bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response byPyronemaspecies
Authors: Bruns Thomas D. , Chung Judy A. , Carver Akiko A. , Glassman Sydney I. 
Published: September 2019

AbstractWe have designed a simple, inexpensive system for the studying the response of soil microbes to fire. This system allows one to create post-fire environments in soil in reproducible and realistic ways. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near peak temperature for a significant time, and is accurately predicted by the log of soil depth and the mass charcoal burned. Flash fuels that left no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response byPyronema, a well-known genus of postfire fungus, from uninoculated forest soil within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change significantly with the fire, although there is an overall reduction in richness and evenness. Extrapolating from the physical relationships we predict soil heating effects in wild fires are likely to be very patchy across the forest floor but the width of a survivable “goldilocks zone” will stay relatively constant across a range of fuel loads. We further predict that a necromass zone above it, which represents an open niche for pyrophilous microbes, increases in size rapidly with addition of fuel, and then remains nearly constant over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities.
Inhibiting the copper efflux system in microbes as a novel approach for developing antibiotics
Authors: Meir Aviv , Lepechkin-Zilbermintz Veronica , Kahremany Shirin , Schwerdtfeger Fabian , Gevorkyan-Airapetov Lada , Munder Anna , Viskind Olga , Gruzman Arie , Ruthstein Sharon 
Published: September 2019

AbstractFive out of six people receive at least one antibiotic prescription per year. However, the ever-expanding use of antibiotics in medicine, agriculture, and food production has accelerated the evolution of antibiotic-resistant bacteria, which, in turn, made the development of novel antibiotics based on new molecular targets a priority in medicinal chemistry. One way of possibly combatting resistant bacterial infections is by inhibiting the copper transporters in prokaryotic cells. Copper is a key element within all living cells, but it can be toxic in excess. Both eukaryotic and prokaryotic cells have developed distinct copper regulation systems to prevent its toxicity. Therefore, selectively targeting the prokaryotic copper regulation system might be an initial step in developing next-generation antibiotics. One such system is the Gram-negative bacterial CusCFBA efflux system. CusB is a key protein in this system and was previously reported to play an important role in opening the channel for effluxviasignificant structural changes upon copper binding while also controlling the assembly and disassembly process of the entire channel. In this study, we aimed to develop novel peptide copper channel blockers, designed byin silicocalculations based on the structure of CusB. Using a combination of magnetic resonance spectroscopy and various biochemical methods, we found a lead peptide that promotes copper-induced cell toxicity. Targeting copper transport in bacteria has not yet been pursued as an antibiotic mechanism of action. Thus, our study lays the foundation for discovering novel antibiotics.Author SummaryHerein, we apply a novel approach for the development of a new generation of antibiotics based on copper toxicity. In cells, copper ions are double-edge swords. On the one hand, various enzymes depend on them as cofactors for catalysis, but on the other hand, they are highly toxic. Thus, cells have developed sophisticated regulation systems to very precisely control copper concentration. Prokaryotic organisms are more sensitive to copper than eukaryotic systems, and therefore they employ additional copper transporters that have no homology in the eukaryotic cells in general and specifically in the human cell. Here, we suggest to take advantage of this fact, by developing inhibitors against one of the bacterial copper transporter: CusCBA. The adaptor protein within this transporter, CusB, plays a critical role in the opening of the whole transporter. We designed a peptide that interfere with its proper function and assembly, and therefore inhibits the opening of the transporter upon copper stress. This study lays the foundation for designing better and novel antibiotics.
The role of the diencephalon in the guidance of thalamocortical axons in mice
Authors: Quintana-Urzainqui Idoia , Pablo Hernández-Malmierca P , Clegg James M. , Li Ziwen , Kozić Zrinko , Price David J 
Published: September 2019

AbstractThalamocortical axons (TCAs) cross several tissues on their journey to the cortex. Mechanisms must be in place along the route to ensure they connect with their targets in an orderly fashion. The ventral telencephalon acts as an instructive tissue, but the importance of the diencephalon in TCA mapping is unknown. We report that disruption of diencephalic development by Pax6 deletion results in a thalamocortical projection containing mapping errors. We used conditional mutagenesis to test whether these errors are due to the disruption of pioneer projections from prethalamus to thalamus and found that, while this correlates with abnormal TCA fasciculation, it does not induce topographical errors. To test whether the thalamus contains navigational cues for TCAs, we used slice culture transplants and gene expression studies. We found the thalamic environment is instructive for TCA navigation and that the molecular cues Netrin1 and Semaphorin3a are likely to be involved. Our findings indicate that the correct topographic mapping of TCAs onto the cortex requires the order to be established from the earliest stages of their growth by molecular cues in the thalamus itself.
NHJ-1 regulates canonical non-homologous end joining inCaenorhabditis elegans
Authors: Vujin Aleksandar , Jones Steven J. , Zetka Monique 
Published: September 2019

