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Importance of latrine communication in European rabbits shifts along a rural–to–urban gradient
(2016)
Background: Information transfer in mammalian communication networks is often based on the deposition of excreta in latrines. Depending on the intended receiver(s), latrines are either formed at territorial boundaries (between-group communication) or in core areas of home ranges (within-group communication). The relative importance of both types of marking behavior should depend, amongst other factors, on population densities and social group sizes, which tend to differ between urban and rural wildlife populations. Our study is the first to assess (direct and indirect) anthropogenic influences on mammalian latrine-based communication networks along a rural-to-urban gradient in European rabbits (Oryctolagus cuniculus) living in urban, suburban and rural areas in and around Frankfurt am Main (Germany).
Results: The proportion of latrines located in close proximity to the burrow was higher at rural study sites compared to urban and suburban ones. At rural sites, we found the largest latrines and highest latrine densities close to the burrow, suggesting that core marking prevailed. By contrast, latrine dimensions and densities increased with increasing distance from the burrow in urban and suburban populations, suggesting a higher importance of peripheral marking.
Conclusions: Increased population densities, but smaller social group sizes in urban rabbit populations may lead to an increased importance of between-group communication and thus, favor peripheral over core marking. Our study provides novel insights into the manifold ways by which man-made habitat alterations along a rural-to-urban gradient directly and indirectly affect wildlife populations, including latrine-based communication networks.
Xenorhabdus and Photorhabdus bacteria are gaining more and more attention as a subject of research because of their unique yet similar life cycle with nematodes and insects. This work focused on the secondary metabolites that are produced by Xenorhabdus and Photorhabdus. With the help of modern HPLC-MS methodologies and increasingly available bacterial genome sequences, the structures of unknown secondary metabolites could be elucidated and thus their biosynthesis pathways could be proposed, too.
The first paper reported 17 depsipeptides termed xentrivalpeptides produced by the bacterium Xenorhabdus sp. 85816. Xentrivalpeptide A could be isolated from the bacterial culture as the main component. The structure of xentrivalpeptide A was elucidated by NMR and the Marfey´s method. The remaining xentrivalpeptides were exclusively identified by feeding experiments and MS fragmentation patterns.
The second paper described the discovery and isolation of xenoamicin A from Xenorhabdus mauleonii DSM17908. Additionally, other xenoamicin derivatives from Xenorhabdus doucetiae DSM17909 were analyzed by means of feeding experiments and MS fragmentation patterns. The xenoamicin biosynthesis gene cluster was identified in Xenorhabdus doucetiae DSM17909.
The manuscript for publication focused on the biosynthesis of anthraquinones in Photorhabdus luminescens. The Type II polyketide synthase for the biosynthesis of anthraquinone derivatives was discovered in P. luminescens in a previous publication by the Bode group,1 in which a partial reaction mechanism for the biosynthesis has been proposed. The manuscript reported in this thesis however elucidated the biosynthetic mechanisms in a greater detail as compared to the previous publication. Particularly, the biosynthetic mechanism was deciphered through heterologous expression of anthraquinone biosynthesis (ant) genes in E. coli. Additionally, deactivation of the genes antG encoding a putative CoA ligase and antI encoding a putative hydrolase, was performed in P. luminescens. Selected ant genes were over-expressed in E. coli as well as the corresponding proteins purified for in vitro assays. Model compounds were chemically synthesized as possible substrates of AntI and were used for in vitro assays. Here, it was revealed that the CoA ligase AntG played an essential role in the activation of the ACP AntF. Furthermore, a chain shortening mechanism by the hydrolase AntI was identified and was further confirmed by in vitro assays using model compounds. Additionally, this chain shortening mechanism was supported by homology based structural modeling of AntI.
