bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rice glycosyltransferase UGT706F1 functions in heat tolerance through glycosylating flavonoids under the regulation of transcription factor MYB61
Authors: Zhao Shuman , Ma Yuqing , Ding Yi , Dong Guangrui , Liu Chonglin , Ma Xinmei , Hou Bingkai 
Published: February 2025

SUMMARYGlobal metabolic and transcriptional reprogramming is a common event in plant abiotic stress responses, however, the relevant molecular mechanisms remain largely unknown. Here, we characterized the physiological function and molecular mechanism for the rice UGT706F1. We found that UGT706F1 can be potently induced by high temperature. Its overexpression can markedly enhance the heat tolerance of rice through improving the capacity of scavenging reactive oxygen species, whereas its functional deletion results in heat sensitivity in rice. To investigate the regulatory mechanism of UGT706F1 in response to high temperature, we carried out extensive screening of the in vitro enzymatic activity of UGT706F1 and discovered that UGT706F1 exhibits broad‐spectrum activity toward flavonoid compounds. Through targeted flavonoid metabolomics analysis, we further revealed that the overexpression of UGT706F1 elevated the content of diverse flavonoids and flavonoid glycosides in rice. Subsequently, via transcriptome analysis, we found that following heat treatment, the overexpression of UGT706F1 was capable of enhancing the transcriptional activity of those genes including the flavonoid synthases, heat shock factors, heat shock proteins, glutathione S‐transferase, and various antioxidant enzymes. Furthermore, we identified an R2R3 MYB‐type transcription factor MYB61 and demonstrated that MYB61 could directly bind the promoter of UGT706F1 and activate the transcription of UGT706F1. The overexpression of MYB61 also enhanced the heat tolerance and increased flavonoid glycosides. Overall, this study unveiled a novel pathway of the plant heat tolerance response mediated by MYB61‐UGT706F1 module and identified a new UGT player for the metabolic and transcriptional regulation under high‐temperature circumstance.
Chlamydomonas reinhardtii, Volvox carteri and related green algae accumulate ketocarotenoids not in vegetative cells but in zygospores
Authors: Schwarz Sonja , Bauch Matthias , Schmitt Volker , Hallmann Armin , Lohr Martin 
Published: February 2025

SUMMARYZygospores of green alga such as Chlamydomonas reinhardtii, Volvox carteri or Dunaliella salina display a bright orange color indicative of carotenoids, yet there have been no reports on their pigment composition. The genomes of these algae contain genes for homologs of the β‐carotene ketolase (BKT) from the well‐known astaxanthin producer Haematococcus pluvialis, that were assumed to be pseudogenes, because none of these species has been reported to accumulate astaxanthin or other ketocarotenoids. Here, we show that C. reinhardtii and V. carteri synthesize ketocarotenoids specifically in zygospores. Contrary to the vegetative aplanospores of H. pluvialis, the major ketocarotenoid in zygospores of C. reinhardtii is not astaxanthin but 4‐ketolutein. Moreover, the ketocarotenoids in maturing zygospores are not synthesized de novo but from carotenoids of the photosynthetic apparatus liberated by a massive breakdown of thylakoid membranes. In line with this conclusion, incubation of zygospores at 9°C instead of 22°C resulted in a reduced thylakoid breakdown and only low amounts of ketocarotenoids, while the accumulation of storage lipids was less affected. Furthermore, we show the full‐length BKT from C. reinhardtii to catalyze the ketolation of both α‐carotene and lutein in carotenogenic bacteria. We also detected putative BKT genes in the genomes of various other green algae not yet known to synthesize ketocarotenoids, suggesting a zygospore‐specific accumulation of ketocarotenoids to be common among Chlamydomonadales. Our observation that zygospores of C. reinhardtii accumulate ketocarotenoids together with storage lipids sheds light on the physiology of a largely unexplored algal life stage crucial for survival and propagation.
Posttranslational regulation of plant membrane transporters
Authors: Niño‐González María , Duque Paula 
Published: February 2025

