570 Biowissenschaften; Biologie
Refine
Year of publication
- 2010 (132) (remove)
Document Type
- Article (65)
- Part of Periodical (35)
- Doctoral Thesis (32)
Language
- English (132) (remove)
Has Fulltext
- yes (132)
Is part of the Bibliography
- no (132)
Keywords
- new species (3)
- Arzneimitteldesign (2)
- Computational chemistry (2)
- Neotropis (2)
- aging (2)
- faunal survey (2)
- taxonomy (2)
- temperature (2)
- Aleyrodidae (1)
- Alignment <Biochemie> (1)
Institute
- Biowissenschaften (46)
- Biochemie und Chemie (22)
- Medizin (12)
- Pharmazie (6)
- Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) (6)
- Exzellenzcluster Makromolekulare Komplexe (5)
- Institut für Ökologie, Evolution und Diversität (4)
- Frankfurt Institute for Advanced Studies (FIAS) (3)
- Sonderforschungsbereiche / Forschungskollegs (3)
- Zentrum für Arzneimittelforschung, Entwicklung und Sicherheit (ZAFES) (2)
- Geographie (1)
- Georg-Speyer-Haus (1)
- Geowissenschaften (1)
- Informatik (1)
- Institut für sozial-ökologische Forschung (ISOE) (1)
- Physik (1)
- Starker Start ins Studium: Qualitätspakt Lehre (1)
Proteins of the Omp85 family are conserved in all kingdoms of life. They mediate protein transport across or protein insertion into membranes and reside in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. Omp85 proteins contain a C-terminal transmembrane β-barrel and a soluble N terminus with a varying number of polypeptide-transport-associated or POTRA domains. Here we investigate Omp85 from the cyanobacterium Anabaena sp. PCC 7120. The crystallographic three-dimensional structure of the N-terminal region shows three POTRA domains, here named P1 to P3 from the N terminus. Molecular dynamics simulations revealed a hinge between P1 and P2 but in contrast show that P2 and P3 are fixed in orientation. The P2-P3 arrangement is identical as seen for the POTRA domains from proteobacterial FhaC, suggesting this orientation is a conserved feature. Furthermore, we define interfaces for protein-protein interaction in P1 and P2. P3 possesses an extended loop unique to cyanobacteria and plantae, which influences pore properties as shown by deletion. It now becomes clear how variations in structure of individual POTRA domains, as well as the different number of POTRA domains with both rigid and flexible connections make the N termini of Omp85 proteins versatile adaptors for a plentitude of functions.
Moderately elevated levels of plasma plant sterols have been suspected to be causally involved in atherosclerosis. The aim of this study was to investigate whether plant sterols and other markers of sterol metabolism predicted all-cause and cardiovascular mortality in participants of the Ludwigshafen Risk and Cardiovascular health (LURIC) study. A total of 1,257 individuals who did not use statins and at baseline had a mean (± SD) age of 62.8 (± 11.0) years were included in the present analysis. Lathosterol, cholestanol, campesterol, and sitosterol were measured to estimate cholesterol synthesis and absorption. The mean (± SD) time of the follow-up for all-cause and cardiovascular mortality was 7.32 (± 2.3) years. All-cause (P = 0.001) and cardiovascular (P = 0.006) mortality were decreased in the highest versus the lowest lathosterol to cholesterol tertile. In contrast, subjects in the third cholestanol to cholesterol tertile had increased all-cause (P < 0.001) and cardiovascular mortality (P = 0.010) compared with individuals in the first tertile. The third campesterol to cholesterol tertile was associated with increased all-cause mortality (P = 0.025). Sitosterol to cholesterol tertiles were not significantly related to all-cause or cardiovascular mortality. The data suggest that high absorption and low synthesis of cholesterol predict increased all-cause and cardiovascular mortality in LURIC participants.
Chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. They possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. Today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. In particular, how proteins cross the third outermost membrane has remained unexplained. We identified a protein in the third outermost membrane of the diatom Phaeodactylum tricornutum with properties comparable to those of the Omp85 family. We demonstrate that the targeting route of P. tricornutum Omp85 parallels that of the translocation channel of the outer envelope membrane of chloroplasts, Toc75. In addition, the electrophysiological properties are similar to those of the Omp85 proteins involved in protein translocation. This supports the hypothesis that P. tricornutum Omp85 is involved in precursor protein translocation, which would close a gap in the fundamental understanding of the evolutionary origin and function of protein import in secondary plastids.
Peroxisome proliferator-activated receptor γ (PPARγ) gained considerable interest as a therapeutic target during chronic inflammatory diseases. Remarkably, the pathogenesis of diseases such as multiple sclerosis or Alzheimer is associated with impaired PPARγ expression. Considering that regulation of PPARγ expression during inflammation is largely unknown, we were interested in elucidating underlying mechanisms. To this end, we initiated an inflammatory response by exposing primary human macrophages to lipopolysaccharide (LPS) and observed a rapid decline of PPARγ1 expression. Because promoter activities were not affected by LPS, we focused on mRNA stability and noticed a decreased mRNA half-life. As RNA stability is often regulated via 3′-untranslated regions (UTRs), we analyzed the impact of the PPARγ-3′-UTR by reporter assays using specific constructs. LPS significantly reduced luciferase activity of the pGL3-PPARγ-3′-UTR, suggesting that PPARγ1 mRNA is destabilized. Deletion or mutation of a potential microRNA-27a/b (miR-27a/b) binding site within the 3′-UTR restored luciferase activity. Moreover, inhibition of miR-27b, which was induced upon LPS exposure, partially reversed PPARγ1 mRNA decay, whereas miR-27b overexpression decreased PPARγ1 mRNA content. In addition, LPS further reduced this decay. The functional relevance of miR-27b-dependent PPARγ1 decrease was proven by inhibition or overexpression of miR-27b, which affected LPS-induced expression of the pro-inflammatory cytokines tumor necrosis factor α (TNFα) and interleukin (IL)-6. We provide evidence that LPS-induced miR-27b contributes to destabilization of PPARγ1 mRNA. Understanding molecular mechanisms decreasing PPARγ might help to better appreciate inflammatory diseases.
Bare incrusted soils are a degradation stage often encountered in the Sahel zone. Our study documents the success of restoration (= regreening) experiments using deep ploughing in an experimental site south of Gorom-Gorom in the Oudalan province of Burkina Faso. We used phytosociological relevés and maximum likelihood classifications of digital photography to analyze changes in vegetation. Plant cover in treated plots was found to be about 20 times higher than in control plots, mean species richness more than twice as high. Therefore, this promising restoration method should be tested also in other Sahelian regions. Our approach to combine phytosociological relevés and maximum likelihood classifications of digital photography proved to be very useful.
Background: Early inner ear development requires the strict regulation of cell proliferation, survival, migration and differentiation, coordinated by the concerted action of extrinsic and intrinsic factors. Deregulation of these processes is associated with embryonic malformations and deafness. We have shown that insulin-like growth factor I (IGF-I) plays a key role in embryonic and postnatal otic development by triggering the activation of intracellular lipid and protein kinases. RAF kinases are serine/threonine kinases that regulate the highly conserved RAS-RAF-MEK-ERK signaling cascade involved in transducing the signals from extracellular growth factors to the nucleus. However, the regulation of RAF kinase activity by growth factors during development is complex and still not fully understood.
