Biowissenschaften
Refine
Year of publication
- 2014 (86) (remove)
Document Type
- Article (72)
- Doctoral Thesis (9)
- Book (3)
- Contribution to a Periodical (2)
Has Fulltext
- yes (86)
Is part of the Bibliography
- no (86)
Keywords
- 3D orientation pattern of ciliary bundles (1)
- Activated Cry1a (1)
- Adaptation (1)
- Angolan giraffe (1)
- Anopheles (1)
- Botswana (1)
- Cell culture (1)
- Chemistry (1)
- Cicer arietinum (1)
- Common ragweed (1)
Institute
- Biowissenschaften (86)
- Senckenbergische Naturforschende Gesellschaft (20)
- Biodiversität und Klima Forschungszentrum (BiK-F) (19)
- Institut für Ökologie, Evolution und Diversität (12)
- Medizin (7)
- Präsidium (7)
- Geowissenschaften (6)
- Biochemie und Chemie (5)
- Exzellenzcluster Makromolekulare Komplexe (5)
- Buchmann Institut für Molekulare Lebenswissenschaften (BMLS) (2)
Non-coding RNAs (ncRNAs) play various roles during central nervous system development. MicroRNAs (miRNAs) are a class of ncRNAs that exert their function together with argonaute proteins by post-transcriptional gene silencing of messenger RNAs (mRNAs). Several studies provide evidence for alterations in miRNA expression in patients with neurodegenerative diseases. Among these is huntington‘s disease (HD), a dominantly inherited fatal disorder characterized by deregulation of neuronal-specific mRNAs as well as miRNAs. Recently, next-generation sequencing (NGS) miRNA profiles from human HD and neurologically normal control brain tissues were reported. Five consistently upregulated miRNAs affect the expression of genes involved in neuronal differentiation, neurite outgrowth, cell death and survival. We re-analyzed the NGS data publicly available in array express and detected nineteen additional differentially expressed miRNAs. Subsequently, we connected these miRNAs to genes implicated in HD development and network analysis pointed to miRNA-mediated downregulation of twenty-two genes with roles in the pathogenesis as well as treatment of the disease. In silico prediction and reporter systems prove that levels of BDNF, a central node in the miRNA-mRNA regulatory network, can be post-transcriptionally controlled by upregulated miR-10b-5p and miR-30a-5p. Reduced BDNF expression is associated with neuronal dysfunction and death in HD. Moreover, the 3’UTR of CREB1 harbors a predicted binding site for these two miRNAs. CREB1 is similarly downregulated in HD and overexpression decreased susceptibility to 3-nitropropionic-induced toxicity in a cell model. In contradiction to these observations, it is presumed that miR-10b-5p upregulation in HD exerts a neuroprotective role in response to the mutation in the huntingtin gene. Therefore, the function of miR-10b-5p and especially its effect on BDNF expression in HD requires further academic research.
In vitro investigation of genes identified by genome-wide association studies of Parkinson's disease
(2014)
Natural products (NPs) have been a rich source for pharmaceutically used anti-infectives and other drugs. However, the application of anti-infectives inevitably causes the development of resistant and multiresistant pathogens, which have to be treated with novel anti-infectives. The industrial research for novel anti-infectives has been concentrating on members of the bacterial Actinomycetales for a long time. Due to several reasons, e.g. the rediscovery of already known NPs, pharmaceutical companies abandoned their NP-research and focused on drug development based on combinatorial chemistry. However, the limited structural diversity of merely synthetic compound libraries has not been a fruitful source for bioactive compounds. Hence the discovery of novel bioactive NPs as a source for anti-infectives is still of economical and humanitarian interest and will remain to be an important branch of research in the future. One strategy to circumvent the rediscovery of bioactive NPs is the analysis of yet unexplored bacterial taxa. Based on this assumption, this work aimed at the discovery of novel NPs from the entomopathogenic bacterial genera Xenorhabdus and Photorhabdus and other promising taxa, as well as the investigation of their biosynthesis. ...
