bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal Gut Microbial Changes Predict RecurrentClostridium difficilein Patients with and without Ulcerative Colitis
Authors: Lee Allen A. , Rao Krishna , Limsrivilai Julajak , Gillilland Merritt , Malamet Benjamin , Briggs Emily , Young Vincent B. , Higgins Peter DR 
Published: May 2019

ABSTRACTBackgroundUlcerative colitis (UC) carries an increased risk of primary and recurrentClostridium difficileinfection (rCDI) and CDI is associated with UC flares. We hypothesized that specific fecal microbial changes associate with UC flare and rCDI.MethodsWe conducted a prospective observational cohort study of 57 patients with UC and CDI, CDI only, and UC flare only. Stool samples were collected at baseline, at the end of antibiotic therapy, and after reconstitution for 16S rRNA sequencing. The primary outcomes were recurrent UC flare and rCDI. Logistic regression and Lasso models were constructed for analysis.ResultsThere were 21 (45.7%) patients with rCDI, while 11 (34.4%) developed UC flare. Patients with rCDI demonstrated significant inter-individual (P=.008) and intra-individual differences (P=.004 relative to baseline samples) in community structure by Jensen-Shannon distance (JSD) compared with non-rCDI. Two cross-validated models identified by Lasso regression predicted risk of rCDI: a baseline model with female gender, hospitalization for UC in the past year, increased Ruminococcaceae and Verrucomicrobia, and decreased Eubacteriaceae, Enterobacteriaceae, Lachnospiraceae, and Veillonellaceae (AuROC=0.94); and a model 14 days after completion of antibiotics with female gender, increased Shannon diversity, Ruminococcaceae and Enterobacteriaceae, and decreased community richness and Faecalibacterium (AuROC=0.9). Adding JSD between baseline and post-treatment samples to the latter model improved fit (AuROC=0.94). A baseline model including UC hospitalization in the past year and increased Bacteroidetes showed good fit characteristics for predicting increased risk of UC flare (AuROC=0.88).ConclusionFecal microbial features at baseline and following therapy predict rCDI risk in patients with and without UC. These results may help risk stratify patients to guide management.
Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans
Authors: Knaus Brian J. , Tabima Javier F. , Shakya Shankar K. , Judelson Howard S. , Grünwald Niklaus J. 
Published: May 2019

AbstractThe plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative genomic analysis of 47 high coverage genomes to infer changes in genic copy number. We included samples from sexual populations at the center of origin as well as several dominant clonal lineages sampled worldwide. We conclude that sexual populations at the center of origin are diploid as was the lineage that caused the famine, while modern clonal lineages showed increased copy number (3x). Copy number variation (CNV) was found genome-wide and did not to adhere to the two-speed genome hypothesis. Although previously reported, tetraploidy was not found in any of the genomes evaluated. We propose a model of super-fit clone emergence supported by the epidemiological record (e.g., EU_13_A2, US-11, US-23) whereby higher copy number provides fitness leading to replacement of prior clonal lineages.
Community-level signatures of ecological succession in natural bacterial communities
Authors: Pascual-García Alberto , Bell Thomas 
Published: May 2019

AbstractA central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We present an integrative top-down analysis of over 700 bacterial communities sampled from water-filled beech tree-holes in the United Kingdom at distances between <5m to >100km, combining an analyses of community composition (16S rRNA sequencing) with assays of community functional capacity (exo-enzymatic activities, ATP production, CO2 dissipation and yield). The communities were grown in laboratory conditions in a complex growth medium, what allowed us to investigate the relationship between composition and function, excluding confounding environmental factors. We found a distance-decay trend in the similarity of the communities, and simulated data allowed us to reject the hypothesis that stochastic processes dominated the assembly of the communities, suggesting that niche effects prevailed. Consistent with this idea, clustering of communities lead us to identify six distinct community classes encompassing samples collected at often distant locations. Using structural equation modelling, we explored how functions were interrelated, demonstrating that a representative functional signature can be associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions with PiCRUST. Notably, this approach allowed us to show that these classes contain distinct genetic repertoires reflecting community-level ecological strategies. We finally formulated an over-arching ecological hypothesis about how local conditions drive succession in these habitats. The ecological strategies resemble the classical distinction between r- and K-strategists and could be extrapolated to other systems, suggesting that a coarse grained picture of microbial ecological succession may be explained by relatively simple ecological mechanisms.
De-risking drug discovery of intracellular targeting peptides: screening strategies to eliminate false-positive hits
Authors: Ng Simon , Juang Yu-Chi , Chandramohan Arun , Kristal Kaan Hung Yi , Sadruddin Ahmad , Yuen Tsz Ying , Ferrer Fernando J. , Lee Xue’Er Cheryl , Xi Liew , Johannes Charles W. , Brown Christopher J. , Kannan Srinivasaraghavan , Aronica Pietro G. , Berglund Nils , Verma Chandra S. , Liu Lijuan , Stoeck Alexander , Sawyer Tomi K. , Partridge Anthony W. , Lane David P. 
Published: May 2019