Methodology/Principal Findings: By using a combination of qRT-PCR, Western blotting, immunohistochemistry and in situ hybridization, we show that C-RAF and B-RAF are expressed during the early development of the chicken inner ear in specific spatiotemporal patterns. Moreover, later in development B-RAF expression is associated to hair cells in the sensory patches. Experiments in ex vivo cultures of otic vesicle explants demonstrate that the influence of IGF-I on proliferation but not survival depends on RAF kinase activating the MEK-ERK phosphorylation cascade. With the specific RAF inhibitor Sorafenib, we show that blocking RAF activity in organotypic cultures increases apoptosis and diminishes the rate of cell proliferation in the otic epithelia, as well as severely impairing neurogenesis of the acoustic-vestibular ganglion (AVG) and neuron maturation.
Conclusions/Significance: We conclude that RAF kinase activity is essential to establish the balance between cell proliferation and death in neuroepithelial otic precursors, and for otic neuron differentiation and axonal growth at the AVG.
Naturally, the floodplains of Central Asian rivers harbour riparian, so-called ‘Tugai’ forests, reeds with Phragmites australis, and shrub communities which form a mosaic depending on the variety of available ground water. In recent decades, these natural ecosystems have been strongly altered anthropogenically or even completely destroyed. In order to restore those ecosystems, knowledge on vegetation, ecosystem dynamics, and natural regeneration processes is essential. In our study, we present results of ecological investigations at the Tarim River. We gathered comprehensive data on soil, vegetation, forest stand age, tree vitality, river course dynamics, and land use and brought it to the landscape level. Thus, recommendations are derived for the maintenance of these floodplain ecosystems, in particular with regard to their biological diversity.
The Ucayali River originates in the high Andean Mountains near the city of Cusco in Peru. After about 1,600 km, it joins with the Marañón River. Both the Ucayali River and the Marañón River are sources of the Amazon. From 2001 to 2005, the Ministry of Transport and Communication of Peru funded a study to determine the navigability of the Ucayali River. In the process, an extensive data set was acquired including hydrological and sedimentological data as well as a comprehensive topographical survey of the riverbed. Since the Ucayali River has experienced no stream channel modification in the past, the available data provide information about the flow pattern for a natural stream and insight into a reference ecosystem. This paper offers the first analysis of the available data and a sediment transport calculation for the Ucayali River.
In recent decades, the number of streams on the Canary Islands has decreased dramatically due to the non-sustainable consumption of water for agriculture and tourism. Natural reaches of streams with an endemic macroinvertebrate fauna do, however, still exist in protected areas of Tenerife and La Gomera. Those reaches serve as a reference to develop an assessment method for streams on islands. This method takes into account common parameters such as water quality and hydromorphology, while emphasizing biodiversity and endemism. The latter concepts as they relate to stream conservation are important in both nature conservation and protection of species as many endemic aquatic organisms are endangered.
This study represents the first comprehensive biological and hydrochemical investigation of small coastal ponds in the saltmarsh dominated Tijuana Estuary, southern California (U.S.). Special attention is given to the brackish water biotopes.
Different salinities and considerable fluctuations in water level characterized these shallow ponds and restrict the biological settlement. Fluctuations of salinities ranged from brackish water to hyperhaline water conditions. Due to different salinity levels, the ponds vary in hydrochemistry, macroinvertebrate species composition and plant communities. The macroinvertebrate community of the brackish waters were dominated by Gastropoda, Odonata, and Coleoptera containing a mixture of freshwater/brackish water species and marine macroinvertebrates. Typical plants of the brackish habitat were Typha domingensis (Southern cattail), and Scirpus californicus (California bulrush) associated with Juncus acutus (Siny rush). These brackish habitats with a wide range of salinity fluctuations are sparsely colonized but represent a niche for typical highly adaptable species. Especially, it is a biotope for species with a wide range of salt tolerance. Therefore, endangered species occurred besides introduced or invasive species in the ponds of the Tijuana Estuary. This fact has to be taken into account in case of wetland restoration. Due to the freshwater influence, the restoration of brackish habitats focuses on the problem of invasive species.
