bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethanol-induced conditioned place preference and aversion differentially alter plasticity in the bed nucleus of stria terminalis
Authors: Pati Dipanwita , Pina Melanie M. , Kash Thomas L.
Published: January 2019

Contextual cues associated with drugs of abuse, such as ethanol, can trigger craving and drug seeking behavior. Pavlovian procedures, such as place conditioning, have been widely used to study the rewarding/aversive properties of drugs and the association between environmental cues and drug seeking. Previous research has shown that ethanol as an unconditioned stimulus can induce a strong conditioned place preference (CPP) or aversion (CPA) in rodents. However, the neural mechanisms underlying ethanol induced reward and aversion have not been thoroughly investigated. The bed nucleus of the stria terminalis (BNST), an integral part of the extended amygdala, is engaged by both rewarding and aversive stimuli and plays a role in ethanol seeking behavior. Here, we used ex-vivo slice physiology to probe learning-induced synaptic plasticity in the BNST following ethanol-induced CPP and CPA. Male DBA/2J mice (2-3 months old) were conditioned using previously reported ethanol-induced CPP/CPA procedures. Ethanol-induced CPP was associated with increased neuronal excitability in the ventral BNST (vBNST). Conversely, ethanol-induced CPA resulted in a significant decrease in spontaneous glutamatergic transmission without alterations in GABAergic signaling. Ethanol-CPA also led to significant increase in paired pulse ratio at excitatory synapses, suggestive of a decrease in presynaptic glutamate release. Collectively, these data demonstrate that the vBNST is involved in the modulation of contextual learning associated with both the rewarding and the aversive properties of ethanol in mice.
Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)
Authors: Tandon Kshitij , Chiang Pei-Wen , Lu Chih-Ying , Wada Naohisa , Yang Shan-Hua , Chan Ya-Fan , Chen Ping-Yun , Chang Hsiao-Yu , Chou Ming-Shean , Chen Wen-Ming , Tang Sen-Lin
Published: January 2019

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase—a dddD gene homolog found in all E. acroporae strains—and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.
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

Populations 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

It 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

Fusion 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

Mycobacterium 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

Commonly 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

Single-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

Background

Clinical 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 Results

Our 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.

Conclusions

We 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

Mature 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

Pseudomonas 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.

Importance

Pseudomonas 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

Cellular 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.
Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation
Authors: Gibson B.A. , Doolittle L.K. , Jensen L.E. , Gamarra N. , Redding S. , Rosen M.K.
Published: January 2019

Genomic DNA is highly compacted in the nucleus of eukaryotic cells as a nucleoprotein assembly called chromatin1. The basic unit of chromatin is the nucleosome, where ∼146 base pair increments of the genome are wrapped and compacted around the core histone proteins2,3. Further genomic organization and compaction occur through higher order assembly of nucleosomes4. This organization regulates many nuclear processes, and is controlled in part by histone post-transtranslational modifications and chromatin-binding proteins. Mechanisms that regulate the assembly and compaction of the genome remain unclear5,6. Here we show that in the presence of physiologic concentrations of mono- and divalent salts, histone tail-driven interactions drive liquid-liquid phase separation (LLPS) of nucleosome arrays, resulting in substantial condensation. Phase separation of nucleosomal arrays is inhibited by histone acetylation, whereas histone H1 promotes phase separation, further compaction, and decreased dynamics within droplets, mirroring the relationship between these modulators and the accessibility of the genome in cells7-10. These results indicate that under physiologically relevant conditions, LLPS is an intrinsic behavior of the chromatin polymer, and suggest a model in which the condensed phase reflects a genomic “ground state” that can produce chromatin organization and compaction in vivo. The dynamic nature of this state could enable known modulators of chromatin structure, such as post-translational modifications and chromatin binding proteins, to act upon it and consequently control nuclear processes such as transcription and DNA repair. Our data suggest an important role for LLPS of chromatin in the organization of the eukaryotic genome.
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

The 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.
An Improved Human smORF Annnotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq
Authors: Martinez Thomas F. , Chu Qian , Donaldson Cynthia , Tan Dan , Shokhirev Maxim N. , Saghatelian Alan
Published: January 2019

Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs, providing an approach to select smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.
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

Background

Our 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.

Results

Species 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.

Conclusions

A 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

Background

Single-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.

Results

We 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.

