bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into regeneration from the genome, transcriptome and metagenome analysis ofEisenia fetida
Authors: Bhambri Aksheev , Dhaunta Neeraj , Patel Surendra Singh , Hardikar Mitali , Srikakulam Nagesh , Shridhar Shruti , Vellarikkal Shamsudheen , Suryawanshi Hemant , Pandey Rajesh , Jayarajan Rijith , Verma Ankit , Kumar Vikram , Bhatt Abhishek , Gautam Pradeep , Rai Manish , Khan Jameel Ahmed , Fromm Bastian , Peterson Kevin J. , Scaria Vinod , Sivasubbu Sridhar , Pillai Beena 
Published: August 2017

AbstractEarthworms show a wide spectrum of regenerative potential with certain species likeEisenia fetidacapable of regenerating more than two-thirds of their body while other closely related species, such asParanais litoralisseem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaeteCapitella telata, and the freshwater leechHelobdella robustahave been sequenced and studied. The terrestrial annelids, in spite of their ecological relevance and unique biochemical repertoire, are represented by a single rough genome draft ofEisenia fetida(North American isolate), which suggested that extensive duplications have led to a large number of HOX genes in this annelid. Herein, we report the draft genome sequence ofEisenia fetida(Indian isolate), a terrestrial redworm widely used for vermicomposting assembled using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm, showed that many miRNA gene families have also undergone extensive duplications. Genes for several important proteins such as sialidases and neurotrophins were identified by RNA sequencing of tissue samples. We also usedde novoassembled RNA-Seq data to identify genes that are differentially expressed during regeneration, both in the newly regenerating cells and in the adjacent tissue. Sox4, a master regulator of TGF-beta induced epithelial-mesenchymal transition was induced in the newly regenerated tissue. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. The metagenome of the worm, characterized using 16S rRNA sequencing, revealed the identity of several bacterial species that reside in the nephridia of the worm. Comparison of the bodywall and cocoon metagenomes showed exclusion of hereditary symbionts in the regenerated tissue. In summary, we present extensive genome, transcriptome and metagenome data to establish the transcriptome and metagenome dynamics during regeneration.
Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments
Authors: Brunk Elizabeth , Chang Roger L. , Xia Jing , Hefzi Hooman , Yurkovich James T. , Kim Donghyuk , Buckmiller Evan , Wang Harris , Yang Chen , Palsson Bernhard O. , Church George M. , Lewis Nathan E. 
Published: August 2017

AbstractAcross all domains of life, elaborate control mechanisms regulate proteins, pathways, and cell phenotypes as organisms adapt to ever-changing environments. Post-translational modifications (PTMs) allow cells to rapidly and reversibly regulate molecular pathways, but it remains unclear how individual PTMs regulate fitness. Here, we studied >130 PTM sites inEscherichia colito unravel how PTMs regulate cell metabolism and fitness in response to environmental changes, such as the glucose-acetate diauxie. Using a new metabolic modeling approach, we found a significant fraction of post-translationally modified enzymes are predicted to control shifts in pathway usage following evolutionarily-important environmental changes. Genetic screens using Multiplex Automated Genome Engineering confirmed that these PTMs impact cellular fitness, especially under dynamically changing environments. Finally, mechanisms of how individual PTMs impact protein function were detailed using molecular dynamics simulations and enzyme assays for enolase, transaldolase, and serine hydroxymethyltransferase. Thus, by integrating whole-cell data and pathway modeling with detailed biochemical analysis, we unraveled how individual PTMs regulate enzymes, pathways, and phenotypes to adapt to sudden environmental changes.
A transgenic zebrafish model for thein vivostudy of the blood and choroid plexus brain barriers using claudin 5
Authors: van Leeuwen Lisanne Martine , Evans Robert J. , Jim Kin Ki , Verboom Theo , Fang Xiaoming , Bojarczuk Aleksandra , Malicki Jarema , Andrew Johnston Simon , Marijke van der Sar Astrid 
Published: August 2017

