bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multiplexed RT-PCR Assay for Nanopore Whole Genome Sequencing of Tilapia lake virus (TiLV)
Authors: Delamare-Deboutteville Jerome , Meemetta Watcharachai , Pimsannil Khaettareeya , Sangpo Pattiya , Gan Han Ming , Mohan Chadag Vishnumurthy , Dong Ha Thanh , Senapin Saengchan 
Published: April 2023

ABSTRACTTilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.
Rapid dissemination of host-metabolism-manipulating transposon-like entities via integrative and conjugative elements
Authors: Colombi Elena , Bertels Frederic , Doulcier Guilhem , McConnell Ellen , Pichugina Tatyana , Sohn Kee Hoon , Straub Christina , McCann Honour , Rainey Paul B. 
Published: April 2023

AbstractIntegrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness, yet ICEs that carry accessory genes encoding functions other than antimicrobial resistance remain poorly characterized.Recent observation of the rapid acquisition of ICEs in a pandemic lineage ofPseudomonas syringaepv.actinidaeled to investigation of the structural and functional diversity of these elements among a diverse array ofP. syringae. Fifty-three unique ICE types were identified across multiple phylogroups. These ICEs display distinct evolutionary histories compared to their bacterial hosts, are highly recombinogenic, exhibit a conserved structure and are punctuated by hotspots of accessory gene integration. Many carry a 16 kb transposon-like entity (Tn6212) that shows little polymorphism indicating recent dissemination. Deletion of Tn6212did not alter pathogen growthin planta, but mutants displayed significant fitness defects when grown on TCA cycle intermediates. These were largely attributable to a single LysR regulator. RNA-seq analysis of a set of nested Tn6212deletions confirmed a central role of LysR in enhanced expression of more than 300 genes and down-regulation of genes controlling expression of energetically demanding loci. Together the transcriptional data indicate a major role for Tn6212in manipulation of bacterial metabolism with primary effects on RNA degradation, protein synthesis and potential diversion of ATP to growth.
Latent Representations in Hippocampal Network Model Co-Evolve with Behavioral Exploration of Task Structure
Authors: Cone Ian , Clopath Claudia 
Published: April 2023

AbstractReal-life behavioral tasks are often complex and depend on abstract combinations of sensory stimuli and internal logic. To successfully learn these tasks, animals must pair actions or decisions to the task’s complex structure. The hippocampus has been shown to contain fields which represent complex environmental and task variables, including place, lap, evidence accumulation, etc. Altogether, these representations have been hypothesized to form a “cognitive map” which encodes the complex real-world structure underlying behavior. However, it is still unclear how biophysical plasticity mechanisms at the single cell level can lead to the population-wide evolution of task-relevant maps. In this work we present a biophysically plausible model comprised of a recurrent hippocampal network and an action network, in which the latent representational structure co-evolves with behavior in a task-dependent manner. We demonstrate that the network develops latent structures that are needed for solving the task and does not integrate latent structures which do not support task learning. We show that, in agreement with experimental data, cue-dependent “splitters” can only be induced at the single cell level if the task requires a split representation to solve. Finally, our model makes specific predictions on how biases in behavior result from experimentally testable biases in the underlying latent representation.
Introduction of Barnase/Barstar in soybean produces a rescuable male sterility system for hybrid breeding
Authors: Szeluga Nicole , Baldrich Patricia , DelPercio Ryan , Meyers Blake C. , Frank Margaret H. 
Published: April 2023

AbstractHybrid breeding for increased vigor has been used for over a century to boost agricultural outputs without requiring higher inputs. While this approach has led to some of the most substantial gains in crop productivity, breeding barriers have fundamentally limited soybean (Glycine max) from reaping the benefits of hybrid vigor. Soybean makes inconspicuous flowers that self-fertilize before opening, and thus are not readily amenable to outcrossing. In this study, we demonstrate that the Barnase/Barstar male sterility/male rescue system can be used in soybean to produce hybrid seeds. By expressing the cytotoxic ribonuclease, Barnase, under a tapetum-specific promoter in soybean anthers, we are able to completely block pollen maturation, creating male-sterile plants. We show that fertility can be rescued in the F1 generation of these Barnase-expressing lines when they are crossed with pollen from plants that express the Barnase inhibitor, Barstar. Importantly, we found that the successful rescue of male fertility is dependent on the relative dosage of Barnase and Barstar. When Barnase and Barstar were expressed under the same tapetum-specific promoter, the F1 offspring remained male-sterile. When we expressed Barstar under a relatively stronger promoter than Barnase, we were able to achieve a successful rescue of male fertility in the F1 generation. This work demonstrates the successful implementation of a biotechnology approach to produce fertile hybrid offspring in soybean.
daf-42is an evolutionarily young gene essential for dauer development inCaenorhabditis elegans
Authors: Lim Daisy S. , Kim Jun , Kim Wonjoo , Kim Nari , Lee Sang-Hee , Lee Daehan , Lee Junho 
Published: April 2023