Conclusions

VPAC 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.
The role ofCaulobactercell surface structures in colonization of the air-liquid interface
Authors: Fiebig Aretha
Published: January 2019

In aquatic environments,Caulobacterspp. are often present at the boundary between liquid and air known as the neuston. I report an approach to study temporal features ofCaulobacter crescentuscolonization and pellicle biofilm development at the air-liquid interface, and have defined the role of cell surface structures in this process. At this interface,C. crescentusinitially forms a monolayer of cells bearing a surface adhesin known as the holdfast. When excised from the liquid surface, this monolayer strongly adheres to glass. The monolayer subsequently develops into a three-dimensional structure that is highly enriched in clusters of stalked cells known as rosettes. As this pellicle film matures, it becomes more cohesive and less adherent to a glass surface. A mutant strain lacking a flagellum does not efficiently reach the surface, and strains lacking type IV pili exhibit defects in organization of the three-dimensional pellicle. Strains unable to synthesize holdfast fail to accumulate at the boundary between air and liquid and do not form a pellicle. Phase contrast images support a model whereby the holdfast functions to trapC. crescentuscells at the air-liquid boundary. Unlike the holdfast, neither the flagellum nor type IV pili are required forC. crescentusto partition to the air-liquid interface. While it is well established that the holdfast enables adherence to solid surfaces, this study provides evidence that the holdfast has physicochemical properties required for partitioning of non-motile mother cells to the air-liquid interface, which facilitates colonization of this microenvironment.

Importance

In aquatic environments the boundary at the air interface is often highly enriched with nutrients and oxygen. Colonization of this niche likely confers a significant fitness advantage in many cases. This study provides evidence that the cell surface adhesin known as a holdfast enablesCaulobacter crescentusto partition to and colonize the air-liquid interface. Additional surface structures including the flagellum and type IV pili are important determinants of colonization and biofilm formation at this boundary. Considering that holdfast-like adhesins are broadly conserved inCaulobacterspp. and other members of the diverse classAlphaproteobacteria, these surface structures may function broadly to facilitate colonization of air-liquid boundaries in a range of ecological contexts including freshwater, marine, and soil ecosystems.
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Authors: Takahashi Hiro , Hayashi Noriya , Yamashita Yui , Naito Satoshi , Takahashi Anna , Fuse Kazuyuki , Satou Kenji , Endo Toshinori , Kojima Shoko , Onouchi Hitoshi
Published: January 2019

Background

Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST betweenArabidopsisand any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.

Results

To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 88 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved in wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.

Conclusions

This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.
S. cerevisiaeSrs2 helicase ensures normal recombination intermediate metabolism during meiosis and prevents accumulation of Rad51 aggregates
Authors: Hunt Laura J , Ahmed Emad , Kaur Hardeep , Ahuja Jasvinder , Hulme Lydia , Chou Ta-Chung , Lichten Michael , Goldman Alastair SH
Published: January 2019

We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilizes Rad51-DNA filaments, and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction ofsrs2mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalized with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity, and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards inter-homologue strand invasion characteristic of normal meiosis.srs2mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division.
Integrin cytoplasmic domain and pITAM compete for spleen tyrosine kinase binding
Authors: Antenucci Lina , Hellman Maarit , Hytönen Vesa P. , Permi Perttu , Ylänne Jari
Published: January 2019

In hematopoietic tissues cell-cell communication involves immunoreceptors and specialized cell adhesion receptors that both mediate intracellular signals. Spleen tyrosine kinase (Syk) is a non-receptor tyrosine kinase involved in the downstream signaling of both immunoreceptors tyrosine activation motif (ITAM) receptors and integrin family cell adhesion receptors. Both phosphorylated ITAM (pITAM) and integrins bind to the regulatory domain of Syk composed of two Src homology 2 (SH2) domains. The interaction with pITAM is mediated by binding of a specific phosphotyrosine to each of the SH2 domains, leading to conformational changes and Syk kinase activation. Integrins bind to the interdomain A segment between the two SH2 domains and to the N-terminal SH2 domain, but the detailed binding site is not known. In order to map the binding site, we performed NMR titration experiments. We found that integrin cytoplasmic domain peptide induced chemical shift changes near the IA segment and at the phosphotyrosine binding site of the N-terminal SH2 domain of Syk. These changes were distinct, but partially overlapping with those induced by pITAM peptide. We were also able to show that pITAM peptide inhibited integrin binding to Syk regulatory domain. These results suggest that ITAM receptors and integrins cannot bind simultaneously to Syk, but provide two distinct routes for Syk activation.
Managing genomic variant calling workflows with Swift/T
Authors: Ahmed Azza E. , Heldenbrand Jacob , Asmann Yan , Fadlelmola Faisal M. , Katz Daniel S. , Kendig Katherine , Kendzior Matthew C. , Li Tiffany , Ren Yingxue , Rodriguez Elliott , Weber Matthew R. , Wozniak Justin M. , Zermeno Jennie , Mainzer Liudmila S.
Published: January 2019

