Kaiserslautern - Fachbereich Biologie
Refine
Year of publication
Document Type
- Doctoral Thesis (133)
- Article (37)
- Master's Thesis (1)
- Review (1)
- Working Paper (1)
Keywords
- Streptococcus pneumoniae (8)
- Apoptosis (4)
- Ackerschmalwand (3)
- Resistenz (3)
- Affinitätschromatographie (2)
- Arabidopsis (2)
- Beta-Lactam-Resistenz (2)
- Biogeographie (2)
- Blattschneiderameisen (2)
- Botrytis cinerea (2)
Faculty / Organisational entity
Synthetic Biology is revolutionizing biological research by introducing principles of mechanical engineering, including the standardization of genetic parts and standardized part assembly routes. Both are realized in the Modular Cloning (MoClo) strategy. MoClo allows for the rapid and robust assembly of individual genes and multigene clusters, enabling iterative cycles of gene design, construction, testing, and learning in short time. This is particularly true if generation times of target organisms are short, as is the case for the unicellular green alga Chlamydomonas reinhardtii. Testing a gene of interest in Chlamydomonas with MoClo requires two assembly steps, one for the gene of interest itself and another to combine it with a selection marker. To reduce this to a single assembly step, we constructed five new destination vectors. They contain genes conferring resistance to commonly used antibiotics in Chlamydomonas and a site for the direct assembly of basic genetic parts. The vectors employ red/white color selection and, therefore, do not require costly compounds like X-gal and IPTG. mCherry expression is used to demonstrate the functionality of these vectors.
Cellular membranes can serve as barriers between subcellular compartments, but they can also interact to form dynamically regulated membrane contact sites between a specific pair of organelles. Focussing on plants, this article discusses local redox environments and the current knowledge on membrane contact sites as examples for the dividing and connecting functions of membranes, respectively.
The precise regulation of synaptic connectivity is essential for the processing of information in the brain. Any aberrant loss of synaptic connectivity due to genetic mutations will disrupt information flow in the nervous system and may represent the underlying cause of psychiatric or neurodegenerative diseases. Therefore, identification of the molecular mechanisms controlling synaptic plasticity and maintenance is essential for our understanding of neuronal circuits in development and disease.
Loss of USP28 and SPINT2 expression promotes cancer cell survival after whole genome doubling
(2021)
Background
Whole genome doubling is a frequent event during cancer evolution and shapes the cancer genome due to the occurrence of chromosomal instability. Yet, erroneously arising human tetraploid cells usually do not proliferate due to p53 activation that leads to CDKN1A expression, cell cycle arrest, senescence and/or apoptosis.
Methods
To uncover the barriers that block the proliferation of tetraploids, we performed a RNAi mediated genome-wide screen in a human colorectal cancer cell line (HCT116).
Results
We identified 140 genes whose depletion improved the survival of tetraploid cells and characterized in depth two of them: SPINT2 and USP28. We found that SPINT2 is a general regulator of CDKN1A transcription via histone acetylation. Using mass spectrometry and immunoprecipitation, we found that USP28 interacts with NuMA1 and affects centrosome clustering. Tetraploid cells accumulate DNA damage and loss of USP28 reduces checkpoint activation, thus facilitating their proliferation.
Conclusions
Our results indicate three aspects that contribute to the survival of tetraploid cells: (i) increased mitogenic signaling and reduced expression of cell cycle inhibitors, (ii) the ability to establish functional bipolar spindles and (iii) reduced DNA damage signaling.
The plasma membrane harbors a specific set of transmembrane proteins which enable diverse cellular functions such as nutrient uptake, ion homeostasis and cellular signaling. The surface levels of these proteins need to be dynamically regulated to allow for plastic changes in cellular behaviour e. g. upon cell stress or during neuronal communication. Endocytosis is a powerful mechanism for quickly adapting the surface proteome via protein internalization. Here, I discuss how endocytosis contributes to brain function and counteracts cell stress.
Heterocystous Cyanobacteria of the genus Nodularia form major blooms in brackish waters, while terrestrial Nostoc species occur worldwide, often associated in biological soil crusts. Both genera, by virtue of their ability to fix N2 and conduct oxygenic photosynthesis, contribute significantly to global primary productivity. Select Nostoc and Nodularia species produce the hepatotoxin nodularin and whether its production will change under climate change conditions needs to be assessed. In light of this, the effects of elevated atmospheric CO2 availability on growth, carbon and N2 fixation as well as nodularin production were investigated in toxin and non-toxin producing species of both genera. Results highlighted the following:
Biomass and volume specific biological nitrogen fixation (BNF) rates were respectively almost six and 17 fold higher in the aquatic Nodularia species compared to the terrestrial Nostoc species tested, under elevated CO2 conditions.
