bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining single-cell RNA-sequencing with a molecular atlas unveils new markers for C. elegans neuron classes
Authors: Lorenzo Ramiro , Onizuka Michiho , Defrance Matthieu , Laurent Patrick 
Published: November 2019

AbstractSingle-cell RNA-sequencing (scRNA-seq) of the Caenorhabditis elegans (C. elegans) nervous system offers the unique opportunity to obtain a partial expression profile for each neuron within a known connectome. Building on recent scRNA-seq data [1] and on a molecular atlas describing the expression pattern of ~800 genes at the single cell resolution [2], we designed an iterative clustering analysis aiming to match each cell-cluster to the ~100 anatomically defined neuron classes of C. elegans. This heuristic approach successfully assigned 58 clusters to their corresponding neuron class. Another 11 clusters grouped neuron classes sharing close molecular signatures and 7 clusters were not assigned. Based on these 76 molecular profiles, we designed 15 new neuron class-specific promoters validated in vivo. Amongst them, 10 represent the only specific promoter reported to this day, expanding the list of neurons amenable to genetic manipulations. Finally, we observed a differential expression of functionally relevant genes between sensory-, inter-, and motor neurons in C. elegans, suggesting the mode of functional diversification may vary accordingly to the neuronal modalities.
CyTOF reveals phenotypically-distinct human blood neutrophil populations differentially correlated with melanoma stage
Authors: Zhu Yanfang Peipei , Eggert Tobias , Araujo Daniel J. , Vijayanand Pandurangan , Ottensmeier Christian H. , Hedrick Catherine C. 
Published: November 2019

ABSTRACTUnderstanding neutrophil heterogeneity and its relationship to disease progression has become a recent focus of cancer research. Indeed, several studies have identified neutrophil subpopulations associated with pro- or anti-tumoral functions. However, this work has been hindered by the lack of widely-accepted markers with which to define neutrophil subpopulations. To identify markers of neutrophil heterogeneity in cancer, we utilized single-cell cytometry by time-of-flight (CyTOF) coupled with high-dimensional analysis on blood samples from treatment-naïve, melanoma patients. Our efforts allowed us to identify 7 blood-neutrophil clusters, including 2 previously identified individual populations. Interrogation of these neutrophil subpopulations revealed a positive trend between specific clusters and disease stage. Finally, we recapitulated these 7 blood-neutrophil populations via flow cytometry and found that they exhibit diverse capacities for phagocytosis and reactive oxygen species (ROS) production in vitro. In summary, our data provide a refined consensus on neutrophil-heterogeneity markers, enabling a prospective functional evaluation in patients with solid tumors.KEY POINTSCyTOF analysis reveals 7 blood neutrophil clusters correlating with melanoma stage in treatment-naïve patients.Neutrophil clusters by unbiased-calling are recapitulated by flow cytometry and harbor diverse phagocytic and ROS-producing capacities.
Formation of human long intergenic non-coding RNA genes and pseudogenes: ancestral sequences are key players
Authors: Delihas Nicholas 
Published: November 2019

AbstractPathways leading to formation of non-coding RNA and protein genes are varied and complex. We report finding a highly conserved repeat sequence present in both human and chimpanzee genomes that appears to have originated from a common primate ancestor. This sequence is repeatedly copied in human chromosome 22 (chr22) low copy repeats (LCR22) or segmental duplications and forms twenty-one different genes, which include human long intergenic non-coding RNA (lincRNA) gene and pseudogene families, as well as the gamma-glutamyltransferase (GGT) protein gene family and the RNA pseudogenes that originate from GGT sequences. In sharp contrast, only predicted protein genes stem from the homologous repeat sequence present in chr22 of chimpanzee. The data point to an ancestral DNA sequence, highly conserved through evolution and duplicated in humans by chromosomal repeat sequences that serves as a functional genomic element in the development of new and diverse genes in humans and chimpanzee.
An abundant quiescent stem cell population inDrosophilaMalpighian tubules protects principal cells from kidney stones
Authors: Wang Chenhui , Spradling Allan C. 
Published: November 2019

