bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional screening of β-Glucanase Producing Actinomycetes Strains from Western Ghats ecosystems of Kerala, India
Authors: Edison Lekshmi K. , Pradeep N. S.
Published: April 2020

Screening of potential soil actinomycetes is static at infant phase because less than one part of soil biodiversity has been explored. An important factor considered before isolating microorganisms with potential application is understanding the biodiversity and environmental features associated with growth. Search of distinctive enzymes from unusual ecological habitats are highly fascinating and have great opportunities that may also pointed the developments in high throughput screening programs. In the present study Western Ghats hot spot regions of Kerala has been explored for the actinomycetes strains with beta glucanase activity. A total of 127 actinomycetes strains were isolated. After qualitative primary screening 106 strains (83%) produced exo-β-1,4-glucanase enzyme and 79 strains (62%) produced endo-β-1,3-glucanase enzyme. The quantitative secondary screening confirmed the strains TBG-MR17 and TBG-AL13 recognised as respective dominant producers of exo-β-1,4-glucanase and endo-β-1,3-glucanase enzymes. The study reveals the richness of the Western Ghats soils with innumerable actinomycetes having potential β-glucanase activities.
Long Noncoding RNA Derived from LncRNA–mRNA Co-expression Networks Modulates the Locust Phase Change
Authors: Li Ting , Chen Bing , Yang Pengcheng , Wang Depin , Du Baozhen , Kang Le
Published: April 2020

Long noncoding RNAs (lncRNAs) regulate various biological processes from gene expression to animal behavior. Although protein-coding genes, microRNAs, and neuropeptides play important roles in the regulation of phenotypic plasticity in migratory locust, empirical studies on the function of lncRNAs in the process remain limited. Here, we applied high-throughput RNA-seq to characterize the expression patterns of lncRNAs and mRNAs in the time course of the locust phase change. LncRNAs displayed more rapid response at the early stages of the time-course treatments than mRNA expression. Functional annotations demonstrated that early changed lncRNAs employed different pathways in isolation and crowding processes to cope up with the changes in population density. Finally, two overlapping hub lncRNA loci in the crowding and isolation networks were screened to be functionally verified. Experimental validation indicated that LNC1010057 could act as a potential regulator to modulate the locust phase change. This work offers new insights into the mechanism underlying the locust phase change and expands the scope of lncRNA functions in animal behavior.
Algal growth at environmentally relevant concentrations of suspended solids: implications for microplastic hazard assessment
Authors: Gorokhova Elena , Ek Karin , Reichelt Sophia
Published: April 2020

Hazard assessment of microplastic is challenging because standard toxicity testing is mostly developed for soluble (at least partially) chemicals. Adverse effects can occur when test organisms are exposed to turbid environments with various particulate matter (PM), both natural, such as sediment, and anthropogenic, such as microplastic. It is, therefore, relevant to compare responses to PM exposure between the microplastic and other suspended solids present at ecologically relevant concentrations; this can be done by using reference materials when assessing hazard potential of microplastics. Here, we evaluated growth inhibition in unicellular algaRaphidocelis subcapitataexposed to different suspended solids (microplastic, kaolin, and cellulose; 10, 100 and 1000 mg/L) during 72 h; algae without added solids were used as a control. In addition, aggregate formation in the exposure systems was analyzed using particle size distribution data. At 10 and 100 mg/L, no adverse growth effects were observed in any treatments; moreover, algal growth was significantly stimulated in kaolin and cellulose treatments compared to the control. However, at 1000 mg/L, all tested materials exerted growth inhibition, with no significant differences among the treatments. The comparison among particle size distributions across the treatments showed that both PM concentration and size of the particle aggregates were significant growth predictors for all materials tested. Therefore, at high concentrations, both natural and anthropogenic materials have similar capacity to cause adverse effects in algal growth inhibition tests, which must be taken into account in hazard assessment of plastic litter.
Gray Matter alterations in MS and CIS: a Coordinate based Meta-analysis and regression
Authors: Singh Sonika , Tench Christopher , Tanasescu Radu , Constantinescu Cris
Published: April 2020

The purpose of this coordinate based meta-analysis (CBMA) was to summarise the available evidence related to regional grey matter (GM) changes in patients with multiple sclerosis (MS) and clinically isolated syndrome (CIS). CBMA is a way to find the consistent results across multiple independent studies that are otherwise not easily comparable due to methodological differences. The coordinate based random effect size (CBRES) meta-analysis method utilizes the reported coordinates (foci of the clusters of GM loss) and Z score standardised by number of subjects, controlling type I error rate by false cluster discovery rate (FCDR). Thirty-four published articles reporting forty-five independent studies using voxel-based morphometry (VBM) for the assessment of GM atrophy between MS or CIS patients and healthy controls were identified from electronic databases. The primary meta-analysis identified clusters of spatially consistent cross-study reporting of GM atrophy; subgroup analyses and meta-regression were also performed. This meta-analysis demonstrates consistent areas of GM loss in MS or CIS, in the form of significant clusters. Some clusters also demonstrate correlation with disease duration.
Studies on trans-sutural distraction osteogenesis-related genes based on transcriptome sequencing
Authors: Wang Baicheng , Xue Hongyu , Tong Haizhou , Zhang Peiyang , Wang Mei , Sun Yidan , Zhao Zhenmin
Published: April 2020

