3) transect design is appropriate for analyzing ecosystem changes in site gradients and over time; (4) both the study design and the individual methods should be standardized to compare the data collected worldwide; and (5) a long-term perspective is important to quantify the degree and direction of species changes and to validate species distribution models. (6) Finally we suggest to develop experimental altitudinal approaches to overcome the addressed problems of biodiversity surveys.
Heat stress transcription factors (Hsfs) play essential role in heat stress response and thermotolerance by controlling the transcriptional activation of heat stress response (HSR) genes including molecular chaperones. Plant Hsf families show a striking multiplicity, with more than 20 members in the many plant species. Among Hsfs, HsfA1s act as the master regulators of heat stress (HS) response and HsfA2 becomes one of the most abundant Hsfs during HS. Using transgenic plans with suppressed expression of HsfA2 we have shown that this Hsf is involved in acquired thermotolerance of S. lycopersicum cv Moneymaker as HsfA2 is required for high expression and maintenance of increased levels of Hsps during repeated cycles of HS treatment.
Interestingly, HsfA2 undergoes temperature-dependent alternative splicing (AS) which results in the generation of seven transcript variants. Three of these transcripts (HsfA2-Iα-γ), generated due to alternative splicing of a second, newly identified intron encode for the full length protein involved in acquired thermotolerance. Another 3 transcripts (HsfA2-IIIα-γ) are generated due to alternative splicing in intron 1, leading in all cases to a premature termination codon and targeting of these transcripts for degradation via the non-sense mRNA decay mechanism (NMD).
Interestingly, excision of intron 2, results into the generation of a second previously unreported protein isoform, annotated as HsfA2-II. HsfA2-II shows similar transcriptional activity to the full-length protein HsfA2-I in the presence of HsfA1a but lacks the nuclear export signal (NES) required for nucleocytoplasmic shuttling which allows efficient nuclear retention and stimulation of transcription of HS-induced genes. Furthermore, stability assays showed that HsfA2-II exhibits lower protein stability compared to HsfA2-I.
The presence of a second intron and the generation of a second protein isoform we identified in other Solanaceae species as well. Remarkably, we observed major differences in the splicing efficiency of HsfA2 intron 2 among different tomato species. Several wild tomato accessions exhibit higher splicing efficiency that favors the generation of HsfA2-II, while in these species the splice variant HsfA2-Iγ is absent. This natural variation in splicing efficiency specifically occurring at temperatures around 37.5oC is associated with the presence of 3 intronic polymorphisms. In the case of wild species these polymorphisms seemingly restrict the binding of RS2Z36, identified as a putative splicing silencer for HsfA2 intron 2.
Tomato accessions with the polymorphic “wild” HsfA2 show enhanced thermotolerance against a direct severe heat stress incident due to the stronger increase of Hsps and other stress induced genes. Introgression of the “wild” S. pennellii HsfA2 locus into the cultivar M82, resulted in enhanced seedling thermotolerance highlighting the potential use of the polymorphic HsfA2 for breeding.
We conclude that alterations in the splicing efficiency of HsfA2 have contributed to the adaption of tomato species to different environments and these differences might be directly related to natural variation in their thermotolerance.
The retrograde response constitutes an important signalling pathway from mitochondria to the nucleus which induces several genes to allow compensation of mitochondrial impairments. In the filamentous ascomycete Podospora anserina, an example for such a response is the induction of a nuclear-encoded and iron-dependent alternative oxidase (AOX) occurring when cytochrome-c oxidase (COX) dependent respiration is affected. Several long-lived mutants are known which predominantly or exclusively respire via AOX. Here we show that two AOX-utilising mutants, grisea and PaCox17::ble, are able to compensate partially for lowered OXPHOS efficiency resulting from AOX-dependent respiration by increasing mitochondrial content. At the physiological level this is demonstrated by an elevated oxygen consumption and increased heat production. However, in the two mutants, ATP levels do not reach WT levels. Interestingly, mutant PaCox17::ble is characterized by a highly increased release of the reactive oxygen species (ROS) hydrogen peroxide. Both grisea and PaCox17::ble contain elevated levels of mitochondrial proteins involved in quality control, i. e. LON protease and the molecular chaperone HSP60. Taken together, our work demonstrates that AOX-dependent respiration in two mutants of the ageing model P. anserina is linked to a novel mechanism involved in the retrograde response pathway, mitochondrial biogenesis, which might also play an important role for cellular maintenance in other organisms.
Shrew-1, also called AJAP1, is a transmembrane protein associated with E-cadherin-mediated adherence junctions and a putative tumor suppressor. Apart from its interaction with β-catenin and involvement in E-cadherin internalization, little structure or function information exists. Here we explored shrew-1 expression during postnatal differentiation of mammary gland as a model system. Immunohistological analyses with antibodies against either the extracellular or the cytoplasmic domains of shrew-1 consistently revealed the expression of full-length shrew-1 in myoepithelial cells, but only part of it in luminal cells. While shrew-1 localization remained unaltered in myoepithelial cells, nuclear localization occurred in luminal cells during lactation. Based on these observations, we identified two unknown shrew-1 transcript variants encoding N-terminally truncated proteins. The smallest shrew-1 protein lacks the extracellular domain and is most likely the only variant present in luminal cells. RNA analyses of human tissues confirmed that the novel transcript variants of shrew-1 exist in vivo and exhibit a differential tissue expression profile. We conclude that our findings are essential for the understanding and interpretation of future functional and interactome analyses of shrew-1 variants.
The crystal structure of the bovine Rieske iron-sulfur protein indicates a sulfur atom (S-1) of the iron-sulfur cluster and the sulfur atom (Sgamma) of a cysteine residue that coordinates one of the iron atoms form hydrogen bonds with the hydroxyl groups of Ser-163 and Tyr-165, respectively. We have altered the equivalent Ser-183 and Tyr-185 in the Saccharomyces cerevisiae Rieske iron-sulfur protein by site-directed mutagenesis of the iron-sulfur protein gene to examine how these hydrogen bonds affect the midpoint potential of the iron-sulfur cluster and how changes in the midpoint potential affect the activity of the enzyme. Eliminating the hydrogen bond from the hydroxyl group of Ser-183 to S-1 of the cluster lowers the midpoint potential of the cluster by 130 mV, and eliminating the hydrogen bond from the hydroxyl group of Tyr-185 to Sgamma of Cys-159 lowers the midpoint potential by 65 mV. Eliminating both hydrogen bonds has an approximately additive effect, lowering the midpoint potential by 180 mV. Thus, these hydrogen bonds contribute significantly to the positive midpoint potential of the cluster but are not essential for its assembly. The activity of the bc1 complex decreases with the decrease in midpoint potential, confirming that oxidation of ubiquinol by the iron-sulfur protein is the rate-limiting partial reaction in the bc1 complex, and that the rate of this reaction is extensively influenced by the midpoint potential of the iron-sulfur cluster.
This paper deals with the control exerted by the mitochondrial translocator FLX1, which catalyzes the movement of the redox cofactor FAD across the mitochondrial membrane, on the efficiency of ATP production, ROS homeostasis, and lifespan of S. cerevisiae. The deletion of the FLX1 gene resulted in respiration-deficient and small-colony phenotype accompanied by a significant ATP shortage and ROS unbalance in glycerol-grown cells. Moreover, the flx1Δ strain showed H2O2 hypersensitivity and decreased lifespan. The impaired biochemical phenotype found in the flx1Δ strain might be justified by an altered expression of the flavoprotein subunit of succinate dehydrogenase, a key enzyme in bioenergetics and cell regulation. A search for possible cis-acting consensus motifs in the regulatory region upstream SDH1-ORF revealed a dozen of upstream motifs that might respond to induced metabolic changes by altering the expression of Flx1p. Among these motifs, two are present in the regulatory region of genes encoding proteins involved in flavin homeostasis. This is the first evidence that the mitochondrial flavin cofactor status is involved in controlling the lifespan of yeasts, maybe by changing the cellular succinate level. This is not the only case in which the homeostasis of redox cofactors underlies complex phenotypical behaviours, as lifespan in yeasts.
The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa - Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae) - by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant 'hot-spot' for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general.