As a part of the interdisciplinary research project ”Integration of nature protection goals with organic farming: an the example from the Hessian ”state domain” [Staatsdomäne] area Frankenhausen”, different restoration measures have been carried out within this site, 15 km north of Kassel. Since 1998, intensive conventional agricultural practices have been substituted with organic farming here. One intention of the agricultural restructuring was to realise nature protection goals in cooperation with sustainable organic agricultural production.
The hydrologic portion of the project addresses both the implementation of restoration measures in rivers and streams and their scientific monitoring. Starting in July 2007, several restoration measures were carried out in the hydrologic systems of the Jungfernbach and Esse streams within the Frankenhausen site. Both systems are formed by typical loess streams (catchment size about 9 km2) which had been heavily degraded for several hundred years by intensive agriculture. The most important restoration measures were removal of a piped section of a tributary of the Jungfernbach at Totenhof, restoration of biological passability by removal of weirs and substitution of narrow pipes under farm paths, relocation of a section of the Jungfernbach from the edge of the floodplain to its original location in the centre, widening of narrow sections and partial raising of the deepened stream bed by means of rough ramps (stone bars) and racks made of oak wood or iron.
These physical restoration measures were accompanied by a scientific monitoring programme comprising morphological, hydrochemical and biological (aquatic macrophytes, aquatic macroinvertebrates, fish and amphibians) aspects.
The aim of this study was to document the original ecological conditions, the restoration measures and the early ecological effects on the stream sections for the first six months following restoration as a basis for further ecological monitoring.
The restoration measures effected clear morphological changes in cross-section and passability. The chemical condition of the streams showed slight changes in some aspects following the restoration, e. g. a reduction of phosphorus, magnesium and potassium concentration. Other than macrophytic algae in the newly shaped sections, aquatic macrophytes did not develop over the winter season before the end of the monitoring phase in April 2008. Within the newly shaped stream sections of a small tributary and of the Jungfernbach, up to 14 aquatic macroinvertebrate taxa started to colonise the new habitats 6 months after restoration.
Fish fauna were very poorly represented in the streams and included only a few specimens of brown trout (Salmo trutta). This did not change markedly after restoration, possibly due to the isolation of the population caused by impassable weirs downstream of the investigation area.
The survival of the approximately 1,000 artificial ponds in the Pfälzerwald (Palatinate Forest) biosphere reserve is endangered as they continue to be abandoned, but a large number of them have conservation and historical value. An overall management concept is needed as the high costs for restoration and the requirements of the EU Water Framework Directive regarding river continuity will make it impossible to maintain all of the ponds. Most of the ponds are migration barriers for fish and aquatic invertebrates. The assessment methods presented here are based on readily available data for the evaluation of the ecological and cultural-historical importance of the ponds, their implications within the landscape, and their (often negative) impact on stream ecology. The assessment of the condition of the ponds’ manmade structures leads to conclusions about the urgency for action. The assessment classes are linked with recommendations for action. In the synopsis of all assessments, management concepts emerge for the individual ponds, and priority lists of ponds can be generated that point out where actions are preferential.
The use of water buffalos for landscape maintenance started ten years ago in Germany. Now, more than 2,100 buffalos are kept by about 90 breeders, and first results concerning their usefulness for landscape management are available. Buffalos are mainly used on particularly wet sites which cannot be grazed by cattle or other domestic animals. Although grazing of wetlands, river banks and water bodies is still controversial, early results from literature and our own research clearly indicate the beneficial impact of moderate grazing on such sites for birds, amphibians, vegetation and insects. This paper presents a short literature review and the first results of the BUBALUS project at Brandenburg University of Technology (BTU) and general experience from other projects.