SummaryAdultDrosophilaMalpighian tubules have low rates of cell turnover but are vulnerable to damage caused by stones, like their mammalian counterparts, kidneys. We show thatDrosophilarenal stem cells (RSCs) comprise a unique, unipotent regenerative compartment. RSCs respond only to loss of nearby principal cells (PCs), cells critical for maintaining ionic balance. Perhaps due to the large size of PCs they are outnumbered by RSCs, which replace each lost cell with multiple PCs of lower ploidy. RSCs share a developmental origin with highly active intestinal stem cells (ISCs), and like ISCs generate daughters by asymmetric Notch signaling, yet RSCs remain quiescent in the absence of damage. Nevertheless, the capacity for RSC-mediated repair extends the lifespan of flies carrying kidney stones. We propose that abundant, RSC-like stem cells exist in other tissues with low rates of turnover where they may have been mistaken for differentiated tissue cells.
PHYTOCHROME INTERACTING FACTORs Trigger Environmentally Responsive Chromatin Dynamics
Authors: Willige Björn C. , Zander Mark , Phan Amy , Garza Renee M. , Trigg Shelly A. , He Yupeng , Nery Joseph R. , Chen Huaming , Ecker Joseph R. , Chory Joanne 
Published: November 2019

AbstractThe pivotal interplay between light receptors and PHYTOCHROME INTERACTING FACTORs (PIFs) serves as an essential regulatory hub that perceives and integrates environmental cues into the plant’s transcriptional networks. A critical control component of environmentally-responsive gene networks is the histone variant H2A.Z which provides transcriptional plasticity and prevents undesired gene activation. However, the functional relationship between PIF transcription factors and H2A.Z is only poorly understood. Here, we describe a genomic approach that utilizes the rapid and reversible light-mediated manipulation of PIF7 activity to visualize PIF7 DNA binding and H2A.Z occupancy kinetics. Strikingly, PIFs shape the H2A.Z landscape in a light quality-dependent manner. In addition, we observed that PIFs initiate H2A.Z eviction through direct interaction with EIN6 ENHANCER (EEN), a subunit of INO80 chromatin remodeling complex. These studies uncover a previously unknown PIF-INO80 regulatory module controlling plant growth in response to rapid environmental changes.One-sentence summaryA PIF-INO80 module controls light quality-dependent H2A.Z dynamics.
Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants
Authors: Zhang Siwei , Zhang Hanwen , Qiao Min , Zhou Yifan , Zhao Siming , Kozlova Alena , Shi Jianxin , Sanders Alan R. , Wang Gao , Sengupta Subhajit , West Siobhan , Streit Michael , Cowan Chad A. , Chen Mengjie , Pang Zhiping P. , Gejman Pablo V. , He Xin , Duan Jubao 
Published: November 2019

AbstractFunctional interpretation of noncoding disease variants, which likely regulate gene expression, has been challenging. Chromatin accessibility strongly influences gene expression during neurodevelopment; however, to what extent genetic variants can alter chromatin accessibility in the context of brain disorders/traits is unknown. Using human induced pluripotent stem cell (iPSC)-derived neurons as a neurodevelopmental model, we identified abundant open-chromatin regions absent in adult brain samples and thousands of genetic variants exhibiting allele-specific open-chromatin (ASoC). ASoC variants are overrepresented in brain enhancers, transcription-factor-binding sites, and quantitative-trait-loci associated with gene expression, histone modification, and DNA methylation. Notably, compared to open chromatin regions and other commonly used functional annotations, neuronal ASoC variants showed much stronger enrichments of risk variants for various brain disorders/traits. Our study provides the first snapshot of the neuronal ASoC landscape and a powerful framework for prioritizing functional disease variants.One Sentence SummaryAllele-specific open chromatin informs functional disease variants
Detection and treatment strategy for Tritrichomonas muris in the common laboratory mouse
Authors: Da Costa Andreia S. , Graham Tisha M. , Duncan Jennifer A. , Pillai Smitha P.S. , Lund Jennifer M. 
Published: November 2019