Ribosomes are large ribonucleoprotein complexes that are fundamental for protein synthesis. Ribosomes are ribozymes because their catalytic functions such as peptidyl transferase and peptidyl-tRNA hydrolysis depend on the rRNA. rRNA is a heterogeneous biopolymer comprising of at least 112 chemically modified residues that are believed to expand its topological potential. In the present study, we established a comprehensive modification profile of Saccharomyces cerevisiae’s 18S and 25S rRNA using a high resolution Reversed-Phase High Performance Liquid Chromatography (RP-HPLC). A combination of mung bean nuclease assay, rDNA point mutants and snoRNA deletions allowed us to systematically map all ribose and base modifications on both rRNAs to a single nucleotide resolution. We also calculated approximate molar levels for each modification using their UV (254nm) molar response factors, showing sub-stoichiometric amount of modifications at certain residues. The chemical nature, their precise location and identification of partial modification will facilitate understanding the precise role of these chemical modifications, and provide further evidence for ribosome heterogeneity in eukaryotes.
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...
The worldwide use of neonicotinoid pesticides has caused concern on account of their involvement in the decline of bee populations, which are key pollinators in most ecosystems. Here we describe a role of non-neuronal acetylcholine (ACh) for breeding of Apis mellifera carnica and a so far unknown effect of neonicotinoids on non-target insects. Royal jelly or larval food are produced by the hypopharyngeal gland of nursing bees and contain unusually high ACh concentrations (4–8 mM). ACh is extremely well conserved in royal jelly or brood food because of the acidic pH of 4.0. This condition protects ACh from degradation thus ensuring delivery of intact ACh to larvae. Raising the pH to ≥5.5 and applying cholinesterase reduced the content of ACh substantially (by 75–90%) in larval food. When this manipulated brood was tested in artificial larval breeding experiments, the survival rate was higher with food supplemented by 100% with ACh (6 mM) than with food not supplemented with ACh. ACh release from the hypopharyngeal gland and its content in brood food declined by 80%, when honeybee colonies were exposed for 4 weeks to high concentrations of the neonicotinoids clothianidin (100 parts per billion [ppb]) or thiacloprid (8,800 ppb). Under these conditions the secretory cells of the gland were markedly damaged and brood development was severely compromised. Even field-relevant low concentrations of thiacloprid (200 ppb) or clothianidin (1 and 10 ppb) reduced ACh level in the brood food and showed initial adverse effects on brood development. Our findings indicate a hitherto unknown target of neonicotinoids to induce adverse effects on non-neuronal ACh which should be considered when re-assessing the environmental risks of these compounds. To our knowledge this is a new biological mechanism, and we suggest that, in addition to their well documented neurotoxic effects, neonicotinoids may contribute to honeybee colony losses consecutive to a reduction of the ACh content in the brood food.
Embryonale Stammzellen (ESCs) sind ein wichtiges Werkzeug zur Untersuchung der frühen embryonalen Entwicklung. ESCs können mit Hilfe neuer Technologien zur Modifikation von Genen (z.B. mit dem CRISPR/Cas9 System) genetisch manipuliert werden. Daraus resultierende „knockout“ ES Zelllinien können helfen, die physiologische Rolle von Proteinen während der Differenzierung zu verstehen.
Transkriptionsfaktoren, die schnell und spezifisch Signalwege regulieren, spielen während der Embryonalentwicklung und während der Differenzierung von ESCs in vielen verschiedenen Zelltypen eine essentielle Rolle. Der Transkriptionsregulator „Far Upstream Binding Protein 1“ (FUBP1) ist ein Protein, welches eine ganz bestimmte einzelsträngige DNA Sequenz, das „Far Upstream Sequenz Element“, erkennt, bindet, und dadurch Gene wie z.B c-myc oder p21 reguliert. Mit der Entwicklung zweier Fubp1 Genfallen Mausstämme (Fubp1 GT) sollte die Frage nach der physiologischen Funktion von FUBP1 beantwortet werden. Die homozygoten FUBP1-defizienten GT Embryonen sterben im Mutterleib ungefähr am Tag E15.5 der Embryonalentwicklung. Sie sind kleiner als Wildtypembryonen und zeigen ein anämisches Aussehen. Daher wurden diese Mausmodelle hinsichtlich der Hämatopoese untersucht, die zu diesem Zeitpunkt vor allem in der Leber stattfindet. Es konnte eine signifikante Reduktion der hämatopoetischen Stammzellen (HSCs) festgestellt werden und zusätzlich war die langfristige Repopulation der FUBP1-/--Stammzellen im Knochenmark in Transplantationsexperimenten reduziert.
