bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication
Authors: Wang Weitao , Klein Kyle , Proesmans Karel , Yang Hongbo , Marchal Claire , Zhu Xiaopeng , Borrman Tyler , Hastie Alex , Weng Zhiping , Bechhoefer John , Chen Chun-Long , Gilbert David M. , Rhind Nicholas
Published: August 2020

DNA replication is regulated by the location and timing of replication initiation. Therefore, much effort has been invested in identifying and analyzing the sites of human replication initiation. However, the heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual initiation site utilization in metazoans has made mapping the location and timing of replication initiation in human cells difficult. A potential solution to the problem of human replication mapping is single-molecule analysis. However, current approaches do not provide the throughput required for genome-wide experiments. To address this challenge, we have developed Optical Replication Mapping (ORM), a high-throughput single-molecule approach to map newly replicated DNA, and used it to map early initiation events in human cells. The single-molecule nature of our data, and a total of more than 2000-fold coverage of the human genome on 27 million fibers averaging ~300 kb in length, allow us to identify initiation sites and their firing probability with high confidence. In particular, for the first time, we are able to measure genome-wide the absolute efficiency of human replication initiation. We find that the distribution of human replication initiation is consistent with inefficient, stochastic initiation of heterogeneously distributed potential initiation complexes enriched in accessible chromatin. In particular, we find sites of human replication initiation are not confined to well-defined replication origins but are instead distributed across broad initiation zones consisting of many initiation sites. Furthermore, we find no correlation of initiation events between neighboring initiation zones. Although most early initiation events occur in early-replicating regions of the genome, a significant number occur in late-replicating regions. The fact that initiation sites in typically late-replicating regions have some probability of firing in early S phase suggests that the major difference between initiation events in early and late replicating regions is their intrinsic probability of firing, as opposed to a qualitative difference in their firing-time distributions. Moreover, modeling of replication kinetics demonstrates that measuring the efficiency of initiation-zone firing in early S phase suffices to predict the average firing time of such initiation zones throughout S phase, further suggesting that the differences between the firing times of early and late initiation zones are quantitative, rather than qualitative. These observations are consistent with stochastic models of initiation-timing regulation and suggest that stochastic regulation of replication kinetics is a fundamental feature of eukaryotic replication, conserved from yeast to humans.
A putative origin of insect chemosensory receptors in the last common eukaryotic ancestor
Authors: Benton Richard , Dessimoz Christophe , Moi David
Published: August 2020

The insect chemosensory repertoires of Gustatory Receptors (GRs) and Odorant Receptors (ORs) together represent one of the largest families of ligand-gated ion channels. Previous analyses have identified homologous “Gustatory Receptor-Like (GRL)” proteins across Animalia, but the evolutionary origin of this novel class of ion channels is unknown. We describe a survey of unicellular eukaryotic genomes for GRLs, identifying several candidates in fungi, protists and algae that contain many structural features characteristic of animal GRLs. The existence of these proteins in unicellular eukaryotes, together withab initioprotein structure predictions, supports homology between GRLs and a large family of uncharacterised plant proteins containing the DUF3537 domain. Together, this evidence suggests an origin of this protein family in the last common eukaryotic ancestor.
Identification and characterization of distinct murine brown adipocyte lineages
Authors: Karlina Ruth , Lutter Dominik , Miok Viktorian , Fischer David , Altun Irem , Schöttl Theresa , Schorpp Kenji , Israel Andreas , Cero Cheryl , Johnson James W. , Kapser-Fischer Ingrid , Böttcher Anika , Keipert Susanne , Feuchtinger Annette , Graf Elisabeth , Strom Tim , Walch Axel , Lickert Heiko , Walzthoeni Thomas , Heinig Matthias , Theis Fabian J. , García-Cáceres Cristina , Cypess Aaron M. , Ussar Siegfried
Published: August 2020

Brown adipose tissue (BAT) plays an important role in the regulation of body weight and glucose homeostasis. While increasing evidence supports white adipose tissue heterogeneity, little is known about heterogeneity within murine BAT. Using single cell RNA sequencing of the stromal vascular fraction of murine BAT and analysis of 67 brown preadipocyte and adipocyte clones we unravel heterogeneity within brown preadipocytes. Statistical analysis of gene expression profiles from these clones identifies markers distinguishing brown adipocyte lineages. We confirm the presence of distinct brown adipocyte populationsin vivousing three identified markers; Eif5, Tcf25, and Bin1. Functionally, we demonstrate that loss of Bin1 enhances UCP1 expression and mitochondrial respiration, suggesting that Bin1 marks a dormant brown adipocyte type. The existence of multiple brown adipocyte lineages suggests distinct functional properties of BAT depending on its cellular composition, with potentially distinct function in thermogenesis and the regulation of whole body energy homeostasis.
Anin vitrotumorigenesis model based on live cell-generated oxygen and nutrient gradients
Authors: Gilmore Anne C. , Flaherty Sarah J. , Somasundaram Veena , Scheiblin David A. , Lockett Stephen J. , Wink David A. , Heinz William F.
Published: August 2020