SummaryMaintaining a specific pathogen-free (SPF) mouse colony is critical to avoid potentially confounding variables introduced by unknown infections. Here, we report an instance of protozoan Tritrichomonas muris (T. muris) infection of mice within an SPF facility. Although T. muris has been considered a commensal organism, we observed instances of asymmetric infection in gene-knockout mice as compared to wild-type mice. We utilized treatment with metronidazole and confirmed successful elimination of T. muris from our SPF colony using extraction of fecal DNA followed by PCR detection. We propose that T. muris testing should be considered for SPF mice, particularly in immunity studies.
High Yield Monolayer Graphene Grids for Near-Atomic Resolution Cryo-Electron Microscopy
Authors: Han Yimo , Fan Xiao , Wang Haozhe , Zhao Fang , Tully Christopher G. , Kong Jing , Yao Nan , Yan Nieng 
Published: November 2019

AbstractCryogenic electron microscopy (cryo-EM) has become one of the most powerful techniques to reveal the atomic structures and working mechanisms of biological macromolecules. New designs of the cryo-EM grids—aimed at preserving thin, uniform vitrified ice and improving protein adsorption—have been considered a promising approach to achieving higher resolution with the minimal amount of materials and data. Here, we describe a method for preparing graphene cryo-EM grids with 99% monolayer graphene coverage that allows for more than 70% grid squares for effective data acquisition with improved image quality and protein density. Using our graphene grids, we have achieved 2.6 Å resolution for streptavidin, with a molecular weight of 52 kDa, from 11,000 particles. Our graphene grids increase the density of examined soluble, membrane, and lipo-proteins by at least five times, affording the opportunity for structural investigation of challenging proteins which cannot be produced in large quantity. In addition, our method employs only simple tools that most structural biology laboratories can access. Moreover, our approach allows for customized grid designs targeting specific proteins, due to its broad compatibility with a variety of nanomaterials.Significance statementSingle particle cryogenic electron microscopy (cryo-EM) represents the cutting-edge technology to determine three-dimensional atomic structures of bio-macromolecules. However, issues of cryo-sample preparation limit the cryo-EM to achieve higher resolution. Here, we demonstrated a high yield, monolayer graphene supporting film to improve the cryo-sample quality. Using our approach, we have achieved so far, the highest resolution structure of the smallest protein by cryo-EM with the minimal number of datasets. Our technique paves the way for universal cryo-sample preparation for near-atomic resolution cryo-EM.
Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data
Authors: Huang Qianhui , Liu Yu , Du Yuheng , Garmire Lana X. 
Published: November 2019

AbstractAnnotating cell types is a critical step in single cell RNA-Seq (scRNA-Seq) data analysis. Some supervised/semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking to provide practical guidelines. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-Seq analysis. In this study, we evaluated ten cell-type annotation methods publicly available as R packages. Eight of them are popular methods developed specifically for single cell research (Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, SCINA). The other two methods are repurposed from deconvoluting DNA methylation data: Linear Constrained Projection (CP) and Robust Partial Correlations (RPC). We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data. We assessed the accuracy through intra-dataset and inter-dataset predictions, the robustness over practical challenges such as gene filtering, high similarity among cell types, and increased classification labels, as well as the capabilities on rare and unknown cell-type detection. Overall, methods such as Seurat, SingleR, CP, RPC and SingleCellNet performed well, with Seurat being the best at annotating major cell types. Also, Seurat, SingleR, CP and RPC are more robust against down-sampling. However, Seurat does have a major drawback at predicting rare cell populations, and it is suboptimal at differentiating cell types that are highly similar to each other, while SingleR and RPC are much better in these aspects. All the codes and data are available at: https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark.
Abundance, density, and social structure of African forest elephants (Loxodonta cyclotis) in a human-modified landscape in southwestern Gabon
Authors: Brand Colin M. , Johnson Mireille B. , Parker Lillian D. , Maldonado Jesús E. , Korte Lisa , Vanthomme Hadrien , Alonso Alfonso , Ruiz-Lopez Maria Jose , Wells Caitlin P. , Ting Nelson 
Published: November 2019

