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Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein - a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here.
Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago.
Aldehyde oxidase (AOX1) is an enzyme with broad substrate specificity, catalyzing the oxidation of a wide range of endogenous and exogenous aldehydes as well as N-heterocyclic aromatic compounds. In humans, the enzyme’s role in phase I drug metabolism has been established and its importance is now emerging. However, the true physiologic function of AOX1 in mammals is still unknown. Further, numerous single-nucleotide polymorphisms (SNPs) have been identified in human AOX1. SNPs are a major source of interindividual variability in the human population, and SNP-based amino acid exchanges in AOX1 reportedly modulate the catalytic function of the enzyme in either a positive or negative fashion. For the reliable analysis of the effect of amino acid exchanges in human proteins, the existence of reproducible expression systems for the production of active protein in ample amounts for kinetic, spectroscopic, and crystallographic studies is required. In our study we report an optimized expression system for hAOX1 in Escherichia coli using a codon-optimized construct. The codon-optimization resulted in an up to 15-fold increase of protein production and a simplified purification procedure. The optimized expression system was used to study three SNPs that result in amino acid changes C44W, G1269R, and S1271L. In addition, the crystal structure of the S1271L SNP was solved. We demonstrate that the recombinant enzyme can be used for future studies to exploit the role of AOX in drug metabolism, and for the identification and synthesis of new drugs targeting AOX when combined with crystallographic and modeling studies.
Seit der Einführung von Antibiotika in die medizinische Behandlung von bakteriellen Infektionskrankheiten existiert ein Wettlauf zwischen der Evolution von Bakterienresistenzen und der Entwicklung wirksamer Antibiotika. Während bis in die 80er Jahre verstärkt an neuen Antibiotika geforscht wurde, gewinnen multiresistente Keime heute zunehmend die Oberhand. Um einzelne Pathogene erfolgreich nachzuweisen und zu bekämpfen, ist ein grundlegendes Wissen über den Erreger unumgänglich. Bakterielle Proteine, die bei einer Infektion vorrangig vom Immunsystem prozessiert und präsentiert werden, könnten für die Entwicklung von Impfstoffen oder gezielten Therapeutika nützlich sein. Auch für die Diagnostik wären diese immundominanten Proteine interessant. Allerdings herrscht ein Mangel an Wissen über spezifische Antigene vieler pathogener Bakterien, die eine eindeutige Diagnostik eines einzelnen Erregers erlauben würden.
Daher wurden in dieser Arbeit vier verschiedene Humanpathogene mittels Phage Display untersucht: Neisseria gonorrhoeae, Neisseria meningitidis, Borrelia burgdorferi und Clostridium difficile. Hierfür wurden aus der genomischen DNA der vier Erreger Bibliotheken konstruiert und durch wiederholte Selektion und Amplifikation, dem sogenannten Panning, immunogene Proteine isoliert. Für alle Erreger bis auf C. difficile wurden immunogene Proteine aus den jeweiligen Bibliotheken isoliert. Die identifizierten Proteine von N. meningitidis und B. burgdorferi waren größtenteils bekannt, konnten aber in dieser Arbeit durch Phage Display verifiziert werden. Für N. gonorrhoeae wurden 21 potentiell immunogene Oligopeptide isoliert, von denen sechs Proteine als neue zuvor unbeschriebene Proteine mit immunogenem Charakter identifiziert wurden. Von den Phagen-präsentierten Oligopeptide der 21 immunogenen Proteine wurden Epitopmappings mit verschiedenen polyklonalen Antikörpern durchgeführt, um immunogene Bereiche näher zu identifizieren und zu charakterisieren. Bei zehn Proteinen wurden lineare Epitope eindeutig mit drei polyklonalen Antikörpern identifiziert, von fünf weiteren Proteinen waren Epitope mit mindestens einem Antikörper detektierbar. Für eine weitere Charakterisierung der ermittelten Epitope wurden Alaninscans durchgeführt, die eine detaillierte Auskunft über kritische Aminosäuren für die Bindung des Antikörpers an das Epitop geben.
Ausgehend von dem neu identifizierten Protein mit immunogenem Charakter NGO1634 wurden 26 weitere Proteine aufgrund ihrer funktionellen Ähnlichkeit ausgewählt und mithilfe bioinformatischer Analysen auf ihre Eignung zur Entwicklung einer diagnostischen Anwendung analysiert. Durch Ausschluss der meisten Proteine aufgrund ihrer Lokalisation, Membrantopologie oder unspezifischen Proteinsequenz wurden scFv-Antikörper gegen acht Proteine mittels Phage Display generiert und anschließend als scFv-Fc-Fusionsantikörper produziert und charakterisiert.
Die hier identifizierten Proteine und linearen Epitope könnten einen Ansatzpunkt für die Entwicklung einer diagnostischen oder therapeutischen Anwendung bieten. Lineare Epitopsequenzen werden häufig für die Impfstoffentwicklung eingesetzt, sodass vor allem die in dieser Arbeit bestimmten Epitope von Membranproteinen interessante Kandidaten für weitere Untersuchungen in diese Richtung sind. Durch weitere Untersuchungen könnten möglicherweise unbekannte Virulenzfaktoren entdeckt werden, deren Inhibierung einen entscheidenden Einfluss auf Infektionen haben könnten.
The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined.
Mammalian aldehyde oxidases (AOXs; EC1.2.3.1) are a group of conserved proteins belonging to the family of molybdo-flavoenzymes along with the structurally related xanthine dehydrogenase enzyme. AOXs are characterized by broad substrate specificity, oxidizing not only aromatic and aliphatic aldehydes into the corresponding carboxylic acids, but also hydroxylating a series of heteroaromatic rings. The number of AOX isoenzymes expressed in different vertebrate species is variable. The two extremes are represented by humans, which express a single enzyme (AOX1) in many organs and mice or rats which are characterized by tissue-specific expression of four isoforms (AOX1, AOX2, AOX3, and AOX4). In vertebrates each AOX isoenzyme is the product of a distinct gene consisting of 35 highly conserved exons. The extant species-specific complement of AOX isoenzymes is the result of a complex evolutionary process consisting of a first phase characterized by a series of asynchronous gene duplications and a second phase where the pseudogenization and gene deletion events prevail. In the last few years remarkable advances in the elucidation of the structural characteristics and the catalytic mechanisms of mammalian AOXs have been made thanks to the successful crystallization of human AOX1 and mouse AOX3. Much less is known about the physiological function and physiological substrates of human AOX1 and other mammalian AOX isoenzymes, although the importance of these proteins in xenobiotic metabolism is fairly well established and their relevance in drug development is increasing. This review article provides an overview and a discussion of the current knowledge on mammalian AOX.
1. Migration conveys an immense challenge, especially for juvenile birds coping with enduring and risky journeys shortly after fledging. Accordingly, juveniles exhibit considerably lower survival rates compared to adults, particularly during migration. Juvenile white storks (Ciconia ciconia), which are known to rely on adults during their first fall migration presumably for navigational purposes, also display much lower annual survival than adults.
2. Using detailed GPS and body acceleration data, we examined the patterns and potential causes of age-related differences in fall migration properties of white storks by comparing first-year juveniles and adults. We compared juvenile and adult parameters of movement, behaviour and energy expenditure (estimated from overall dynamic body acceleration) and placed this in the context of the juveniles’ lower survival rate.
3. Juveniles used flapping flight vs. soaring flight 23% more than adults and were estimated to expend 14% more energy during flight. Juveniles did not compensate for their higher flight costs by increased refuelling or resting during migration. When juveniles and adults migrated together in the same flock, the juvenile flew mostly behind the adult and was left behind when they separated. Juveniles showed greater improvement in flight efficiency throughout migration compared to adults which appears crucial because juveniles exhibiting higher flight costs suffered increased mortality.
4. Our findings demonstrate the conflict between the juveniles’ inferior flight skills and their urge to keep up with mixed adult–juvenile flocks. We suggest that increased flight costs are an important proximate cause of juvenile mortality in white storks and likely in other soaring migrants and that natural selection is operating on juvenile variation in flight efficiency.
Ice-rich permafrost coasts in the Arctic are highly sensitive to climate warming and erode at a pace that exceeds the global average. Permafrost coasts deliver vast amounts of organic carbon into the nearshore zone of the Arctic Ocean. Numbers on flux exist for particulate organic carbon (POC) and total or soil organic carbon (TOC, SOC). However, they do not exist for dissolved organic carbon (DOC), which is known to be highly bioavailable. This study aims to estimate DOC stocks in coastal permafrost as well as the annual flux into the ocean. DOC concentrations in ground ice were analyzed along the ice-rich Yukon coast (YC) in the western Canadian Arctic. The annual DOC flux was estimated using available numbers for coast length, cliff height, annual erosion rate, and volumetric ice content in different stratigraphic horizons. Our results showed that DOC concentrations in ground ice range between 0.3 and 347.0mgL(-1) with an estimated stock of 13.63.0gm(-3) along the YC. An annual DOC flux of 54.90.9Mgyr(-1) was computed. These DOC fluxes are low compared to POC and SOC fluxes from coastal erosion or POC and DOC fluxes from Arctic rivers. We conclude that DOC fluxes from permafrost coasts play a secondary role in the Arctic carbon budget. However, this DOC is assumed to be highly bioavailable. We hypothesize that DOC from coastal erosion is important for ecosystems in the Arctic nearshore zones, particularly in summer when river discharge is low, and in areas where rivers are absent.
Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein – a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here.
Background: Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)). Methods: Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (beta 2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-beta 2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human beta 2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human beta 2GPI or after CL-micelle absorption. Results: Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM a beta 2GPI and aCL. Anti-CL and anti-beta 2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and beta 2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized beta 2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-beta 2GPI humoAbs. Conclusions: The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1.
Pancreatic secretory zymogen-granule membrane glycoprotein 2 (GP2) has been identified to be a major autoantigenic target in Crohn’s disease patients. It was discussed recently that a long and a short isoform of GP2 exists whereas the short isoform is often detected by GP2-specific autoantibodies. In the outcome of inflammatory bowel diseases, these GP2-specific autoantibodies are discussed as new serological markers for diagnosis and therapeutic monitoring. To investigate this further, camelid nanobodies were generated by phage display and selected against the short isoform of GP2 in order to isolate specific tools for the discrimination of both isoforms. Nanobodies are single domain antibodies derived from camelid heavy chain only antibodies and characterized by a high stability and solubility. The selected candidates were expressed, purified and validated regarding their binding properties in different enzyme-linked immunosorbent assays formats, immunofluorescence, immunohistochemistry and surface plasmon resonance spectroscopy. Four different nanobodies could be selected whereof three recognize the short isoform of GP2 very specifically and one nanobody showed a high binding capacity for both isoforms. The KD values measured for all nanobodies were between 1.3 nM and 2.3 pM indicating highly specific binders suitable for the application as diagnostic tool in inflammatory bowel disease.
Monoclonal antibodies are highly valuable tools in biomedicine but the generation by hybridoma technology is very time-consuming and elaborate. In order to circumvent the consisting drawbacks an in vitro immunization approach was established by which murine as well as human monoclonal antibodies against a viral coat protein could be developed. The in vitro immunization process was performed by isolation of murine hematopoietic stem cells or human monocytes and an in vitro differentiation into immature dendritic cells. After antigen loading the cells were co-cultivated with naive T and B lymphocytes for three days in order to obtain antigen-specific B lymphocytes in culture, followed by fusion with murine myeloma cells or human/murine heteromyeloma cells. Antigen-specific hybridomas were selected and the generated antibodies were purified and characterized in this study by ELISA, western blot, gene sequencing, affinity measurements. Further the characteristics were compared to a monoclonal antibody against the same target generated by conventional hybridoma technology. Isotype detection revealed a murine IgM and a human IgG4 antibody in comparison to an IgG1 for the conventionally generated antibody. The antibodies derived from in vitro immunization showed indeed a lower affinity for the antigen as compared to the conventionally generated one, which is probably based on the significantly shorter B cell maturation (3 days) during the immunization process. Nevertheless, they were suitable for building up a sandwich based detection system. Therefore, the in vitro immunization approach seems to be a good and particularly fast alternative to conventional hybridoma technology.
Background
Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)).
Methods
Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption.
Results
Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs.
Conclusions
The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1.
Epitope mapping is crucial for the characterization of protein-specific antibodies. Commonly, small overlapping peptides are chemically synthesized and immobilized to determine the specific peptide sequence. In this study, we report the use of a fast and inexpensive planar microbead chip for epitope mapping. We developed a generic strategy for expressing recombinant peptide libraries instead of using expensive synthetic peptide libraries. A biotin moiety was introduced in vivo at a defined peptide position using biotin ligase. Peptides in crude Escherichia coli lysate were coupled onto streptavidin-coated microbeads by incubation, thereby avoiding tedious purification procedures. For read-out we used a multiplex planar microbead chip with size- and fluorescence-encoded microbead populations. For epitope mapping, up to 18 populations of peptide-loaded microbeads (at least 20 microbeads per peptide) displaying the primary sequence of a protein were analyzed simultaneously. If an epitope was recognized by an antibody, a secondary fluorescence-labeled antibody generated a signal that was quantified, and the mean value of all microbeads in the population was calculated. We mapped the epitopes for rabbit anti-PA28 gamma (proteasome activator 28 gamma) polyclonal serum, for a murine monoclonal antibody against PA28 gamma, and for a murine monoclonal antibody against the hamster polyoma virus major capsid protein VP1 as models. In each case, the identification of one distinct peptide sequence out of up to 18 sequences was possible. Using this approach, an epitope can be mapped multiparametrically within three weeks. (C) 2016 Elsevier B.V. All rights reserved.
Background:
Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental
property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions
are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial
clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda
(insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate
the link between size and diversity within this ancient and highly diverse lineage.
Results:
The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally
distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions
typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a
negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these
two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within
Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution
within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes
including significant phylogenetic conservatism.
Conclusions:
Based on our findings we suggest that the use of models derived from well-studied but atypical clades,
such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results
indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect
diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large
timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available
data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may
collectively enhance our understanding of this key component of terrestrial ecosystems.
Jeden Tag werden unzählige Mengen an medizinischen Patientendaten in Krankenhäusern und Arztpraxen digital gespeichert. Für Forschungszwecke werden diese Daten bisher größtenteils nicht verwendet. Ziel dieser Arbeit ist es täglich anfallende anonymisierte Patientendaten, die aus einer Praxis für ganzheitliche Innere Medizin stammen, zu analysieren. Aufgrund mangelnder Kooperation seitens des Anbieters der Praxissoftware konnten die Patientendaten nicht automatisch extrahiert werden. Daher wurde eine Auswahl an Diagnosen und anthropometrischen Parametern manuell in eine Datenbank übertragen. Informationen über die Behandlung wurden dabei nicht berücksichtigt. Data-Mining Verfahren ermöglichen die Forschung auf der Grundlage von alltäglichen Patientendaten. Durch die Anwendung maschinellen Lernens kann Präventionsmedizin und die Überwachung von Behandlungsverläufen unterstützt werden.
Das Potenzial der Analyse dieser sonst weitgehend ungenutzten Daten wird anhand von Untersuchungen zur Komorbidität verdeutlicht. Dabei zeigt sich, dass einerseits das Metabolische Syndrom und dessen Komponenten zusammen mit Krebserkrankungen ein Cluster bilden und andererseits psychosomatische Störungen vermehrt mit Autoimmunerkrankungen der Schilddrüse auftreten. Außerdem wird eine noch nicht schulmedizinisch anerkannte Stoffwechselerkrankung, die Hämopyrrollaktamurie (HPU) untersucht. Diese lässt sich durch eine vermehrte Ausscheidung von Pyrrolen im Urin nachweisen. Bezüglich der Patienten bei denen ein HPU-Test vorliegt, weisen 84 % einen erhöhten Titer auf. Diese Beobachtung steht im Widerspruch zur vorherigen Annahme, dass in etwa 10 % der Bevölkerung von HPU betroffen sind.
Präventives Handeln ermöglicht es Gesundheit zu erhalten. Zu diesem Zweck ist es notwen- dig Krankheiten möglichst früh zu erkennen. In dieser Studie können Entscheidungsbaum-Modelle die Hashimoto Thyreoiditis mit einer Genauigkeit von 87.5 % bei einem Patienten diagnostizieren. Defizite durch die fehlenden Informationen über die medikamentöse Behandlung werden anhand des Modells zur Vorhersage von Hypothyreoiditis (Genauigkeit von 60.9 %) aufgezeigt.
Mit Hilfe von STATIS, das auf einer Erweiterung der Hauptkomponentenanalyse basiert, die es ermöglicht mehrere Tabellen simultan zu vergleichen, wurde der Behandlungsverlauf von 20 Patienten über einen Zeitraum von fünf Jahren überwacht. Anhand von Hypertonie wird gezeigt, dass sich sich die Patenten bezüglich Ihrer Laborwerte voneinander unterscheiden und sich Muster für Krankheiten erkennen lassen.
Diese Arbeit demonstriert den Nutzen, der durch die vermehrte Analyse alltäglicher hochdimensionaler und heterogener Daten erbracht werden kann.
Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites
(2016)
Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.
Background:
Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize
survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different
levels of gene expression.
Results:
Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of
Arabidopsis thaliana
to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is
modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of
genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are
likely candidates to play a role in regulating translation of those genes.
Conclusions:
Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids
is maintained upon heat exposure.
