bluuebunny/crossref_metadata_2025_split huggingface dataset:
A theoretical approach for discriminating accurately intrinsic pattern of biological systems and recognizing three kind soybean proteomes
Authors: Zou Huabin 
Published: July 2018

Abstractproteomics is able to reveal plentiful information related to different physiological and pathological states of biology. Further, the determination of accurately proteomic pattern is the essential platform for deeply proteomic research. While this has been somewhat ignored so far. In this article the quantitative standard Pg=61%, a biological similarity constant for discriminating accurately intrinsic proteomic patterns was established depending on biological common heredity and variation information equation in symmetric variation state. On the other hand, a novel theoretical method was proposed for linearly dividing nonlinear data sequence into linear segments. The proteomes of three kind soybeans were precisely distinguished from one another by analyzing their infrared fingerprint spectra relying on this theoretically systemic approach. Additionally, methods employed in this paper enable us to quickly, accurately and quantitatively determine the proteomic patterns without using any prior knowledge and learning samples, and without using electrophoresis, high performance liquid chromatography-mass spectrometry techniques, which are high cost, time-consuming. This approach provide us with an excellent one for quickly accurate determining biological species, physiological states and diagnosing pathological states based on proteomes.
Characterizing molecular flexibility by combining lRMSD measures
Authors: Cazals F. , Tetley R. 
Published: July 2018

AbstractThe root mean square deviation (RMSD) and the least RMSD are two widely used similarity measures in structural bioinformatics. Yet, they stem from global comparisons, possibly obliterating locally conserved motifs. We correct these limitations with the so-called combined RMSD, which mixes independent lRMSD measures, each computed with its own rigid motion. The combined RMSD can be used to compare (quaternary) structures based on motifs defined from the sequence (domains, SSE), or to compare structures based on structural motifs yielded by local structural alignment methods.We illustrate the benefits of combined RMSD over the usual RMSD on three problems, namely (i) the analysis of conformational changes based on combined RMSD of rigid structural motifs (case study: a class II fusion protein), (ii) the calculation of structural phylogenies (case study: class II fusion proteins), and (iii) the assignment of quaternary structures for hemoglobin. Using these, we argue that the combined RMSD is a tool a choice to perform positive and negative discrimination of degree of freedom, with applications to the design of move sets and collective coordinates.Combined RMSD are available within the Structural Bioinformatics Library (http://sbl.inria.fr).
A centrosome calcium signal is essential for mammalian cell mitosis
Authors: Helassa Nordine , Nugues Charlotte , Burgoyne Robert D , Haynes Lee P 
Published: July 2018

AbstractTo generate a complex multicellular organism like a human requires enormous expansion in cell numbers and this is achieved predominantly through mitosis. Defects in mitosis can lead to premature ageing and cancer so understanding how it is regulated has important implications for human disease. Early data from plant and invertebrate model systems indicated that calcium (Ca2+) could influence mitosis. Here we explore this key question in the cell biology of mammalian cells by targeting high affinity genetically encoded Ca2+sensors to mitosis specific subcellular locations. We reveal a prolonged yet spatially restricted Ca2+signal at the centrosomes of mitotic cells using an actin-targeted Ca2+sensor. Local depletion of Ca2+at centrosomes using flash-photolysis of the caged Ca2+chelator diazo-2 arrests mitosis and we provide evidence that this signal emanates from the endoplasmic reticulum. In summary, we characterize a centrosomal Ca2+signal as a functionally essential input into mitosis. This extends our understanding of the complex regulatory network controlling cell division and pinpoints Ca2+as an important controller of this fundamental process.
Hybrid sequence-structure based HMM models leverage the identification of homologous proteins: the example of class II fusion proteins
Authors: Tetley R. , Guardado-Calvo P. , Fedry J. , Rey F. , Cazals F. 
Published: July 2018

