bluuebunny/crossref_metadata_2025 huggingface dataset:
Notes on the threatened lowland forests of Mt Cameroon and their endemics including Drypetes njonji sp. nov., with a key to species of Drypetes sect. Stipulares (Putranjivaceae)
Authors: Cheek Martin , Ndam Nouhou , Budden Andrew
Published: November 2019

Background and aims

This paper reports a further discovery of a new endemic threatened species to science in the context of long-term botanical surveys in the lowland coastal forests of Mount Cameroon specifically and generally in the Cross River-Sanaga interval of west-central Africa. These studies focus on species discovery and conservation through the Tropical Important Plant Areas programme.

Methods

Normal practices of herbarium taxonomy have been applied to study the material collected. The relevant collections are stored in the Herbarium of the Royal Botanic Gardens, Kew, London and at the Limbe Botanic Garden, Limbe, and the Institute of Research in Agronomic Development – National Herbarium of Cameroon, Yaoundé.

Key results

New species to science continue to be discovered from Mt Cameroon. Most of these species are rare, highly localised, and threatened by habitat destruction. These discoveries increase the justification for improved conservation management of surviving habitat. Drypetes njonji is described as an additional species new to science and appears to be endemic to the lowland coastal forests at the foot of Mt Cameroon. It is placed in and keyed out in Sect. Stipulares, a group confined to Lower Guinea. The conservation status of Drypetes njonji is assessed as Endangered (EN B1+2ab(iii)) according to the 2012 criteria of IUCN. An updated overview of the lowland plant endemics of Mt Cameroon is presented.
From plant populations to communities: using hierarchical trait environment relationships to reveal within ecosystem filtering
Authors: Deschamps Lucas , Proulx Raphaël , Gross Nicolas , Rheault Guillaume , Maire Vincent
Published: November 2019

Explaining the existence of highly diverse plant communities under strong abiotic filtering is a long-standing challenge in ecology. Hierarchical aspects of abiotic and biotic filters are rarely taken into account and studies focus mainly on community-level aggregated patterns. Because variations in biotic conditions might take place in short abiotic gradient and within the tolerance of species in regional pool, it is likely that biotic filtering will select individuals within species and adjust population characteristics. To challenge this idea, we replicated a diversity gradient in four highly contrasted wetlands with an almost complete species turn-over, sampling individuals in communities irrespective of their taxonomic identities or status. Using hierarchical distributional modelling, we analyzed the variation of the mean and dispersion of functional trait space at the ecosystem, community and species level. We found that the abiotic differences between ecosystems filtered species contrasted in their growth/nutrient conservation trade-off, while within ecosystems community variation were mainly due to the partitioning of canopy and leaf adaptations to light conditions. We found strong species-specific functional and demographic responses of dominant species along the diversity gradient, especially for traits linked to biomass and space occupation. Two contrasted strategies emerged, with species using plasticity to maintain equally dense populations, while others used plasticity to become overwhelmingly abundant when in favorable conditions. Our results demonstrate that within ecosystems, variation in biotic conditions selects individuals within populations, revealing the importance of phenotypic variation for a species to be maintained in more or less diverse communities. Because phenotypic variations are related to demographic responses, it offers a way to link the study of species diversity and eco-evolutionary dynamics.
Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats
Authors: Sajko Sara , Grishkovskaya Irina , Kostan Julius , Graewert Melissa , Setiawan Kim , Trübestein Linda , Niedermüller Korbinian , Gehin Charlotte , Sponga Antonio , Puchinger Martin , Gavin Anne-Claude , Leonard Thomas , Svergun Dimitri , Smith Terry K. , Morriswood Brooke , Djinovic-Carugo Kristina
Published: November 2019

