bluuebunny/crossref_metadata_2025 huggingface dataset:
Simplified geometric representations of protein structures identify complementary interaction interfaces
Authors: McCafferty Caitlyn L. , Marcotte Edward M. , Taylor David W.
Published: December 2019

Protein-protein interactions are critical to protein function, but three-dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting for molecular motions to optimize rigid 3D translations and rotations. However, such approaches can be computationally expensive, and faster, less accurate approximations may prove useful for large-scale prediction and assembly of 3D structures of multi-protein complexes. We asked if a reduced representation of protein geometry retains enough information about molecular properties to predict pairwise protein interaction interfaces that are tolerant of limited structural rearrangements. Here, we describe a cuboid transformation of 3D protein accessible surfaces on which molecular properties such as charge, hydrophobicity, and mutation rate can be easily mapped, implemented in the MorphProt package. Pairs of surfaces are compared to rapidly assess partner-specific potential surface complementarity. On two available benchmarks of 85 overall known protein complexes, we observed F1 scores (a weighted combination of precision and recall) of 19-34% at correctly identifying protein interaction surfaces, comparable to more computationally intensive 3D docking methods in the annual Critical Assessment of PRedicted Interactions. Furthermore, we examined the effect of molecular motion through normal mode simulation on a benchmark receptor-ligand pair and observed no marked loss of predictive accuracy for distortions of up to 6 Å RMSD. Thus, a cuboid transformation of protein surfaces retains considerable information about surface complementarity, offers enhanced speed of comparison relative to more complex geometric representations, and exhibits tolerance to conformational changes.
The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes
Authors: Sierra Maria A. , Bhattacharya Chandrima , Ryon Krista , Meierovich Sophie , Shaaban Heba , Westfall David , Mohammad Rawhi , Kuchin Katerina , Afshinnekoo Ebrahim , Danko David C. , Mason Christopher E.
Published: December 2019

The Microbe Directory (TMD) is a comprehensive database of annotations for microbial species collating features such as gram-stain, capsid-symmetry, resistance to antibiotics and more. This work presents a significant improvement to the original Microbe Directory (2018). This update adds 68,852 taxa, many new annotation features, an interface for the statistical analysis of microbiomes based on TMD features, and presents a portal for the broad community to add or correct entries. This update also adds curated lists of gene annotations which are useful for characterizing microbial genomes. Much of the new data in TMD is sourced from a set of databases and independent studies collating these data into a single quality controlled and curated source. This will allow researchers and clinicians to have easier access to microbial data and provide for the possibility of serendipitous discovery of otherwise unexpected trends.
Molecular Basis for the Evolved Instability of a Human G-Protein Coupled Receptor
Authors: Chamness Laura M. , Zelt Nathan B. , Kuntz Charles P. , Bender Brian J. , Penn Wesley D. , Ziarek Joshua J. , Meiler Jens , Schlebach Jonathan P.
Published: December 2019

Membrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Though they function at the plasma membrane, mammalian GnRHRs tend to accumulate within the secretory pathway. Their apparent instability is believed to have evolved in response to selection for attenuated GnRHR activity. Nevertheless, the structural basis of this adaptation remains unclear. We find that this adaptation coincides with a C-terminal truncation and an increase in the polarity of its transmembrane (TM) domains. This enhanced polarity compromises the translocon-mediated cotranslational folding of two TM domains. Moreover, replacing a conserved polar residue in TM6 with an ancestral hydrophobic residue partially restores GnRHR expression with minimal impact on function. An evolutionary analysis suggests variations in the polarity of this residue are associated with reproductive differences. Our findings suggest the marginal energetics of cotranslational folding can be exploited to tune membrane protein fitness.
CeutaOPEN: Individual-based field observations of breeding snowy ploversCharadrius nivosus
Authors: Eberhart-Phillips Luke J. , Cruz-López Medardo , Lozano-Angulo Lydia , del Ángel Salvador Gómez , Rojas-Abreu Wendoly , Küpper Clemens
Published: December 2019

Shorebirds (partimmembers of order Charadriiformes) have a global distribution and exhibit remarkable variation in ecological and behavioural traits that are pertinent to many core questions in the fields of evolutionary ecology and conservation biology. Shorebirds are also relatively convenient to study in the wild as they are ground nesting and often occupy open habitats that are tractable to monitor. Here we present a database documenting the reproductive ecology of 1,600 individually marked snowy plovers (Charadrius nivosus) monitored between 2006 and 2016 at Bahía de Ceuta (23°54 N, 106°57 W) – an important breeding site in north-western Mexico. The database encompasses various morphological, behavioural, and fitness-related traits of males and females along with spatial and temporal population dynamics. This open resource will serve as an important data repository for addressing overarching questions in avian ecology and wetland conservation during an era of big data and global collaborative science.
Characterization of the phototoxicity, chemigenetic profile, and mutational signatures of the chemotherapeutic CX-5461 inCaenorhabditis elegans
Authors: Ye Frank B. , Hamza Akil , Singh Tejomayee , Flibotte Stephane , Hieter Philip , O’Neil Nigel J.
Published: December 2019