In der vorliegenden Arbeit wurde die Rolle von FUBP1 in einem weiteren Stammzellsystem analysiert und gleichzeitig seine Bedeutung in anderen Zelltypen der frühen Embryonalentwicklung untersucht.
Die Quantifizierung der FUBP1 Expression in den ESCs und während der Differenzierung zu sogenannten `embryoid bodies` (EBs) zeigten eine starke Expression auf mRNA- und auf Proteinebene. Nach der erfolgreichen Optimierung der Differenzierung von murinen ESCs wurden Fubp1 „knockout“ (KO) ESC Klone mit Hilfe der CRISPR/Cas9 Technologie etabliert. Die molekularbiologische Analyse der ESCs zeigte eine signifikante Erhöhung der Oct4 mRNA-Expression, während Nanog und die Differenzierungsmarker Brachyury, Nestin und Sox17 unverändert und in vergleichbarer Menge zu den Kontrollen vorhanden waren. Während der Differenzierung der Fubp1 KO Klone zu EBs zeigte sich eine signifikante Reduktion mesodermaler Marker wie Flk-1, SnaiI, Snai2, Bmp4 und FgfR2. Mit Hilfe durchflusszytometrischer Analysen bestätigte sich die verzögerte Bildung mesodermaler Zellen (Brachyury- und Flk-1-exprimierender Zellen) in den Fubp1 KO Klonen der EBs an den Tagen 3, 4 und 5 nach Beginn der Differenzierung.
Die Anwendung einer Ko-Kultivierung auf OP9 Zellen zur Differenzierung der ESCs in hämatopoetische Linien sollte zeigen, ob der Fubp1 KO ESCs ein Defekt in der frühen Entwicklung hämatopoetischer Stammzellen zu beobachten ist. Erneut konnte am Tag 5 der ESC-Differenzierung in der OP9 Ko-Kultur eine signifikante Reduktion der mesodermalen (Flk-1+) Zellen festgestellt werden. Die weitere Differenzierung zu hämatopoetischen CD45+ Zellen zeigte jedoch keinen Unterschied im prozentualen Anteil CD45+ Zellen am Tag 12 der Differenzierung. Auch die gezielte Differenzierung zu erythroiden Zellen durch Zugabe des Zytokins EPO zum Medium zeigte keinen signifikanten Unterschied im Differenzierungsgrad der erythroiden Zellen zwischen Kontroll- und Fubp1 KO Klonen.
In weiteren Experimenten habe ich in dieser Arbeit die Expression von FUBP1 in WT Embryos an den Tagen E9.5 und E13.5 der Embryonalentwicklung untersucht. Hierbei zeigte sich in beiden Entwicklungsstadien eine immunhistochemische Anfärbung von FUBP1 in den meisten Zellen des Embryos. Die Annahme, dass die Abwesenheit von FUBP1 in der Embryonalentwicklung zu verstärkten apoptotischen Vorgängen führen könnte und gleichzeitig die massive Expansion von Zellen gestört sein könnte wurde mit Hilfe immunhistochemischer Färbung von „cleaved Caspase 3“ (Apoptosemarker) und „Ki-67“ (Proliferationsmarker) in den homozygoten Fubp1 GT Embryos an den Tagen E9.5 und E13.5 nicht bestätigt.
Die Ergebnisse dieser Arbeit lassen darauf schließen, dass die Regulation von Apoptose und Proliferation durch FUBP1 während der Embryonalentwicklung nicht die Hauptrolle von FUBP1 darstellt. Es zeigte sich jedoch, dass FUBP1 als Transkriptionsregulator wichtig für die mesodermale Differenzierung von ESCs ist. Zu beobachten war, dass es in den FUBP1-defizienten ESCs zu einer Verzögerung der mesodermalen Differenzierung kommt. Es konnte bereits gezeigt werden, dass FUBP1 essenziell für die Selbsterneuerung von HSCs ist. Dies macht deutlich, dass FUBP1 neben der Proliferation und Apoptose ein breiteres Spektrum an Signalwegen reguliert, die für Stammzellen und deren Differenzierung von Bedeutung sind.
