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Disruption of the zinc finger gene GLI3 has been shown to be the cause of Greig cephalopolysyndactyly syndrome (GCPS), at least in some GCPS translocation patients. To characterize this genomic region on human chromosome 7p13, we have isolated a VAC contig of more than 1000 kb including the GLI3 gene. In this contig the gene itself spans at least 200-250 kb. A CpG island is located in the vicinity of the 5' region of the known GLI3 cDNA, implying a potential promoter region.
No abstract available
The auditory system is an exquisitely complex sensory organ dependent upon the synchronization of numerous processes for proper function. The molecular characterization of hereditary hearing loss is complicated by extreme genetic heterogeneity, wherein hundreds of genes dispersed genome-wide play a central and irreplaceable role in normal hearing function. The present study explores this area on a genome-wide and single gene basis for the detection of genetic mutations playing critical roles in human hearing.
This work initiated with a high resolution SNP array study involving 109 individuals. A 6.9 Mb heterozygous deletion on chromosome 4q35.1q35.2 was identified in a syndromic patient that was in agreement with a chromosome 4q deletion syndrome diagnosis. A 99.9 kb heterozygous deletion of exons 58-64 in USH2A was identified in one patient. Two homozygous deletions and five heterozygous deletions in STRC (DFNB16) were also detected. The homozygous deletions alone were enough to resolve the hearing impairment in the two patients. A Sanger sequencing assay was developed to exclude a pseudogene with a high percentage sequence identity to STRC from the analysis, which further solved three of the six heterozygous deletion patients with the hemizygous, in silico predicted pathogenic mutations c.2726A>T (p.H909L), c.4918C>T (p.L1640F), and c.4402C>T (p.R1468X). A single patient who was copy neutral for STRC and without pathogenic copy number variations had compound heterozygous mutations [c. 2303_2313+1del12 (p.G768Vfs*77) and c.5125A>G (p.T1709A)] in STRC. It has been shown that STRC has been previously underestimated as a hearing loss gene. One additional patient is described who does not have pathogenic copy number variation but is the only affected member of his family having hearing loss with a paternally segregating translocation t(10;15)(q26.13;q21.1).
Twenty-four patients without chromosomal aberrations and the above described patient with an USH2A heterozygous deletion were subjected to a targeted hearing loss gene next generation sequencing panel consisting of either 80 or 129 hearing-relevant genes. The patient having the USH2A heterozygous deletion also disclosed a second mutation in this gene [c.2276G>T (p.C759F)]. This compound heterozygous mutation is the most likely cause of hearing loss in this patient. Nine mutations in genes conferring autosomal dominant hearing loss [ACTG1 (DFNA20/26); CCDC50 (DFNA44); EYA4 (DFNA10); GRHL2 (DFNA28); MYH14 (DFNA4A); MYO6 (DFNA22); TCF21 and twice in MYO1A (DFNA48)] and four genes causing autosomal recessive hearing loss were detected [GJB2 (DFNB1A); MYO7A (DFNB2); MYO15A (DFNB3), and USH2A]. Nine normal hearing controls were also included. Statistical significance was achieved comparing controls and patients that revealed an excess of mutations in the hearing loss patients compared to the control group. The family with the GRHL2 c.1258-1G>A mutation is only the second family published worldwide with a mutation described in this gene to date, supporting the initial claim of this gene causing DFNA28 hearing loss. Audiogram analysis of five affected family members uncovered the progressive nature of DFNA28 hearing impairment. Regression analysis predicted the annual threshold deterioration in each of the five family members with multiple audiograms available over a number of years.