The spherical vaterite CaCO3 microcrystals are nowadays widely used as sacrificial templates for fabrication of various microcarriers made of biopolymers (e.g., proteins, nucleic acids, enzymes) due to porous structure and mild template elimination conditions. Here, we demonstrated for the first time that polymer microcarriers with tuned internal nanoarchitecture can be designed by employing the CaCO3 crystals of controlled porosity. The layer-by-layer deposition has been utilized to assemble shell-like (hollow) and matrix-like (filled) polymer capsules due to restricted and free polymer diffusion through the crystal pores, respectively. The crystal pore size in the range of few tens of nanometers can be adjusted without any additives by variation of the crystal preparation temperature in the range 745 degrees C. The temperature-mediated growth mechanism is explained by the Ostwald ripening of nanocrystallites forming the crystal secondary structure. Various techniques including SEM, AFM, CLSM, Raman microscopy, nitrogen adsorptiondesorption, and XRD have been employed for crystal and microcapsule analysis. A three-dimensional model is introduced to describe the crystal internal structure and predict the pore cutoff and available surface for the pore diffusing molecules. Inherent biocompatibility of CaCO3 and a possibility to scale the porosity in the size range of typical biomacromolecules make the CaCO3 crystals extremely attractive tools for template assisted designing tailor-made biopolymer-based architectures in 2D to 3D targeted at drug delivery and other bioapplications.
Molecularly imprinted polymers (MIPs) for the recognition of proteins are expected to possess high affinity through the establishment of multiple interactions between the polymer matrix and the large number of functional groups of the target. However, while highly affine recognition sites need building blocks rich in complementary functionalities to their target, such units are likely to generate high levels of nonspecific binding. This paradox, that nature solved by evolution for biological receptors, needs to be addressed by the implementation of new concepts in molecular imprinting of proteins. Additionally, the structural variability, large size and incompatibility with a range of monomers made the development of protein MIPs to take a slow start. While the majority of MIP preparation methods are variants of chemical polymerization, the polymerization of electroactive functional monomers emerged as a particularly advantageous approach for chemical sensing application. Electropolymerization can be performed from aqueous solutions to preserve the natural conformation of the protein templates, with high spatial resolution and electrochemical control of the polymerization process. This review compiles the latest results, identifying major trends and providing an outlook on the perspectives of electrosynthesised protein-imprinted MIPs for chemical sensing. (C) 2016 Elsevier B.V. All rights reserved.
Phenothiazine-modified redox hydrogels were synthesized and used for the wiring of the aldehyde oxidoreductase PaoABC to electrode surfaces. The effects of the pH value and electrode surface modification on the biocatalytic activity of the layers were studied in the presence of vanillin as the substrate. The enzyme electrodes were successfully employed as bioanodes in vanillin/O-2 biofuel cells in combination with a high potential bilirubin oxidase biocathode. Open circuit voltages of around 700 mV could be obtained in a two compartment biofuel cell setup. Moreover, the use of a rather hydrophobic polymer with a high degree of crosslinking sites ensures the formation of stable polymer/enzyme films which were successfully used as bioanode in membrane-less biofuel cells. (C) 2015 Elsevier B.V. All rights reserved.
Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pK(a) of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase.
Recruitment of European eels (Anguilla anguilla) has declined to the extent that they have been added to the IUCN Red List of Threatened Species. Therefore, it is critical to ensure that eels complete their outward river migration in order to contribute to the available spawning stock. We conducted a 4-year (2007-2011) telemetry study to understand the migratory behaviour and potential impact of environmental factors on the eel during this critical life stage. Out of 399 female eels tagged with acoustic transmitters, only 28% demonstrated clear downstream migratory behaviour. Fifty-five percent were detected exhibiting no downstream migration behaviour and 17% were not detected at any monitoring station. Movement patterns of downstream-migrating (silver) eels were characterized by nocturnal activity and seasonal migration, with distinct peaks in autumn and spring. Migration was often discontinuous and exhibited phases of active locomotion and expanded stopovers. The most important determinants of movement activity were water temperature, cumulative precipitation and moonlight, although the significance varied by season and location in the river basin. Our results evidence a discontinuous, stepwise migration over an extended period. Furthermore, our findings indicate that migration success depends on holding duration prior to tagging and environmental predictors with varying importance depending on the season, as well as the locations of capture, tagging and release. Copyright (c) 2015 John Wiley & Sons, Ltd.
Offending and mortality
(2016)
Background: Previous research has shown that offenders are at increased risk to die prematurely, but the etiology of this association is still unknown. Moreover, most previous studies use relatively short follow-up periods and do not take into account variation within the offender population with respect to frequency, timing and types of offenses. Method: Using conviction data for a number of families at high-risk of offending born on average in 1932, we study mortality in both offenders and non-offenders, from a similar socio-economic background, until 2007. We condition on life expectancy of the parents, age, gender, year of birth and marital status. We investigate associations between mortality and offending for different types of offenses: violent offenses, property offenses, weapons offenses, drugs offenses and driving under influence. Results: In general, offending sample members were not significantly more likely to have died than non offending sample members. Compared to the general population, however, both the offending and non offending sample members were at increased risk to die. Sample members who were convicted for driving under the influence of alcohol or weapons offenses were at increased risk to die prematurely compared to non-offending sample members. Conclusions: The relationship between offending in general and mortality is largely spurious. Limitations: The use of official conviction data might have influenced the results. (C) 2015 Elsevier Ltd. All rights reserved.
East Africa hosts a striking diversity of terrestrial ecosystems, which vary both in space and time due to complex regional topography and a dynamic climate. The structure and functioning of these ecosystems under this environmental setting can be studied with dynamic vegetation models (DVMs) in a spatially explicit way. Yet, regional applications of DVMs to East Africa are rare and a comprehensive validation of such applications is missing. Here, we simulated the present-day and mid-Holocene vegetation of East Africa with the DVM, LPJ-GUESS and we conducted an exhaustive comparison of model outputs with maps of potential modern vegetation distribution, and with pollen records of local change through time. Overall, the model was able to reproduce the observed spatial patterns of East African vegetation. To see whether running the model at higher spatial resolutions (10′ × 10′) contribute to resolve the vegetation distribution better and have a better comparison scale with the observational data (i.e. pollen data), we run the model with coarser spatial resolution (0.5° × 0.5°) for the present-day as well. Both the area- and point-wise comparison showed that a higher spatial resolution allows to better describe spatial vegetation changes induced by the complex topography of East Africa. Our analysis of the difference between modelled mid-Holocene and modern-day vegetation showed that whether a biome shifts to another is best explained by both the amount of change in precipitation it experiences and the amount of precipitation it received originally. We also confirmed that tropical forest biomes were more sensitive to a decrease in precipitation compared to woodland and savanna biomes and that Holocene vegetation changes in East Africa were driven not only by changes in annual precipitation but also by changes in its seasonality.
Tubers of potato (Solanum tuberosum L.), one of the most important crops, are a prominent example for an efficient production of storage starch. Nevertheless, the synthesis of this storage starch is not completely understood. The plastidial phosphorylase (Phol; EC 2.4.11) catalyzes the reversible transfer of glucosyl residues from glucose-1-phosphate to the non-reducing end of alpha-glucans with the release of orthophosphate. Thus, the enzyme is in principle able to act during starch synthesis. However, so far under normal growth conditions no alterations in tuber starch metabolism were observed. Based on analyses of other species and also from in vitro experiments with potato tuber slices it was supposed, that Phol has a stronger impact on starch metabolism, when plants grow under low temperature conditions. Therefore, we analyzed the starch content, granule size, as well as the internal structure of starch granules isolated from potato plants grown under low temperatures. Besides wild type, transgenic potato plants with a strong reduction in the Phol activity were analyzed. No significant alterations in starch content and granule size were detected. In contrast, when plants were cultivated at low temperatures the chain length distributions of the starch granules were altered. Thus, the granules contained more short glucan chains. That was not observed in the transgenic plants, revealing that Pho1 in wild type is involved in the formation of the short glucan chains, at least at low temperatures. (C) 2016 Elsevier Masson SAS. All rights reserved.
