Showing papers by "Braunschweig University of Technology published in 2017"

A guiding map for inflammation

Abstract: Biologists, physicians and immunologists have contributed to the understanding of the cellular participants and biological pathways involved in inflammation. Here, we provide a general guide to the cellular and humoral contributors to inflammation as well as to the pathways that characterize inflammation in specific organs and tissues.

Designing Human Antibodies by Phage Display

Abstract: With six approved products and more than 60 candidates in clinical testing, human monoclonal antibody discovery by phage display is well established as a robust and reliable source for the generation of therapeutic antibodies. While a vast diversity of library generation philosophies and selection strategies have been conceived, the power of molecular design offered by controlling the in vitro selection step is still to be recognized by a broader audience outside of the antibody engineering community. Here, we summarize some opportunities and achievements, e.g., the generation of antibodies which could not be generated otherwise, and the design of antibody properties by different panning strategies, including the adjustment of kinetic parameters.

Not just amyloid: physiological functions of the amyloid precursor protein family

Abstract: Amyloid precursor protein (APP) gives rise to the amyloid-β peptide and thus has a key role in the pathogenesis of Alzheimer disease. By contrast, the physiological functions of APP and the closely related APP-like proteins (APLPs) remain less well understood. Studying these physiological functions has been challenging and has required a careful long-term strategy, including the analysis of different App-knockout and Aplp-knockout mice. In this Review, we summarize these findings, focusing on the in vivo roles of APP family members and their processing products for CNS development, synapse formation and function, brain injury and neuroprotection, as well as ageing. In addition, we discuss the implications of APP physiology for therapeutic approaches.

Review of the Current State of UAV Regulations

Abstract: UAVs—unmanned aerial vehicles—facilitate data acquisition at temporal and spatial scales that still remain unachievable for traditional remote sensing platforms. However, current legal frameworks that regulate UAVs present significant barriers to research and development. To highlight the importance, impact, and diversity of UAV regulations, this paper provides an exploratory investigation of UAV regulations on the global scale. For this, the methodological approach consists of a research synthesis of UAV regulations, including a thorough literature review and a comparative analysis of national regulatory frameworks. Similarities and contrasting elements in the various national UAV regulations are explored including their statuses from the perspectives of past, present, and future trends. Since the early 2000s, countries have gradually established national legal frameworks. Although all UAV regulations have one common goal—minimizing the risks to other airspace users and to both people and property on the ground—the results reveal distinct variations in all the compared variables. Furthermore, besides the clear presence of legal frameworks, market forces such as industry design standards and reliable information about UAVs as public goods are expected to shape future developments.

The ins and outs of microorganism–electrode electron transfer reactions

Abstract: Electron transfer between microorganisms and an electrode — even across long distances — enables the former to live by coupling to an electronic circuit. Such a system integrates biological metabolism with artificial electronics; studying these systems adds to our knowledge of charge transport in the chemical species involved, as well as, perhaps most importantly, to our knowledge of charge transport and chemistry at the cell–electrode interfaces. This understanding may lead to microbial electrochemical systems finding widespread application, particularly in the energy sector. Bioelectrochemical systems have already shown promise for electricity generation, as well as for the production of biochemical and chemical feedstocks, and with improvement are likely to give rise to viable applications. Electrodes colonized by microbial electrocatalysts can serve as useful components in the electrosynthesis of valuable chemical products. This Review outlines the mechanisms by which electrons are transferred between microorganisms and electrodes, and describes the challenges involved in designing robust and efficient systems.

The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

Abstract: Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bio-acoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.

Nitric oxide function in plant abiotic stress

Abstract: Abiotic stress is one of the main threats affecting crop growth and production. An understanding of the molecular mechanisms that underpin plant responses against environmental insults will be crucial to help guide the rational design of crop plants to counter these challenges. A key feature during abiotic stress is the production of nitric oxide (NO), an important concentration dependent, redox-related signalling molecule. NO can directly or indirectly interact with a wide range of targets leading to the modulation of protein function and the reprogramming of gene expression. The transfer of NO bioactivity can occur through a variety of potential mechanisms but chief among these is S-nitrosylation, a prototypic, redox-based, post-translational modification. However, little is known about this pivotal molecular amendment in the regulation of abiotic stress signalling. Here, we describe the emerging knowledge concerning the function of NO and S-nitrosylation during plant responses to abiotic stress.

Future Challenges in Heterogeneous Catalysis: Understanding Catalysts under Dynamic Reaction Conditions.

Abstract: In the future, (electro-)chemical catalysts will have to be more tolerant towards a varying supply of energy and raw materials. This is mainly due to the fluctuating nature of renewable energies. For example, power-to-chemical processes require a shift from steady-state operation towards operation under dynamic reaction conditions. This brings along a number of demands for the design of both catalysts and reactors, because it is well-known that the structure of catalysts is very dynamic. However, in-depth studies of catalysts and catalytic reactors under such transient conditions have only started recently. This requires studies and advances in the fields of 1) operando spectroscopy including time-resolved methods, 2) theory with predictive quality, 3) kinetic modelling, 4) design of catalysts by appropriate preparation concepts, and 5) novel/modular reactor designs. An intensive exchange between these scientific disciplines will enable a substantial gain of fundamental knowledge which is urgently required. This concept article highlights recent developments, challenges, and future directions for understanding catalysts under dynamic reaction conditions.