This report provides a brief review of the 20th annual meeting of the German Language Branch of the Society of Environmental Toxicology and Chemistry (SETAC GLB) held from September 7th to 10th 2015 at ETH (Swiss Technical University) in Zurich, Switzerland. The event was chaired by Inge Werner, Director of the Swiss Centre for Applied Ecotoxicology (Ecotox Centre) Eawag-EPFL, and organized by a team from Ecotox Centre, Eawag, Federal Office of the Environment, Federal Office of Agriculture, and Mesocosm GmbH (Germany). Over 200 delegates from academia, public agencies and private industry of Germany, Switzerland and Austria attended and discussed the current state of science and its application presented in 75 talks and 83 posters. In addition, three invited keynote speakers provided new insights into scientific knowledge ‘brokering’, and—as it was the International Year of Soil—the important role of healthy soil ecosystems. Awards were presented to young scientists for best oral and poster presentations, and for best 2014 master and doctoral theses. Program and abstracts of the meeting (mostly in German) are provided as Additional file 1.
This case study reports on an e-learning course on good academic practice, compulsory for doctoral students of the central graduate academy GRADE at the Goethe University in Frankfurt (Germany). The tool comprises of six closely linked web based trainings. They are designed as a virtual PhD, depicting the different phases of a doctorate and covering the various aspects of good academic practice and potential fields of academic misconduct.
The first step in methanol metabolism in methylotrophic yeasts, the oxidation of methanol and higher alcohols with molecular oxygen to formaldehyde and hydrogen peroxide, is catalysed by alcohol oxidase (AOX), a 600-kDa homo-octamer containing eight FAD cofactors. When these yeasts are grown with methanol as the carbon source, AOX forms large crystalline arrays in peroxisomes. We determined the structure of AOX by cryo-electron microscopy at a resolution of 3.4 Å. All residues of the 662-amino acid polypeptide as well as the FAD are well resolved. AOX shows high structural homology to other members of the GMC family of oxidoreductases, which share a conserved FAD binding domain, but have different substrate specificities. The preference of AOX for small alcohols is explained by the presence of conserved bulky aromatic residues near the active site. Compared to the other GMC enzymes, AOX contains a large number of amino acid inserts, the longest being 75 residues. These segments are found at the periphery of the monomer and make extensive inter-subunit contacts which are responsible for the very stable octamer. A short surface helix forms contacts between two octamers, explaining the tendency of AOX to form crystals in the peroxisomes.
Background: Bacteria within the genus Photorhabdus maintain mutualistic symbioses with nematodes in complicated lifecycles that also involves insect pathogenic phases. Intriguingly, these bacteria are rich in biosynthetic gene clusters that produce compounds with diverse biological activities. As a basis to better understand the life cycles of Photorhabdus we sequenced the genomes of two recently discovered representative species and performed detailed genomic comparisons with five publically available genomes.
Results: Here we report the genomic details of two new reference Photorhabdus species. By then conducting genomic comparisons across the genus, we show that there are several highly conserved biosynthetic gene clusters. These clusters produce a range of bioactive small molecules that support the pathogenic phase of the integral relationship that Photorhabdus maintain with nematodes.
Conclusions: Photorhabdus contain several genetic loci that allow them to become specialist insect pathogens by efficiently evading insect immune responses and killing the insect host.
Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict some novel compounds that are probably involved in cell-cell communication, differing to known communication systems. We identify several gene clusters, which may represent novel signaling mechanisms and demonstrate the natural product potential of Legionella.