Species-rich wet grasslands in floodplains are on focus of European nature conservation policy. However, since the seventies of the last century large areas with grasslands in floodplains have been meliorated, ploughed and used for intensive cropping in Germany. Therefore, restoration strategies for large-scale conversion of former arable land into species-rich grasslands and integration into a long-term sustainable land use regime are needed. Dealing with large areas in restoration projects causes high costs which often exceed the possibilities of NGO’s or other stakeholders. Aiming to develop and implement new cost-efficient strategies for restoration and long-term management of wetlands on former arable land local NGO’s and the Anhalt University of Applied Sciences started a co-operation within a project in a heavily degraded floodplain in the Elbe river valley. Up to now, more than 40 ha former arable land was successively bought and immediately grazed by large herbivores (Heck-cattle and Przewalski-horses). The local farmers apply a year-round grazing regime without additional feeding and low stocking density. Scientific evaluation of the project progress and experiments with different re-vegetation variants (natural recovery, hay transfer, seeding of commercial seed mixture) revealed the following results: (1) on former arable land immediate grazing with large herbivores without additional feeding is possible and leads to a successive development of typical grassland communities with low nutrient status, (2) integration of old pastures into the grazing system enhances colonization of native grassland species alongside animal tracks, (3) seeding of a commercial seed mixture impedes the colonization of native grassland species, (4) transfer of species-rich hay accelerates the colonization rate of several grassland species, and (5) highest cover of target species was found on regularly wet sites. Therefore, we conclude that grazing with large herbivores proved to be successful in converting former arable land into species-rich grasslands. Nevertheless, rising of the groundwater table is most important for further development of species-rich wet grasslands in the Wulfener Bruch.
The restoration of ecosystems has become a major challenge throughout the world in the 21st century (see comprehensive surveys from, e. g. Temperton et al. 2004, van Andel & Aronson 2006, Walker et al. 2007, and Zerbe & Wiegleb 2009). Due to non-sustainable land use and inefficient use of natural resources, many ecosystems have been degraded or completely destroyed. Consequently, the functioning of ecosystems has been severely affected and many ecosystem services have been lost.
While many different RNA aptamers have been identified that bind to a plethora of small molecules only very few are capable of acting as engineered riboswitches. Even for aptamers binding the same ligand large differences in their regulatory potential were observed. We address here the molecular basis for these differences by using a set of unrelated neomycin-binding aptamers. UV melting analyses showed that regulating aptamers are thermally stabilized to a significantly higher degree upon ligand binding than inactive ones. Regulating aptamers show high ligand-binding affinity in the low nanomolar range which is necessary but not sufficient for regulation. NMR data showed that a destabilized, open ground state accompanied by extensive structural changes upon ligand binding is important for regulation. In contrast, inactive aptamers are already pre-formed in the absence of the ligand. By a combination of genetic, biochemical and structural analyses, we identified a switching element responsible for destabilizing the ligand free state without compromising the bound form. Our results explain for the first time the molecular mechanism of an engineered riboswitch.
FIAS Scientific Report 2009
(2010)
In this Annual Report we present some of the ongoing activities of FIAS and of the associated graduate
school, the “Frankfurt International Graduate School for Science” (FIGSS) in the year 2009. The main part of the Report consists of a collection of short reports describing the research projects of scientists working at or associated with FIAS.
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.
The estimation model PhytoCalc allows a non-destructive quantification of dry weight and nutrient pools of understorey plants in forests by using the relationship between species biomass, cover and mean shoot length. The model has been validated with independent samples in several German forest types and can be a useful tool in forest monitoring. However, in open areas within forests (e.g. clearcuts), the current model version underestimates biomass and produces unreliable nutrient pool estimations. Thus, tissue density, as approximated by leaf dry matter content (LDMC), is systematically higher under high light compared to low light conditions. We demonstrate that the ratio of LDMC under clearcut conditions to LDMC under forest conditions can be used to adjust the PhytoCalc model to clearcut conditions. We investigated the LDMC ratio of five exemplary species commonly occurring on clearcuts. Integrating the square of the ratio as a correction factor improved estimates of biomass to more than 70% fit between observations and predictions. Results also suggest this ratio can be used to correct nutrient concentrations modelled in PhytoCalc, which tend to be overestimated in clearcuts. As morphological groups of plant species exhibit significantly different ratios, we advise using group-specific correction factors for clearcut adjustments in the future.