MORN (Membrane Occupation and Recognition Nexus) repeat proteins have a wide taxonomic distribution, being found in both prokaryotes and eukaryotes. Despite this ubiquity, they remain poorly characterised at both a structural and a functional level compared to other common repeats. In functional terms, they are often assumed to be lipid-binding modules that mediate membrane targeting. We addressed this putative activity by focusing on a protein composed solely of MORN repeats –Trypanosoma bruceiMORN1. Surprisingly, no evidence for binding to membranes or lipid vesicles by TbMORN1 could be obtained either in vivo or in vitro. Conversely, TbMORN1 did interact with individual phospholipids. High- and low-resolution structures of the MORN1 protein fromTrypanosoma bruceiand homologous proteins from the parasitesToxoplasma gondiiandPlasmodium falciparumwere obtained using a combination of macromolecular crystallography, small-angle X-ray scattering, and electron microscopy. This enabled a first structure-based definition of the MORN repeat itself. Furthermore, all three structures dimerised via their C-termini in an antiparallel configuration. The dimers could form extended or V-shaped quaternary structures depending on the presence of specific interface residues. This work provides a new perspective on MORN repeats, showing that they are protein-protein interaction modules capable of mediating both dimerisation and oligomerisation.
A circuit mechanism for irrationalities in decision-making and NMDA receptor hypofunction: behaviour, computational modelling, and pharmacology
Authors: Cavanagh Sean E. , Lam Norman H. , Murray John D. , Hunt Laurence T. , Kennerley Steven W.
Published: November 2019

Decision-making biases can be systematic features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases in health and disease. Monkeys performed an evidence integration task in which they showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a neural mechanism for this behaviour. Because NMDA receptor (NMDA-R) hypofunction is a leading hypothesis for neuropathology in schizophrenia, we simulated behavioural effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were tested experimentally using the NMDA-R antagonist ketamine, yielding changes in decision-making consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent.

Significance

People can make apparently irrational decisions because of underlying features in their decision circuitry. Deficits in the same neural circuits may also underlie debilitating cognitive symptoms of neuropsychiatric patients. Here, we reveal a neural circuit mechanism explaining an irrationality frequently observed in healthy humans making binary choices – the pro-variance bias. Our circuit model could be perturbed by introducing deficits in either excitatory or inhibitory neuron function. These two perturbations made specific, dissociable predictions for the types of irrational decisionmaking behaviour produced. We used the NMDA-R antagonist ketamine, an experimental model for schizophrenia, to test if these predictions were relevant to neuropsychiatric pathophysiology. The results were consistent with impaired excitatory neuron function, providing important new insights into the pathophysiology of schizophrenia.
Aversion of the invasive Asian longhorned tick to the white-footed mouse, the dominant reservoir of tick-borne pathogens in the United States
Authors: Ronai Isobel , Tufts Danielle M. , Diuk-Wasser Maria A.
Published: November 2019

The Asian longhorned tick (Haemaphysalis longicornis) was reported for the first time in the United States of America in 2017 and has now spread across 12 states. The potential of this invasive tick vector to transmit pathogens will be determined through its association to native hosts, such as the white-footed mouse (Peromyscus leucopus) which is the primary reservoir for the causative agent of Lyme disease (Borrelia burgdorferi) and other zoonotic pathogens. We placed larval H. longicornis on P. leucopus, 65% of the larvae (n = 40) moved off the host within a short period of time and none engorged. In contrast, larval black-legged ticks (Ixodes scapularis) did not move from where they were placed in the ear of the mouse. We then conducted a laboratory behavioural assay to assess the interaction of H. longicornis with the hair of potential mammalian host species in the United States of America. H. longicornis larvae were less likely to enter the hair zone of P. leucopus and humans compared to the hair of domestic cats, domestic dogs, and white-tailed deer. Our study identifies a tick-host hair interaction behaviour, which can be quantified in a laboratory assay to predict tick-host associations and provides insights into how ticks select a host.
Landscape structure shapes tree seedlings’ diversity at multiple spatial scales in a fragmented tropical rainforest
Authors: Nicasio-Arzeta Sergio , Zermeño-Hernández Isela E. , Maza-Villalobos Susana , Benítez-Malvido Julieta
Published: November 2019