Anthropogenic changes in climate and land use are driving changes in migration patterns of birds worldwide. Spatial changes in migration have been related to long-term temperature trends, but the intrinsic mechanisms by which migratory species adapt to environmental change remain largely unexplored. We show that, for a long-lived social species, older birds with more experience are critical for innovating new migration behaviours. Groups containing older, more experienced individuals establish new overwintering sites closer to the breeding grounds, leading to a rapid population-level shift in migration patterns. Furthermore, these new overwintering sites are in areas where changes in climate have increased temperatures and where food availability from agriculture is high, creating favourable conditions for overwintering. Our results reveal that the age structure of populations is critical for the behavioural mechanisms that allow species to adapt to global change, particularly for long-lived animals, where changes in behaviour can occur faster than evolution.
The acoustic startle response (ASR) and its modulation by non-startling prepulses, presented shortly before the startle-eliciting stimulus, is a broadly applied test paradigm to determine changes in neural processing related to auditory or psychiatric disorders. Modulation by a gap in background noise as a prepulse is especially used for tinnitus assessment. However, the timing and frequency-related aspects of prepulses are not fully understood. The present study aims to investigate temporal and spectral characteristics of acoustic stimuli that modulate the ASR in rats and gerbils. For noise-burst prepulses, inhibition was frequency-independent in gerbils in the test range between 4 and 18 kHz. Prepulse inhibition (PPI) by noise-bursts in rats was constant in a comparable range (8–22 kHz), but lower outside this range. Purely temporal aspects of prepulse–startle-interactions were investigated for gap-prepulses focusing mainly on gap duration. While very short gaps had no (rats) or slightly facilitatory (gerbils) influence on the ASR, longer gaps always had a strong inhibitory effect. Inhibition increased with durations up to 75 ms and remained at a high level of inhibition for durations up to 1000 ms for both, rats and gerbils. Determining spectral influences on gap-prepulse inhibition (gap-PPI) revealed that gerbils were unaffected in the limited frequency range tested (4–18 kHz). The more detailed analysis in rats revealed a variety of frequency-dependent effects. Gaps in pure-tone background elicited constant and high inhibition (around 75%) over a broad frequency range (4–32 kHz). For gaps in noise-bands, on the other hand, a clear frequency-dependency was found: inhibition was around 50% at lower frequencies (6–14 kHz) and around 70% at high frequencies (16–20 kHz). This pattern of frequency-dependency in rats was specifically resulting from the inhibitory effect by the gaps, as revealed by detailed analysis of the underlying startle amplitudes. An interaction of temporal and spectral influences, finally, resulted in higher inhibition for 500 ms gaps than for 75 ms gaps at all frequencies tested. Improved prepulse paradigms based on these results are well suited to quantify the consequences of central processing disorders.
In the adult mammalian brain stem cells within defined neurogenic niches retain the capacity for lifelong de novo generation of neurons. The subventricular zone (SVZ) of the lateral ventricles and the subgranular layer (SGL) of the hippocampal dentate gyrus (DG) have been identified as the two major sites of adult neurogenesis. Moreover, the third ventricle in the hypothalamus is emerging as a new neurogenic niche in the adult brain. Extracellular purine and pyrimidine nucleotides are involved in the control of both embryonic and adult neuro-genesis. These nucleotides act via ionotropic P2X or metabotropic P2Y receptors and studies of the adult SVZ and the DG provide strong evidence that ATP promotes progenitor cell proliferation in this stem cell rich regions. Previous studies have shown that the extracellular nucleotide-hydrolyzing enzyme NTPDase2 is highly expressed by adult neural stem and progenitor cells of the SVZ and the rostral migratory stream (RMS), the hippocampal SGL, and the third ventricle. NTPDase2 preferentially hydrolyzes extracellular nucleoside triphosphates (NTPs) and, to a lower extent, diphosphates, thus modulating their effect on nearby nucleotide receptors. Deletion of the enzyme increases extracellular NTP concentrations, and might indicate roles of purinergic signaling in adult neurogenesis. As shown by enzyme histochemistry, genetic deletion of NTPDase2 essentially eliminates ATPase activity in neurogenic niches but does not affect protein expression levels and activity of other ectonucleotidases. Lack of NTPDase2 leads to expansion of the hippocampal stem cell pool as well as of the inter-mediate progenitor type-2 cells. Cell expansion is lost at around type-3 stage, paralleled by increased labeling for caspase-3, indicating increased apoptosis, and decreased levels in CREB phosphorylation in doublecortin-expressing cells, diminishing survival in this cell population. In line with increased cell death, P2Y12 receptor-expressing microglia is enriched at the hilus orientated side of the granule cell layer. These data strongly suggest that NTPDase2 functions as central homeostatic regulator of nucleotide-mediated neural progenitor cell proliferation and expansion in the adult brain by balancing extracellular nucleotide concentrations and activation of purinergic receptors.