AbstractCanonical non-homologous end joining (cNHEJ) is a near-universally conserved pathway for the repair of DNA double-strand breaks (DSBs). While the cNHEJ pathway encompasses more than a dozen factors in vertebrates and is similarly complex in other eukaryotes, in the nematodeC. elegansthe entire known cNHEJ toolkit consists of two proteins that comprise the Ku ring complex,cku-70andcku-80, and the terminal ligaselig-4. Here, we report the discovery ofnhj-1as the fourth cNHEJ factor inC. elegans. Observing a difference in the phenotypic response to ionizing radiation (IR) between two lines of the wild type N2 strain, we mapped the locus causative of IR-sensitivity to a candidate on chromosome V. Using CRISPR-Cas9 mutagenesis, we show that disrupting thenhj-1sequence induces IR-sensitivity in an IR-resistant background. Double mutants ofnhj-1and the cNHEJ factorslig-4orcku-80do not exhibit additive IR-sensitivity, arguing thatnhj-1is a member of the cNHEJ pathway. Furthermore, like the loss oflig-4,the loss ofnhj-1in thecom-1genetic background, in which meiotic DSBs are repaired by cNHEJ instead of homologous recombination, increased the number of DAPI-staining bodies in diakinesis, consistent with increased chromosome fragmentation in the absence of cNHEJ repair. Finally, we show that NHJ-1 localizes to many somatic nuclei in the L1 larva, but not the primordial germline, which is in accord with a role in the predominantly somatically active cNHEJ. Althoughnhj-1shares no sequence homology with other known eukaryotic cNHEJ factors and is taxonomically restricted to the Rhadbitid family, its discovery underscores the evolutionary plasticity of even highly conserved pathways, and may represent a springboard for further characterization of cNHEJ inC. elegans.
Single-cell resolution view of the transcriptional landscape of developingDrosophilaeye
Authors: Ejsmont Radoslaw Kamil , Houser Grace , Garcia Natalia Mora , Topp Sara Fonseca , Danda Natalia , Wong-Chung Agnes , Hassan Bassem A. 
Published: September 2019

AbstractFaithful and reliable quantification of gene expression at a single-cell level is an outstanding challenge in developmental biology. Most existing approaches face a trade-off between the signal to noise ratio, resolution, and sensitivity. Here, we present a novel approach for in situ quantification of gene expression in a developing tissue. Our pipeline combines computational prediction of transcription factor targets, gene tagging, fluorescent reporter imaging, state-of-the-art image analysis, and automated cell-type identification. By applying this approach to identify the sequence of quantitative changes in gene expression which govern the development of theDrosophilaneural retina, we demonstrate the feasibility of our method. We analyze the targets of Atonal (Ato), a transcription factor that controls the transition from eye disc progenitor cell to photoreceptor neurons. We utilized recombineering and genomic engineering to tag all predicted Ato targets with novel transcriptional reporters. These reporters enable following the expression of both regulator and regulated genes to accurately quantify their expression levels in individual cells. Our complete computational pipeline identifies nuclei in the eye discs and detects different states of cells as they progress through differentiation. Based on detailed gene expression analysis, our technique revealed genes likely to be direct Ato targets and provided insight into how gene expression changes drive the specification of photoreceptors.
To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes
Authors: Jefferies Damien , Khalid Syma 
Published: September 2019

AbstractOuter membrane vesicles (OMVs) are spherical liposomes that are secreted by almost all forms of Gram-negative bacteria. The nanospheres contribute to bacterial pathogenesis by trafficking molecular cargo from bacterial membranes to target cells at the host-pathogen interface. We have simulated the interaction of OMVs with host cell membranes to understand why OMV uptake depends on the length of constituent lipopolysaccharide macromolecules. Using coarse-grained molecular dynamics simulations, we show that lipopolysaccharide lipid length affects OMV shape at the host-pathogen interface: OMVs with long (smooth-type) lipopolysaccharide lipids retain their spherical shape when they interact with host cell membranes, whereas OMVs with shorter (rough-type) lipopolysaccharide lipids distort and spread over the host membrane surface. In addition, we show that OMVs preferentially coordinate domain-favoring ganglioside lipids within host membranes to enhance curvature and affect the local lipid composition. We predict that these differences in shape preservation affect OMV internalization on long timescales: spherical nanoparticles tend to be completely enveloped by host membranes, whereas low sphericity nanoparticles tend to remain on the surface of cells.
Structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: a functional marker based approach
Authors: Barka Geleta Dugassa , Caixeta Eveline Teixeira , Ferreira Sávio Siqueira , Zambolim Laércio 
Published: September 2019

