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Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.
Environmental change is likely to have a strong impact on biodiversity, and many species may shift their distribution in response. In this study, we aimed at projecting the availability of suitable habitat for an endangered amphibian species, the Fire-bellied toad Bombina bombina, in Brandenburg (north-eastern Germany). We modelled a potential habitat distribution map based on (1) a database with 10,581 presence records for Bombina from the years 1990 to 2009, (2) current estimates for ecogeographical variables (EGVs) and (3) the future projection of these EGVs according to the statistical regional model, respectively, the soil and water integrated model, applying the maximum entropy approach (Maxent). By comparing current and potential future distributions, we evaluated the projected change in distribution of suitable habitats and identified the environmental variables most associated with habitat suitability that turned out to be climatic variables related to the hydrological cycle. Under the applied scenario, our results indicate increasing habitat suitability in many areas and an extended range of suitable habitats. However, even if the environmental conditions in Brandenburg may change as predicted, it is questionable whether the Fire-bellied toad will truly benefit, as dispersal abilities of amphibian species are limited and strongly influenced by anthropogenic disturbances, that is, intensive agriculture, habitat destruction and fragmentation. Furthermore, agronomic pressure is likely to increase on productive areas with fertile soils and high water retention capacities, indeed those areas suitable for B. bombina. All these changes may affect temporary pond hydrology as well as the reproductive success and breeding phenology of toads.
Increasing attempts are made to understand the factors responsible for both the demographic and genetic depletion in amphibian populations. Landscape genetics aims at a spatially explicit correlation of genetic population parameters to landscape features. Using data from the endangered fire-bellied toad Bombina bombina in Brandenburg (Northeastern Germany), we performed an environmental niche factor analysis (ENFA), relating demographic (abundance) and genetic (diversity at 17 microsatellite loci and partial sequences of the mitochondrial control region in 434 individuals from 16 populations) parameters to ecological and anthropogenic variables such as temperature, precipitation, soil wetness, water runoff, vegetation density, and road/traffic impact. We found significant correlations between road disturbance and observed heterozygosity and between soil wetness and mitochondrial diversity. As the influences of the environmental variables can differ between different indicators for genetic diversity, population size and abundance data, our ENFA-based landscape genetics approach allows us to put various aspects of long- versus short term effective population size and genetic connectivity into an ecological and spatially explicit context, enabling potentially even forecast assessment under future environmental scenarios.
The contractile vacuole (CV) is an osmoregulatory organelle found exclusively in algae and protists. In addition to expelling excessive water out of the cell, it also expels ions and other metabolites and thereby contributes to the cell's metabolic homeostasis. The interest in the CV reaches beyond its immediate cellular roles. The CV's function is tightly related to basic cellular processes such as membrane dynamics and vesicle budding and fusion; several physiological processes in animals, such as synaptic neurotransmission and blood filtration in the kidney, are related to the CV's function; and several pathogens, such as the causative agents of sleeping sickness, possess CVs, which may serve as pharmacological targets. The green alga Chlamydomonas reinhardtii has two CVs. They are the smallest known CVs in nature, and they remain relatively untouched in the CV-related literature. Many genes that have been shown to be related to the CV in other organisms have close homologues in C. reinhardtii. We attempted to silence some of these genes and observe the effect on the CV. One of our genes, VMP1, caused striking, severe phenotypes when silenced. Cells exhibited defective cytokinesis and aberrant morphologies. The CV, incidentally, remained unscathed. In addition, mutant cells showed some evidence of disrupted autophagy. Several important regulators of the cell cycle as well as autophagy were found to be underexpressed in the mutant. Lipidomic analysis revealed many meaningful changes between wild-type and mutant cells, reinforcing the compromised-autophagy observation. VMP1 is a singular protein, with homologues in numerous eukaryotic organisms (aside from fungi), but usually with no relatives in each particular genome. Since its first characterization in 2002 it has been associated with several cellular processes and functions, namely autophagy, programmed cell-death, secretion, cell adhesion, and organelle biogenesis. It has been implicated in several human diseases: pancreatitis, diabetes, and several types of cancer. Our results reiterate some of the observations in VMP1's six reported homologues, but, importantly, show for the first time an involvement of this protein in cell division. The mechanisms underlying this involvement in Chlamydomonas, as well as other key aspects, such as VMP1's subcellular localization and interaction partners, still await elucidation.
