bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis
Authors: Anciaux Yoann , Lambert Amaury , Ronce Ophelie , Roques Lionel , Martin Guillaume 
Published: January 2019

AbstractPopulations may genetically adapt to severe stress that would otherwise cause their extirpation. Recent theoretical work, combining stochastic demography with Fisher’s geometric model of adaptation, has shown how evolutionary rescue becomes unlikely beyond some critical intensity of stress. Increasing mutation rates may however allow adaptation to more intense stress, raising concerns about the effectiveness of treatments against pathogens. This previous work assumes that populations are rescued by the rise of a single resistance mutation. However, even in asexual organisms, rescue can also stem from the accumulation of multiple mutations in a single genome. Here, we extend previous work to study the rescue process in an asexual population where the mutation rate is sufficiently high so that such events may be common. We predict both the ultimate extinction probability of the population and the distribution of extinction times. We compare the accuracy of different approximations covering a large range of mutation rates. Moderate increase in mutation rates favors evolutionary rescue. However, larger increase leads to extinction by the accumulation of a large mutation load, a process called lethal mutagenesis. We discuss how these results could help design “evolution-proof” anti-pathogen treatments that even highly mutable strains could not overcome.
Effects of Parcellation and Threshold on Brain Connectivity Measures
Authors: Lacy T.C. , Robinson P.A. 
Published: January 2019

AbstractIt is shown that the statistical properties of connections between regions of the brain and their dependence on coarse-graining and thresholding in published data can be reproduced by a simple distance-based physical connectivity model. This allows studies with differing parcellation and thresholding to be interrelated objectively, and for the results of future studies on more finely grained or differently thresholded networks to be predicted. The dependence of network measures on thresholding and parcellation implies that chosen brain regions can appear to form a small world network in many studies, even though the network of individual neurons may not be a small world network itself.
A Bimolecular Multicelular complementation system for the detection of syncytium formation: A new methodology for the identification of entry inhibitors
Authors: García-Murria María Jesús , Expósito-Domínguez Neus , Mingarro Ismael , Martinez-Gil Luis 
Published: January 2019

AbstractFusion of viral and cellular membranes is a key step during the viral life cycle. Enveloped viruses trigger this process by means of specialized viral proteins expressed on their surface, the so called viral fusion proteins. There are multiple assays to analyze the viral entry including those that focus on the cell-cell fusion induced by some viral proteins. These methods often rely on the identification of multinucleated cells (syncytium) as a result of cell membrane fusions. In this manuscript, we describe a novel methodology for the study of cell-cell fusion. Our approach, named Bimolecular Multicelular Complementation (BiMuC), provides an adjustable platform to investigate qualitatively and quantitatively the formation of a syncytium. Furthermore, we demonstrated that our procedure meets the requirements of a drug discovery approach and performed a proof of concept small molecule high-throughput screening to identify compounds that could block the entry of the emerging Nipah virus.
Select β-lactam combinations exhibit synergy against Mycobacterium abscessus in vitro
Authors: Story-Roller Elizabeth , Maggioncalda Emily C. , Lamichhane Gyanu 
Published: January 2019

ABSTRACTMycobacterium abscessus (Mab) is a nontuberculous mycobacterium that causes invasive pulmonary infections in patients with structural lung disease. Mab is intrinsically resistant to several classes of antibiotics and an increasing number of strains isolated from patients exhibit resistance to most antibiotics considered for treatment of Mab infections. Therefore, there is an unmet need for new regimens with improved efficacy to treat this disease. Synthesis of the essential cell wall peptidoglycan in Mab is achieved via two enzyme classes, L,D- and D-D-transpeptidases, with each class preferentially inhibited by different subclasses of β-lactam antibiotics. We hypothesized that a combination of two β-lactams that comprehensively inhibit the two enzyme classes will exhibit synergy in killing Mab. Paired combinations of antibiotics tested for in vitro synergy against Mab included dual β-lactams, a β-lactam and a β-lactamase inhibitor, and a β-lactam and a rifamycin. Of the initial 206 combinations screened, 24 pairs exhibited synergy. 13/24 pairs were combinations of two β-lactams. 12/24 pairs brought the minimum inhibitory concentrations of both drugs to within the therapeutic range. Additionally, synergistic drug pairs significantly reduced the frequency of selection of spontaneous resistant mutants. These novel combinations of currently-available antibiotics may offer viable immediate treatment options against highly-resistant Mab infections.
Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression
Authors: Wulftange William J. , Rose Michelle A. , Garmendia-Cedillos Marcial , Silva Davi da , Poprawski Joanna E. , Srinivasachar Dhruv , Sullivan Taylor , Lim Langston , Bliskovsky Valery V. , Hall Matthew D. , Pohida Thomas J. , Robey Robert W. , Morgan Nicole Y. , Gottesman Michael M. 
Published: January 2019