Trans-sutural distraction osteogenesis (TSDO) is an important approach to improve mid-face hypoplasia. In recent years, many studies have been carried out on physical mechanisms of TSDO; however, it’s specific cytological and molecular mechanisms are still unclear. In this study, we performed transcriptome sequencing analysis in Sprague Dawley rats at 1 and 2 weeks after suture osteogenesis and compared RNA expression levels between experimental and control groups. At one week, enrichment pathways were mainly up-regulated in muscle- and bone-related pathways. By contrast, pathways of the immune system showed a state of inhibition and down-regulation, especially for B cells; the main immune pathways showed significant down-regulation. However, two weeks later, the experimental group showed positive up-regulation of the pathways related to DNA synthesis and replication, cell cycle, and chromosome replication. At the same time, the immune pathways that were down-regulated in the first week were up-regulated in the second week. In other words, the up-regulated muscle- and bone-related pathways show opposite trends. The expression of bone- and myogenesis-related transcriptome was up-regulated and the immune-related pathways were down-regulated in the experimental group at 1 week. At 2 weeks, the pathways related to bone- and muscle were down-regulated, while those related to cell cycle regulation and DNA replication were up-regulated. These results suggest that musculoskeletal-related molecules may play an important role during suture osteogenesis at 1 week, and immune regulation may be involved in this process; however, at 2 weeks, molecules related to cell proliferation and replication may be a major role.
Transcriptional profiling and single-cell chimerism analysis identifies human tissue resident T cells in the human skin after allogeneic stem cell transplantation
Authors: de Almeida Gustavo P. , Lichtner Peter , Mädler Sophia , Chu Chang-Feng , Zielinski Christina E.
Published: April 2020

Tissue resident memory T cells (TRM) have recently emerged as crucial cellular players for host defense in a wide variety of tissues and barrier sites. Mouse models revealed that they are maintained long-termin locounlike recirculating effector memory T cells (TEM). Insights into the maintenance and regulatory checkpoints of human tissue resident T cells (TRM) remain scarce, especially due to the obstacles in tracking T cells over time and system-wide in humans. We present a clinical model that allowed us to overcome these limitations. We demonstrate that allogeneic stem cell transplantation resulted in compartmentalization of host T cells in the human skin despite complete donor T cell chimerism in the blood, thus unmasking long-term persistence of tissue resident T cell subsets of host origin within the diverse skin T cell community. Single-cell transcriptional profiling paired with single-cell chimerism analysis provided an in-depth characterization of thesebona fideskin resident T cells. Their phenotype, functions and regulatory checkpoints may serve therapeutic strategies for the treatment of autoimmune diseases and chronic infections, where their specific depletion versus maintenance, respectively, will have to be harnessed pharmaceutically.
Capture-based enrichment ofTheileria parvaDNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity
Authors: Palmateer Nicholas C , Tretina Kyle , Orvis Joshua , Ifeonu Olukemi O , Crabtree Jonathan , Drabék Elliott , Pelle Roger , Awino Elias , Gotia Hanzel T , Munro James B , Tallon Luke , Morrison W Ivan , Daubenberger Claudia A , Nene Vish , Knowles Donald P , Bishop Richard P , Silva Joana C
Published: April 2020

Theileria parvais an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissibleT. parvabut not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associatedT. parvapopulations. Here, we describe a capture-based target enrichment approach that enables, for the first time,de novoassembly of nearly completeT. parvagenomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derivedT. parvaparasites.De novogenome assemblies generated for cattle genotypes differ from the reference by ∼54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derivedT. parvagenome, which is larger than the genome from the reference, cattle-derived, Muguga strain. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derivedT. parvaand the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an averageFST, genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derivedT. parvaparasites more commonly seen between, rather than within, species, with clear implications for vaccine development. The DNA capture approach used provides clear advantages over alternativeT. parvaDNA enrichment methods used previously and enables in-depth comparative genomics in this apicomplexan parasite.
On the temporally flexible structure of plant-pollinator interaction networks
Authors: CaraDonna Paul J. , Waser Nickolas M.
Published: April 2020

