bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence-based gene models for structural and functional annotations of the oil palm genome
Authors: Kuang Lim Chan , Tatarinova Tatiana V. , Rosli Rozana , Amiruddin Nadzirah , Azizi Norazah , Halim Mohd Amin Ab , Nik Mohd Sanusi Nik Shazana , Nagappan Jayanthi , Ponomarenko Petr , Triska Martin , Solovyev Victor , Firdaus-Raih Mohd , Sambanthamurthi Ravigadevi , Murphy Denis , Low Eng Ti Leslie 
Published: February 2017

AbstractThe advent of rapid and inexpensive DNA sequencing has led to an explosion of data that must be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including a comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We annotated 26,087 oil palm genes integrated from two gene-prediction pipelines, Fgenesh++ and Seqping. As case studies, we conducted comprehensive investigations on intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the current gene prediction set is of high quality. 3,672 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further scrutiny of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstock, and we identified 42 key genes involved in fatty-acid biosynthesis in oil palm mesocarp and kernel. These results provide an important resource for studies on plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops.
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interaction networks
Authors: Simpkins Scott W. , Nelson Justin , Deshpande Raamesh , Li Sheena C. , Piotrowski Jeff S. , Wilson Erin H. , Gebre Abraham A. , Okamoto Reika , Yoshimura Mami , Costanzo Michael , Yashiroda Yoko , Ohya Yoshikazu , Osada Hiroyuki , Yoshida Minoru , Boone Charles , Myers Chad L. 
Published: March 2017

AbstractChemical-genetic interactions – observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes – contain rich functional information linking compounds to their cellular modes of action. To systematically identify these interactions, an array of mutants is challenged with a compound and monitored for fitness defects, generating a chemical-genetic interaction profile that provides a quantitative, unbiased description of the cellular function(s) perturbed by the compound. Genetic interactions, obtained from genome-wide double-mutant screens, provide a key for interpreting the functional information contained in chemical-genetic interaction profiles. Despite the utility of this approach, integrative analyses of genetic and chemical-genetic interaction networks have not been systematically evaluated. We developed a method, called CG-TARGET (Chemical Genetic Translation via A Reference Genetic nETwork), that integrates large-scale chemical-genetic interaction screening data with a genetic interaction network to predict the biological processes perturbed by compounds. CG-TARGET compared favorably to a baseline enrichment approach across a variety of benchmarks, achieving similar accuracy while substantially improving the ability to control the false discovery rate of biological process predictions. We applied CG-TARGET to a recent screen of nearly 14,000 chemical compounds inSaccharomyces cerevisiae, integrating this dataset with the globalS. cerevisiaegenetic interaction network to prioritize over 1500 compounds with high-confidence biological process predictions for further study. Upon investigation of the compatibility of chemical-genetic and genetic interaction profiles, we observed that one-third of observed chemical-genetic interactions contributed to the highest-confidence biological process predictions and that negative chemical-genetic interactions overwhelmingly formed the basis of these predictions. We present here a detailed characterization of the CG-TARGET method along with experimental validation of predicted biological process targets, focusing on inhibitors of tubulin polymerization and cell cycle progression. Our approach successfully demonstrates the use of genetic interaction networks in the functional annotation of compounds to biological processes.
Clay-induced DNA double-strand breaks underlay genetic diversity, antibiotic resistance and could be a molecular basis for asbestos-induced cancer
Authors: González-Tortuero Enrique , Rodríguez-Beltran Jerónimo , Radek Renate , Blázquez Jesús , Rodríguez-Rojas Alexandro 
Published: February 2017