b-Type cytochromes
(1980)
Chlamydia trachomatis (Ctr) can persist over extended times within their host cell and thereby establish chronic infections. One of the major inducers of chlamydial persistence is interferon-gamma (IFN-γ) released by immune cells as a mechanism of immune defence. IFN-γ activates the catabolic depletion of L-tryptophan (Trp) via indoleamine-2,3-dioxygenase (IDO), resulting in persistent Ctr. Here, we show that IFN-γ induces the downregulation of c-Myc, the key regulator of host cell metabolism, in a STAT1-dependent manner. Expression of c-Myc rescued Ctr from IFN-γ-induced persistence in cell lines and human fallopian tube organoids. Trp concentrations control c-Myc levels most likely via the PI3K-GSK3β axis. Unbiased metabolic analysis revealed that Ctr infection reprograms the host cell tricarboxylic acid (TCA) cycle to support pyrimidine biosynthesis. Addition of TCA cycle intermediates or pyrimidine/purine nucleosides to infected cells rescued Ctr from IFN-γ-induced persistence. Thus, our results challenge the longstanding hypothesis of Trp depletion through IDO as the major mechanism of IFN-γ-induced metabolic immune defence and significantly extends the understanding of the role of IFN-γ as a broad modulator of host cell metabolism.
Chlamydia trachomatis, an obligate intracellular human pathogen, is the world’s leading cause of infection related blindness and the most common, bacterial sexually transmitted disease. In order to establish an optimal replicative niche, the pathogen extensively interferes with the physiology of the host cell. Chlamydia switches in its complex developmental cycle between the infectious non-replicative elementary bodies (EBs) and the non-infectious replicative reticulate bodies (RBs). The transformation to RBs, shortly after entering a host cell, is a crucial process in infection to start chlamydial replication. Currently it is unknown how the transition from EBs to RBs is initiated. In this thesis, we could show that, in an axenic media approach, L glutamine uptake by the pathogen is crucial to initiate the EB to RB transition. L-glutamine is converted to amino acids which are used by the bacteria to synthesize peptidoglycan. Peptidoglycan inturn is believed to function in separating dividing Chlamydia. The glutamine metabolism is reprogrammed in infected cells in a c-Myc-dependent manner, in order to accomplish the increased requirement for L-glutamine. Upon a chlamydial infection, the proto-oncogene c-Myc gets upregulated to promote host cell glutaminolysis via glutaminase GLS1 and the L-glutamine transporter SLC1A5/ASCT2. Interference with this metabolic reprogramming leads to limited growth of C. trachomatis. Besides the active infection, Chlamydia can persist over a long period of time within the host cell whereby chronic and recurrent infections establish. C. trachomatis acquire a persistent state during an immune attack in response to elevated interferon-γ (IFN-γ) levels. It has been shown that IFN-γ activates the catabolic depletion of L-tryptophan via indoleamine 2,3-dioxygenase (IDO), resulting in the formation of non-infectious atypical chlamydial forms. In this thesis, we could show that IFN-γ depletes the key metabolic regulator c-Myc, which has been demonstrated to be a prerequisite for chlamydial development and growth, in a STAT1-dependent manner. Moreover, metabolic analyses revealed that the pathogen de routs the host cell TCA cycle to enrich pyrimidine biosynthesis. Supplementing pyrimidines or a-ketoglutarate helps the bacteria to partially overcome the persistent state. Together, the results indicate a central role of c-Myc induced host glutamine metabolism reprogramming and L-glutamine for the development of C. trachomatis, which may provide a basis for anti-infectious strategies. Furthermore, they challenge the longstanding hypothesis of L-tryptophan shortage as the sole reason for IFN-γ induced persistence and suggest a pivotal role of c-Myc in the control of the C. trachomatis dormancy.