Travelling waves are the physical basis of frequency discrimination in many vertebrate and invertebrate taxa, including mammals, birds, and some insects. In bushcrickets (Tettigoniidae), the crista acustica is the hearing organ that has been shown to use sound-induced travelling waves. Up to now, data on mechanical characteristics of sound-induced travelling waves were only available along the longitudinal (proximal-distal) direction. In this study, we use laser Doppler vibrometry to investigate in-vivo radial (anterior-posterior) features of travelling waves in the tropical bushcricket Mecopoda elongata. Our results demonstrate that the maximum of sound-induced travelling wave amplitude response is always shifted towards the anterior part of the crista acustica. This lateralization of the travelling wave response induces a tilt in the motion of the crista acustica, which presumably optimizes sensory transduction by exerting a shear motion on the sensory cilia in this hearing organ.
The mitochondrial kinase PINK1 and the ubiquitin ligase Parkin are participating in quality control after CCCP- or ROSinduced mitochondrial damage, and their dysfunction is associated with the development and progression of Parkinson’s disease. Furthermore, PINK1 expression is also induced by starvation indicating an additional role for PINK1 in stress response. Therefore, the effects of PINK1 deficiency on the autophago-lysosomal pathway during stress were investigated. Under trophic deprivation SH-SY5Y cells with stable PINK1 knockdown showed downregulation of key autophagic genes, including Beclin, LC3 and LAMP-2. In good agreement, protein levels of LC3-II and LAMP-2 but not of LAMP-1 were reduced in different cell model systems with PINK1 knockdown or knockout after addition of different stressors. This downregulation of autophagic factors caused increased apoptosis, which could be rescued by overexpression of LC3 or PINK1. Taken together, the PINK1-mediated reduction of autophagic key factors during stress resulted in increased cell death, thus defining an additional pathway that could contribute to the progression of Parkinson’s disease in patients with PINK1 mutations.
Noise-induced hearing loss is one of the most common auditory pathologies, resulting from overstimulation of the human cochlea, an exquisitely sensitive micromechanical device. At very low frequencies (less than 250 Hz), however, the sensitivity of human hearing, and therefore the perceived loudness is poor. The perceived loudness is mediated by the inner hair cells of the cochlea which are driven very inadequately at low frequencies. To assess the impact of low-frequency (LF) sound, we exploited a by-product of the active amplification of sound outer hair cells (OHCs) perform, so-called spontaneous otoacoustic emissions. These are faint sounds produced by the inner ear that can be used to detect changes of cochlear physiology. We show that a short exposure to perceptually unobtrusive, LF sounds significantly affects OHCs: a 90 s, 80 dB(A) LF sound induced slow, concordant and positively correlated frequency and level oscillations of spontaneous otoacoustic emissions that lasted for about 2 min after LF sound offset. LF sounds, contrary to their unobtrusive perception, strongly stimulate the human cochlea and affect amplification processes in the most sensitive and important frequency range of human hearing.
Bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. The basic molecular quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase producing acyl-homoserine lactones (AHLs) as signaling molecules, and a LuxR-type receptor detecting the AHLs to control expression of specific genes. However, many proteobacteria possess one or more unpaired LuxR-type receptors that lack a cognate LuxI-like synthase, referred to as LuxR solos. The enteric and insect pathogenic bacteria of the genus Photorhabdus harbor an extraordinarily high number of LuxR solos, more than any other known bacteria, and all lack a LuxI-like synthase. Here, we focus on the presence and the different types of LuxR solos in the three known Photorhabdus species using bioinformatics analyses. Generally, the N-terminal signal-binding domain (SBD) of LuxR-type receptors sensing AHLs have a motif of six conserved amino acids that is important for binding and specificity of the signaling molecule. However, this motif is altered in the majority of the Photorhabdus-specific LuxR solos, suggesting the use of other signaling molecules than AHLs. Furthermore, all Photorhabdus species contain at least one LuxR solo with an intact AHL-binding motif, which might allow the ability to sense AHLs of other bacteria. Moreover, all three species have high AHL-degrading activity caused by the presence of different AHL-lactonases and AHL-acylases, revealing a high quorum quenching activity against other bacteria. However, the majority of the other LuxR solos in Photorhabdus have a N-terminal so-called PAS4-domain instead of an AHL-binding domain, containing different amino acid motifs than the AHL-sensors, which potentially allows the recognition of a highly variable range of signaling molecules that can be sensed apart from AHLs. These PAS4-LuxR solos are proposed to be involved in host sensing, and therefore in inter-kingdom signaling. Overall, Photorhabdus species are perfect model organisms to study bacterial communication via LuxR solos and their role for a symbiotic and pathogenic life style.