The accumulation and distribution of characteristic secondary products in the different organs of an Aloe plant (A. succotrina Lam.) were studied by high performance liquid chromatography for the first time. In the leaves of the Aloe plant, only anthrone-C-glycosyls of the 7-hydroxyaloin type and, for the first time in plant material, the free anthraquinone 7-hydroxyaloeemodin were found. In contrast to previous reports on the distribution of secondary products in Aloe plants, anthrone-C-glycosyls were also detected in flowers, bracts and the inflorescence axis of the species examined. Aloesaponol I, a tetrahydroanthracene aglycone, was only present in the underground organs and in the stem. The 2-alkylchromone-C-glucosyl aloeresin B showed no specific occurrence as it was found in every type of organ. Based on these results and the findings of recent studies on Aloe roots and flowers, a distribution scheme of polyketide types in the Aloe plant was established. It suggests a separate and independent anthranoid metabolism for underground Aloe organs and stem on the one hand, and for leaves and inflorescence organs on the other hand. In the latter structures anthranoid metabolism seems to be additionally compartmentalized as the anthranoid pro files of inflorescence organs and leaves differ in two points relevant to anthranoid biosynthe sis: firstly, the occurrence of anthrone aglycones and secondly, the individual content of corresponding anthrone-C-glucosyl diastereomers.
Bacteria are true artists of survival, which rapidly adapt to environmental changes like pH shifts, temperature changes and different salinities. Upon osmotic shock, bacteria are able to counteract the loss of water by the uptake of potassium ions. In many bacteria, this is accomplished by the major K+ uptake system KtrAB. The system consists of the K+-translocating channel subunit KtrB, which forms a dimer in the membrane, and the cytoplasmic regulatory RCK subunit KtrA, which binds non-covalently to KtrB as an octameric ring. This unique architecture differs strongly from other RCK-gated K+ channels like MthK or GsuK, in which covalently tethered cytoplasmic RCK domains regulate a single tetrameric pore. As a consequence, an adapted gating mechanism is required: The activation of KtrAB depends on the binding of ATP and Mg2+ to KtrA, while ADP binding at the same site results in inactivation, mediated by conformational rearrangements. However, it is still poorly understood how the nucleotides are exchanged and how the resulting conformational changes in KtrA control gating in KtrB is still poorly understood.
Here,I present a 2.5-Å cryo-EM structure of ADP-bound, inactive KtrAB, which for the first time resolves the N termini of both KtrBs. They are located at the interface of KtrA and KtrB, forming a strong interaction network with both subunits. In combination with functional and EPR data we show that the N termini, surrounded by a lipidic environment, play a crucial role in the activation of the KtrAB system. We are proposing an allosteric network, in which an interaction of the N termini with the membrane facilitates MgATP-triggered conformational changes, leading to the active, conductive state.
Gram-negative bacteria maintain an intrinsic resistance mechanism against entry of noxious compounds by utilizing highly efficient efflux pumps. The E. coli AcrAB-TolC drug efflux pump contains the inner membrane H+/drug antiporter AcrB comprising three functionally interdependent protomers, cycling consecutively through the loose (L), tight (T) and open (O) state during cooperative catalysis. Here, we present 13 X-ray structures of AcrB in intermediate states of the transport cycle. Structure-based mutational analysis combined with drug susceptibility assays indicate that drugs are guided through dedicated transport channels toward the drug binding pockets. A co-structure obtained in the combined presence of erythromycin, linezolid, oxacillin and fusidic acid shows binding of fusidic acid deeply inside the T protomer transmembrane domain. Thiol cross-link substrate protection assays indicate that this transmembrane domain-binding site can also accommodate oxacillin or novobiocin but not erythromycin or linezolid. AcrB-mediated drug transport is suggested to be allosterically modulated in presence of multiple drugs.
The radiation-sensitive mutant pso4-1 of Saccharomyces cerevisiae shows a pleiotropic phenotype, including sensitivity to DNA cross-linking agents, nearly blocked sporulation and reduced mutability. We have cloned the putative yeast DNA repair gene PSO4 from a genomic library by complementation of the blocked UV-induced mutagenesis and of sporulation in diploids homozygous for pso4-1. Sequence analysis revealed that gene PSO4 consists of 1512 bp located upstream of UBI4 on chromosome XII and encodes a putative protein of 56.7 kDa. PSO4 is allelic to PRP19, a gene encoding a spliceosome-associated protein, but shares no significant homology with other yeast genes. Gene disruption with a destroyed reading frame of our PSO4 clone resulted in death of haploid cells, confirming the finding that PSO4/PRP19 is an essential gene. Thus, PSO4 is the third essential DNA repair gene found in the yeast S.cerevisiae.
All-optical closed-loop voltage clamp for precise control of muscles and neurons in live animals
(2023)
Excitable cells can be stimulated or inhibited by optogenetics. Since optogenetic actuation regimes are often static, neurons and circuits can quickly adapt, allowing perturbation, but not true control. Hence, we established an optogenetic voltage-clamp (OVC). The voltage-indicator QuasAr2 provides information for fast, closed-loop optical feedback to the bidirectional optogenetic actuator BiPOLES. Voltage-dependent fluorescence is held within tight margins, thus clamping the cell to distinct potentials. We established the OVC in muscles and neurons of Caenorhabditis elegans, and transferred it to rat hippocampal neurons in slice culture. Fluorescence signals were calibrated to electrically measured potentials, and wavelengths to currents, enabling to determine optical I/V-relationships. The OVC reports on homeostatically altered cellular physiology in mutants and on Ca2+-channel properties, and can dynamically clamp spiking in C. elegans. Combining non-invasive imaging with control capabilities of electrophysiology, the OVC facilitates high-throughput, contact-less electrophysiology in individual cells and paves the way for true optogenetic control in behaving animals.
The paper provides an updated checklist of the alien flora of Turkey with information on its structure. The alien flora of Turkey comprises 340 taxa, among which there are 321 angiosperms, 17 gymnosperms and two ferns. Of the total number of taxa, 228 (68%) are naturalized and 112 (32%) are casual. There are 275 neophytes (172 naturalized and 103 casual) and 61 archaeophytes (52 naturalized and 9 casual); four species could not be classified with respect to the residence time. In addition, 47 frequently planted taxa with a potential to escape are also listed. The richest families are Asteraceae (38 taxa), Poaceae (30), Fabaceae (23) and Solanaceae (22). As for the naturalized alien plants, the highest species richness is found in Asteraceae (31 taxa), Poaceae (22), Amaranthaceae (18) and Solanaceae (15). The majority of alien taxa are perennial (63.8% of the total number of taxa with this life history assigned, including those with multiple life histories), annuals contribute 33.8% and 2.4% are biennial aliens. Among perennials the most common life forms are phanerophytes, of which 20.3% are trees and 12.6% shrubs; woody vines, stem succulents, and aquatic plants are comparatively less represented. Most of the 340 alien taxa introduced to Turkey have their native ranges in Americas (44.7%) and Asia (27.6%). Of other regions, 9.1% originated in Africa, 4.4% in Eurasia, 3.8% in Australia and Oceania and 3.5% in the Mediterranean. The majority of taxa (71.9%) were introduced intentionally, whereas the remaining (28.1%) were introduced accidentally. Among the taxa introduced intentionally, the vast majority are ornamental plants (55.2%), 10.0% taxa were introduced for forestry and 6.7% as crops. Casual alien plants are most commonly found in urban and ruderal habitats (40.1%) where naturalized taxa are also often recorded (27.3%). Plants that occur as agricultural weeds are typically naturalized rather than casual (16.0% vs 7.1%, respectively). However, (semi)natural habitats in Turkey are often invaded by alien taxa, especially by those that are able to naturalize.
Background: The industrial production of various alcohols from organic carbon compounds may be performed at high rates and with a low risk of contamination using thermophilic microorganisms as whole-cell catalysts. Thermoanaerobacter species that thrive around 50–75 °C not only perform fermentation of sugars to alcohols, but some also utilize different organic acids as electron acceptors, reducing them to their corresponding alcohols. Results: We purified AdhE as the major NADH- and AdhB as the major NADPH-dependent alcohol dehydrogenase (ADH) from the cell extract of the organic acid-reducing Thermoanaerobacter sp. strain X514. Both enzymes were present in high amounts during growth on glucose with and without isobutyrate, had broad substrate spectra including different aldehydes, with high affinities (< 1 mM) for acetaldehyde and for NADH (AdhE) or NADPH (AdhB). Both enzymes were highly thermostable at the physiological temperature of alcohol production. In addition to AdhE and AdhB, we identified two abundant AdhA-type ADHs based on their genes, which were recombinantly produced and biochemically characterized. The other five ADHs encoded in the genome were only expressed at low levels. Conclusions: According to their biochemical and kinetic properties, AdhE and AdhB are most important for ethanol formation from sugar and reduction of organic acids to alcohols, while the role of the two AdhA-type enzymes is less clear. AdhE is the only abundant aldehyde dehydrogenase for the acetyl-CoA reduction to aldehydes, however, acid reduction may also proceed directly by aldehyde:ferredoxin oxidoreductase. The role of the latter in bio-alcohol formation from sugar and in organic acid reduction needs to be elucidated in future studies.