Ecological communities consist of species that are joined in complex networks of interspecific interaction. The interactions that networks depict often form and dissolve rapidly, but this temporal variation is not well integrated into our understanding of the causes and consequences of network structure. If interspecific interactions exhibit temporal flexibility across time periods over which organisms co-occur, then the emergent structure of the corresponding network may also be temporally flexible, something that a temporally-static perspective would miss. Here, we use an empirical system to examine short-term flexibility in network structure (connectance, nestedness, and specialization), and in individual species interactions that contribute to that structure. We investigated weekly plant-pollinator networks in a subalpine ecosystem across three summer growing seasons. To link the interactions of individual species to properties of their networks, we examined weekly temporal variation in species’ contributions to network structure. As a test of the potential robustness of networks to perturbation, we also simulated the random loss of species from weekly networks. We then compared the properties of weekly networks to the properties of cumulative networks that aggregate field observations over each full season. A week-to-week view reveals considerable flexibility in the interactions of individual species and their contributions to network structure. For example, species that would be considered relatively generalized across their entire activity period may be much more specialized at certain times, and at no point as generalized as the cumulative network may suggest. Furthermore, a week-to-week view reveals corresponding temporal flexibility in network structure and potential robustness throughout each summer growing season. We conclude that short-term flexibility in species interactions leads to short-term variation in network properties, and that a season-long, cumulative perspective may miss important aspects of the way in which species interact, with implications for understanding their ecology, evolution, and conservation.
A Powerful Method for Pleiotropic Analysis under Composite Null Hypothesis Identifies Novel Shared Loci Between Type 2 Diabetes and Prostate Cancer
Authors: Ray Debashree , Chatterjee Nilanjan
Published: April 2020

Summary

There is increasing evidence that pleiotropy, the association of multiple traits with the same genetic variants/loci, is a very common phenomenon. Cross-phenotype association tests are often used to jointly analyze multiple traits from a GWAS. The underlying methods, however, are often designed to test the global null hypothesis that there is no association of a genetic variant with any of the traits, the rejection of which does not implicate pleiotropy. In this article, we propose a new statistical approach, PLACO, for specifically detecting pleiotropic loci between two traits by considering an underlying composite null hypothesis that a variant is associated with none or only one of the traits. We propose testing the null hypothesis based on the product of the Z-statistics of the SNPs across two studies and derive a null distribution of the test statistic in the form of a mixture distribution that allows for fractions of SNPs to be associated with none or only one of the traits. We borrow approaches from the statistical literature on mediation analysis that allow asymptotic approximation of the null distribution avoiding estimation of nuisance parameters related to mixture proportions and variance components. Simulation studies demonstrate that the proposed method can maintain type I error and can achieve major power gain over alternative simpler methods that are typically used for testing pleiotropy. PLACO allows correlation in summary statistics between studies that may arise due to sharing of controls between disease traits. Application of PLACO to publicly available summary data from two large case-control GWAS of Type 2 Diabetes and of Prostate Cancer implicated a number of novel shared genetic regions nearZBTB38(3q23),RGS17(6q25.3),HAUS6(9p22.1),UBAP2(9p13.3),RAPSN(11p11.2),AKAP6(14q12),KNL1(15q15) andZNF236(18q23).
Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
Authors: Abrouk Michael , Ahmed Hanin Ibrahim , Cubry Philippe , Šimoníková Denisa , Cauet Stéphane , Bettgenhaeuser Jan , Gapa Liubov , Pailles Yveline , Scarcelli Nora , Couderc Marie , Zekraoui Leila , Kathiresan Nagarajan , Čížková Jana , Hřibová Eva , Doležel Jaroslav , Arribat Sandrine , Bergès Hélène , Wieringa Jan J. , Gueye Mathieu , Kane Ndjido A. , Leclerc Christian , Causse Sandrine , Vancoppenolle Sylvie , Billot Claire , Wicker Thomas , Vigouroux Yves , Barnaud Adeline , Krattinger Simon G.
Published: April 2020

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we established high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
RbAp46/48LIN-53and HAT-1 are required for initial CENP-AHCP-3deposition and de novo centromere formation inCaenorhabditis elegansembryos
Authors: Lin Zhongyang , Yee Yuen Karen Wing
Published: April 2020

