bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acceptable symbiont cell size differs among cnidarian species and may limit symbiont diversity
Authors: Biquand Elise , Okubo Nami , Aihara Yusuke , Rolland Vivien , Hayward David C , Hatta Masayuki , Minagawa Jun , Maruyama Tadashi , Takahashi Shunichi 
Published: March 2017

Abstract
Reef-building corals form symbiotic relationships with dinoflagellates of the genus Symbiodinium. Symbiodinium are genetically and physiologically diverse, and corals may be able to adapt to different environments by altering their dominant Symbiodinium phylotype. Notably, each coral species associates only with specific Symbiodinium phylotypes, and consequently the diversity of symbionts available to the host is limited by the species specificity. Currently, it is widely presumed that species specificity is determined by the combination of cell-surface molecules on the host and symbiont. Here we show experimental evidence supporting a new model to explain at least part of the specificity in coral–Symbiodinium symbiosis. Using the laboratory model Aiptasia–Symbiodinium system, we found that symbiont infectivity is related to cell size; larger Symbiodinium phylotypes are less likely to establish a symbiotic relationship with the host Aiptasia. This size dependency is further supported by experiments where symbionts were replaced by artificial fluorescent microspheres. Finally, experiments using two different coral species demonstrate that our size-dependent-infection model can be expanded to coral–Symbiodinium symbiosis, with the acceptability of large-sized Symbiodinium phylotypes differing between two coral species. Thus the selectivity of the host for symbiont cell size can affect the diversity of symbionts in corals.
Chance and necessity in the genome evolution of endosymbiotic bacteria of insects
Authors: Sabater-Muñoz Beatriz , Toft Christina , Alvarez-Ponce David , Fares Mario A 
Published: March 2017

Abstract
An open question in evolutionary biology is how does the selection–drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host–symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria. Experimental evolution of Escherichia coli under strong genetic drift revealed remarkable similarities in the mutational spectrum, genome reduction patterns and gene losses to endosymbiotic bacteria of insects. Interestingly, the transcriptome of the experimentally evolved lines showed a generalized deregulation of the genome that affected genes encoding proteins involved in mutational buffering, regulation and amino acid biosynthesis, patterns identical to those found in endosymbiotic bacteria. Our results indicate that drift has shaped endosymbiotic associations through a change in the functional landscape of bacterial genes and that the host had only a small role in such a shift.
Defining the functional traits that drive bacterial decomposer community productivity
Authors: Evans Rachael , Alessi Anna M , Bird Susannah , McQueen-Mason Simon J , Bruce Neil C , Brockhurst Michael A 
Published: March 2017

Abstract
Microbial communities are essential to a wide range of ecologically and industrially important processes. To control or predict how these communities function, we require a better understanding of the factors which influence microbial community productivity. Here, we combine functional resource use assays with a biodiversity–ecosystem functioning (BEF) experiment to determine whether the functional traits of constituent species can be used to predict community productivity. We quantified the abilities of 12 bacterial species to metabolise components of lignocellulose and then assembled these species into communities of varying diversity and composition to measure their productivity growing on lignocellulose, a complex natural substrate. A positive relationship between diversity and community productivity was caused by a selection effect whereby more diverse communities were more likely to contain two species that significantly improved community productivity. Analysis of functional traits revealed that the observed selection effect was primarily driven by the abilities of these species to degrade β-glucan. Our results indicate that by identifying the key functional traits underlying microbial community productivity we could improve industrial bioprocessing of complex natural substrates.
An alternative polysaccharide uptake mechanism of marine bacteria
Authors: Reintjes Greta , Arnosti Carol , Fuchs Bernhard M , Amann Rudolf 
Published: March 2017

