bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea
Authors: Warwick-Dugdale Joanna , Tian Funing , Michelsen Michelle , Cronin Dylan R , Moore Karen , Farbos Audrey , Chittick Lauren , Bell Ashley , Buchholz Holger H , Parsons Rachel J , Zayed Ahmed A , Allen Michael J , Sullivan Matthew B , Temperton Ben 
Published: September 2022

ABSTRACTIn the summer months, the waters of the Sargasso Sea are nutrient-limited and strongly stratified, serving as a model system for the predicted warmer and nutrient-limited oceans of the Anthropocene. The dominant microorganisms of surface waters are key drivers of the global carbon cycle. However, the viruses of the Sargasso Sea that shape these host communities and influence host biogeochemical function are not well understood. Here, we apply a hybrid sequencing approach that combines short- and long reads to survey Sargasso Sea phage communities via metagenomics at the viral maximum (80m) and mesopelagic (200m) depths. Taxonomically, we identified 2,301 Sargasso Sea phage populations (~species-level taxonomy) across 186 genera. Over half of the phage populations lacked representation in other global ocean viral metagenomes, whilst 177 phage genera lacked representation in phage isolate databases. Viral fraction and cell-associated viral communities captured in short-read data were distinct and decoupled at both depths, possibly indicating low active lytic viral replication in the Sargasso Sea, with viral turnover occurring across periods longer than the sampling period of three days. Inclusion of long read data was critical for (1) the identification of 79 ecologically important and common viral genomes; (2) capturing the extent of viral genome microdiversity; and (3) enabling the recovery of hypervariable regions in viral genomes predicted to encode proteins involved in host recognition, DNA synthesis and DNA packaging. Host prediction was only possible for ~4% of viral populations. Genomes of phages known to infect Prochlorococcus and Pelagibacter were poorly represented in our data, supporting recent evidence of low infection levels in the dominant bacterial taxa of oligotrophic regions.SubjectsBioinformatics, Genomics, Marine Biology, Microbiology, VirologySequence data accession numbersPRJNA767318
The assessment of cortical hemodynamic responses induced by tubuloglomerular feedback using in vivo imaging
Authors: Lee Blaire , Postnov Dmitry D. , Sørensen Charlotte M. , Sosnovtseva Olga 
Published: September 2022

AbstractThe tubuloglomerular feedback (TGF) mechanism is crucial in modulating renal hemodynamics and glomerular filtration rate in individual nephrons. Our study aimed to evaluate the TGF-induced vascular responses by comparing the effects of two transport inhibitors with different sites and mechanisms of action. We assessed cortical hemodynamics with high-resolution laser speckle contrast imaging, which enabled the evaluation of blood flow individual micro-vessels and analysis of their dynamical patterns in the time-frequency domain. We demonstrated that a systemic administration of a loop diuretic abolishes TGF-mediated hemodynamic responses. Furthermore, we showed that the local microcirculatory blood flow decreased, and the TGF reset in response to reduced proximal reabsorption elicited by systemic administration of a sodium-glucose co-transporter 2 inhibitor, phlorizin.
PIKfyve is required for phagosomal Rab7 acquisition and the delivery and fusion of early macropinosomes to phagosomes
Authors: Vines James H. , Buckley Catherine M. , King Jason S. 
Published: September 2022

AbstractPhagosome maturation is tightly regulated to ensure efficient delivery of the complex arsenal of antimicrobial activities that kill and digest captured microbes. Like other endocytic pathways, phagosome maturation is regulated by a combination of Rab GTPases and phosphoinositide signalling lipids (PIPs) which define membrane identity and recruit specific effectors. PIKfyve is a PI-5 kinase, which converts PI(3)P to PI(3,5)P2on endosomes. Disruption of PIKfyve results in severe defects in phagosomal maturation but the underlying mechanism remains unclear. Here, we use the model professional phagocyte,Dictyostelium discoideumto dissect the role of PIKfyve in the crucial first steps of phagosome maturation. We find that, although early Rab5 dynamics are unaffected, loss of PIKfyve prevents phagosomes from acquiring Rab7 by fusion with a pool of Rab7 and V-ATPase positive endosomes. By following PIP dynamics using our recently characterised PI(3,5)P2-probe SnxA, we delineate multiple subpopulations of Rab7-positive endosomes that fuse sequentially with phagosomes. We identify one of these as PI(3,5)P2-positive macropinosomes, which dock and fuse with phagosomes in a PIKfyve-dependent manner. We therefore show thatDictyosteliumphagosomes primarily accumulate Rab7 by vesicular fusion rather than from a cytosolic pool, and that this requires PIKfyve. In particular PI(3,5)P2defines a specific subset of fusogenic macropinosomes, which we propose enables content mixing and the efficient bulk delivery of lysosomal components to phagosomes.
Single and Multi-trait Genomic Prediction for agronomic traits inEuterpe edulis
Authors: Canal Guilherme Bravim , Barreto Cynthia Aparecida Valiati , de Almeida Francine Alves Nogueira , Zaidan Iasmine Ramos , do Couto Diego Pereira , Azevedo Camila Ferreira , Nascimento Moysés , Ferreira Marcia Flores da Silva , Ferreira Adésio 
Published: September 2022