The tumor microenvironment (TME) is multi-cellular, spatially heterogenous, and contains cell-generated gradients of soluble molecules. Current cell-based model systems lack this complexity or are difficult to interrogate microscopically. We present a 2D live-cell chamber that approximates the TME and demonstrate that breast cancer cells and macrophages generate hypoxic and nutrient gradients, self-organize, and have spatially varying phenotypes along the gradients, leading to new insights into tumorigenesis.
St. Jude Cloud—a Pediatric Cancer Genomic Data Sharing Ecosystem
Authors: McLeod Clay , Gout Alexander M. , Zhou Xin , Rahbarinia Delaram , Thrasher Andrew , Newman Scott , Birch Kirby , Macias Michael , Finkelstein David , Sunny Jobin , Mudunuri Rahul , Orr Brent A. , Treadway Madison , Davidson Bob , Ard Tracy , Swistak Andrew , Wiggins Stephanie , Foy Scott , Brady Samuel W. , Wang Jian , Sioson Edgar , Wang Shuoguo , Michael J. Robert , Liu Yu , Ma Xiaotu , Patel Aman , Edmonson Michael N. , Wilkinson Mark R. , Frantz Andrew , Chang Ti-Cheng , Tian Liqing , Lei Shaohua , Meyer Christopher , Thangaraj Naina , Tater Pamella , Kandali Vijay , Ma Singer , Nguyen Tuan , Serang Omar , McGuire Irina , Robison Nedra , Gentry Darrell , Tang Xing , Palmer Lance , Wu Gang , Suh Ed , Tanner Leigh , McMurry James , Lear Matthew , Wang Zhaoming , Wilson Carmen , Cheng Yong , Weiss Mitch , Armstrong Gregory T. , Robison Leslie L. , Yasui Yutaka , Nichols Kim E. , Ellison David W. , Bangur Chitanya , Mullighan Charles G. , Baker Suzanne J. , Dyer Michael , Miller Geralyn , Rusch Michael , Daly Richard , Perry Keith , Downing James R. , Zhang Jinghui
Published: August 2020

Effective data sharing is key to accelerating research that will improve the precision of diagnoses, efficacy of treatments and long-term survival of pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a cloud-based data sharing ecosystem developed via collaboration between St. Jude Children’s Research Hospital, DNAnexus, and Microsoft, for accessing, analyzing and visualizing genomic data from >10,000 pediatric cancer patients, long-term survivors of pediatric cancer and >800 pediatric sickle cell patients. Harmonized genomic data totaling 1.25 petabyes on St. Jude Cloud include 12,104 whole genomes, 7,697 whole exomes and 2,202 transcriptomes, which are freely available to researchers worldwide. The resource is expanding rapidly with regular data uploads from St. Jude’s prospective clinical genomics programs, providing public access as soon as possible rather than holding data back until publication. Three interconnected apps within the St. Jude Cloud ecosystem—Genomics Platform, Pediatric Cancer Knowledgebase (PeCan) and Visualization Community—provide a unique experience for simultaneously performing advanced data analysis in the cloud and enhancing the pediatric cancer knowledgebase. We demonstrate the value of the St. Jude Cloud ecosystem through use cases that classify 48 pediatric cancer subtypes by gene expression profiling and map mutational signatures across 35 subtypes of pediatric cancer.
Decoding the physical principles of two-component biomolecular phase separation
Authors: Zhang Yaojun , Xu Bin , Weiner Benjamin G. , Meir Yigal , Wingreen Ned S.
Published: August 2020

Cells possess a multiplicity of non-membrane bound compartments, which form via liquid-liquid phase separation. These condensates assemble and dissolve as needed to enable central cellular functions. One important class of condensates is those composed of two associating polymer species that form one-to-one specific bonds. What are the physical principles that underlie phase separation in such systems? To address this question, we employed coarse-grained molecular dynamics simulations to examine how the phase boundaries depend on polymer valence, stoichiometry, and binding strength. We discovered a striking phenomenon – for sufficiently strong binding, phase separation is suppressed at rational polymer stoichiometries, which we termed the magic-ratio effect. We further developed an analytical dimer-gel theory that confirmed the magic-ratio effect and disentangled the individual roles of polymer properties in shaping the phase diagram. Our work provides new insights into the factors controlling the phase diagrams of biomolecular condensates, with implications for natural and synthetic systems.
Double-transmembrane domain of SNAREs decelerates the fusion by increasing the protein-lipid mismatch
Authors: Bu Bing , Tian Zhiqi , Li Dechang , Zhang Kai , Chen Wei , Ji Baohua , Diao Jiajie
Published: August 2020

SNARE is the essential mediator of membrane fusion that highly relies on the molecular structure of SNAREs. For instance, the protein syntaxin-1 involving in neuronal SNAREs, has a single transmembrane domain (sTMD) leading to fast fusion, while the syntaxin 17 has a V-shape double TMDs (dTMDs), taking part in the autophagosome maturation. However, it is not clear how the TMD structure influences the fusion process. Here, we demonstrate that the dTMDs significantly reduce fusion rate compared with the sTMD by using an in vitro reconstitution system. Through theoretical analysis, we reveal that the V-shape dTMDs can significantly increase protein-lipid mismatch, thereby raising the energy barrier of the fusion, and that increasing the number of SNAREs can reduce the energy barrier or protein-lipid mismatch. This study provides a physical-chemical mechanistic understanding of SNARE-regulated membrane fusion.
Factors influencing the accuracy and precision in dating single gene trees
Authors: Louvel Guillaume , Crollius Hugues Roest
Published: August 2020