BRENDA in 2017: new perspectives and new tools in BRENDA.

Abstract: The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations. External data and links complete the data with sequences and 3D structures. A total of 206 000 enzyme ligands provide functional and structural data. BRENDA offers a complex query tool engine allowing the users an efficient access to the data via different search methods and explorers. The new design of the BRENDA entry page and the enzyme summary pages improves the user access and the performance. New interactive and intuitive BRENDA pathway maps give an overview on biochemical processes and facilitate the visualization of enzyme, ligand and organism information in the biochemical context. SCOPe and CATH, databases for protein structure classification, are included. New online and video tutorials provide online training for the users. BRENDA is freely available for academic users.

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

Abstract: Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

Abstract: The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Further to its role in the tricarboxylic acid cycle, αKG is an essential cofactor for αKG-dependent dioxygenases such as Egl-9 family hypoxia inducible factor 1 (EGLN1) and the ten-eleven translocation (TET) family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG, leading to EGLN1-mediated HIF1α protein degradation. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. By contrast, overexpression of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation through altered TET activity. AML with high levels of BCAT1 (BCAT1high) displayed a DNA hypermethylation phenotype similar to cases carrying a mutant isocitrate dehydrogenase (IDHmut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate. High levels of BCAT1 strongly correlate with shorter overall survival in IDHWTTET2WT, but not IDHmut or TET2mut AML. Gene sets characteristic for IDHmut AML were enriched in samples from patients with an IDHWTTET2WTBCAT1high status. BCAT1high AML showed robust enrichment for leukaemia stem-cell signatures, and paired sample analysis showed a significant increase in BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1α stability and regulation of the epigenomic landscape, mimicking the effects of IDH mutations. Our results suggest the BCAA-BCAT1-αKG pathway as a therapeutic target to compromise leukaemia stem-cell function in patients with IDHWTTET2WT AML.

Telling your secrets without page faults: stealthy page table-based attacks on enclaved execution

Abstract: Protected module architectures, such as Intel SGX, enable strong trusted computing guarantees for hardware-enforced enclaves on top a potentially malicious operating system. However, such enclaved execution environments are known to be vulnerable to a powerful class of controlled-channel attacks. Recent research convincingly demonstrated that adversarial system software can extract sensitive data from enclaved applications by carefully revoking access rights on enclave pages, and recording the associated page faults. As a response, a number of state-of-the-art defense techniques has been proposed that suppress page faults during enclave execution. This paper shows, however, that page table-based threats go beyond page faults. We demonstrate that an untrusted operating system can observe enclave page accesses without resorting to page faults, by exploiting other side-effects of the address translation process. We contribute two novel attack vectors that infer enclaved memory accesses from page table attributes, as well as from the caching behavior of unprotected page table memory. We demonstrate the effectiveness of our attacks by recovering EdDSA session keys with little to no noise from the popular Libgcrypt cryptographic software suite.

Actin assembly mechanisms at a glance.

Abstract: The actin cytoskeleton and associated motor proteins provide the driving forces for establishing the astonishing morphological diversity and dynamics of mammalian cells. Aside from functions in protruding and contracting cell membranes for motility, differentiation or cell division, the actin cytoskeleton provides forces to shape and move intracellular membranes of organelles and vesicles. To establish the many different actin assembly functions required in time and space, actin nucleators are targeted to specific subcellular compartments, thereby restricting the generation of specific actin filament structures to those sites. Recent research has revealed that targeting and activation of actin filament nucleators, elongators and myosin motors are tightly coordinated by conserved protein complexes to orchestrate force generation. In this Cell Science at a Glance article and the accompanying poster, we summarize and discuss the current knowledge on the corresponding protein complexes and their modes of action in actin nucleation, elongation and force generation.

Phylotranscriptomic consolidation of the jawed vertebrate timetree.

Abstract: Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost-effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calcul a ting genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates. The use of genomic data to reconstruct phylogenetic relationships is powerful but challenging. Here, the authors develop a bioinformatics pipeline and use phylogenomic datasets to reconstruct the evolutionary relationships of jawed vertebrates.