AbstractUnder adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauer endures unfavorable environments and interacts with host animals to access favorable environments, thus playing a critical role in survival. Here, we report that inCaenorhabditis elegans,daf-42is essential for development into the dauer stage, as the null mutant ofdaf-42exhibited a “no viable dauer” phenotype in which no viable dauers were obtained in any dauer-inducing conditions. Long-term time lapse microscopy of synchonized larvae revealed thatdaf-42is involved in developmental changes from the pre-dauer L2d stage to the dauer stage.daf-42encodes large, disordered proteins of various sizes that are expressed in and secreted from the seam cells within a narrow time window shortly before the molt into dauer stage. Transcriptome analysis showed that the transcription of genes involved in larval physiology and dauer metabolism are highly affected by thedaf-42 mutation. Contrary to the notion that essential genes that control the life and death of an organism may well be conserved across diverse species,daf-42is an evolutionarily young gene conserved only in theCaenorhabditisgenus. Our study shows that dauer formation is a vital process that is controlled not only by conserved genes but also by newly emerged genes, providing important insights into evolutionary mechanisms.
How Do Deer Respiratory Epithelial Cells Weather The Initial Storm of SARS-CoV-2?
Authors: Davila Kaitlyn M. Sarlo , Nelli Rahul K. , Phadke Kruttika S. , Ruden Rachel M. , Yongming Sang , Bellaire Bryan H. , Gimenez-Lirola Luis G. , Miller Laura C. 
Published: April 2023

ABSTRACTThe potential infectivity of SARS-CoV-2 in animals raises a public health and economic concern, particularly the high susceptibility of white-tailed deer (WTD) to SARS-CoV-2. The disparity in the disease outcome between humans and WTD is very intriguing, as the latter are often asymptomatic, subclinical carriers of SARS-CoV-2. To date, no studies have evaluated the innate immune factors responsible for the contrasting SARS-CoV-2-associated disease outcomes in these mammalian species. A comparative transcriptomic analysis in primary respiratory epithelial cells of human (HRECs) and WTD (Deer-RECs) infected with SARS-CoV-2 was assessed throughout 48 hours post inoculation (hpi). Both HRECs and Deer-RECs were susceptible to SARS-COV-2, with significantly (P< 0.001) lower virus replication in Deer-RECs. The number of differentially expressed genes (DEG) gradually increased in Deer-RECs but decreased in HRECs throughout the infection. The ingenuity pathway analysis of DEGs further identified that genes commonly altered during SARS-CoV-2 infection mainly belong to cytokine and chemokine response pathways mediated via IL-17 and NF-κB signaling pathways. Inhibition of the NF-κB signaling in the Deer-RECs pathway was predicted as early as 6 hpi. The findings from this study could explain the lack of clinical signs reported in WTD in response to SARS-CoV-2 infection as opposed to the severe clinical outcomes reported in humans.HIGHLIGHTSWhite-tailed deer primary respiratory epithelial cells are susceptible to SARS- CoV-2 without causing hyper cytokine gene expression.Downregulation of IL-17 and NF-κB signaling pathways after SARS-CoV-2 infection could be key to the regulated cytokine response in deer cells.Deer innate immune system could play a critical role in early antiviral and tissue repair response following SARS-CoV-2 infection.
Integrated multi-omics approach reveals the role of SPEG in skeletal muscle biology including its relationship with myospryn complex
Authors: Li Qifei , Lin Jasmine , Luo Shiyu , Schmitz-Abe Klaus , Agrawal Rohan , Meng Melissa , Moghadaszadeh Behzad , Beggs Alan H. , Liu Xiaoli , Perrella Mark A. , Agrawal Pankaj B. 
Published: April 2023