Biotic-dispersed tree seedling species are fundamental for the maintenance of the structure and function of forest patches in fragmented rainforest landscapes. Nonetheless, the effects of landscape structure and the spatial scale at which operates on seedling α- and β-diversity is unknown. Using a multi-scale approach, we assessed the relative effect of landscape composition (i.e., percentage of old-growth/secondary forest cover), configuration (i.e., aggregation/density of forest patches) and connectivity (i.e., structural and functional) on α- and β-diversity of biotic-dispersed seedlings in 16 forest patches in the Lacandona rainforest, Mexico. We assessed these effects at 13 spatial scales (from 300 to 1500 m radius, at 100 m intervals) for three α- and β-diversity orders (rare, common and dominant species). We found that patch aggregation increased species richness and reduced β-diversity of common and dominant species at similar spatial scales (500 to 600 m). Additionally, functional connectivity had a positive effect on the β-diversity of rare species in the 800 m spatial extent. These effects suggest that landscape configuration and functional connectivity sustain seedling diversity by preserving seed rain richness and the presence of large terrestrial herbivorous mammals. In contrast, the percentage of secondary forest matrix was detrimental for all α-diversity orders and the β-diversity of common and dominant species. Forthcoming conservation strategies should prevent deforestation, increase habitat amount and promote functional connectivity of forest-dependent fauna through matrix management actions.
Global Transcriptome Characterization and Assembly of Thermophilic AscomyceteChaetomium thermophilum
Authors: Singh Amit , Schermann Géza , Reislöhner Sven , Kellner Nikola , Hurt Ed , Brunner Michael
Published: November 2019

A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genomeChaetomium thermophilumhas been reported previously, but it is limited to open reading frames (ORFs) of genes and contains only a few noncoding transcripts. In this study, we identified and annotated by deep RNA sequencing full-length transcripts ofC.thermophilum.We annotated 7044 coding genes and a large number of noncoding genes (n=4567). Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help understanding the gene regulatory landscape inC.thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species. The R packages for gene and GO annotation database can be found underhttps://www.bzh.uni-heidelberg.de/brunner/Chaetomium_thermophilum.
Histone methyltransferase DOT1L controls state-specific identity during B cell differentiation
Authors: Aslam Muhammad Assad , Alemdehy Mir Farshid , Kwesi-Maliepaard Eliza Mari , Caganova Marieta , Pardieck Iris N. , van den Brand Teun , Muhaimin Fitriari Izzatunnisa , van Welsem Tibor , de Rink Iris , Song Ji-Ying , de Wit Elzo , Arens Ramon , Rajewsky Klaus , Jacobs Heinz , van Leeuwen Fred
Published: November 2019

Differentiation of naïve peripheral B cells into terminally differentiated plasma cells is characterized by epigenetic alterations, yet the epigenetic mechanisms that control B cell fate remain unclear. Here we identified a central role for the histone H3K79 methyltransferase DOT1L in controlling B cell differentiation. Murine B cells lackingDot1Lfailed to establish germinal centers (GC) and normal humoral immune responsesin vivo.In vitro, activated B cells showed aberrant differentiation and prematurely acquired plasma cell features. Mechanistically, combined epigenomics and transcriptomics analysis revealed that DOT1L promotes expression of a pro-proliferative, pro-GC program. In addition, DOT1L supports the repression of an anti-proliferative, plasma cell differentiation program by maintaining expression of the H3K27 methyltransferaseEzh2, the catalytic component of Polycomb Repressor Complex 2 (PRC2). Our findings show that DOT1L is a central modulator of the core transcriptional and epigenetic landscape in B cells, establishing an epigenetic barrier that warrants B cell naivety and GC B cell differentiation.
Oceans apart: Heterogeneous patterns of parallel evolution in sticklebacks
Authors: Fang Bohao , Kemppainen Petri , Momigliano Paolo , Feng Xueyun , Merilä Juha
Published: November 2019