AbstractWe present a sequence-structure based method characterizing a set of functionally related proteins exhibiting low sequence identity and loose structural conservation. Given a (small) set of structures, our method consists of three main steps. First, pairwise structural alignments are combined with multi-scale geometric analysis to produce structural motifs i.e. regions structurally more conserved than the whole structures. Second, the sub-sequences of the motifs are used to build profile hidden Markov models (HMM) biased towards the structurally conserved regions. Third, these HMM are used to retrieve from UniProtKB proteins harboring signatures compatible with the function studied, in a bootstrap fashion.We apply these hybrid HMM to investigate two questions related to class II fusion proteins, an especially challenging class since known structures exhibit low sequence identity (less than 15%) and loose structural similarity (of the order of 15Å in lRMSD). In a first step, we compare the performances of our hybrid HMM against those of sequence based HMM. Using various learning sets, we show that both classes of HMM retrieve unique species. The number of unique species reported by both classes of methods are comparable, stressing the novelty brought by our hybrid models. In a second step, we use our models to identify 17 plausible HAP2-GSC1 candidate sequences in 10 different drosophila melanogaster species. These models are not identified by the PFÅM family HAP2-GCS1 (PF10699), stressing the ability of our structural motifs to capture signals more subtle than whole Pfam domains.In a more general setting, our method should be of interest for all cases functional families with low sequence identity and loose structural conservation.Our software tools are available from the FunChaT package of the Structural Bioinformatics Library (http://sbl.inria.fr).
Overexpression of Arabidopsis ubiquitin ligase AtPUB46 enhances tolerance to drought and oxidative stress
Authors: Adler Guy , Mishra Amit Kumar , Maymon Tzofia , Raveh Dina , Bar-Zvi Dudy 
Published: July 2018

AbstractThe U-Box E3 ubiquitin ligase, AtPUB46, functions in the drought response: T-DNA insertion mutants of this single paralogous gene are hypersensitive to water- and oxidative stress (Adler et al. BMC Plant Biology 17:8, 2017). Here we analyze the phenotype of AtPUB46 overexpressing (OE) plants. AtPUB46-OE show increased tolerance to water stress and have smaller leaf blades and reduced stomatal pore area and stomatal index compared with wild type (WT). Despite this, the rate of water loss from detached rosettes is similar in AtPUB46-OE and WT plants. Germination of AtPUB46-OE seeds was less sensitive to salt than WT whereas seedling greening was more sensitive. We observed a complex response to oxidative stress applied by different agents: AtPUB46-OE plants were hypersensitive to H2O2 but hyposensitive to methyl viologen. AtPUB46-GFP fusion protein is cytoplasmic, however, in response to H2O2 a considerable proportion translocates to the nucleus. We conclude that the differential stress phenotype of the AtPUB46-OE does not result from its smaller leaf size but from a change in the activity of a stress pathway(s) regulated by a degradation substrate of the AtPUB46 E3 and also from a reduction in stomatal pore size and index.Accession NumbersSequence data for this article can be found in: The Arabidopsis Information Resource database (http://www.arabidopsis.org) under accession numbers At5G18320 (PUB46).
Mutation of sequences flanking and separating transcription factor binding sites in a Drosophila enhancer significantly alter its output
Authors: Li Xiao-Yong , Eisen Michael B. 
Published: July 2018

AbstractHere we explore how mutating different sequences in an enhancer that regulates patterned gene expression in Drosophila melanogaster embryos can affect its output. We used quantitative imaging to analyze the effects of a wide variety of mutations in the hunchback distal anterior enhancer. This enhancer has been shown to respond to the anterior morphogen Bicoid, but we found that mutations in only one of the five strong Bicoid sites in the enhancer has a significant effect on its binding. The pioneer factor Zelda, which binds to this enhancer and is the only other factor implicated in its activity besides Bicoid. However, we found that mutations of all its sites only has modest effect that is limited to reduction of its output in more posterior regions of the embryo, where Bicoid levels are low. In contrast to the modest effects of mutating known transcription factor binding sites, randomizing the sequences between Zelda and Bicoid sites significantly compromised enhancer activity. Finer mapping suggested that the sequences that determine activity are broadly distributed in the enhancer. Mutations in short sequences flanking Bicoid binding sites have stronger effects than mutations to Bicoid sites themselves, highlighting the complex and counterintuitive nature of the relationship between enhancer sequence and activity.
An amphipathic helix enables septins to sense micron-scale membrane curvature
Authors: Cannon Kevin S. , Woods Benjamin L. , Crutchley John M. , Gladfelter Amy S. 
Published: July 2018