Genomic variant discovery is frequently performed using the GATK Best Practices variant calling pipeline, a complex workflow with multiple steps, fans/merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Here we describe a wrapper for the GATK-based variant calling workflow using the Swift/T parallel scripting language. Standard built-in features include the flexibility to split by chromosome before variant calling, optionally permitting the analysis to continue when faulty samples are detected, and allowing users to analyze multiple samples in parallel within each cluster node. The use of Swift/T conveys two key advantages: (1) Thanks to the embedded ability of Swift/T to transparently operate in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.,) a single workflow is trivially portable across numerous clusters; (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, conditional on the analyst’s choice, which makes the workflow easy to maintain. This modular design permits separation of the workflow into multiple stages and the request of resources optimal for each stage of the pipeline. While Swift/T’s implicit data-level parallelism eliminates the need for the developer to code parallel analysis of multiple samples, it does make debugging of the workflow a bit more difficult, as is the case with any implicitly parallel code. With the above features, users have a powerful and portable way to scale up their variant calling analysis to run in many traditional computer cluster architectures.

https://github.com/ncsa/Swift-T-Variant-Calling

http://swift-t-variant-calling.readthedocs.io/en/latest/
Crystal structure of trans-bis[2-(1H-benzotriazol-1-yl)acetato-κO]bis(ethanolamine-κ2
N,O)copper(II)
Authors: Alieva Guloy K. , Ashurov Jamshid M. , Kadirova Shahnoza A. , Ibragimov Bakhtiyar T. , Zakhidov Kasim A.
Published: January 2019

The reaction of 2-(1H-benzotriazol-1-yl)acetic acid (HBTA; C8H7N3O2) and monoethanolamine (MEA; C2H7NO) with CuCl2·2H2O resulted in the formation of the title complex, [Cu(C8H6N3O2)2(C2H7NO)2] or [Cu(BTA)2(MEA)2]. Its asymmetric unit comprises one BTA anion coordinating to the Cu2+ cation (site symmetry \overline{1}) through the carboxyl O atom, and one MEA ligand chelating the metal cation by two heteroatoms (O and N). The equatorial Cu—O and Cu—N bond lengths are similar at 2.029 (1) and 1.980 (2) Å, respectively, while the length of the axial Cu—O bond is considerably greater [2.492 (2) Å], as is typical for Jahn–Teller-distorted systems. An intramolecular hydrogen bond is present between the hydroxy group of the MEA ligand and the non-coordinating O atom of the carboxylate group. Intermolecular hydrogen bonding involving the amino function of the MEA ligand and the carboxylate group results in eight-membered rings with an R
2
2(8) graph-set motif. The molecules are further linked by C—H...π interactions involving the triazole rings and methylene groups of MEA, thus generating an overall three-dimensional supramolecular framework.
A fresh view on particle swarm optimization to develop a precise model for predicting rock fragmentation
Authors: Sayevand Khosro , Arab Hossein
Published: January 2019

Purpose

The purpose of this paper is to propose a gauge for the convergence of the deterministic particle swarm optimization (PSO) algorithm to obtain an optimum upper bound for PSO algorithm and also developing a precise equation for predicting the rock fragmentation, as important aims in surface mines.

Design/methodology/approach

In this study, a database including 80 sets of data was collected from 80 blasting events in Shur river dam region, in Iran. The values of maximum charge per delay (W), burden (B), spacing (S), stemming (ST), powder factor (PF), rock mass rating (RMR) and D80, as a standard for evaluating the fragmentation, were measured. To check the performance of the proposed PSO models, artificial neural network was also developed. Accuracy of the developed models was evaluated using several statistical evaluation criteria, such as variance account for, R-square (R2) and root mean square error.

Findings

Finding the upper bounds for the difference between the position and the best position of particles in PSO algorithm and also developing a precise equation for predicting the rock fragmentation, as important aims in surface mines.