AbstractThe noninvasive monitoring of population size and demography is critical to effective conservation, but forest living taxa can be difficult to directly observe due to elusiveness and/or inaccessible habitat. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters focusing specifically on population size and density using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas, which is considered a global stronghold for forest elephants in southwestern Gabon. Additionally, we examined forest elephant sociality through analysis of social networks, predicting that we would find matrilineal structure as exhibited by savanna elephants and other forest elephants. Given 95% confidence intervals, we estimate the size of the population in the sampled area to be between 754 and 1,502 individuals and our best density estimate ranges from 0.47 to 0.80 elephants per km2. When extrapolated across the entire Industrial Corridor, this estimate suggests an elephant population size of 3,033 to 6,043 in this area based on abundance or 1,684 to 2,832 based on density, which is 40 – 83% smaller than previously suggested. Furthermore, our social network analysis revealed approximately half of network components included females with different mitochondrial haplotypes; this suggests a wider range of variation in forest elephant sociality than has previously been reported. This study emphasizes the threatened status of forest elephants and demonstrates the need to further refine baseline estimates of population size and knowledge on social behavior in this taxon, both of which will aid in determining how population dynamics in this keystone species may be changing through time in relation to increasing conservation threats.
The antimalarial natural product salinipostin A identifies essential α/β serine hydrolases involved in lipid metabolism inP. falciparumparasites
Authors: Yoo Euna , Schulze Christopher J. , Stokes Barbara H. , Onguka Ouma , Yeo Tomas , Mok Sachel , Gnädig Nina F. , Zhou Yani , Kurita Kenji , Foe Ian T. , Terrell Stephanie M. , Boucher Michael J. , Cieplak Piotr , Linington Roger G. , Long Jonathan Z. , Uhlemann Anne-Catrin , Weerapana Eranthie , Fidock David A. , Bogyo Matthew 
Published: November 2019

SUMMARYSalinipostin A (Sal A) is a potent antimalarial marine natural product with an undefined mechanism of action. Using a Sal A-derived activity-based probe, we identify its targets in thePlasmodium falciparumparasite. All of the identified proteins contain α/β serine hydrolase domains, and several are essential for parasite growth. One of the essential targets displays high homology to human monoacylglycerol lipase (MAGL) and is able to process lipid esters including a MAGL acylglyceride substrate. This Sal A target is inhibited by the anti-obesity drug Orlistat, which disrupts lipid metabolism and produces disorganized and stalled schizonts similar to Sal A. Resistance selections yielded parasites that showed only minor reductions in sensitivity and that acquired mutations in a protein linked to drug resistance inToxoplasma gondii. This inability to evolve efficient resistance mechanisms combined with the non-essentiality of human homologs makes the serine hydrolases identified here promising antimalarial targets.
Biomolecular AFM viewer
Authors: Amyot Romain , Flechsig Holger 
Published: November 2019

AbstractWe developed a stand-alone software which allows to transform biomolecular structures and movies of their conformational dynamics into a representation which corresponds to the outcome of biomolecular atomic force microscopy (AFM) experiments, such as high-speed AFM. The software implements a high degree of usability. An integrated highly versatile molecular viewer allows the visualization of structures and their corresponding simulated AFM representations in arbitrary orientations. The obtained results can be conveniently exported as still images and movies. We provide a demonstration of our biomolecular AFM viewer by applying it to several proteins from the Protein Data Bank, and to a molecular movie of conformational transitions between two protein structures obtained from a modelling server.
Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples
Authors: Street Teresa L. , Barker Leanne , Sanderson Nicholas D. , Kavanagh James , Hoosdally Sarah , Cole Kevin , Newnham Robert , Selvaratnam Mathyruban , Andersson Monique , Llewelyn Martin J. , O’Grady Justin , Crook Derrick W. , Eyre David W. ,   the GonFast Investigators Group, Rees Joanna , Lord Emily , Soni Suneeta , Richardson Celia , Jessop Joanne , Adams Tanya 
Published: November 2019

AbstractBackgroundEmpirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance.MethodsWe investigated if Nanopore sequencing can detect sufficient N. gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. We used N. gonorrhoeae spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced whilst minimizing contaminating host DNA.ResultsIn simulated infections the Qiagen UCP Pathogen Mini kit provided the highest ratio N. gonorrhoeae to human DNA and the most consistent results. Depletion of human DNA with saponin increased N. gonorrhoeae yields in simulated infections, but decreased yields in clinical samples. In ten urine samples from men with symptomatic urethral gonorrhoea, ≥87% coverage of an N. gonorrhoeae reference genome was achieved in all samples, with ≥92% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections if ≥104 CFU/ml of N. gonorrhoeae was present, sequencing of the large majority of the genome was frequently achieved. N. gonorrhoeae could also be detected from urine in cobas PCR Media tubes and from urethral swabs, and in the presence of simulated Chlamydia co-infection.ConclusionUsing Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture.
Identification of a novel tedizolid resistance mutation in rpoB of methicillin-resistant Staphylococcus aureus
Authors: Shen Tianwei , Penewit Kelsi , Waalkes Adam , Xu Libin , Salipante Stephen J. , Nath Abhinav , Werth Brian J. 
Published: November 2019

AbstractA tedizolid-resistant isolate of MRSA was selected by serial passage. Whole genome sequencing revealed only a single nucleotide variant in rpoB. Cross-resistance to linezolid, chloramphenicol, and quinupristin-dalfopristin was observed but susceptibility to other drugs including rifampin was unchanged. Models of the RNA-polymerase-ribosomal complex revealed that the mutated residue was unlikely to interact directly with the oxazolidinone binding site. This is the first time that rpoB mutation has been associated with resistance to the PhLOPSa antimicrobials.
High-sensitivity assessment of phagocytosis by persistent association-based normalization
Authors: de Neergaard Therese , Sundwall Martin , Nordenfelt Pontus 
Published: November 2019

AbstractPhagocytosis is measured as a functional outcome in many research fields but can be challenging to quantify accurately, with no robust method available for cross-laboratory reproducibility. Here, we identified a simple, measurable parameter – persistent prey-phagocyte association – to use for normalization and dose-response analysis. We apply this in a straightforward analytical method, persistent association-based normalization (PAN), where first the multiplicity of prey (MOP) ratio needed to elicit half of the phagocytes to associate persistently (MOP50) is determined. MOP50is then applied to normalize for experimental factors, with adhesion and internalization analyzed separately. We use THP-1 cells and different prey and opsonization conditions to compare the PAN method to standard ways of assessing phagocytosis, and find it better in all cases, with increased robustness, sensitivity, and reproducibility. The approach is easily incorporated into most existing phagocytosis assays and allows for reproducibly comparing results across experiments and laboratories with high sensitivity.
The Pleiades cluster of fungal effector genes inhibit host defenses
Authors: Navarrete Fernando , Grujic Nenad , Stirnberg Alexandra , Aleksza David , Gallei Michelle , Adi Hazem , Bindics Janos , Trujillo Marco , Djamei Armin 
Published: November 2019

SummaryBiotrophic plant pathogens secrete effector proteins to manipulate the host physiology. Effectors suppress defenses and induce an environment favorable to disease development. Sequence-based prediction of effector function is difficulted by their rapid evolution rate. In the maize pathogen Ustilago maydis, effector-coding genes frequently organize in clusters. Here we describe the functional characterization of the pleiades, a cluster of ten symplastic effectors. Deletion of the pleiades leads to strongly impaired virulence and accumulation of reactive oxygen species (ROS) in infected tissue. Eight of the Pleiades suppress the production of ROS upon perception of pathogen associated molecular patterns (PAMPs). Although genetically redundant, the Pleiades target different host components. The paralogs Taygeta1 and Merope1 suppress ROS production in either the cytoplasm or nucleus, respectively. Merope1 targets and promotes the autoubiquitination activity of RFI2, a conserved family of E3 ligases that regulates the production of PAMP-triggered ROS burst and influences flowering time in plants.