SUMMARYThe movement of substances across biological membranes is often constrained by physical or energetic barriers, requiring the action of transporter proteins embedded within the lipidic bilayer. These transporters also provide finely tuned regulation of substrate fluxes, essential for maintaining cellular function under both normal and stress conditions. Consequently, transporters are subject to multiple levels of tight regulation, including posttranslational modifications (PTMs). Here, we review the current knowledge on PTMs affecting plant membrane transporters and their impact on protein function. The attachment of chemical groups to protein residues enables rapid modulation of transporter functions, influencing a wide range of protein characteristics. Phosphorylation stands out as the most common PTM, affecting transporter attributes such as activation status, localization and substrate specificity. In turn, ubiquitination acts as a signal for downregulation, either by targeting the transporters for proteasomal degradation or by triggering their endocytosis and subsequent vacuolar sorting. The roles of other, less common PTMs remain unclear, as limited examples exist and recent advances have been sparse. The complex dynamics of substrate transport, which require precise flux magnitudes and directions, appear to demand multi‐layered control of the associated transporters. In consequence, further research is needed to investigate individual PTMs affecting transporters, as well as the interplay of multiple PTMs on a single transporter, to better understand how gradual modulation of protein function is achieved.
(Re)wilding London: Fabric, politics, and aesthetics
Authors: Turnbull Jonathon , Fry Tom , Lorimer Jamie 
Published: February 2025

AbstractRewilding has become established as a new mode of nature conservation. There is a growing body of science, ambitious landscape‐scale plans, and increasing political will. But until recently, cities and the urban were neglected; the idea of urban rewilding seen as oxymoronic. Of late, however, there has been a shift, with growing enthusiasm amongst metropolitan authorities, civil society, and citizens in major cities like London, New York, Toronto, and Melbourne, as well as smaller cities around the world. Noting a dearth of research on urban rewilding, this paper proffers an agenda for future geographical research into this emerging mode of urban nature conservation. The paper deploys the spatial‐optical metaphor of diffraction, which originates in feminist science studies, to explore how rewilding as a socioecological practice developed in rural areas is changed when it encounters the urban, drawing on recent work in urban theory to trace how the urban might inform a new model of rewilding better equipped for the novel ecosystems and political configurations of the increasingly urban Anthropocene. It begins by defining how the sociomaterial urban fabric diffracts rewilding's practices and principles. It then examines how the distinct political economy of cities shapes the power dynamics of urban rewilding. The aesthetic dimensions of urban rewilding are then highlighted as important factors shaping how this emerging mode of urban nature recovery unfolds. In conclusion, we note how the nascency of urban rewilding presents opportunities for geographers to prefigure a progressive mode of Anthropocene conservation, and we advocate an affirmative style of critique that allies with practitioners and policy‐makers. We establish future priorities for research into urban rewilding, including exploring minoritarian cultures of nature, comparative analysis of diverse cases, and examination of rural–urban linkages.
Keep Calm and Make a Blacklist: Child Labour and International Trade
Authors: Cifarelli Flavia 
Published: February 2025

ABSTRACTI investigate how the provision of information regarding the use of child labour in foreign production affects imports, using a staggered adoption design. I exploit a list, published annually by the US Department of Labor, with information on tradable goods produced using child labour in different countries. I find that the inclusion in the list leads to a decrease in US imports from that country equal to 15%, taking into account potential spillover effects. I provide evidence suggesting that this effect is not due to any change in price but is driven by a reduction in both US firms' intermediate input demand and demand by US final consumers, with the former channel being slightly larger.
Preliminary determination of bacterial contamination of whole blood units in a Ghanaian blood bank: Providing evidence to improve transfusion safety
Authors: Aidoo Nana Benyin , Ramirez‐Arcos Sandra , Gillard Laurie , Azumah Daniel Edem , Adatsi Angela 
Published: February 2025