Die Kernhülle ist eine hoch spezialisierte Membran, die den eukaryotischen Zellkern umgibt. Sie besteht aus der äußeren und der inneren Kernmembran, die über die Kernporenkomplexe miteinander verbunden werden. Die Kernhülle reguliert nicht nur den Transport von Makromolekülen zwischen dem Nukleoplasma und dem Zytoplasma, sie dient auch der Verankerung des Chromatins und des Zytoskeletts. Durch diese Interaktionen hilft die Kernhülle, den Zellkern innerhalb der Zelle und die Chromosomen innerhalb des Zellkerns zu positionieren, und reguliert dadurch die Expression bestimmter Gene. In höheren Eukaryoten durchlaufen sowohl die Kernhülle, als auch die Kernporenkomplexe während der Zellteilung strukturelle Veränderungen. Zu Beginn der Mitose werden sie abgebaut, um sich am Ende der Mitose in den Tochterzellen erneut zu bilden. Die molekularen Mechanismen, die zum Wiederaufbau der Kernhülle führen, sind kaum geklärt. Ein geeignetes System, um bestimmte Ereignisse bei der Kernhüllenbildung zu untersuchen, liefert das zellfreie System aus Xenopus Eiern und Spermienchromatin (Lohka 1998). Es konnte bereits früher gezeigt werden, dass es im Eiextrakt von Xenopus laevis mindestens zwei verschiedene Vesikelpopulationen gibt, die zur Bildung der Kernhülle beitragen. Eine der Vesikelpopulationen bindet an Chromatin, fusioniert dort und bildet eine Doppelmembran. Die andere Vesikelpopulation bindet an die bereits vorhandene Doppelmembran und sorgt für die Ausbildung der Kernporenkomplexe. Ziel dieser Arbeit war es, diese beiden Membranfraktionen zu isolieren und zu charakterisieren, wobei das Hauptinteresse in der porenbildenden Membranfraktion lag. Durch Zentrifugation über einen diskontinuierlichen Zuckergradienten konnten die Membranvesikel in zwei verschiedene Vesikelfraktionen aufgetrennt werden. Eine Membranfraktion konnte aus der 40%igen Zuckerfraktion („40% Membranfraktion“) isoliert werden, die andere aus der 30%igen Zuckerfraktion („30% Membranfraktion“). Die verschiedenen Membranfraktionen wurden zu in vitro Kernen gegeben, in denen die Kernporen durch vorausgegangene Bildung von Annulate Lamellae depletiert worden waren. Nach Zugabe der 30% Membranfraktion konnte die Bildung von funktionalen Kernporen beobachtet werden. Im Gegensatz dazu zeigte die 40% Membranfraktion keine porenbildenden Eigenschaften. Unter Verwendung eines vereinfachten Systems, bestehend aus Zytosol, Spermienchromatin und den Membranen, wurde gezeigt, dass die 40% Membranfraktion an Chromatin bindet und ausreichend ist, um eine kontinuierliche Doppelmembran ohne Kernporen zu bilden. Die 30% Membranfraktion besitzt keine Chromatinbindungseigenschaften und wird aktiv entlang von Mikrotubuli zu den porenlosen Kernen transportiert. Dort interagiert sie mit der chromatingebundenen 40% Membranfraktion und induziert die Porenbildung. Nach dem Vergleich der Proteinzusammensetzung der beiden Membranfraktionen, konnte das Major Vault Protein (MVP) nur in der porenbildenden Membranfraktion gefunden werden. MVP ist die Hauptstrukturkomponente der Vault-Komplexe, einem Ribonukleo-proteinpartikel, der in den meisten eukaryotischen Zellen vorhanden ist (Kedersha et al., 1991). Bemerkenswerterweise wird über die Funktion der Vault-Komplexe, trotz ihrer übiquitären Expression und ihrem Vorkommen in fast allen eukaryotischen Zellen, immer noch diskutiert. Um mehr über die Funktion und die Lokalisation der Vaults/MVP zu lernen, wurden die Vaults in Anlehnung an die Methode von Kedersha und Rome (1986) aus Xenopus Eiern isoliert. Zusätzlich wurde rekombinantes Xenopus MVP hergestellt, das unter anderem für die Produktion von Antikörpern in Meerschweinchen verwendet wurde. Um herauszufinden, ob die Anwesenheit von MVP in der 30% Membranfraktion in direktem Zusammenhang mit deren porenbildender Eigenschaft steht, wurden gereinigte Vault-Komplexe oder rekombinantes MVP, das alleine ausreichend ist, um in sich zu den charakteristischen Vault-Strukturen zusammenzulagern, zu porenlosen Kernen gegeben. Sowohl gereinigte Vault-Komplexe, als auch rekombinantes MVP waren in der Lage in den porenlosen Kernen die Bildung von funktionalen Kernporen zu induzieren. Untersuchungen zur Lokalisation von MVP zeigten, dass MVP teilweise an der Kernhülle und den Kernporenkomplexen lokalisiert, während der Großteil an MVP zytoplasmatisch vorliegt. Dies sind die ersten Daten, die Vaults/MVP mit der Kernporenbildung in Verbindung bringen. Deshalb bietet diese Arbeit die Grundlage, um diese unerwartete Rolle der Vaults in Zukunft genauer zu charakterisieren.