Background: Otic neurons and sensory cells derive from common progenitors whose transition into mature cells requires the coordination of cell survival, proliferation and differentiation programmes. Neurotrophic support and survival of post-mitotic otic neurons have been intensively studied, but the bases underlying the regulation of programmed cell death in immature proliferative otic neuroblasts remains poorly understood. The protein kinase AKT acts as a node, playing a critical role in controlling cell survival and cell cycle progression. AKT is activated by trophic factors, including insulin-like growth factor I (IGF-I), through the generation of the lipidic second messenger phosphatidylinositol 3-phosphate by phosphatidylinositol 3-kinase (PI3K). Here we have investigated the role of IGF-dependent activation of the PI3K-AKT pathway in maintenance of otic neuroblasts.
Methodology/Principal Findings: By using a combination of organotypic cultures of chicken (Gallus gallus) otic vesicles and acoustic-vestibular ganglia, Western blotting, immunohistochemistry and in situ hybridization, we show that IGF-I-activation of AKT protects neural progenitors from programmed cell death. IGF-I maintains otic neuroblasts in an undifferentiated and proliferative state, which is characterised by the upregulation of the forkhead box M1 (FoxM1) transcription factor. By contrast, our results indicate that post-mitotic p27Kip-positive neurons become IGF-I independent as they extend their neuronal processes. Neurons gradually reduce their expression of the Igf1r, while they increase that of the neurotrophin receptor, TrkC.
Conclusions/Significance: Proliferative otic neuroblasts are dependent on the activation of the PI3K-AKT pathway by IGF-I for survival during the otic neuronal progenitor phase of early inner ear development.
Argonaute 2 (AGO2) is an indispensable component of the RNA-induced silencing complex, operating at the translational or posttranscriptional level. It is compartmentalized into structures such as GW- and P-bodies, stress granules and adherens junctions as well as the midbody. Here we show using immunofluorescence, image and bioinformatic analysis and cytogenetics that AGO2 also resides in membrane protrusions such as open- and close-ended tubes. The latter are cytokinetic bridges where AGO2 colocalizes at the midbody arms with cytoskeletal components such as α-Τubulin and Aurora B, and various kinases. AGO2, phosphorylated on serine 387, is located together with Dicer at the midbody ring in a manner dependent on p38 MAPK activity. We further show that AGO2 is stress sensitive and important to ensure the proper chromosome segregation and cytokinetic fidelity. We suggest that AGO2 is part of a regulatory mechanism triggered by cytokinetic stress to generate the appropriate micro-environment for local transcript homeostasis.
Alkylglycerol monooxygenase (AGMO) is a tetrahydrobiopterin (BH4)-dependent enzyme with major expression in the liver and white adipose tissue that cleaves alkyl ether glycerolipids. The present study describes the disclosure and biological characterization of a candidate compound (Cp6), which inhibits AGMO with an IC50 of 30–100 µM and 5–20-fold preference of AGMO relative to other BH4-dependent enzymes, i.e., phenylalanine-hydroxylase and nitric oxide synthase. The viability and metabolic activity of mouse 3T3-L1 fibroblasts, HepG2 human hepatocytes and mouse RAW264.7 macrophages were not affected up to 10-fold of the IC50. However, Cp6 reversibly inhibited the differentiation of 3T3-L1 cells towards adipocytes, in which AGMO expression was upregulated upon differentiation. Cp6 reduced the accumulation of lipid droplets in adipocytes upon differentiation and in HepG2 cells exposed to free fatty acids. Cp6 also inhibited IL-4-driven differentiation of RAW264.7 macrophages towards M2-like macrophages, which serve as adipocyte progenitors in adipose tissue. Collectively, the data suggest that pharmacologic AGMO inhibition may affect lipid storage.
The accumulation of functionally impaired mitochondria is a key event in aging. Previous works with the fungal aging model Podospora anserina demonstrated pronounced age-dependent changes of mitochondrial morphology and ultrastructure, as well as alterations of transcript and protein levels, including individual proteins of the oxidative phosphorylation (OXPHOS). The identified protein changes do not reflect the level of the whole protein complexes as they function in-vivo. In the present study, we investigated in detail the age-dependent changes of assembled mitochondrial protein complexes, using complexome profiling. We observed pronounced age-depen-dent alterations of the OXPHOS complexes, including the loss of mitochondrial respiratory supercomplexes (mtRSCs) and a reduction in the abundance of complex I and complex IV. Additionally, we identified a switch from the standard complex IV-dependent respiration to an alternative respiration during the aging of the P. anserina wild type. Interestingly, we identified proteasome components, as well as endoplasmic reticulum (ER) proteins, for which the recruitment to mitochondria appeared to be increased in the mitochondria of older cultures. Overall, our data demonstrate pronounced age-dependent alterations of the protein complexes involved in energy transduction and suggest the induction of different non-mitochondrial salvage pathways, to counteract the age-dependent mitochondrial impairments which occur during aging.
Enhanced apoptosis and elevated levels of reactive oxygen species (ROS) play a major role in aging. In addition, several neurodegenerative diseases are associated with increased oxidative stress and apoptosis in neuronal tissue. Antioxidative treatment has neuro-protective effects. The aim of the present study was to evaluate changes of susceptibility to apoptotic cell death by oxidative stress in aging and its inhibition by the antioxidant Ginkgo biloba extract EGb761. We investigated basal and ROS-induced levels of apoptotic lymphocytes derived from the spleen in young (3 months) and old (24 months) mice. ROS were induced by 2-deoxy-D-ribose (dRib) that depletes the intracellular pool of reduced glutathione. Lymphocytes from aged mice accumulate apoptotic cells to a significantly higher extent under basal conditions compared to cells from young mice. Treatment with dRib enhanced this difference, implicating a higher sensitivity to ROS in aging. Apoptosis can be reduced in vitro by treatment with EGb761. In addition, mice were treated daily with 100mg/kg EGb761 per os over a period of two weeks. ROS-induced apoptosis was significantly reduced in the EGb761 group. Interestingly, this effect seemed to be more pronounced in old mice.
The relevance of physiological immune aging is of great interest with respect to determining disorders with pathologic immune function in aging individuals. In recent years, the relevance of changes in peripheral lymphocytes in age-associated neurologic diseases has become more evident. Due to the lack of immunological studies, covering more than one event after mitogenic activation, we envisaged a new concept in the present study, aiming to investigate several events, starting from T cell receptor (TCR) ligation up to T cell proliferation. In addition, we addressed the question whether changes are present in the subsets (CD4, CD8) with aging. Phosphorylation of tyrosine residues declines with increasing age in CD4+ cells. Fewer levels of CD69 positive cells after 4 h mitogenic activation, altered expression of cytokines (IL2, IFN-gamma and TNF-alpha; 22 h) and lower proliferation (72 h) were determined in aging. Moreover, it could be shown that CD8+ lymphocytes react more effectively to mitogenic stimulation with reference to CD69 expression and proliferation in both age groups (<35 and >60 years old). These data indicate that T cell activation, mediated by TCR engagement, is significantly impaired in aging and both subsets are affected. However, bypassing the TCR does not fully restore T cell function, indicating that there are more mechanisms involved than impaired signal transduction through TCR only. The results will be discussed in relation to their relevance in neurodegenerative and psychiatric disorders.
Apoptosis seems to be involved in immunosenescence associated with aging. Moreover, in lymphocytes (PBL) of patients with Alzheimer's disease, an increased susceptibility to the apoptotic pathway has been described possibly due to impaired protection of oxidative stress. Accordingly, it seemed to be of particular interest to investigate the contribution of normal aging to the susceptibility from human lymphocytes to programmed cell death. We could show that PBL from elderly individuals (>60 years) accumulate apoptosing cells to a significant higher extent in spontaneous and activation-induced cell death compared to younger controls (<35 years). Treatment with the oxidative stressor 2-deoxy-D-ribose or with agonistic-CD95-antibody pronounced this effect even more implicating a higher sensitivity to reactive oxygen species and a higher functional CD95 expression, respectively. In addition, expression of the activation markers HLA-DR and CD95 was significantly increased in CD3+-cells of aged subjects, while expression of CD25 did not seem to be affected by age. Expression of Bcl-2 was increased in aging and correlated with the number of apoptotic cells.