Cryo-electron tomography provides a snapshot of the cellular proteome. With template matching, the spatial positions of various macromolecular complexes within their native cellular context can be detected. However, the growing awareness of the reference bias introduced by the cross-correlation based approaches, and more importantly the lack of a reliable confidence measurement in the selection of these macromolecular complexes, has restricted the use of these applications. Here we propose a heuristic, in which the reference bias is measured in real space in an analogous way to the R-free value in X-ray crystallography. We measure the reference bias within the mask used to outline the area of the template, and do not modify the template itself. The heuristic works by splitting the mask into a working and a testing area in a volume ratio of 9:1. While the working area is used during the calculation of the cross-correlation function, the information from both areas is explored to calculate the M-free score. We show using artificial data, that the M-free score gives a reliable measure for the reference bias. The heuristic can be applied in template matching and in sub-tomogram averaging. We further test the applicability of the heuristic in tomograms of purified macromolecules, and tomograms of whole Mycoplasma cells.
Cryptochrome 1a, located in the UV/violet-sensitive cones in the avian retina, is discussed as receptor molecule for the magnetic compass of birds. Our previous immunohistochemical studies of chicken retinae with an antiserum that labelled only activated cryptochrome 1a had shown activation of cryptochrome 1a under 373 nm UV, 424 nm blue, 502 nm turquoise and 565 nm green light. Green light, however, does not allow the first step of photoreduction of oxidized cryptochromes to the semiquinone. As the chickens had been kept under ‘white’ light before, we suggested that there was a supply of the semiquinone present at the beginning of the exposure to green light, which could be further reduced and then re-oxidized. To test this hypothesis, we exposed chickens to various wavelengths (1) for 30 min after being kept in daylight, (2) for 30 min after a 30 min pre-exposure to total darkness, and (3) for 1 h after being kept in daylight. In the first case, we found activated cryptochrome 1a under UV, blue, turquoise and green light; in the second two cases we found activated cryptochrome 1a only under UV to turquoise light, where the complete redox cycle of cryptochrome can run, but not under green light. This observation is in agreement with the hypothesis that activated cryptochrome 1a is found as long as there is some of the semiquinone left, but not when the supply is depleted. It supports the idea that the crucial radical pair for magnetoreception is generated during re-oxidation.
Background: Malaria is still a priority public health problem of Nepal where about 84% of the population are at risk. The aim of this paper is to highlight the past and present malaria situation in this country and its challenges for long-term malaria elimination strategies.
Methods: Malariometric indicator data of Nepal recorded through routine surveillance of health facilities for the years between 1963 and 2012 were compiled. Trends and differences in malaria indicator data were analysed.
Results: The trend of confirmed malaria cases in Nepal between 1963 and 2012 shows fluctuation, with a peak in 1985 when the number exceeded 42,321, representing the highest malaria case-load ever recorded in Nepal. This was followed by a steep declining trend of malaria with some major outbreaks. Nepal has made significant progress in controlling malaria transmission over the past decade: total confirmed malaria cases declined by 84% (12,750 in 2002 vs 2,092 in 2012), and there was only one reported death in 2012. Based on the evaluation of the National Malaria Control Programme in 2010, Nepal recently adopted a long-term malaria elimination strategy for the years 2011–2026 with the ambitious vision of a malaria-free Nepal by 2026. However, there has been an increasing trend of Plasmodium falciparum and imported malaria proportions in the last decade. Furthermore, the analysis of malariometric indicators of 31 malaria-risk districts between 2004 and 2012 shows a statistically significant reduction in the incidence of confirmed malaria and of Plasmodium vivax, but not in the incidence of P. falciparum and clinically suspected malaria.
Conclusions: Based on the achievements the country has made over the last decade, Nepal is preparing to move towards malaria elimination by 2026. However, considerable challenges lie ahead. These include especially, the need to improve access to diagnostic facilities to confirm clinically suspected cases and their treatment, the development of resistance in parasites and vectors, climate change, and increasing numbers of imported cases from a porous border with India. Therefore, caution is needed before the country embarks towards malaria elimination.