In order to further characterize the role of purinergic signaling in adult neurogenesis, the ADP-sensitive P2Y13 receptor was identified as a potential candidate whose activation might inhibit neurogenesis in the hippocampal dentate gyrus and the newly identified neurogenic niche at the third ventricle. Deletion of P2ry13 increased progenitor cell proliferation and long-term progenitor survival as well as new neuron formation in the hippocampal neurogenic niche. This was further paralleled by increased thickening of the granule cell layer, CREB phosphorylation, and expression of the neuronal activity marker c-Fos. Increased progenitor cell proliferation and progenitor survival persist in aged P2ry13 knockout animals. However, in the ventral dentate gyrus proliferation and expansion levels of progenitor cells did not differ significantly from the wild type. This study strongly supports the notion that extracellular nucleotides significantly contribute to the control of adult neurogenesis in the dentate gyrus in situ. Data in this work suggest that activation of the P2Y13 receptor dampens progenitor cell proliferation, new neuron formation, and neuronal activity. In contrast to several in vitro studies and studies in the SVZ in situ, a contribution of the ATP/ADP-sensitive P2Y1 receptor could not be confirmed in the dentate gyrus in vivo.
To unravel implications of purinergic signaling and P2Y13 receptor action in the control of adult hypothalamic neurogenesis a pilot study was performed. Mice null for P2ry13 revealed increased progenitor cell proliferation at the third ventricle as well as long-term progeny survival and new neuron formation in the hypothalamus. In contrast to results obtained in the dentate gyrus expression of the neuronal activity marker c-Fos was significantly decreased in hypothalamic nuclei, indicating increased inhibition of appetite-regulating neuronal circuits by surplus neurons in knockout animals. These data provide first evidence that extracellular nucleotide signaling contributes to the control of adult hypothalamic neurogenesis in situ. Activation of the P2Y13 receptor inhibits progenitor cell proliferation, long-term survival and neuron formation and therefore controls inhibition of appetite-regulating circuits in the adult rodent hypothalamus.
Juvenile neuronal ceroid-lipofuscinosis (JNCL) is a rare lysosomal storage disease in children with lethal outcome and no therapy. The origin of JNCL has been traced to autosomal recessive mutations in the CLN3 gene, and ~85% of the JNCL patients harbor a 1.02 kb deletion that removes the exons 7 and 8 and the surrounding intronic DNA (CLN3Δex7/8). So far, structure, function and localization of the CLN3 protein remain elusive. However, there is strong evidence that CLN3 modulates a process or condition that is essential in many cellular pathways. Lipid metabolism and antero-/retrograde transport, two mechanisms CLN3 was previously implicated in, fulfill these requirements. Notably, also a bioactive group of glycosphingolipids referred to as gangliosides is tightly interrelated with these functions. Furthermore, a-series gangliosides have been shown to be involved in the development and sustenance of the brain, where they are essential for neurite outgrowth and cell survival. Defects in ganglioside metabolism were shown to play a crucial role in many lysosomal storage disorders. However, the contribution of gangliosides to NCL pathology is largely unknown.
The present study analyzed central enzymes and metabolites of the a-series ganglioside pathway in a JNCL cell model. The core finding was, thereby, the reduced amount of the neuroprotective ganglioside GM1 in homozygous CbCln3Δex7/8 cells. This was caused by the enhanced action of the GM1-degrading multimeric enzyme complex and in particular, by the upregulation of protein levels and increased enzyme activity of β-galactosidase (Glb1).