In previous investigations an impact of cellular copper homeostasis on ageing of the ascomycete Podospora anserina has been demonstrated. Here we provide new data indicating that mitochondria play a major role in this process. Determination of copper in the cytosolic fraction using total reflection X-ray fluorescence spectroscopy analysis and eGfp reporter gene studies indicate an age-related increase of cytosolic copper levels. We show that components of the mitochondrial matrix (i.e. eGFP targeted to mitochondria) become released from the organelle during ageing. Decreasing the accessibility of mitochondrial copper in P. anserina via targeting a copper metallothionein to the mitochondrial matrix was found to result in a switch from a copper-dependent cytochrome-c oxidase to a copper-independent alternative oxidase type of respiration and results in lifespan extension. In addition, we demonstrate that increased copper concentrations in the culture medium lead to the appearance of senescence biomarkers in human diploid fibroblasts (HDFs). Significantly, expression of copper-regulated genes is induced during in vitro ageing in medium devoid of excess copper suggesting that cytosolic copper levels also increase during senescence of HDFs. These data suggest that the identified molecular pathway of age-dependent copper dynamics may not be restricted to P. anserina but may be conserved from lower eukaryotes to humans.
Nitric oxide (NO)-sensitive soluble guanylyl cyclase (sGC) is the major cytosolic receptor for NO, catalyzing the conversion of GTP to cGMP. In a search for proteins specifically interacting with human sGC, we have identified the multidomain protein AGAP1, the prototype of an ArfGAP protein with a GTPase-like domain, Ankyrin repeats, and a pleckstrin homology domain. AGAP1 binds through its carboxyl terminal portion to both the α1 and β1 subunits of sGC. We demonstrate that AGAP1 mRNA and protein are co-expressed with sGC in human, murine, and rat cells and tissues and that the two proteins interact in vitro and in vivo. We also show that AGAP1 is prone to tyrosine phosphorylation by Src-like kinases and that tyrosine phosphorylation potently increases the interaction between AGAP1 and sGC, indicating that complex formation is modulated by reversible phosphorylation. Our findings may hint to a potential role of AGAP1 in integrating signals from Arf, NO/cGMP, and tyrosine kinase signaling pathways.
The human 5-lipoxygenase (5-LO), encoded by the ALOX5 gene, is the key enzyme in the formation of pro-inflammatory leukotrienes. ALOX5 gene transcription is strongly stimulated by calcitriol (1α, 25-dihydroxyvitamin D3) and TGFβ (transforming growth factor-β). Here, we investigated the influence of MLL (activator of transcript initiation), AF4 (activator of transcriptional elongation) as well as of the leukemogenic fusion proteins MLL-AF4 (ectopic activator of transcript initiation) and AF4-MLL (ectopic activator of transcriptional elongation) on calcitriol/TGFβ-dependent 5-LO transcript elongation. We present evidence that the AF4 complex directly interacts with the vitamin D receptor (VDR) and promotes calcitriol-dependent ALOX5 transcript elongation. Activation of transcript elongation was strongly enhanced by the AF4-MLL fusion protein but was sensitive to Flavopiridol. By contrast, MLL-AF4 displayed no effect on transcriptional elongation. Furthermore, HDAC class I inhibitors inhibited the ectopic effects caused by AF4-MLL on transcriptional elongation, suggesting that HDAC class I inhibitors are potential therapeutics for the treatment of t(4;11)(q21;q23) leukemia.
Bioaerosols are considered to play a relevant role in atmospheric processes, but their sources, properties, and spatiotemporal distribution in the atmosphere are not yet well characterized. In the Amazon Basin, primary biological aerosol particles (PBAPs) account for a large fraction of coarse particulate matter, and fungal spores are among the most abundant PBAPs in this area as well as in other vegetated continental regions. Furthermore, PBAPs could also be important ice nuclei in Amazonia. Measurement data on the release of fungal spores under natural conditions, however, are sparse. Here we present an experimental approach to analyze and quantify the spore release from fungi and other spore-producing organisms under natural and laboratory conditions. For measurements under natural conditions, the samples were kept in their natural environment and a setup was developed to estimate the spore release numbers and sizes as well as the microclimatic factors temperature and air humidity in parallel to the mesoclimatic parameters net radiation, rain, and fog occurrence. For experiments in the laboratory, we developed a cuvette to assess the particle size and number of newly released fungal spores under controlled conditions, simultaneously measuring temperature and relative humidity inside the cuvette. Both approaches were combined with bioaerosol sampling techniques to characterize the released particles using microscopic methods. For fruiting bodies of the basidiomycetous species, Rigidoporus microporus, the model species for which these techniques were tested, the highest frequency of spore release occurred in the range from 62 % to 96 % relative humidity. The results obtained for this model species reveal characteristic spore release patterns linked to environmental or experimental conditions, indicating that the moisture status of the sample may be a regulating factor, whereas temperature and light seem to play a minor role for this species. The presented approach enables systematic studies aimed at the quantification and validation of spore emission rates and inventories, which can be applied to a regional mapping of cryptogamic organisms under given environmental conditions.
Bioaerosols are considered to play a relevant role in atmospheric processes, but their sources, properties and spatiotemporal distribution in the atmosphere are not yet well characterized. In the Amazon Basin, primary biological aerosol particles (PBAP) account for a large fraction of coarse particulate matter, and fungal spores are among the most abundant PBAP there as well as in other vegetated continental regions. furthermore, PBAP could also be important ice nuclei in Amazonia. Measurement data on the release of fungal spores under natural conditions, however, are sparse. Here we present an experimental approach to analyze and quantify the spore release from fungi and other spore producing organisms under natural and laboratory conditions. For measurements under natural conditions, the samples were kept in their natural environment and a setup was developed to estimate the spore release numbers and sizes together with the microclimatic factors temperature and air humidity, as well as the mesoclimatic parameters net radiation, rain, and fog occurrence. For experiments in the laboratory, we developed a cuvette to assess the particle size and number of newly released fungal spores under controlled conditions, simultaneously measuring temperature and relative humidity inside the cuvette. Both approaches were combined with bioaerosol sampling techniques to characterize the released particles by microscopic methods. For fruiting bodies of the basidiomycetous species, Rigidoporus microporus, the model species for which these techniques were tested, the highest frequency of spore release occurred in the range of 62 and 96 % relative humidity. The results obtained for this model species reveal characteristic spore release patterns linked to environmental or experimental conditions, indicating that the moisture status of the sample may be a regulating factor, while temperature and light seem to play a minor role for this species. The presented approach enables systematic studies aimed at the quantification and validation of spore emission rates and inventories, which can be applied to a regional mapping of cryptogamic organisms under given environmental conditions.
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
Core Facilities (CF) for advanced light microscopy (ALM) have become indispensable support units for research in the life sciences. Their organizational structure and technical characteristics are quite diverse, although the tasks they pursue and the services they offer are similar. Therefore, throughout Europe, scientists from ALM‐CFs are forming networks to promote interactions and discuss best practice models. Here, we present recommendations for ALM‐CF operations elaborated by the workgroups of the German network of ALM‐CFs, German Bio‐Imaging (GerBI). We address technical aspects of CF planning and instrument maintainance, give advice on the organization and management of an ALM‐CF, propose a scheme for the training of CF users, and provide an overview of current resources for image processing and analysis. Further, we elaborate on the new challenges and opportunities for professional development and careers created by CFs. While some information specifically refers to the German academic system, most of the content of this article is of general interest for CFs in the life sciences.
Two main types of methods are used in gene therapy: integrating vectors and nuclease-based genome engineering. Nucleases are site-specific and are efficient for knock-outs, but inefficient at inserting long DNA sequences. Integrating vectors perform this task with high efficiency, but their insertion occurs at random genomic positions. This can result in transformation of target cells, which leads to severe adverse events in a gene therapy context. Thus, it is of great interest to develop novel genome engineering tools that combine the advantages of both technologies. The main focus of this thesis is on generating such a targetable integrating vector.