Cyanobacteria produce about 40 percent of the world’s primary biomass, but also a variety of often toxic peptides such as microcystin. Mass developments, so called blooms, can pose a real threat to the drinking water supply in many parts of the world. This study aimed at characterizing the biological function of microcystin production in one of the most common bloom-forming cyanobacterium Microcystis aeruginosa.
In a first attempt, the effect of elevated light intensity on microcystin production and its binding to cellular proteins was studied. Therefore, conventional microcystin quantification techniques were combined with protein-biochemical methods. RubisCO, the key enzyme for primary carbon fixation was a major microcystin interaction partner. High light exposition strongly stimulated microcystin-protein interactions. Up to 60 percent of the total cellular microcystin was detected bound to proteins, i.e. inaccessible for standard quantification procedures. Underestimation of total microcystin contents when neglecting the protein fraction was also demonstrated in field samples. Finally, an immuno-fluorescence based method was developed to identify microcystin producing cyanobacteria in mixed populations.
The high light induced microcystin interaction with proteins suggested an impact of the secondary metabolite on the primary metabolism of Microcystis by e.g. modulating the activity of enzymes. For addressing that question, a comprehensive GC/MS-based approach was conducted to compare the accumulation of metabolites in the wild-type of Microcystis aeruginosa PCC 7806 and the microcystin deficient ΔmcyB mutant. From all 501 detected non-redundant metabolites 85 (17 percent) accumulated significantly different in either of both genotypes upon high light exposition. Accumulation of compatible solutes in the ΔmcyB mutant suggests a role of microcystin in fine-tuning the metabolic flow to prevent stress related to excess light, high oxygen concentration and carbon limitation.
Co-analysis of the widely used model cyanobacterium Synechocystis PCC 6803 revealed profound metabolic differences between species of cyanobacteria. Whereas Microcystis channeled more resources towards carbohydrate synthesis, Synechocystis invested more in amino acids. These findings were supported by electron microscopy of high light treated cells and the quantification of storage compounds. While Microcystis accumulated mainly glycogen to about 8.5 percent of its fresh weight within three hours, Synechocystis produced higher amounts of cyanophycin. The results showed that the characterization of species-specific metabolic features should gain more attention with regard to the biotechnological use of cyanobacteria.
Protein-metal coordination complexes are well known as active centers in enzymatic catalysis, and to contribute to signal transduction, gas transport, and to hormone function. Additionally, they are now known to contribute as load-bearing cross-links to the mechanical properties of several biological materials, including the jaws of Nereis worms and the byssal threads of marine mussels. The primary aim of this thesis work is to better understand the role of protein-metal cross-links in the mechanical properties of biological materials, using the mussel byssus as a model system. Specifically, the focus is on histidine-metal cross-links as sacrificial bonds in the fibrous core of the byssal thread (Chapter 4) and L-3,4-dihydroxyphenylalanine (DOPA)-metal bonds in the protective thread cuticle (Chapter 5).
Byssal threads are protein fibers, which mussels use to attach to various substrates at the seashore. These relatively stiff fibers have the ability to extend up to about 100 % strain, dissipating large amounts of mechanical energy from crashing waves, for example. Remarkably, following damage from cyclic loading, initial mechanical properties are subsequently recovered by a material-intrinsic self-healing capability. Histidine residues coordinated to transition metal ions in the proteins comprising the fibrous thread core have been suggested as reversible sacrificial bonds that contribute to self-healing; however, this remains to be substantiated in situ. In the first part of this thesis, the role of metal coordination bonds in the thread core was investigated using several spectroscopic methods. In particular, X-ray absorption spectroscopy (XAS) was applied to probe the coordination environment of zinc in Mytilus californianus threads at various stages during stretching and subsequent healing. Analysis of the extended X-ray absorption fine structure (EXAFS) suggests that tensile deformation of threads is correlated with the rupture of Zn-coordination bonds and that self-healing is connected with the reorganization of Zn-coordination bond topologies rather than the mere reformation of Zn-coordination bonds. These findings have interesting implications for the design of self-healing metallopolymers.
