bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos
Authors: Fenelon Kelli D. , Gao Fan , Borad Priyanshi , Abbasi Shiva , Pachter Lior , Koromila Theodora 
Published: December 2022

AbstractDuring development, embryonic patterning systems direct a set of initially uncommitted pluripotent cells to differentiate into a variety of cell types and tissues. A core network of transcription factors, such as Zelda/POU5F1, Odd-paired (Opa)/ZIC and Ocelliless (Oc)/OTX, are conserved across animals. While Opa is essential for a second wave of zygotic activation after Zelda, it is unclear whether Opa drives head cell specification past gastrulation onset, in theDrosophilaembryo. Our hypothesis is that Opa and Oc are interacting with distinct cis-regulatory regions for shaping cell fates in the embryonic head. Using super-resolution microscopy and epigenomic meta-analysis of single cell RNAseq datasets we find thatopa’s andoc’s overlapping expression domains are dynamic in the head region, with both factors being simultaneously transcribed at the blastula stage. However, analysis of single-embryo RNAseq data reveals a subgroup of Opa-bound genes to be Opa-independent in the cellularized embryo. Interrogation of these genes against Oc ChIPseq combined with in situ data, suggests that Opa is competing with Oc for the regulation of a subgroup of genes later in gastrulation. Specifically, we find that Oc binds to late, head-specific enhancers independently and activates them in a head-specific wave of zygotic transcription, suggesting distinct roles for Oc in the blastula and gastrula stages.
Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease
Authors: Craig Rory J. 
Published: December 2022

ABSTRACTHUH endonucleases of the Rep (replication protein) class mediate the replication of highly diverse plasmids and viral genomes across all domains of life. Reps also function as transposases, and three evolutionarily independent groups of transposable elements (TEs) mobilised by Reps have been described: the prokaryotic insertion sequences IS200/IS605and IS91/ISCR, and the eukaryotic Helitrons. Here I present Replitrons, a new group of eukaryotic transposons encoding Rep HUH endonuclease. Replitron transposases feature Rep with one catalytic Tyr (Y1) as their only recognised domain, contrasting with Helitron transposases that feature Rep with two Tyr (Y2) and a fused helicase domain (i.e. RepHel). Protein clustering found no link between Replitron transposases and described Rep transposases, and instead recovered a weak association with Reps of circular Rep-encoding single stranded (CRESS) DNA viruses and their related plasmids (pCRESS). The predicted tertiary structure of the transposase ofReplitron-1, the founding member of the group that is active in the green algaChlamydomonas reinhardtii, closely resembles that of CRESS-DNA viruses and other HUH endonucleases. Replitrons are present in at least three eukaryotic supergroups and reach high copy numbers in non-seed plant genomes. Replitron DNA sequences generally feature short direct repeats at, or potentially near, their termini. Finally, I characterisecopy-and-paste de novoinsertions ofReplitron-1using long-read sequencing ofC. reinhardtiiexperimental lines. Overall, these results support an ancient and evolutionarily independent origin of Replitrons, in line with other major groups of eukaryotic TEs. This work substantially expands the known diversity of both transposons and HUH endonucleases in eukaryotes.
Japanese Encephalitis Virus NS1’ Protein regulates the expression and distribution of TIM-1 to promote viral infection
Authors: Liang Zhenjie , Xie Shengda , Pan Junhui , Yang Xingmiao , Jiao Wenlong , Cao Ruibing 
Published: December 2022