AbstractBackground and ObjectivesTransfusion‐associated bacterial sepsis poses a significant risk to patient safety. This study aimed to determine the rate of bacterial contamination of whole blood (WB) collected at the Cape Coast Teaching Hospital (CCTH) as a quality control and quality assurance activity.Materials and MethodsOne‐hundred and three WB units collected between January and April of 2018 were screened for bacterial contamination. Bacteria isolated from positive cultures were identified and subjected to antimicrobial testing. WB recipients were followed up for clinical symptoms.ResultsOf the 103 WB units tested, 33 (32%) were contaminated with bacteria. Gram‐positive organisms accounted for 67% of the isolates, including coagulase‐negative Staphylococcus, Staphylococcus aureus and Bacillus spp., while Gram‐negative bacteria comprised 33% of the isolates, with Citrobacter freundii, Serratia marcescens, Escherichia coli and Providencia stuartii being identified. Resistance to antibiotics varied between species. No septic transfusion events were reported involving WB units tested in this study.ConclusionThe high percentage of contaminated WB units collected at the CCTH provided evidence‐based data for the implementation of improved donor skin disinfection processes and the use of blood diversion pouches in 2019. These approaches allowed CCTH to comply with Ghanaian regulatory entities.
The Role of Embodied Carbon in Sustainable Construction: A Review of Qatar's Practices and Perspectives
Authors: Rayaru Kandiyil Dilba , Sadique Monower , Lee Denise , Amoako-Attah Joseph , Al Mufti Rafal 
Published: February 2025

Abstract
This study explores the urgent need for an embodied carbon (EC) assessment framework within Qatar's construction sector, driven by the country's rapid development and high carbon intensity in construction materials, such as cement and steel. Employing a systematic literature review through the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology and Visualization of Similarities (VOS) viewer for bibliometric analysis, this study identifies major gaps in Qatar-specific EC data and regulation. It highlights global best practices, particularly those from countries with mandated EC regulations, and discusses their potential adaptation to Qatar's unique environmental and economic context. This study advocates the establishment of a comprehensive EC database to inform construction practices aligned with Qatar's sustainability goals under its National Vision 2030. The findings suggest that a regionally adapted EC framework would significantly aid Qatar in reducing greenhouse gas emissions, given the country's heavy reliance on energy-intensive materials and its extreme climate. The study concludes with recommendations for the policy integration of EC assessments in Qatar's building sector, aiming to support sustainable urban development and climate resilience in the face of intensifying environmental challenges.
Optimization of Chamber Structure and Ignition of a Rotary Engine Based on the Multi-Population-Subgroup Genetic Algorithm
Authors: Wen Huan , Zou Run , Li Liangyu , Sun Qinghai , Wang Nana , Su Tiexiong 
Published: February 2025

Abstract
The rotary engine (RE) is characterized by high-speed and a long and narrow combustion chamber. This leads to problems such as uneven distribution of the fuel–air mixture, difficulty in the ignition, and difficulty in rapid propagation of the flame to the trailing side of the combustion chamber, which in turn has an adverse impact on its combustion efficiency. In view of this, this study proposed a multi-population-subgroup genetic algorithm (MPSGA) with a faster convergence rate and more significant optimization based on the multi-population genetic algorithm. The performance of the optimization method was verified by test functions. This method is applied to the comprehensive matching optimization of chamber structure and ignition of the RE to significantly improve the combustion performance. The results showed that compared to the original scheme, the best matching scheme of the chamber structure parameters and ignition parameters of the RE obtained by using the MPSGA increased the explosive pressure by 39.3% and the thermal efficiency by 9.8%.
Review of BCG immunotherapy for bladder cancer
Authors: Liatsos George D. , Mariolis Ilias , Hadziyannis Emilia , Bamias Aristotelis , Vassilopoulos Dimitrios 
Published: February 2025