The byssus cuticle is a protective coating surrounding the fibrous thread core that is both as hard as an epoxy and extensible up to 100 % strain before cracking. It was shown previously that cuticle stiffness and hardness largely depend on the presence of Fe-DOPA coordination bonds. However, the byssus is known to concentrate a large variety of metals from seawater, some of which are also capable of binding DOPA (e.g. V). Therefore, the question arises whether natural variation of metal composition can affect the mechanical performance of the byssal thread cuticle. To investigate this hypothesis, nanoindentation and confocal Raman spectroscopy were applied to the cuticle of native threads, threads with metals removed (EDTA treated), and threads in which the metal ions in the native tissue were replaced by either Fe or V. Interestingly, replacement of metal ions with either Fe or V leads to the full recovery of native mechanical properties with no statistical difference between each other or the native properties. This likely indicates that a fixed number of metal coordination sites are maintained within the byssal thread cuticle – possibly achieved during thread formation – which may provide an evolutionarily relevant mechanism for maintaining reliable mechanics in an unpredictable environment.
While the dynamic exchange of bonds plays a vital role in the mechanical behavior and self-healing in the thread core by allowing them to act as reversible sacrificial bonds, the compatibility of DOPA with other metals allows an inherent adaptability of the thread cuticle to changing circumstances. The requirements to both of these materials can be met by the dynamic nature of the protein-metal cross-links, whereas covalent cross-linking would fail to provide the adaptability of the cuticle and the self-healing of the core. In summary, these studies of the thread core and the thread cuticle serve to underline the important and dynamic roles of protein-metal coordination in the mechanical function of load-bearing protein fibers, such as the mussel byssus.
Inferring gene regulatory networks and cellular phases from time-resolved transcriptomics data
(2014)
The adaptation of cell growth and proliferation to environmental changes is essential for the surviving of biological systems. The evolutionary conserved Ser/Thr protein kinase “Target of Rapamycin” (TOR) has emerged as a major signaling node that integrates the sensing of numerous growth signals to the coordinated regulation of cellular metabolism and growth. Although the TOR signaling pathway has been widely studied in heterotrophic organisms, the research on TOR in photosynthetic eukaryotes has been hampered by the reported land plant resistance to rapamycin. Thus, the finding that Chlamydomonas reinhardtii is sensitive to rapamycin, establish this unicellular green alga as a useful model system to investigate TOR signaling in photosynthetic eukaryotes.
The observation that rapamycin does not fully arrest Chlamydomonas growth, which is different from observations made in other organisms, prompted us to investigate the regulatory function of TOR in Chlamydomonas in context of the cell cycle. Therefore, a growth system that allowed synchronously growth under widely unperturbed cultivation in a fermenter system was set up and the synchronized cells were characterized in detail. In a highly resolved kinetic study, the synchronized cells were analyzed for their changes in cytological parameters as cell number and size distribution and their starch content. Furthermore, we applied mass spectrometric analysis for profiling of primary and lipid metabolism. This system was then used to analyze the response dynamics of the Chlamydomonas metabolome and lipidome to TOR-inhibition by rapamycin
The results show that TOR inhibition reduces cell growth, delays cell division and daughter cell release and results in a 50% reduced cell number at the end of the cell cycle. Consistent with the growth phenotype we observed strong changes in carbon and nitrogen partitioning in the direction of rapid conversion into carbon and nitrogen storage through an accumulation of starch, triacylglycerol and arginine. Interestingly, it seems that the conversion of carbon into triacylglycerol occurred faster than into starch after TOR inhibition, which may indicate a more dominant role of TOR in the regulation of TAG biosynthesis than in the regulation of starch.
