bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthogonality of shell proteins across BMC subclasses in cyanobacteria
Authors: MacCready Joshua S. , Dwyer Matthew E. , Kerfeld Cheryl A. , Ducat Daniel C. 
Published: March 2024

AbstractBacterial microcompartments (BMC) are protein-based organelles broadly distributed across all bacterial phyla and subclassified into ≥60 functional variants. Despite their evolutionary and metabolic diversity, shell proteins that structurally compose the BMC surface are closely related across BMC classes. Herein, we sought to identify molecular and physiological features that could promote independent operation of more than one BMC type within the same cell by reducing inter-organelle cross-talk of shell proteins. We heterologously expressed shell proteins from the structurally well-defined BMC ofHaliangium ochraceum(HO) withinSynechococcus elongatusPCC 7942, a model cyanobacterium containing the β-carboxysome. We find considerable cross-reactivity of the HO hexameric shell protein (HO BMC-H) with components of the β-carboxysome; HO BMC-H can integrate into carboxysomes, disrupt its ultrastructural organization, and impair its associated CO2fixation reactions.S. elongatusis unable to maintain the integrity of the β-carboxysome over time when HO BMC-H is expressed in the absence of one or more of three broad strategies that act to increase the orthogonality between HO and carboxysome BMC shell proteins: i) reduced expression of promiscuous shell proteins; ii) sequestration of free HO BMC-H proteins via co-expression of other members of the same HO shell protein class, or; iii) heterologous expression of BMC positional system proteins McdAB (Maintenance ofcarboxysomedistribution AB), revealing a putative moonlighting function of the McdAB protein family. Our results have implications for bacteria that encode more than one BMC within their genome and may have translational implications for the use of engineered BMCs for biotechnological applications.
Assessment of risk perception and determinants of mpox for strengthening community engagement in local populations in Cameroon
Authors: Tambo Ernest , Noungoue Ngounou Pamela J. , Njobet Marie Paule N. , Tappa Ngo T. , Ngogang Jeanne , Hunter Mikayla , Shaw Souradet Y. , Rimoin Anne W. , Mbala-Kingebeni Placide , Kindrachuk Jason ,   the International Mpox Research Consortium
Published: March 2024

BackgroundThis study assessed the current state of knowledge, including social determinants of health considerations, regarding mpox acquisition and severity in Southwest and Littoral regions, Cameroon.MethodsThis was a descriptive cross-sectional study carried out with mpox cases from Southwest and Littoral regions. Perceived knowledge and determinants of mpox were assessed via a self-reported questionnaire. Descriptive and inferential statistical analyses were performed.ResultsA total of 394 participants took part in the study. With respect to the socio-demographic characteristic of the study population, 356 (89.4%) were Cameroonians, 267 (67.1%) were females, and 261 (65.60%) were students. With regards to mpox knowledge, 278 (69.8%) of the respondents declared that mpox is caused by a virus, with 12 (3.0%) individuals responding that the signs and symptoms associated with mpox were back and/or muscle pain, skin rash, fever, pustules, and exhaustion. Knowledge scores were found to be dependent on socio-demographic background. Based on socio-behavioral determinants of mpox, 348 (87.4%) of the participants reported consumption of wild game (bushmeat) and 92 (23.1%) participants reported that mpox can be treated traditionally in their culture. Regarding epidemiological determinants, 42 (10.6%) participants reported that mpox can be transmitted through direct contact with lesions, 120 (30.2%) reported prior smallpox infection, and 47(11.8%) reported prior mpox infection. Based on risk factors reported, 180 (46.7%) of the participants had close contact with confirmed or probable cases of mpox and 196 (49.2%) were present in healthcare facilities where mpox cases were managed.ConclusionMultiple knowledge gaps regarding mpox and MPXV were documented in the population in Southwest and Littoral regions of Cameroon. Reported social and behavioral determinants included the state of instability of the southwest region and population displacement in the bushes/forests, wild game consumption without proper cooking and poor hygiene were associated with mpox infection risk perception and vulnerability. On the epidemiological aspects increased instability, travel out of town, and limited remote rural chickenpox vaccination coverage were reported to increase risk, vulnerability, and spread of mpox within these endemic communities.
Improved genome sequence and annotation ofCutaneotrichosporon oleaginosusATCC 20509
Authors: Nijsse Bart , Duman-Özdamar Zeynep Efsun , Verbokkem Janine A. C. , Butler Derek , Suarez-Diez Maria , Julsing Mattijs K. 
Published: March 2024