An important model system for the study of genomic mechanisms underlying parallel ecological adaptation in the wild is the three-spined stickleback (Gasterosteus aculeatus), which has repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies have identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes, but these are typically based on limited geographic sampling and are biased towards studies in the Eastern Pacific. We analysed population genomic data from marine and freshwater ecotypes of three-spined sticklebacks with from a comprehensive global collection of marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Our findings highlight that most signatures of parallel evolution were unique to the Eastern Pacific. Trans-oceanic marine and freshwater differentiation was only found in a very limited number of genomic regions, including three chromosomal inversions. Using both simulations and empirical data, we demonstrate that this is likely due to both the stochastic loss of freshwater-adapted alleles during founder events during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which have reduced the amount of standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the existence of highly elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is also consistent with a secondary contact scenario between marine and freshwater populations that have evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies focused on Eastern Pacific populations have led us to believe, parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.
Inhibiting endoplasmic reticulum stress decreases tumor burden in a mouse model for hepatocellular carcinoma
Authors: Pavlovic Natasa , Calitz Carlemi , Thanapirom Kessarin , Mazza Giuseppe , Rombouts Krista , Gerwins Pär , Heindryckx Femke
Published: November 2019

Hepatocellular carcinoma (HCC) is a liver tumor that arises in patients with cirrhosis. Hepatic stellate cells are key players in the progression of HCC, as they create a fibrotic micro-environment and produce growth factors and cytokines that enhance tumor cell proliferation and migration. We assessed the role of endoplasmic reticulum (ER) stress in the cross-talk between stellate cells and HCC-cells. Mice with a fibrotic HCC were treated with the IRE1α-inhibitor 4μ8C, which reduced tumor burden and collagen deposition. By co-culturing HCC-cells with stellate cells, we found that HCC-cells induce ER-stress in stellate cells, thereby contributing to their activation. Inhibiting IRE1α blocked stellate cell activation, which inhibited tumor cell proliferation and migration in different in vitro 2D and 3D co-cultures. Our results suggest that IRE1α is an important mediator in the communication between stellate cells and cancer cells and components of the ER-stress pathway may be therapeutically relevant for HCC-patients.

Impact statement

IRE1α is an important mediator in the communication between stellate cells and cancer cells and components of the ER-stress pathway may be therapeutically relevant for liver cancer.
Cortisol-induced signatures of stress in the fish microbiome
Authors: Webster Tamsyn M. Uren , Rodriguez-Barreto Deiene , Consuegra Sofia , Garcia de Leaniz Carlos
Published: November 2019

Stress experienced in intensive aquaculture can compromise fish growth, condition and immunity. Microbiome disruption may contribute to these adverse health effects, but little is known about how stress affects fish microbial communities. Here, we specifically examined the effects of stress-induced cortisol production on the fish microbiome. We exposed juvenile Atlantic salmon to a mild confinement stressor for two weeks. We then measured cortisol in the plasma, skin-mucus and faeces, and characterised the skin and faecal microbiome. Faecal and skin cortisol concentrations increased in fish exposed to confinement stress, and were positively correlated with plasma cortisol. Elevated faecal cortisol was associated with pronounced changes in the diversity and structure of the faecal microbiome. In particular, we identified a marked decline in probiotic Lactobacillales (Carnobacteriumsp.) and an increase in pro-inflammatory and pathogenic taxa within the classes Clostridia and Gammaproteobacteria. In contrast, skin-mucus cortisol concentrations were lower and not associated with any detectable changes in the skin microbiome. Our results demonstrate that cortisol disrupts the gut microbiome, which may, in turn, contribute to the adverse effects of stress on fish health. They also highlight the value of using non-invasive faecal samples to monitor stress, including simultaneous determination of cortisol and stress-responsive bacteria.
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

Single-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

Understanding 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 POINTS

CyTOF 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

Pathways 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

AdultDrosophilaMalpighian 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

The 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 summary

A 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

Functional 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 Summary

Allele-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

Maintaining 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

Cryogenic 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 statement

Single 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

Annotating 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

The 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

Salinipostin 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

We 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

Background

Empirical 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.

Methods

We 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.

Results

In 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.