ABSTRACTThe central nervous system (CNS) has specific barriers that protect the brain from potential threats and tightly regulate molecular transport. Despite the critical functions of the CNS barriers, the mechanisms underlying their development and function are not well understood, and there are very limited experimental models for their study. Claudin 5 is a tight junction protein required for blood brain barrier (BBB) and choroid plexus (CP) barrier structure and function in humans. Here, we show that the geneclaudin 5ais the zebrafish orthologue with high fidelity expression, in the BBB and CP barriers, that demonstrates the conservation of the BBB and CP between humans and zebrafish. Expression ofclaudin 5acorrelates with developmental tightening of the BBB and is restricted to a subset of the brain vasculature clearly delineating the BBB. We show thatclaudin 5aexpressing cells of the CP are ciliated ependymal cells that drive fluid flow in the brain ventricles. Finally, we find that CP development precedes BBB development and thatclaudin 5aexpression occurs simultaneously with angiogenesis. Thus, our novel transgenic zebrafish represents an ideal model to study CNS barrier development and function, critical in understanding the mechanisms underlying CNS barrier function in health and disease.
Determining the optimal number of independent components for reproducible transcriptomic data analysis
Authors: Kairov Ulykbek , Cantini Laura , Greco Alessandro , Molkenov Askhat , Czerwinska Urszula , Barillot Emmanuel , Zinovyev Andrei 
Published: August 2017

AbstractBackgroundIndependent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data.ResultsHere we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets.ConclusionsWe suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.
The psychological arrow of time and the human brain dynamics of event ordering
Authors: Gauthier Baptiste , Pestke Karin , Wassenhove Virginie van 
Published: August 2017

AbstractWhen navigating the real-world, the spatiotemporal sequencing of events is intrinsically bound to one’s physical trajectory; when recollecting the past or imagining the future, the temporal and spatial dimension of events can be independently manipulated. Yet, the rules enabling the flexible use of spatial and temporal cognitive maps likely differ in one major way as time is directional (oriented from past-to-future) whereas space is not. Using combined magneto- and electroencephalography, we sought to capture such differences by characterizing time-resolved brain activity while participants mentally ordered memories from different mental perspectives in time (past/future) or space (west/east). We report two major neural dissociations underlying the mental ordering of events in time and in space: first, brain responses evoked by the temporal order and the temporal distance of events-to-self dissociated at early and late latencies, respectively whereas spatial order and distance of events-to-self elicited late brain responses simultaneously. Second, brain responses distinguishing self-position in time and the temporal order of events involved sources in the hippocampal formation; spatial perspective, order and distance did not. These results suggest that the neural dynamics evoked by the temporal ordering of a series of events retrieved from long-term memory, i.e. the psychological time arrow, entails dedicated cognitive processes in the hippocampal formation that are fundamentally distinct from the mapping of spatial location.
Asymmetric MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin
Authors: Zawadzka Katarzyna , Zawadzki Pawel , Baker Rachel , Rajasekar Karthik V. , Sherratt David J. , Arciszewska Lidia K. 
Published: August 2017

AbstractTheEscherichia coliSMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerization domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head, forming an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerization is preserved during this interaction, MukF directs the formation of dimer of dimers MukBEF complexes, observed previouslyin vivo. The MukF N- and C-terminal domains stimulate ATPase independently and additively, consistent with them each targeting only one of the two MukB ATPase active sites in the asymmetric complex. We demonstrate that MukF interaction with the MukB neck turns over during cycles of ATP binding and hydrolysisin vivoand that impairment of this interaction leads to MukBEF release from chromosomes.
Gene markers for exon capture and phylogenomics in ray-finned fishes
Authors: Jiang Jiamei , Yuan Hao , Zheng Xin , Wang Qian , Kuang Ting , Li Jingyan , Liu Junning , Song Shuli , Wang Weicai , Cheng Fangyaun , Li Hongjie , Huang Junman , Li Chenhong 
Published: August 2017

AbstractGene capture coupled with the next generation sequencing has become one of the favorable methods in subsampling genomes for phylogenomic studies. Many target gene markers have been developed in plants, sharks, frogs, reptiles and others, but few have been reported in the ray-finned fishes. Here, we identified a suite of “single-copy” protein coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and 11 orders) of ray-finned fishes. Sorting through the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray-finned fishes at different taxonomic level. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may fill a gap in the tool kit of phylogenomic study in vertebrates.
The molecular mechanism of N-acetylglucosamine side-chain attachment to the Lancefield group A Carbohydrate inStreptococcus pyogenes
Authors: Rush Jeffrey S. , Edgar Rebecca J. , Deng Pan , Chen Jing , Zhu Haining , van Sorge Nina M. , Morris Andrew J. , Korotkov Konstantin V. , Korotkova Natalia 
Published: August 2017