ABSTRACTCommonly used monolayer cancer cell cultures fail to provide a physiologically relevant environment in terms of oxygen delivery. Here, we describe a three-dimensional bioreactor system where cancer cells are grown in Matrigel in modified 6-well plates. Oxygen is delivered to the cultures through a polydimethylsiloxane (PDMS) membrane at the bottom of the wells, with microfabricated PDMS pillars to control oxygen delivery. The plates receive 3% oxygen from below and 0% oxygen at the top surface of the media, providing a gradient of 3% to 0% oxygen. We compared growth and transcriptional profiles for cancer cells grown in Matrigel in the bioreactor, 3D cultures grown in 21% oxygen, and cells grown in a standard hypoxia chamber at 3% oxygen. Additionally, we compared gene expression of conventional 2D monolayer culture and 3D Matrigel culture in 21% oxygen. We conclude that controlled oxygen delivery may provide a more physiologically relevant 3D system.
Dynamic pseudo-time warping of complex single-cell trajectories
Authors: Do Van Hoan , Blažević Mislav , Monteagudo Pablo , Borozan Luka , Elbassioni Khaled , Laue Sören , Ringeling Francisca Rojas , Matijević Domagoj , Canzar Stefan 
Published: January 2019

AbstractSingle-cell RNA sequencing enables the construction of trajectories describing the dynamic changes in gene expression underlying biological processes such as cell differentiation and development. The comparison of single-cell trajectories under two distinct conditions can illuminate the differences and similarities between the two and can thus be a powerful tool. Recently developed methods for the comparison of trajectories rely on the concept of dynamic time warping (dtw), which was originally proposed for the comparison of two time series. Consequently, these methods are restricted to simple, linear trajectories. Here, we adopt and theoretically link arboreal matchings to dtw and propose an algorithm to compare complex trajectories that more realistically contain branching points that divert cells into different fates. We implement a suite of exact and heuristic algorithms suitable for the comparison of trajectories of different characteristics in our tool Trajan. Trajan automatically pairs similar biological processes between conditions and aligns them in a globally consistent manner. In an alignment of singlecell trajectories describing human muscle differentiation and myogenic reprogramming, Trajan identifies and aligns the core paths without prior information. From Trajan’s alignment, we are able to reproduce recently reported barriers to reprogramming. In a perturbation experiment, we demonstrate the benefits in terms of robustness and accuracy of our model which compares entire trajectories at once, as opposed to a pairwise application of dtw. Trajan is available at https://github.com/canzarlab/Trajan.
Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3
Authors: Dainis Alexandra , Tseng Elizabeth , Clark Tyson A. , Hon Ting , Wheeler Matthew , Ashley Euan 
Published: January 2019

ABSTRACTBackgroundClinical sequencing has traditionally focused on genomic DNA through the use of targeted panels and exome sequencing, rather than investigating the potential transcriptomic consequences of disease-associated variants. RNA sequencing has recently been shown to be an effective additional tool for identifying disease-causing variants. We here use targeted long-read genome and transcriptome sequencing to efficiently and economically identify molecular consequences of a rare, disease-associated variant in hypertrophic cardiomyopathy (HCM).Methods and ResultsOur study, which employed both Pacific Biosciences SMRT sequencing and Oxford Nanopore Technologies MinION sequencing, as well as two RNA targeting strategies, identified alternatively-spliced isoforms that resulted from a splice-site variant containing allele in HCM. These included a predicted in-frame exon-skipping event, as well as an abundance of additional isoforms with unexpected intron-inclusion, exon-extension, and pseudo-exon events. The use of long-read RNA sequencing allowed us to not only investigate full length alternatively-spliced transcripts but also to phase them back to the variant-containing allele.ConclusionsWe suggest that targeted, long-read RNA sequencing in conjunction with genome sequencing may provide additional molecular evidence of disease for rare or de novo variants in cardiovascular disease, as well as providing new information about the consequence of these variants on downstream RNA and protein expression.
Plant seeds are primed by herbivore-induced plant volatiles
Authors: Maurya Abhinav K. , Pazouki Leila , Frost Christopher J. 
Published: January 2019