Improved binding of Glb1 to substrate-carrying membranes was provided by an increase in LBPA levels. In combination with other smaller alterations in the ganglioside pattern, a shift towards less complex gangliosides became present. The resulting loss of neuroprotection may be the reason for the multifocal pathology in homozygous CbCln3Δex7/8 cells.
The second part of the present study investigated the cellular mechanisms behind the altered ganglioside profile with regard to the potential role of CLN3. Here, the anterograde transport of GM1 to the plasma membrane presented a positive correlation with the amount of full-length CLN3. In case of the truncated protein this correlation was missing, resulting in reduced PM staining with CTxB-FITC. However, transfection of full-length CLN3 in these cells restored the CTxB-FITC intensity. Based on the neuroprotective role of GM1, the corresponding increase in GM1 levels may be the cause for the restoration effects observed in previous studies using full-length CLN3. Hence, administration of GM1 was expected to improve cell viability of homozygous CbCln3Δex7/8 cells and beyond that to rescue potentially some disease phenotypes. However, no effect could be observed. The reason for this may be reduced caveolar uptake and the mislocalization of ganglioside GM1 to the trans-Golgi network (TGN) and redirection towards degradative compartments.
Both are in line with the idea of an impaired endocytic flux in CLN3 deficiency. The observed localization of CLN3 in the TGN suggests a potential role for CLN3 in the lipid sorting machinery, subsequently altering membrane composition and its regulatory functions. The resulting imbalance may affect many of the cellular processes impaired in JNCL.
Background: One aspect of premating isolation between diverging, locally-adapted population pairs is female mate choice for resident over alien male phenotypes. Mating preferences often show considerable individual variation, and whether or not certain individuals are more likely to contribute to population interbreeding remains to be studied. In the Poecilia mexicana-species complex different ecotypes have adapted to hydrogen sulfide (H2S)-toxic springs, and females from adjacent non-sulfidic habitats prefer resident over sulfide-adapted males. We asked if consistent individual differences in behavioral tendencies (animal personality) predict the strength and direction of the mate choice component of premating isolation in this system.
Results: We characterized focal females for their personality and found behavioral measures of ‘novel object exploration’, ‘boldness’ and ‘activity in an unknown area’ to be highly repeatable. Furthermore, the interaction term between our measures of exploration and boldness affected focal females’ strength of preference (SOP) for the resident male phenotype in dichotomous association preference tests. High exploration tendencies were coupled with stronger SOPs for resident over alien mating partners in bold, but not shy, females. Shy and/or little explorative females had an increased likelihood of preferring the non-resident phenotype and thus, are more likely to contribute to rare population hybridization. When we offered large vs. small conspecific stimulus males instead, less explorative females showed stronger preferences for large male body size. However, this effect disappeared when the size difference between the stimulus males was small.
Conclusions: Our results suggest that personality affects female mate choice in a very nuanced fashion. Hence, population differences in the distribution of personality types could be facilitating or impeding reproductive isolation between diverging populations depending on the study system and the male trait(s) upon which females base their mating decisions, respectively.
50 years of amino acid hydrophobicity scales : revisiting the capacity for peptide classification
(2016)
Background: Physicochemical properties are frequently analyzed to characterize protein-sequences of known and unknown function. Especially the hydrophobicity of amino acids is often used for structural prediction or for the detection of membrane associated or embedded β-sheets and α-helices. For this purpose many scales classifying amino acids according to their physicochemical properties have been defined over the past decades. In parallel, several hydrophobicity parameters have been defined for calculation of peptide properties. We analyzed the performance of separating sequence pools using 98 hydrophobicity scales and five different hydrophobicity parameters, namely the overall hydrophobicity, the hydrophobic moment for detection of the α-helical and β-sheet membrane segments, the alternating hydrophobicity and the exact ß-strand score.