AbstractAutosomal-recessive mutations inSPEG(striated muscle preferentially expressed protein kinase) have been linked to centronuclear myopathy. Loss of SPEG is associated with defective triad formation, abnormal excitation-contraction coupling, and calcium mishandling in skeletal muscles. To elucidate the underlying molecular pathways, we have utilized multi-omics tools and analysis to obtain a comprehensive view of the complex biological processes. We identified that SPEG interacts with myospryn complex proteins (CMYA5, FSD2, RyR1), and SPEG deficiency results in myospryn complex abnormalities. In addition, transcriptional and protein profiles of SPEG-deficient muscle revealed defective mitochondrial function including aberrant accumulation of enlarged mitochondria on electron microscopy. Furthermore, SPEG regulates RyR1 phosphorylation at S2902, and its loss affects JPH2 phosphorylation at multiple sites. On analyzing the transcriptome, the most dysregulated pathways affected by SPEG deficiency included extracellular matrix-receptor interaction and peroxisome proliferator-activated receptors signaling, which may be due to defective triad and mitochondrial abnormalities. In summary, we have elucidated the critical role of SPEG in triad as it works closely with myospryn complex, phosphorylates JPH2 and RyR1, and demonstrated that its deficiency is associated with mitochondrial abnormalities. This study emphasizes the importance of using multi-omics techniques to comprehensively analyze the molecular anomalies of rare diseases.SynopsisWe have previously linked mutations inSPEG(striated preferentially expressed protein) with a recessive form of centronuclear myopathy and/or dilated cardiomyopathy and have characterized a striated muscle-specific SPEG-deficient mouse model that recapitulates human disease with disruption of the triad structure and calcium homeostasis in skeletal muscles. In this study, we applied multi-omics approaches (interactomic, proteomic, phosphoproteomic, and transcriptomic analyses) in the skeletal muscles of SPEG-deficient mice to assess the underlying pathways associated with the pathological and molecular abnormalities.SPEG interacts with myospryn complex proteins (CMYA5, FSD2, RyR1), and its deficiency results in myospryn complex abnormalities.SPEG regulates RyR1 phosphorylation at S2902, and its loss affects JPH2 phosphorylation at multiple sites.SPEGα and SPEGβ have different interacting partners suggestive of differential function.Transcriptome analysis indicates dysregulated pathways of ECM-receptor interaction and peroxisome proliferator-activated receptor signaling.Mitochondrial defects on the transcriptome, proteome, and electron microscopy, may be a consequence of defective calcium signaling.
Invasive plant species interact with drought to shift key functions and families in the native rhizosphere
Authors: Ettinger Cassandra L. , LaForgia Marina L. 
Published: April 2023

AbstractInteractions between species invasions and climate change have the potential to drive changes in plant communities more than either factor alone. One pathway through which these effects can occur is via changes to the rhizosphere microbial community. Invasive plants can alter the taxonomic and functional makeup of these microbial communities, which may affect natives’ abilities to compete with invaders. At the same time, climate change is leading to more frequent extreme wet and dry events, shifting the composition of microbial taxa available in the soil. Understanding the response of plant communities to these combined global change drivers requires a comprehensive approach that assesses the relationship between plant competition and belowground rhizosphere microbial community responses. Here we use a field experiment in a California grassland with a set of six native annual forbs (i.e., wildflowers) and three invasive annual grasses to test how competition with invasive plants alters both identity and function in the native rhizosphere microbiome, and whether competition between these groups interacts with rainfall to amplify or ameliorate these microbial shifts. Metagenomics of rhizosphere communities revealed that drought combined with competition from invaders altered a higher number of functions and families in the native rhizosphere compared to invasive competition alone or drought alone. This suggests invasion-driven shifts in the microbial community may be involved in weakening natives’ ability to cope with climate change, especially drought. Understanding the role of the microbial community under invasion and climate change may be critical to mitigating the negative effects of these interacting global change drivers on native communities.
Identification of FacZ as a division site placement factor inStaphylococcus aureus
Authors: Bartlett Thomas M. , Sisley Tyler A. , Mychack Aaron , Walker Suzanne , Baker Richard W. , Rudner David Z. , Bernhardt Thomas G. 
Published: April 2023

SUMMARYStaphylococcus aureusis a gram-positive pathogen responsible for life-threatening infections that are difficult to treat due to antibiotic resistance. The identification of new vulnerabilities in essential processes like cell envelope biogenesis represents a promising avenue towards the development of anti-staphylococcal therapies that overcome resistance. To this end, we performed cell sorting-based enrichments forS. aureusmutants with defects in envelope integrity and cell division. We identified many known envelope biogenesis factors as well as a large collection of new factors with roles in this process. Mutants inactivated for one of the hits, the uncharacterized SAOUHSC_01855 protein, displayed aberrant membrane invaginations and multiple FtsZ cytokinetic ring structures. This factor is broadly distributed among Firmicutes, and its inactivation inB. subtilissimilarly caused division and membrane defects. We therefore renamed the protein FacZ (Firmicute-associatedcoordinator ofZ-rings). InS. aureus, inactivation of the conserved cell division protein GpsB suppressed the division and morphological defects offacZmutants. Additionally, FacZ and GpsB were found to interact directly in a purified system. Thus, FacZ is a novel antagonist of GpsB function with a conserved role in controlling division site placement inS. aureusand other Firmicutes.
HIV post-exposure prophylaxis adherence due to needle stick and sharp injuries
Authors: Osoo Moses Odhiambo , Otieno George Ochieng’ , Halestrap Peter 
Published: April 2023