SUMMARY

For several decades, intravesical
Bacillus
Calmette–Guérin (iBCG) immunotherapy has been the gold standard adjuvant treatment for high-risk and selected intermediate-risk patients with non-muscle-invasive bladder cancer (NMIBC). In this review, the mechanisms of iBCG immune-mediated anti-cancer activity and resistance are presented. Furthermore, a literature review of short-term and systemic iBCG-related side effects was performed. A high incidence (75.5%) of iBCG-related short-term, self-limiting adverse events was observed, while more severe iBCG-related local/systemic complications (iBCG-rL/SCs) that required medical treatment or hospitalization occurred at a lower rate (2.35%). Disseminated was the most common form of iBCG-rSCs, while two-thirds of the cases were classified as infectious. The implementation of molecular-based techniques resulted in significantly higher diagnostic rates. Anti-tuberculous treatment (ATT) is the mainstay of treatment, while in patients with any iBCG-rL/SC form involving the vasculature, ATT should be combined with surgery. Local and osteoarticular forms have the lowest mortality, but their management necessitates severe and debilitating surgical procedures. The overall iBCG-attributed mortality in patients with iBCG-rL/SC was 7.4%, with disseminated, vascular, and lung involvements exhibiting the highest rates. Given the global shortage of BCG for the last two decades, as well as the paucity of effective options for iBCG-refractory or relapsing NMIBC patients, new therapeutic strategies are being tested with promising early results.
Accessible support at a national scale: the use and value of virtual learning assistants across multiple undergraduate institutions
Authors: Pribbenow Christine M. , Harrington D'Andrew , Rele Chinmay P. , Sandlin Katie M. , Leung Wilson , Lopatto David , Reed Laura K. 
Published: February 2025

ABSTRACT

The Genomics Education Partnership (GEP;
thegep.org
) is a collaboration of more than 260 faculty from over 200 colleges and universities across the continental United States and Puerto Rico, all of whom are engaged in bringing Course-based Undergraduate Research Experiences (CUREs) centered in genomics and bioinformatics to their students. The purpose of the GEP-CURE is to ensure all undergraduate students have access to research experiences in genomics, regardless of the funding and resources available at their institutions. The GEP community provides many resources to facilitate implementation of the genomics curriculum at collaborating institutions, including extensive support for both faculty and undergraduate students. Faculty receive training to implement the curriculum, ongoing professional development, access to updated curriculum, and a community of practitioners. During the COVID-19 pandemic, the GEP developed a virtual learning assistant (LA) program to provide real-time support in GEP activities and research to all students, regardless of their institution, while they were participating in the GEP-CURE. A mixed-methods descriptive study was conducted about this program and draws from quantitative data gathered about the scope and use of the program, as well as the value of the program, as indicated by the undergraduates themselves from their post-course survey responses. Additionally, seven LAs who served in this role between 2021 and 2023 participated in interviews to help the GEP better understand how this resource was used by GEP students, the needs of the students, and to identify the conditions in which this resource could be replicated in other courses.
The DnaJK chaperone of
Bacillus subtilis
post-transcriptionally regulates gene expression through the YlxR(RnpM)/RNase P complex
Authors: Ogura Mitsuo , Kanesaki Yu , Yoshikawa Hirofumi , Haga Koki 
Published: February 2025