Foreign DNA microinjected into theCaenorhabditis elegansgermline forms episomal extra-chromosomal arrays, or artificial chromosomes (ACs), in embryos. Injected linear, short DNA fragments concatemerize into high molecular weight (HMW)-DNA arrays that are visible as punctate DAPI-stained foci in oocytes, which undergo chromatinization and centromerization in embryos. The inner centromere, inner and outer kinetochore components, including AIR-2, CENP-AHCP-3, Mis18BP1KNL-2and BUB-1, assemble onto the nascent ACs during the first mitosis. Yet, due to incomplete DNA replication of the nascent ACs, centromeric proteins are not oriented at the poleward faces of the nascent ACs in mitosis, resulting in lagging ACs. The DNA replication efficiency of ACs improves over several cell cycles. We found that a condensin subunit, SMC-4, but not the replicative helicase component, MCM-2, facilitatesde novoCENP-AHCP-3deposition on nascent ACs. Furthermore, H3K9ac, H4K5ac, and H4K12ac are highly enriched on newly chromatinized ACs. HAT-1 and RbAp46/48LIN-53, which are essential forde novocentromere formation and segregation competency of nascent ACs, also hyperacetylate histone H3 and H4. Different from centromere maintenance on endogenous chromosomes, where Mis18BP1KNL-2functions upstream of RbAp46/48LIN-53, RbAp46/48LIN-53depletion causes the loss of both CENP-AHCP-3and Mis18BP1KNL-2initial deposition atde novocentromeres on ACs.
Designing Feature-Controlled Humanoid Antibody Discovery Libraries Using Generative Adversarial Networks
Authors: Amimeur Tileli , Shaver Jeremy M. , Ketchem Randal R. , Taylor J. Alex , Clark Rutilio H. , Smith Josh , Van Citters Danielle , Siska Christine C. , Smidt Pauline , Sprague Megan , Kerwin Bruce A. , Pettit Dean
Published: April 2020

We demonstrate the use of a Generative Adversarial Network (GAN), trained from a set of over 400,000 light and heavy chain human antibody sequences, to learn the rules of human antibody formation. The resulting model surpasses commonin silicotechniques by capturing residue diversity throughout the variable region, and is capable of generating extremely large, diverse libraries of novel antibodies that mimic somatically hypermutated human repertoire response. This method permits us to rationally designde novohumanoid antibody libraries with explicit control over various properties of our discovery library. Through transfer learning, we are able to bias the GAN to generate molecules with key properties of interest such as improved stability and developability, lower predicted MHC Class II binding, and specific complementarity-determining region (CDR) characteristics. These approaches also provide a mechanism to better study the complex relationships between antibody sequence and molecular behavior, bothin vitroandin vivo. We validate our method by successfully expressing a proof-of-concept library of nearly 100,000 GAN-generated antibodies via phage display. We present the sequences and homology-model structures of example generated antibodies expressed in stable CHO pools and evaluated across multiple biophysical properties. The creation of discovery libraries using ourin silicoapproach allows for the control of pharmaceutical properties such that these therapeutic antibodies can provide a more rapid and cost-effective response to biological threats.
Mechanistic modeling of the SARS-CoV-2 disease map
Authors: Rian Kinza , Esteban-Medina Marina , Hidalgo Marta R. , Çubuk Cankut , Falco Matias M. , Loucera Carlos , Gunyel Devrim , Ostaszewski Marek , Peña-Chilet María , Dopazo Joaquín
Published: April 2020

Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map in which the detailed activity of the human signaling circuits related to the viral infection and the different antiviral responses, including immune and inflammatory activities, can be inferred from gene expression experiments. Moreover, given to the mechanistic properties of the model, the effect of potential interventions, such as knock-downs, over-expression or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied in specific conditions. By providing a holistic, systems biology approach to the understanding of the complexities of the viral infection process, this tool will become an important asset in the search for efficient antiviral treatments.

The tool is freely available at:http://hipathia.babelomics.org/covid19/
DenovoIdentification of Cross-linked Peptides via Isotope Coded Linkage Tags
Authors: Gunawardena Harsha P.
Published: April 2020

An isotope labeled cross-linker (asymmetric d4-DTSSP) was developed to streamline the efforts required for the detection of cross-linked peptides. The cross-linking and mass spectrometry strategy we call Isotope Tagging of Interacting Proteins (iTIP) has improved the specificity of detecting cross-linked peptides and the accurate identification of the interacting peptide sequences via the incorporation of isotopic signatures that are readily observed in the MS/MS spectra. All tryptic peptides derived from the cross-linking reactions of a protein complex are first subjected to ETD-MS2which results in the facile cleavage of the cross-linker at the disulfide bond and the release of inter-linked polypeptide chains that are detected as a pair of peaks (doublets) in the MS2spectrum. The constituent peptide halves that are tagged by the heavy/light ends of the cross-linker are easily mass-selected from all other fragment ions, and each polypeptide half is then subjected to CID or HCD-MS3for identification. The MS3spectra are subjected to conventional database search strategies available for the sequencing of linear or non-cross-linked peptides. The confident identification of each polypeptide is further assisted by the presence of a stable isotope labeled fragment ions that localizes the cross-linked site on the polypeptide sequence.
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Authors: Mao Ting-Ru , Liu Ye-Wei , Meegaskumbura Madhava , Yang Jian , Ellepola Gajaba , Senevirathne Gayani , Fu Cheng-Hai , Gross Joshua B. , Pie Marcio R.
Published: April 2020