Originality/value

For the first time, the convergence of the deterministic PSO is studied in this study without using the stagnation or the weak chaotic assumption. The authors also studied application of PSO inpredicting rock fragmentation.
Modelling of ice rubble in the punch shear tests with cohesive 3D discrete element method
Authors: Sorsimo Arto , Heinonen Jaakko
Published: January 2019

Purpose

This paper aims to simulate a punch shear test of partly consolidated ice ridge keel by using a three-dimensional discrete element method. The authors model the contact forces between discrete ice blocks with Hertz–Mindlin contact model. For freeze bonds between the ice blocks, the authors apply classical linear cohesion model with few modifications. Based on punch shear test simulations, the authors are able to determine the main characteristics of an ice ridge from the material parameters of the ice and freeze bonds.

Design/methodology/approach

The authors introduced a discrete model for ice that can be used for modelling of ice ridges. The authors started with short introduction to current status with ice ridge modelling. Then they introduced the model, which comprises Hertz–Mindlin contact model and freeze bond model with linear cohesion and softening. Finally, the authors presented the numerical results obtained using EDEM is commercial Discrete Element Modeling software (EDEM) and analysed the results.

Findings

The Hertz–Mindlin model with cohesive freeze bonds and linear softening is a reasonable model for ice rubble. It is trivial that the ice blocks within the ice ridge are not spherical particles, but according to results, the representation of ice blocks as spheres gave promising results. The simulation results provide information on how the properties of freeze bond affect the results of punch shear test. Thus, the simulation results can be used to approximate the freeze bonds properties within an ice ridge when experimental data are available.

Research limitations/implications

As the exact properties of ice rubble are unknown, more research is required both in experimental and theoretical fields of ice rubble mechanics.

Originality/value

Based on this numerical study, the authors are able to determine the main characteristics of an ice ridge from material parameters of ice and freeze bonds. Furthermore, the authors conclude that the model creates a promising basis for further development in other applications within ice mechanics.
Evaluating local vulnerability and organisational resilience to frequent flooding in Africa: the case of Northern Cameroon
Authors: Bang Henry , Miles Lee , Gordon Richard
Published: January 2019

Purpose

The purpose of this paper is to evaluate local vulnerability and organisational resilience including coping/adaptive capacity to climate risks, specifically frequent flooding in Northern Cameroon.

Design/methodology/approach

The research is exploratory/deductive and draws upon qualitative methods, secondary and empirical techniques supplemented by semi-structured qualitative interviews with senior disaster managers. Secondary information sources, which include peer review articles, government reports/plans, newspaper articles and other grey literature, enhanced the analysis.

Findings

The research findings have unveiled the physical and social vulnerability of Northern Cameroon to frequent flooding. Results also show that institutional performance for flood management in Cameroon is ineffective, and adaptive capacity is highly deficient. Cameroon’s legislative framework for flood management is weak, and this exacerbates the poor implementation of structural and non-structural flood management measures. Results also indicate issues with relief, evacuation and foreign assistance in flood management. Recommendations that focus on enhancing capacity of response to frequent flooding via reducing vulnerabilities, managing resilience and enhancing adaptive capacity are provided.

Originality/value

Using Gallopin’s (2006) model of vulnerability, this paper makes a distinct contribution by offering insights into the role of adaptive capacity in disaster management systems in developing (African) countries via an evaluation of vulnerabilities and organisational resilience to repeated flooding in Northern Cameroon.
The crossover effect of work–family conflict among hotel employees
Authors: Pan Su-Ying , Yeh Ying-Jung
Published: January 2019

Purpose

Work–family research has established the existence of a crossover effect, wherein a given perception is transferable between two intimate persons. However, little research has been done to delineate this crossover process. Therefore, grounded in the conservation of resources theory, the present study aims to examine why and how a supervisor’s work–family conflict (WFC) is related to his or her subordinates’ WFC. The authors focus on three resource-related mechanisms and explore the consequences of subordinates’ WFC.

Design/methodology/approach

Questionnaire surveys were collected from 180 supervisor–subordinate dyads from five hotels. Mplus was used to test the framework.

Findings

The results support the notion that supervisor’s negative affect and subordinate’s workload account for the crossover effect of WFC. Moreover, subordinates’ WFC is found to be related to lower job satisfaction and higher turnover intention.

Research limitations/implications

The current study highlights the downward effect of supervisors’ WFC, a phenomenon that has been understudied in the extant research. Alternative mediators or moderators in the relationship between supervisors’ WFC and subordinates’ WFC can be explored by future research.

Practical implications

Hotels should help supervisors to effectively manage the work and family dynamic through training and changing the “face time” culture.

Originality/value

Grounded in the conservation of resources theory, the authors propose a framework that incorporates WFC into the crossover model.