QuestionThe empirical evidence of root herbivory effects on plant community composition and co-existence is contradictory. This originates from difficulties connected to below-ground research and confinement of experimental studies to a small range of environmental conditions. Here we suggest coupling experimental data with an individual-based model to overcome the limitations inherent in either approach. To demonstrate this, we investigated the consequences of root herbivory, as experimentally observed on individual plants, on plant competition and co-existence in a population and community context under different root herbivory intensities (RHI), fluctuating and constant root herbivore activity and grazing along a resource gradient. LocationBerlin, Germany, glasshouse; Potsdam, Germany, high performance cluster computer. MethodsThe well-established community model IBC-Grass was adapted to allow for a flexible species parameterization and to include annual species. Experimentally observed root herbivory effects on performance of eight common grassland plant species were incorporated into the model by altering plant growth rates. We then determined root herbivore effects on plant populations, competitive hierarchy and consequences for co-existence and community diversity. ResultsRoot herbivory reduced individual biomass, but temporal fluctuation allowed for compensation of herbivore effects. Reducing resource availability strongly shifted competitive hierarchies, with, however, more similar hierarchies along the gradient under root herbivory, pointing to reduced ecological species differences. Consequently, negative effects on co-existence and diversity prevailed, with the exception of a few positive effects on co-existence of selected species pairs. Temporal fluctuation alleviated but did not remove negative root herbivore effects, despite of the stronger influence of intra- compared to interspecific competition. Grazing in general augmented co-existence. Most interestingly, grazing interacted with RHI and resource availability by promoting positive effects of root herbivory. ConclusionsThrough integrating experimental data on the scale of individual plants with a simulation model we verified that root herbivory could affect plant competition with consequences for species co-existence. Our approach demonstrates the benefit that accrues when empirical and modelling approaches are brought more closely together, and that gathering data on distinct processes and under specific conditions, combined with appropriate models, can be used to answer challenging research questions in a more general way.
Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of Stat6-knockout mouse studies together with STAT6 ChIP-seq data and our own gene expression time series data during Th2 cell differentiation. We focused on transcription factors (TFs), cytokines, and cytokine receptors and delineated 59 positively and 41 negatively STAT6-regulated genes, which were used to construct a transcriptional network around STAT6. The network illustrates that important and well-known TFs for Th2 cell differentiation are positively regulated by STAT6 and act either as activators for Th2 cells (e.g., Gata3, Atf3, Satb1, Nfil3, Maf, and Pparg) or as suppressors for other Th cell subpopulations such as Th1 (e.g., Ar), Th17 (e.g., Etv6), or iTreg (e.g., Stat3 and Hifla) cells. Moreover, our approach reveals 11 TFs (e.g., Atf5, Creb3l2, and Asb2) with unknown functions in Th cell differentiation. This fact together with the observed enrichment of asthma risk genes among those regulated by STAT6 underlines the potential value of the data integration strategy used here. Thus, our results clearly support the opinion that data integration is a useful tool to delineate complex physiological processes.
Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative realtime polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.
The intensification of agricultural practices has led to a severe decrease in grassland biodiversity. Although there is strong evidence that organic farming can reduce the negative impacts of land use, knowledge regarding the most beneficial management system for species richness on organic grasslands is still scarce. This study examines differences in the biodiversity of plants and butterflies on rotationally and continuously grazed pastures as well as on meadows cut twice per year on two large organic suckler cow farms in NE Germany. Vegetation and flower abundance, as factors likely to influence butterfly abundance and diversity, were compared and used to explain the differences. The data attained by vegetation assessments and monthly transect inspections from May to August were analyzed using descriptive statistics and nonparametric methods. The abiotic site conditions of the studied plots had more influence on plant species numbers than the management method. Dry and nutrient-poor areas (mainly poor types of Cynosurion) and undrained wet fens (Calthion) were important for phytodiversity, measured by the absolute number of species, indicator species for ecologically valuable grasslands and the Shannon Index. Meadows tended to have more indicator species than pastures, where small-scale special sites such as wet depressions were crucial for plant diversity. Butterfly diversity was very low, and 90% of the recorded butterflies were individuals of the generalist species Pieris napi. Butterfly abundance depended mainly on occurrence of specific habitat types and specific larval host plants. Supply of flowers was crucial only in certain time periods. Differences in butterfly abundance between the management systems could be explained by the site conditions of the studied grasslands. We conclude that meadows are more favorable to support ecologically valuable plant species; however, their extension is contradictory to the organic farming method of suckler cows maintained outside of stables. Rotationally grazed pastures could be a compromise that would enhance the temporal heterogeneity of flower abundance and vegetation structure. The plant diversity on pastures should be improved by less intensive grazing on special sites and plant species enrichment by means of hay transfer. For enhancing butterfly diversity we suggest to reduce land use intensity especially on poor soils. Considering the economic perspective of the farms, small parts of the agricultural area could be sufficient if connectivity to other suitable habitats is assured. Flower abundance and diversity of larval host plants could be promoted by high diversity of farming practices as well as preserving small uncut strips of meadows.
The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.
Ecological niches of organisms vary across geographical space, but niche shift patterns between regions and the underlying mechanisms remain largely unexplored. We studied shifts in the pH niche of 42 temperate forest plant species across a latitudinal gradient from northern France to boreo-nemoral Sweden. We asked 1) whether species restrict their niches with increasing latitude as they reach their northern range margin (environmental constraints); 2) whether species expand their niches with increasing latitude as regional plant species richness decreases (competitive release); and 3) whether species shift their niche position toward more acidic sites with increasing latitude as the relative proportion of acidic soils increases (local adaptation). Based on 1458 vegetation plots and corresponding soil pH values, we modelled species response curves using Huisman-Olff-Fresco models. Four niche measures (width, position, left and right border) were compared among regions by randomization tests. We found that with increasing latitude, neutrophilic species tended to retreat from acidic sites, indicating that these species retreat to more favorable sites when approaching their range margin. Alternatively, these species might benefit from enhanced nitrogen deposition on formerly nutrient-poor, acidic sites in southern regions or lag behind in post-glacial recolonization of potential habitats in northern regions. Most acidophilic species extended their niche toward more base-rich sites with increasing latitude, indicating competitive release from neutrophilic species. Alternatively, acidophilic species might benefit from optimal climatic conditions in the north where some have their core distribution area. Shifts in the niche position suggested that local adaptation is of minor importance. We conclude that shifts in the pH niche of temperate forest plants are the rule, but the directions of the niche shifts and possible explanations vary. Our study demonstrates that differentiating between acidophilic and neutrophilic species is crucial to identify general patterns and underlying mechanisms.
Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation.
Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
Functionally diverse communities can adjust their species composition to altered environmental conditions, which may influence food web dynamics. Trait-based aggregate models cope with this complexity by ignoring details about species identities and focusing on their functional characteristics (traits). They describe the temporal changes of the aggregate properties of entire communities, including their total biomasses, mean trait values, and trait variances. The applicability of aggregate models depends on the validity of their underlying assumptions that trait distributions are normal and exhibit small variances. We investigated to what extent this can be expected to work by comparing an innovative model that accounts for the full trait distributions of predator and prey communities to a corresponding aggregate model. We used a food web structure with well-established trade-offs among traits promoting mutual adjustments between prey edibility and predator selectivity in response to selection. We altered the shape of the trade-offs to compare the outcome of the two models under different selection regimes, leading to trait distributions increasingly deviating from normality. Their biomass and trait dynamics agreed very well for stabilizing selection and reasonably well for directional selection, under which different trait values are favored at different times. However, for disruptive selection, the results of the aggregate model strongly deviated from the full trait distribution model that showed bimodal trait distributions with large variances. Hence, the outcome of aggregate models is reliable under ideal conditions but has to be questioned when confronted with more complex selection regimes and trait distributions, which are commonly observed in nature.
Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure.
A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites
(2016)
Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.
The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain alpha-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.
Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity.
Practical use of many bioelectronic and bioanalytical devices is limited by the need of expensive materials and time consuming fabrication. Here we demonstrate the use of nickel electrodes as a simple and cheap solid support material for bioelectronic applications. The naturally nanostructured electrodes showed a surprisingly high electromagnetic surface enhancement upon light illumination such that immobilization and electron transfer reactions of the model redox proteins cytochrome b(5) (Cyt b(5)) and cytochrome c (Cyt c) could be followed via surface enhanced resonance Raman spectroscopy. It could be shown that the nickel surface, when used as received, promotes a very efficient binding of the proteins upon preservation of their native structure. The immobilized redox proteins could efficiently exchange electrons with the electrode and could even act as an electron relay between the electrode and solubilized myoglobin. Our results open up new possibility for nickel electrodes as an exceptional good support for bioelectronic devices and biosensors on the one hand and for surface enhanced spectroscopic investigations on the other hand. (C) 2016 Elsevier B.V. All rights reserved.
Microelectrodes modified with electropolymerized plumbagin (PLG) were used for the generation of superoxide radical (O-2(center dot-)) and hydrogen peroxide (H2O2) during oxygen reduction reaction (ORR) in an aqueous medium, specifically in serum-free cell culture media. This is enabled by the specific design of a polymer film on the microelectrode. The generation and diffusion of O-2(center dot-) during electrocatalytic ORR at a positionable PLG polymer-modified microelectrode was followed by fluorescence microscopy with the selective dye 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) and by amperometric detection using a cytochrome c-modified electrode at + 0.13 V. H2O2 production, either by direct oxygen reduction or as product of O-2(center dot-) disproportionation, was monitored by the reaction with Amplex UltraRed. The PLG polymer-modified microelectrodes were used to expose mammalian B6-RPE07 retinal cells to defined local fluxes of reactive oxygen species (ROS), and cellular responses and morphological alterations were observed. The use of a controllable source of ROS opens many possibilities to study how living cells respond to the presence of a certain flux of specific ROS.
Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic beta-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha-and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single "fusion loop". We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal "tail" that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens.
A loss of dehydration tolerance in wheat seedlings on the fifth day following imbibition is associated with a disturbance in cellular redox homeostasis, as documented by a shift of the reduced/oxidized glutathione ratio to a more oxidized state and a significant increase in the ratio of protein thiols to the total thiol group content. Therefore, the identification and characterization of redox-sensitive proteins are important steps toward understanding the molecular mechanisms of the loss of dehydration tolerance. In the present study, proteins that were differentially expressed between fully turgid (control), dehydrated tolerant (four-day-old) and dehydrated sensitive (six-day-old) wheat seedlings were analysed. Protein spots having at least a significant (p < 0.05) two-fold change in protein abundance were selected by Delta2D as differentially expressed, identified by MALDI-TOF and LC-MS/MS, and classified according to their function. The observed changes in the proteomic patterns of the differentially S-nitrosylated and S-glutathionylated proteins were highly specific in dehydration-tolerant and-sensitive wheat seedlings. The metabolic function of these proteins indicates that dehydration tolerance is mainly related to nucleic acids, protein metabolism, and energy metabolism. It has been proven that leaf-specific thionins BTH6 and DB4, chloroplastic 50S ribosomal protein L16, phospholipase A1-II delta, and chloroplastic thioredoxin M2 are both S-nitrosylated and S-glutathionylated upon water deficiency. Our results revealed the existence of interplay between S-nitrosylation and S-glutathionylation, two redox-regulated protein posttranslational modifications that could enhance plant defence mechanisms and/or facilitate the acclimation of plants to unfavourable environmental conditions. (C) 2016 Elsevier Masson SAS. All rights reserved.
Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA:: SnRK1 alpha 2 in a snrk1 alpha 1 knock out background (snrk1 alpha 1/alpha 2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1 alpha 1/alpha 2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1 alpha 1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1 alpha 1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1 alpha 1/alpha 2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.
Groundwater influx can significantly contribute to nutrient and carbon budgets of lakes, and its influence is the strongest in littoral areas dominated by macrophytes and periphyton. We have reviewed the effects of groundwater-borne nitrogen and phosphorus and dissolved inorganic and organic carbon (DIC, DOC) on these benthic primary producers in lakes. We develop a hypothesis for groundwater effects including the less studied impacts of periphyton shading on macrophytes. Groundwater-borne nutrients and DIC promote both macrophytes and periphyton. Direct studies on groundwater-borne DOC effects are lacking, but coloured DOC contributes to light attenuation and thus can restrict the growth of benthic primary producers. We predict that above certain threshold levels of nutrient influx by groundwater, periphyton and macrophyte biomass should decline owing to shading by phytoplankton and periphyton, respectively. However, because of their higher light requirements, those thresholds should be lower for macrophytes. For macrophytes, a threshold level is also predicted for a shift from DIC limitation to light limitation. Differences in light requirements are expected to result in lower thresholds of DOC loading for declines of macrophytes than periphyton.
Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5 end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1.
The origin of ambling horses
(2016)
Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called ‘gaited’ horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th–11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date.
Although many birds are socially monogamous, most (>75%) studied species are not strictly genetically monogamous, especially under high breeding density. We used molecular tools to reevaluate the reproductive strategy of the socially monogamous white stork (Ciconia ciconia) and examined local density effects. DNA samples of nestlings (Germany, Spain) were genotyped and assigned relationships using a two-program maximum likelihood classification. Relationships were successfully classified in 79.2% of German (n = 120) and 84.8% of Spanish (n = 59) nests. For each population respectively, 76.8% (n = 73) and 66.0% (n = 33) of nests contained only full-siblings, 10.5% (n = 10) and 18.0% (n = 9) had half-siblings (at least one nestling with a different parent), 3.2% (n = 3) and 10.0% (n = 5) had unrelated nestlings (at least two nestlings, each with different parents), and 9.5% (n = 9) and 6.0% (n = 3) had “not full-siblings” (could not differentiate between latter two cases). These deviations from strict monogamy place the white stork in the 59th percentile for extra-pair paternity among studied bird species. Although high breeding density generally increases extra-pair paternity, we found no significant association with this species’ mating strategies. Thus although genetic monogamy is indeed prominent in the white stork, extra-pair paternity is fairly common compared to other bird species and cannot be explained by breeding density.
The creation of electron transfer (ET) chains based on the defined arrangement of enzymes and redox proteins on electrode surfaces represents an interesting approach within the field of bioelectrocatalysis. In this study, we investigated the ET reaction of the flavin-dependent enzyme fructose dehydrogenase (FDH) with the redox protein cytochrome c (cyt c). Two different pH optima were found for the reaction in acidic and neutral solutions. When cyt c was adsorbed on an electrode surface while the enzyme remained in solution, ET proceeded efficiently in media of neutral pH. Interprotein ET was also observed in acidic media; however, it appeared to be less efficient. These findings suggest that two different ET pathways between the enzyme and cyt c may occur. Moreover, cyt c and FDH were immobilized in multiple layers on an electrode surface by means of another biomacromolecule: DNA (double stranded) using the layer -by -layer technique. The biprotein multilayer architecture showed a catalytic response in dependence on the fructose concentration, indicating that the ET reaction between both proteins is feasible even in the immobilized state. The electrode showed a defined response to fructose and a good storage stability. Our results contribute to the better understanding of the ET reaction between FDH and cyt c and provide the basis for the creation of all-biomolecule based fructose sensors the sensitivity of which can be controlled by the layer preparation.
Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.
We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong σ70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
During starch metabolism, the phosphorylation of glucosyl residues of starch, to be more precise of amylopectin, is a repeatedly observed process. This phosphorylation is mediated by dikinases, the glucan, water dikinase (GWD) and the phosphoglucan, water dikinase (PWD). The starch-related dikinases utilize ATP as dual phosphate donor transferring the terminal gamma-phosphate group to water and the beta-phosphate group selectively to either C6 position or C3 position of a glucosyl residue within amylopectin. By the collaborative action of both enzymes, the initiation of a transition of alpha-glucans from highly ordered, water-insoluble state to a less order state is realized and thus the initial process of starch degradation. Consequently, mutants lacking either GWD or PWD reveal a starch excess phenotype as well as growth retardation. In this review, we focus on the increased knowledge collected over the last years related to enzymatic properties, the precise definition of the substrates, the physiological implications, and discuss ongoing questions.
Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources.
A new sequestrate Lactarius species was found in a humid evergreen tropical rainforest dominated by Fabaceae of the subfamily Caesalpinioideae in Cameroon, Central Africa. It is described here as new to science and is named Lactarius megalopterus, referring to its spore ornamentation of extraordinarily high wings. Anatomical characters and molecular systematic analyses confirm its relationship to Lactarius subgenus Plinthogali. Phylogenetic analyses based on two nuclear DNA regions revealed its close relationship to Lactarius angiocarpus, which is also an angiocarpous species from Zambia in Africa. Molecular studies have shown that tuber-like, sequestrate sporocarps evolved independently in several lineages of Basidiomycota. The findings of sequestrate fungi in tropical rainforests raise questions regarding the evolutionary benefit of enclosing the spore-producing hymenium. The enclosure of spore-producing tissue has often been associated with the protection of the delicate hymenium against desiccation in arid habitats or against frost in cold habitats. However, these cannot be the selective factors in warm and humid areas like the tropics. This controversy is exemplarily studied and discussed in the family of Russulaceae, especially in the genus Lactarius. Characters shown by the angiocarpous sporocarp of the new Lactarius, such as thick-walled statismospores, an aromatic smell and mild taste, can be interpreted as adaptations to endozoochorous spore dispersal by mammals. Therefore, here we prefer the alternative hypothesis that sequestrate sporocarps are the result of adaptation to endozoochorous spore dispersal.
Norway spruce (Picea abies) is periodically attacked by the bark beetle Ips typographus and its fungal associate, Endoconidiophora polonica, whose infection is thought to be required for successful beetle attack. Norway spruce produces terpenoid resins and phenolics in response to fungal and bark beetle invasion. However, how the fungal associate copes with these chemical defenses is still unclear. In this study, we investigated changes in the phenolic content of Norway spruce bark upon E. polonica infection and the biochemical factors mediating these changes. Although genes encoding the rate-limiting enzymes in Norway spruce stilbene and flavonoid biosynthesis were actively transcribed during fungal infection, there was a significant time-dependent decline of the corresponding metabolites in fungal lesions. In vitro feeding experiments with pure phenolics revealed that E. polonica transforms both stilbenes and flavonoids to muconoid-type ring-cleavage products, which are likely the first steps in the degradation of spruce defenses to substrates that can enter the tricarboxylic acid cycle. Four genes were identified in E. polonica that encode catechol dioxygenases carrying out these reactions. These enzymes catalyze the cleavage of phenolic rings with a vicinal dihydroxyl group to muconoid products accepting a wide range of Norway spruce-produced phenolics as substrates. The expression of these genes and E. polonica utilization of the most abundant spruce phenolics as carbon sources both correlated positively with fungal virulence in several strains. Thus, the pathways for the degradation of phenolic compounds in E. polonica, initiated by catechol dioxygenase action, are important to the infection, growth, and survival of this bark beetle-vectored fungus and may play a major role in the ability of I. typographus to colonize spruce trees.