ABSTRACTJapanese encephalitis virus (JEV) is a mosquito-borneFlavivirus, which may cause severe encephalitis in humans, horses, and other animals. TIM-1 has been identified to be a receptor that promotes various viruses to enter into target cells in recent years. In the present study, we found that TIM-1 protein was significantly increased in A549 cells at the late stage of JEV infection, while the transcription levels of TIM-1 remained unaltered. Interestingly, we found that NS1’ protein plays a key role in increasing the expression of TIM-1 in cells infected with JEV. Further, we found that the NS1’ protein also efficiently regulates TIM-1 protein to distribute in the cytoplasm in JEV-infected cells, and the amount of TIM-1 protein located on the cell membrane was reduced instead. As a consequence, NS1’ protein antagonize TIM-1 mediated viral restriction for further viral infection and propagation in the late stage of infection. In molecular mechanism, the molecular weight of TIM-1 increased a bit in the present of NS1’. Expression of NEU1 down-regulated TIM-1 expression and oseltamivir treatment increased the expression of TIM-1. Therefore, our data indicated that JEV NS1’ protein facilitated the sialylation modification of TIM-1 to up-regulate the level of TIM-1 expression and regulate its distribution. Collectively, our study revealed that JEV NS1’ protein regulates the expression and distribution of TIM-1 by facilitating its sialylation to antagonize TIM-1-mediated JEV restriction for further infection. Understanding the functional interplays between TIM-1 and NS1’ proteins will offer new insights into virushost interaction.IMPORTANCET-cell immunoglobulin and mucin domain protein 1 (TIM-1) is known to promote cellular entry of various enveloped viruses. We discovered a novel phenomenon of dynamic expression and functional regulation of TIM-1 during JEV infection. Firstly, TIM-1 protein increased in the cytoplasm at the late stage of JEV infection. Furthermore, JEV NS1’ protein up-regulated the intracellular expression of TIM-1 and antagonize TIM-1-mediated viral restriction for further viral infection. In molecular mechanism, JEV NS1’ protein facilitated the sialylation of TIM-1 to increase the level of TIM-1 expression and cytoplasm distribution. Taken together, at the late stage of infection, JEV employs a strategy in which NS1’ promotes JEV release by promoting the sialylation of TIM-1, causing it to be primarily localized in the cytoplasm. Therefore, we discovered new functions of TIM-1 and JEV NS1’ during the process of JEV infection, and provide a new insight into the interactions between JEV and cell hosts.
Diversity and ecological function of urease-producing bacteria in the cultivation environment ofGracilariopsis lemaneiformis
Authors: Pei Pengbing , Du Hong , Aslam Muhammad , Wang Hui , Ye Peilin , Li Tangcheng , Liang Honghao , Zhang Zezhi , Ke Xiao , Lin Qi , Chen Weizhou 
Published: December 2022

AbstractUrease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolysis of urea. They play an important role in marine nitrogen cycle. However, there is still incomplete understanding of UPB and their ecological functions in the cultivation environment of red macroalageGracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake byG. lemaneiformis. Total 34 isolates belonging to four main bacterial phyla i.e. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay andureCgene cloning. Our data revealed that only 8 strains were found containing urease. These all UPB exhibited different urease activities by Berthelot reaction colorimetry assay. Furthermore, UPB with highest urease activity was selected to use as co-culture withG. lemaneiformisto explore its role in terms of promotion or inhibition of nitrogen uptake byG. lemaneiformis. The results showed that the urea consumption in culture media and the total cellular nitrogen inG. lemaneiformisfound increased significantly in the UPB-co culture group than control i.e. in the sterile group (p< 0.05). Similarity, isotopic assay revealed that δ15N contents ofG. lemaneiformiswas significant higher in the UPB-co culture than in the control where δ15N-urea was the only nitrogen source in the culture media, indicating the UPB helpedG. lemaneiformisto absorb more nitrogen from urea. Moreover, the highest content of δ15N was found inG. lemaneiformiswith epiphytic bacteria, as compared to sterilized (control) showing that epiphytic bacteria along with UPB have compound effects in helpingG. lemaneiformisabsorb more nitrogen in urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be important player in the marine nitrogen cycling.ImportanceTo the best of our knowledge, this is the first study ever conducted to isolate the culturable UPB from the cultivation environment ofG. lemaneiformisby urea agar chromogenic medium assay, and also evaluate the effects of UPB on urea utilization inG. lemaneiformisby stable isotopic tracer technique. This study provides a new insight into the mechanism of organic nitrogen uptake and utilization inG. lemaneiformis, and is of great significance for a better understanding of the ecological role of functional bacteria (e.g. urease-producing bacteria) in the marine nitrogen cycling.
Motility mediates satellite formation in confined biofilms
Authors: Cordero Mireia , Mitarai Namiko , Jauffred Liselotte 
Published: December 2022