Background: While the use of plastic materials has generated huge societal benefits, the "plastic age" comes with downsides: One issue of emerging concern is the accumulation of plastics in the aquatic environment. Here, so-called microplastics (MP), fragments smaller than 5 mm, are of special concern because they can be ingested throughout the food web more readily than larger particles. Focusing on freshwater MP, we briefly review the state of the science to identify gaps of knowledge and deduce research needs.
State of the science: Environmental scientists started investigating marine (micro)plastics in the early 2000s. Today, a wealth of studies demonstrates that MP have ubiquitously permeated the marine ecosystem, including the polar regions and the deep sea. MP ingestion has been documented for an increasing number of marine species. However, to date, only few studies investigate their biological effects. The majority of marine plastics are considered to originate from land-based sources, including surface waters. Although they may be important transport pathways of MP, data from freshwater ecosystems is scarce. So far, only few studies provide evidence for the presence of MP in rivers and lakes. Data on MP uptake by freshwater invertebrates and fish is very limited.
Knowledge gaps: While the research on marine MP is more advanced, there are immense gaps of knowledge regarding freshwater MP. Data on their abundance is fragmentary for large and absent for small surface waters. Likewise, relevant sources and the environmental fate remain to be investigated. Data on the biological effects of MP in freshwater species is completely lacking. The accumulation of other freshwater contaminants on MP is of special interest because ingestion might increase the chemical exposure. Again, data is unavailable on this important issue.
Conclusions: MP represent freshwater contaminants of emerging concern. However, to assess the environmental risk associated with MP, comprehensive data on their abundance, fate, sources, and biological effects in freshwater ecosystems are needed. Establishing such data critically depends on a collaborative effort by environmental scientists from diverse disciplines (chemistry, hydrology, ecotoxicology, etc.) and, unsurprisingly, on the allocation of sufficient public funding.
Background: The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have been conducted, their resolution is low, mainly due to limited sampling. Detailed knowledge about the genetic variation and phylogeography of the South African giraffe (G. c. giraffa) and the Angolan giraffe (G. c. angolensis) is lacking. We investigate genetic variation among giraffe matrilines by increased sampling, with a focus on giraffe key areas in southern Africa.
Results: The 1,562 nucleotides long mitochondrial DNA dataset (cytochrome b and partial control region) comprises 138 parsimony informative sites among 161 giraffe individuals from eight populations. We additionally included two okapis as an outgroup. The analyses of the maternally inherited sequences reveal a deep divergence between northern and southern giraffe populations in Africa, and a general pattern of distinct matrilineal clades corresponding to their geographic distribution. Divergence time estimates among giraffe populations place the deepest splits at several hundred thousand years ago.
Conclusions: Our increased sampling in southern Africa suggests that the distribution ranges of the Angolan and South African giraffe need to be redefined. Knowledge about the phylogeography and genetic variation of these two maternal lineages is crucial for the development of appropriate management strategies.
Mit dem Namen Gerhard Quinkert verbindet man in Frankfurt vor allem die Öffnung der Chemie für die Biologie. Das war damals ein außergewöhnlicher Schritt, der dank einer gezielten Berufungspolitik realisiert wurde. Der Organische Chemiker hat das "Frankfurter Modell" Ende der 1970er Jahre entwickelt.
Three neonicotinoids, imidacloprid, clothianidin and thiacloprid, agonists of the nicotinic acetylcholine receptor in the central brain of insects, were applied at non-lethal doses in order to test their effects on honeybee navigation. A catch-and-release experimental design was applied in which feeder trained bees were caught when arriving at the feeder, treated with one of the neonicotinoids, and released 1.5 hours later at a remote site. The flight paths of individual bees were tracked with harmonic radar. The initial flight phase controlled by the recently acquired navigation memory (vector memory) was less compromised than the second phase that leads the animal back to the hive (homing flight). The rate of successful return was significantly lower in treated bees, the probability of a correct turn at a salient landscape structure was reduced, and less directed flights during homing flights were performed. Since the homing phase in catch-and-release experiments documents the ability of a foraging honeybee to activate a remote memory acquired during its exploratory orientation flights, we conclude that non-lethal doses of the three neonicotinoids tested either block the retrieval of exploratory navigation memory or alter this form of navigation memory. These findings are discussed in the context of the application of neonicotinoids in plant protection.