The integrating vector used in this project is the Sleeping Beauty (SB) transposon, a DNA transposon characterized by high activity across a wide range of cells. The SB transposase was combined with an RNA-guided Cas9 nuclease domain. This nuclease component was meant to direct transposase integration to specific targets defined by RNAs. The SB transposase was fused to cleavage-inactivated Cas9 (dCas9) to tether it to the target sites. In addition, adapter proteins consisting of dCas9 and domains non-covalently interacting with SB transposase or the SB transposon were generated. All constituent domains of these fusion proteins were tested in enzymatic assays and almost all enzymatic activities could be verified.
Combining the fusion protein dCas9-SB100X with a gRNA binding a sequence from the AluY repetitive element resulted in a weak, but statistically significant enrichment around sites bound by the gRNA. This enrichment was ca. 2-fold and occurred within a 300 bp window downstream of target sites, or within the AluY element.
Targeting with adapter proteins and targeting of other targets (L1 elements or single-copy targets) did not result in statistically significant effects. Single-copy targets tested included the HPRT gene and three specifically selected GSH targets that were known to be receptive to SB insertions. The combination with a more sequence-specific transposase mutant also failed to increase specificity to a level allowing targeting of single-copy loci. Genome-wide analysis of insertions however demonstrated, that dCas9-SB100X has a different insertion profile than SB100X, regardless of the gRNA used.
As low efficiency of retargeting is likely a consequence of the high background activity of the SB100X transposase in the fusion constructs, a SB mutant with reduced DNA affinity, SB(C42), was generated. For this mutant, transposition activity was partly dependent on a dCas9 domain being supplied with a multi-copy target gRNA, specifically a 2-fold increase in the presence of a AluY-directed gRNA. Whether using this mutant results in improved targeting remains to be determined.
In a side project, an attempt was made to direct SB insertions to ribosomal DNA by fusing the transposase to a nucleolar protein. This fusion transposase partially localized to nucleoli and insertions catalyzed by this transposase were found to be enriched in nucleolus organizer regions (NORs) and nucleolus-associated domains (NADs).
The aim of a second side project was increasing the ratio between homology-directed repair (HDR) and non-homologous end-joining (NHEJ) at Cas9-mediated double-strand breaks (DSBs). To achieve this, Cas9 was fused to DNA-interacting domains and corresponding binding sequences were fused to the homology donors. While an increased HDR/NHEJ ration could be observed for the fusion proteins, it was not dependent on the presence on the binding sequences in the donor molecules.
In the adult mammalian central nervous system, two defined neurogenic regions retain the capacity to generate new neurons throughout adulthood, namely the subependymal zone (SEZ) at the lateral ventricles and the subgranular layer of the hippocampus (SGL). Adult neurogenesis consists of a whole set of events including proliferation, fate specification, migration, survival and finally synaptic integration of newly born neurons. Each of these events is controlled by the interplay of numerous factors. In this study two signalling systems were analysed with regard to their functional role in adult neurogenesis in vivo, namely the purinergic system and the growth factor EGF. Neither short- nor long-term application of the P2Y receptor agonists UTP and ADPβS and the P2Y receptor antagonist suramin into the lateral ventricle of adult mice altered cell responses as compared to vehicle controls in vivo. In contrast, analysis of the expansion rates of cultured neural stem cells (NSCs) from knockout mice revealed a strong increase in the number of NSCs from NTPDase2-/- mice, whereas cell numbers of NSCs from P2Y1-/- and P2Y2-/- mice were significantly reduced in comparison to wildtype levels. Notably, in vivo proliferation rates were potently elevated in the SGL and the SEZ of NTPDase2-deficient mice. However, in vivo proliferation in both neurogenic niches of the single receptor knockout mice P2Y1-/- and P2Y2-/- and P2Y1-/- P2Y2-/-double-knockout mice did not differ significantly from the wildtype. In mice lacking the P2Y2 receptor the survival of newly born neurons in the hippocampal granule cell layer was significantly increased. These data provide the first line of evidence that purinergic signalling is involved in the control of neural stem cells behaviour not only in vitro but also in vivo. In order to further characterise the role of epidermal growth factor (EGF) in adult neurogenesis, transit amplifying precursors (TAPs) and type B astrocytes were identified as EGF-responsive cell populations following ventricular EGF injection, whereas ependymal cells, neuroblasts and NG2-positive cells did not or only to a minor extent respond to EGF injection. These EGF-responsive cell populations were found on both, the septal as well as striatal lateral ventricle walls. Long-term ventricular EGF infusion for 6d, 1. increased cell proliferation of both ventricle walls revealing a gradient along the rostro-caudal axis, 2. altered the balance between neuronal and macroglial cell fates to generate oligodendrocyte precursors and 3. lead to an entire remodelling of the classical architecture of the SEZ.
Bisphenols and phthalates, chemicals frequently used in plastic products, promote obesity in cell and animal models. However, these well-known metabolism disrupting chemicals (MDCs) represent only a minute fraction of all compounds found in plastics. To gain a comprehensive understanding of plastics as a source of exposure to MDCs, we characterized all chemicals present in 34 everyday products using nontarget high-resolution mass spectrometry and analyzed their joint adipogenic activities by high-content imaging. We detected 55,300 chemical features and tentatively identified 629 unique compounds, including 11 known MDCs. Importantly, chemicals that induced proliferation, growth, and triglyceride accumulation in 3T3-L1 adipocytes were found in one third of the products. Since the majority did not target peroxisome proliferator-activated receptor γ, the effects are likely to be caused by unknown MDCs. Our study demonstrates that daily-use plastics contain potent mixtures of MDCs and can, therefore, be a relevant yet underestimated environmental factor contributing to obesity.
Teaser Plastics contain a potent mixture of chemicals promoting adipogenesis, a key process in developing obesity.
Bisphenols and phthalates, chemicals frequently used in plastic products, promote obesity in cell and animal models. However, these well-known metabolism-disrupting chemicals (MDCs) represent only a minute fraction of all compounds found in plastics. To gain a comprehensive understanding of plastics as a source of exposure to MDCs, we characterized the chemicals present in 34 everyday products using nontarget high-resolution mass spectrometry and analyzed their joint adipogenic activities by high-content imaging. We detected 55,300 chemical features and tentatively identified 629 unique compounds, including 11 known MDCs. Importantly, the chemicals extracted from one-third of the products caused murine 3T3-L1 preadipocytes to proliferate, and differentiate into adipocytes, which were larger and contained more triglycerides than those treated with the reference compound rosiglitazone. Because the majority of plastic extracts did not activate the peroxisome proliferator-activated receptor γ and the glucocorticoid receptor, the adipogenic effects are mediated via other mechanisms and, thus, likely to be caused by unknown MDCs. Our study demonstrates that daily-use plastics contain potent mixtures of MDCs and can, therefore, be a relevant yet underestimated environmental factor contributing to obesity.
Acetobacterium woodii utilizes the Wood‐Ljungdahl pathway for reductive synthesis of acetate from carbon dioxide. However, A. woodii can also perform non‐acetogenic growth on 1,2‐propanediol (1,2‐PD) where instead of acetate, equal amounts of propionate and propanol are produced as metabolic end products. Metabolism of 1,2‐PD occurs via encapsulated metabolic enzymes within large proteinaceous bodies called bacterial microcompartments. While the genome of A. woodii harbours 11 genes encoding putative alcohol dehydrogenases, the BMC‐encapsulated propanol‐generating alcohol dehydrogenase remains unidentified. Here, we show that Adh4 of A. woodii is the alcohol dehydrogenase required for propanol/ethanol formation within these microcompartments. It catalyses the NADH‐dependent reduction of propionaldehyde or acetaldehyde to propanol or ethanol and primarily functions to recycle NADH within the BMC. Removal of adh4 gene from the A. woodii genome resulted in slow growth on 1,2‐PD and the mutant displayed reduced propanol and enhanced propionate formation as a metabolic end product. In sum, the data suggest that Adh4 is responsible for propanol formation within the BMC and is involved in redox balancing in the acetogen, A. woodii.