AbstractSome natural clays and synthetic nanofibres present in the environment have a severe impact on human health. After several decades of research, the molecular mechanism of how asbestos induce cancers is not well understood. Different fibres, including asbestos, can penetrate the membrane and introduce DNA in both, bacterial and eukaryotic cells. Incubating Escherichia coli with sepiolite, a clayey material, and asbestos under friction forces, both fibres cause double-strand breaks in bacteria. Since antibiotics and clays are used together in animal husbandry, the mutagenic effect of these fibres might constitute a pathway to antibiotic resistance due to the friction provided by peristalsis of the gut from farm animals in addition to the previously proposed horizontal gene transfer. Moreover, we raise the possibility that the same mechanism could generate bacteria diversity in natural scenarios with a role in the evolution of species. Finally, we provide a new model on how asbestos may promote mutagenesis and cancer based on the observed mechanical genotoxicity.
Inferring individual-level processes from population-level patterns in cultural evolution
Authors: Kandler Anne , Wilder Bryan , Fortunato Laura 
Published: February 2017

AbstractOur species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.
BECon: A tool for interpreting DNA methylation findings from blood in the context of brain
Authors: Edgar Rachel , Jones Meaghan J , Meaney Michael J , Turecki Gustavo , Kobor Michael S 
Published: February 2017

AbstractTissue differences are one of the largest contributors to variability in the human DNA methy-lome. Despite the tissue specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well documented. Here we aimed to provide a resource to the community to aid interpretation of blood based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data we have made available metrics on: the variability of CpGs in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance;https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood based human DNA methylation results, in the context of brain.
Community evolution increases plant productivity at low diversity
Authors: van Moorsel Sofia J. , Hahl Terhi , Wagg Cameron , De Deyn Gerlinde B. , Flynn Dan F.B. , Zuppinger-Dingley Debra , Schmid Bernhard 
Published: February 2017

ABSTRACTSpecies extinctions from local communities can negatively affect ecosystem functioning. Ecological mechanisms underlying these impacts are well studied but the role of evolutionary processes is rarely assessed. Using a long-term field experiment, we tested whether natural selection in plant communities increased the effects of biodiversity on productivity. We re-assembled communities with 8-year co-selection history adjacent to communities with identical species composition but no history of co-selection (“naïve communities”). Monocultures and in particular mixtures of two to four co-selected species were more productive than their corresponding naïve communities over four years in soils with or without co-selected microbial communities. At the highest diversity level of eight plant species, no such differences were observed. Our findings suggest that plant community evolution can lead to rapid increases in ecosystem functioning at low diversity but may take longer at high diversity. This effect was not modified by treatments that simulated additional co-evolutionary processes between plants and soil organisms.
Multiplexed confocal and super-resolution fluorescence imaging of cytoskeletal and neuronal synapse proteins
Authors: Guo Syuan-Ming , Veneziano Remi , Gordonov Simon , Li Li , Park Demian , Kulesa Anthony B. , Blainey Paul C. , Cottrell Jeffrey R. , Boyden Edward S. , Bathe Mark 
Published: February 2017

ABSTRACTNeuronal synapses contain dozens of protein species whose expression levels and localizations are key determinants of synaptic transmission and plasticity. The spectral properties of fluorophores used in conventional microscopy limit the number of measured proteins to four species within a given sample. The ability to perform high-throughput confocal or super-resolution imaging of many proteins simultaneously without limitation in target number imposed by this spectral limit would enable large-scale characterization of synaptic protein networks in situ. Here, we introduce PRISM: Probe-based Imaging for Sequential Multiplexing, a method that sequentially utilizes either high affinity Locked Nucleic Acid (LNA) or low affinity DNA probes to enable diffraction-limited confocal and PAINT-based super-resolution imaging. High-affinity LNA probes offer high-throughput, confocal-based imaging compared with PAINT, which uses low affinity probes to realize localization-based super-resolution imaging. Simultaneous immunostaining of all targets is performed prior to imaging, followed by sequential LNA/DNA probe exchange that requires only minutes under mild wash conditions. We apply PRISM to quantify the co-expression levels and nanometer-scale organization of one dozen cytoskeletal and synaptic proteins within individual neuronal synapses. Our approach is scalable to dozens of target proteins and is compatible with high-content screening platforms commonly used to interrogate phenotypic changes associated with genetic and drug perturbations in a variety of cell types.
Elastic Multi-Scale Mechanisms: Computation and Biological Evolution
Authors: Diaz Ochoa Juan G. 
Published: February 2017