AbstractDiscovery of false-positive target binding, due to assay interference or aggregation, presents a significant problem for drug discovery programs. These issues may often be unrealized and could lead researchers astray if not subject to independent verification of reproducibility and/or on-target mechanism of action. Although well-documented for small molecules, this issue has not been widely explored for peptide modality. As a case study, we demonstrate that two purported KRas inhibitors, stapled peptide SAH-SOS1A and macrocyclic peptide cyclorasin 9A5, exemplify false-positive molecules – both in terms of their sub-micromolar KRas binding affinities and their on-target cellular activities. We observed that the apparent binding of fluorescein-labeled SAH-SOS1A given by a fluorescence polarization assay is sensitive to detergent. False-positive readouts can arise from peptide adsorption to the surface of microplates. Hence, we used surface plasmon resonance and isothermal titration calorimetry to unambiguously show that both SAH-SOS1A and cyclorasin 9A5 are non-binders for KRas. Thermal shift assay and hydrogen-deuterium exchange mass spectrometry further demonstrate that both peptides destabilize KRas and induce unfolding of the protein. Furthermore, both peptides caused significant release of intracellular lactate dehydrogenase, suggesting that membrane rupture rather than on-target activity is accountable for their reported cytotoxicity. Finally, both peptides exhibited off-target activities by inhibiting the proliferation of U-2 OS and A549 cells, despite their independency of the KRas signaling pathway. Our findings demonstrate the critical need to employ orthogonal binding assays and cellular counter-screens to de-risk false-positive molecules. More rigorous workflows should lead to improved data and help obviate inadvertent scientific conclusions.Significance statementFalse positive molecule hits occur frequently in high-throughput screens and can contaminate the scientific literature. This has become an increasingly serious issue in small molecule drug discovery and chemical probe development and it is not surprising that peptides may be similarly prone to assay interference. Using KRas as a target and two known macrocyclic peptide inhibitors as a case study, we clearly show that reporter-free biophysical assays and cellular counter-screens offer the solution to detect and de-risk the potential of false-positive compounds. We further discuss the advantages, limitations and overall strategic importance of such methods.
Clinical manifestations and phenotypic analysis of new ANK1 gene mutations in 12 Chinese children with hereditary spherocytosis
Authors: Xie Fei , Lei Lei , Cai Bin , Gan Lu , Gao Yu , Liu Xiaoying , Zhou Lin , Jiang Jinjin 
Published: May 2019