New anti-cancer therapeutics require extensivein vivocharacterization to identify endogenous and exogenous factors affecting efficacy, to measure toxicity and mutagenicity, and to determine genotypes resulting in therapeutic sensitivity or resistance. We usedCaenorhabditis elegansas a platform with which to characterize properties of anti-cancer therapeutic agentsin vivo. We generated a map of chemigenetic interactions between DNA damage response mutants and common DNA damaging agents. We used this map to investigate the properties of the new anti-cancer therapeutic CX-5461. We phenocopied the photoreactivity observed in CX-5461 clinical trials and found that CX-5461 generates reactive oxygen species when exposed to UVA radiation. We demonstrated that CX-5461 is a mutator, resulting in both large copy number variations and a high frequency of single nucleotide variations (SNVs). CX-5461-induced SNVs exhibited a distinct mutational signature. Consistent with the wide range of CX-5461-induced mutation types, we found that multiple repair pathways were needed for CX-5461 tolerance. Together, the data fromC. elegansdemonstrate that CX-5461 is a multimodal DNA damaging agent with strong similarity to ellipticines, a class of antineoplastic agents, and to anthracycline-based chemotherapeutics.
Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution
Authors: Sun Zhiyi , Vaisvila Romualdas , Yan Bo , Baum Chloe , Saleh Lana , Samaranayake Mala , Guan Shengxi , Dai Nan , Corrêa Ivan R. , Pradhan Sriharsa , Davis Theodore B. , Evans Thomas C. , Ettwiller Laurence M.
Published: December 2019

The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisulfite treated DNA we applied a new enzymatic deamination approach, termed EM-seq (Enzymatic Methyl-seq) to long-range sequencing technologies. Our methodology, named LR-EM-seq (Long Range Enzymatic Methyl-seq) preserves the integrity of DNA allowing long-range methylation profiling of 5-mC and 5-hmC over several kilobases of genomic DNA. When applied to known differentially methylated regions (DMR), LR-EM-seq achieves phasing of over 5 kb resulting in broader and better defined DMRs compared to previously reported. This result demonstrated the importance of phasing methylation for biologically relevant questions and the applicability of LR-EM-seq for long range epigenetic analysis at single molecule and single nucleotide resolution.
The Nucleome Data Bank: Web-based Resources to Simulate and Analyze the Three-Dimensional Genome
Authors: Contessoto Vinícius G. , Cheng Ryan R. , Hajitaheri Arya , Dodero-Rojas Esteban , Mello Matheus F. , Lieberman-Aiden Erez , Wolynes Peter G. , Pierro Michele Di , Onuchic José N.
Published: December 2019

We introduce the Nucleome Data Bank, a web-based platform to simulate and analyze the three-dimensional organization of genomes. The Nucleome Data Bank enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and FISH data, as well as multiple observations of chromosomal dynamicsin vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the Nucleome Data Bank freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate three-dimensional structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The Nucleome Data Bank aims to be a shared resource to biologists, biophysicists, and all genome scientists. The Nucleome Data Bank (NDB) is available athttps://ndb.rice.edu.
New Tools for Genetically Targeting Myeloid Populations in the Central Nervous System
Authors: McKinsey Gabriel L. , Lizama Carlos O. , Keown-Lang Amber E. , Niu Abraham , Chee Elin , Santander Nicolas , Arnold Thomas D.
Published: December 2019

As the resident macrophages of the brain and spinal cord, microglia are crucial for the phagocytosis of infectious agents, apoptotic cells and synapses. Developmentally, microglia originate from the embryonic yolk sac and serve important roles in the sculpting of neonatal neural circuits. During brain injury or infection, bone-marrow derived macrophages invade neural tissue, making it difficult to distinguish between invading macrophages and resident microglia. In addition to circulation-derived monocytes, other non-microglial central nervous system (CNS) macrophage subtypes include borderzone (meningeal and perivascular) and choroid plexus macrophages. To distinguish between resident microglia and these other CNS macrophage subtypes, we generated aP2ry12-CreERmouse line. P2RY12 is a microglial-specific nucleotide sensing GPCR that is important for microglial response to tissue damage. Using immunofluorescent labeling and flow cytometry experiments, we show thatP2ry12-CreERrecombination is exceptionally specific to parenchymal microglia. We also perform ribosome immunoprecipitations and transcriptional profiling ofP2ry12-CreERrecombined cells, using a Cre-dependentRpl22-HAmouse line. By identifying genes enriched in this dataset that are not correspondingly enriched in a broaderCx3CR1-CreER; Rpl22dataset, we isolate a number of borderzone macrophage-specific transcripts, including the genePF4. Using aPF4-Cremouse line, we show thatPF4expression robustly marks borderzone macrophages. Together, we demonstrate two new methods to genetically target distinct CNS macrophage subtypes.
Dihydroartemisinin-loaded Magnetic Nanoparticles for Enhanced Chemodynamic Therapy
Authors: Guo Shengdi , Yao Xianxian , Jiang Qin , Wang Kuang , Zhang Yuanying , Peng Haibao , Tang Jing , Yang Wuli
Published: December 2019