Abstract
Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered—using super-resolution structured illumination microscopy—that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS). Fluorescence in situ hybridisation identified these organisms as members of the bacterial phyla Bacteroidetes and Planctomycetes and the gammaproteobacterial genus Catenovulum. Simultaneous membrane staining with nile red indicated that the FLA-PS labelling occurred in the cell but not in the cytoplasm. The dynamics of FLA-PS staining was further investigated in pure culture experiments using Gramella forsetii, a marine member of Bacteroidetes. The staining patterns observed in environmental samples and pure culture tests are consistent with a ‘selfish’ uptake mechanisms of larger oligosaccharides (&gt;600 Da), as demonstrated for gut Bacteroidetes. Ecologically, this alternative polysaccharide uptake mechanism secures substantial quantities of substrate in the periplasmic space, where further processing can occur without diffusive loss. Such a mechanism challenges the paradigm that hydrolysis of HMW substrates inevitably yields low-molecular-weight fragments that are available to the surrounding community and demonstrates the importance of an alternative mechanism of polysaccharide uptake in marine bacteria.
Origins of chemoreceptor curvature sorting in Escherichia coli
Authors: Draper Will , Liphardt Jan 
Published: March 2017

AbstractBacterial chemoreceptors organize into large clusters at the cell poles. Despite a wealth of structural and biochemical information on the system’s components, it is not clear how chemoreceptor clusters are reliably targeted to the cell pole. Here, we quantify the curvature-dependent localization of chemoreceptors in live cells by artificially deforming growing cells of Escherichia coli in curved agar microchambers, and find that chemoreceptor cluster localization is highly sensitive to membrane curvature. Through analysis of multiple mutants, we conclude that curvature sensitivity is intrinsic to chemoreceptor trimers-of-dimers, and results from conformational entropy within the trimer-of-dimers geometry. We use the principles of the conformational entropy model to engineer curvature sensitivity into a series of multi-component synthetic protein complexes. When expressed in E. coli, the synthetic complexes form large polar clusters, and a complex with inverted geometry avoids the cell poles. This demonstrates the successful rational design of both polar and anti-polar clustering, and provides a synthetic platform on which to build new systems.
Isolation and Characterization of Encephalomyocarditis Virus from Dogs in China
Authors: Luo Ya-Kun , Liang Lin , Tang Qing-Hai , Zhou Ling , Shi Li-Jun , Cong Ying-Ying , Lin Wen-Cheng , Cui Shang-Jin 
Published: March 2017

AbstractEncephalomyocarditis virus (EMCV) is as a potential zoonotic agent with a wide host range. Here, we describe an EMC virus isolate, identified as EMCV C15, which was successfully obtained from the serum of dogs from animal hospitals. Virus production in cell culture was confirmed by EMCV-specific real-time RT-PCR, indirect immunofluorescence assays and electron microscopy. In addition, the open reading frame sequence (ORF) of the EMCV C15 virus was determined. From sequence comparison and phylogenetic analysis among 24 reference EMCV strains, it appears that the EMCV C15 strain is closely genetically related to strain BEL2887A/91 (>99.0% nucleotide identity). In artificially challenged dogs, the heart and brain were important targets of EMCV C15. This study provides genetic and pathogenic characterization of the EMCV C15 strain isolated in Beijing and calls for sustained surveillance of EMCV infection in China to support better prevention and control of the disease.
The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene/photosynthetic Bradyrhizobium symbiosis
Authors: Nouwen Nico , Arrighi Jean-François , Cartieaux Fabienne , Chaintreuil Clémence , Gully Djamel , Klopp Christophe , Giraud Eric 
Published: March 2017