AbstractObjectiveTo summarize the clinical features and laboratory examination of ANK1 gene in 12 children with hereditary spherocytosis in China, and to determine the genetic mutations in those children.MethodsThe clinical data of children and their parents were collected and analyzed. The sequence of related genes was analyzed by second-generation sequencing technology. The suspected pathogenic mutations were detected by Sanger sequencingResultsNew mutations in the coding region of ANK1 was detected in 12 patients, which caused amino acid changes in the gene encoding, causing structural changes or loss of function.ConclusionANK1 (c.1914_c.1918delTTTG), ANK1 (c.399T>G), ANK1 (c.1564delC), ANK1 (c.4439dupA<br>), ANK1 (c.4510_4513del), ANK1 (c.2961delC), ANK1 (c.2142dupT), ANK1 (c.2858+1G>C), ANK1 (c.3235delG), ANK1 (c.4739A>G), ANK1 (c.2638-2 A>G), ANK1 (c. 4739A>G) mutations in the coding region of the gene are the cause of suspicious disease in these 12 Chinese children. At the same time, second-generation gene sequencing technology is an effective means of confirming HS. Different types of mutations (P=0.388)and different mutation areas (P=0.660)had no significant effect on the severity of anemia. The 12 gene mutation sites in this study have not been included in the human genome database, dbSNP (v138) and ExAC databases. The new ANK1 gene mutations found in HS children can provide further exploration of the genetic etiology of HS in Chinese population.
Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan
Authors: Matsuoka Shunsuke , Sugiyama Yoriko , Sato Hirotoshi , Katano Izumi , Harada Ken , Doi Hideyuki 
Published: May 2019

AbstractGrowing evidence has revealed high diversity and spatial heterogeneity of fungal communities including in local habitats in terrestrial ecosystems. These findings highlight the considerable sampling effort, analysis time, and costs required for the investigation of fungal diversity over large spatial scales. Recently, the analysis of environmental DNA in river water has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. However, previous studies have not investigated the spatial structure of fungal DNA assemblages in river water. In the present study, we investigate fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding in water across different branches of river over forest landscapes. The river water was found to contain both phylogenetically and functionally diverse fungal DNA, including aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, branches. In addition, the assemblages were more similar between spatially closer branches. These results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure can be obtained by investigating the fungal DNA assemblages in river water.
Modality-specific circuits for skylight orientation in the fly visual system
Authors: Sancer Gizem , Kind Emil , Plazaola Haritz , Balke Jana , Pham Tuyen , Hasan Amr , Münch Lucas , Mathejczyk Thomas F. , Wernet Mathias F. 
Published: May 2019

AbstractIn the fly optic lobe ∼800 highly stereotypical columnar microcircuits are arranged retinotopically to process visual information. Differences in cellular composition and synaptic connectivity within functionally specialized columns remains largely unknown. Here we describe the cellular and synaptic architecture in medulla columns located downstream of photoreceptors in the ‘dorsal rim area’ (DRA), where linearly polarized skylight is detected for guiding orientation responses. We show that only in DRA medulla columns, both R7 and R8 photoreceptors target to the bona fide R7 target layer where they form connections with previously uncharacterized, modality-specific Dm neurons: Two morphologically distinct DRA-specific cell types (termed Dm-DRA1 and Dm-DRA2) stratify in separate sublayers and exclusively contact polarization-sensitive DRA inputs, while avoiding overlaps with color-sensitive Dm8 cells. Using the activity-dependent GRASP and trans-Tango techniques, we confirm that DRA R7 cells are synaptically connected to Dm-DRA1, whereas DRA R8 form synapses with Dm-DRA2. Finally, using live imaging of ingrowing pupal photoreceptor axons, we show that DRA R7 and R8 termini reach layer M6 sequentially, thus separating the establishment of different synaptic connectivity in time. We propose that a duplication of R7→Dm circuitry in DRA ommatidia serves as an ideal adaptation for detecting linearly polarized skylight using orthogonal e-vector analyzers.
A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system
Authors: Gillingham Mark A.F. , Montero B. Karina , Wihelm Kerstin , Grudzus Kara , Sommer Simone , Santos Pablo S.C. 
Published: May 2019