AbstractIn many Lactobacillales species (i.e. lactic acid bacteria), peptidoglycan is decorated by polyrhamnose polysaccharides that are critical for cell envelope integrity and cell shape and also represent key antigenic determinants. Despite the biological importance of these polysaccharides, their biosynthetic pathways have received limited attention. The important human pathogen,Streptococcus pyogenes, synthesizes a key antigenic surface polymer—the Lancefield group A carbohydrate (GAC). GAC is covalently attached to peptidoglycan and consists of a polyrhamnose polymer, with N-acetylglucosamine (GlcNAc) side chains, which is an essential virulence determinant. The molecular details of the mechanism of polyrhamnose modification with GlcNAc are currently unknown. In this report, using molecular genetics, analytical chemistry and mass spectrometry analysis, we demonstrated that GAC biosynthesis requires two distinct undecaprenol-linked GlcNAc-lipid intermediates: GlcNAc-pyrophosphorylundecaprenol (GlcNAc-P-P-Und) produced by the GlcNAc-phosphate transferase GacO and GlcNAc-phosphate-undecaprenol (GlcNAc-P-Und) produced by the glycosyltransferase GacI. Further investigations revealed that the GAC polyrhamnose backbone is assembled on GlcNAc-P-P-Und. Our results also suggested that a GT-C glycosyltranferase, GacL, transfers GlcNAc from GlcNAc-P-Und to polyrhamnose. Moreover, GacJ, a small membrane-associated protein, formed a complex with GacI and significantly stimulated its catalytic activity. Of note, we observed that GacI homologs perform a similar function inStreptococcus agalactiaeandEnterococcus faecalis. In conclusion, the elucidation of GAC biosynthesis inS. pyogenesreported here enhances our understanding of how other Gram-positive bacteria produce essential components of their cell wall.
Intra-voxel incoherent motion magnetic resonance imaging of the living human fetus: the technique and within-subject reproducibility
Authors: Jakab András , Tuura Ruth , Kottke Raimund , Kellenberger Christian , Scheer Ianina 
Published: August 2017

AbstractOur purpose was to test the within-subject repeatability of the perfusion fraction, diffusion coefficient and pseudo diffusion coefficient measurements in various fetal organs and in the placenta based on the intra-voxel incoherent motion imaging principle.In uterodiffusion-weighted magnetic resonance imaging was performed on 1.5T and 3.0T clinical scanners with b-factors ranging from 0 to 900 s/mm2 in 16 steps and a tetrahedral diffusion-weighting encoding scheme. Data from 16 pregnant women (maternal age: 34 ± 4.9 years, range: 24.6 −40.8) were included in this pilot study. For 15 cases, IVIM was repeated (maternal age: 33.7 ± 5.2 years, range: 24.6 – 40.8). A bi-exponential model was fitted on the volume-averaged diffusion values and the perfusion fraction (f), diffusion coefficient (d) and pseudo diffusion coefficient (D*) were calculated. Within-subject repeatability was given as the test-retest variability of the IVIM parameters in the fetal frontal cortex, frontal white matter, cerebellum, lungs, kidneys, liver and in the placenta. An in-house developed image processing script was utilized to remove the image frames with excessive motion, and to perform motion correction by using non-linear freeform deformations. For the fetal lungs, liver and the placenta, within-subject variability ranged from 14.4% to 20.4% for f, 12.2% to 14.1% for d and 16.8% to 25.3% for D*. The diffusion coefficients of the investigated brain regions were moderately to highly reproducible (4.8% to 15.2%), however, f and D* showed inferior reproducibility compared to corresponding measures derived for the lungs, liver and placenta. The IVIM-based parameters of the fetal kidney were revealed to be highly variable across scans. Our results indicate that in utero intra-voxel incoherent motion magnetic resonance imaging potentially provides a novel method for examining microvascular perfusion and diffusion in the developing human fetus. The reproducible quantification of the perfusion and diffusion parameters depend greatly upon data quality, fetal and maternal movements, and image post processing to detect and remove corrupted data before calculating the IVIM model.
Enhancement of non-specific immune responses in European sea bass (Dicentrarchus labrax, L. 1758) by geophyte extract injections (Urginea maritimaandMuscari comosum)
Authors: Uluköy Gülşen , Baba Esin , Mammadov Ramazan 
Published: August 2017