Molecular dating is the inference of divergence time from genetic sequences. Knowing the time of appearance of a taxon sets the evolutionary context by connecting it with past ecosystems and species. Knowing the divergence times of gene lineages would provide a context to understand adaptation at the genomic level. However, molecular clock inference faces uncertainty due to the variability of the rate of substitution between species, between genes and between sites within genes. When dating speciations, per-lineage rate variability can be informed by fossil calibrations, and gene-specific rates can be either averaged out or modeled by concatenating multiple genes. By contrast when dating gene-specific events, fossil calibrations only inform about speciation nodes and concatenation does not apply to divergences other than speciations.

This study aims at benchmarking the accuracy of molecular dating applied to single gene trees, and identify how it is affected by gene tree characteristics. We analyze 5205 alignments of genes from 21 Primates in which no duplication or loss is observed. We also simulated alignments based on characteristics from Primates under a relaxed clock model, to analyze the dating accuracy. Divergence times were estimated with the bayesian program Beast2.

From the empirical dataset, we find that the date estimates deviate more from the median age with shorter alignments, high rate heterogeneity between branches and low average rate, features that underlie the amount of dating information in alignments, hence statistical power. The smallest deviation is associated with core biological functions such as ATP binding, cellular organization and anatomical development, categories that are expected to be under strong negative selection.We then investigated the accuracy of dating with simulated alignments, by controlling the three above parameters separately. It confirmed the factors of precision, but also revealed biases when branch rates are highly heterogeneous. This suggests that in the case of the relaxed uncorrelated molecular clock, biases arise from the tree prior when calibrations are lacking and rate heterogeneity is high. Our study finally reports the scale of the gene tree features that influence the dating consistency with median ages, so that comparisons can be made with other genes and taxa. To tackle the molecular dating of events only observed in single gene trees, like deep coalescence, horizontal gene transfers and gene duplications, future models should overcome the lack of power due to limited information from single genes.
The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes
Authors: Yuan Xianlin , li liangping
Published: August 2020

SARS-CoV-2 has rapidly transmitted worldwide and results in the COVID-19 pandemic. Spike glycoprotein on surface is a key factor of viral transmission, and has appeared a lot of variants due to gene mutations, which may influence the viral antigenicity and vaccine efficacy. Here, we used bioinformatic tools to analyze B-cell epitopes of prototype S protein and its 9 common variants. 12 potential linear and 53 discontinuous epitopes of B-cells were predicted from the S protein prototype. Importantly, by comparing the epitope alterations between prototype and variants, we demonstrate that B-cell epitopes and antigenicity of 9 variants appear significantly different alterations. The dominant D614G variant impacts the potential epitope least, only with moderately elevated antigenicity, while the epitopes and antigenicity of some mutants(V483A, V367F, etc.) with small incidence in the population change greatly. These results suggest that the currently developed vaccines should be valid for a majority of SARS-CoV-2 infectors. This study provides a scientific basis for large-scale application of SARS-CoV-2 vaccines and for taking precautions against the probable appearance of antigen escape induced by genetic variation after vaccination.

Author Summary

The global pandemic of SARS-CoV-2 has lasted for more than half a year and has not yet been contained. Until now there is no effective treatment for SARS-CoV-2 caused disease (COVID-19). Successful vaccine development seems to be the only hope. However, this novel coronavirus belongs to the RNA virus, there is a high mutation rate in the genome, and these mutations often locate on the Spike proteins of virus, the gripper of the virus entering the cells. Vaccination induce the generation of antibodies, which block Spike protein. However, the Spike protein variants may change the recognition and binding of antibodies and make the vaccine ineffective. In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. We discovered the variability in antigenicity among the mutants, for instance, in the more widespread D614G variant the change of epitope was least affected, only with slight increase of antigenicity. However, the antigenic epitopes of some mutants change greatly. These results could be of potential importance for future vaccine design and application against SARS-CoV2 variants.
Molecular Characterization of Carbapenem-ResistantAcinetobacter baumanniiClinical Isolates from Egyptian Patients
Authors: Hassan Reem M , Salem Sherifa T , Mostafa Hassan Saly Ismail , Hegab Asmaa Sayed , Elkholy Yasmine S
Published: August 2020

Acinetobacter baumannii(A. baumannii) represents a global threat owing to its ability to resist most of the currently available antimicrobial agents. Moreover, emergence of carbapenem resistantA. baumannii(CR-AB) isolates limits the available treatment options. Enzymatic degradation by variety of ß-lactamases, have been identified as the most common mechanism of carbapenem resistance inA. baumannii. The alarming increase in the prevalence of CR-AB necessitates continuous screening and molecular characterization to appreciate the problem. The present study was performed to assess the prevalence and characterize carbapenemases among 206 CR-AB isolated from various clinical specimens collected from different intensive care units at Kasr Al-Aini Hospital.