Recently, chemodynamic therapy (CDT) has represented a new approach for cancer treatment with low toxicity and side effects. Nonetheless, it has been a challenge to improve the therapeutic effect through increasing the amount of reactive oxygen species (ROS). Herein, we increased the amount of ROS agents in the Fenton-like reaction by loading dihydroartemisinin (DHA) which was an artemisinin (ART) derivative containing peroxide groups, into magnetic nanoparticles (MNP), thereby improving the therapeutic effect of CDT. Blank MNP were almost non-cytotoxic, whereas three MNP loading ART-based drugs, MNP-ART, MNP-DHA, and MNP-artesunate (MNP-AS), all showed significant killing effect on breast cancer cells (MCF-7 cells), in which MNP-DHA were the most potent. What’s more, the MNP-DHA showed high toxicity to drug-resistant breast cancer cells (MCF-7/ADR cells), demonstrating its ability to overcome multidrug resistance (MDR). The study revealed that MNP could produce ferrous ions under the acidic condition of tumor microenvironment, which catalyzed DHA to produce large amounts of ROS, leading to cell death. Further experiments also showed that the MNP-DHA had significant inhibitory effect on another two aggressive breast cancer cell lines (MDA-MB-231 and MDA-MB-453 cells), which indicated that the great potential of MNP-DHA for the treatment of intractable breast cancers.
Advanced Whole Genome Sequencing Using an Entirely PCR-free Massively Parallel Sequencing Workflow
Authors: Shen Hanjie , Liu Pengjuan , Li Zhanqing , Chen Fang , Jiang Hui , Shi Shiming , Xi Yang , Li Qiaoling , Wang Xiaojue , Zhao Jing , Liang Xinming , Xie Yinlong , Wang Lin , Tian Wenlan , Berntsen Tam , Alexeev Andrei , Luo Yinling , Gong Meihua , Li Jiguang , Xu Chongjun , Barua Nina , Drmanac Snezana , Dai Sijie , Mi Zilan , Ren Han , Lin Zhe , Chen Ao , Zhang Wenwei , Mu Feng , Xu Xun , Zhao Xia , Jiang Yuan , Drmanac Radoje
Published: December 2019

Background

Systematic errors can be introduced from DNA amplification during massively parallel sequencing (MPS) library preparation and sequencing array formation. Polymerase chain reaction (PCR)-free genomic library preparation methods were previously shown to improve whole genome sequencing (WGS) quality on the Illumina platform, especially in calling insertions and deletions (InDels). We hypothesized that substantial InDel errors continue to be introduced by the remaining PCR step of DNA cluster generation. In addition to library preparation and sequencing, data analysis methods are also important for the accuracy of the output data.In recent years, several machine learning variant calling pipelines have emerged, which can correct the systematic errors from MPS and improve the data performance of variant calling.

Results

Here, PCR-free libraries were sequenced on the PCR-free DNBSEQ™ arrays from MGI Tech Co., Ltd. (referred to as MGI) to accomplish the first true PCR-free WGS which the whole process is truly not only PCR-free during library preparation but also PCR-free during sequencing. We demonstrated that PCR-based WGS libraries have significantly (about 5 times) more InDel errors than PCR-free libraries.Furthermore, PCR-free WGS libraries sequenced on the PCR-free DNBSEQ™ platform have up to 55% less InDel errors compared to the NovaSeq platform, confirming that DNA clusters contain PCR-generated errors.In addition, low coverage bias and less than 1% read duplication rate was reproducibly obtained in DNBSEQ™ PCR-free using either ultrasonic or enzymatic DNA fragmentation MGI kits combined with MGISEQ-2000. Meanwhile, variant calling performance (single-nucleotide polymorphisms (SNPs) F-score>99.94%, InDels F-score>99.6%) exceeded widely accepted standards using machine learning (ML) methods (DeepVariant or DNAscope).