AbstractIn the most studied rhizobium-legume interactions, the host plant supplies the symbiont with homocitrate, an essential co-factor of the nitrogenase enzyme complex, via the expression of a nodule-specific homocitrate synthase FEN1. Photosynthetic bradyrhizobia interacting with Nod factor (NF) dependent and NF-independent Aeschynomene legumes are able to synthesize homocitrate themselves as they contain a nifV gene encoding a homocitrate synthase. Here, we show that in the model strain ORS285, nifV is required for free-living and symbiotic dinitrogen fixation with NF-independent Aeschynomene species. In contrast, in symbiosis with NF-dependent Aeschynomene species, the nifV requirement for efficient nitrogen fixation was found to be host plant dependent. Interestingly, orthologs of FEN1 were found in both NF-dependent and NF-independent Aeschynomene species. However, a high nodule specific induction of FEN1 expression was only observed in A. afraspera, a host plant in which nifV is not required for symbiotic dinitrogen fixation. These data indicate that efficient symbiotic nitrogen fixation in many of the tested Aeschynomene species requires rhizobial homocitrate synthesis. Considering that more than 10% of the fully sequenced rhizobium strains do contain a nifV gene, the Aeschynomene/photosynthetic Bradyrhizobium interaction is likely not the only rhizobium/legume symbiosis where rhizobial nifV expression is required.
Eμ and 3′RR IgH enhancers show hierarchic unilateral dependence in mature B-cells
Authors: Saintamand A. , Vincent-Fabert C. , Marquet M. , Ghazzaui N. , Magnone V. , Pinaud E. , Cogné M. , Denizot Y. 
Published: March 2017

AbstractEnhancer and super-enhancers are master regulators of cell fate. While they act at long-distances on adjacent genes, it is unclear whether they also act on one another. The immunoglobulin heavy chain (IgH) locus is unique in carrying two super-enhancers at both ends of the constant gene cluster: the 5′Eμ super-enhancer promotes VDJ recombination during the earliest steps of B-cell ontogeny while the 3′ regulatory region (3′RR) is essential for late differentiation. Since they carry functional synergies in mature B-cells and physically interact during IgH locus DNA looping, we investigated if they were independent engines of locus remodelling or if their function was more intimately intermingled, their optimal activation then requiring physical contact with each other. Analysis of chromatin marks, enhancer RNA transcription and accessibility in Eμ- and 3′RR-deficient mice show, in mature activated B-cells, an unilateral dependence of this pair of enhancers: while the 3′RR acts in autonomy, Eμ in contrast likely falls under control of the 3′RR.
The G2A receptor (GPR132) contributes to oxaliplatin-induced mechanical pain hypersensitivity
Authors: Hohmann Stephan W. , Angioni Carlo , Tunaru Sorin , Lee Seungkyu , Woolf Clifford J. , Offermanns Stefan , Geisslinger Gerd , Scholich Klaus , Sisignano Marco 
Published: March 2017

AbstractChemotherapy-induced peripheral neuropathic pain (CIPN) is a common and severe debilitating side effect of many widely used cytostatics. However, there is no approved pharmacological treatment for CIPN available. Among other substances, oxaliplatin causes CIPN in up to 80% of treated patients. Here, we report the involvement of the G-protein coupled receptor G2A (GPR132) in oxaliplatin-induced neuropathic pain in mice. We found that mice deficient in the G2A-receptor show decreased mechanical hypersensitivity after oxaliplatin treatment. Lipid ligands of G2A were found in increased concentrations in the sciatic nerve and dorsal root ganglia of oxaliplatin treated mice. Calcium imaging and patch-clamp experiments show that G2A activation sensitizes the ligand-gated ion channel TRPV1 in sensory neurons via activation of PKC. Based on these findings, we conclude that targeting G2A may be a promising approach to reduce oxaliplatin-induced TRPV1-sensitization and the hyperexcitability of sensory neurons and thereby to reduce pain in patients treated with this chemotherapeutic agent.
Elicitation of resistance and associated defense responses in Trichoderma hamatum induced protection against pearl millet downy mildew pathogen
Authors: Siddaiah Chandra Nayaka , Satyanarayana Niranjan Raj , Mudili Venkataramana , Kumar Gupta Vijai , Gurunathan Selvakumar , Rangappa Shobith , Huntrike Shekar Shetty , Srivastava Rakesh Kumar 
Published: March 2017