All isolates were confirmed to beA. baumanniiby detection of the blaOXA-51-like gene. Molecular screening of 13 common Ambler class bla carbapenemases genes in addition to insertion sequence (IS-1)upstreamOXA-23 was performed by using four sets of multiplex PCR, followed by identification using gene sequencing technology. Among the investigated genes, the prevalence of blaOXA-23, and blaOXA-58 were 77.7%, and 1.9%, respectively. The ISAba1was detected in 10% of the blaOXA-23 positive isolates. The prevalence of metallo-β-lactamases (MBLs) studied; blaNDM-1, blaSPM, blaVIM, blaSIM-1 were 11.7%, 6.3%, 0.5%, and 0.5% respectively. One of class A; bla KPC was detected in 10.7% of the investigated isolates. blaOXA-24/40, blaIMP, blaGES, blaVEB and blaGIM were not detected in any of the studied isolates. Moreover, 18.4% of the isolates have shown to harbor two or more of the screened bla genes. We concluded that the most prevalent type of ß-lactamases genes among CR-AB isolates collected from Egyptian patients were blaOXA-23 followed by blaNDM-1 and blaKPC.

Author summary

Carbapenem-resistantA. baumanniihas become a real global health threat. The aim of the present study was to characterize and to assess the prevalence of carbapenemases among 206 CR-AB clinical isolates from Egyptian patients. We concluded that the most prevalent type of ß-lactamases genes among CR-AB isolates collected from Egyptian patients were blaOXA-23 followed by blaNDM-1 and blaKPC. In this study, ISAba1was detected upstream 10% of blaOXA-23 positive isolates only which indicates that the spread of resistance amongAcinetobacterisolates could be either chromosomal or plamid-mediated.
Distinct Cellular Strategies Determine Sensitivity to Mild Drought of Arabidopsis Natural Accessions
Authors: Chen Ying , Dubois Marieke , Vermeersch Mattias , Inzé Dirk , Vanhaeren Hannes
Published: August 2020

The world-wide distribution ofArabidopsis thaliana(Arabidopsis) accessions imposes different types of evolutionary pressures, which contributes to various responses of these accessions to environmental stresses. Drought stress responses have been well studied, particularly in Columbia, a common Arabidopsis accession. However, the reactions to drought stress are complex and our understanding of which of these responses contribute to the plant’s tolerance to mild drought is very limited. Here, we studied the mechanisms by which natural accessions react to mild drought at a physiological and molecular level during early leaf development. We documented variations in mild drought tolerance among natural accessions and used transcriptome sequencing of a drought-sensitive accession, ICE163, and a drought-tolerant accession, Yeg-1, to get insights into the mechanisms underlying this tolerance. This revealed that ICE163 preferentially induces jasmonates and anthocyanin-related pathways, which are beneficial in biotic stress defense, while Yeg-1 has a more pronounced activation of abscisic acid signaling, the classical abiotic stress response. Related physiological traits, including content of proline, anthocyanins and ROS, stomatal closure and cellular leaf parameters, were investigated and linked to the transcriptional responses. We conclude that most of these processes constitute general drought response mechanisms that are regulated similarly in drought-tolerant and -sensitive accessions. However, the capacity to close stomata and maintain cell expansion under mild drought appeared to be major factors that contribute to a better leaf growth under mild drought.

One-sentence summary

This paper demonstrates that an efficient closure of stomata and maintenance of cell expansion during drought conditions are crucial to maximally preserve plant growth during water deficit.
Non-autonomous regulation of germline stem cell proliferation by somatic MPK-1/MAPK activity inC. elegans
Authors: Robinson-Thiewes Sarah , Dufour Benjamin , Martel Pier-Olivier , Lechasseur Xavier , Brou Amani Ange Danielle , Roy Vincent , Chen Yunqing , Kimble Judith , Narbonne Patrick
Published: August 2020

Extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) is a major positive regulator of cell proliferation that is often upregulated in cancer. Yet few studies have addressed ERK/MAPK regulation of proliferation within a complete organism. TheC. elegansERK/MAPK ortholog MPK-1 is best known for its control of somatic organogenesis and germline differentiation, but it also stimulates germline stem cell proliferation. Here we identify tissue-specific MPK-1 isoforms and characterize their distinct roles in germline function. The germline-specific MPK-1B isoform promotes germline differentiation, but has no apparent role in germline stem cell proliferation. By contrast, the soma-specific MPK-1A isoform promotes germline proliferation non-autonomously. Indeed, MPK-1A functions in the intestine or somatic gonad to promote germline proliferation, independently of its other known roles. We propose that a non-autonomous role of ERK/MAPK in stem cell proliferation may be conserved across species and other tissue types, with major clinical implications for cancer and other diseases.
Small RNA directs symbiosis, virulence, and natural products biosynthesis in entomopathogenic bacteria
Authors: Neubacher Nick , Tobias Nicholas J. , Huber Michaela , Cai Xiaofeng , Glatter Timo , Pidot Sacha J. , Stinear Timothy P. , Lütticke Anna Lena , Papenfort Kai , Bode Helge B.
Published: August 2020