Recent molecular phylogenetic reconstruction of the monocot Hypoxidaceae implies that the genus Curculigo is non-monophyletic. Curculigo seychellensis occurs on the Seychelles islands and is part of an isolated though geographically well-defined clade. However, Curculigo seychellensis differs in a wide range of character-states from other species of Curculigo and from the genus Hypoxidia, representing the sister clade of C. seychellensis. Therefore, we here propose a new-though monotypic-genus, endemic to the Seychelles: Friedmannia. A detailed reasoning combined with a whole set of new data is presented. A neotype for the genus and the species is designated here.
Microthlaspi is a predominantly Eurasian genus which also occurs in the northernmost parts of Africa (Maghreb). The most widespread species of the genus is M. perfoliatum, which can be found from Sweden to Algeria and from Portugal to China. The other species are thought to have much more confined distribution ranges, often covering only a few hundred kilometres. This is also believed for the diploid M. erraticum, which was recently re-appraised as a taxon independent from the tetra- to hexaploid M. perfoliatum. Previously, M. erraticum was believed to be present only in Central Europe, from the East of France to Slovenia. In order to gain a deeper understanding of the ecology, evolution and migration history of Microthlaspi it was the focus of the current study to investigate, if M. erraticum is present in habitats outside Central Europe, but with microclimates similar to Central Europe. It is demonstrated that M. erraticum is much more widespread than previously thought, while other lineages apart from M. perfoliatum s.str. and M. erraticum seem to have restricted distribution ranges. The latter species was observed from the Alps and their foreland, the Balkans, the mountainous areas around the Black Sea, Southern Siberia, as well as the Altai and Tien Shan mountains. This demonstrates a widespread occurrence of this easily-overlooked species. (C) 2016 Elsevier GmbH. All rights reserved.
The interplay between soil structure, roots, and microbiota as a determinant of plant-soil feedback
(2016)
Plant-soil feedback (PSF) can influence plant community structure via changes in the soil microbiome. However, how these feedbacks depend on the soil environment remains poorly understood. We hypothesized that disintegrating a naturally aggregated soil may influence the outcome of PSF by affecting microbial communities. Furthermore, we expected plants to differentially interact with soil structure and the microbial communities due to varying root morphology. We carried out a feedback experiment with nine plant species (five forbs and four grasses) where the training phase consisted of aggregated versus disintegrated soil. In the feedback phase, a uniform soil was inoculated in a fully factorial design with soil washings from conspecific- versus heterospecific-trained soil that had been either disintegrated or aggregated. This way, the effects of prior soil structure on plant performance in terms of biomass production and allocation were examined. In the training phase, soil structure did not affect plant biomass. But on disintegrated soil, plants with lower specific root length (SRL) allocated more biomass aboveground. PSF in the feedback phase was negative overall. With training on disintegrated soil, conspecific feedback was positively correlated with SRL and significantly differed between grasses and forbs. Plants with higher SRL were likely able to easily explore the disintegrated soil with smaller pores, while plants with lower SRL invested in belowground biomass for soil exploration and seemed to be more susceptible to fungal pathogens. This suggests that plants with low SRL could be more limited by PSF on disintegrated soils of early successional stages. This study is the first to examine the influence of soil structure on PSF. Our results suggest that soil structure determines the outcome of PSF mediated by SRL. We recommend to further explore the effects of soil structure and propose to include root performance when working with PSF.
Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
Synthetic biology aims at designing and engineering organisms. The engineering process typically requires the establishment of suitable DNA constructs generated through fusion of multiple protein coding and regulatory sequences. Conventional cloning techniques, including those involving restriction enzymes and ligases, are often of limited scope, in particular when many DNA fragments must be joined or scar-free fusions are mandatory. Overlap-based-cloning methods have the potential to overcome such limitations. One such method uses seamless ligation cloning extract (SLiCE) prepared from Escherichia coli cells for straightforward and efficient in vitro fusion of DNA fragments. Here, we systematically characterized extracts prepared from the unmodified E. coli strain DH10B for SLiCE-mediated cloning and determined DNA sequence-associated parameters that affect cloning efficiency. Our data revealed the virtual absence of length restrictions for vector backbone (up to 13.5 kbp) and insert (90 bp to 1.6 kbp). Furthermore, differences in GC content in homology regions are easily tolerated and the deletion of unwanted vector sequences concomitant with targeted fragment insertion is straightforward. Thus, SLiCE represents a highly versatile DNA fusion method suitable for cloning projects in virtually all molecular. and synthetic biology projects. (C) 2016 Elsevier Inc. All rights reserved.
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no: such increase of the radius of gyration (R-g). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination Of single-molecule Forster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius, with denaturant concentration obtained by 2f-FCS,and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant;induced unfolded state expansion, and to identify the Most likely sources of earlier discrepancies.
Background: Non-typhoid Salmonella Typhimurium (S. Typhimurium) accounts for a high number of registered salmonellosis cases, and O-serotyping is one important tool for monitoring epidemiology and spread of the disease. Moreover, variations in glucosylated O-antigens are related to immunogenicity and spread in the host. However, classical autoagglutination tests combined with the analysis of specific genetic markers cannot always reliably register phase variable glucose modifications expressed on Salmonella O-antigens and additional tools to monitor O-antigen glucosylation phenotypes of S. Typhimurium would be desirable. Results: We developed a test for the phase variable O-antigen glucosylation state of S. Typhimurium using the tailspike proteins (TSP) of Salmonella phages 9NA and P22. We used this ELISA like tailspike adsorption (ELITA) assay to analyze a library of 44 Salmonella strains. ELITA was successful in discriminating strains that carried glucose 1-6 linked to the galactose of O-polysaccharide backbone (serotype O1) from non-glucosylated strains. This was shown by O-antigen compositional analyses of the respective strains with mass spectrometry and capillary electrophoresis. The ELITA test worked rapidly in a microtiter plate format and was highly O-antigen specific. Moreover, TSP as probes could also detect glucosylated strains in flow cytometry and distinguish multiphasic cultures differing in their glucosylation state. Conclusions: Tailspike proteins contain large binding sites with precisely defined specificities and are therefore promising tools to be included in serotyping procedures as rapid serotyping agents in addition to antibodies. In this study, 9NA and P22TSP as probes could specifically distinguish glucosylation phenotypes of Salmonella on microtiter plate assays and in flow cytometry. This opens the possibility for flow sorting of cell populations for subsequent genetic analyses or for monitoring phase variations during large scale O-antigen preparations necessary for vaccine production.
We report on the pH-dependent bioelectrocatalytic activity of the redox enzyme xanthine dehydrogenase (XDH) in the presence of sulfonated polyaniline PMSA1 (poly(2-methoxyaniline-5-sulfonic acid)-co-aniline). Ultraviolet-visible (UV-vis) spectroscopic measurements with both components in solution reveal electron transfer from the hypoxanthine (HX)-reduced enzyme to the polymer. The enzyme shows bioelectrocatalytic activity on indium tin oxide (ITO) electrodes, when the polymer is present. Depending on solution pH, different processes can be identified. It can be demonstrated that not only product-based communication with the electrode but also efficient polymer-supported bioelectrocatalysis occur. Interestingly, substrate dependent catalytic currents can be obtained in acidic and neutral solutions, although the highest activity of XDH with natural reaction partners is in the alkaline region. Furthermore, operation of the enzyme electrode without addition of the natural cofactor of XDH is feasible. Finally, macroporous ITO electrodes have been used as an immobilization platform for the fabrication of HX-sensitive electrodes. The study shows that the efficient polymer/enzyme interaction can be advantageously combined with the open structure of an electrode material of controlled pore size, resulting in good processability, stability, and defined signal transfer in the presence of a substrate.
The honeybee hypopharyngeal gland consists in numerous units, each comprising a secretory cell and a canal cell. The secretory cell discharges its products into a convoluted tubular membrane system, the canaliculus, which is surrounded at regular intervals by rings of actin filaments. Using probes for various membrane components, we analyze the organization of the secretory cells relative to the apicobasal configuration of epithelial cells. The canaliculus was defined by labeling with an antibody against phosphorylated ezrin/radixin/moesin (pERM), a marker protein for the apical membrane domain of epithelial cells. Anti-phosphotyrosine visualizes the canalicular system, possibly by staining the microvillar tips. The open end of the canaliculus leads to a region in which the secretory cell is attached to the canal cell by adherens and septate junctions. The remaining plasma membrane stains for Na,K-ATPase and spectrin and represents the basolateral domain. We also used fluorophore-tagged phalloidin, anti-phosphotyrosine and anti-pERM as probes for the canaliculus in order to describe fine-structural changes in the organization of the canalicular system during the adult life cycle. These probes in conjunction with fluorescence microscopy allow the fast and detailed three-dimensional analysis of the canalicular membrane system and its structural changes in a developmental mode or in response to environmental factors.