On Millimeter Wave and THz Mobile Radio Channel for Smart Rail Mobility

Abstract: As a widely acknowledged efficient and green transportation model, rail traffic is expected to evolve into a new era of “smart rail mobility” whereby infrastructure, trains, and travelers will be interconnected to achieve optimized mobility, higher safety, and lower costs. Thus, a seamless high-data rate wireless connectivity with up to dozens of gigahertz bandwidth is required. Such a huge bandwidth requirement motivates the exploration of the underutilized millimeter (mm) wave and terahertz (THz) bands. In this paper, the motivations for developing millimeter wave and THz communications for railway are clarified by first defining the applications and scenarios required for smart rail mobility. Ray-tracing simulations at 100 GHz imply that to form high-gain directional antenna beams, dynamic beamforming strategies and advanced handover design are critical for the feasibility of THz communications to enable smart rail mobility.

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.

Abstract: The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.

Harvesting the unexplored potential of European waste materials for road construction

Abstract: This paper demonstrates how a considerable amount of waste produced in the urban and peri-urban environment can be recycled in asphalt roads. The example presented is from Europe, however, the barriers and conclusions are universal. It was shown that various waste materials such as glass, asphalt, concrete, wood, plastics etc. have a potential for re-use in asphalt roads. The available quantities of the European target waste materials that would otherwise be incinerated or disposed in landfills were considered. It was shown that there is high potential in Europe for recycling in road construction, in particular, under the hypothetical scenario where 33% of new roads would be made of the target waste materials (excluding RAP which is already recycled), it is estimated that 16% of the available waste quantities could be recycled in roads. Four hypothetical roads were analysed showing a considerable savings in costs, CO2 and energy in comparison to conventional asphalt mixtures using all virgin components.

Xenon isotopes in 67P/Churyumov-Gerasimenko show that comets contributed to Earth's atmosphere

Abstract: The origin of cometary matter and the potential contribution of comets to inner-planet atmospheres are long-standing problems. During a series of dedicated low-altitude orbits, the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) on the Rosetta spacecraft analyzed the isotopes of xenon in the coma of comet 67P/Churyumov-Gerasimenko. The xenon isotopic composition shows deficits in heavy xenon isotopes and matches that of a primordial atmospheric component. The present-day Earth atmosphere contains 22 ± 5% cometary xenon, in addition to chondritic (or solar) xenon.

Targeting Neuroinflammation to Treat Alzheimer’s Disease

Abstract: Over the past few decades, research on Alzheimer's disease (AD) has focused on pathomechanisms linked to two of the major pathological hallmarks of extracellular deposition of beta-amyloid peptides and intra-neuronal formation of neurofibrils. Recently, a third disease component, the neuroinflammatory reaction mediated by cerebral innate immune cells, has entered the spotlight, prompted by findings from genetic, pre-clinical, and clinical studies. Various proteins that arise during neurodegeneration, including beta-amyloid, tau, heat shock proteins, and chromogranin, among others, act as danger-associated molecular patterns, that-upon engagement of pattern recognition receptors-induce inflammatory signaling pathways and ultimately lead to the production and release of immune mediators. These may have beneficial effects but ultimately compromise neuronal function and cause cell death. The current review, assembled by participants of the Chiclana Summer School on Neuroinflammation 2016, provides an overview of our current understanding of AD-related immune processes. We describe the principal cellular and molecular players in inflammation as they pertain to AD, examine modifying factors, and discuss potential future therapeutic targets.

Combined fit of spectrum and composition data as measured by the Pierre Auger Observatory

Abstract: We present a combined fit of a simple astrophysical model of UHECR sources to both the energy spectrum and mass composition data measured by the Pierre Auger Observatory. The fit has been performed for energies above $5 \cdot 10^{18}$ eV, i.e.~the region of the all-particle spectrum above the so-called "ankle" feature. The astrophysical model we adopted consists of identical sources uniformly distributed in a comoving volume, where nuclei are accelerated through a rigidity-dependent mechanism. The fit results suggest sources characterized by relatively low maximum injection energies, hard spectra and heavy chemical composition. We also show that uncertainties about physical quantities relevant to UHECR propagation and shower development have a non-negligible impact on the fit results.

Determining the bacterial cell biology of Planctomycetes

Abstract: Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail. Super-resolution light microscopy of mutants, cryo-electron tomography, bioinformatic predictions and proteomic analyses support an altered Gram-negative cell plan for Planctomycetes, including a defined outer membrane, a periplasmic space that can be greatly enlarged and convoluted, and an energized cytoplasmic membrane. These conclusions are further supported by experiments performed with two other Planctomycetes, Gemmata obscuriglobus and Rhodopirellula baltica. We also provide experimental evidence that is inconsistent with endocytosis-like macromolecule uptake; instead, extracellular macromolecules can be taken up and accumulate in the periplasmic space through unclear mechanisms.

Photonic Nanostructures Patterned by Thermal Nanoimprint Directly into Organo-Metal Halide Perovskites.

Abstract: Photonic nanostructures are created in organo-metal halide perovskites by thermal nanoimprint lithography at a temperature of 100 °C. The imprinted layers are significantly smoothened compared to the initially rough, polycrystalline layers and the impact of surface defects is substantially mitigated upon imprint. As a case study, 2D photonic crystals are shown to afford lasing with ultralow lasing thresholds at room temperature.