Rapid modulation of gene expression is a key feature for the success of bacteria, particularly for those that rapidly have to adapt to different niches. The lifecycles ofPhotorhabdusandXenorhabdusinvolve a mutualistic association with nematodes as well as an entomopathogenic phase1,2, both of which rely on the production of numerous specialized metabolites (SMs)3,4. Several regulators have been previously implicated in the regulation of SM production in these genera3,4. However, the molecular underpinnings regulating SM production and the role of small regulatory RNAs (sRNAs) in this process are unknown. Here we describe the mechanism underlying RNA-mediated control of SM synthesis. We show that the Hfq-dependent sRNA, ArcZ, is an essential requirement for SM production. We discovered that ArcZ directly base-pairs with the mRNA encoding HexA, a key repressor of SM genes. We further demonstrate that the ArcZ regulon is not restricted to SM production, but rather modulates up to ~15% of the transcriptional output in bothPhotorhabdusandXenorhabdus. Together, our study shows that sRNAs are crucial for SM production in these species, reveals previously unknown targets for biosynthetic pathway manipulations, and offers a new tool for the (over)production, isolation and identification of unknown natural products.
TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell typesin vivo
Authors: Liu Yating , Fischer Anthony D. , St. Pierre Celine L. , Macias-Velasco Juan F. , Lawson Heather A. , Dougherty Joseph D.
Published: August 2020

The alteration of gene expression due to variations in the sequences of transcriptional regulatory elements has been a focus of substantial inquiry in humans and model organisms. However, less is known about the extent to which natural variation contributes to post-transcriptional regulation. Allelic Expression Imbalance (AEI) is a classical approach for studying the association of specific haplotypes with relative changes in transcript abundance. Here, we piloted a new TRAP based approach to associate genetic variation with transcript occupancy on ribosomes in specific cell types, to determine if it will allow examination of Allelic Translation Imbalance (ATI), and Allelic Translation Efficiency Imbalance, using as a test case mouse astrocytesin vivo. We show that most changes of the mRNA levels on ribosomes were reflected in transcript abundance, though ∼1.5% of transcripts have variants that clearly alter loading onto ribosomes orthogonally to transcript levels. These variants were often in conserved residues and altered sequences known to regulate translation such as upstream ORFs, PolyA sites, and predicted miRNA binding sites. Such variants were also common in transcripts showing altered abundance, suggesting some genetic regulation of gene expression may function through post-transcriptional mechanisms. Overall, our work shows that naturally occurring genetic variants can impact ribosome occupancy in astrocytesin vivoand suggests that mechanisms may also play a role in genetic contributions to disease.
The putative phosphate transporter PitB (PP1373) is involved in tellurite uptake in Pseudomonas putida KT2440
Authors: Montenegro Rafael , Vieto Sofía , Wicki-Emmenegger Daniela , Vásquez-Castro Felipe , Coronado-Ruiz Carolina , Fuentes-Schweizer Paola , Calderón Paula , Pereira Reinaldo , Chavarría Max
Published: August 2020

Tellurium oxyanions are chemical species with great toxicity; their presence in the environment has increased because of mining industries and photovoltaic and electronic waste. Recovery strategies based on microorganisms for this metalloid are of interest, but further studies of the transport systems and enzymes responsible for implementing tellurium transformations are required because many mechanisms remain unknown. Here, we investigated the involvement in tellurite uptake of the putative phosphate transporter PitB (PP1373) in soil bacterium Pseudomonas putida KT2440. For this purpose, through a method based on the CRISPR/Cas9 system, we generated a strain deficient in pitB gene and characterized its phenotype on exposing it to varied concentrations of tellurite. Growth curves and Transmission Electronic Microscopy experiments of wild type and ΔpitB showed that both strains were able to internalize tellurite into the cytoplasm and reduce the oxyanion to black nano-sized and rod-shaped tellurium particles, however, ΔpitB strain showed an increased resistance to the tellurite toxic effects. At a concentration of 100 uM tellurite, where the biomass formation of wild type strain decreased by half, we observed a greater ability of ΔpitB to reduce this oxyanion with respect to wild type strain (~38% vs ~16%), which is related by the greater biomass production of ΔpitB and not by a greater consumption of tellurite per cell. The phenotype of the mutant was restored on over-expressing pitB in trans. In summary, our results indicate that PitB is one of several transporters responsible for tellurite uptake in P. putida KT2440.
Global identification of RsmA/N binding sites inPseudomonas aeruginosabyin vivoUV CLIP-seq
Authors: Chihara Kotaro , Barquist Lars , Takasugi Kenichi , Noda Naohiro , Tsuneda Satoshi
Published: August 2020