Epitomized by the well-studied Astyanax mexicanus, cavefishes provide important model organisms to understand adaptations in response to divergent natural selection. However, the spectacular Sinocyclocheilus diversification of China, the most diverse cavefish clade in the world harboring nearly 75 species, demonstrate evolutionary convergence for many traits, yet remain poorly understood in terms of their morphological evolution. Here, using a broad sample of 49 species representative of this diversification, we analyze patterns of Sinocylocheilus evolution in a phylogenetic context. We categorized species into morphs based on eye-related condition: Blind, Micro-eyed (small-eyed), and Normal-eyed and we also considered three habitat types (Troglodytic – cave-restricted; Troglophilic – cave-associated; Surface – outside of caves). Geometric morphometric analyses show Normal-eyed morphs with fusiform shapes being segregated from Blind/Micro-eyed (Eye-regressed) morphs with deeper bodies along the first principal component (“PC”) axis. The second PC axis accounts for shape complexity related to the presence of horns. Ancestral character reconstructions of morphs suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to the typical morphology of ancestral Normal-eyed morphs. Interestingly, only some Blind or Micro-eyed morphs bear horns and they are restricted to a single clade (Clade B) and arising from a Troglodytic ancestral species. Our geophylogeny shows an east-to-west diversification spanning the Pliocene and the Pleistocene, with Troglodytic species dominating karstic subterranean habitats of the plains whereas predominantly Surface species inhabit streams and pools in hills to the west (perhaps due to the scarcity of caves). Integration of morphology, phylogeny and geography suggests Sinocyclocheilus are pre-adapted for cave dwelling. Analyses of evolutionary rates suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 3.3 to 12.5 fold increase in the evolutionary rate of eye regression. Furthermore, body size and eye size have undergone reversals, but horns have not, a trait that seem to require substantial evolutionary time to form. These results, compared to the Astyanax model system, indicate Sinocyclocheilus fishes demonstrate extraordinary morphological diversity and variation, offering an invaluable model system to explore evolutionary novelty.
Procentriole microtubules as drivers of centriole reduplication
Authors: Vasquez-Limeta Alejandra , Sullenberger Catherine , Kong Dong , Lukasik Kimberly , Shukla Anil , Loncarek Jadranka
Published: April 2020

Centriole reduplication leads to the formation of supernumerary centrosomes, which promote cellular transformation, invasion and are a hallmark of tumors. A close association between a mother centriole and a procentriole (engagement), established during centriole duplication, intrinsically blocks reduplication. Premature loss of centriole association predisposes centrioles for reduplication and occurs during various types of cell cycle arrests in the presence of high Polo-like kinase 1 activity. Here we use nano-scale imaging and biochemistry to reveal the processes leading to the loss of centriole association and reduplication. We discover that centriole reduplication is driven by events occurring on procentriole microtubule walls. These events are mechanistically different from mitotic centriole separation driven by Pericentrin and Separase but are similar to the physiological process of centriole distancing occurring in unperturbed cycling G2 cells. We propose a concept in which centriole reduplication is a consequence of hijacked and amplified centriole maturation process.

Highlights

Separase-mediated Pericentrin reorganization is not required for centriole distancing and reduplication in interphase.

Expression of active Plk1 in S phase leads to centrosomal ultrastructural changes resembling G2 phase.

Procentrioles without microtubule walls cannot disengage.

Centriole distancing is intrinsically regulated by the events occurring on procentriole microtubules.
Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy
Authors: Metcalfe Kyle S. , Murali Ranjani , Mullin Sean W. , Connon Stephanie A. , Orphan Victoria J.
Published: April 2020

Archaeal anaerobic methanotrophs (‘ANME’) and sulfate-reducing Deltaproteobacteria (‘SRB’) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partnersin situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA Illumina iTag amplicon libraries prepared from Costa Rica sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescencein situhybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a completenifHDKoperon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression ofnifHin SEEP-SRB1g and diazotrophic activity within ANME-2b/SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain-reaction (HCR-) FISH targetingnifHtranscripts and by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b/SEEP-SRB1g consortia incubated with a headspace containing CH4and15N2revealed differences in cellular15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.
ERK basal and pulsatile activity are differentially regulated in mammalian epidermis to control proliferation and exit from the stem cell compartment
Authors: Hiratsuka Toru , Bordeu Ignacio , Pruessner Gunnar , Watt Fiona M.
Published: April 2020