This study clearly shows, for the first time, a complex picture of metabolic and lipidomic dynamically changes during the cell cycle of Chlamydomonas reinhardtii and furthermore reveals a complex regulation and adjustment of metabolite pools and lipid composition in response to TOR inhibition.
Tierische und menschliche Fäkalien aus Landwirtschaft und Haushalten enthalten zahlreiche obligat und opportunistisch pathogene Mikroorganismen, deren Konzentration u. a. je nach Gesundheitszustand der betrachteten Gruppe schwankt. Neben den Krankheitserregern enthalten Fäkalien aber auch essentielle Pflanzennährstoffe (276) und dienen seit Jahrtausenden (63) als Dünger für Feldfrüchte. Mit der unbedarften Verwendung von pathogenbelastetem Fäkaldünger steigt jedoch auch das Risiko einer Infektion von Mensch und Tier. Diese Gefahr erhöht sich mit der globalen Vernetzung der Landwirtschaft, z. B. durch den Import von kontaminierten Futter- bzw. Lebensmitteln (29).
Die vorliegende Arbeit stellt die milchsaure Fermentation von Rindergülle und Klärschlamm als alternative Hygienisierungsmethode gegenüber der Pasteurisation in Biogasanlagen bzw. gebräuchlichen Kompostierung vor.
Dabei wird ein Abfall der Gram-negativen Bakterienflora sowie der Enterokokken, Schimmel- und Hefepilze unter die Nachweisgrenze von 3 log10KbE/g beobachtet, gleichzeitig steigt die Konzentration der Lactobacillaceae um das Tausendfache. Darüber hinaus wird gezeigt, dass pathogene Bakterien wie Staphylococcus aureus, Salmonella spp., Listeria monocytogenes, EHEC O:157 und vegetative Clostridum perfringens-Zellen innerhalb von 3 Tagen inaktiviert werden. Die Inaktivierung von ECBO-Viren und Spulwurmeiern erfolgt innerhalb von 7 bzw. 56 Tagen. Zur Aufklärung der Ursache der beobachteten Hygienisierung wurde das fermentierte Material auf flüchtige Fettsäuren sowie pH-Wertänderungen untersucht. Es konnte festgestellt werden, dass die gemessenen Werte nicht die alleinige Ursache für das Absterben der Erreger sind, vielmehr wird eine zusätzliche bakterizide Wirkung durch eine mutmaßliche Bildung von Bakteriozinen in Betracht gezogen. Die parasitizide Wirkung wird auf die physikalischen Bedingungen der Fermentation zurückgeführt.
Die methodischen Grundlagen basieren auf Analysen mittels zahlreicher klassisch-kultureller Verfahren, wie z. B. der Lebendkeimzahlbestimmung. Darüber hinaus findet die MALDI-TOF-Massenspektrometrie und die klassische PCR in Kombination mit der Gradienten-Gelelektrophorese Anwendung, um kultivierbare Bakterienfloren zu beschreiben bzw. nicht kultivierbare Bakterienfloren stichprobenartig zu erfassen.
Neben den Aspekten der Hygienisierung wird zudem die Eignung der Methode für die landwirtschaftliche Nutzung berücksichtigt. Dies findet sich insbesondere in der Komposition des zu fermentierenden Materials wieder, welches für die verstärkte Humusakkumulation im Ackerboden optimiert wurde. Darüber hinaus wird die Masseverlustbilanz während der milchsauren Fermentation mit denen der Kompostierung sowie der Verarbeitung in der Biogasanlage verglichen und als positiv bewertet, da sie mit insgesamt 2,45 % sehr deutlich unter den bisherigen Alternativen liegt (73, 138, 458). Weniger Verluste an organischem Material während der Hygienisierung führen zu einer größeren verwendbaren Düngermenge, die auf Grund ihres organischen Ursprungs zu einer Verstärkung des Humusanteiles im Ackerboden beitragen kann (56, 132).