Posttranscriptional regulation of gene expression in bacteria is performed by a complex and hierarchical signaling cascade.Pseudomonas aeruginosaharbors two redundant RNA-binding proteins RsmA/RsmN (RsmA/N), which play a critical role in balancing acute and chronic infections. However,in vivobinding sites on target transcripts and the overall impact on the physiology remains unclear. In this study, we appliedin vivoUV crosslinking immunoprecipitation followed by RNA-sequencing (UV CLIP-seq) to detect RsmA/N binding sites at single-nucleotide resolution and mapped more than 500 peaks to approximately 400 genes directly bound by RsmA/N inP. aeruginosa. This also demonstrated the ANGGA sequence in apical loops skewed towards 5’UTRs as a consensus motif for RsmA/N binding. Genetic analysis combined with CLIP-seq results identified previously unrecognized RsmA/N targets involved in LPS modification. Moreover, the small non-coding RNAs RsmY/RsmZ, which sequester RsmA/N away from target mRNAs, are positively regulated by the RsmA/N-mediated translational repression ofhptB, encoding a histidine phosphotransfer protein, andcafA, encoding a cytoplasmic axial filament protein, thus providing a possible mechanistic explanation for homeostasis of the Rsm system. Our findings present the global RsmA/N-RNA interaction network that exerts pleiotropic effects on gene expression inP. aeruginosa.

IMPORTANCE

The ubiquitous bacteriumPseudomonas aeruginosais notorious as an opportunistic pathogen causing life-threatening acute and chronic infections in immunocompromised patients.P. aeruginosainfection processes are governed by two major gene regulatory systems, namely, the GacA/GacS (GacAS) two-component system and the RNA-binding proteins RsmA/RsmN (RsmA/N). RsmA/N basically function as a translational repressor or activator directly by competing with the ribosome. In this study, we identified hundreds of RsmA/N regulatory target RNAs and the consensus motifs for RsmA/N bindings by UV crosslinkingin vivo. Moreover, our CLIP-seq revealed that RsmA/N posttranscriptionally regulate cell wall organization and exert feedback control on GacAS-RsmA/N systems. Many genes including small regulatory RNAs identified in this study are attractive targets for further elucidating the regulatory mechanisms of RsmA/N inP. aeruginosa.
Power and coherence in the EEG of the rat: impact of behavioral states, cortical area, lateralization and light/dark phases
Authors: Mondino Alejandra , Cavelli Matías , Gonzalez Joaquín , Osorio Lucía , Castro-Zaballa Santiago , Costa Alicia , Vanini Giancarlo , Torterolo Pablo
Published: August 2020

The sleep-wake cycle is constituted by three behavioral states: wakefulness (W), non-REM (NREM) and REM sleep. These states are associated with drastic changes in cognitive capacities, mostly determined by the function of the thalamo-cortical system. Thalamo-cortical activity can be examined by means of the intra-cranial electroencephalogram (iEEG).

With the purpose to study in depth the basal activity of the iEEG in adult rats, we analyzed the spectral power and coherence of the iEEG during W and sleep in the paleocortex (olfactory bulb), as well as in motor, somatosensory and visual neocortical areas. We also analyzed the laterality (right Vs. left hemispheres) of the signals, as well as the iEEG in function of the light and dark phases.

We found that the iEEG power and coherence of the whole spectrum were largely affected by behavioral states and were highly dependent on the cortical areas recorded. We also determined that there are night/day differences in power and coherence during sleep, but not in W. Finally, while we did not find right/left differences in power either in W or sleep, we observed that during REM sleep intra-hemispheric coherence differs between both hemispheres.

We conclude that the iEEG dynamics is highly dependent on the cortical area and behavioral states. We also determine that there are light/dark phases disparities in the iEEG that emerge during sleep, and that intra-hemispheric connectivity differs between both hemispheres only during REM sleep.
Gene expression patterns in chordate embryonic development suggest partial applicability of Haeckel’s postulates
Authors: Guo Song , Hu Haiyang , Xu Chuan , Irie Naoki , Khaitovich Philipp
Published: August 2020

The relationship between embryonic development and evolution historically investigated based on embryo morphology, could now be reassessed using mRNA expression endophenotype. Here, we investigated the applicability of von Baer’s and Haeckel’s arguments at mRNA expression level by comparing the developmental changes among nine evolutionarily distinct species: from oyster to mouse. In agreement with models based on von Baer’s postulates, up to 36% of mRNA expression indicated nearly linear conservation of species’ developmental programs. By contrast, 5-15% of developmental expression profiles, enriched in neural genes, displayed an alignment pattern compatible with the terminal edition paradigm proposed by Haeckel. Thus, the development-evolution relationship based on mRNA expression agrees with early concepts based on embryo morphology and demonstrates that the corresponding patterns coexist in chordate development.
Transcutaneous vagus nerve stimulation in humans induces pupil dilation and attenuates alpha oscillations
Authors: Sharon Omer , Fahoum Firas , Nir Yuval
Published: August 2020