AbstractCutaneotrichosporon oleaginosusis an oleaginous yeast with a high content of fatty acids and can accumulate more than 40% of its weight in lipids. It can grow on a wide range of carbon sources and side streams such as crude glycerol. The genome sequence ofC. oleaginosusATCC 20509 is reported here to contribute to its development as a biotechnological platform for producing microbial oils.
Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales
Authors: Haro-Moreno Jose M. , López-Pérez Mario , Molina-Pardines Carmen , Rodriguez-Valera Francisco 
Published: March 2024

ABSTRACTWe have used single-amplified genomes (SAGs) and long-read metagenomics to examine the diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order. OBCs are notorious for their diversity and have been used to type strains in pathogens and saprophytes, but their patterns of variation in free-living bacteria are little known. We found that, for these marine heterotrophic bacteria, the diversity is comparable to that of saprophytes, such as Enterobacteriales i.e. nearly each strain carries a different OBC. However, although OBC inheritance was largely vertical, the existence of some shared clusters allowed a comparative analysis. The OBCs diverge along with the genome, which is taken as indicative of old horizontal gene transfer (HGT) events. Only 14 cases of recent HGT were detected and they happened independently of taxonomy or location. Thus, although the O-chain is a major phage receptor in Gram-negative bacteria, the exchange of the complete cluster seems to play a minor role in the phage-bacterium arms-race. By long-read metagenomics, we could detect 380 different OBCs in a single sampling site in the Mediterranean. A single population (single species and sample) of the endemic Ia.3/VII genomospecies had a set of 158 OBCs of which 130 were different. This large diversity in clonal lineages might reflect the large amount of metabolic pathways required to deal with the enormous chemical diversity of dissolved organic matter in the ocean.
Designing a Novel 3D Scaffold for Multiepitope Vaccine Development: Engineering Ag85a Protein for Enhanced Stability and Antigenicity
Authors: Mondal Torsha , Rahman Shakilur , Das Amit Kumar , Hazra Ditipriya , Roychowdhury Amlan 
Published: March 2024

ABSTRACTDesigning multi epitope vaccine (MEV) by reverse vaccinology has become immensely important in the area of vaccine research due to the emergence of new pathogens as well as rise of multi drug resistant old evils like tuberculosis. Administering a vaccine may have the best possibility to save mankind from these unforeseeable events. The strategy of designing a MEV in-silico lies in a few basic steps, including procuring the amino acid sequence of the B cell and T cell epitopes from literature search, bioinformatics approach to construct a potent immunogen capable of eliciting both humoral and cell mediated response. But the challenge lies in the construction of a stable protein with a compact tertiary structure. Merely joining the epitopes one after another, may not be sufficient to achieve this. In this study, a methodology has been detailed to tackle this great challenge using a simple approach of protein engineering. A scaffold based MEV has been designed for the very first time against Mtb by converting a vaccine candidate protein, Ag85A into a scaffold by truncating its non-immunogenic regions so the gaps could be filled by the highly immunogenic epitopes. The stability of the MEV was estimated by molecular dynamics simulation.
The effect of laboratory diet and feeding on growth parameters in zebrafish
Authors: Hillman Courtney , Cooper Austin H. , Ram Pooja , Parker Matthew O. 
Published: March 2024