There was a direct correlation between elevated CO2 and decreased dry weight specific cellular nodularin content in a diazotrophically grown terrestrial Nostoc species, and the aquatic Nodularia species, regardless of nitrogen availability.
Elevated atmospheric CO2 levels were correlated to a reduction in biomass specific BNF rates in non-toxic Nodularia species.
Nodularin producers exhibited stronger stimulation of net photosynthesis rates (NP) and growth (more positive Cohen’s d) and less stimulation of dark respiration and BNF per volume compared to non-nodularin producers under elevated CO2 levels.
This study is the first to provide information on NP and nodularin production under elevated atmospheric CO2 levels for Nodularia and Nostoc species under nitrogen replete and diazotrophic conditions.
Endocytosis of the amyloid precursor protein (APP) is critical for generation of β-amyloid, aggregating in Alzheimer's disease. APP endocytosis depending on the intracellular NPTY motif is well investigated, whereas involvement of the YTSI (also termed BaSS) motif remains controversial. Here, we show that APP lacking the YTSI motif (ΔYTSI) displays reduced localization to early endosomes and decreased internalization rates, similar to APP ΔNPTY. Additionally, we show that the YTSI-binding protein, PAT1a interacts with the Rab5 activator RME-6, as shown by several independent assays. Interestingly, knockdown of RME-6 decreased APP endocytosis, whereas overexpression increased the same. Similarly, APP ΔNPTY endocytosis was affected by PAT1a and RME-6 overexpression, whereas APP ΔYTSI internalization remained unchanged. Moreover, we could show that RME-6 mediated increase of APP endocytosis can be diminished upon knocking down PAT1a. Together, our data identify RME-6 as a novel player in APP endocytosis, involving the YTSI-binding protein PAT1a.
Habitat fragmentation and forest management have been considered to drastically alter the nature of forest ecosystems globally. However, much uncertainty remains regarding the causative mechanisms mediating temperate forest responses, such as forest physical environment and the structure of woody plant assemblages, regardless of the role these forests play for global sustainability. In this paper, we examine how both habitat fragmentation and timber exploitation via silvicultural operations affect these two factors at local and habitat spatial scales in a hyper-fragmented landscape of mixed beech forests spanning more than 1500 km2 in SW Germany. Variables were recorded across 57 1000 m2 plots covering four habitats: small forest fragments, forest edges within large control forests, as well as managed and unmanaged forest interior sites. As expected, forest habitats differed in disturbance level, physical conditions and community structure at plot and habitat scale. Briefly, diversity of plant assemblages differed across all forest habitats (highest in edge forests) and correlated with integrative indices of edge, fragmentation and management effects. Surprisingly, managed and unmanaged forests did not differ in terms of species richness at local spatial scale, but managed forests exhibited a clear signal of physical/floristic homogenization as species promoted by silviculture proliferated; i.e. impoverished communities at landscape scale. Moreover, functional composition of plant communities responded to the microclimatic regime within forest fragments, resulting in a higher prevalence of species adapted to these microclimatic conditions. Our results underscore the notion that forest fragmentation and silvicultural management (1) promote changes in microclimatic regimes, (2) alter the balance between light-demanding and shade-adapted species, (3) support diverse floras across forest edges, and (4) alter patterns of beta diversity. Hence, in human-modified landscapes edge-affected habitats can be recognized as biodiversity reservoirs in contrast to impoverished managed interior forests. Furthermore, our results ratify the role of unmanaged forests as a source of environmental variability, species turnover, and distinct woody plant communities.
The amyloid precursor protein (APP) is a key molecular component of Alzheimer’s disease (AD) pathogenesis. Proteolytic APP processing generates various cleavage products, including extracellular amyloid beta (Aβ) and the cytoplasmic APP intracellular domain (AICD). Although the role of AICD in the activation of kinase signaling pathways is well established in the context
of full-length APP, little is known about intracellular effects of the AICD fragment, particularly within discrete neuronal compartments. Deficits in fast axonal transport (FAT) and axonopathy documented in AD-affected neurons prompted us to evaluate potential axon-autonomous effects of the AICD fragment for the first time. Vesicle motility assays using the isolated squid axoplasm
preparation revealed inhibition of FAT by AICD. Biochemical experiments linked this effect to aberrant activation of selected axonal kinases and heightened phosphorylation of the anterograde motor protein conventional kinesin, consistent with precedents showing phosphorylation-dependent regulation of motors proteins powering FAT. Pharmacological inhibitors of these kinases alleviated the AICD inhibitory effect on FAT. Deletion experiments indicated this effect requires a sequence encompassing the NPTY motif in AICD and interacting axonal proteins containing a phosphotyrosinebinding domain. Collectively, these results provide a proof of principle for axon-specific effects of AICD, further suggesting a potential mechanistic framework linking alterations in APP processing, FAT deficits, and axonal pathology in AD.