Gene therapy has garnered increasing interest over recent decades. Several therapies employing gene transfer mechanisms have been developed, and, of these, adeno-associated virus (AAV) vectors have demonstrated viability for use with in vivo gene therapy. Several AAV-based therapeutics have received regulatory approval in the last few years including those for retinal disease, spinal muscular atrophy or aromatic L-amino acid decarboxylase deficiency. Lately, with the introduction of novel liver-directed AAV vector-based therapeutics for the treatment of haemophilia A and B, gene therapy has attracted significant attention in the hepatology community, with the liver increasingly recognised as a target for gene therapy. However, the introduction of foreign DNA into hepatocytes is associated with a risk of hepatic reactions, with raised ALT (alanine aminotransferase) and AST (aspartate aminotransferase) being – so far – the most commonly reported side effects. The complete mechanisms underlying the ALT flairs remain to be determined and the long-term risks associated with these new treatments is not yet known. The liver community is increasingly being asked to support liver-directed gene therapy to mitigate potential liver associated harm. In this review, we focus on AAV vector-based gene therapy, shedding light on this promising technique and its remarkable success in haemophilia, with a special focus on hepatic complications and their management in daily clinical practice.
Signal-dependent regulation of actin dynamics is essential for many cellular processes, including directional cell migration. In particular, cell migration is initiated by lamellipodia, actin-based protrusions of the plasma membrane. The formation of these protruding structures require incessant assembly and disassembly of actin filaments. The Arp2/3 complex and WAVE proteins are essential for both lamellipodium formation and its dynamics. WAVEs mediate the activation of the Arp2/3 complex downstream of the small GTPase Rac, thus being critical for Rac- and RTK-induced actin polymerization and cell migration. The WAVE-family proteins are always found associated with multiprotein complexes. The most abundant WAVE-based complex is referred to as the WANP (WAVE2-Abi-1-Nap1-PIR121) complex. IQGAP1 is a huge scaffolding protein with multiple protein-interacting domains. IQGAP1 participates in many fundamental activities, including regulation of the actin cytoskeleton, mitogenic, adhesive and migratory responses, as well as in cell polarity and cellular trafficking. IQGAP1 binds to N-WASP, thus raising the possibility that it might control actin nucleation by the Arp2/3 complex. In this study, IQGAP1 was found co-immunoprecipitated not only with WAVE, but also with the endogenous WANP-complex subunits. Correspondingly, IQGAP1 associated to both anti-WAVE and anti-Abi-1 immuno-complexes. Pull-down experiments proved that IQGAP1 binds directly to the WANP-complex subunits. Physical interaction between IQGAP1 and the reconstituted WANP complex could also be demonstrated. Together, these data indicate that IQGAP1 is an accessory component of the WANP complex. Interestingly, the IQGAP-WANP complex disassembled after either EGF stimulation or transfection with constitutively active Cdc42 and Rac1. HeLa cells devoid of IQGAP1 showed diminished and less persistent ruffling upon EGF, but not HGF, stimulation in comparison with the control. This phenotype was accompanied by a strong reduction in chemotaxis towards both growth factors, which was as dramatic as in WANP-complex knockdown (KD) cells. Moreover, GM130 and Giantin showed a polarized and flat ribbon-like pattern in control cells, as it is expected for cis- and cis/medial-Golgi markers. Conversely, small and dispersed vesicular structures were found in both IQGAP1 KD and WANP-complex KD cells. Importantly, Arp2/3-complex silencing resulted in the same phenotypes. Consistently, Brefeldin A-induced disassembly of the Golgi strongly inhibited the IQGAP1-WANP-complex interaction and chemotaxis towards EGF in wild-type cells. The re-expression of an RNAi-resistant wild-type IQGAP1 in IQGAP1 KD cells fully rescued both the ruffling abilities and Golgi structure. A constitutively active mutant, unable to bind to neither Rac1 /Cdc42 nor the WANP complex, could reconstitute only the former defect. Hence, this study shows that actin dynamics regulated by the IQGAP1-WANP complex controls Golgi-apparatus architecture and its contribution to cell chemotaxis. The working model here proposes that at the Golgi apparatus, recruitment of the WANP complex by IQGAP1 leads to the assembly of actin filaments required to maintain the appropriated Golgi morphology. The dissociation of the complex may be required to allow the remodeling of the Golgi membranes in order to respond following a chemoattractant gradient.
Background: Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments.
Results: We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction.
Conclusions: Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation.
Lysosomes are major degradative organelles that contain enzymes capable of breaking down proteins, nucleic acids, carbohydrates, and lipids. In the last decade, new discoveries have traced also important roles for lysosomes as signalling hubs, affecting metabolism, autophagy and pathogenic infections. Therefore, maintenance of a healthy lysosome population is of utmost importance to the cell to respond to both stress conditions and also homeostatic signalling. For example, for minor perturbations to the lysosomal membrane, the cell activates repair processes which seal membrane nicks. For more extensive damage, autophagy is activated to remove damaged organelles from the cell. on the other hand, during pathogen invasion host cells have also evolved mechanisms to hijack the endolysosomal pathway to facilitate their own growth and replication in host cells.
The first part of the thesis work focuses on a lysosomal regeneration program which is activated under conditions where the entire lysosomal pool of the cell is damaged. Upon extensive membrane damage induced by the lysosomotropic drug LLOMe, the cell activates a regeneration pathway which helps in the formation of new functional lysosomes by recycling damaged membranes. I have identified the molecules important for this novel pathway of lysosomal regeneration and showed how the protein TBC1D15 orchestrates this process to regenerate functional organelles from completely damaged membrane masses in the first 2 hours following lysosomal membrane damage. This process resembles the process of auto- lysosomal reformation (ALR)- involving the formation of lysosomal tubules which are extended along microtubules and cleaved in a dynamin2 dependent manner to form proto-lysosomes which develop into fully functional mature lysosomes. These lysosomal tubules are closely associated with ATG8 positive autophagosomal membranes and require ATG8 proteins to bind to the lysophagy receptor LIMP2 on damaged membranes. This process is physiologically important under conditions of crystal nephropathy where calcium oxalate crystals induce damage to lysosomal membranes in nephrons in kidney disease.
The second part of the thesis shows how the endolysosomal system of the cell is hijacked by the bacteriaLegionella pneumophila. During Legionella infection the formation of conventional ATG8 positive autophagosomes are blocked due to the protease activity of the bacterial effector protein RavZ which cleaves lipidated ATG8 proteins from autophagosomal membranes. The SidE effectors of Legionella modify STX17 and SNAP29 by the process of non-canonical ubiquitination called phosphoribose-linked serine ubiquitination (PR-Ub). These proteins are essential for the formation of the autophagosomal SNARE complex which is used for fusion of the autophagosome with the lysosome. Upon Legionella infection, PR-UB of STX17 aids in formation of autophagosome-like replication vacuoles. ThesevacuolesdonotfusewiththelysosomebecauseSNAP29isalsoPR-Ubmodified. PR-UbofSTX17 and SNAP29 sterically blocks the formation of the autophagosomal-SNARE complex thereby preventing fusion of the autophagosome with the lysosome. As a result, Legionella can replicate in autophagosome- like vacuoles which do not undergo lysosomal degradation. In absence of PR-Ub modified STX17, bacterial replication is compromised when measured by bacterial replication assays in lung epithelial (A549) cells.
Taken together, this thesis highlights two important aspects of the autophagy-lysosomal system- how it responds to extensive membrane damage and its importance in Legionella pneumophila infection. Extensive damage to lysosomal membranes triggers a rapid regeneration process to partially restore lysosomal function before the effects of TFEB dependent lysosomal biogenesis becomes apparent. On the other hand, Legionella pneumophila infection segregates the lysosomes from the rest of the endo-lysosomal system by blocking autophagosome-lysosome fusion. Though lysosomes remain active, they are incapable of degrading pathogens since pathogen containing vacuoles do not fuse with the lysosome.
Summary statement When echolocating under demanding conditions e.g. noisy, narrow space, or cluttered environments, frugivorous bats adapt their call pattern by increasing the call rate within biosonar groups.
Abstract For orientation, echolocating bats emit biosonar calls and use echoes arising from call reflections. They often pattern their calls into groups which increases the rate of sensory feedback over time. Insectivorous bats emit call groups at a higher rate when orienting in cluttered compared to uncluttered environments. Frugivorous bats increase the rate of call group emission when they echolocate in noisy environments. Here, calls emitted by conspecifics potentially interfere with the bat’s biosonar signals and complicate the echolocation behavior. To minimize the information loss followed by signal interference, bats may profit from a temporally increased sensory acquisition rate, as it is the case for the call groups. In frugivorous bats, it remains unclear if call group emission represents an exclusive adaptation to avoid interference by signals from other bats or if it represents an adaptation that allows to orient under demanding environmental conditions. Here, we compared the emission pattern of the frugivorous bat Carollia perspicillata when the bats were flying in noisy versus silent, narrow versus wide or cluttered versus non-cluttered corridors. According to our results, the bats emitted larger call groups and they increased the call rate within the call groups when navigating in narrow, cluttered, or noisy environments. Thus, call group emission represents an adaptive behavior when the bats orient in complex environments.