AbstractPopularly known as juçaizeiro,Euterpe edulishas been gaining prominence in the fruit growing sector and has demanded the development of superior genetic materials. As it is a native species and still little studied, the application of more sophisticated techniques can result in higher gains with less time. Until now, there are no studies that apply genomic prediction for this crop, especially in multi-trait analysis. In this sense, this study aimed to apply new methods and breeding techniques for the juçaizeiro, to optimize this breeding program through the application of genomic selection. This data consisted of 275 juçaizeiro genotypes from a population of Rio Novo do Sul-ES, Brazil. The genomic prediction was performed using the multi-trait (G-BLUP MT) and single-trait (G-BLUP ST) models and the selection of superior matrices was based on the selection index of Mulamba and Mock. Similar results for predictive ability were observed for both models. However, the G-BLUP ST model provided greater selection gains when compared to the G-BLUP MT. For this reason, the genomic estimated breeding values (GEBVs) from the G-BLUP ST were used to select the six superior genotypes (UFES.A.RN.390, UFES.A.RN.386, UFES.A.RN.080, UFES.A.RN.383, UFES.S.RN.098, and UFES.S.RN.093), to provide superior genetic materials for the development of seedlings and implantation of productive orchards, which will meet the demands of the productive, industrial and consumer market.Key messageIn the first genomic selection study forEuterpe edulis, substantial gains for multiple traits of fruit production was reported. This is a key factor for the sustainable use of the species in the Atlantic Forest.
Drought adaptability of different subspecies of tetraploid wheat (Triticum turgidum) under contrasting moisture conditions: association with solvent retention capacity and quality-related traits
Authors: Saeidnia F. , Shoormij F. , Mirlohi A. , Soleimani Kartalaei E. , Mohammadi M. , Sabzalian M. R. 
Published: September 2022

AbstractFew prior efforts have been made to investigate the genetic potential of different subspecies of Triticum turgidum for drought tolerance and their quality-related traits compared with common wheat (Triticum aestivum) and to identify the association among agronomic, micronutrients, and quality-related traits, especially under climate change conditions. In this research, grain quality, technological properties of flour, and some agronomic traits were studied in 33 wheat genotypes from six different subspecies of Triticum turgidum along with three cultivars of Triticum aestivum in the field, applying a well-watering (WW) and a water stress (WS) environment during two growing seasons. A high degree of variation was observed among genotypes for all evaluated traits, demonstrating that selection for these traits would be successful. Consequences of water stress were manifested as declined DM, TGW, GY, and LASRC; and significantly increased GPC, ZEL, GH, WAF, WSRC, SuSRC, and SCSRC compared to the well-watering condition. The reductions in the unextractable polymeric protein fraction and glutenin-to-gliadin ratio indicated a poorer grain yield quality, despite higher protein content. This study showed that the early-maturing genotypes had higher water absorption and pentosan, and therefore are more suitable for bread baking. In contrast, late-maturing genotypes are ideal for cookie and cracker production. Two subspecies of T. turgidum ssp. durum and T. turgidum ssp. dicoccum with high micronutrient densities and quality-related traits, and T. turgidum ssp. oriental due to having high values of grain protein content can be used to improve the quality of T. aestivum through cross-breeding programs. Based on the association of different traits with SRC values and other quality-related traits and PCA results, contrasting genotypes can be used to develop mapping populations for genome studies of grain quality and functional properties of flour in future studies.
The homeobox transcription factor DUXBL controls exit from totipotency
Authors: Vega-Sendino Maria , Olbrich Teresa , Stein Paula , Tillo Desiree , Carey Grace I. , Savy Virginia , Saykali Bechara , Domingo Catherine N. , Maity Tapan K. , Jenkins Lisa M. , Williams Carmen J. , Ruiz Sergio 
Published: September 2022