NO donors and Arg remove dormancy of apple embryos and stimulate germination. Compounds lowering NO level (cPTIO, L -NAME, CAN) strengthen dormancy. Embryo transition from dormancy state to germination is linked to increased nitric oxide synthase (NOS)-like activity. Germination of embryos is associated with declined level of biotin containing proteins and nitrated proteins in soluble protein fraction of root axis. Pattern of nitrated proteins suggest that storage proteins are putative targets of nitration. Nitric oxide (NO) acts as a key regulatory factor in removal of seed dormancy and is a signal necessary for seed transition from dormant state into germination. Modulation of NO concentration in apple (Malus domestica Borkh.) embryos by NO fumigation, treatment with NO donor (S-nitroso-N-acetyl-d,l-penicillamine, SNAP), application of 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO), N (omega)-nitro-l-arginine methyl ester (l-NAME), canavanine (CAN) or arginine (Arg) allowed us to investigate the NO impact on seed dormancy status. Arg analogs and NO scavenger strengthened embryo dormancy by lowering reactive nitrogen species level in embryonic axes. This effect was accompanied by strong inhibition of NOS-like activity, without significant influence on tissue NO2 (-) concentration. Germination sensu stricto of apple embryos initiated by dormancy breakage via short term NO treatment or Arg supplementation were linked to a reduced level of biotinylated proteins in root axis. Decrease of total soluble nitrated proteins was observed at the termination of germination sensu stricto. Also modulation of NO tissue status leads to modification in nitrated protein pattern. Among protein bands that correspond to molecular mass of approximately 95 kDa, storage proteins (legumin A-like and seed biotin-containing protein) were identified, and can be considered as good markers for seed dormancy status. Moreover, pattern of nitrated proteins suggest that biotin containing proteins are also targets of nitration.
Parental care is widespread among vertebrates and the observed patterns of parental care and investment are extremely diverse. Among amphibians, caecilians (Gymnophiona) exhibit considerable variation in reproductive modes, including both oviparity and viviparity, combined with highly unusual investment strategies (e.g. skin-feeding and intrauterine feeding). In the present study, current knowledge on the reproductive modes is integrated into an analysis of the evolutionary scenario of parental investment of caecilians. Phylogenetically basal caecilians possessing a biphasic life cycle that includes an aquatic larval stage invest in macrolecithal eggs directly corresponding to size at hatching. Some phylogenetically derived caecilians (i.e. the Teresomata) have a smaller clutch size and show a reduction to either medium-yolked (mesolecithal) or small-yolked (microlecithal) eggs. Via alternative pathways of parental investment, such as intrauterine feeding in viviparous taxa and maternal dermatotrophy in oviparous taxa, teresomatan caecilians increase both offspring size and quality. However, more data regarding reproductive biology are needed to obtain a fully resolved understanding of the evolution of reproduction in caecilian amphibians. (C) 2016 The Linnean Society of London
A new electrochemical MIP sensor for the most frequently used drug paracetamol (PAR) was prepared by electropolymerization of mixtures containing the template molecule and the functional monomers ophenylenediamine, resorcinol and aniline. The imprinting factor of 12 reflects the effective target binding to the MIP as compared with the non-imprinted electropolymer. Combination of the MIP with a nonspecific esterase allows the measurement of phenacetin - another analgesic drug. In the second approach the PAR containing sample solution was pretreated with tyrosinase in order to prevent electrochemical interferences by ascorbic acid and uric acid. Interference-free indication at a very low electrode potential without fouling of the electrode surface was achieved with the o-phenylenediamine: resorcinol-based MIP.
Polymer multicomponent coatings such as multilayers mimic an extracellular, matrix (ECM) that attracts significant attention for the use of the multilayers as functional supports for advanced cell culture and tissue engineering. Herein, biodegradation and molecular transport in hyaluronan/polylysine multilayers coated with gold nanoparticles were described. Nanoparticle coating acts as a semipermeable barrier that governs molecular transport into/from the multilayers, and makes them biodegradation-resistant. Model protein lysozyme (mimics of ECM-soluble signals) diffuses into the multilayers as fast- and, slow-diffusing populations existing in an equilibrium,. Such a. composite system may have high potential to be exploited as degradation-resistant drug-delivery platforms suitable for cell-based applications.
We utilized femtosecond time-resolved resonant inelastic X-ray scattering and ab initio theory to study the transient electronic structure and the photoinduced molecular dynamics of a model metal carbonyl photocatalyst Fe(CO)(5) in ethanol solution. We propose mechanistic explanation for the parallel ultrafast intra-molecular spin crossover and ligation of the Fe(CO)(4) which are observed following a charge transfer photoexcitation of Fe(CO)(5) as reported in our previous study [ Wernet et al., Nature 520, 78 (2015)]. We find that branching of the reaction pathway likely happens in the (1)A(1) state of Fe(CO)(4). A sub-picosecond time constant of the spin crossover from B-1(2) to B-3(2) is rationalized by the proposed B-1(2) -> (1)A(1) -> B-3(2) mechanism. Ultrafast ligation of the B-1(2) Fe(CO)(4) state is significantly faster than the spin-forbidden and diffusion limited ligation process occurring from the B-3(2) Fe(CO)(4) ground state that has been observed in the previous studies. We propose that the ultrafast ligation occurs via B-1(2) -> (1)A(1) -> (1)A'Fe(CO)(4)EtOH pathway and the time scale of the (1)A(1) Fe(CO)(4) state ligation is governed by the solute-solvent collision frequency. Our study emphasizes the importance of understanding the interaction of molecular excited states with the surrounding environment to explain the relaxation pathways of photoexcited metal carbonyls in solution. (C) 2016 Author(s).
The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS
(2016)
The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction.
Phenomic experiments are carried out in large-scale plant phenotyping facilities that acquire a large number of pictures of hundreds of plants simultaneously. With the aid of automated image processing, the data are converted into genotype-feature matrices that cover many consecutive days of development. Here, we explore the possibility of predicting the biomass of the fully grown plant from early developmental stage image-derived features. We performed phenomic experiments on 195 inbred and 382 hybrid maizes varieties and followed their progress from 16 days after sowing (DAS) to 48 DAS with 129 image-derived features. By applying sparse regression methods, we show that 73% of the variance in hybrid fresh weight of fully-grown plants is explained by about 20 features at the three-leaf-stage or earlier. Dry weight prediction explained over 90% of the variance. When phenomic features of parental inbred lines were used as predictors of hybrid biomass, the proportion of variance explained was 42 and 45%, for fresh weight and dry weight models consisting of 35 and 36 features, respectively. These models were very robust, showing only a small amount of variation in performance over the time scale of the experiment. We also examined mid-parent heterosis in phenomic features. Feature heterosis displayed a large degree of variance which resulted in prediction performance that was less robust than models of either parental or hybrid predictors. Our results show that phenomic prediction is a viable alternative to genomic and metabolic prediction of hybrid performance. In particular, the utility of early-stage parental lines is very encouraging. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
Microviridins are a family of ribosomally synthesized and post-translationally modified peptides with a highly unusual architecture featuring non-canonical lactone as well as lactam rings. Individual variants specifically inhibit different types of serine proteases. Here we have established an efficient in vitro reconstitution approach based on two ATP-grasp ligases that were constitutively activated using covalently attached leader peptides and a GNAT-type N-acetyltransferase. The method facilitates the efficient in vitro one-pot transformation of microviridin core peptides to mature microviridins. The engineering potential of the chemo-enzymatic technology was demonstrated for two synthetic peptide libraries that were used to screen and optimize microviridin variants targeting the serine proteases trypsin and subtilisin. Successive analysis of intermediates revealed distinct structure-activity relationships for respective target proteases.
The importance of intraspecific trait variability for community dynamics and ecosystem functioning has been underappreciated. There are theoretical reasons for predicting that species that differ in intraspecific trait variability will also differ in their effects on ecosystem functioning, particularly in variable environments. We discuss whether species with greater trait variability are likely to exhibit greater temporal stability in their population dynamics, and under which conditions this might lead to stability in ecosystem functioning. Resolving this requires us to consider several questions. First, are species with high levels of variation for one trait equally variable in others? In particular, is variability in response and effects traits typically correlated? Second, what is the relative contribution of local adaptation and phenotypic plasticity to trait variability? If local adaptation dominates, then stability in function requires one of two conditions: (i) individuals of appropriate phenotypes present in the environment at high enough frequencies to allow for populations to respond rapidly to the changing environment, and (ii) high levels of dispersal and gene flow. While we currently lack sufficient information on the causes and distribution of variability in functional traits, filling in these key data gaps should increase our ability to predict how changing biodiversity will alter ecosystem functioning.
ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.
Citizen science has been gaining momentum in the United States and Europe, where citizens are literate and often interested in science. However, in developing countries, which have a dire need for environmental data, such programs are slow to emerge, despite the large and untapped human resources in close proximity to areas of high biodiversity and poorly known floras and faunas. Thus, we propose that the parataxonomist and paraecologist approach, which originates from citizen-based science, is well suited to rural areas in developing countries. Being a paraecologist or a parataxonomist is a vocation and entails full-time employment underpinned by extensive training, whereas citizen science involves the temporary engagement of volunteers. Both approaches have their merits depending on the context and objectives of the research. We examined 4 ongoing paraecologist or parataxonomist programs in Costa Rica, India, Papua New Guinea, and southern Africa and compared their origins, long-term objectives, implementation strategies, activities, key challenges, achievements, and implications for resident communities. The programs supported ongoing research on biodiversity assessment, monitoring, and management, and participants engaged in non-academic capacity development in these fields. The programs in Southern Africa related to specific projects, whereas the programs in Costa Rica, India, and Papua New Guinea were designed for the long term, provided sufficient funding was available. The main focus of the paraecologists’ and parataxonomists’ activities ranged from collection and processing of specimens (Costa Rica and Papua New Guinea) or of socioeconomic and natural science data (India and Southern Africa) to communication between scientists and residents (India and Southern Africa). As members of both the local land user and research communities, paraecologists and parataxonomists can greatly improve the flow of biodiversity information to all users, from local stakeholders to international academia.
Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator-prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to previous studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.
Interactions between plants and soil microorganisms influence individual plant performance and thus plant-community composition. Most studies on such plant-soil feedbacks (PSFs) have been performed under controlled greenhouse conditions, whereas no study has directly compared PSFs under greenhouse and natural field conditions. We grew three grass species that differ in local abundance in grassland communities simultaneously in the greenhouse and field on field-collected soils either previously conditioned by these species or by the general grassland community. As soils in grasslands are typically conditioned by mixes of species through the patchy and heterogeneous plant species’ distributions, we additionally compared the effects of species-specific versus non-specific species conditioning on PSFs in natural and greenhouse conditions. In almost all comparisons PSFs differed between the greenhouse and field. In the greenhouse, plant growth in species-specific and non-specific soils resulted in similar effects with neutral PSFs for the most abundant species and positive PSFs for the less abundant species. In contrast, in the field all grass species tested performed best in non-specific plots, whereas species-specific PSFs were neutral for the most abundant and varied for the less abundant species. This indicates a general beneficial effect of plant diversity on PSFs in the field. Controlled greenhouse conditions might provide valuable insights on the nominal effects of soils on plants. However, the PSFs observed in greenhouse conditions may not be the determining drivers in natural plant communities where their effects may be overwhelmed by the diversity of abiotic and biotic above- and belowground interactions in the field.
Arf-like Protein 3 (ARL3) Regulates Protein Trafficking and Ciliogenesis in Mouse Photoreceptors
(2016)
Arf-like protein 3 (ARL3) is a ubiquitous small GTPase expressed in ciliated cells of plants and animals. Germline deletion of Arl3 in mice causes multiorgan ciliopathy reminiscent of Bardet-Biedl or Joubert syndromes. As photoreceptors are elegantly compartmentalized and have cilia, we probed the function of ARL3 (ADP-ribosylation factor (Arf)-like 3 protein) by generating rod photoreceptor-specific (prefix (rod)) and retina-specific (prefix (ret)) Arl3 deletions. In predegenerate (rod)Arl3(-/-) mice, lipidated phototransduction proteins showed trafficking deficiencies, consistent with the role of ARL3 as a cargo displacement factor for lipid-binding proteins. By contrast, (ret)Arl3(-/-) rods and cones expressing Cre recombinase during embryonic development formed neither connecting cilia nor outer segments and degenerated rapidly. Absence of cilia infers participation of ARL3 in ciliogenesis and axoneme formation. Ciliogenesis was rescued, and degeneration was reversed in part by subretinal injection of adeno-associated virus particles expressing ARL3-EGFP. The conditional knock-out phenotypes permitted identification of two ARL3 functions, both in the GTP-bound form as follows: one as a regulator of intraflagellar transport participating in photoreceptor ciliogenesis and the other as a cargo displacement factor transporting lipidated protein to the outer segment. Surprisingly, a farnesylated inositol polyphosphate phosphatase only trafficked from the endoplasmic reticulum to the Golgi, thereby excluding it from a role in photoreceptor cilia physiology.
The amyloid precursor protein (APP) and its paralogs, amyloid precursor-like protein 1 (APLP1) and APLP2, are metalloproteins with a putative role both in synaptogenesis and in maintaining synapse structure. Here, we studied the effect of zinc on membrane localization, adhesion, and secretase cleavage of APP, APLP1, and APLP2 in cell culture and rat neurons. For this, we employed live-cell microscopy techniques, a microcontact printing adhesion assay and ELISA for protein detection in cell culture supernatants. We report that zinc induces the multimerization of proteins of the amyloid precursor protein family and enriches them at cellular adhesion sites. Thus, zinc facilitates the formation of de novo APP and APLP1 containing adhesion complexes, whereas it does not have such influence on APLP2. Furthermore, zinc-binding prevented cleavage of APP and APLPs by extracellular secretases. In conclusion, the complexation of zinc modulates neuronal functions of APP and APLPs by (i) regulating formation of adhesion complexes, most prominently for APLP1, and (ii) by reducing the concentrations of neurotrophic soluble APP/APLP ectodomains.
Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations.
Growth and developmental processes are occasionally accompanied by multiple rounds of DNA replication, known as endoreduplication. Coordination between endoreduplication and cell size regulation often plays a crucial role in proper organogenesis and cell differentiation. Here, we report that the level of correlation between ploidy and cell volume is different in the outer and inner cell layers of leaves of Arabidopsis thaliana using a novel imaging technique. Although there is a well-known, strong correlation between ploidy and cell volume in pavement cells of the epidermis, this correlation was extremely weak in palisade mesophyll cells. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells. We therefore propose that the correlation between ploidy and cell volume is regulated by cell identity.
The production of toxic metabolites by cyanobacterial blooms represents a significant threat to the health of humans and ecosystems worldwide. Here we summarize the current state of the knowledge regarding the genetics, biosynthesis and regulation of well-characterized cyanotoxins, including the microcystins, nodularin, cylindrospermopsin, saxitoxins and antitoxins, as well as the lesser-known marine toxins (e.g. lyngbyatoxin, aplysiatoxin, jamaicamides, barbamide, curacin, hectochlorin and apratoxins). (C) 2015 Elsevier B.V. All rights reserved.
analysis
(2016)
The development of ‘omics’ technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of ‘omics’ data integration together with an overview of available statistical methods and tools.
Wastewater samples from a Swedish chemi-thermo-mechanical pulp (CTMP) mill collected at different purification stages in a wastewater treatment plant (WWTP) were analyzed with an amperometric enzyme-based biosensor array in a flow-injection system. In order to resolve the complex composition of the wastewater, the array consists of several sensing elements which yield a multidimensional response. We used principal component analysis (PCA) to decompose the array's responses, and found that wastewater with different degrees of pollution can be differentiated. With the help of partial least squares regression (PLS-R), we could link the sensor responses to the toxicity parameter, as well as to global organic pollution parameters (COD, BOD, and TOC). From investigating the influences of individual sensors in the array, it was found that the best models were in most cases obtained when all sensors in the array were included in the PLS-R model. We find that fast simultaneous determination of several global environmental parameters characterizing wastewaters is possible with this kind of biosensor array, in particular because of the link between the sensor responses and the biological effect onto the ecosystem into which the wastewater would be released. In conjunction with multivariate data analysis tools, there is strong potential to reduce the total time until a result is yielded from days to a few minutes.
Background: Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. Results: The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Conclusions: Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.
Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
Arf-like proteins (ARLs) are ubiquitously expressed small G proteins of the RAS superfamily. In photoreceptors, ARL2 and ARL3 participate in the trafficking of lipidated membrane-associated proteins and colocalize in the inner segment with UNC119A and PDE delta. UNC119A and PDE delta are acyl-and prenyl-binding proteins, respectively, involved in trafficking of acylated (transducin-alpha subunit, nephrocystin NPHP3) and prenylated proteins (GRK1, PDE6). Germline Arl3 knockout mice do not survive beyond postnatal day 21 and display ciliary defects in multiple organs (kidney, liver and pancreas) as well as retinal degeneration. Conditional knockouts will be necessary to delineate mechanisms of protein transport in retina disease.