ABSTRACTBacteria have spectacular survival capabilities and can spread in many, vastly different environments. For instance, when pathogenic bacteria infect a host, the cells expand through proliferation and squeezing through narrow pores and elastic matrices. However, the exact role of surface structures and matrix elasticity in colony expansion and morphogenesis is still largely unknown. Here we show howsatellitecolonies emerge around biofilms embedded in semi-soft agar in controlledin vitroassays. We tested how extra-cellular structures – important for biofilm formation and motility – control this morphology. Moreover, we identify the range of extra-cellular matrix elasticity, where this morphology is possible. When paralleled with mathematical modelling, our results demonstrate that satellite formation allows bacterial communities to spread faster. We anticipate that this strategy is important to speed up expansion in various environments while retaining the close interactions and protection provided by the community.
Non-coding autoimmune risk variant accelerates T peripheral helper cell development via ICOS
Authors: Kim Taehyeung , Martínez-Bonet Marta , Wang Qiang , Hackert Nicolaj , Sparks Jeffrey A. , Baglaenko Yuriy , Koh Byung-Hee , Darbousset Roxane , Laza-Briviesca Raquel , Chen Xiaoting , Gutierrez-Arcelus Maria , Westra Harm-Jan , Weirauch Matthew T. , Raychaudhuri Soumya , Rao Deepak A. , Nigrovic Peter A. 
Published: December 2022

ABSTRACTFine-mapping and functional studies implicate rs117701653, a common non-coding variant in theCD28/CTLA4/ICOSlocus, as a contributor to risk for rheumatoid arthritis and type 1 diabetes. Using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated allele reduces affinity for the inhibitory chromosomal regulator SMCHD1 to drive expression of inducible T-cell costimulator (ICOS), enhancing memory CD4+T cell ICOS expression in individuals bearing the risk allele. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells, and in rheumatoid arthritis patients, of blood and joint fluid Tph cells and circulating plasmablasts, suggesting a causal link. Indeed, ICOS ligation accelerates T cell differentiation into CXCR5-PD-1highTph cells producing IL-21 and CXCL13, as does carriage of the rs117701653 risk allele. Thus, mechanistic dissection of a causal non-coding variant in human autoimmunity discloses a new pathway through which ICOS regulates Tph abundance.
Evaluation of microRNA variant maturation prior to genome edition
Authors: Busseau Isabelle , Mockly Sophie , Houbron Élisabeth , Somaï Hedi , Seitz Hervé 
Published: December 2022

* AbstractAssessment of the functionality of individual microRNA/target sites is a crucial issue. Genome editing techniques should theoretically permit a fine functional exploration of such interactions, allowing the mutation of microRNAs or individual binding sites in a completein vivosetting, therefore abrogating or restoring individual interactions on demand. A major limitation to this experimental strategy is the influence of microRNA sequence on its accumulation level, which introduces a confounding effect when assessing phenotypic rescue by compensatorily mutated microRNA and target site. Here we describe a simple assay to identify microRNA variants most likely to accumulate at wild-type levels even though their sequence has been mutated. In this assay, quantification of a reporter construct in cultured cells predicts the efficiency of an early biogenesis step, the Drosha-dependent cleavage of microRNA precursors, which appears to be a major determinant of microRNA accumulation in our variant collection. This system allowed the generation of a mutantDrosophilastrain expressing abantammicroRNA variant at wild-type levels.
The H163A Mutation Unravels an Oxidized Conformation of the SARS-CoV-2 Main Protease and Opens a New Avenue for Anti-Viral Therapeutic Design
Authors: Tran Norman , Dasari Sathish , Barwell Sarah , McLeod Matthew J. , Kalyaanamoorthy Subha , Holyoak Todd , Ganesan Aravindhan 
Published: December 2022

AbstractThe main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro’s susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of a new Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrated a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild-type enzyme. We show that other point mutations can also significantly shift the equilibrium towards this state by altering conformational free energies. New therapeutic strategies against SARS-CoV-2 can be explored by understanding how H163 modulates this equilibrium.
Blockchain innovations and the contribution of the intergovernmental organizations
Authors: Katuu Shadrack 
Published: December 2022

Purpose
The United Nations (UN) is globally acknowledged for its unique role as a convening platform to address humanitarian, peace, security and sustainable development challenges. However, it is not often associated with technological innovation. Blockchain technology, an innovation that emerged in the late 2000s, has generated animated discussions that are led, in the most part, by private sector institutions. A dearth of literature highlights the innovative blockchain projects supported by UN entities. The purpose of this study is to provide an overview of blockchain innovations supported by UN entities and explore opportunities for future studies.

Design/methodology/approach
This paper used an exploratory case study approach with the purpose of providing a broad perspective of blockchain innovations undertaken by UN entities in the quest to meet sustainable and equitable development across the world.