In our rapidly changing world, land use has been recognized as having one of the strongest impacts on species and genetic diversity. The present state of temperate forests in Europe is a product of decisions made by former and current management and policy actions, rather than natural factors. Alterations of crown projection areas, structural complexity of the forest stand caused by thinning and cuttings, and changes in tree species composition caused by regeneration or plantings not only affect forest interior buffering against warming, but also the understorey light environment and nutrient availability. Ultimately, current silvicultural management practices have deep impact on the forest ecosystems, microenvironmental changes and forest floor understorey herbs. In response to environmental changes, plants rely on genetically heritable phenotypic variation, an important level of variation in the population, as it is prerequisite for adaptation. However, until now most studies on plant adaptation to land use focus on grassland management. Yet, studies on the adaptation of forest understorey herbs to forest management have been absent so far. This is important because understanding adaptation of understorey herbs is crucial for biodiversity conservation, forest restoration, and climate change mitigation. Studying current adaptation of understorey herbs to forest management yields insights into the evolutionary consequences of management practices, which could be employed to improve sustainable use of forest habitat.
In sum, my conducted experiments complement each other well and managed to fill in research gaps on the topic of genetically heritable phenotypic variation in understorey herbs and how it is affected by forest management and related microenvironmental variables. I showed that forest management has direct evolutionary consequences on the genetic basis of understorey herbs, but also indirectly through the microenvironment. Furthermore, I revealed that local adaptation and phenotypic plasticity of understorey herbs to forest structural attributes act along continuous gradients. And lastly, I highlighted the important role of intra-individual variation by revealing plastic responses to drought and shading, urging researchers to not ignore this important level of trait variation. Ultimately, understorey herbs in temperate forests employ phenotypic plasticity as a flexible strategy to adapt to varying environmental conditions. By adjusting their leaf characteristics, reproductive investment, and phenology, they can optimize their fitness and survival in response to changes in light availability, resource availability, and seasonal cues. The anthropogenic impact on temperate forests and understorey herbs will continue and likely increase in the future. This should urge foresters to adapt their silvicultural management decisions towards the long-term preservation of genetic diversity and, through this, the evolvability and adaptability of forest understorey herbs and associated organisms. Based on the results shown in my dissertation, variation in forest management regimes and types could be beneficial for promoting genetic diversity within several species of forest understorey herbs. Lastly, in the face of future climatic changes, the mechanisms by which plants can cope with increasing stressful environmental conditions might very well rely heavily on intra-individual variation, providing the necessary rapid plastic adjustment to changing microclimatic conditions within populations and thus increase climate change resilience.
Soil fungal communities are an essential element in the terrestrial ecosystem, however their response to ongoing anthropogenic climate change is currently poorly understood. Fungi are one of the most abundant groups of microbes in soil, they are mainly responsible for the decomposition of organic matter (Baldrian et al., 2012; Buée et al., 2009). By binding carbon in soil, fungi thus maintain an important role in the global carbon cycle (Bardgett et al., 2008). Future climates are likely to influence the communities of belowground microbial organisms (Castro et al., 2010; Deacon et al., 2006). However, how these communities are affected in their diversity, composition, and function after environmental perturbation is insufficiently known.
Molecular techniques using high-throughput sequencing are presently revolutionizing the analysis of complex communities, such as soil fungi. High-throughput metabarcoding enables the recovery of DNA sequence data directly from environmental samples, and DNA sequences from entire communities present in these samples can be simultaneously recovered through massively parallel sequencing reactions (Bik et al., 2012; Taberlet et al., 2012b). This results in more accurate estimation of diversity and community composition and thus provides unprecedented insight into cryptic communities (Lindahl and Kuske, 2014). Yet, challenges associated with these novel techniques include the bioinformatic processing, and the ecological analyses of the large amount of sequence data generated. Most biologists without explicit training in bioinformatics spend a fair amount of time learning how to filter raw sequence data, and customize bioinformatics pipelines specific to their project. To improve the quality of data treatment, and decrease the time needed for the analyses, it is desirable to have bioinformatics pipelines that are easy to use, well explained to researchers not trained in bioinformatics, and adaptable to individual research needs...
This thesis describes the adaptation of Acinetobacter species to dry environments with the soil bacterium A. baylyi and the opportunistic hospital pathogen A. baumanii in its focus. The adaptation of A. baylyi and A. baumannii to osmotic stress was investigated. Compatible solutes that were uptaken from the environment or synthesized de novo to cope with the loss of water at high salinity were identified. The corresponding transporters and enzymes involved were characzerized. In addition, the desiccation resistance of A. baumannii was analyzed to elucidate its survival in hospital environments. The usage of compatible solutes during desiccation stress was analyzed and proteins that were produced were identified.
The availability of water is essential for bacterial life and if environmental conditions are awkward, bacteria have to cope with high salinitiy to prevent loss of water. In this thesis it was shown that A. baylyi synthesizes glutamate and mannitol de novo as compatible solutes in response to osmotic stress to balance the osmotic potential. The pathway for mannitol biosynthesis from Fructose-6-Phosphate (F-6-P) via Mannitol-1-Phosphate (Mtl-1-P) was elucidated and the isolation and characterization of a novel type of biofunctional enzyme was described. Interestingly, the unique bifunctional enzyme MtlD, acting as dehydrogenase and phosphatase, mediates both steps of the mannitol biosynthesis pathway. This enzyme catalyzes the reduction of F-6-P to Mtl-1-P with NADPH as reducing equivalent. The dehydrogenase activity of MtlD was salt dependent and the phosphatase activity was dependent on Mg2+ as cofactor. Phylogenetic analyses revealed that MtlD is broadly distributed among other Acinetobacter strains but not in other phylogenetic tribes.
In this thesis it is also described that, besides de novo synthesis of compatible solutes, A. baylyi takes up glycine betaine (GB) or its precursor choline by different transport systems and uses this solutes as osmoprotectants. The uptake of GB occurs via a secondary transporter (ACIAD3460) of the BCCT family. Choline is taken up as precursor and oxidized to GB by two dehydrogenases. The uptake and use of choline as GB precursor involves two transporters, whose genes are encoded in the bet cluster (BetT1, BetT2), two dehydrogenases (BetA, BetB) and a regulatory protein (BetI). Both transporters differ from each other in structure and function: BetT1 is osmo-independent and active independently of osmotic stress. BetT2 contains - in contrast to BetT1 - a long C-terminal domain for osmo-sensing and its activity highly increases in the presence of high osmolarity. The oxidation of choline occurs independently of the osmolarity of the medium but in the absence of salt stress, GB is exported. In contrast, in the presence of high salinity, GB is accumulated in the cytoplasm to balance the osmotic potential in order to prevent loss of water. The regulation of both transporters, the uptake of choline independently of the osmolarity and the export of GB under isoosmotic conditions are regulated by the transcriptional regulator BetI.
A. baumannii ATCC 19606 was also shown to cope with high salinity. Analogously to A. baylyi, A. baumannii ATCC19606 synthesizes glutamate and mannitol de novo in response to osmotic stress. The genes for the synthesis of these compatible solutes are identical to those found in A. baylyi. This suggests that the solute biosynthesis pathways of A. baumannii and A. baylyi are identical. A. baumannii was also able to take up GB and choline in response to osmotic stress and growth at high salinity was restored upon addition of GB and its precursor choline. The bet cluster was also present in the genome A. baumannii and also contains the two different choline transporters BetT1 and BetT2.
Our suggestion that choline or GB or the utilization of phosphatidylcholine as carbon source led to an increase in the survival under desiccation stress was not confirmed. However, 2D analysis of proteins produced during desiccation stress in A. baumannii led to elevated amounts of proteins implicated in biofilm formation, regulation, cell morphology and general stress response, such as Hsp60 or superoxide dismutase, both might play a role in general stress protection.