AbstractThe geometry of cells is well described by membrane curvature. Septins are filament forming, GTP-binding proteins that assemble on positive, micrometer-scale curvatures. Here, we examine the molecular basis of curvature sensing by septins. We show that differences in affinity and the number of binding sites drive curvature-specific adsorption of septins. Moreover, we find septin assembly onto curved membranes is cooperative and show that geometry influences higher-order arrangement of septin filaments. Although septins must form polymers to stay associated with membranes, septin filaments do not have to span micrometers in length to sense curvature, as we find that single septin complexes have curvature-dependent association rates. We trace this ability to an amphipathic helix (AH) located on the C-terminus of Cdc12. The AH domain is necessary and sufficient for curvature sensing both in vitro and in vivo. These data show that curvature sensing by septins operates at much smaller length scales than the micrometer curvatures being detected.
An actuated neural probe architecture for reducing gliosis-induced recording degradation
Authors: Massey Travis L. , Kuo Leane S. , Fan Jiang Lan , Maharbiz Michel M. 
Published: July 2018

AbstractGlial encapsulation of chronically implanted neural probes inhibits recording and stimulation, and this signal loss is a significant factor limiting the clinical viability of most neural implant topologies for decades-long implantation. We demonstrate a mechanical proof of concept for silicon shank-style neural probes intended to minimize gliosis near the recording sites. Compliant whiskers on the edges of the probe fold inward to minimize tissue damage during insertion. Once implanted to the target depth and retracted slightly, these whiskers splay outward. The splayed tips, on which recording sites could be patterned, extend beyond the typical 50-100 micron radius of a glial scar. The whiskers are micron-scale to minimize or avoid glial scarring. Electrically inactive devices with whiskers of varying widths and curvature were designed and monolithically fabricated from a five-micron silicon-on-insulator (SOI) wafer, and their mechanical functionality was demonstrated in a 0.6% agar brain phantom. Deflection was plotted versus deflection speed, and those that were most compliant actuated successfully. This probe requires no preparation for use beyond what is typical for a shank-style silicon probe.
Predicting subclinical psychotic-like experiences on a continuum using machine learning
Authors: Taylor Jeremy A , Larsen Kit Melissa , Dzafic Ilvana , Garrido Marta I 
Published: July 2018

AbstractPrevious studies applying machine learning methods to psychosis have primarily been concerned with the binary classification of chronic schizophrenia patients and healthy controls. The aim of this study was to use electroencephalographic (EEG) data and pattern recognition to predict subclinical psychotic-like experiences on a continuum between these two extremes in otherwise healthy people. We applied two different approaches to an auditory oddball regularity learning task obtained fromN= 73 participants:A feature extraction and selection routine incorporating behavioural measures, event-related potential components and effective connectivity parameters;Regularisation of spatiotemporal maps of event-related potentials.Using the latter approach, optimal performance was achieved using the response to frequent, predictable sounds. Features within the P50 and P200 time windows had the greatest contribution toward lower Prodromal Questionnaire (PQ) scores and the N100 time window contributed most to higher PQ scores. As a proof-of-concept, these findings demonstrate that EEG data alone are predictive of individual psychotic-like experiences in healthy people. Our findings are in keeping with the mounting evidence for altered sensory responses in schizophrenia, as well as the notion that psychosis may exist on a continuum expanding into the non-clinical population.
Responses of ground-dwelling spider assemblages to changes in vegetation from wet oligotrophic habitats of Western France
Authors: Lafage Denis , Djoudi El Aziz , Perrin Gwenhaël , Gallet Sébastien , Pétillon Julien 
Published: July 2018

AbstractWhile many arthropod species are known to depend, directly or indirectly, on certain plant species or communities, it remains unclear to what extent vegetation shapes assemblages of other taxa, notably spiders. In this study, we tested whether the activity-density, composition, and diversity of ground-dwelling spiders were driven by changes in vegetation structure. Field sampling was conducted using pitfall traps in bogs, heathlands, and grasslands of Brittany (Western France) in 2013. A total of 8576 spider individuals were identified up to the species level (for a total of 141 species), as well as all plant species in more than 300 phytosociological relevés. A generalised linear model showed that spider activity–density was negatively influenced by mean vegetation height and mean Ellenberg value for moisture. Indices of diversity (α, β, and functional diversities) increased with increasing vegetation height and shrub cover (GLMs). Variables driving spider composition were mean vegetation height, dwarf shrub cover, and low shrub cover (results from a redundancy analysis). Spiders, some of the most abundant arthropod predators, are thus strongly influenced by vegetation structure, including ground-dwelling species. Although later successional states are usually seen as detrimental to local biodiversity in Europe, our results suggest that allowing controlled development of the shrub layer could have a positive impact on the diversity of ground-dwelling spiders.
Management performance mapping and the value of information for regional prioritization of management interventions
Authors: Buddenhagen C. E. , Piedra J. Andrade , Forbes G. A. , Kromann P. , Navarrete I. , Thomas-Sharma S. , Xing Y. , Choudhury R. A. , Andersen K. F. , Schulte-Geldermann E. , Garrett K. A. 
Published: July 2018

ABSTRACTPolicymakers and donors often need to identify the locations and settings where technologies are most likely to have important effects, to increase the benefits from agricultural development or extension efforts. Higher quality information may help to target the high-payoff locations. The value of information (VOI) in this context is formalized by evaluating the results of decision making guided by a set of information compared to the results of acting without taking the information into account. We present a framework for management performance mapping that includes evaluating the VOI for decision making about geographic priorities in regional intervention strategies, in case studies of Andean and Kenyan potato seed systems. We illustrate use of Bayesian network models and recursive partitioning to characterize the relationship between seed health and yield responses and environmental and management predictors used in studies of seed degeneration. These analyses address the expected performance of an intervention based on geographic predictor variables. In the Andean example, positive selection of seed from asymptomatic plants was more effective at high altitudes in Ecuador. In the Kenyan example, there was the potential to target locations with higher technology adoption rates and with higher potato cropland connectivity, i.e., a likely more important role in regional epidemics. Targeting training to high performance areas would often provide more benefits than would random selection of target areas. We illustrate how assessing the VOI can help inform targeted development programs and support a culture of continuous improvement for interventions.
Link Your Sites (LYS.py): Coupling your PAML codeml results and homologous protein structures in PyMOL
Authors: Moreta Lys Sanz , da Fonseca Rute Andreia Rodrigues 
Published: July 2018

ABSTRACTThe visualization of the molecular context of an amino acid mutation in a protein structure is crucial for the assessment of its functional impact and to understand its evolutionary implications. Currently, searches for fast evolving amino acid positions using codon substitution models like those implemented in PAML (Z. Yang, 2000) are done in almost complete proteomes, generating large numbers of candidate proteins that require individual structural analyses. Here I present a python wrapper script that integrates the output of PAML with the PyMOL visualization tool to automate the generation of protein structure models where positively selected sites are mapped along with the location of putative functional domains.
Ring nucleases deactivate Type III CRISPR ribonucleases by degrading cyclic oligoadenylate
Authors: Athukoralage Januka S , Rouillon Christophe , Graham Shirley , Grüschow Sabine , White Malcolm F 
Published: July 2018