AbstractDespite being one of the most used laboratory species in biomedical, behavioural and physiological research, the nutritional requirements of zebrafish(Danio rerio)are poorly understood, and no standardised laboratory diet exists. Diet and feeding regimen can significantly impact the welfare of the fish and in turn experimental reproducibility. Consequently, the establishment of a standardised diet and feeding protocol for laboratory zebrafish is imperative to enhance animal welfare, guarantee research reproducibility and advance the economic and environmental sustainability of laboratory dietary practices. The aim of this systematic review was to determine the optimal feed for juvenile zebrafish growth and development. A comprehensive search was conducted in PubMed, Scopus and Google Scholar to identify relevant studies published up to August 2023 and the studies were selected based on the predefined inclusion/exclusion criteria. A total of 1065 articles were identified in the databases, of which 14 were included in this review. We conducted data extraction and risk-of-bias analysis in the included studies. Statistical comparisons for specific growth rate, weight gain (%) and length gain (%) parameters were performed to determine the optimal feed for enhanced juvenile growth. We identify an insect-based diet as optimal for juvenile growth for all three growth parameters. We also identify areas of potential heterogeneity and conclude by encouraging a standardised laboratory diet to ensure reproducible data and encourage zebrafish welfare.
Monitoring the directed evolution to a tripartite genome from a bipartite torradovirus genome
Authors: Turina M. , Nerva L. , Vallino M. , Ciuffo M. , Falk B.W. , Ferriol I. 
Published: March 2024

ABSTRACTWe have previously shown that tomato apex necrosis virus that cannot express the RNA2-ORF1 protein (P21) is not able to systemically infect plant hosts but is not affected in cell autonomous aspects of virus replication/accumulation. Here we attempted to provide P21in transby co-agroinfiltrating the RNA2-ORF1 null constructs (a stop codon mutant and a deletion mutant) with a P21-expressing construct under control of the 35S promoter and containing the 5’ and 3’ UTRs of wild type (WT) RNA2. Such construct when co-agroinfiltrated with the stop codon mutant originates a WT bipartite virus through homologous recombination. More surprisingly, when co-agroinfiltrated with the P21 deletion mutant it cannot immediately complement the mutant, but it serendipitously originates a tripartite virus with an actively replicating P21-expressing RNA3 only after this replicating RNA3 accumulates deletions in a small region inside the original 3’-UTR provided by the cDNA clone. Such virus can be transmitted mechanically and by whiteflies, is competent for virion formation, and its RNA3 is encapsidated. The tripartite virus can be mechanically transferred for eleven generations without losing its infectivity or show major genomic rearrangements. Furthermore, mixing equal amounts of WT and tripartite virus inocula in the same leaf originated plants systemically infected only with the WT virus, showing that the tripartite virus has lower fitness than the WT. To our knowledge this is the first example of a stable virus evolvingin vitrofrom bipartite to tripartite genomic structure from a synthetic construct in a plant virus.
MOB rules: Antibiotic Exposure Reprograms Metabolism to MobilizeBacillus subtilisin Competitive Interactions
Authors: Liu Yongjin , LaBonte Sandra , Brake Courtney , LaFayette Carol , Rosebrock Adam P. , Caudy Amy A. , Straight Paul D. 
Published: March 2024

AbstractAntibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria.Bacillus subtilisresponds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-MobilizedBacillus) to spread across a surface. HowB.subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions thatB. subtilisrequires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two,pdhAandpucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters ofpdhAandpucAexpression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.
Single-cell profiling reveals the intratumor heterogeneity and immunosuppressive microenvironment in cervical adenocarcinoma
Authors: Peng Yang , Yang Jing , Ao Jixing , Li Yilin , Shen Jia , He Xiang , Tang Dihong , Chu Chaonan , Liu Congrong , Weng Liang 
Published: March 2024