AbstractPhysiology-based differentiation of SHgenes andHemileia vastatrixraces is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SHrelated candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SHgenes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SHgenes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.
Long-term potentiation prevents ketamine-induced aberrant neurophysiological dynamics in the hippocampus-prefrontal cortex pathway in vivo
Authors: Lopes-Aguiar Cleiton , Ruggiero Rafael N. , Rossignoli Matheus T. , de Miranda Esteves Ingrid , Santos José Eduardo Peixoto , Romcy-Pereira Rodrigo N. , Leite João P. 
Published: September 2019

ABSTRACTN-methyl-D-aspartate receptor (NMDAr) antagonists such as ketamine (KET) produce psychotic-like behavior in both humans and animal models. NMDAr hypofunction affects normal oscillatory dynamics and synaptic plasticity in key brain regions related with schizophrenia, particularly in the hippocampus and the prefrontal cortex. In contrast, long-term potentiation (LTP) induction is known to increase glutamatergic transmission. Thus, we hypothesized that LTP could mitigate the electrophysiological changes promoted by KET. We recorded HPC-PFC local field potentials and evoked responses in urethane anesthetized rats, before and after KET administration, preceded or not by LTP induction. Our results show that KET promotes an aberrant delta-high-gamma crossfrequency coupling in the PFC and an enhancement in HPC-PFC evoked responses. LTP induction prior to KET attenuates changes in synaptic efficiency and prevents the increase in cortical gamma amplitude comodulation. These findings are consistent with evidence that increased efficiency of glutamatergic receptors attenuates cognitive impairment in animal models of psychosis. Therefore, high-frequency stimulation in HPC may be a useful tool to better understand how to prevent NMDAr hypofunction effects on synaptic plasticity and oscillatory coordination in cortico-limbic circuits.
Systematical analysis reveals the novel function of Cyp2c29 in liver injury
Authors: Wang Qi , Tang Qin , Zhao Lijun , Zhang Qiong , Wu Yuxin , Hu Hui , Liu Lan-Lan , Liu Xiang , Zhu Yanhong , Guo An-Yuan , Yang Xiangliang 
Published: September 2019

AbstractAs a severe lethal cancer, hepatocellular carcinoma (HCC) usually originates from chronic liver injury and inflammation, in which the discovery of key genes is important for HCC prevention. Here, we analyzed the time serial (from 0 week to 30 weeks) transcriptome data of liver injury samples in diethylnitrosamine (DEN)-induced HCC mouse model. Through expression and function analyses, we identified that Cyp2c29 was a key gene continuously downregulated during liver injury. Overexpression of Cyp2c29 suppressed the NF-κB activation, proinflammatory cytokine production and hepatocyte proliferation by increasing its production 14,15-epoxyeicosatrienoic acid (14,15-EET). Furthermore, in vivo Cyp2c29 protected against liver inflammation in liver injury mice models by reversing the expression on functions of cell proliferation, metabolism and inflammation including suppressing NF-κB pathway and compensatory proliferation. CYP2C8 and CYP2C9, two human homologs of mouse Cyp2c29, were decreased in human HCC progression and positively correlated with HCC patient survival. Therefore, through systematical analysis and verification, we identified that Cyp2c29 is a novel gene in liver injury and inflammation, which may be a potential biomarker for HCC prevention and prognosis.
Co-ordinated Ras and Rac activity shapes macropinocytic cups and enables phagocytosis of geometrically diverse bacteria
Authors: Buckley Catherine M. , Pots Henderikus , Gueho Aurelie , Phillips Ben A. , Gilsbach Bernd , Traynor David , Nikolaev Anton , Soldati Thierry , Parnell Andrew J. , Kortholt Arjan , King Jason S. 
Published: September 2019