AbstractThe CRISPR-Cas system provides adaptive immunity against mobile genetic elements in prokaryotes, utilising small CRISPR RNAs which direct effector complexes to degrade invading entities. Type III effector complexes were recently demonstrated to synthesise a novel second messenger, cyclic oligoadenylate (cOA), on binding target RNA. cOA in turn binds to and activates a range of downstream effector proteins including ribonucleases (Csm6/Csx1) and transcription factors via a CARF (CRISPR associated Rossman Fold) domain, inducing an antiviral state in the cell that is important for immunity. The mechanism of the “off-switch” that resets the system is not understood. Here, we report the identification of the nuclease that degrades these cOA ring molecules. The “Ring nuclease” is itself a CARF family protein with a metal independent mechanism, which cleaves cOA4 rings to generate linear di-adenylate species and switches off the antiviral state. The identification of Ring nucleases adds an important insight to the CRISPR-Cas system.
Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
Authors: Grobler Yolande , Yun Chi Y. , Kahler David J. , Bergman Casey M. , Lee Hangnoh , Oliver Brian , Lehmann Ruth 
Published: July 2018

AbstractWolbachia is an intracellular bacterium that infects a remarkable range of insect hosts. Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue, West Nile, and Zika. Remarkably, Wolbachia infection provides insect hosts with resistance to many arboviruses thereby rendering the insects ineffective as vectors. To utilize Wolbachia effectively as a tool against vector-borne viruses a better understanding of the host-Wolbachia relationship is needed. To investigate Wolbachia-insect interactions we used the Wolbachia/Drosophila model that provides a genetically tractable system for studying host-pathogen interactions. We coupled genome-wide RNAi screening with a novel high-throughput fluorescence in situ hybridization (FISH) assay to detect changes in Wolbachia levels in a Wolbachia-infected Drosophila cell line JW18. 1117 genes altered Wolbachia levels when knocked down by RNAi of which 329 genes increased and 788 genes decreased the level of Wolbachia. Validation of hits included in depth secondary screening using in vitro RNAi, Drosophila mutants, and Wolbachia-detection by DNA qPCR. A diverse set of host gene networks was identified to regulate Wolbachia levels and unexpectedly revealed that perturbations of host translation components such as the ribosome and translation initiation factors results in increased Wolbachia levels both in vitro using RNAi and in vivo using mutants and a chemical-based translation inhibition assay. This work provides evidence for Wolbachia-host translation interaction and strengthens our general understanding of the Wolbachia-host intracellular relationship.Author summaryInsects such as mosquitos act as vectors to spread devastating human diseases such as Dengue, West Nile, and Zika. It is critical to develop control strategies to prevent the transmission of these diseases to human populations. A novel strategy takes advantage of an endosymbiotic bacterium Wolbachia pipientis. The presence of this bacterium in insect vectors prevents successful transmission of RNA viruses. The degree to which viruses are blocked by Wolbachia is dependent on the levels of the bacteria present in the host such that higher Wolbachia levels induce a stronger antiviral effect. In order to use Wolbachia as a tool against vector-borne virus transmission a better understanding of host influences on Wolbachia levels is needed. Here we performed a genome-wide RNAi screen in a model host system Drosophila melanogaster infected with Wolbachia to identify host systems that affect Wolbachia levels. We found that host translation can influence Wolbachia levels in the host.
Choline Transporter in α/β core neurons of Drosophila mushroom body non-canonically regulates pupal eclosion and maintains neuromuscular junction integrity
Authors: Hamid Runa , Hajirnis Nikhil , Kushwaha Shikha , Saleem Sadaf , Kumar Vimlesh , Mishra Rakesh K 
Published: July 2018

AbstractInsect mushroom bodies (MB) have an ensemble of synaptic connections well-studied for their role in experience-dependent learning and several higher cognitive functions. MB requires neurotransmission for an efficient flow of information across synapses with the different flexibility to meet the demand of the dynamically changing environment of an insect. Neurotransmitter transporters coordinate appropriate changes for an efficient neurotransmission at the synapse. Till date, there is no transporter reported for any of the previously known neurotransmitters in the intrinsic neurons of MB. In this study, we report a highly enriched expression of Choline Transporter (ChT) in Drosophila MB. We demonstrate that knockdown of ChT in a sub-type of MB neurons called α/β core (α/βc) neurons leads to eclosion failure, peristaltic defect in larvae, and altered NMJ phenotype. These defects were neither observed on knockdown of proteins of the cholinergic locus in α/βc neurons nor by knockdown of ChT in cholinergic neurons. Thus, our study provides insights into non-canonical roles of ChT in MB.