Vagus nerve stimulation (VNS) is widely used to treat drug-resistant epilepsy and depression. While the precise mechanisms mediating its long-term therapeutic effects are not fully resolved, they likely involve locus coeruleus (LC) stimulation via the nucleus of the solitary tract (NTS), which receives afferent vagal inputs. In rats, VNS elevates LC firing and forebrain noradrenaline levels, whereas LC lesions suppress VNS therapeutic efficacy. Non-invasive transcutaneous VNS (tVNS) employs electrical stimulation that targets the auricular branch of the vagus nerve at the cymba conchae of the ear. However, the extent that tVNS mimics VNS remains unclear. Here, we investigated the short-term effects of tVNS in healthy human male volunteers (n=24), using high-density EEG and pupillometry during visual fixation at rest. We compared short (3.4s) trials of tVNS to sham electrical stimulation at the earlobe (far from the vagus nerve branch) to control for somatosensory stimulation. Although tVNS and sham stimulation did not differ in subjective intensity ratings, tVNS led to robust pupil dilation (peaking 4-5s after trial onset) that was significantly higher than following sham stimulation. We further quantified, using parallel factor analysis, how tVNS modulates idle occipital alpha (8-13Hz) activity identified in each participant. We found greater attenuation of alpha oscillations by tVNS than by sham stimulation. This demonstrates that tVNS reliably induces pupillary and EEG markers of arousal beyond the effects of somatosensory stimulation, thus supporting the hypothesis that tVNS elevates noradrenaline and other arousal-promoting neuromodulatory signaling, and mimics invasive VNS.

Significance statement

Current non-invasive brain stimulation techniques are mostly confined to modulating cortical activity, as is typical with transcranial magnetic or transcranial direct/alternating-current electrical stimulation. Transcutaneous vagus nerve stimulation (tVNS) has been proposed to stimulate subcortical arousal-promoting nuclei, though previous studies yielded inconsistent results. Here we show that short (3.4s) tVNS pulses in naïve healthy male volunteers induced transient pupil dilation and attenuation of occipital alpha oscillations. These markers of brain arousal are in line with the established effects of invasive VNS on locus coeruleus-noradrenaline signaling, and support the notion that tVNS mimics VNS. Therefore, tVNS can be used as a tool for studying the means by which endogenous subcortical neuromodulatory signaling affects human cognition, including perception, attention, memory, and decision-making; and also for developing novel clinical applications.
A physical theory of movement in small animals
Authors: Loveless Jane , Garner Alastair , Issa Abdul Raouf , Roberts Ruairí J. V. , Webb Barbara , Prieto-Godino Lucia L. , Ohyama Tomoko , Alonso Claudio R.
Published: August 2020

All animal behaviour must ultimately be governed by physical laws. As a basis for understanding the physics of behaviour in a simple system, we here develop an effective theory for the motion of the larval form of the fruitfly Drosophila melanogaster, and compare it against a quantitative analysis of the real animal’s behaviour. We first define a set of fields which quantify stretching, bending, and twisting along the larva’s antero- posterior axis, and then perform a search in the space of possible theories that could govern the long-wavelength physics of these fields, using a simplified approach inspired by the renormalisation group. Guided by symmetry considerations and stability requirements, we arrive at a unique, analytically tractable free-field theory with a minimum of free parameters. Unexpectedly, we are able to explain a wide-spectrum of features of Drosophila larval behaviour by applying equilibrium statistical mechanics: our theory closely predicts the animals’ postural modes (eigenmaggots), as well as distributions and trajectories in the postural mode space across several behaviours, including peristaltic crawling, rolling, self-righting and unbiased substrate exploration. We explain the low-dimensionality of postural dynamics via Boltzmann suppression of high frequency modes, and also propose and experimentally test, novel predictions on the relationships between different forms of body deformation and animal behaviour. We show that crawling and rolling are dominated by similar symmetry properties, leading to identical dynamics/statistics in mode space, while rolling and unbiased exploration have a common dominant timescale. Furthermore, we are able to demonstrate that self-righting behaviour occurs continuously throughout substrate exploration, owing to the decoupling of stretching, bending, and twisting at low energies. Together, our results demonstrate that relatively simple effective physics can be used to explain and predict a wide range of animal behaviours.
Influence of destination attractiveness factors and travel motivations on rural homestay choice: the moderating role of need for uniqueness
Authors: Dey Banasree , Mathew Jones , Chee-Hua Chin
Published: August 2020

Purpose

Rural homestays have emerged as an interesting option for tourists. This study aims to assess the role of destination attractiveness factors and travel motivations in homestay choice. The moderating role of need for uniqueness towards enhancing these relationships is also examined.

Design/methodology/approach

A survey of 201 Indian tourists who had visited rural homestays in the Uttarakhand state of India was conducted. Data were analyzed using SPSS and WarpPLS, based on structural equation modelling approach.

Findings

Results indicate that two destination attractiveness factors – (a) cultural and rural attractions and (b) destination location and transportation – have a significant association with rural homestay choice. Further, need for uniqueness enhances the relationship between natural attractions and choosing rural homestays.

Originality/value

Although there are several studies on rural homestays, there is scant research on the factors influencing the choice of rural homestays from a tourists’ perspective. Besides, studies on rural homestay tourism have not assessed the role of need for uniqueness in influencing such choices. The implications of the study for destination marketers, homestay operators and owners are discussed which would hopefully aid in attracting discerning tourists to the rural homestays to such regions.
Analysing the impact of COVID-19 on over-the-top media platforms in India
Authors: Madnani Divya , Fernandes Semila , Madnani Nidhi
Published: August 2020

Purpose

The outbreak of COVID-19 saw a robust increase in viewership of over-the-top (OTT) media platforms. This study aims to investigate the impact of COVID-19 on OTT platforms in India, as it has led to reshaping consumer content preferences.