AbstractMature plants can detect and respond to herbivore-induced plant volatiles (HIPVs) by priming or directly activating defenses against future herbivores. Whether other plant life stages can respond to HIPVs in similar manners is poorly understood. For example, seeds are known to respond to a variety of environment cues that are essential for proper germination timing and survival. Seeds may also be exposed to HIPVs prior to germination, and such exposure may affect the growth, development, and defense profiles when the seeds grow into mature plants. Here, we investigated the effect of seed exposure to common HIPVs on growth, reproduction and defense characteristics in the model plants Arabidopsis thaliana and Medicago truncatula. Of all the HIPVs tested, indole specifically reduced both beet armyworm growth on A. thaliana and pea 33 aphid fecundity on M. truncatula. Induction of defense genes was not affected by seed exposure to indole in either plant species, suggesting that seed priming operates independently of induced resistance. Moreover, neither species showed any negative effect of seed exposure to HIPVs on vegetative and reproductive growth. Rather, M. truncatula plants derived from seeds exposed to z-3-hexanol and z-3-hexenyl acetate grew faster and produced larger leaves compared to controls. Our results indicate that seeds are sensitive to specific HIPVs, which represents a novel ecological mechanism of plant-to-plant communication.
Ethanol stimulates trehalose production through a SpoT-DksA-AlgU dependent pathway inPseudomonas aeruginosa
Authors: Harty Colleen E. , Martins Dorival , Doing Georgia , Mould Dallas L. , Clay Michelle E. , Nguyen Dao , Hogan Deborah A. 
Published: January 2019

AbstractPseudomonas aeruginosafrequently resides among ethanol-producing microbes, making its response to these microbially-produced concentrations of ethanol relevant to understanding its biology. Our ranscriptome analysis found that the genes involved in trehalose metabolism were induced by low concentrations of ethanol, and levels of intracellular trehalose increased significantly upon growth with ethanol. The increase in trehalose was dependent on the TreYZ pathway, but not other trehalose metabolic enzymes TreS or TreA. The sigma factor AlgU (AlgT), a homolog of RpoE in other species, was required for increased expression of thetreZgene and trehalose levels, but induction was not controlled by the well-characterized proteolysis of its antisigma factor MucA. Growth with ethanol led to increased SpoT-dependent (p)ppGpp accumulation, which stimulates AlgU-dependent transcription oftreZand other AlgU-regulated genes through DksA, a (p)ppGpp and RNA polymerase binding protein. Ethanol stimulation of trehalose also required acylhomoserine lactone (AHL)-mediated quorum sensing, as induction was not observed in a ΔlasRΔrhlRstrain. A network analysis using a model, eADAGE, built from publicly availableP. aeruginosatranscriptome datasets (1) provided strong support for our model thattreZand co-regulated genes are controlled by both AlgU and AHL-mediated QS (QS). Consistent with (p)ppGpp and AHL-mediated quorum sensing regulation, ethanol, even when added at the time of culture inoculation, stimulatedtreZtranscript levels and trehalose production in cells from post-exponential phase cultures but not from exponential phase cultures. These data highlight the integration of growth and cell density cues in theP. aeruginosatranscriptional response to ethanol.ImportancePseudomonas aeruginosais often found with bacteria and fungi that produce fermentation products including ethanol. At concentrations similar to those produced by environmental microbes, we found that ethanol stimulated expression of trehalose biosynthetic genes and cellular levels of trehalose, a disaccharide that protects against environmental stresses. The induction of trehalose by ethanol required the alternative sigma factor AlgU through DksA and SpoT-dependent (p)ppGpp. Trehalose accumulation also required AHL quorum sensing and only occurred in post-exponential phase cultures. This work highlights how cells integrate cell-density and growth cues in their responses to products made by other microbes and a reveals a new role for (p)ppGpp in the regulation of AlgU activity.
Reconstruction of Par polarity in apolar cells reveals a dynamic process of cortical polarization
Authors: Kono Kalyn , Yoshiura Shigeki , Fujita Ikumi , Okada Yasushi , Shitamukai Atsunori , Shibata Tatsuo , Matsuzaki Fumio 
Published: January 2019