Conclusion

Using 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

A 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

Phagocytosis 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

Biotrophic 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.
The desmosomal cadherin Desmoglein-3 regulates YAP and phospho-YAP in keratinocyte responses to mechanical forces
Authors: Uttagomol Jutamas , Ahmad Usama Sharif , Rehman Ambreen , Huang Yunying , Laly Ana C. , Kang Angray , Soetaert Jan , Chance Randy , Teh Muy-Teck , Connelly John T. , Wan Hong
Published: November 2019

Desmoglein 3 (Dsg3), plays a crucial role in cell-cell adhesion and tissue integrity. Increasing evidence suggests that Dsg3 acts as a regulator of cellular mechanotransduction, but little is known about its direct role in mechanical force transmission. The present study investigated the impact of cyclic strain and substrate stiffness on Dsg3 expression and its role in mechanotransduction. A direct comparison was made with E-cadherin, a well-characterized mechanosensor, in human keratinocytes. Exposure of oral and skin keratinocytes to equiaxial cyclic strain promoted changes in expression and localization of junction assembly proteins. Knockdown of Dsg3 by siRNA blocked strain-induced junctional remodeling of E-cadherin and Myosin IIa. Importantly, the study demonstrated that Dsg3 regulates the expression and localization of YAP, a mechanosensor and an effector of the Hippo pathway. Furthermore, we showed that Dsg3 forms a complex with phospho-YAP and sequestered it to the plasma membrane, while Dsg3 depletion had an impact on both YAP and phospho-YAP in their response to mechanical forces, increasing the sensitivity of keratinocytes to both strain-or substrate rigidity-induced nuclear relocalization of YAP and phospho-YAP. We showed that PKP1 seemed to be the key in such a complex formation since its silencing resulted in Dsg3 disruption at the junctions with concomitant loss of pYAP in the peripheral cytoplasm. Finally, we demonstrated that this Dsg3/YAP pathway has an influence on the expression ofYAP1target genes as well as cell proliferation in keratinocytes. Together, these findings provide evidence of a novel role for Dsg3 in keratinocyte mechanotransduction.
GPSRdocker: A Docker-based Resource for Genomics, Proteomics and Systems biology
Authors: Agrawal Piyush , Kumar Rajesh , Usmani Salman Sadullah , Dhall Anjali , Patiyal Sumeet , Sharma Neelam , Kaur Harpreet , Kumar Vinod , Kaur Dilraj , Jain Shipra , Pande Akshara , Bhalla Sherry , Raghava Gajendra P.S.
Published: November 2019

Background

In past number of web-based resources has been developed in the field of Bioinformatics. These resources are heavily used by scientific community to provide solution for challenges faced by experimental researchers particularly in the field of biomedical sciences. There are number of challenges in utilizing full potential of these services that includes internet speed, limits on computing power, and security of data. In order to enhance utilities of these web-based assets, we developed a docker-based container that integrates large number resources available in literature.

Results

This paper describes GPSRdocker a docker-based container developed for providing wide-range of computational tools in the field of bioinformatics particularly in genomics, proteomics and system biology. Majority of tools integrated in GPSRdocker are based on web services developed at Raghava’s group in last two decades. Broadly, these tools can be categorized in three categories; i) general scripts, ii) supporting software and iii) major standalone software. In order to facilitate students or developers working in the field of bioinformatics, we developed general scripts in Perl and Python. These general-purpose scripts serve as building block for any bioinformatics tools like computing features/descriptors of a protein. Supporting software packages includes SCIKIT, WEKA, SVMlight, and PSI-BLAST; these software packages allow one to develop/implement bioinformatics software. Major Standalone software is core of this container which allows predicting function/class of biomolecules. These tools can be classified broadly in following categories; protein annotation, epitope-based vaccines, prediction of interaction and drug discovery.

Conclusion

A docker-based container has been developed which can be easily run on any operating system as well as it can be directly ported on cloud. Scripts can be run to build pipelines for addressing problems at system level like prediction of vaccine candidate for a pathogen. GPSRdocker including manual is available free for academic use from https://webs.iiitd.edu.in/gpsrdocker.