AbstractEngulfment of extracellular material by phagocytosis or macropinocytosis depends on the ability of cells to generate specialised cup shaped protrusions. To effectively capture and internalise their targets, these cups are organised into a ring or ruffle of actin-driven protrusion encircling a non-protrusive interior domain. These functional domains depend on the combined activities of multiple Ras and Rho family small GTPases, but how their activities are integrated and differentially regulated over space and time is unknown. Here, we show that the amoeba Dictyostelium discoideum coordinates Ras and Rac activity using the multidomain protein RGBARG (RCC1, RhoGEF, BAR and RasGAP-containing protein). We find RGBARG uses a tripartite mechanism of Ras, Rac and phospholipid interactions to localise at the protruding edge and interface with the interior of both macropinocytic and phagocytic cups. There, RGBARG shapes the protrusion by driving Rac activation at the rim whilst suppressing expansion of the active Ras interior domain. Consequently, cells lacking RGBARG form enlarged, flat interior domains unable to generate large macropinosomes. During phagocytosis, we find that disruption of RGBARG causes a geometry-specific defect in engulfing rod-shaped bacteria and ellipsoidal beads. This demonstrates the importance of co-ordinating small GTPase activities during engulfment of more complex shapes and thus the full physiological range of microbes, and how this is achieved in a model professional phagocyte.
Dynamics of the 4D genome during lineage specification, differentiation and maturation in vivo
Authors: Oudelaar A. Marieke , Beagrie Robert A. , Gosden Matthew , de Ornellas Sara , Georgiades Emily , Kerry Jon , Hidalgo Daniel , Carrelha Joana , Shivalingam Arun , El-Sagheer Afaf H. , Telenius Jelena M. , Brown Tom , Buckle Veronica J. , Socolovsky Merav , Higgs Douglas R. , Hughes Jim R. 
Published: September 2019

AbstractMammalian gene expression patterns are controlled by regulatory elements, which interact within Topologically Associating Domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. We developed Tiled-C, a low-input Chromosome Conformation Capture (3C) approach, to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of matched chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. In contrast to previous reports, our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.
An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms
Authors: Kanca Oguz , Zirin Jonathan , Garcia-Marques Jorge , Knight Shannon , Yang-Zhou Donghui , Amador Gabriel , Chung Hyunglok , Zuo Zhongyuan , Ma Liwen , He Yuchun , Lin Wen-Wen , Fang Ying , Ge Ming , Yamamoto Shinya , Schulze Karen L. , Hu Yanhui , Spradling Allan C. , Mohr Stephanie E. , Perrimon Norbert , Bellen Hugo J. 
Published: September 2019

AbstractWe previously reported a CRISPR-mediated knock-in strategy into introns ofDrosophilagenes, generating anattP-FRT-SA-T2A-GAL4-polyA-3XP3-EGFP-FRT-attPtransgenic library for multiple uses (Lee et al., 2018b). The method relied on double stranded DNA (dsDNA) homology donors with ∼1 kb homology arms. Here, we describe three new simpler ways to edit genes in flies. We create single stranded DNA (ssDNA) donors using PCR and add 100 nt of homology on each side of an integration cassette, followed by enzymatic removal of one strand. Using this method, we generated GFP-tagged proteins that mark organelles in S2 cells. We then describe two dsDNA methods using cheap synthesized donors flanked by 100 nt homology arms and gRNA target sites cloned into a plasmid. Upon injection, donor DNA (1 to 5 kb) is released from the plasmid by Cas9. The cassette integrates efficiently and preciselyin vivo. The approach is fast, cheap, and scalable.
PDS5 proteins regulate the length of axial elements and telomere integrity during male mouse meiosis
Authors: Viera Alberto , Berenguer Inés , Ruiz-Torres Miguel , Gómez Rocío , Guajardo Andrea , Barbero José Luis , Losada Ana , Suja José A. 
Published: September 2019

AbstractCohesin cofactors regulate the loading, maintenance and release of cohesin complexes from chromosomes during the mitotic cell cycle but little is known on their role during vertebrate meiosis. One such cofactor is PDS5, which exists in two versions in somatic and germline cells, PDS5A and PDS5B, with unclear functional specificity. Here we have analyzed their distribution and functions in mouse spermatocytes. We show that simultaneous elimination of PDS5A and PDS5B results in severe defects during prophase I while their individual depletion does not, suggesting a functional redundancy of the two factors. Shortened axial/lateral elements and a reduction of early recombination nodules are observed in the absence of both PDS5 proteins. Moreover, telomere integrity and their association to the nuclear envelope are severely compromised. As these defects occur without detectable reduction in chromosome-bound cohesin, we propose that the dynamic behavior of the complex, mediated by PDS5 proteins, is key for successful completion of meiotic prophase I.
DeepMAsED: Evaluating the quality of metagenomic assemblies
Authors: Rojas-Carulla Mateo , Ley Ruth E. , Schölkopf Bernhard , Youngblut Nicholas D. 
Published: September 2019

AbstractMotivation/backgroundMethodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large scale metagenome assemblies.ResultsWe present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates close to a 5% contig misassembly rate in two recent large-scale metagenome assembly publications.ConclusionsDeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modelling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects.AvailabilityDeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED.