bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation of the K+ transporter SlHAK5 of tomato alters pistil morphology, ionome, metabolome and transcriptome in flowers
Authors: Amo Jesús , Jiménez‐Estévez Elisa , Martínez‐Martínez Almudena , Yáñez Adrián , Martínez Vicente , Nieves‐Cordones Manuel , Rubio Francisco 
Published: October 2024

AbstractK+ accumulation in plant tissues is a crucial factor for plant growth and development. The tomato high‐affinity K+ transporter SlHAK5 is essential for root K+ acquisition from low external concentrations. It is also involved in K+ accumulation in pollen and plant fertility as slhak5 KO plants show a low rate of pollen germination, impaired pollen tube growth and parthenocarpic fruits. Here, we present a thorough analysis of slhak5 flowers, which showed relevant defects at the anatomic, ionomic, metabolomic and transcriptomic levels. First, slhak5 flowers exhibited shorter styles and enlarged ovaries that, together with a low number of seeds in fruits from slhak5 X WT crosses, indicated an effect of the slhak5 mutation on female fertility. Second, a lower accumulation of Ca2+, as well as of several metabolites such as amino acids, citric acid and sugars, was observed in mutant flowers, whereas indole‐3‐acetic acid content was increased when compared to the wild‐type. Third, RNAseq conducted on pistils and stamens of wild‐type and slhak5 plants revealed that transport and signalling pathways are significantly enriched in the gene expression analyses of stamens. Thus, it can be concluded that a functional SlHAK5 transporter is required to maintain appropriate Ca2+, metabolite and gene expression levels in flowers, and its absence leads to important reductions in both male and female fertility.
The Political Influence of Proxy Advisors in Campaigns for Ethical Investment: Guiding the Invisible Hand
Authors: Elbra Ainsley , O'Brien Erin , Boersma Martijn 
Published: October 2024

ABSTRACTLarge, listed companies are under increasing pressure to respond to critical issues such as climate change, modern slavery, and the protection of First Nations' heritage. Much of this pressure is exerted by civil society actors through corporate governance mechanisms, including leveraging shareholder rights to lobby firms. At the heart of this process sit largely understudied actors, proxy advisors, who advise large institutional investors on whether to support civil society's claim‐making on companies. The proxy advising industry is an influential duopoly that advises almost all institutional investors globally. This article advances our understanding of how norms are formed to become established market practices. It maps the relational power structures that govern ethical investment and reveals the capacity of proxy advisors to contribute to the cascading of ethical investment norms. In doing so, we argue that markets are not solely guided by exogenous forces but are reflective of the web of social relations between actors. We conclude that despite historically being seen as neutral experts in their role in advising institutional investors, proxy advisors should be viewed as political actors with significant influence over the outcome of social movement campaigns.
Measuring many mindsets: A systematic review of growth mindset domains, and discussion of domain relationships, with implications for growth mindset interventions
Authors: Kyler E. Nathan , Moscicki Michele K. 
Published: October 2024

AbstractResearch into growth mindset, the belief that attributes are malleable, has increased dramatically in the last 30 years, leading to an explosion in the number of mindset domains studied. Given this plethora of mindset domains, there is comparatively little work investigating mindset domain relationships. Further, with expanding interest in growth mindset has come an increase in mindset interventions aimed at increasing growth mindset beliefs, with mixed results. The mindset domain used in intervention messaging is an understudied potential moderator of intervention efficacy, as few domains have been used in interventions, despite the number of domains studied. In this article we raise three questions: (1) How many mindset domains have been studied and what are those domains?; (2) How are beliefs in different mindset domains related to one another?; and (3) How can we use information about existing mindset domains and their relationships to improve mindset intervention efficacy? To address question one, we systematically reviewed the mindset literature between 1995 and 2022 to document studied mindset domains. We then discuss heterogeneity in mindset domain relationship research and suggest how our review can be used to address gaps in this field. Lastly, we describe heterogeneity in mindset intervention efficacy and suggest how to apply our review of mindset domains to examine the impact of the domain used in intervention messaging on efficacy. We aim to stimulate research into understanding mindset domain relationships and how this insight may be applied to mindset interventions to improve people's lives through effectively enhancing their growth mindset beliefs.
Identifying the gene responsible for non‐photochemical quenching reversal in Phaeodactylum tricornutum
Authors: Ware Maxwell A. , Paton Andrew J. , Bai Yu , Kassaw Tessema , Lohr Martin , Peers Graham 
Published: October 2024

SUMMARYAlgae such as diatoms and haptophytes have distinct photosynthetic pigments from plants, including a novel set of carotenoids. This includes a primary xanthophyll cycle comprised of diadinoxanthin and its de‐epoxidation product diatoxanthin that enables the switch between light harvesting and non‐photochemical quenching (NPQ)‐mediated dissipation of light energy. The enzyme responsible for the reversal of this cycle was previously unknown. Here, we identified zeaxanthin epoxidase 3 (ZEP3) from Phaeodactylum tricornutum as the candidate diatoxanthin epoxidase. Knocking out the ZEP3 gene caused a loss of rapidly reversible NPQ following saturating light exposure. This correlated with the maintenance of high concentrations of diatoxanthin during recovery in low light. Xanthophyll cycling and NPQ relaxation were restored via complementation of the wild‐type ZEP3 gene. The zep3 knockout strains showed reduced photosynthetic rates at higher light fluxes and reduced specific growth rate in variable light regimes, likely due to the mutant strains becoming locked in a light energy dissipation state. We were able to toggle the level of NPQ capacity in a time and dose dependent manner by placing the ZEP3 gene under the control of a β‐estradiol inducible promoter. Identification of this gene provides a deeper understanding of the diversification of photosynthetic control in algae compared to plants and suggests a potential target to improve the productivity of industrial‐scale cultures.
Outcome of 21 dogs treated for the portocaval subtype of extrahepatic portosystemic shunts
Authors: Swieton Natalie , Weisse Chick , Zwingenberger Allison L. , Vilaplana Grosso Frederico R. , Carroll Kenneth A. , Scharf Valery F. , Asano Kazushi , Wallace Mandy L. , Arai Shiori , Lipscomb Victoria J. , Amato Nicole S. , Davidson Jacqueline R. , Aly Ali M. 
Published: October 2024

AbstractObjectiveTo assess outcomes of dogs with side‐to‐side portocaval extrahepatic portosystemic shunts (PC‐EHPSS) and poor portal perfusion to the liver treated with medical management alone (MM) or surgical attenuation (SA).Study designMulti‐institutional retrospective study.AnimalsA total of 21 dogs with PC‐EHPSS (14/21 MM and 7/21 SA).MethodsMedical records were reviewed, and data was collected on dogs <12 kg with PC‐EHPSS treated with MM or SA between June 2008 to June 2021. Signalment, clinical signs, postoperative complications, bloodwork values, long‐term clinical outcome, survival, and owner reported quality of life were recorded.ResultsOf 21 dogs included, 10 were mixed breeds and 14 were females. Median age at time of presenting clinical signs was 163 days. At final follow‐up examination (median 1119 days), all SA and 6/14 MM dogs were alive, with a median survival time of 2138 days following treatment onset. In surviving MM dogs, outcome was fair in 3/6 and poor in 3/6. In SA dogs with long‐term follow‐up, outcome was fair in 5/6, and poor in 1/6. A greater proportion of SA dogs had improved bloodwork parameter values at final follow‐up examination, and the mean relative change in final bloodwork values was higher when compared to MM dogs.ConclusionThese findings demonstrate that SA has improved clinical outcomes to MM for PC‐EHPSS; however, SA clinical outcomes appear worse than those previously reported for other EHPSS.Clinical significanceThis information may have implications for expected outcomes in other EHPSS subtypes associated with severely diminished portal perfusion.
Pangenome analysis of
Paenibacillus polymyxa
strains reveals the existence of multiple and functionally distinct
Paenibacillus
species
Authors: Maggi Federica , Giuliodori Anna Maria , Brandi Anna , Cimarelli Lucia , Alcántara Roberto , Pallotti Stefano , Amantini Consuelo , Petrelli Dezemona , Fabbretti Attilio , Spurio Roberto , Napolioni Valerio 
Published: October 2024

ABSTRACT

Paenibacillus polymyxa
, a Gram-positive bacterium commonly found in soil and plant roots, plays an important role in the environment due to its nitrogen-fixing ability and is renowned for producing antibiotics like polymyxin. In this study, we present a robust framework for investigating the evolutionary and taxonomic connections of strains belonging to
P. polymyxa
available at the National Center for Biotechnology Information, as well as five new additional strains isolated at the University of Camerino (Italy), through pangenome analysis. These strains can produce secondary metabolites active against
Staphylococcus aureus
and
Klebsiella pneumoniae
. Employing techniques such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) estimation, OrthoFinder, and ribosomal multilocus sequence typing, we consistently divided these
P. polymyxa
strains into four clusters, which differ significantly in terms of ANI and dDDH percentages, both considered as reference indices for separating bacterial species. Moreover, the strains of Cluster 2 were re-classified as belonging to the
Paenibacillus ottowii
species. By comparing the pangenomes, we identified the core genes of each cluster and analyzed them to recognize distinctive features in terms of biosynthetic/metabolic potential. The comparison of pangenomes also allowed us to pinpoint differences between clusters in terms of genetic variability and the percentage of the genome dedicated to core and accessory genes. In conclusion, the data obtained from our analyses of strains belonging to the
P. polymyxa
species converge toward a necessary reclassification, which will require a fundamental contribution from microbiologists in the near future.

IMPORTANCE

The development of sequencing technologies has led to an exponential increase in microbial sequencing data. Accurately identifying bacterial species remains a challenge because of extensive intra-species variability, the need for multiple identification methods, and the rapid rate of taxonomic changes. A substantial contribution to elucidating the relationships among related bacterial strains comes from comparing their genomic sequences. This comparison also allows for the identification of the “pangenome,” which is the set of genes shared by all individuals of a species, as well as the set of genes that are unique to subpopulations. Here, we applied this approach to
Paenibacillus polymyxa
, a species studied for its potential as a biofertilizer and biocontrol agent and known as an antibiotic producer. Our work highlights the need for a more efficient classification of this bacterial species and provides a better delineation of strains with different properties.
Bacterial acquisition of host fatty acids has far-reaching implications on virulence
Authors: Waters Jack K. , Eijkelkamp Bart A. 
Published: October 2024

SUMMARY
The lipid homeostasis pathways of bacterial pathogens have been studied comprehensively for their biochemical functionality. However, new and refined technologies have supported the interrogation of bacterial lipid and fatty acid homeostasis mechanisms in more complex environments, such as mammalian host niches. In particular, emerging findings on the breadth and depth of host fatty acid uptake have demonstrated their importance beyond merely fatty acid utilization for membrane synthesis, as they can contribute to virulence factor regulation, pathogenesis, and group-based behaviors. Lipid homeostasis is also intertwined with other metabolic and physiological processes in the bacterial cells, which appear to be largely unique per species, but overarching themes can be derived. This review combines the latest biochemical and structural findings and places these in the context of bacterial pathogenesis, thereby shedding light on the far-reaching implications of lipid homeostasis on bacterial success.
In vivo
RNA sequencing reveals a crucial role of Fus3-Kss1 MAPK pathway in
Candida glabrata
pathogenicity
Authors: Mo Xinreng , Yu Xiangtai , Cui Hao , Xiong Kang , Yang Shan , Su Chang , Lu Yang 
Published: October 2024

ABSTRACT

Candida glabrata
is an important and increasingly common pathogen of humans, particularly in immunocompromised hosts. Despite this, little is known about how this fungus causes disease. Here, we applied RNA sequencing and an
in vivo
invasive infection model to identify the attributes that allow this organism to infect hosts. Fungal transcriptomes show a dramatic increase in the expression of Fus3 and Kss1, two mitogen-activated protein kinases (MAPKs), during invasive infection. We further demonstrate that they are both highly induced under a combination of serum and high CO
2
conditions. Deletion of both
FUS3
and
KSS1
, but neither gene alone, results in a reduced fungal burden in organs, as well as in the gastrointestinal tract in the DSS (Dextran Sulfate Sodium)-induced colitis model. Similarly, the defect in persistence in macrophages and attenuated adhesion to epithelial cells are observed when
FUS3
and
KSS1
are both disrupted. The
fus3 kss1
double mutant also displays defects in the induction of virulence attributes such as genes required for iron acquisition and adhesion and in the anti-fungal drug tolerance. The putative downstream transcription factors Ste12 (1), Ste12 (2), Tec1, and Tec2 are found to be involved in the regulation of these virulence attributes. Collectively, our study indicates that an evolutionary conserved MAPK pathway, which regulates mating and filamentous growth in
Saccharomyces cerevisiae
, is critical for
C. glabrata
pathogenicity.

IMPORTANCE

The MAPK signaling pathway, mediated by closely related kinases Fus3 and Kss1, is crucial for controlling mating and filamentous growth in
Saccharomyces cerevisiae
, but this pathway does not significantly impact hyphal development and pathogenicity in
Candida albicans
, a commensal-pathogenic fungus of humans. Furthermore, deletion of Cpk1, the ortholog of Fus3 in pathogenic fungus
Cryptococcus neoformans
, has no effect on virulence. Here, we demonstrate that the MAPK pathway is crucial for the pathogenicity of
Candida glabrata
, a fungus that causes approximately one-third of cases of hematogenously disseminated candidiasis in the United States. This pathway regulates multiple virulence attributes including the induction of iron acquisition genes and adhesins, as well as persistence in macrophages and organs. Our work provides insights into
C. glabrata
pathogenesis and highlights an example in which regulatory rewiring of a conserved pathway confers a virulent phenotype in a pathogen.
Cyclooxygenase-2/prostaglandin E2 pathway orchestrates the replication of infectious bronchitis virus in chicken tracheal explants
Authors: Mahmoud Motamed Elsayed , Ali Ahmed , Farooq Muhammad , Isham Ishara M. , Suhail Sufna M. , Herath-Mudiyanselage Heshanthi , Rahimi Ryan , Abdul-Careem Mohamed Faizal 
Published: October 2024

ABSTRACT

In this study, we investigated the localized pathogenesis of infectious bronchitis virus (IBV) in chicken tracheal organ cultures (TOCs), focusing on the role of inducible cyclooxygenase (COX-2). Two divergent IBV strains, respiratory Connecticut (Conn) A5968 and nephropathogenic Delmarva (DMV)/1639, were studied at 6, 12, 24, and 48 hours post-infection (hpi). Various treatments including exogenous prostaglandin (PGE)2, a selective COX-2 antagonist (SC-236), and inhibitors of PGE2 receptors and Janus kinase (JAK) were administered. IBV genome load and antigen expression were quantified using real-time quantitative PCR and immunohistochemistry. COX-2, interferon (IFN)-α, IFN-β, interleukin (IL)−1β, IL-6, and inducible nitric oxide synthase (iNOS) expressions were measured, along with PGE2 and COX-2 concentrations. IBV genome load and protein expression peaked at 12 and 24 hpi, respectively. Conn A5968-infected TOCs exhibited continuous COX-2 expression for up to 24 hpi, extended PGE2 production up to 48 hpi, and reduced inflammatory cytokine expression. In contrast, DMV/1639-infected TOCs displayed heightened inflammatory cytokine expression, brief COX-2 expression, and PGE2 production. Treatment with IFN-γ, SC-236, PGE2 receptor inhibitors, or JAK inhibitors reduced IBV infection and lesion scores, whereas exogenous PGE2 or IFN-γ pretreatment with a JAK-2 inhibitor augmented infection. These findings shed light on the innate immune regulation of IBV infection in the trachea, highlighting the involvement of the COX-2/PGE2 pathway.

IMPORTANCE
Understanding the localized pathogenesis of infectious bronchitis virus (IBV) within the trachea of chickens is crucial for developing effective control strategies against this prevalent poultry pathogen. This study sheds light on the role of inducible cyclooxygenase (COX-2) and prostaglandin (PGE)2 in IBV pathogenesis using chicken tracheal organ culture (TOC) models. The findings reveal distinct patterns of COX-2 expression, PGE2 production, and immune responses associated with different IBV strains, highlighting the complexity of host-virus interactions. Furthermore, the identification of specific inhibitors targeting the COX-2/PGE2 pathway and Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway provides potential therapeutic avenues for mitigating IBV infection in poultry. Overall, this study contributes to our understanding of the innate immune regulation of IBV infection within the trachea, laying the groundwork for the development of targeted interventions to control IBV outbreaks in poultry populations.
Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach
Authors: Xu Zhilu , Yeoh Yun Kit , Tun Hein M. , Fei Na , Zhang Jingwan , Morrison Mark , Kamm Michael A. , Yu Jun , Chan Francis Ka Leung , Ng Siew C. 
Published: October 2024

ABSTRACT

The reproducibility in microbiome studies is limited due to the lack of one gold-standard operating procedure. The aim of this study was to examine the impact of protocol variations on microbiome composition using metagenomic data sets from a single center. We assessed the variation in a data set consisted of 2,722 subjects, including 9 subcohorts harboring healthy subjects and patients with various disorders, such as inflammatory bowel disease, colorectal cancer, and type 2 diabetes. Two different DNA extraction kits, with or without lyticase, and two sample storage methods were compared. Our results indicated that DNA extraction had the largest impact on gut microbiota diversity among all host factors and sample operating procedures. Healthy subjects matched by age, body mass index, and sample operating methods exhibited reduced, yet significant differences (PERMANOVA,
P
< 0.05) in gut microbiota composition across studies. The variations contributed by DNA extraction were primarily driven by different recovery efficiency of gram-positive bacteria, e.g., phyla Firmicutes and Actinobacteria. This was further confirmed by a parallel comparison of fecal samples from five healthy subjects and a standard mock community. In addition, the DNA extraction method influenced DNA biomass, quality, and the detection of specific lineage-associated diseases. Sample operating approach and batch effects should be considered for cohorts with large sample size or longitudinal cohorts to ensure that source data were appropriately generated and analyzed. Comparison between samples processed with inconsistent methods should be dealt with caution. This study will promote the establishment of a sample operating standard to enhance our understanding of microbiome and translating in clinical practice.

IMPORTANCE
The reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 fecal samples generated from a single research center to examine the extent to which sample storage and DNA extraction influence the quantification of microbial composition and compared this variable with other sources of technical and biological variation. Our research highlights the impact of DNA extraction methods when analyzing microbiome data and suggests that the microbiome profile may be influenced by differences in the extraction efficiency of bacterial species. With metagenomics sequencing being increasingly used in clinical biology, our findings provide insight into the challenges using metagenomics sequencing in clinical diagnostics, where the detection of certain species and its abundance relative to a “healthy reference” is key.