AbstractExplanations based on low level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low level interacting elements with unambiguous, finite and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution (oee). Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution. We introduce a modulus of elasticity to measure the changes in these mechanisms in response to changes in the computed environment. We test this concept in a population of predators and predated cells with chemotactic mechanisms and demonstrate how the selection of a given mechanism depends on the entire population. We finally explore this concept in different frameworks and postulate that the identification of predictive mechanisms is only successful with small elasticity modulus.
The reactivation of reprogramming factors within human blastocysts by using ATP contribute to human blastocyst development
Authors: Takemura Takashi , Okabe Midori 
Published: February 2017

AbstractScientists worldwide have been unable to replicate the stimulus-triggered acquisition of pluripotency (STAP) cells and/or the STAP phenomenon. However, investigations into STAP cells and/or the STAP phenomenon by RIKEN CDB in Japan found that ATP (adenosine 5’-triphosphate disodium salt hydrate) can upregulate Oct3/4 (POU5F1: POU domain, class 5, transcription factor 1) and Nanog mRNA expression in mouse hepatocytes.On the other hand, no studies have investigated whether ATP can contribute to human blastocyst development. Here we show the reactivation of reprogramming factors within human blastocysts by appropriate ATP treatment (1 mM for 2 days) can contribute to human blastocyst development.In conclusion, although ATP treatment could not replicate STAP cells and/or the STAP phenomenon by scientists worldwide, appropriate ATP treatment (1 mM for 2 days) in cultured human blastocysts with totipotency would be helpful for infertility women.
Bacterial tail anchors can target to the mitochondrial outer membrane
Authors: Bal Güleycan Lutfullahoğlu , Keskin Abdurrahman , Seferoğlu Ayşe Bengisu , Dunn Cory D. 
Published: February 2017

ABSTRACTDuring the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was refashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol. Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacteriumEscherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeastSaccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM. Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.
Comparing arenavirus infection patterns in experimentally and naturally infected rodent hosts
Authors: Mariën Joachim , Borremans Benny , Gryseels Sophie , Vanden Broecke Bram , Becker-Ziaja Beate , Makundi Rhodes , Massawe Apia , Reijniers Jonas , Leirs Herwig 
Published: February 2017

AbstractInfectious diseases of wildlife are typically studied using data on antibody and pathogen presence/level. In order to interpret these data, it is necessary to know the course of antibodies and pathogen presence/levels after infection. Such data are typically collected using experimental infection studies in which host individuals are inoculated in the laboratory and sampled over an extended period, but because laboratory conditions are controlled and much less variable than natural conditions, the immune response and pathogen dynamics may differ. Here, we compared Morogoro arenavirus infection patterns between naturally and experimentally infected multimammate mice (Mastomys natalensis). Longitudinal samples were collected during three months of bi-weekly trapping in Morogoro, Tanzania, and antibody titer and viral RNA presence were determined to assess whether the natural temporal patterns are similar to those previously observed in the laboratory. A good match with laboratory data was found for 52% of naturally infected individuals, while most of the mismatches can be explained by the presence of chronically infected individuals (35%), maternal antibodies (10%) and an antibody detection limit (25%). These results suggest that while laboratory data are useful for interpreting field samples, there can still be differences due to conditions that were not tested in the laboratory.Important noticeThis is a pre-print version of the manuscript, made available through bioRxiv.org. Note that this manuscript has not yet been peer-reviewed, and has been submitted to a peer-reviewed journal.
Constraint-based modeling identifies new putative targets to fight colistin-resistantA. baumanniiinfections
Authors: Presta Luana , Bosi Emanuele , Mansouri Leila , Dijkshoorn Lenie , Fani Renato , Fondi Marco 
Published: February 2017