Findings
This study found 25 blockchain projects by 13 UN entities in 19 countries. The geographical spread of the case studies revealed that two studies have global jurisdiction, five studies in Africa, three in Europe, four in Latin America and the Caribbean and 11 in Asia, Oceania and the Middle East. Of the 19 countries, three had two projects each. Two countries had three projects and the rest had one project each. Of the 13 UN entities, three dominated with UNICEF (part of six projects), UNDP (part of 10 projects) and WFP (part of four projects). Finally, the 25 projects were divided among three categories of blockchain use cases, as defined by UN guidance documents. Five case studies focused on immutable record keeping, five on transfer of value and 15 on smart contracts.

Originality/value
This study offers a unique overview of blockchain efforts within UN entities. It provides a platform for future studies to reveal implicit assumptions, contrasting explanations and casual connections.
A feminist-affordance lens: examining the power outcomes of the actualization of smartphone affordances
Authors: Salamoun Randa , Karam Charlotte M. , Abdallah Crystel 
Published: December 2022

PurposeThe authors explore the entanglement of smartphone technology and power in this paper. This paper explores the following question: In what ways does the actualization of smartphone affordances result in empowering outcomes (i.e. increase or reduce oppression) in the daily lives of refugees? Leveraging both affordance and feminist theories, the authors develop a hybrid lens bringing attention to the contextualized relationship between social process goals and affordances for sociality, upon which the authors introduce the notion of “goal-affordance interrelations”. The authors then trace how the actualization of these interrelations increases or reduces oppression.Design/methodology/approachUsing an abductive approach, the authors analyze 32 semi-structured interview transcriptions conducted with Syrian refugees in Lebanon.FindingsThe analysis in this study reveals four categories of social process goals (meet financial needs, satisfy security needs, communicate and learn and maintain pre-existing social ties) that are intimate components of contextually meaningful affordances. When actualized, the goal–affordance interrelations fundamentally shape refugee experiences of power outcomes. The findings suggest forms of empowerment where powerlessness, marginalization, violence and exploitation are perceived to be reduced. Actualization outcomes are also found to increase perceived oppression. Additionally, the findings reveal that not all interrelations are actualized, such that the anticipation of an oppressive power outcome may limit the actualization of affordances for sociality.Originality/valueThis research raises considerations concerning technology and oppression, and that efforts to empower refugees through technology should critically question whether the lived experiences of oppression will be reduced. The findings of this study reveal various forms of less empowering (i.e. oppressive) outcomes for the refugees sampled, they also point to the potential politicization of the actualization of goal–affordance interrelations.
Graduate readiness for a professional career in accounting – an investigation of employers’ perspectives in Fiji
Authors: Roy Sandhiya 
Published: December 2022

Purpose
The purpose of this paper is to identify and gain recent insights into the extent to which skills expectation gap exists from the perspective of employers in a Pacific Island country, including the competencies perceived essential within the work context of accountants and the support provided by employers to accounting graduates to address the skills expectation gap.

Design/methodology/approach
Using the expectation–performance gap framework developed by Bui and Porter (2010), this study collects and analyses data via semi-structured interviews with employers at chartered accounting firms, large- and medium-sized commercial and industrial firms in Fiji.

Findings
Majority of the employers indicated that graduates from the Fijian universities are adequately prepared and have acquired the necessary attributes to perform at the workplace. However, employers expect universities to do a little more in terms of developing confidence and improving ability to apply theoretical knowledge to practice. The findings also outline that the institutional-, social- and student-related constraints directly affect the quality of graduates, which are not in control of academics.

Research limitations/implications
It is noted that graduate capabilities are developed over two different learning environments. This study focused on how universities prepared graduates to perform at the workplace from the perspective of employers. This serves as a basis for future research to investigate effectiveness of trainings provided by employers to graduates to enable them into becoming successful accounting professionals.

Originality/value
This study adds clarifications to the debate on academic–practice gap by providing recent insights into the extent to which graduates demonstrate capabilities to perform in the accounting profession, the prevailing issues with graduate capabilities and the employers’ contribution towards strengthening graduate capabilities.
Disentangling direct and indirect effects of extreme events on coastal wetland communities
Authors: Davis Courtney L. , Walls Susan C. , Barichivich William J. , Brown Mary E. , Miller David A. W. 
Published: December 2022

Abstract

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population‐ and community‐level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions.

We extended static structural equation modelling approaches to incorporate system dynamics in a multi‐year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system.

We used data from an 8‐year study (2009–2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species‐specific and community‐level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands.

We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non‐lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland‐specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland‐breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change.

Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.