AbstractBackgroundCervical adenocarcinoma (ADC) is more aggressive compared to other types of cervical cancer (CC), such as squamous cell carcinoma (SCC). The tumor immune microenvironment (TIME) and tumor heterogeneity are recognized as pivotal factors in cancer progression and therapy. However, the disparities in TIME and heterogeneity between ADC and SCC are poorly understood.MethodsWe performed single-cell RNA sequencing on 11 samples of ADC tumor tissues, with other 4 SCC samples served as controls. The immunochemistry and multiplexed immunofluorescence were conducted to validate our findings.ResultsCompared to SCC, ADC exhibited unique enrichments in several sub-clusters of epithelial cells with elevated stemness and hyper-malignant features, including the Epi_10_CYSTM1 cluster. ADC displayed a highly immunosuppressive environment characterized by the enrichment of regulatory T cells (Tregs) and tumor-promoting neutrophils. The Epi_10_CYSTM1 cluster recruits Tregs via ALCAM-CD6 signaling, while Tregs reciprocally induce stemness in the Epi_10_CYSTM1 cluster through TGFβ signaling. Importantly, our study revealed that the Epi_10_CYSTM1 cluster could serve as a valuable predictor of lymph node metastasis for CC patients.ConclusionsThis study highlights the significance of ADC-specific cell clusters in establishing a highly immunosuppressive microenvironment, ultimately contributing to the heightened aggressiveness and poorer prognosis of ADC compared to SCC.
The value of research activities “other than” publishing articles: reflections on an experimental workshop series
Authors: Chahed Yasmine , Charnock Robert , Du Rietz Dahlström Sabina , Lennon Niels Joseph , Palermo Tommaso , Parisi Cristiana , Pflueger Dane , Sundström Andreas , Toh Dorothy , Yu Lichen 
Published: March 2024

PurposeThe purpose of this essay is to explore the opportunities and challenges that early-career researchers (ECRs) face when they seek to contribute to academic knowledge production through research activities “other than” those directly focused on making progress with their own, to-be-published, research papers in a context associated with the “publish or perish” (PoP) mentality.Design/methodology/approachDrawing broadly on the notion of technologies of humility (Jasanoff, 2003), this reflective essay develops upon the experiences of the authors in organizing and participating in a series of nine workshops undertaken between June 2013 and April 2021, as well as the arduous process of writing this paper itself. Retrospective accounts, workshop materials, email exchanges and surveys of workshop participants provide the key data sources for the analysis presented in the paper.FindingsThe paper shows how the organization of the workshops is intertwined with the building of a small community of ECRs and exploration of how to address the perceived limitations of a “gap-spotting” approach to developing research ideas and questions. The analysis foregrounds how the workshops provide a seemingly valuable research experience that is not without contradictions. Workshop participation reveals tensions between engagement in activities “other than” working on papers for publication and institutionalized pressures to produce publication outputs, between the (weak) perceived status of ECRs in the field and the aspiration to make a scholarly contribution, and between the desire to develop a personally satisfying intellectual journey and the pressure to respond to requirements that allow access to a wider community of scholars.Originality/valueOur analysis contributes to debates about the ways in which seemingly valuable outputs are produced in academia despite a pervasive “publish or perish” mentality. The analysis also shows how reflexive writing can help to better understand the opportunities and challenges of pursuing activities that might be considered “unproductive” because they are not directly related to to-be-published papers.
The influence of board policy setting on firm performance in Malaysia: the interacting effect of capital structure
Authors: Khatib Saleh F.A. , Abdullah Dewi Fariha , Al Amosh Hamzeh 
Published: March 2024