Conclusions

Enabled by the new PCR-free library preparation kits, ultra high-thoughput PCR-free sequencers and ML-based variant calling, true PCR-free DNBSEQ™ WGS provides a powerful solution for improving WGS accuracy while reducing cost and analysis time, thus facilitating future precision medicine, cohort studies, and large population genome projects.
Low basal expression and slow induction of IFITM3 puts immune cells at risk of influenza A infection
Authors: Wellington Dannielle , Yin Zixi , Zhang Liwei , Forbester Jessica , Kite Kerry , Laurenson-Schafer Henry , Makvandi-Nejad Shokouh , Jin Boquan , Bowes Emma , Manoharan Krishnageetha , Maldonado-Perez David , Verill Clare , Humphreys Ian , Dong Tao
Published: December 2019

The interferon-induced transmembrane protein, IFITM3, has been shown to restrict influenza virus infection in murine andin vitrosettings for ten years, but no explanation has been found to explain why this virus infection is so highly contagious and infects most individuals it comes in contact with. We confirm that the expression level of IFITM3 plays a role in determining the level of viral infection through manipulation of IFITM3 levels with interferon (IFN) stimulation and overexpression systems. Low basal expression may put some immune cells, including lymphocytes and lung-resident macrophages, at risk of influenza virus infection. Investigating the induction of IFITM3 by IFN, we find a strong preference for Type I IFN in IFITM3 induction in both cell lines and primary human cells. While myeloid cells can increase expression following stimulation by Type I IFN, lymphocytes show minimal induction of IFITM3 following IFN stimulation, suggesting that they are always at risk of viral infection. Surprisingly, we found that the time it takes for maximal induction of IFITM3 is relatively slow for an interferon-stimulated gene at around 36 hours. Low basal expression and slow induction of IFITM3 could increase the risk of influenza virus infection in selected immune cells.

Importance

Influenza virus infection remains one of the top ten threats to global health, causing significant deaths and hospitalisations across the world each year. Understanding mechanisms for controlling influenza virus infection remain a priority. The interferon-induced transmembrane protein IFITM3 can restrict influenza infection by limiting replication of the virus. The precise mechanisms of how IFITM3 reduced replication of influenza are unknown, although it is predicted to prevent release of viral contents into the cytosol by preventing pore formation on the endosomal compartments where it is suggested to reside. Here we have shown that the expression level of IFITM3 is important in determining the control of influenza virus infection. We find an expression pattern for IFITM3 that varies based on cell type, tissue locality, differentiation state and cell naivety, all of which highlights cells that may be at the highest risk of influenza infection.
A single-cell atlas of the human healthy airways
Authors: Deprez Marie , Zaragosi Laure-Emmanuelle , Truchi Marin , Garcia Sandra Ruiz , Arguel Marie-Jeanne , Lebrigand Kevin , Paquet Agnès , Pee’r Dana , Marquette Charles-Hugo , Leroy Sylvie , Barbry Pascal
Published: December 2019

Rationale

The respiratory tract constitutes an elaborated line of defense based on a unique cellular ecosystem. Single-cell profiling methods enable the investigation of cell population distributions and transcriptional changes along the airways.

Methods

We have explored cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12thdivision of the airway tree.

Results

The resulting atlas is composed of a high percentage of epithelial cells (89.1%), but also immune (6.2%) and stromal (4.7%) cells with peculiar cellular proportions in different sites of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4,PI3,SIX3) and tracheobronchial (SCGB1A1,TFF3) airways. By contrast, cell-type specific gene expression was stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuro-endocrine (PNEC) and brush cells, which are likely derived from a common population of precursor cells. We also report a population ofKRT13positive cells with a high percentage of dividing cells which are reminiscent of “hillock” cells previously described in mouse.

Conclusions

Robust characterization of this unprecedented large single-cell cohort establishes an important resource for future investigations. The precise description of the continuum existing from nasal epithelium to successive divisions of lung airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.
Transcriptomic responses to hypoxia in endometrial and decidual stromal cells
Authors: Rytkönen Kalle T. , Heinosalo Taija , Mahmoudian Mehrad , Ma Xinghong , Perheentupa Antti , Elo Laura L. , Poutanen Matti , Wagner Günter P.
Published: December 2019