All forms of restriction, from caloric to amino acid to glucose restriction, have been established in recent years as therapeutic options for various diseases, including cancer. However, usually there is no direct comparison between the different restriction forms. Additionally, many cell culture experiments take place under static conditions. In this work, we used a closed perfusion culture in murine L929 cells over a period of 7 days to compare methionine restriction (MetR) and glucose restriction (LowCarb) in the same system and analysed the metabolome by liquid chromatography mass spectrometry (LC-MS). In addition, we analysed the inhibition of glycolysis by 2-deoxy-D-glucose (2-DG) over a period of 72 h. 2-DG induced very fast a low-energy situation by a reduced glycolysis metabolite flow rate resulting in pyruvate, lactate, and ATP depletion. Under perfusion culture, both MetR and LowCarb were established on the metabolic level. Interestingly, over the period of 7 days, the metabolome of MetR and LowCarb showed more similarities than differences. This leads to the conclusion that the conditioned medium, in addition to the different restriction forms, substantially reprogramm the cells on the metabolic level.
Chlamydia trachomatis is an obligate intracellular human pathogen that grows inside a membranous, cytosolic vacuole termed an inclusion. Septins are a group of 13 GTP-binding proteins that assemble into oligomeric complexes and that can form higher-order filaments. We report here that the septins SEPT2, -9, -11, and probably -7 form fibrillar structures around the chlamydial inclusion. Colocalization studies suggest that these septins combine with F actin into fibers that encase the inclusion. Targeting the expression of individual septins by RNA interference (RNAi) prevented the formation of septin fibers as well as the recruitment of actin to the inclusion. At the end of the developmental cycle of C. trachomatis, newly formed, infectious elementary bodies are released, and this release occurs at least in part through the organized extrusion of intact inclusions. RNAi against SEPT9 or against the combination of SEPT2/7/9 substantially reduced the number of extrusions from a culture of infected HeLa cells. The data suggest that a higher-order structure of four septins is involved in the recruitment or stabilization of the actin coat around the chlamydial inclusion and that this actin recruitment by septins is instrumental for the coordinated egress of C. trachomatis from human cells. The organization of F actin around parasite-containing vacuoles may be a broader response mechanism of mammalian cells to the infection by intracellular, vacuole-dwelling pathogens. IMPORTANCE Chlamydia trachomatis is a frequent bacterial pathogen throughout the world, causing mostly eye and genital infections. C. trachomatis can develop only inside host cells; it multiplies inside a membranous vacuole in the cytosol, termed an inclusion. The inclusion is covered by cytoskeletal "coats" or "cages," whose organization and function are poorly understood. We here report that a relatively little-characterized group of proteins, septins, is required to organize actin fibers on the inclusion and probably through actin the release of the inclusion. Septins are a group of GTP-binding proteins that can organize into heteromeric complexes and then into large filaments. Septins have previously been found to be involved in the interaction of the cell with bacteria in the cytosol. Our observation that they also organize a reaction to bacteria living in vacuoles suggests that they have a function in the recognition of foreign compartments by a parasitized human cell.
Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing
(2016)
Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing.
Most parasites and parasitoids are adapted to overcome defense mechanisms of their specific hosts and hence colonize a narrow range of host species. Accordingly, an increase in host functional or phylogenetic dissimilarity is expected to increase the species diversity of parasitoids. However, the local diversity of parasitoids may be driven by the accessibility and detectability of hosts, both increasing with increasing host abundance. Yet, the relative importance of these two mechanisms remains unclear. We parallelly reared communities of saproxylic beetle as potential hosts and associated parasitoid Hymenoptera from experimentally felled trees. The dissimilarity of beetle communities was inferred from distances in seven functional traits and from their evolutionary ancestry. We tested the effect of host abundance, species richness, functional, and phylogenetic dissimilarities on the abundance, species richness, and Shannon diversity of parasitoids. Our results showed an increase of abundance, species richness, and Shannon diversity of parasitoids with increasing beetle abundance. Additionally, abundance of parasitoids increased with increasing species richness of beetles. However, functional and phylogenetic dissimilarity showed no effect on the diversity of parasitoids. Our results suggest that the local diversity of parasitoids, of ephemeral and hidden resources like saproxylic beetles, is highest when resources are abundant and thereby detectable and accessible. Hence, in some cases, resources do not need to be diverse to promote parasitoid diversity.