Climate change will have severe consequences on Eastern Boundary Upwelling Systems (EBUS). They host the largest fisheries in the world supporting the life of millions of people due to their tremendous primary production. Therefore, it is of utmost importance to better understand predicted impacts like alternating upwelling intensities and light impediment on the structure and the trophic role of protistan plankton communities as they form the basis of the food web. Numerical models estimate the intensification of the frequency in eddy formation. These ocean features are of particular importance due to their influence on the distribution and diversity of plankton communities and the access to resources, which are still not well understood even to the present day. My PhD thesis entails two subjects conducted during large-scaled cooperation projects REEBUS (Role of Eddies in Eastern Boundary Upwelling Systems) and CUSCO (Coastal Upwelling System in a Changing Ocean).
Subject I of my study was conducted within the multidisciplinary framework REEBUS to investigate the influence of eddies on the biological carbon pump in the Canary Current System (CanCS). More specifically, the aim was to find out how mesoscale cyclonic eddies affect the regional diversity, structure, and trophic role of protistan plankton communities in a subtropical oligotrophic oceanic offshore region.
Samples were taken during the M156 and M160 cruises in the Atlantic Ocean around Cape Verde during July and December 2019, respectively. Three eddies with varying ages of emergence and three water layers (deep chlorophyll maximum DCM, right beneath the DCM and oxygen minimum zone OMZ) were sampled. Additional stations without eddy perturbation were analyzed as references. The effect of oceanic mesoscale cyclonic eddies on protistan plankton communities was analyzed by implementing three approaches. (i) V9 18S rRNA gene amplicons were examined to analyze the diversity and structure of the plankton communities and to infer their role in the biological carbon pump. (ii) By assigning functional traits to taxonomically assigned eDNA sequences, functional richness and ecological strategies (ES) were determined. (iii) Grazing experiments were conducted to assess abundance and carbon transfer from prokaryotes to phagotrophic protists.
All three eddies examined in this study differed in their ASV abundance, diversity, and taxonomic composition with the most pronounced differences in the DCM. Dinoflagellates were the most abundant taxa in all three depth layers. Other dominating taxa were radiolarians, Discoba and haptophytes. The trait-approach could only assign ~15% of all ASVs and revealed in general a relatively high functional richness. But no unique ES was determined within a specific eddy. This indicates pronounced functional redundancy, which is recognized to be correlated with ecosystem resilience and robustness by providing a degree of buffering capacity in the face of biodiversity loss. Elevated microbial abundances as well as bacterivory were clearly associated to mesoscale eddy features, albeit with remarkable seasonal fluctuations. Since eddy activity is expected to increase on a global scale in future climate change scenarios, cyclonic eddies could counteract climate change by enhancing carbon sequestration to abyssal depths. The findings demonstrate that cyclonic eddies are unique, heterogeneous, and abundant ecosystems with trapped water masses in which characteristic protistan plankton develop as the eddies age and migrate westward into subtropical oligotrophic offshore waters. Therefore, eddies influence regional protistan plankton diversity qualitatively and quantitatively.
Subject II of my PhD project contributed to the CUSCO field campaign to identify the influence of varying upwelling intensities in combination with distinct light treatments on the whole food web structure and carbon pump in the Humboldt Current System (HCS) off Peru. To accomplish such a task, eight offshore-mesocosms were deployed and two light scenarios (low light, LL; high light, HL) were created by darkening half of the mesocosms. Upwelling was simulated by injecting distinct proportions (0%, 15%, 30% and 45%) of collected deep-water (DW) into each of the moored mesocosms. My aim was to examine the changes in diversity, structure, and trophic role of protistan plankton communities for the induced manipulations by analyzing the V9 18S rRNA gene amplicons and performing short-term grazing experiments.
The upwelling simulations induced a significant increase in alpha diversity under both light conditions. In austral summer, reflected by HL conditions, a generally higher alpha diversity was recorded compared to the austral winter simulation, instigated by LL treatment. Significant alterations of the protistan plankton community structure could likewise be observed. Diatoms were associated to increased levels of DW addition in the mimicked austral winter situation. Under nutrient depletion, chlorophytes exhibited high relative abundances in the simulated austral winter scenario. Dinoflagellates dominated the austral summer condition in all upwelling simulations. Tendencies of reduced unicellular eukaryotes and increased prokaryotic abundances were determined under light impediment. Protistan-mediated mortality of prokaryotes also decreased by ~30% in the mimicked austral winter scenario.
The findings indicate that the microbial loop is a more relevant factor in the structure of the food web in austral summer and is more focused on the utilization of diatoms in austral winter in the HCS off Peru. It was evident that distinct light intensities coupled with multiple upwelling scenarios could lead to alterations in biochemical cycles, trophic interactions, and ecosystem services. Considering the threat of climate change, the predicted relocation of EBUS could limit primary production and lengthen the food web structure with severe socio-economic consequences.