Human reproductive success depends on a properly decidualized uterine endometrium that allows implantation and the formation of the placenta. At the core of the decidualization process are endometrial stromal fibroblasts (ESF) that differentiate to decidual stromal cells (DSC). As variations in oxygen levels are functionally relevant in endometrium both upon menstruation and during placentation, we assessed the transcriptomic responses to hypoxia in ESF and DSC. In both cell types hypoxia upregulated genes in classical hypoxia pathways such as glycolysis and the epithelial mesenchymal transition. In DSC hypoxia restored an ESF like transcriptional state for a subset of transcription factors that are known targets of the progesterone receptor, suggesting that hypoxia partially interferes with progesterone signaling. In both cell types hypoxia modified transcription of several inflammatory transcription factors that are known regulators of decidualization, including decreased transcription ofSTATsand increased transcription ofCEBPs. We observed that hypoxia upregulated genes had a significant overlap with genes previously detected to be upregulated in endometriotic stromal cells. Promoter analysis of the genes in this overlap suggested the hypoxia upregulated Jun/Fos and CEBP transcription factors as potential drivers of endometriosis-associated transcription. Using immunohistochemistry we observed increased expression of JUND and CEBPD in endometriosis lesions compared to healthy endometria. Overall the findings suggest that hypoxic stress establishes distinct transcriptional states in ESF and DSC, and that hypoxia influences the expression of genes that contribute to the core gene regulation of endometriotic stromal cells.
OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module specifying phloem identity
Authors: Wallner Eva-Sophie , Tonn Nina , Shi Dongbo , Luzzietti Laura , Wanke Friederike , Hunziker Pascal , Xu Yingqiang , Jung Ilona , Lopéz-Salmerón Vadir , Gebert Michael , Wenzl Christian , Lohmann Jan U. , Harter Klaus , Greb Thomas
Published: December 2019

Spatial specificity of cell fate decisions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How a phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBE3 forms a central module with the phloem- specific SMXL5 protein for establishing phloem identity inArabidopsis thaliana. By protein interaction studies and phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins form a complex in nuclei of phloem stem cells where they establish a phloem-specific chromatin profile. This profile allows expression ofOPS,BRX,BAM3, andCVP2genes acting as mediators of phloem differentiation. Our findings demonstrate that OBE3/SMXL5 protein complexes establish nuclear features essential for determining phloem cell fate and highlight how a combination of ubiquitous and local regulators generate specificity of developmental decisions in plants.
Disentangling microbial associations from hidden environmental and technical factors via latent graphical models
Authors: Kurtz Zachary D. , Bonneau Richard , Müller Christian L.
Published: December 2019

Detecting community-wide statistical relationships from targeted amplicon-based and metagenomic profiling of microbes in their natural environment is an important step toward understanding the organization and function of these communities. We present a robust and computationally tractable latent graphical model inference scheme that allows simultaneous identification of parsimonious statistical relationships among microbial species and unobserved factors that influence the prevalence and variability of the abundance measurements. Our method comes with theoretical performance guarantees and is available within the SParse InversE Covariance estimation for Ecological ASsociation Inference (SPIEC-EASI) framework (‘SpiecEasi’ R-package). Using simulations, as well as a comprehensive collection of amplicon-based gut microbiome datasets, we illustrate the method’s ability to jointly identify compositional biases, latent factors that correlate with observed technical covariates, and robust statistical microbial associations that replicate across different gut microbial data sets.
Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes
Authors: Verma Rahul K , Kalyakulina Alena , Giuliani Cristina , Shinde Pramod , Kachhvah Ajay Deep , Ivanchenko Mikhail , Jalan Sarika
Published: December 2019

Networks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We have studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mt-DNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects and variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clusteringrevealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral ‘RSRS50’ variant 10398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.
Competition for access to mates predicts female-specific ornamentation and polyandry
Authors: Murray Rosalind L. , Herridge Elizabeth J. , Ness Rob W. , Wiberg R. Axel W. , Bussière Luc F.
Published: December 2019

Sexually selected ornaments are highly variable and the factors that drive variation in ornament expression are not always clear. Rare instances of female-specific ornament evolution (such as in some dance fly species) are particularly puzzling. While some evidence suggests that such rare instances represent straightforward reversals of sexual selection intensity, the distinct nature of trade-offs between ornaments and offspring pose special constraints in females. To examine whether competition for access to mates generally favours heightened ornament expression, we built a phylogeny and conducted a comparative analysis of Empidinae dance fly taxa that display ornate female-specific ornaments. We show that species with more female-biased operational sex ratios in lek-like mating swarms have greater female ornamentation, and in taxa with more ornate females, polyandry is increased. These findings support the hypothesis that ornament diversity in dance flies depends on female receptivity, which is associated with contests for nutritious nuptial gifts provided by males. Moreover, our results suggest that increases in female receptivity lead to higher levels of polyandry and sperm competition among males. The incidence of both heightened pre-mating sexual selection on females and post-mating selection on males contradicts assertions that sex-roles are straightforwardly reversed in dance flies.
XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing
Authors: Winkelman Jared T. , Pukhrambam Chirangini , Vvedenskaya Irina O. , Zhang Yuanchao , Taylor Deanne M. , Shah Premal , Ebright Richard H. , Nickels Bryce E.
Published: December 2019

Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a “stepping” mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a “scrunching” mechanism, has not. We report a method that directly defines RNAP-active-center position relative to DNAin vivowith single-nucleotide resolution (XACT-seq; crosslink-between-active-center-and-template sequencing). We apply this method to detect and quantify pausing in initial transcription at 411(∼4,000,000) promoter sequencesin vivo, inEscherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4-5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard-coded by sequence elements similar to those for transcription-elongation pausing.
Spatiotemporal analysis of host cell modification during herpes simplex virus 1 replication
Authors: Scherer Katharina M. , Manton James D. , Soh Timothy K. , Mascheroni Luca , Connor Viv , Crump Colin M. , Kaminski Clemens F.
Published: December 2019

Herpesviruses are large and complex viruses, and have a long evolutionary history with their host species. One poorly understood, but important, area in virus-host interaction is the extensive remodelling of intracellular organelles and morphology that occurs during active viral replication. We have constructed a recombinant reporter virus that allowed us to classify four distinct stages in the infection cycle of herpes simplex virus 1. Single-cell analysis of the impact of the viral load on replication dynamics demonstrates the utility of this times-tamping method for tracking the infection cycle. High-resolution microscopy analysis of cellular structures in live and fixed cells in concert with our dual-fluorescent reporter virus have enabled us to generate a detailed overview over the spatial and temporal organisation of the cytoskeleton and organelles during viral replication. This provides the first systems-level analysis of the morphological changes involved in viral replication.
GABA signalling in guard cells acts as a ‘stress memory’ to optimise plant water loss
Authors: Xu Bo , Long Yu , Feng Xueying , Zhu Xujun , Sai Na , Chirkova Larissa , Herrmann Johannes , Okamoto Mamoru , Hedrich Rainer , Gilliham Matthew
Published: December 2019

The non-protein amino acid γ-aminobutyric acid (GABA) has been proposed to be an ancient messenger for cellular communication conserved across biological kingdoms. GABA has well-defined signalling roles in animals; however, whilst GABA accumulates in plants under stress it has not been determined if, how, where and when GABA acts as an endogenous plant signalling molecule. Here, we establish that endogenous GABA is abona fideplant signal, acting via a mechanism not found in animals. GABA antagonises stomatal movement in response to opening and closing stimuli in multiple plant families including dicot and monocot crops. UsingArabidopsis thaliana, we show guard cell GABA production is necessary and sufficient to influence stomatal aperture, transpirational water loss and drought tolerance via inhibition of stomatal guard cell plasma membrane and tonoplast-localised anion transporters. This study proposes a novel role for GABA – as a ‘stress memory’ – opening new avenues for improving plant stress tolerance.
Microglial homeostasis requires balanced CSF-1/CSF-2 receptor signaling
Authors: Chitu Violeta , Biundo Fabrizio , Shlager Gabriel G. L. , Park Eun S. , Wang Ping , Gulinello Maria E. , Gokhan Solen , Ketchum Harmony C. , Saha Kusumika , DeTure Michael A. , Dickson Dennis W. , Wszolek Zbignew K. , Zheng Deyou , Croxford Andrew L. , Becher Burkhard , Sun Daqian , Mehler Mark F. , Stanley E. Richard
Published: December 2019

CSF-1Rhaploinsufficiency causes adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP). Previous studies in theCsf1r+/-mouse model of ALSP hypothesized a central role of elevated cerebralCsf2expression. Here we show that monoallelic deletion ofCsf2rescues most behavioral deficits and histopathological changes inCsf1r+/-mice by preventing microgliosis and eliminating most microglial transcriptomic alterations, including those indicative of oxidative stress and demyelination. We also show elevation ofCsf2transcripts and of several CSF-2 downstream targets in the brains of ALSP patients, demonstrating that the mechanisms identified in the mouse model are functional in man. Our data provide new insights into the mechanisms underlying ALSP. Since both increasedCSF2levels and decreased microglialCsf1rexpression have also been reported in Alzheimer’s disease and multiple sclerosis, we suggest that the unbalanced CSF-1R/CSF-2 signaling we describe in the present study may contribute to the pathogenesis of other neurodegenerative conditions.

Highlights

ALSP is aCSF1R-deficiency dementia associated with increasedCSF2expression

InCsf1r+/-ALSP mice CSF-2 promotes microgliosis by direct signaling in microglia

TargetingCsf2improves cognition, myelination and normalizes microglial function

CSF-2 is a therapeutic target in ALSP
Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation ofListeria monocytogenesin epithelial cells
Authors: Peron-Cane Caroline , Fernandez José-Carlos , Leblanc Julien , Wingertsmann Laure , Gautier Arnaud , Desprat Nicolas , Lebreton Alice
Published: December 2019