Mars is one of the best candidates among planetary bodies for supporting life. The presence of water in the form of ice and atmospheric vapour together with the availability of biogenic elements and energy are indicators of the possibility of hosting life as we know it. The occurrence of permanently frozen ground – permafrost, is a common phenomenon on Mars and it shows multiple morphological analogies with terrestrial permafrost. Despite the extreme inhospitable conditions, highly diverse microbial communities inhabit terrestrial permafrost in large numbers. Among these are methanogenic archaea, which are anaerobic chemotrophic microorganisms that meet many of the metabolic and physiological requirements for survival on the martian subsurface. Moreover, methanogens from Siberian permafrost are extremely resistant against different types of physiological stresses as well as simulated martian thermo-physical and subsurface conditions, making them promising model organisms for potential life on Mars. The main aims of this investigation are to assess the survival of methanogenic archaea under Mars conditions, focusing on methanogens from Siberian permafrost, and to characterize their biosignatures by means of Raman spectroscopy, a powerful technology for microbial identification that will be used in the ExoMars mission. For this purpose, methanogens from Siberian permafrost and non-permafrost habitats were subjected to simulated martian desiccation by exposure to an ultra-low subfreezing temperature (-80ºC) and to Mars regolith (S-MRS and P-MRS) and atmospheric analogues. They were also exposed to different concentrations of perchlorate, a strong oxidant found in martian soils. Moreover, the biosignatures of methanogens were characterized at the single-cell level using confocal Raman microspectroscopy (CRM). The results showed survival and methane production in all methanogenic strains under simulated martian desiccation. After exposure to subfreezing temperatures, Siberian permafrost strains had a faster metabolic recovery, whereas the membranes of non-permafrost methanogens remained intact to a greater extent. The strain Methanosarcina soligelidi SMA-21 from Siberian permafrost showed significantly higher methane production rates than all other strains after the exposure to martian soil and atmospheric analogues, and all strains survived the presence of perchlorate at the concentration on Mars. Furthermore, CRM analyses revealed remarkable differences in the overall chemical composition of permafrost and non-permafrost strains of methanogens, regardless of their phylogenetic relationship. The convergence of the chemical composition in non-sister permafrost strains may be the consequence of adaptations to the environment, and could explain their greater resistance compared to the non-permafrost strains. As part of this study, Raman spectroscopy was evaluated as an analytical technique for remote detection of methanogens embedded in a mineral matrix. This thesis contributes to the understanding of the survival limits of methanogenic archaea under simulated martian conditions to further assess the hypothetical existence of life similar to methanogens on the martian subsurface. In addition, the overall chemical composition of methanogens was characterized for the first time by means of confocal Raman microspectroscopy, with potential implications for astrobiological research.