The enrichment of deadwood is essential for the conservation of saproxylic biodiversity in managed forests. However, existing strategies focus on a cost‐intensive increase of deadwood amount, while largely neglecting increasing deadwood diversity.
Deadwood objects, that is logs and branches, from six tree species were experimentally sun exposed, canopy shaded and artificially shaded for 4 years, after which the alpha‐, beta‐ and gamma‐diversity of saproxylic beetles, wood‐inhabiting fungi and spiders were analysed. Analyses of beta‐diversity included the spatial distance between exposed deadwood objects. A random‐drawing procedure was used to identify the combination of tree species and sun exposure that yielded the highest gamma‐diversity at a minimum of exposed deadwood amount.
In sun‐exposed plots, species numbers in logs were higher than in shaded plots for all taxa, while in branches we observed the opposite for saproxylic beetles. Tree species affected the species numbers only of saproxylic beetles and wood‐inhabiting fungi. The beta‐diversity of saproxylic beetles and wood‐inhabiting fungi among logs was influenced by sun exposure and tree species, but beta‐diversity of spiders by sun exposure only. For all saproxylic taxa recorded in logs, differences between communities increased with increasing spatial distance.
A combination of canopy‐shaded Carpinus logs and sun‐exposed Populus logs resulted in the highest species numbers of all investigated saproxylic taxa among all possible combinations of tree species and sun‐exposure treatments.
Synthesis and applications. We recommend incorporating the enrichment of different tree species and particularly the variation in sun exposure into existing strategies of deadwood enrichment. Based on the results of our study, we suggest to combine the logs of softwood broadleaf tree species (e.g. Carpinus, Populus), hardwood broadleaf tree species (e.g. Quercus) and coniferous tree species (e.g. Pinus) under different conditions of sun exposure and distribute them spatially in a landscape to maximize the beneficial effects on overall diversity.
Tree species diversity is important to maintain saproxylic beetle diversity in managed forests. Yet, knowledge about the conservational importance of single tree species and implications for forest management and conservation practices are lacking.
We exposed freshly cut branch‐bundles of 42 tree species, representing tree species native and non‐native to Europe, under sun‐exposed and shaded conditions for 1 year. Afterwards, communities of saproxylic beetles were reared ex situ for 2 years. We tested for the impact of tree species and sun exposure on alpha‐, beta‐, and gamma‐diversity as well as composition of saproxylic beetle communities. Furthermore, the number of colonised tree species by each saproxylic beetle species was determined.
Tree species had a lower impact on saproxylic beetle communities compared to sun exposure. The diversity of saproxylic beetles varied strongly among tree species, with highest alpha‐ and gamma‐diversity found in Quercus petraea. Red‐listed saproxylic beetle species occurred ubiquitously among tree species. We found distinct differences in the community composition of broadleaved and coniferous tree species, native and non‐native tree species as well as sun‐exposed and shaded deadwood.
Our study enhances the understanding of the importance of previously understudied and non‐native tree species for the diversity of saproxylic beetles. To improve conservation practices for saproxylic beetles and especially red‐listed species, we suggest a stronger incorporation of tree species diversity and sun exposure of into forest management strategies, including the enrichment of deadwood from native and with a specific focus on locally rare or silviculturally less important tree species.