Results: Most of the scales are capable of discriminating between transmembrane α-helices and transmembrane β-sheets, but assignment of peptides to pools of soluble peptides of different secondary structures is not achieved at the same quality. The separation capacity as measure of the discrimination between different structural elements is best by using the five different hydrophobicity parameters, but addition of the alternating hydrophobicity does not provide a large benefit. An in silico evolutionary approach shows that scales have limitation in separation capacity with a maximal threshold of 0.6 in general. We observed that scales derived from the evolutionary approach performed best in separating the different peptide pools when values for arginine and tyrosine were largely distinct from the value of glutamate. Finally, the separation of secondary structure pools via hydrophobicity can be supported by specific detectable patterns of four amino acids.
Conclusion: It could be assumed that the quality of separation capacity of a certain scale depends on the spacing of the hydrophobicity value of certain amino acids. Irrespective of the wealth of hydrophobicity scales a scale separating all different kinds of secondary structures or between soluble and transmembrane peptides does not exist reflecting that properties other than hydrophobicity affect secondary structure formation as well. Nevertheless, application of hydrophobicity scales allows distinguishing between peptides with transmembrane α-helices and β-sheets. Furthermore, the overall separation capacity score of 0.6 using different hydrophobicity parameters could be assisted by pattern search on the protein sequence level for specific peptides with a length of four amino acids.
Along with barley and rice, maize provides staple food for more than half of the world population. Maize ears are regularly infected with fungal pathogens of the Fusarium genus, which, besides reducing yield, also taint grains with toxic metabolites. In an earlier work, we have shown that maize ears infection with single Fusarium strains was detectable through volatile sensing. In nature, infection most commonly occurs with more than a single fungal strain; hence we tested how the interactions of two strains would modulate volatile emission from infected ears. For this purpose, ears of a hybrid and a dwarf maize variety were simultaneously infected with different strains of Fusarium graminearum and F. verticillioides and, the resulting volatile profiles were compared to the ones of ears infected with single strains. Disease severity, fungal biomass, and the concentration of the oxylipin 9-hydroxy octadecadienoic acid, a signaling molecule involved in plant defense, were monitored and correlated to volatile profiles. Our results demonstrate that in simultaneous infections of hybrid and dwarf maize, the most competitive fungal strains had the largest influence on the volatile profile of infected ears. In both concurrent and single inoculations, volatile profiles reflected disease severity. Additionally, the data further indicate that dwarf maize and hybrid maize might emit common (i.e., sesquiterpenoids) and specific markers upon fungal infection. Overall this suggests that volatile profiles might be a good proxy for disease severity regardless of the fungal competition taking place in maize ears. With the appropriate sensitivity and reliability, volatile sensing thus appears as a promising tool for detecting fungal infection of maize ears under field conditions.
Rhythms, i.e. periodic sequences of events or states, are a ubiquitous feature of physiological systems such as the heart, the lungs or the brain. For the brain in particular, the diversity of rhythms is remarkable, ranging from low frequency rhythms in the slow/delta band (0.5-4 Hz) during sleep to gamma band oscillations (30-120 Hz) rhythms during alert behavior, all expressed in various brain areas and at various spatial scales. To understand whether these rhythms subserve a function for the organism it is important to also understand the underlying mechanisms that generate them. While the generation of some rhythms appear to be well-understood, e.g. sleep spindles, others such as the cortical beta rhythm (13-30 Hz) have remained elusive.
Understanding the generation of a brain rhythm involves multiple spatial scales, from identifying intracellular mechanisms such as the contribution of individual transmembrane currents to studying how specific neuronal populations or areas affect the full physiological rhythm present in the intact, highly interconnected brain. The aim of this work has been to delineate the mechanistic contributions of individual brain areas to the in vivo generation of two particular rhythms present in efferent areas: (1) The first part of this work studies the influence of thalamocortical neurons on cortical slow/delta waves (0.5-4 Hz) of sleep that are sometimes also present in awake animals. (2) The second part is about the contribution of primary visual cortex to the beta rhythm (13-30 Hz) in extrastriate cortex of awake behaving animals.
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...