ABSTRACTUpon exit from the totipotent 2-cell (2C) embryo stage, the 2C-associated transcriptional program needs to be efficiently silenced. However, the molecular mechanisms involved in this process remain mostly unknown. Here, we demonstrate that the 2C-specific transcription factor DUX directly induces the expression of DUXBL to promote this silencing. Indeed, DUX expression in Duxbl-knockout ESC causes increased induction of the 2C-transcriptional program, whereas DUXBL overexpression impairs 2C-associated transcription. CUT&RUN analyses show that DUXBL gains accessibility to DUX-bound regions in DUX-induced ESC while it is unable to bind those regions in uninduced cells. Mechanistically, we determined that DUXBL interacts with TRIM24 and TRIM33, two members of the tripartite motif superfamily involved in gene silencing and co-localizes with them in nuclear foci upon DUX expression. Furthermore, DUXBL downregulation in mouse zygotes leads to a penetrant 2C-stage arrest. Our data reveals an unexpected role for DUXBL in controlling the exit from totipotency.
Expression of thioredoxin-1 in the ASJ neuron corresponds with and enhances intrinsic regenerative capacity under lesion conditioning inC. elegans
Authors: Grooms Noa W.F. , Fitzgerald Michael Q. , Zuckerman Binyamin , Ureña Samuel E. , Weinberger Leor S. , Chung Samuel H. 
Published: September 2022

AbstractA conditioning lesion of the peripheral sensory axon triggers robust central axon regeneration in mammals. We trigger conditioned regeneration in theC. elegansASJ neuron by laser surgery or genetic disruption of sensory pathways. Conditioning upregulatestrx-1expression, as indicated bytrx-1promoter-driven green fluorescent protein and fluorescence in situ hybridization, suggestingtrx-1levels and associated fluorescence indicate regenerative capacity. Redox activity oftrx-1functionally enhances conditioned regeneration, but both redox-dependent and –independent activity inhibit non-conditioned regeneration. Six strains isolated in a forward genetic screen for reduced fluorescence, which suggests diminished regenerative potential, also show reduced axon outgrowth. We demonstrate an association betweentrx-1expression and the conditioned state that we leverage to rapidly assess regenerative capacity.
A neuron that regulates locomotion makes a potential sensory cilium lying over the C. elegans egg-laying apparatus
Authors: Christie Nakeirah T.M. , Koelle Michael R. 
Published: September 2022

AbstractThe neural circuit for C. elegans egg laying has been studied intensively for decades, yet it is not clear that its known components can account for how egg-laying and locomotion behaviors are coordinated. We found that the two PVP neurons, which release neuropeptides that promote roaming locomotion, make previously-undescribed branches that terminate in large wing-shaped endings directly over the egg-laying apparatus. The PVP branches occur in hermaphrodites but not males and develop during the L4 larval stage when the egg-laying system also develops. The PVP wing is located at the junction between the uterus and the vulva, adjacent to neurons that control egg laying, and surrounded by cells that we found label with a glial marker. The morphology of the PVP wing and its envelopment within possible glial cells are consistent with the hypothesis that the PVP wing is a sensory cilium. Although PVP is reported to express sensory receptor homologs, we have been unable to detect PVP expression of more specific markers of neural cilia, and we have also not detected strong PVP defects in the daf-19 mutant, which does show defects in known neural cilia. The PVPs are extraordinarily sensitive to expression of transgenes, which cause developmental and possibly functional defects in these neurons. This has prevented us from recording or manipulating PVP activity to determine its functional roles. Thus, the intriguing hypothesis that PVP is a sensory neuron that might coordinate egg laying and locomotion will remain speculative until better methods to manipulate PVP can be developed.
Analysis of polygenic selection in purebred and crossbred pig genomes using Generation Proxy Selection Mapping
Authors: Grohmann Caleb J. , Shull Caleb M. , Crum Tamar E. , Schwab Clint , Safranski Timothy J. , Decker Jared E. 
Published: September 2022

AbstractBackgroundArtificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time, termed polygenic selection, at causal loci and the surrounding genomic regions. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied Generation Proxy Selection Mapping (GPSM), a genome-wide association analysis of SNP genotype (38,294 to 46,458 SNPs) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8,447 pigs per population) to identify loci responding to artificial selection over a span of five to ten years. Gene-drop simulation analyses were conducted to validate GPSM results. Selection signatures within and across each population of pigs were compared in the context of commercial pork production.ResultsForty-nine to 854 loci were identified by GPSM as under selection (Q-values less than 0.10) across 15 subsets of pigs based on population combinations. The number of significant associations increased as populations of pigs were pooled. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were identified when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations.ConclusionsThis work confirms the efficacy and accuracy of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. Identified polygenic selection highlights loci important to swine production.
Roles at crossroads: complexities and conflicts surrounding management accountants' roles based on evidence from the Sri Lankan context
Authors: Sivabalachandran Thenuja , Gooneratne Tharusha 
Published: September 2022