Fluctuation in signal transduction pathways is frequently observed during mammalian development. However, its role in regulating stem cells has not been explored. Here we tracked spatiotemporal ERK MAPK dynamics in human epidermal stem cells. While stem cells and differentiated cells were distinguished by high and low stable basal ERK activity, respectively, we also found cells with pulsatile ERK activity. Transitions from Basalhi-Pulselo(stem) to Basalhi-Pulsehi, Basalmid-Pulsehi, and Basallo-Pulselo(differentiated) cells occurred in expanding keratinocyte colonies and in response to a range of differentiation stimuli. Pharmacological inhibition of ERK induced differentiation only when cells were in the Basalmid-Pulsehistate. Basal ERK activity and pulses were differentially regulated by DUSP10 and DUSP6, leading us to speculate that DUSP6-mediated ERK pulse downregulation promotes initiation of differentiation whereas DUSP10-mediated downregulation of mean ERK activity promotes and stabilizes post-commitment differentiation. Quantification of MAPK1/3, DUSP6 and DUSP10 transcripts in individual cells demonstrated that ERK activity is controlled both transcriptionally and post-transcriptionally. When cells were cultured on a topography that mimics the epidermal-dermal interface, spatial segregation of mean ERK activity and pulses was observed. In vivo imaging of mouse epidermis revealed a patterned distribution of basal cells with pulsatile ERK activity and downregulation was linked to the onset of differentiation. Our findings demonstrate that ERK MAPK signal fluctuations link kinase activity to stem cell dynamics.

Significance

Understanding how intracellular signaling cascades control cell fate is a key issue in stem cell biology. Here we show that exit from the stem cell compartment in mammalian epidermis is characterised by pulsatile ERK MAPK activity. Basal activity and pulses are differentially regulated by DUSP10 and DUSP6, two phosphatases that have been shown previously to regulate differentiation commitment in the epidermis. ERK activity is controlled both transcriptionally and post-transcriptionally. Spatial segregation of mean ERK activity and pulses is observed both in reconstituted human epidermis and in mouse epidermis. Our findings demonstrate the tight spatial and temporal regulation of ERK MAPK expression and activity in mammalian epidermis.
High performance intensiometric direct- and inverse-response genetically encoded biosensors for citrate
Authors: Zhao Yufeng , Shen Yi , Wen Yurong , Campbell Robert E.
Published: April 2020

Motivated by the growing recognition of citrate as a central metabolite in a variety of biological processes associated with healthy and diseased cellular states, we have developed a series of high-performance genetically encoded citrate biosensors suitable for imaging of citrate concentrations in mammalian cells. The design of these biosensors was guided by structural studies of the citrate-responsive sensor histidine kinase, and took advantage of the same conformational changes proposed to propagate from the binding domain to the catalytic domain. Following extensive engineering based on a combination of structure guided mutagenesis and directed evolution, we produced an inverse-response biosensor (ΔF/Fmin~ 18) designated Citroff1 and a direct-response biosensor (ΔF/Fmin~ 9) designated Citron1. We report the x-ray crystal structure of Citron1 and demonstrate the utility of both biosensors for qualitative and quantitative imaging of steady-state and pharmacologically-perturbed citrate concentrations in live cells.
Treated HIV Infection Alters Phenotype But Not HIV-specific Function of Peripheral Blood Natural Killer Cells
Authors: Zhao Nancy Q. , Ferreira Anne-Maud , Grant Philip M. , Holmes Susan , Blish Catherine A.
Published: April 2020

Natural killer (NK) cells are the predominant antiviral cells of the innate immune system, and may play an important role in acquisition and disease progression of HIV. While untreated HIV infection is associated with distinct alterations in the peripheral blood NK cell repertoire, less is known about how NK phenotype is altered in the setting of long-term viral suppression with antiretroviral therapy (ART), as well as how NK memory can impact functional responses. As such, we sought to identify changes in NK cell phenotype and function using high-dimensional mass cytometry to simultaneously analyze both surface and functional marker expression of peripheral blood NK cells in a cohort of ART-suppressed, HIV+ patients and HIV-healthy controls. We found that the NK cell repertoire following IL-2 treatment was altered in individuals with treated HIV infection compared to healthy controls, with increased expression of markers including NKG2C and CD2, and decreased expression of CD244 and NKp30. Using co-culture assays with autologous,in vitroHIV-infected CD4 T cells, we identified a subset of NK cells with enhanced responsiveness to HIV-1-infected cells, but no differences in the magnitude of anti-HIV NK cell responses between the HIV+ and HIV-groups. In addition, by profiling of NK cell receptors on responding cells, we found similar phenotypes of HIV-responsive NK cell subsets in both groups. Lastly, we identified clusters of NK cells that are altered in individuals with treated HIV infection compared to healthy controls, but found that these clusters are distinct from those that respond to HIVin vitro. As such, we conclude that while chronic, treated HIV infection induces a reshaping of the IL-2-stimulated peripheral blood NK cell repertoire, it does so in a way that does not make the repertoire more HIV-specific.
Discovering the Molecular Determinants ofPhaeobacter inhibenssusceptibility toPhaeobacterphage MD18
Authors: Urtecho Guillaume , Campbell Danielle E. , Hershey David M. , Whitaker Rachel J. , O’Toole George A.
Published: April 2020