ABSTRACTGenotyping novel complex multigene systems is particularly challenging in non-model organisms. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most next-generation sequencing genotyping pipelines have been validated in non-model systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable. Further hindering accurate genotyping, the relationship between artefacts and copy number variation (CNV) within a PCR remains poorly described. Here we investigate the latter by experimentally combining multiple known major histocompatibility complex (MHC) haplotypes of a model organism (chicken, Gallus gallus, 43 artificial genotypes with 2-13 alleles per amplicon). In addition to well defined “optimal” primers, we simulated a non-model species situation by designing “naive” primers, with sequence data from closely related Galliform species. We applied a novel open-source genotyping pipeline (ACACIA) to the data, and compared its performance with another, previously published, pipeline. ACACIA yielded very high allele calling accuracy (>98%). Non-chimeric artefacts increased linearly with increasing CNV but chimeric artefacts leveled when amplifying more than 4-6 alleles. As expected, we found heterogeneous amplification efficiency of allelic variants when co-amplifying multiple loci. Using our validated ACACIA pipeline and the example data of this study, we discuss in detail the pitfalls researchers should avoid in order to reliably genotype complex multigene systems. ACACIA and the datasets used in this study are publicly available at GitLab and FigShare (https://gitlab.com/psc_santos/ACACIAandhttps://figshare.com/projects/ACACIA/66485).
Programmed Switch in The Mitochondrial Degradation Pathways During Human Retinal Ganglion Cell Differentiation from Stem Cells is Critical for RGC Survival
Authors: Das Arupratan , Bell Claire M. , Berlinicke Cynthia A. , Marsh-Armstrong Nicholas , Zack Donald J. 
Published: May 2019

ABSTRACTRetinal ganglion cell (RGC) degeneration is the root cause for vision loss in glaucoma as well as in other forms of optic neuropathies. Genetic analysis indicated abnormal mitochondrial quality control (MQC) as a major risk factor for optic neuropathies. However, nothing is known on how MQC regulates human retinal ganglion cell (hRGC) health and survival. Human pluripotent stem cells (hPSCs) provide opportunity to differentiate hRGCs and understand the abnormal MQC associated hRGC degeneration in great detail. Degradation of damaged mitochondria is a very critical step of MQC, here we have used stem cell derived hRGCs to understand the damaged mitochondrial degradation pathways for hRGC survival. Using pharmacological methods, we have investigated the role of the proteasomal and endo-lysosomal pathways in degrading damaged mitochondria in hRGCs and their precursor stem cells. We find that upon mitochondrial damage with the proton uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP), hRGCs more efficiently degraded mitochondria than their precursor stem cells. We further identified that for degrading damaged mitochondria, stem cells predominantly use the ubiquitine-proteasome system (UPS) while hRGCs use the endo-lysosomal pathway. UPS inhibition causes apoptosis in stem cells, while hRGC viability is dependent on the endo-lysosomal pathway but not on the UPS pathway. This suggests manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating glaucoma. Endo-lysosome dependent cell survival is also conserved for other human neurons as differentiated human cerebral cortical neurons also degenerated upon endo-lysosomal inhibition but not for the proteasome inhibition.SIGNIFICANCE STATEMENTUsing human stem cells we have shown a switch in the mitochondrial degradation pathway during hRGC differentiation where endo-lysosomal pathway becomes the predominant pathway for cellular homeostasis and hRGC survival which is also true for human cortical neurons. These findings suggest manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating glaucoma as well as for other neurodegenerative diseases.
The coordination of spindle-positioning forces during the asymmetric division of theC. eleganszygote is revealed by distinct microtubule dynamics at the cortex
Authors: Bouvrais H. , Chesneau L. , Cunff Y. Le , Fairbrass D. , Soler N. , Pastezeur S. , Pécot T. , Kervrann C. , Pécréaux J. 
Published: May 2019

ABSTRACTIn theCaenorhabditis eleganszygote, astral microtubules generate forces, pushing against and pulling from the cell periphery. They are essential to position the mitotic spindle. By measuring the dynamics of astral microtubules at the cortex, we revealed the presence of two populations, residing there for 0.4 s and 1.8 s, which correspond to the pulling and pushing events, respectively. Such an experiment offers a unique opportunity to monitor both forces that position the spindle under physiological conditions and study their variations along the anteroposterior axis (space) and the mitotic progression (time). By investigating pulling-force-generating events at the microscopic level, we showed that an anteroposterior asymmetry in dynein on-rate – encoding pulling-force imbalance – is sufficient to cause posterior spindle displacement. The regulation by spindle position – reflecting the number of microtubule contacts in the posterior-most region – reinforces this imbalance only in late-anaphase. Furthermore, we exhibited the first direct proof that the force-generator increasing persistence to pull (processivity) accounts for the temporal control of pulling force throughout mitosis. We thus propose a three-fold control of pulling force, by the polarity, spindle position and mitotic progression. Focusing on pushing force, we discovered a correlation between its density and the stability of the spindle position during metaphase, which strongly suggests that the pushing force contributes to maintaining the spindle at the cell centre. This force remains constant and symmetric along the anteroposterior axis during the division. The pulling one increases in intensity and becomes dominant at anaphase. In conclusion, the two-population study enabled us to decipher the complex regulation of the spindle positioning during cell division.
Novel differential linear B-cell epitopes to identify Zika and dengue virus infections in patients
Authors: Amrun Siti Naqiah , Yee Wearn-Xin , Bakar Farhana Abu , Lee Bernett , Kam Yiu-Wing , Lum Fok-Moon , Tan Jeslin J.L. , Lim Vanessa W.X. , Watthanaworawit Wanitda , Ling Clare , Nosten Francois , Renia Laurent , Leo Yee-Sin , Ng Lisa F.P. 
Published: May 2019