Real-time imaging of bacterial virulence factor dynamics is hampered by the limited number of fluorescent tools suitable for tagging secreted effectors. Here, we demonstrated that the fluorogenic reporter FAST could be used to tag secreted proteins, and we implemented it to monitor infection dynamics in epithelial cells exposed to the human pathogenListeria monocytogenes(Lm). By tracking individual FAST-labelled vacuoles afterLminternalisation into cells, we unveiled the heterogeneity of residence time inside entry vacuoles. Although half of the bacterial population escaped within 13 minutes after entry, 12% of bacteria remained entrapped over an hour inside long term vacuoles, and sometimes much longer, regardless of the secretion of the pore-forming toxin listeriolysin O (LLO). We imaged LLO-FAST in these long-term vacuoles, and showed that LLO enabledLmto proliferate inside these compartments, reminiscent of what had been previously observed for SpaciousListeria-containing phagosomes (SLAPs). Unexpectedly, inside epithelial SLAP-like vacuoles (eSLAPs),Lmproliferated as fast as in the host cytosol. eSLAPs thus constitute an alternative replication niche in epithelial cells that might promote the colonization of host tissues.

Author summary

Bacterial pathogens secrete virulence factors to subvert their hosts; however, monitoring bacterial secretion in real-time remains challenging. Here, we developed a convenient method that enabled fluorescent imaging of secreted proteins in live microscopy, and applied it to the human pathogenListeria monocytogenes.Listeriahas been described to invade cells and proliferate in their cytosol; it is first internalized inside vacuoles, from where it escapes thanks to the secretion of virulence factors that disrupt membranes. Our work revealed the existence, in human epithelial cells, of a population ofListeriathat failed to escape vacuoles but instead multiplied efficiently therein, despite -and in fact, thanks to— the active secretion of a toxin that permeates membranes. This intravacuolar niche may provideListeriawith an alternative strategy to colonize its host.
Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas
Authors: Machado Fabricio Brum , Moharana Kanhu C. , Almeida-Silva Fabricio , Gazara Rajesh K. , Pedrosa-Silva Francisnei , Coelho Fernanda S. , Grativol Clícia , Venancio Thiago M.
Published: December 2019

Soybean (Glycine max[L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past five years generated an enormous amount of RNA-seq data, encompassing various tissues, developmental conditions, and genotypes. In this study, we have collected data from 1,298 publicly available soybean transcriptome samples, processed the raw sequencing reads, and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52,737/56,044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground, and seed/seed-related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1,349 genes showed heavily biased expression patterns towards particular tissues. A transcript-level analysis revealed that 95% (70,963/74,490) of the known transcripts overlap with those reported here, whereas 3,256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user-friendly web interface athttp://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.
Germlinede novomutation rates on exons versus introns in humans
Authors: Rodriguez-Galindo Miguel , Casillas Sònia , Weghorn Donate , Barbadilla Antonio
Published: December 2019

A main assumption of molecular population genetics is that genomic mutation rate does not depend on sequence function. Challenging this assumption, a recent study has found a reduction in the mutation rate in exons compared to introns in somatic cells. This reduction was ascribed to an enhanced exonic mismatch repair system activity. If this reduction happens also in the germline, it can compromise studies of population genomics, including the detection of the footprint of selection when using introns as proxies of neutrality. Here we compiled and analyzed published germlinede novomutation (DNM) data to test if the exonic mutation rate is also reduced in germ cells. We detected ascertainment bias in studies using DNM data from diseased probands and investigated the impact of extended nucleotide context onde novomutation rate. After controlling for these factors, we found no reduction in the mutation rate in exons compared to introns in the germline genome, in contrast to what has been previously described in somatic cells. Therefore, there is no evidence of an enhanced mismatch repair system activity in exons with respect to adjacent introns in germline cells.
Anin vitroquantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias
Authors: Wilson Jennifer L. , Lu Dan , Corr Nick , Fullerton Aaron , Lu James
Published: December 2019

Myelosuppression is one of the most common and severe adverse events associated with anti-cancer therapies and can be a source of drug attrition. Current mathematical modeling methods for assessing cytopenia risk rely on indirect measurements of drug effects and primarily focus on single lineage responses to drugs. However, anti-cancer therapies have diverse mechanisms with varying degrees of effect across hematopoietic lineages. To improve predictive understanding of drug-induced myelosuppression, we developed a quantitative systems pharmacology (QSP) model of hematopoiesisin vitrofor quantifying the effects of anti-cancer agents on multiple hematopoietic cell lineages. We calibrated the system parameters of the model to cell kinetics data without treatment and then validated the model by showing that the inferred mechanisms of anti-proliferation and/or cell-killing are consistent with the published mechanisms for three classes of drugs with different mechanisms of action. Using a set of compounds as a sample set, we then analyzed novel compounds to predict their mechanisms and magnitude of myelosuppression. Further, these quantitative mechanisms are valuable for the development of translationalin vivomodels to predict clinical cytopenia effects.

Author Summary

Reduced bone marrow activity and levels of mature blood cells is an undesirable side effect of many anti-cancer therapies. Selecting promising lead compounds for further development requires understanding of potential myelosuppressive effects. However, existing preclinical experiments and modeling formulations fail to consider drug effects on multiple blood cell types or the mechanistic differences between how drugs induced myelosuppression. Here we developed a quantitative systems pharmacology (QSP) model that estimates a drug candidate’s effect on multiple precursor and mature blood cell lineages and further distinguishes how the drug affects these populations - through cell-killing or anti-proliferation mechanisms. This modeling formalism is valuable for vetting compounds for therapeutic development and for further translational modeling to anticipate the clinical effects of compounds.
Handling and Packaging of Medical Bags at the Acute Disaster Site Under High Temperature Conditions
Authors: Ando Wataru , Imamura Yumika , Nagashima Hideyuki , Kondo Kouji , Nakamura Kazunori , Otori Katsuya
Published: December 2019

The handling of medical bags in high temperature disaster sites has not been fully evaluated. In this study, medical bags were assessed in the closed, semi-opened, and opened state, with and without heat insulating material (HIM) and a coolant. The bags were heated for 300 minutes at 35 or 40°C, and the internal temperature was measured. closed and semi-opened bags were able to limit temperature increases in the central part of the bag at both 35 and 40°C to a greater extent than opened bags. When coolant and HIM were used in closed and semi-opened bags, the internal temperature was significantly lower than that seen in the opened state at 40°C (P < 0.01 and P < 0.001, respectively). In conclusion, in high temperature disaster sites, medical bags should be maintained in a semi-opened or closed state using a HIM and coolant.
Soil solution in Swiss forest stands: a 20 year’s time series
Authors: Braun Sabine
Published: December 2019

The chemistry of the soil solution is influenced by atmospheric deposition of air pollutants, by exchange processes between the soil matrix and the soil solution and by processes between the rhizosphere and the soil. At sites of the Intercantonal Long-term Forest Observation Programme in Switzerland the soil solution has been monitored since 1998 in a number of forest plots growing from 9 to 47 sites in a wide range of soil conditions and air pollution impacts. The results show various site-specific developments of soil acidification. At sites with already advanced acidification (pH < 4.2), the acidification indicators remained rather stable at high levels, possibly due to the high buffering capacity of the aluminum buffer (pH 4.2 – 3.8). In contrast, in less acidified sites the acidification still progressed further which is reflected by e.g. the ongoing decrease of the base cation to aluminum ratio. Main driver of the acidification is the high N deposition which provokes cation loss and impedes sustainable nutrient balances for tree nutrition in the majority of plots examined. On an average for the years 2005-2017, N leaching rates were 9.4 kg N ha-1yr-1, ranging from 0.04 to 53 kg N ha-1yr-1. Three plots with high N input show very low N leaching, suggesting that N leaching may not always be a good eutrophication indicator. Both N deposition and N leaching have decreased since the year 2000 but the latter trend is partly also due to increased drought.
Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Authors: Ghosh Arpan C. , Tattikota Sudhir G. , Liu Yifang , Comjean Aram , Hu Yanhui , Barrera Victor , Ho Sui Shannan J. , Perrimon Norbert
Published: December 2019

PDGF/VEGF ligands regulate a plethora of biological processes in multicellular organisms via autocrine, paracrine and endocrine mechanisms. Here, we investigated organ-specific roles of Drosophila PDGF/VEGF-like factors (Pvfs). We combine genetic approaches and single-nuclei sequencing to demonstrate that muscle-derived Pvf1 signals to the Drosophila hepatocyte-like cells/oenocytes to suppress lipid synthesis by activating the Pi3K/Akt1/mTOR signaling cascade in the oenocytes. Additionally, we show that this signaling axis regulates the rapid expansion of adipose tissue lipid stores observed in newly eclosed flies. Flies emerge after pupation with limited adipose tissue lipid stores and lipid levels are progressively restored via lipid synthesis. We find that pvf1 expression in the adult muscle increase rapidly during this stage and that muscle-to-oenocyte Pvf1 signaling inhibits restoration of adipose tissue lipid stores as the process reaches completion. Our findings provide the first evidence in a metazoan of a PDGF/VEGF ligand acting as a myokine that regulates systemic lipid homeostasis by activating mTOR in hepatocyte-like cells.

Highlights

Muscle specific Pvf1 protects mature adult flies from obesity

Single-nuclei RNA sequencing reveals that PvR, the receptor for Pvf1, is highly expressed in the Drosophila hepatocyte-like cells/oenocytes.

PvR is required specifically in oenocytes to protect adult flies from obesity

Muscle-to-oenocyte Pvf1 signaling activates PvR/Pi3K/Akt1/mTOR in the oenocytes to suppress lipid synthesis

Muscle-derived Pvf1 helps terminate the rapid expansion of adipose tissue lipid stores in newly eclosed flies