Over the past centuries, anthropogenic utilization has fundamentally changed the appearance of European forest ecosystems. Constantly growing and changing demands have led to an enormous decline in ecological key elements and a structural homogenization of most forests. These changes have been accompanied by widespread declines of many forest-dwelling and especially saproxylic, i.e. species depending on deadwood. In order to counteract this development, various conservation strategies have been developed, but they primarily focus on a quantitative deadwood enrichment. However, the diversity of saproxylic species is furthermore driven by a variety of abiotic and biotic determinants as well as interactions between organisms. A detailed understanding of these processes has so far been largely lacking. The aim of the present thesis was therefore to improve the existing ecological knowledge of determinants influencing saproxylic species and species communities in order to provide the basis for evidence-based and adapted conservation measures.
In chapter II of this thesis, I first investigated the impact of sun exposure, tree species, and their combination on saproxylic beetles, wood-inhabiting fungi, and spiders. Therefore, logs and branches of six tree species were set up under different sun exposures in an experimental approach. The impact of sun exposure and tree species strongly differed among single saproxylic taxa as well as diameters of deadwood. All investigated taxa were affected by sun exposure, whereby sun exposure resulted in a higher alpha-diversity of taxa recorded in logs and a lower alpha-diversity of saproxylic beetles reared from branches compared to shading by canopy. Saproxylic beetles and wood-inhabiting fungi as obligate saproxylic species were additionally affected by tree species. In logs, the respective impact of both determinants also resulted in divergent community compositions. Finally, a rarefaction/extrapolation method was used to evaluate the effectiveness of different combinations of tree species and sun exposure for the conservation of saproxylic species diversity. Based on this procedure, a combination of broadleaved and coniferous as well as hard- and softwood tree species was identified to support preferably high levels of saproxylic species diversity.
The aim of chapter III was to evaluate the individual conservational importance of tree species for the protection of saproxylic beetles. For this, the list of tree species sampled for saproxylic beetles was increased to 42 different tree species. The considered tree species represented large parts of taxonomic and phylogenetic diversity native to Central Europe as well as the most important non-native tree species of silvicultural interest. Freshly cut branches were set up for one year and saproxylic beetles were reared afterwards for two subsequent years.
The study revealed that some tree species, in particular Quercus sp., host a particular high diversity of saproxylic beetles, but tree species with a comparatively medium or low overall diversity were likewise important for red-listed saproxylic beetle species. Compared to native tree species, non-native tree species hosted a similar overall species diversity of saproxylic beetles but differed in community composition.
In chapter IV, I finally analysed the interactions of host beetle diversity and the diversity of associated parasitoids by using experimentally manipulated communities of saproxylic beetles and parasitoid Hymenoptera as a model system. Classical approaches of species identification for saproxylic beetles were combined with DNA-barcoding for parasitoid Hymenoptera. The diversity of the host communities was inferred from their phylogenetic composition as well as differences in seven functional traits. Abundance, species richness, and Shannon-diversity of parasitoid Hymenoptera increased with increasing host abundance. However, the phylogenetic and functional dissimilarity of host communities showed no influence on the species communities of parasitoid Hymenoptera. The results clearly indicate an abundance-driven system in which the general availability, not necessarily the diversity of potential hosts, is decisive.
In summary, the present thesis corroborates the general importance of deadwood heterogeneity for the diversity of saproxylic species by combining different experimental approaches. In order to increase their efficiency, conservation strategies for saproxylic species should generally promote deadwood from different tree species under different conditions of sun exposure on landscape-level in addition to the present enrichment of a certain deadwood amount. The most effective combinations of tree species should consider broadleaved and coniferous as well as hard- and softwood tree species. Furthermore, in addition to dominant tree species, special attention should be given to native, subdominant, silviculturally unimportant, and rare tree species.