AbstractBackgroundRecent Zika virus (ZIKV) outbreaks challenged existing laboratory diagnostic standards, especially for serology-based methods. Due to the genetic and structural similarity of ZIKV with other flaviviruses, this results in cross-reactive antibodies which confounds serological interpretations.MethodsPlasma from Singapore ZIKV patients was screened longitudinally for antibody responses and neutralizing capacities against ZIKV. Samples from healthy controls, ZIKV and DENV patients were further assessed using ZIKV and DENV peptides of precursor membrane (prM), envelope (E) or non-structural 1 (NS1) viral proteins in a peptide-based ELISA for epitope identification. Identified epitopes were re-validated and diagnostically evaluated using sera of patients with DENV, bacteria or unknown infections from Thailand.ResultsLong-lasting ZIKV-neutralizing antibodies were elicited during ZIKV infection. Thirteen potential linear B-cell epitopes were identified and of these, four common flavivirus, three ZIKV-specific, and one DENV-specific differential epitopes had more than 50% sensitivities and specificities. Notably, ZIKV-specific peptide 26 on domain I/II of E protein (amino acid residues 271-288) presented 80% sensitivity and 85.7% specificity. Importantly, the differential epitopes also showed significance in differentiating non-flavivirus patient samples.ConclusionsLinear B-cell epitope candidates to differentiate ZIKV and DENV infections were identified, providing the first step towards the design of a much-needed serology-based assay.
Myeloid Lineage Enhancers Drive Oncogene Synergy in CEBPA/CSF3R Mutant Acute Myeloid Leukemia
Authors: Braun Theodore P. , Okhovat Mariam , Coblentz Cody , Carratt Sarah A. , Foley Amy , Schonrock Zachary , Nevonen Kimberly , Davis Brett , Garcia Brianna , LaTocha Dorian , Weeder Benjamin R. , Grzadkowski Michal R. , Estabrook Joey C. , Manning Hannah G. , Watanabe-Smith Kevin , Smith Jenny L. , Leonti Amanda R. , Ries Rhonda E. , Jeng Sophia , McWeeney Shannon , Genua Cristina Di , Drissen Roy , Nerlov Claus , Meshinchi Soheil , Carbone Lucia , Druker Brian J. , Maxson Julia E. 
Published: May 2019

ABSTRACTAcute Myeloid Leukemia (AML) develops due to the acquisition of mutations from multiple functional classes. Here, we demonstrate that activating mutations in the granulocyte colony stimulating factor receptor (CSF3R), cooperate with loss of function mutations in the transcription factor CEBPA to promote acute leukemia development. This finding of mutation-synergy is broadly applicable other mutations that activate the JAK/STAT pathway or disrupt CEBPA function (i.e. activating mutations in JAK3 and Core Binding Factor translocations). The interaction between these distinct classes of mutations occurs at the level of myeloid lineage enhancers where mutant CEBPA prevents activation of subset of differentiation associated enhancers. To confirm this enhancer-dependent mechanism, we demonstrate that CEBPA mutations must occur as the initial event in AML initiation, confirming predictions from clinical sequencing data. This improved mechanistic understanding will facilitate therapeutic development targeting the intersection of oncogene cooperativity.