AbstractThe immunomodulatory effects of bulb extracts from the geophyte plantsMuscari comosum(MC) andUrginea maritima(UM) on a non-spesific immune responses of European sea bass were investigated. Ethanol extracts were administered via intraperitoneal injection at doses of 0.5mg/fish and 2mg/fish in PBS. Non-spesific immune parameters such as Nitro blue tetrazolium (NBT) positive cells, serum lysozyme, total protein, total number of leukocytes, leukocyte cell type percentages and specific growth rates were investigated on the 1st, 7th, 14th, 21st, 28th and 35th days following the injection. The results indicate that receiving injections with MC and UM enhances some non-specific immune parameters in European sea bass. Total protein in serum was not enhanced. Activation occured on the 14thday and 21stday and this positive effects started to decrease following days. The appropriate dosage to achieve this enhancement was determined to be 0.5 mg/fish for UM and 2 mg/fish for MC. This preliminary study indicates that these doses yield the best results to promote the health status of European sea bass in intensive aquaculture.
Optogenetic inhibition reveals distinct roles for basolateral amygdala activity at discrete timepoints during risky decision making
Authors: Orsini Caitlin A. , Hernandez Caesar M. , Singhal Sarthak , Kelly Kyle B. , Frazier Charles J. , Bizon Jennifer L. , Setlow Barry 
Published: August 2017

AbstractDecision making is a multifaceted process, consisting of several distinct phases that likely require different cognitive operations. Previous work showed that the basolateral amygdala (BLA) is a critical substrate for decision making involving risk of punishment; however, it is unclear how the BLA is recruited at different stages of the decision process. To this end, the current study used optogenetics to inhibit the BLA during specific task phases in a model of risky decision making (Risky Decision-making Task; RDT) in which rats choose between a small, “safe” reward and a large reward accompanied by varying probabilities of footshock punishment. Rats received intra-BLA microinjections of viral vectors carrying either halorhodopsin (eNpHR3.0-mCherry) or mCherry alone (control) followed by optic fiber implants and were trained in the RDT. Laser stimulation during the task occurred during either intertrial interval, deliberation, or reward outcome phases, the latter of which was further divided into the three possible outcomes (small, safe; large, unpunished; large, punished). Inhibition of the BLA selectively during the deliberation phase decreased choice of the large, risky outcome (decreased risky choice). In contrast, BLA inhibition selectively during delivery of the large, punished outcome increased risky choice. Inhibition had no effect during the other phases, nor did it affect performance in control rats. Collectively, these data indicate that the BLA can either inhibit or promote choice of risky options, depending on the phase of the decision process in which it is active.Significance StatementTo date, most behavioral neuroscience research on neural mechanisms of decision making has employed techniques that preclude assessment of distinct phases of the decision process. Here we show that optogenetic inhibition of the basolateral amygdala (BLA) has opposite effects on choice behavior in a rat model of risky decision making depending on the phase in which inhibition occurs. BLA inhibition during a period of deliberation between small, safe and large, risky outcomes decreased risky choice. In contrast, BLA inhibition during receipt of the large, punished outcome increased risky choice. These findings highlight the importance of temporally targeted approaches to understand neural substrates underlying complex cognitive processes. More importantly, they reveal novel information about dynamic BLA modulation of risky choice.
Contributions of different prefrontal cortical regions to abstract rule acquisition and reversal in monkeys
Authors: Camera Giancarlo La , Bouret Sebastien , Richmond Barry J. 
Published: August 2017

AbstractThe ability to learn and follow abstract rules relies on intact prefrontal regions including the lateral prefrontal cortex (LPFC) and the orbitofrontal cortex (OFC). Here, we investigate the specific roles of these brain regions in learning rules that depend critically on the formation of abstract concepts as opposed to simpler input-output associations. To this aim, we tested monkeys with bilateral removals of either LPFC or OFC on a rapidly learned task requiring the formation of the abstract concept of same vs. different. While monkeys with OFC removals were significantly slower than controls at both acquiring and reversing the concept-based rule, monkeys with LPFC removals were not impaired in acquiring the task, but were significantly slower at rule reversal. Neither group was impaired in the acquisition or reversal of a delayed visual cue-outcome association task without a concept-based rule. These results suggest that OFC is essential for the implementation of a concept-based rule, whereas LPFC seems essential for its modification once established.