AbstractAcinetobacter baumanniiis a clinical threat to human health, causing major infection outbreaks worldwide. As new drugs against Gram-negative bacteria do not seem to be forthcoming, and due to the microbial capability of acquiring multi-resistance, there is an urgent need for novel therapeutic targets. Here we have derived a list of new potential targets by means of metabolic reconstruction and modelling ofA. baumanniiATCC 19606. By integrating constraint-based modelling with gene expression data, we simulated microbial growth in normal and stressful conditions (i.e. following antibiotic exposure). This allowed us to describe the metabolic reprogramming that occurs in this bacterium when treated with colistin (the currently adopted last-line treatment) and identify a set of genes that are primary targets for developing new drugs againstA. baumannii, including colistin-resistant strains. It can be anticipated that the metabolic model presented herein will represent a solid and reliable resource for the future treatment ofA. baumanniiinfections.
A unifying mechanism for the biogenesis of prokaryotic membrane proteins co-operatively integrated by the Sec and Tat pathways
Authors: Tooke Fiona J. , Babot Marion , Chandra Govind , Buchanan Grant , Palmer Tracy 
Published: February 2017

AbstractThe vast majority of polytopic membrane proteins are inserted into the cytoplasmic membrane of prokaryotes by the general secretory (Sec) pathway. However, a subset of monotopic proteins that contain non-covalently-bound redox cofactors depend on the twin-arginine translocase (Tat) machinery for membrane integration. Recently actinobacterial Rieske iron-sulfur cluster-containing proteins were identified as an unusual class of membrane proteins that require both the Sec and Tat pathways for the insertion of their three transmembrane domains (TMDs). The Sec pathway inserts the first two TMDs of these proteins co-translationally, but releases the polypeptide prior to the integration of TMD3 to allow folding of the cofactor-containing domain and its translocation by Tat. Here we have investigated features of theStreptomyces coelicolorRieske polypeptide that modulate its interaction with the Sec and Tat machineries. Mutagenesis of a highly conserved loop region between Sec-dependent TMD2 and Tat-dependent TMD3 shows that it plays no significant role in coordinating the activities of the two translocases, but that a minimum loop length of approximately eight amino acids is required for the Tat machinery to recognise TMD3. Instead we show that a combination of relatively low hydrophobicity of TMD3, coupled with the presence of C-terminal positively-charged amino acids, results in abortive insertion of TMD3 by the Sec pathway and its release at the cytoplasmic side of the membrane. Bioinformatic analysis identified two further families of polytopic membrane proteins that share features of dual Sec-Tat-targeted membrane proteins. A predicted heme-molybdenum cofactor-containing protein with five TMDs, and a polyferredoxin also with five predicted TMDs, are encoded across bacterial and archaeal genomes. We demonstrate that membrane insertion of representatives of each of these newly-identified protein families is dependent on more than one protein translocase, with the Tat machinery recognising TMD5. Importantly, the combination of low hydrophobicity of the final TMD and the presence of multiple C-terminal positive charges that serve as critical Sec-release features for the actinobacterial Rieske protein also dictate Sec release in these further protein families. Therefore we conclude that a simple unifying mechanism governs the assembly of dual targeted membrane proteins.
Lycopene: A natural antioxidant for anhydrous buffalo milk fat
Authors: Siwach Ruby , Tokas Jayanti , Seth Raman 
Published: March 2017

The potential of lycopene extract, to enhance the shelf life of anhydrous buffalo milk fat, at five levels, viz. 30, 60, 90, 120 and 150 ppm, was evaluated. Lycopene was found significantly (P < 0.05) effective in preventing the development of oxidative rancidity. The overall preference score for samples containing 30, 60, 90, 120 and 150 ppm of lycopene were 7.43, 7.60, 7.80, 7.96 and 7.90, respectively, and found to be significantly higher than the control (no lycopene, 6.79). The overall preference score with 200 ppm BHA was 7.94, which was not significantly different from ghee samples containing 120 and 150 ppm lycopene.