AbstractEndophytic Trichoderma hamatum UoM 13 isolated from pearl millet roots was evaluated for its efficiency to suppress downy mildew disease. Under laboratory conditions, T. hamatum seed treatment significantly enhanced pearl millet seed germination and seedling vigor. T. hamatum seed treatment resulted in systemic and durable immunity against pearl millet downy mildew disease under greenhouse and field conditions. T. hamatum treated seedlings responded to downy mildew infection with high lignification and callose deposition. Analysis of defense enzymes showed that T. hamatum treatment significantly enhanced the activities of glucanase, peroxidase, phenylalanine ammonia-lyase, and polyphenol oxidase in comparison to untreated control. RT-PCR analysis revealed differentially expressed transcripts of the defense enzymes and PR-proteins in treated, untreated, and checks, wherein PR-1, PR-5, and cell wall defense HRGPs were significantly over expressed in treated seedlings as against their lower expression in controls. T. hamatum treatment significantly stimulated endogenous salicylic acid (SA) levels and significantly upregulated important SA biosynthesis gene isochorismate synthase. The results indicated that T. hamatum UoM13 treatment induces resistance corresponding to significant over expression of endogenous SA, important defense enzymes, PR-proteins, and HRGPs, suggesting that SA biosynthetic pathway is involved in pearl millet for mounting systemic immunity against downy mildew pathogen.
A clear bias in parental origin of de novo pathogenic CNVs related to intellectual disability, developmental delay and multiple congenital anomalies
Authors: Ma Ruiyu , Deng Linbei , Xia Yan , Wei Xianda , Cao Yingxi , Guo Ruolan , Zhang Rui , Guo Jing , Liang Desheng , Wu Lingqian 
Published: March 2017

AbstractCopy number variation (CNV) is of great significance in human evolution and disorders. Through tracing the parent-of-origin of de novo pathogenic CNVs, we are expected to investigate the relative contributions of germline genomic stability on reproductive health. In our study, short tandem repeat (STR) and single nucleotide polymorphism (SNP) were used to determine the parent-of-origin of 87 de novo pathogenic CNVs found in unrelated patients with intellectual disability (ID), developmental delay (DD) and multiple congenital anomalies (MCA). The results shown that there was a significant difference on the distribution of the parent-of-origin for different CNVs types (Chi-square test, p = 4.914 × 10−3). An apparently paternal bias existed in deletion CNVs and a maternal bias in duplication CNVs, indicating that the relative contribution of paternal germline variations is greater than that of maternal to the origin of deletions, and vice versa to the origin of duplications. By analyzing the sequences flanking the breakpoints, we also confirmed that non-allelic homologous recombination (NAHR) served as the major mechanism for the formation of recurrent CNVs whereas non-SDs-based mechanisms played a part in generating rare non-recurrent CNVs and might relate to the paternal germline bias in deletion CNVs.
Chronic exposure to a neonicotinoid increases expression of antimicrobial peptide genes in the bumblebee Bombus impatiens
Authors: Simmons William R. , Angelini David R. 
Published: March 2017

AbstractBumblebees are important pollinators in wild and agricultural settings. In recent decades pollinator declines have been linked to the effects of increased pesticide use and the spread of disease. Synergy between these factors has been suggested, but no physiological mechanism has been identified. This study examines the connection between neonicotinoid exposure and innate immune function in the bumblebee Bombus impatiens, which is an important wild and commercial pollinator in eastern North America. Experimental colonies in the field were enclosed and provided pollen and sugar syrup containing an agriculturally relevant range of imidacloprid concentrations. Bumblebees were collected from colonies over four weeks, and the expression of antimicrobial peptides was measured using multiplex quantitative real time PCR. Significant increases in the expression of abaecin, apidaecin and hymenoptaecin were found over time in treatments receiving moderate to high concentrations of the pesticide. Responses were dependent on time of exposure and dose. These results indicate that immune function in bumblebees is affected by neonicotinoid exposure and suggest a physiological mechanism by which neonicotinoids may impact the innate immune function of bumblebee pollinators in wild and agricultural habitats.
Causal mechanisms of seismo-EM phenomena during the 1965–1967 Matsushiro earthquake swarm
Authors: Enomoto Yuji , Yamabe Tsuneaki , Okumura Nobuo 
Published: March 2017