Background: Endometriosis is characterized by the presence of functional endometrial tissue outside of the uterine cavity. It affects 1 in 10 women of reproductive age. This chronic condition commonly leads to consequences such as pelvic pain, dysmenorrhea, infertility and an elevated risk of epithelial ovarian cancer. Despite the prevalence of endometriosis and its impact on women's lives, there are relatively few in vitro and in vivo models available for studying the complex disease biology, pathophysiology, and for use in the preclinical development of novel therapies. The goal of this study was to develop a novel three-dimensional (3D) cell culture model of ovarian endometriosis and to test whether it is more reflective of endometriosis biology than traditional two dimensional (2D) monolayer cultures.
Methods: A novel ovarian endometriosis epithelial cell line (EEC16) was isolated from a 34-year old female with severe endometriosis. After characterization of cells using in vitro assays, western blotting and RNA-sequencing, this cell line and a second, already well characterized endometriosis cell line, EEC12Z, were established as in vitro 3D spheroid models. We compared biological features of 3D spheroids to 2D cultures and human endometriosis lesions using immunohistochemistry and real-time semi-quantitative PCR.
Results: In comparison to normal ovarian epithelial cells, EEC16 displayed features of neoplastic transformation in in vitro assays. When cultured in 3D, EEC16 and EEC12Z showed differential expression of endometriosis-associated genes compared to 2D monolayer cultures, and more closely mimicked the molecular and histological features of human endometriosis lesions.
Conclusions: To our knowledge, this represents the first report of an in vitro spheroid model of endometriosis. 3D endometriosis models represent valuable experimental tools for studying EEC biology and the development of novel therapeutic approaches.
Strong seasonal variability of hygric and thermal soil conditions are a defining environmental feature in northern Australia. However, how such changes affect the soil–atmosphere exchange of nitrous oxide (N2O), nitric oxide (NO) and dinitrogen (N2) is still not well explored. By incubating intact soil cores from four sites (three savanna, one pasture) under controlled soil temperatures (ST) and soil moisture (SM) we investigated the release of the trace gas fluxes of N2O, NO and carbon dioxide (CO2). Furthermore, the release of N2 due to denitrification was measured using the helium gas flow soil core technique. Under dry pre-incubation conditions NO and N2O emissions were very low (<7.0 ± 5.0 μg NO-N m−2 h−1; <0.0 ± 1.4 μg N2O-N m−2 h−1) or in the case of N2O, even a net soil uptake was observed. Substantial NO (max: 306.5 μg N m−2 h−1) and relatively small N2O pulse emissions (max: 5.8 ± 5.0 μg N m−2 h−1) were recorded following soil wetting, but these pulses were short lived, lasting only up to 3 days. The total atmospheric loss of nitrogen was generally dominated by N2 emissions (82.4–99.3% of total N lost), although NO emissions contributed almost 43.2% to the total atmospheric nitrogen loss at 50% SM and 30 °C ST incubation settings (the contribution of N2 at these soil conditions was only 53.2%). N2O emissions were systematically higher for 3 of 12 sample locations, which indicates substantial spatial variability at site level, but on average soils acted as weak N2O sources or even sinks. By using a conservative upscale approach we estimate total annual emissions from savanna soils to average 0.12 kg N ha−1 yr−1 (N2O), 0.68 kg N ha−1 yr−1 (NO) and 6.65 kg N ha−1 yr−1 (N2). The analysis of long-term SM and ST records makes it clear that extreme soil saturation that can lead to high N2O and N2 emissions only occurs a few days per year and thus has little impact on the annual total. The potential contribution of nitrogen released due to pulse events compared to the total annual emissions was found to be of importance for NO emissions (contribution to total: 5–22%), but not for N2O emissions. Our results indicate that the total gaseous release of nitrogen from these soils is low and clearly dominated by loss in the form of inert nitrogen. Effects of seasonally varying soil temperature and moisture were detected, but were found to be low due to the small amounts of available nitrogen in the soils (total nitrogen <0.1%).