Bacteriophage technologies have immense potential as antibiotic therapies and in genetic engineering. Understanding the mechanisms that bacteriophages implement to infect their hosts will allow researchers to manipulate these systems and adapt them to specific bacterial targets. Here, we isolated a bacteriophage capable of infecting the marine alphaproteobacteriumPhaeobacter inhibensand dissected its mechanism of infection.Phaeobacterphage MD18, a novel species of bacteriophage isolated in Woods Hole, MA, exhibits potent lytic ability againstP. inhibensand appears to be of theSiphoviridaemorphotype. Consistent with this finding, the sequence of the MD18 revealed significant similarity to another siphophage, the recently discoveredRoseobacterphage DSS3P8. We incubated MD18 with a library of barcodedP. inhibenstransposon insertion mutants and identified 22 genes that appear to be required for phage predation of this host. Network analysis of these genes using genomic position, GO term enrichment, and protein associations reveals that these genes are enriched for roles in assembly of a type IV pilus (T4P) and regulators of cellular morphology. Our results suggest that T4P serve as receptors for a novel marine virus that targetsP. inhibens.

Importance

Bacteriophages are useful non-antibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identifiesPhaeobacterphage MD18, the first documented phage ofPhaeobacter inhibens, a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggests that theP

haeobacterphage MD18 has evolved to enhance its replication inP. inhibensby adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis ofP. inhibenstransposon insertion mutants identifies genes that modulate host susceptibility to phage MD18 and implicates the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship betweenP. inhibensand an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.
Activation of cytoplasmic dynein through microtubule crossbridging
Authors: Chakraborty Manas , Toleikis Algirdas , Siddiqui Nida , Cross Robert A. , Straube Anne
Published: April 2020

Cytoplasmic dynein is the main microtubule-minus-end-directed transporter of cellular cargo in animal cells [1, 2]. Cytoplasmic dynein also functions in the organisation and positioning of mitotic spindles [3, 4] and the formation of ordered microtubule arrays in neurons and muscle [5, 6]. Activation of the motor for cargo transport is thought to require formation of a complex with dynactin and a cargo adapter [7-10]. Here we show that recombinant human dynein can crossbridge neighbouring microtubules and can be activated by this crossbridging to slide and polarity-sort microtubule bundles. While single molecules of human dynein are predominantly static or diffusive on single microtubules, they walk processively for 1.5 μm on average along the microtubule bundles they form. Speed and force output of dynein are doubled on bundles compared to single microtubules, indicating that the crossbridging dynein steps equivalently on two microtubules. Our data are consistent with a model of autoactivation through the physical separation of dynein motor domains when crossbridging two microtubules. This enables cytoplasmic dynein to function effectively as a microtubule organiser and transporter without needing to first form a complex with dynactin and a cargo adapter.
Simulation studies of a vision intruder detection system
Authors: Rzucidło Paweł , Rogalski Tomasz , Jaromi Grzegorz , Kordos Damian , Szczerba Piotr , Paw Andrzej
Published: April 2020

Purpose

The purpose of this paper is to describe simulation research carried out for the needs of multi-sensor anti-collision system for light aircraft and unmanned aerial vehicles.

Design/methodology/approach

This paper presents an analysis related to the practical possibilities of detecting intruders in the air space with the use of optoelectronic sensors. The theoretical part determines the influence of the angle of view, distance from the intruder and the resolution of the camera on the ability to detect objects with different linear dimensions. It has been assumed that the detection will be effective for objects represented by at least four pixels (arranged in a line) on the sensor matrix. In the main part devoted to simulation studies, the theoretical data was compared to the obtained intruders’ images. The verified simulation environment was then applied to the image processing algorithms developed for the anti-collision system.

Findings

A simulation environment was obtained enabling reliable tests of the anti-collision system using optoelectronic sensors.

Practical implications

The integration of unmanned aircraft operations in civil airspace is a serious problem on a global scale. Equipping aircraft with autonomous anti-collision systems can help solve key problems. The use of simulation techniques in the process of testing anti-collision systems allows the implementation of test scenarios that may be burdened with too much risk in real flights.

Social implications

This paper aims for possible improvement of safety in light-sport aviation.