AbstractThe 1965–1967 Matsushiro earthquake swarm in central Japan exhibited two unique characteristics. The first was a hydro-mechanical crust rupture resulting from degassing, volume expansion of CO2/water, and a crack opening within the critically stressed crust under a strike-slip stress. The other was, despite the lower total seismic energy, the occurrence of complexed seismo-electromagnetic (seismo-EM) phenomena of the geomagnetic intensity increase, unusual earthquake lights (EQLs) and atmospheric electric field (AEF) variations. Although the basic rupture process of this swarm of earthquakes is reasonably understood in terms of hydro-mechanical crust rupture, the associated seismo-EM processes remain largely unexplained. Here, we describe a series of seismo-EM mechanisms involved in the hydro-mechanical rupture process, as observed by coupling the electric interaction of rock rupture with CO2 gas and the dielectric-barrier discharge of the modelled fields in laboratory experiments. We found that CO2 gases passing through the newly created fracture surface of the rock were electrified to generate pressure-impressed current/electric dipoles, which could induce a magnetic field following Biot-Savart’s law, decrease the atmospheric electric field and generate dielectric-barrier discharge lightning affected by the coupling effect between the seismic and meteorological activities.
Mechanistic and structural basis of bioengineered bovine Cathelicidin-5 with optimized therapeutic activity
Authors: Sahoo Bikash R. , Maruyama Kenta , Edula Jyotheeswara R. , Tougan Takahiro , Lin Yuxi , Lee Young-Ho , Horii Toshihiro , Fujiwara Toshimichi 
Published: March 2017

AbstractPeptide-drug discovery using host-defense peptides becomes promising against antibiotic-resistant pathogens and cancer cells. Here, we customized the therapeutic activity of bovine cathelicidin-5 targeting to bacteria, protozoa, and tumor cells. The membrane dependent conformational adaptability and plasticity of cathelicidin-5 is revealed by biophysical analysis and atomistic simulations over 200 μs in thymocytes, leukemia, and E. coli cell-membranes. Our understanding of energy-dependent cathelicidin-5 intrusion in heterogeneous membranes aided in designing novel loss/gain-of-function analogues. In vitro findings identified leucine-zipper to phenylalanine substitution in cathelicidin-5 (1–18) significantly enhance the antimicrobial and anticancer activity with trivial hemolytic activity. Targeted mutants of cathelicidin-5 at kink region and N-terminal truncation revealed loss-of-function. We ensured the existence of a bimodal mechanism of peptide action (membranolytic and non-membranolytic) in vitro. The melanoma mouse model in vivo study further supports the in vitro findings. This is the first structural report on cathelicidin-5 and our findings revealed potent therapeutic application of designed cathelicidin-5 analogues.
A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungi
Authors: Polaino Silvia , Villalobos-Escobedo José M. , Shakya Viplendra P. S. , Miralles-Durán Alejandro , Chaudhary Suman , Sanz Catalina , Shahriari Mahdi , Luque Eva M. , Eslava Arturo P. , Corrochano Luis M. , Herrera-Estrella Alfredo , Idnurm Alexander 
Published: March 2017

AbstractLight is an environmental signal perceived by most eukaryotic organisms and that can have major impacts on their growth and development. The MadC protein in the fungusPhycomyces blakesleeanus(Mucoromycotina) has been postulated to form part of the photosensory input for phototropism of the fruiting body sporangiophores, but themadCgene has remained unidentified since the 1960s whenmadCmutants were first isolated. In this study themadCgene was identified by positional cloning. AllmadCmutant strains contain loss-of-function point mutations within a gene predicted to encode a GTPase activating protein (GAP) for Ras. ThemadCgene complements theSaccharomyces cerevisiaeRas-GAPira1mutant and the encoded MadC protein interacts withP. blakesleeanusRas homologs in yeast two-hybrid assays, indicating that MadC is a regulator of Ras signaling. Deletion of the homolog in the filamentous ascomyceteNeurospora crassaaffects the circadian clock output, yielding a pattern of asexual conidiation similar to aras-1mutant that is used in circadian studies inN. crassa. Thus, MadC is unlikely to be a photosensor, yet is a fundamental link in the photoresponses from blue light perceived by the conserved White Collar complex with Ras signaling in two distantly-related filamentous fungal species.