AbstractCellular polarization is fundamental for various biological processes. The Par network system is conserved for cellular polarization. Its core complex consists of Par3, Par6, and aPKC. However, the dynamic processes that occur during polarization are not well understood. Here, we artificially reconstructed Par-dependent polarity using non-polarizedDrosophilaS2 cells expressing all three components endogenously in the cytoplasm. The results indicated that elevated Par3 expression induces cortical localization of the Par-complex at the interphase. Its asymmetric distribution goes through three steps: emergence of cortical dots, development of island-like structures with dynamic amorphous shapes, repeating fusion and fission, and polarized clustering of the islands. Our findings also showed that these islands contain a meshwork of unit-like segments. Par-complex patches resembling Par-islands exist inDrosophilamitotic neuroblasts. Thus, this reconstruction system provides an experimental paradigm to study features of the assembly process and structure of Par-dependent cell-autonomous polarity.
An ESCRT-LEM domain inner nuclear membrane protein surveillance system is poised to directly monitor the integrity of the nuclear envelope barrier and nuclear transport system
Authors: Thaller David J. , Allegretti Matteo , Borah Sapan , Ronchi Paolo , Beck Martin , Lusk C. Patrick 
Published: January 2019

AbstractThe integrity of the nuclear envelope membranes coupled to the diffusion barrier and selective transport properties of nuclear pore complexes (NPCs) are a prerequisite for the robust segregation of nucleoplasm and cytoplasm. Recent work supports that mechanical membrane disruption or perturbation to NPC assembly can trigger an ESCRT-dependent surveillance system that seals nuclear envelope pores: how these pores are sensed and sealed remains to be fully defined. Here, we show that the principal components of the nuclear envelope surveillance system in yeast, which includes the ESCRT Chm7 and the integral inner nuclear membrane (INM) protein Heh1, are spatially segregated by the nuclear transport system. Specifically, at steady state Chm7 is actively restricted from the nucleus by Crm1/Xpo1. Consistent with the idea that it is the exposure of the INM that triggers surveillance, the expression of a transmembrane anchor and the winged helix domain of Heh1 is sufficient to recruit and activate Chm7 at a membrane interface. Correlative light electron tomography under conditions of Chm7 hyper-activation further show the formation of an elaborate network of fenestrated sheets at the INM and suggest ER-membrane delivery at sites of nuclear envelope herniation. Our data point to a model in which exposure of Chm7 to Heh1, driven by any perturbation in the nuclear envelope barrier would lead to local nuclear envelope remodeling to promote membrane sealing. Our findings have implications for disease mechanisms associated with defects in NPC assembly and nuclear envelope integrity.
A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals
Authors: Quattrini Andrea M. , Wu Tiana , Soong Keryea , Jeng Ming-Shiou , Benayahu Yehuda , McFadden Catherine S. 
Published: January 2019

AbstractBackgroundOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral,Sinularia.ResultsSpecies delimitations using two widely used DNA barcode markers,mtMutSand 28S rDNA, were incongruent with one another and with the morphospecies identifications, likely due to incomplete lineage sorting. In contrast, 12 of the 15 morphospecies examined formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of >6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation inSinularia.ConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.
VPAC: Variational projection for accurate clustering of single-cell transcriptomic data
Authors: Chen Shengquan , Hua Kui , Cui Hongfei , Jiang Rui 
Published: January 2019

AbstractBackgroundSingle-cell RNA-sequencing (scRNA-seq) technologies have advanced rapidly in recent years and enabled the quantitative characterization at a microscopic resolution. With the exponential growth of the number of cells profiled in individual scRNA-seq experiments, the demand for identifying putative cell types from the data has become a great challenge that appeals for novel computational methods. Although a variety of algorithms have recently been proposed for single-cell clustering, such limitations as low accuracy, inferior robustness, and inadequate stability greatly impede the scope of applications of these methods.ResultsWe propose a novel model-based algorithm, named VPAC, for accurate clustering of single-cell transcriptomic data through variational projection, which assumes that single-cell samples follow a Gaussian mixture distribution in a latent space. Through comprehensive validation experiments, we demonstrate that VPAC can not only be applied to datasets of discrete counts and normalized continuous data, but also scale up well to various data dimensionality, different dataset size and different data sparsity. We further illustrate the ability of VPAC to detect genes with strong unique signatures of a specific cell type, which may shed light on the studies in system biology. We have released a user-friendly python package of VPAC in Github (https://github.com/ShengquanChen/VPAC). Users can directly import our VPAC class and conduct clustering without tedious installation of dependency packages.ConclusionsVPAC enables highly accurate clustering of single-cell transcriptomic data via a statistical model. We expect to see wide applications of our method to not only transcriptome studies for fully understanding the cell identity and functionality, but also the clustering of more general data.