AbstractBackgroundHealthcare workers frequently experience needle sticks and other sharp injuries, which are among the most prevalent types of occupational accident in hospital settings. Studies indicate that approximately 50% of these devices are contaminated with blood, exposing users to potential infections from blood-borne pathogens such as HIV. Despite the efficacy of post-exposure prophylaxis in lowering the risk of HIV transmission, ensuring consistent adherence to this treatment regimen remains a widely acknowledged challenge.ObjectiveThis study aimed to assess healthcare workers’ adherence to HIV post-exposure prophylaxis following needlestick and sharp injuries at Kijabe Hospital, Kenya, between February 2017 and June 2022.MethodA retrospective chart review was conducted on healthcare workers who were started on HIV PEP following a reported occupational exposure due to needle sticks and sharp injuries between February 2017 and June 2022.ResultIn total, 136 healthcare workers were exposed to needle sticks and sharp injuries. The majority of exposures (82.3%) were at a high risk of HIV transmission. The overall adherence rate to the 28-day HIV-PEP course was 26%. Healthcare workers were more likely to complete HIV-PEP when the source’s HIV status was positive than when it was negative [ 42.4% vs. 11.8%; p = 0.001]. The drug regimen (TDF/3TC/DTG) was significantly associated with default treatment (aOR, 5.0 (95% CI 2.0 – 11.0) (p= 0.001) compared with patients using the TDF/3TC/ATVr regimen.ConclusionOur study found that 74% of healthcare workers did not complete the full 28-day course of HIV post-exposure prophylaxis (PEP) as recommended, indicating a significant issue with adherence. This highlights the need for strategies to improve compliance and ensure occupational health. Additionally, as there is limited research on HIV PEP completion rates among healthcare workers in Kenya, these findings will contribute valuable knowledge in this area.
ATR2Cala2fromArabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition
Authors: Kim Dae Sung , Woods-Tör Alison , Cevik Volkan , Furzer Oliver J. , Li Yufei , Ma Wenbo , Tör Mahmut , Jones Jonathan D. G. 
Published: April 2023

SummaryArabidopsisCol-0 RPP2A and RPP2B confer recognition ofArabidopsisdowny mildew (Hyaloperonospora arabidopsidis[Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2effector was unknown.To revealATR2Cala2, an F2population was generated from a cross betweenHpa-Cala2 andHpa-Noks1. We identified ATR2Cala2as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition ofATR2Cala2and its effector function were verified by biolistic bombardment, ectopic expression andHpainfection.ATR2Cala2is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. InATR2Emoy2andATR2Noks1alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression ofATR2Cala2under 35S promoter inArabidopsisandNicotiana benthamianaenhances disease susceptibility.Two additional Col-0 TIR-NLR (TNL) genes (RPP2CandRPP2D) adjacent toRPP2AandRPP2Bare quantitatively required for full resistance toHpa-Cala2.We comparedRPP2haplotypes in multipleArabidopsisaccessions and showed that all 4 genes are present in all ATR2Cala2-recognizing accessions.
Developing a benchmark for supplier code of conducts – lessons learned from Bayer’s journey towards sustainable procurement and research opportunities
Authors: van Hoek Remko , Udesen Thomas 
Published: April 2023

PurposeSupplier codes of conduct are amongst the most widely used practices in sustainable procurement programs. While there are limitations and risks involved in using supplier codes of conduct (including the risk of greenwashing, a weak link to action and the inability of supplier to comply), there is only a modest amount of research on the topic, other than content analysis. We aim to contribute to research both lessons learned, over a two-decade period, about the implementation and use of a supplier code of conduct from a case study, as well as, to suggest further research that can support the industry and enrich insight into the effective adoption of supply codes of conduct.Design/methodology/approachThanks to the support of our co-author from Bayer we are able to share lessons learned by the global procurement team of Bayer and use these as a basis for suggesting questions for further research. The approach of this paper centres on the adoption and implementation of the supplier code of conduct in an effort to complement existing research on supplier codes of conduct that is largely focused on code of conduct content, less on the implementation of codes of conduct. The collaboration with our co-author from Bayer enables direct access to experiences and managerial perspectives. By considering the two-decade journey towards more sustainable supply chain management at Bayer, we are able to achieve a longitudinal perspective on adoption and implementation aspects.FindingsBayer ensures personal and community engagement in its sustainable procurement program in order to drive action and improve decision making along the value chains. The company regularly updates its code of conduct to stay aligned with its maturity and complements the code of conduct with a continuous improvement focus, supported by both generic and industry-specific consortia. The company has not yet been able to establish direct visibility into the conduct of tier 2 and up suppliers.Originality/valueThis paper helps close a gap in the literature and provides input into industry efforts in one of the most widely used practices in sustainable procurement. We hope that the research questions that we developed based on the first 20+ years of Bayer’s learning journey towards sustainable procurement will inspire research that can impact industry efforts towards creating a more sustainable future.