Metabolic systems tend to exhibit steady states that can be measured in terms of their concentrations and fluxes. These measurements can be regarded as a phenotypic representation of all the complex interactions and regulatory mechanisms taking place in the underlying metabolic network. Such interactions determine the system's response to external perturbations and are responsible, for example, for its asymptotic stability or for oscillatory trajectories around the steady state. However, determining these perturbation responses in the absence of fully specified kinetic models remains an important challenge of computational systems biology. Structural kinetic modeling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a parameterised representation of the system's Jacobian matrix in which the model parameters encode information about the enzyme-metabolite interactions. Stability criteria can be derived by generating a large number of structural kinetic models (SK-models) with randomly sampled parameter sets and evaluating the resulting Jacobian matrices. The parameter space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Because the sampled parameters are equivalent to the elasticities used in metabolic control analysis (MCA), the results are easy to interpret biologically. In this project, the SKM framework was extended by several novel methodological improvements. These improvements were evaluated in a simulation study using a set of small example pathways with simple Michaelis Menten rate laws. Afterwards, a detailed analysis of the dynamic properties of the neuronal TCA cycle was performed in order to demonstrate how the new insights obtained in this work could be used for the study of complex metabolic systems. The first improvement was achieved by examining the biological feasibility of the elasticity combinations created during Monte Carlo sampling. Using a set of small example systems, the findings showed that the majority of sampled SK-models would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion was formulated that mitigates such infeasible models and the application of this criterion changed the conclusions of the SKM experiment. The second improvement of this work was the application of supervised machine-learning approaches in order to analyse SKM experiments. So far, SKM experiments have focused on the detection of individual enzymes to identify single reactions important for maintaining the stability or oscillatory trajectories. In this work, this approach was extended by demonstrating how SKM enables the detection of ensembles of enzymes or metabolites that act together in an orchestrated manner to coordinate the pathways response to perturbations. In doing so, stable and unstable states served as class labels, and classifiers were trained to detect elasticity regions associated with stability and instability. Classification was performed using decision trees and relevance vector machines (RVMs). The decision trees produced good classification accuracy in terms of model bias and generalizability. RVMs outperformed decision trees when applied to small models, but encountered severe problems when applied to larger systems because of their high runtime requirements. The decision tree rulesets were analysed statistically and individually in order to explore the role of individual enzymes or metabolites in controlling the system's trajectories around steady states. The third improvement of this work was the establishment of a relationship between the SKM framework and the related field of MCA. In particular, it was shown how the sampled elasticities could be converted to flux control coefficients, which were then investigated for their predictive information content in classifier training. After evaluation on the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle with respect to their intrinsic mechanisms responsible for stability or instability. The findings showed that several elasticities were jointly coordinated to control stability and that the main source for potential instabilities were mutations in the enzyme alpha-ketoglutarate dehydrogenase.
African weakly electric fishes (Mormyridae) underwent an outstanding adaptive radiation (about 200 species), putatively owing to their ability to communicate through species-specific weak electric signals. The electric organ discharge (EOD) is produced by muscle-derived electrocytes organized in piles to form an electric organ. Despite the importance of this trait as a prezygotic isolation mechanism, genomic resources remained limited. We present here a first draft of the skeletal muscle and electric organ transcriptomes from the weakly electric fish species Campylomormyrus compressirostris, obtained using the Illumina HiSeq2000 sequencing technology. Approximately 6.8 Gbp of cDNA sequence data were produced from both tissues, resulting in 57268109 raw reads for the skeletal muscle and 46934923 for the electric organ, and assembled de novo into 46143 and 89270 contigs, respectively. About 50% of both transcriptomes were annotated after protein databases search. The two transcriptomes show similar profiles in terms of Gene Ontology categories composition. We identified several candidate genes which are likely to play a central role in the production and evolution of the electric signal. For most of these genes, and for many other housekeeping genes, we were able to obtain the complete or partial coding DNA sequences (CDS), which can be used for the development of primers to be utilized in qRT-PCR experiments. We present also the complete mitochondrial genome and compare it to those available from other weakly electric fish species. Additionally, we located 1671 SSR-containing regions with their flanking sites and designed the relative primers. This study establishes a first step in the development of genomic tools aimed at understanding the role of electric communication during speciation.
Plants are sessile organisms that gauge stressful conditions to ensure survival and reproductive success. While plants in nature often encounter chronic or recurring stressful conditions, the strategies to cope with those are poorly understood. Here, we demonstrate the involvement of ARGONAUTE1 and the microRNA pathway in the adaptation to recurring heat stress (HS memory) at the physiological and molecular level. We show that miR156 isoforms are highly induced after HS and are functionally important for HS memory. miR156 promotes sustained expression of HS-responsive genes and is critical only after HS, demonstrating that the effects of modulating miR156 on HS memory do not reflect preexisting developmental alterations. miR156 targets SPL transcription factor genes that are master regulators of developmental transitions. SPL genes are posttranscriptionally downregulated by miR156 after HS, and this is critical for HS memory. Altogether, the miR156-SPL module mediates the response to recurring HS in Arabidopsis thaliana and thus may serve to integrate stress responses with development.