ADAM15 protein amplifies focal adhesion kinase phosphorylation under genotoxic stress conditions
(2012)
ADAM15, a disintegrin and metalloproteinase, is capable of counteracting genotoxic stress-induced apoptosis by the suppression of caspase-3 activation. A cell line expressing the membrane-bound ADAM15 without its cytoplasmic tail, however, lost this anti-apoptotic property, suggesting a crucial role of the intracellular domain as a scaffold for recruitment of survival signal-transducing kinases. Accordingly, an enhanced phosphorylation of FAK at Tyr-397, Tyr-576, and Tyr-861 was detected upon genotoxic stress by camptothecin in ADAM15-transfected T/C28a4 cells, but not in transfectants expressing an ADAM15 mutant without the cytoplasmic tail. Accordingly, a specific binding of the cytoplasmic ADAM15 domain to the C terminus of FAK could be shown by mammalian two-hybrid, pulldown, and far Western studies. In cells expressing full-length ADAM15, a concomitant activation of Src at Tyr-416 was detected upon camptothecin exposure. Cells transfected with a chimeric construct consisting of the extracellular IL-2 receptor α-chain and the cytoplasmic ADAM15 domain were IL-2-stimulated to prove that the ADAM15 tail can transduce a percepted extracellular signal to enhance FAK and Src phosphorylation. Our studies further demonstrate Src binding to FAK but not a direct Src interaction with ADAM15, suggesting FAK as a critical intracellular adaptor for ADAM15-dependent enhancement of FAK/Src activation. Moreover, the apoptosis induction elicited by specific inhibitors (PP2, FAK 14 inhibitor) of FAK/Src signaling was significantly reduced by ADAM15 expression. The newly uncovered counter-regulatory response to genotoxic stress in a chondrocytic survival pathway is potentially also relevant to apoptosis resistance in neoplastic growth.
ADAM15, which belongs to the family of the disintegrin and metalloproteinases, is a multi-domain transmembrane protein. A strongly upregulated expression of ADAM15 is found in inflamed synovial membranes from articular joints affected by osteoarthritis and especially rheumatoid arthritis (RA). During the chronic inflammatory process in RA the synovial membrane gets hyperplastic, resulting eventually in the formation of a pannus tissue, which can invade into the adjacent cartilage and bone thereby destroying their integrity. Previously, the expression of ADAM15 in fibroblasts of the RA synovial membrane was found to confer a significant anti-apoptotic response upon triggering of the Fas receptor, which resulted in the activation of two survival kinases, focal adhesion kinase (FAK) and Src. The Fas receptor, also named CD95, belongs to the death receptor family of the tumor necrosis factor receptors and stimulation of Fas/CD95 by its ligand FasL results in the execution of apoptotic cell death in synovial membranes of RA patients. However, the occurrence of apoptotic cell death in vivo in RA synovial tissues is considerably low despite the presence of FasL at high concentrations in the chronically inflamed joint. Accordingly, a general apoptosis resistance is a characteristic of RA-synovial fibroblasts that contributes considerably to the formation the hyperplastic aggressive pannus tissue. The objective of this study was to investigate the mechanisms underlying the capability of ADAM15 to transform FasL-mediated death- inducing signals into pro-survival activation of Src and FAK in rheumatoid arthritis fibroblasts (RASFs).
In the present study, the down-regulation of ADAM15 by RNA interference resulted in a significant increase of caspase 3/7 activity upon stimulation of the Fas receptor in RASFs. Likewise, chondrocytes expressing a deletion mutant of ADAM15 (ΔC), lacking the cytoplasmic domain, revealed increased caspase activities upon Fas ligation in comparison to cells transfected with full-length ADAM15, clearly demonstrating the importance of the cytoplasmic domain for an increased apoptosis resistance. Furthermore, activation of the Fas receptor triggered the phosphorylation of Src at Y416, which results in the active conformation of Src, as well as the phosphorylation of FAK at Y576/577 and Y861 – the target tyrosines phosphorylated by Src - in full-length ADAM15-transfected chondrocytes. However, cells transfected with ADAM15 mutant (ΔC) or with vector control did not exhibit any activation of Src and FAK upon Fas ligation. This suggested the presence of an as yet unknown protein interaction mediating the Fas triggered activation of the two kinases.
In order to identify this mechanism, the application of signal transduction inhibitors interfering with Calcium signaling either by inhibiting calmodulin with trifluoperazine (TFP) or the Calcium release-activated channel (CRAC/Orai1) with BTP-2 efficiently inhibited the phosphorylation of FAK and Src, revealing a role of calmodulin, the major Ca2+ sensor in cells, in ADAM15-dependent and Fas-elicited activation of the two survival kinases. Also, a direct Ca2+ -dependent binding of calmodulin to ADAM15 could be demonstrated by pull-down assays using calmodulin-conjugated sepharose and by protein binding assays using the recombinant cytoplasmic domain of ADAM15 and calmodulin.
Furthermore, it could be demonstrated in living synovial fibroblasts by double immunofluorescence stainings that triggering the Fas receptor by its ligand FasL or a Fas-activating antibody resulted in the recruitment of calmodulin to ADAM15 as well as to the Fas receptor in patch-like structures at the cell membrane. Simultaneously, Src associated with calmodulin was shown to become engaged in an ADAM15 complex, also containing cytoplasmic-bound FAK, by co-immunoprecipitations.
Additional studies were performed to analyze the efficacy of TFP and BTP-2 on apoptosis induction in synovial fibroblasts from 10 RA patients. Using caspase 3/7 and annexin V stainings for determining apoptosis, it could be shown that both inhibitors did not possess any apoptosis inducing capacity. However, when co-incubated with FasL both compounds synergistically enhanced apoptosis rates in the RASFs. Moreover, an additional silencing of ADAM15 revealed a further significant rise in apoptosis rates upon incubation with FasL/TFP or FasL/BTP-2, providing unequivocal evidence for an involvement of ADAM15 in facilitating apoptosis resistance in RASFs.
Taken together, these results demonstrate that ADAM15 provides a scaffold for the formation of calmodulin-dependent pro-survival signaling complexes upon CRAC/Orai1 coactivation by Fas ligation, which provides a new potential therapeutic target to break the apoptosis resistance in RASFs that critically contributes to joint destruction in RA.
Background: Gastrulation is a key transition in embryogenesis; it requires self-organized cellular coordination, which has to be both robust to allow efficient development and plastic to provide adaptability. Despite the conservation of gastrulation as a key event in Metazoan embryogenesis, the morphogenetic mechanisms of self-organization (how global order or coordination can arise from local interactions) are poorly understood.
Results: We report a modular structure of cell internalization in Caenorhabditis elegans gastrulation that reveals mechanisms of self-organization. Cells that internalize during gastrulation show apical contractile flows, which are correlated with centripetal extensions from surrounding cells. These extensions converge to seal over the internalizing cells in the form of rosettes. This process represents a distinct mode of monolayer remodeling, with gradual extrusion of the internalizing cells and simultaneous tissue closure without an actin purse-string. We further report that this self-organizing module can adapt to severe topological alterations, providing evidence of scalability and plasticity of actomyosin-based patterning. Finally, we show that globally, the surface cell layer undergoes coplanar division to thin out and spread over the internalizing mass, which resembles epiboly.
Conclusions: The combination of coplanar division-based spreading and recurrent local modules for piecemeal internalization constitutes a system-level solution of gradual volume rearrangement under spatial constraint. Our results suggest that the mode of C. elegans gastrulation can be unified with the general notions of monolayer remodeling and with distinct cellular mechanisms of actomyosin-based morphogenesis.
Poster presentation: Our work deals with the self-organization [1] of a memory structure that includes multiple hierarchical levels with massive recurrent communication within and between them. Such structure has to provide a representational basis for the relevant objects to be stored and recalled in a rapid and efficient way. Assuming that the object patterns consist of many spatially distributed local features, a problem of parts-based learning is posed. We speculate on the neural mechanisms governing the process of the structure formation and demonstrate their functionality on the task of human face recognition. The model we propose is based on two consecutive layers of distributed cortical modules, which in turn contain subunits receiving common afferents and bounded by common lateral inhibition (Figure 1). In the initial state, the connectivity between and within the layers is homogeneous, all types of synapses – bottom-up, lateral and top-down – being plastic. During the iterative learning, the lower layer of the system is exposed to the Gabor filter banks extracted from local points on the face images. Facing an unsupervised learning problem, the system is able to develop synaptic structure capturing local features and their relations on the lower level, as well as the global identity of the person at the higher level of processing, improving gradually its recognition performance with learning time. ...