Das Zytokin Bone Morphogenetic Protein-2 (BMP-2) gehört als Mitglied der Transforming Growth Factor ß-Superfamilie zu einer großen Gruppe eng verwandter Wachstums- und Differenzierungsfaktoren. Es spielt eine entscheidende Rolle bei Bildung und Regeneration von Knorpel und Knochen und während verschiedener Prozesse der embryonalen Entwicklung. Durch Sezernierung des Proteins und anschließende Diffusion in der extrazellulären Matrix (EZM) ausgehend vom Ort der Sekretion unterliegt sein Wirkungsgrad einem abnehmenden Konzentrationsgradienten. BMP-2 bindet neben der hochaffinen Bindung an seinen spezifischen Rezeptor unter anderem auch an die extrazelluläre Matrix. So konnte in Vorarbeiten bereits durch Deletion der basischen Heparinbindungsstelle des BMP-2, die sich im N-terminalen Bereich befindet, eine Wirkungsverstärkung des Proteins in einem in vitro- Experiment, dem Hühnergliedmaßentest, erreicht werden, da die konkurrierende Bindung an Heparinbindungsstellen der EZM wegfällt. Im Tiermodell konnte jedoch ein genau umgekehrter Effekt dieser Mutante im Vergleich mit dem Wildtyp gezeigt werden, da in vivo die Diffusion des Moleküls durch Bindung an die EZM begrenzt und es so lokal an seinem Wirkungsort konzentriert wird. Von diesen Vorbefunden ausgehend war das Ziel der Arbeit die Klonierung und Expression von Mutanten des BMP-2, bei denen durch schrittweise Modifizierung der Heparinbindungsstelle die Bindung des Proteins an Heparin und deren Einfluß auf die Rezeptorbindung charakterisiert werden sollte. Dazu wurden zwei Mutanten des BMP-2 mit Verdopplung eines bzw. beider basischer Aminosäuretripletts kloniert, da diesem basischen Bereich im N-Terminus die eigentliche Bindung an Heparin zugeschrieben wird. Nach Expression, Renaturierung und säulenchromatographischer Aufreinigung der Proteine konnte in dieser Arbeit in drei verschiedenen funktionellen in vitro-Tests eine abnehmende Wirkung der Mutanten gezeigt werden. Neben dem biophysikalischen Nachweis der apparenten Affinitäten der Mutanten zu Rezeptor und Matrix in Biacore-Messungen konnte die Änderung des Wirkungsgrades auch in einem Zellkulturassay mit einer Maus-Fibroblasten-Zellinie durch Messung der Alkalischen Phosphatase und im Hühnergliedmaßentest gezeigt werden. In in vivo Experimenten bleibt eine entsprechende zu erwartende Wirkungsverstärkung dieser beiden Mutanten nachzuweisen, die im Hinblick auf einen therapeutischen Einsatz bei gewünschtem Ersatz zerstörten Knochens relevant werden könnte.
Biodiversity is in rapid decline worldwide. These declines are more pronounced in areas that are currently biodiversity rich, but economically poor – essentially describing many tropical regions in the Global South where landscapes are dominated by smallholder agriculture. Agriculture is an important driver of biodiversity decline, through habitat destruction and unsustainable practices. Ironically, agriculture itself is dependent on a range of ecosystem services, such as pollination and pest control, provided by biodiversity. Biodiversity on fields and the delivery of ecosystem services to crops is often closely tied to the composition of the surrounding landscape – complex landscapes with a higher proportion of (semi-)natural habitats tend to support a high abundances and biodiversity of pollinators and natural enemies that are beneficial to crop production. However, past landscape scale studies have focused primarily on industrialized agricultural landscapes in the Global North, and context dependent differences between regions and agricultural systems are understudied. Smallholder agriculture supports 2 billion people worldwide and contributes to over half the world’s food supply. Yet smallholders, particularly in sub-Saharan Africa, are underrepresented in research investigating the consequences of landscape change and agricultural practices. Where research in smallholder agriculture is conducted, the focus is often on commodity crops, such as cacao, and less on crops that are directly consumed by smallholder households, though the loss of services to these crops could potentially impact the most vulnerable farmers the hardest. Agroecology – a holistic and nature-based approach to agriculture, provides an alternative to unsustainable input-intensive agriculture. Agroecology has been found to benefit smallholders through improved agronomical and food-security outcomes. Co-benefits of agroecological practices with biodiversity and ecosystem services are assumed, but not often empirically tested. In addition, the local and landscape effects on biodiversity and ecosystem services are more commonly studied in isolation, but their potentially interactive effects are so far little explored. Our study region in northern Malawi exemplifies many challenges experienced by smallholder farmers throughout sub-Saharan Africa and more generally in the Global South. Malawi is located in a global biodiversity hotspot, but biodiversity is threatened by rapid habitat loss and a push for input-intensive agriculture by government and other stakeholders. In contrast, agroecology has been effectively promoted and implemented in the study region. We investigated how land-use differences and the agroecological practices affects biodiversity and ecosystem services of multiple taxa in a maize-bean intercropping system (Chapter 2), and pollination of pumpkin (Chapter 3) and pigeon pea (Chapter 4). Additionally, the effects of local and landscape scale shrub- to farmland habitat conversion was investigated on butterfly communities, as well as the potential for agroecology to mitigate these effects (Chapter 5).