Design/methodology/approach

The authors have conducted primary research by doing a survey and focus group discussion. The first study has focused on the impact of various factors such as time, content, convenience, satisfaction and work from home (WFH) on OTT platforms during the COVID-19 crisis and the second study has focused on change in behavior of people before and during lockdown using visual representation.

Findings

The findings of this study show that lockdown has played a major role in the increase in viewership of OTT platforms, as people working from home are also using OTT platforms more. The average hours spent on OTT have increased from 0–2 to 2–5 h and average spending that users are willing to make on OTT platforms is Rs 100–300 (per month). The satisfaction level of customers is directly related to space to watch with family, time to use OTT platforms, the quality of content on OTT platforms and preference of OTT platform over television. Also, factors such as age group, occupation, city and income groups also determine the usage of the OTT platform.

Originality/value

The main contribution of this paper is to analyze the customer needs that impact their satisfaction level.
Effect of SCF on automobile industry performance during sales promotional schemes
Authors: Chirra Sricharan , Kumar Dinesh
Published: August 2020

Purpose

In today's competitive market subject to various uncertainties, supply chain flexibility (SCF) arose as a potential weapon to enhance the firm's performance. This paper model the effect of SCF on automobile industry performance during sales promotional schemes (SPS), which has turned out to be one of the most important marketing tools.

Design/methodology/approach

In view of the literature and the expert opinion taken from an automobile OEM, the SCFs and performance measures pertaining to the SPS environment have been identified. For the purpose of ranking the SCFs with respect to the performance measures, the Interpretive Ranking Process (IRP) has been applied using the direct contact method as a means for establishing the contextual relationships between SCFs and performance measures and to draw the interpreting reasons behind them.

Findings

The findings of this study along with the validity and stability of the results assessed through the system graphs and sensitivity analysis demonstrate that flexibility at the procurement end followed by the organizational end has the highest impact on the performance of the company during SPS.

Originality/value

Analysis of SCFs in regard to performance measures during SPS helps improve supply chain performance and offer valuable insights to the practicing managers in decision-making. This study augments the flexibility literature, by clubbing the two independent research streams, SCF and SPS.
How managerial coaching promotes employees' affective commitment and individual performance
Authors: Ribeiro Neuza , Nguyen Tam , Duarte Ana Patrícia , Torres de Oliveira Rui , Faustino Catarina
Published: August 2020

Purpose

This study sought to provide a more comprehensive understanding of how managers' coaching skills can affect individual performance through the mediating role of affective commitment.

Design/methodology/approach

The sample included 198 employees from diverse organizations. Based on an online survey, respondents assessed their managers' coaching skills and reported their own individual performance and affective commitment to their organization.

Findings

The findings show that managers' coaching skills have a positive impact on individual performance and affective commitment, with the latter mediating the relationship between the first two variables.

Research limitations/implications

Additional studies with larger samples are needed to understand more fully not only the impact of managers' coaching skills on individual performance but also other psychosocial variables affecting that relationship.

Practical implications

Organizations can increase employees' affective commitment and individual performance by encouraging managers to integrate more coaching skills into their leadership styles.

Originality/value

This study is the first to integrate managers' coaching skills, affective commitment and individual performance into a single research model, thereby extending previous research on this topic.
Mobile money as a financial inclusion instrument: what are the determinants?
Authors: Amoah Anthony , Korle Kofi , Asiama Rexford Kweku
Published: August 2020

Purpose

This paper seeks to examine the motivating factors that propel people to use mobile money in the Greater Accra Region (GAR) of Ghana. The authors posit that the behaviour of a person, in terms of the choice and means of transaction, cannot be explained solely by utility-maximizing assumptions or rationality. Thus, other socio-cultural and psychological factors are crucial in determining whether a person will use mobile money.

Design/methodology/approach

This study uses a cross-sectional design to obtain primary data on 733 households from the GAR of Ghana to determine the drivers of mobile money use. Given the binary nature of the dependent variable, a logit model and its marginal effects are estimated. Furthermore, parametric and non-parametric statistical tests are used to examine gender effect and mobile money use.

Findings

The study finds that technology savvy cohorts (youthful age cohorts), available services such as phone credit recharge, education and income are among the key determinants of mobile money use in Ghana. Furthermore, parametric and non-parametric tests of mobile money use on gender show a statistically significant difference in gender use of mobile money, albeit, marginal. The findings imply that consistent use of mobile money to access social and economic services can go a long way in promoting financial inclusion, financial empowerment and general wellbeing of people.

Originality/value

Households in developing countries especially Ghana have rapidly embraced mobile money technology. However, what determines the household level of adoption, to the best of our knowledge, is unknown and yet to be tested. This study bridges that gap in the empirical literature as well as contributes to policy decisions.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-05-2020-0271