Strong seasonal variability of hygric and thermal soil conditions are a defining environmental feature in Northern Australia. However, how such changes affect the soil–atmosphere exchange of nitrous oxide (N2O), nitric oxide (NO) and dinitrogen (N2) is still 5 not well explored. By incubating intact soil cores from four sites (3 savanna, 1 pasture) under controlled soil temperatures (ST) and soil moisture (SM) we investigated the release of the trace gas fluxes of N2O, NO and carbon dioxide (CO2). Furthermore, the release of N2 due to denitrification was measured using the helium gas flow soil core technique. Under dry pre-incubation conditions NO and N2O emission were very low (< 7.0± 5.0 μgNO-Nm−2 h−1; < 0.0± 1.4 μgN2O-Nm−2 h−1) or in case of N2O, even a net soil uptake was observed. Substantial NO (max: 306.5 μgNm−2 h−1) and relatively small N2O pulse emissions (max: 5.8±5.0 μgNm−2 h−1) were recorded following soil wetting, but these pulses were short-lived, lasting only up to 3 days. The total atmospheric loss of nitrogen was dominated by N2 emissions (82.4–99.3% of total N lost), although NO emissions contributed almost 43.2% at 50% SM and 30 °C ST. N2O emissions were systematically higher for 3 of 12 sample locations, which indicates substantial spatial variability at site level, but on average soils acted as weak N2O sources or even sinks. Emissions were controlled by SM and ST for N2O and CO2, ST and pH for NO, and SM and pH for N2.
In old and heavily weathered soils, the availability of P might be so small that the primary production of plants is limited. However, plants have evolved several mechanisms to actively take up P from the soil or mine it to overcome this limitation. These mechanisms involve the active uptake of P mediated by mycorrhiza, biotic de-occlusion through root clusters, and the biotic enhancement of weathering through root exudation. The objective of this paper is to investigate how and where these processes contribute to alleviate P limitation on primary productivity. To do so, we propose a process-based model accounting for the major processes of the carbon, water, and P cycles including chemical weathering at the global scale. Implementing P limitation on biomass synthesis allows the assessment of the efficiencies of biomass production across different ecosystems. We use simulation experiments to assess the relative importance of the different uptake mechanisms to alleviate P limitation on biomass production. We find that active P uptake is an essential mechanism for sustaining P availability on long timescales, whereas biotic de-occlusion might serve as a buffer on timescales shorter than 10 000 yr. Although active P uptake is essential for reducing P losses by leaching, humid lowland soils reach P limitation after around 100 000 yr of soil evolution. Given the generalized modelling framework, our model results compare reasonably with observed or independently estimated patterns and ranges of P concentrations in soils and vegetation. Furthermore, our simulations suggest that P limitation might be an important driver of biomass production efficiency (the fraction of the gross primary productivity used for biomass growth), and that vegetation on old soils has a smaller biomass production rate when P becomes limiting. With this study, we provide a theoretical basis for investigating the responses of terrestrial ecosystems to P availability linking geological and ecological timescales under different environmental settings.
Genome-wide association studies are widely used to correlate phenotypic traits with genetic variants. These studies usually compare the genetic variation between two groups to single out certain Single Nucleotide Polymorphisms (SNPs) that are linked to a phenotypic variation in one of the groups. However, it is necessary to have a large enough sample size to find statistically significant correlations. Direct-To-Consumer (DTC) genetic testing can supply additional data: DTC-companies offer the analysis of a large amount of SNPs for an individual at low cost without the need to consult a physician or geneticist. Over 100,000 people have already been genotyped through Direct-To-Consumer genetic testing companies. However, this data is not public for a variety of reasons and thus cannot be used in research. It seems reasonable to create a central open data repository for such data. Here we present the web platform openSNP, an open database which allows participants of Direct-To-Consumer genetic testing to publish their genetic data at no cost along with phenotypic information. Through this crowdsourced effort of collecting genetic and phenotypic information, openSNP has become a resource for a wide area of studies, including Genome-Wide Association Studies. openSNP is hosted at http://www.opensnp.org, and the code is released under MIT-license at http://github.com/gedankenstuecke/snpr.