PurposeThe literature has dealt with the relationship between board characteristics (BC) and firm performance (FP) on a large scale. However, it yielded inconsistent results. Thus, this paper aims to examine the indirect relationship between BC and FP through the mediating role of the capital structure (CS).Design/methodology/approachThis study used a sample of 528 non-financial companies listed on Bursa Malaysia from 2015 to 2019. Also, a two-step system generalised method of moments estimation technique was applied.FindingsThe results show that board diversity and the frequency of board meetings positively affect financial performance, and it is negatively influenced by board turnover, size and independence. Also, the results indicate a positive relationship between the independence of the board and all CS variables. Importantly, the findings support the policy-setting role of the board of directors where CS (measured by total debt and short-term debt) suppresses some governance mechanisms’ detrimental effect on FP. Hence, the board of directors, apart from the monitoring function, introduce various policies (financial and non-financial) that enhance the overall performance of companies.Originality/valueThese results are consistent with the agency’s perspective that management practices in selecting the optimal capital reduce agency costs and improve performance. The findings contribute to developing a broader theoretical framework that accounts for the policy-setting role of the board of directors. The current study model of corporate governance offers insight for policymakers into the role of corporate governance other than monitoring functions in organisations and how CS should be taken into consideration with corporate governance and FP association.
Exploring causes of ineffective material management and impact on successful project deliverables in civil engineering construction projects in Sri Lanka
Authors: Pararajasingam Ramgy , Waidyasekara Anuradha Samarajeewa , Victar Hasith Chathuranga 
Published: March 2024

Purpose
Construction material management plays a significant role in achieving successful project delivery of a construction project. However, ineffective material management is a critical issue in the construction industry, especially in developing economies, of which Sri Lanka is not an exception. Therefore, this study aims to focus on exploring the causes of ineffective material management practices in civil engineering construction projects in Sri Lanka and their impact on successful project delivery.

Design/methodology/approach
Furthermore, the literature findings were validated through the preliminary survey. Subsequently, a quantitative research approach was adopted to pursue the research aim. Questionnaire responses were obtained from 215 construction professionals in civil engineering projects who were selected using the judgemental and snowball sampling techniques. Collected data were analysed through Statistical Package for the Social Sciences (SPSS) V26 and Microsoft Excel 2016.

Findings
Moreover, the study revealed that material price fluctuation, shortage of material in the market, delay in material procurement, inadequate planning and delays in material delivery are the most frequent causes of ineffective material management in civil engineering projects. In addition, it was evidenced that most ineffective material management practices cause both time and cost overruns in civil engineering construction projects. Most respondents emphasized inadequate planning, inadequate qualified and experienced staff, lack of supervision and lack of leadership as the causes for both time and cost overruns.

Originality/value
The study was concluded by proposing strategies for effective material management. Education/training/enlightenment of staff in charge of materials management, use of software like Microsoft Project, Primavera and similar software to eliminate manual errors in material management, and providing clear specifications to suppliers were the most agreed strategies for effective material management in civil engineering construction projects.
Big data and the management of libraries in the era of the Fourth Industrial Revolution: implications for policymakers
Authors: Ajani Yusuf Ayodeji , Adefila Emmanuel Kolawole , Olarongbe Shuaib Agboola , Enakrire Rexwhite Tega , Rabiu Nafisa 
Published: March 2024

Purpose
This study aims to examine Big Data and the management of libraries in the era of the Fourth Industrial Revolution and its implications for policymakers in Nigeria.

Design/methodology/approach
A qualitative methodology was used, involving the administration of open-ended questionnaires to librarians from six selected federal universities located in Southwest Nigeria.

Findings
The findings of this research highlight that a significant proportion of librarians are well-acquainted with the relevance of big data and its potential to positively revolutionize library services. Librarians generally express favorable opinions concerning the relevance of big data, acknowledging its capacity to enhance decision-making, optimize services and deliver personalized user experiences.

Research limitations/implications
This study exclusively focuses on the Nigerian context, overlooking insights from other African countries. As a result, it may not be possible to generalize the study’s findings to the broader African library community.

Originality/value
To the best of the authors’ knowledge, this study is unique because the paper reported that librarians generally express favorable opinions concerning the relevance of big data, acknowledging its capacity to enhance decision-making, optimize services and deliver personalized user experiences.