Originality/value

This paper conducts verification of classic flight simulator software suitability for carrying out anti-collision systems tests and development of a flight simulator platform dedicated to such tests.
Modelling of the reference STARs procedures in the context of RPAS integration in non-segregated airspace
Authors: Lichoń Daniel
Published: April 2020

Purpose

This work presents the part of the research in the integration of the remotely piloted aircraft systems (RPAS) in non-segregated airspace. The purpose of this study is to elaborate the reference shape of the Standard Instrument Arrivals (STARs) procedures of controlled airports. The STARs parameters are unique for the aerodromes and depend on navigational aids (NAVAIDs), manoeuvres and aircraft categories. Therefore, the elaboration of reference shapes was advisable in the context of RPAS integration research.

Design/methodology/approach

The models were based on the procedure design guidelines by International Civil Aviation Organization. The statistics of existing STARs were prepared using Aeronautical Information Publications to determine the representative procedural parameters. Construction of procedural shapes required to define the nominal flight path and tolerance areas.

Findings

In statistics, the standard deviation of distances was below the determined reference mean values, thus the models were convergent with existing procedures.

Research limitations/implications

The modelling was limited to initial, intermediate, final and missed approach segments. Arrival segment was not modelled. NAVAIDs include Instrument Landing System Category 1 (in final and missed approach) and very high-frequency omni-directional ranging or global navigation satellite systems (in initial and intermediate approach segments).

Practical implications

Prepared models may be used in research in the integration of the new types of aerial vehicles in existing air traffic management systems.

Originality/value

The reference STARs possess commonly used procedural manoeuvres (straight-in, turn, racetrack and base turn) and different NAVAIDs. The parameters of approach segments were determined as representative of the existing procedures. Moreover, the models are suitable to place at arbitrary origin and runway axis bearing.
Do we follow the crowd on social media? Experimental evidence on consumer attitudes in the contexts of NeWOM and firm crisis response
Authors: Suwandee Sasithorn , Lertwannawit Aurathai , Racela Olimpia C. , Boonchoo Pattana
Published: April 2020

Purpose

This study applies social network theory to examine the moderating effects of two online social media network characteristics, namely homophily and consensus, on the influence of negative electronic word of mouth (NeWOM) and of firm crisis response on consumer attitude toward a company.

Design/methodology/approach

Hypotheses were tested using a mixed-model experimental design of three between-subjects factors, including manipulations of homophily (high vs low), consensus (high vs low), and firm crisis response (accommodative vs defensive), and one repeated measure within-subjects factor of attitude toward the company at three different points in time (A0, A1, A2). Data were collected from 328 Thai participants who were randomly assigned to one of the eight experimental conditions.

Findings

High homophily and high consensus online social media network conditions worsen the negative impact of NeWOM on consumer attitudes. However, high homophily and high consensus strengthen the positive influence of an accommodative response in regaining favorable attitude toward the company. Low homophily and low consensus negate the impact of the firm's defensive response, preventing any further deterioration of attitude toward the company.

Practical implications

Marketers need to understand the relational patterns among members of online social media networks in order to assess the extent to which consumers are influenced by others in the network. In doing so, the firm can better anticipate and manage the impact of NeWOM and can launch an appropriate response strategy that optimizes the recovery, or minimizes the deterioration, of lost company image and reputation.

Originality/value

This study provides a dynamic view of consumer attitudes and highlights the substantial impact that others in the online social media network have on consumers' evaluation of NeWOM and of firm recovery efforts.
Integrative perceived values influencing consumers' attitude and behavioral responses toward mobile location-based advertising: an empirical study in Vietnam
Authors: Le Cu Xuan , Wang Hu
Published: April 2020

Purpose

The purpose of this paper is to examine a proposed model of location-based advertising (LBA) effectiveness upon the influence of integrative perceived values on consumers' attitude and behavioral responses in the immaturity of LBA in Vietnam.

Design/methodology/approach

A survey research method was utilized to collect data from mobile users. A real sample of 459 respondents was deemed and the Structural Equation Modeling (SEM) was applied to analyze data.

Findings

The results unveil that contextual offers, social facilitation, and advertising values have significantly positive effects on attitude; in turn, attitude mediates between these factors and purchase intention, information seeking and recommendation behaviors. Moreover, social facilitation is a significant stimulator of purchase intention. Otherwise, perceived encroached risk negatively impacts attitude.

Practical implications

Marketers should capture considerable attention to mobile natives' conscious awareness about a mechanism of tailoring their enthusiasm and behavioral responses at the embryonic stage of LBA growth in emerging countries like Vietnam.

Originality/value

This study fills the gap in the current literature by simultaneously exploring the importance of integrative perceived values to construct a hypothetical framework of consumers' responses and performance based on the uses and gratifications theory, inclusive perceived behavioral control derived from theory of planned behavior, associated with contextual value from the nature of LBA.