PurposeDrawing insights from finance and non-finance managers in Sri Lanka, this study unveils complexities and conflicts surrounding the roles of management accountants and the nature of role construction stemming from differing expectations of non-finance managers and external influences.Design/methodology/approachThis paper adopts the qualitative methodology and leans on role theory and new institutional sociology (NIS), as these dual theories complement each other and enable a holistic understanding of management accountants' roles, complexities and conflicts.FindingsThe findings reveal that in fulfilling their roles on par with divisional goals, amid expectations of non-finance managers and external influences, management accountants face various complexities and conflicts. Furthermore, in navigating through their roles, understanding the operational realities of work organizations and business sectors and negotiating with non-finance managers is vital.Research limitations/implicationsThis research draws evidence from a selection of finance and non-finance managers. Thus the findings are not expected to be generalized to business firms in Sri Lanka.Practical implicationsThis paper offers practitioner insights into how management accountants could construct their roles in different organizational settings, balancing the expectations of non-finance managers and external influences.Originality/valueDespite its importance, complexities and conflicts surrounding management accountants' roles amid multiple influences have attracted scant research attention. Hence this paper is a noteworthy addition to the literature. Besides, using role theory and NIS in tandem although apt, has not been the focus of prior researchers in delving into this phenomenon.
Choice-based games and resilience building of gender nonconforming individuals: a phenomenological study
Authors: Cantrell Yuri , Zhu Xiaohua Awa 
Published: September 2022

PurposeNarrative-driven, choice-based games, games that allow gamers to make decisions regarding the game characters and storylines, can bring forth emotional changes in their players and offer empathy during scenarios that a player may not experience in real-world situations. Therefore, they can be used as tools to help with gender nonconforming (GNC) individuals’ resilience regarding their gender identities. This study explores GNC peoples’ game-playing experiences with choice-based games, especially how such experiences help them gain resilience and shape their gender identities.Design/methodology/approachThis study follows the classic phenomenological approach to understanding the experience of GNC gamers’ resilience experience from their own perspectives. In-depth interviews were conducted with 12 GNC participants, aged between 18 and 34. Each interview lasted 45–90 minutes. Interviews were transcribed and coded using NVivo R1. The essence of meanings was identified using themes and interpreted through qualitative analysis.FindingsThis paper identified six gender- and resilience-related common themes within GNC people’s gaming experiences, including 1) character creation: exploring gender identity through an avatar; 2) self-exploration and experimentation in games; 3) resonating experiences; 4) positive inclusive features in games; 5) storytelling and involving the player and 6) your actions have meaning.Practical implicationsThe themes, patterns and game features identified in this study may provide insight into potential resilience-building activities for GNC people. They may inform digital mental health interventions, information services and game design practices.Social implicationsEquity, inclusion and social justice have become a significant theme in today’s society. This study focuses on a marginalized community, GNC people and their mental health and resilience building. Results of the study will contribute to the understanding of this community and may inspire more intervention methods to help them cope with stress and difficult situations.Originality/valueResearch on gaming’s health benefits for the general population has been abundant, but studies about using games to help the LGBTQ+ community have been largely overlooked until recent years. Research on casual games’ mental benefits for LGBTQ+ people is particularly lacking. This research is one of the first in-depth, comprehensive investigations of GNC individuals’ resilience experiences with a particular type of casual video games, choice-based games. The phenomenological study offers rich description of gaming and gender identity exploration from gamers’ viewpoints.
The concept of integration in an IPD context: a grounded theory review
Authors: Rankohi Sara , Bourgault Mario , Iordanova Ivanka 
Published: September 2022

PurposeRecent construction literature has been focusing more on integrative contracting approaches such as integrated project delivery (IPD). However, conceptual studies on integration in IPD literature are scattered and fragmented, that is, most of the studies only focused on the segmented dimension of integration. A systemic understanding of the concepts of integration in IPD project-based context is still lacking. To fill this gap, this paper analyzes two aspects of integration (dimensions and directions) in IPD literature and explores their extent in construction projects.Design/methodology/approachGrounded theory review and focus group discussion approaches were employed to perform a thorough conceptual review of the literature, frame the research into the theory and increase the fundamental understanding of the concept of integration in IPD literature.FindingsIn this study, IPD integrating techniques were identified and their integration dimensions and directions were discussed. Results show that integration in the project-based environment of IPD is a multidimensional construct. Based on organizational, contractual and operational characteristics of IPD projects, twenty-four integration mechanisms were identified and framed into seven clusters. The integration directions over project life-cycle were demonstrated in three contexts: (1) an on-site construction project, delivered traditionally, (2) an on-site construction project, delivered with IPD and (3) an off-site construction project, delivered with IPD.Originality/valueThis paper gathers the segments of integration into a comprehensive overview, which can help researchers and practitioners explore elements of IPD project success more precisely. A theoretical framework of integration clusters is developed, based on IPD literature. The impact of IPD on on-site versus off-site construction is illustrated from an integration direction perspective. Finally, future areas of studies for researchers and practitioners about the concept of integration in an IPD context are discussed. This paper provides a point of departure for future theoretical and empirical explorations.