The display of foreign polypeptides and proteins on the surface of viruses or cells provides an important tool for the engineering of biomolecules and the analysis of their interactions with binding partners. The most extensively used display platform is the coat protein of the filamentous bacteriophage (Smith, 1985). Phage display libraries have often been selected for polypeptides, e.g. single chain (sc) antibodies that bind to a protein of interest, but in vivo selection could only be demonstrated for peptides so far. An alternative display platform is the retrovirus murine leukemia virus (MLV). Here, polypeptides are displayed at the N-terminus of the viral envelope glycoprotein. Proof of principle for this platform was demonstrated for protease substrate libraries, which can be selected through coupling proteolytic activation with viral infectivity (Buchholz et al., 1998). Selection of the library CX4A on living cells resulted in viruses with more than three orders of magnitude improved spreading efficiency through tumor cells (Hartl et al., 2005). Also scAb libraries have recently been displayed and selected using retroviruses (Urban et al., 2005). The library scFvlibxMo displays the repertoire of phage display preselected sc antibodies for laminin-1 binding. The retrovirus based selection process resulted in laminin-specific sc antibodies with improved expression levels in mammalian cells.
This thesis describes the in vivo (i.e. in mouse tumor models) selection of the C-X4-A and scFvlibxMo for tumor homing upon systemic delivery.
For selection of the protease substrate library C-X4-A a subcutaneous tumor was induced in SCID mice followed by three systemic injections of the library. The selection process was monitored over a period of 34 days. After the incubation period mice were sacrificed and virus load in organs and tumor determined. PCR analysis after 34 days showed that virus from the library had preferentially infected the tumor. Sequence analysis showed the selection of protease substrates with the most prominent one with a frequency of over 65%. The four most prominent protease substrate variants where reconstituted into the original viral backbone for further investigation (C-SK-A, C-HI-A, C-HM-A and C-HS-A). Interestingly, these viruses exhibited a reduced spreading capacity in vitro on HT1080 cells as compared to the C-AK-A virus, which had previously been selected on HT1080 cells. When assayed for tumor homing, however, viruses C-HI-A and C-HS-A had clearly improved in comparison to C-AK-A. Tumor tissue had been infected at rates of over 55% while virus load of extratumoral organs was very low (infection rates <0.7 for C-HS-A and <0.02 for C-HI-A). Tumor targeting capacity had thus been improved over 10-fold by the in vivo selection of the C-X4-A library.
The experimental set up for the in vivo selection of the scFvlibxMo library was performed according to that of the C-X4-A library. Fingerprint analysis of the selected viruses that infected tumor tissue resulted in the identification of seven antibody variants showing unique CDR3 sequences. Two prominent clones (M49T-A and M49T-B) were cloned back into the MoMLV genome for further analysis of the reconstituted viruses. While variant B bound laminin-1 efficiently, variant A was unable to do so, although it was selected at highest frequency (76%). Both reconstituted viruses were equally well infectious and spread through HT1080rec1 cells at a similar efficiency as MoMLV. In an in vivo competition experiment the selected viruses clearly out-competed a laminin-1 binding reference virus L36xMo for tumor homing. To understand the molecular driving forces behind the in vivo selection process the epitope of the selected scFv M49T-A was identified using a phage peptide library approach. In silico analysis led to the identification of a small group of possible antigens, including tenascin, fibronectin and collagen.
The data described in this thesis demonstrate that the retrovirus display platform is capable of allowing the in vivo selection of protease substrates and scFvs. Notably, the replication competence of the system introduced an additional level of complexity to the library. The performed in vivo selections significantly enhanced tumor tropism. Selective infection of tumor cells combined with transfer of anti-tumoral genes is an attractive strategy for cancer therapy being in focus of current research. The viruses selected in this thesis build prime candidates for targeted retrovirus based tumor therapy.