Background
Landscape composition is known to affect both beneficial insect and pest communities on crop fields. Landscape composition therefore can impact ecosystem (dis)services provided by insects to crops. Though landscape effects on ecosystem service providers have been studied in large-scale agriculture in temperate regions, there is a lack of representation of tropical smallholder agriculture within this field of study, especially in sub-Sahara Africa. Legume crops can provide important food security and soil improvement benefits to vulnerable agriculturalists. However, legumes are dependent on pollinating insects, particularly bees (Hymenoptera: Apiformes) for production and are vulnerable to pests. We selected 10 pigeon pea (Fabaceae: Cajunus cajan (L.)) fields in Malawi with varying proportions of semi-natural habitat and agricultural area within a 1 km radius to study: (1) how the proportion of semi-natural habitat and agricultural area affects the abundance and richness of bees and abundance of florivorous blister beetles (Coleoptera: Melloidae), (2) if the proportion of flowers damaged and fruit set difference between open and bagged flowers are correlated with the proportion of semi-natural habitat or agricultural area and (3) if pigeon pea fruit set difference between open and bagged flowers in these landscapes was constrained by pest damage or improved by bee visitation.
Methods
We performed three, ten-minute, 15 m, transects per field to assess blister beetle abundance and bee abundance and richness. Bees were captured and identified to (morpho)species. We assessed the proportion of flowers damaged by beetles during the flowering period. We performed a pollinator and pest exclusion experiment on 15 plants per field to assess whether fruit set was pollinator limited or constrained by pests.
Results
In our study, bee abundance was higher in areas with proportionally more agricultural area surrounding the fields. This effect was mostly driven by an increase in honeybees. Bee richness and beetle abundances were not affected by landscape characteristics, nor was flower damage or fruit set difference between bagged and open flowers. We did not observe a positive effect of bee density or richness, nor a negative effect of florivory, on fruit set difference.
Discussion
In our study area, pigeon pea flowers relatively late—well into the dry season. This could explain why we observe higher densities of bees in areas dominated by agriculture rather than in areas with more semi-natural habitat where resources for bees during this time of the year are scarce. Therefore, late flowering legumes may be an important food resource for bees during a period of scarcity in the seasonal tropics. The differences in patterns between our study and those conducted in temperate regions highlight the need for landscape-scale studies in areas outside the temperate region.
Binding of proteins to DNA is usually considered 1D with one protein bound to one DNA molecule. In principle, proteins with multiple DNA binding domains could also bind to and thereby cross-link different DNA molecules. We have investigated this possibility using high-mobility group A1 (HMGA1) proteins, which are architectural elements of chromatin and are involved in the regulation of multiple DNA-dependent processes. Using direct stochastic optical reconstruction microscopy (dSTORM), we could show that overexpression of HMGA1a-eGFP in Cos-7 cells leads to chromatin aggregation. To investigate if HMGA1a is directly responsible for this chromatin compaction we developed a DNA cross-linking assay. We were able to show for the first time that HMGA1a can cross-link DNA directly. Detailed analysis using point mutated proteins revealed a novel DNA cross-linking domain. Electron microscopy indicates that HMGA1 proteins are able to create DNA loops and supercoils in linearized DNA confirming the cross-linking ability of HMGA1a. This capacity has profound implications for the spatial organization of DNA in the cell nucleus and suggests cross-linking activities for additional nuclear proteins.