ABSTRACT

To survive in harsh natural environments, translation and mRNA metabolism must be tightly and coordinately controlled, as saving biological costs increases fitness. However, the roles of protein chaperones in this control system are unclear. This study proposes the novel aspect of the link between translation and mRNA metabolism, that is, the co-translational DnaJK chaperone activity is involved in changes in mRNA metabolism by RNase P. We found that the expression of
proBA,
which encodes proline biosynthetic enzymes, is regulated by
ylxR
(
rnpM
) through the
proBA
promoter. YlxR(RnpM), which is associated with RNase P, was also involved in the posttranscriptional regulation of
proBA
. To clarify this posttranscriptional regulation, we screened transposon (Tn)-inserted mutants for cells with low
proB::lacZ
expression and identified the DnaJK chaperone as a regulator of
proB
. To explore the possibility that the complex of YlxR(RnpM) and RNase P might work with DnaJK, we performed an epistatic analysis using the
lacZ
fusions, which revealed that the regulation of
proB
by DnaJK/YlxR(RnpM)/RNase P, that is, co-translational chaperone activity, controlled mRNA metabolism. RNA sequencing analysis of cells deficient in the RNA component of RNase P (
rnpB
) revealed that 261 genes were upregulated in the
rnpB
::Tn strain. Among them, we identified
yoyD/yodF, besA
, and
epeXE,
which were also under the control of DnaJK/YlxR(RnpM)/RNase P regulatory cascade. Finally, we performed yeast two-hybrid analysis using DnaK as bait and identified two genes,
spoIVCA
and
nupG
, whose expression was post-transcriptionally regulated by DnaJK but independent of YlxR(RnpM). These results suggest a broader role for posttranscriptional gene regulation by DnaJK.

IMPORTANCE

Bacillus subtilis
lacking the DnaJK chaperone has not been reported to exhibit a distinct phenotype. However, our study revealed proline-dependent growth in a minimal medium in the
dnaJ
::Tn strain. Inhibition of
spoIVCA
expression in this strain was identified as a probable cause of the sporulation deficiency in previous and current studies using a single cell-level analysis. We also observed posttranscriptional regulation of
proBA
by the DnaJK and YlxR(RnpM)/RNase P complex. LacZ analyses of
proB::lacZ
in different backgrounds suggested that the above regulation ultimately functions in mRNA metabolism. In DnaJK-deficient cells, the nascent peptide may be misfolded, and if DnaJK chaperone activity is lost, such a signal may be transferred to RNase P. Therefore,
proBA
mRNA may be degraded in an RNase P-dependent manner if the misfolding of the polypeptide translated from this mRNA is detected. This system is useful for reducing the biological costs of futile mRNA elongation.
Stress adaptation under
in vitro
evolution influences survival and metabolic phenotypes of clinical and environmental strains of
Vibrio cholerae
El-Tor
Authors: Adade Nana Eghele , Ahator Stephen Dela , García-Romero Inmaculada , Algarañás Macarena , Appiah Vincent , Valvano Miguel A. , Duodu Samuel 
Published: February 2025

ABSTRACT

Bacterial adaptation to stress can lead to phenotypic variants with diverse levels of niche competitiveness, pathogenicity, and antimicrobial resistance. In this work, we employed experimental evolution to investigate whether exposure to various stress conditions results in new phenotypic and metabolic properties in clinical and environmental strains of
Vibrio cholerae
. Our findings revealed the emergence of variants with metabolic and genetic variations and enhanced survival under stress compared to the parental isolates. Phenotypic changes in the evolved variants included colony morphology, biofilm formation, and the appearance of proteolytic and hemolytic activities. The variants demonstrated metabolic changes in the preferred use of carbon, nitrogen, phosphorous, and sulfur substrates, while the genetic changes included single nucleotide polymorphisms (SNPs), breakpoints, translocations, and single nucleotide insertions and deletions. Mutations in genes encoding EAL and HD-GYP domain-containing proteins correlated with increased biofilm formation and different colony morphotypes. The combined analysis of the metabolic and genomic data pointed to pathways implicated in stress survival. The environmental strains were generally more pathogenic than the clinical strains in the
Galleria mellonella
infection model prior to the experimental evolution, and these differences did not change in the evolved variants. This study highlights the contribution of stress conditions as drivers for the evolution of genetic modifications and metabolic adaptation in
V. cholerae
, which may explain the continuous evolution of El-Tor biotype strains toward variants with improved survival in the environment.

IMPORTANCE

How
Vibrio cholerae
, the causative agent of cholera, survives during the periods between outbreaks remains a critical question. Using experimental evolution based on serial bacterial passages in culture media mimicking diverse environmental stress conditions, we investigated whether clinical and environmental isolates of
V. cholerae
develop changes in survival and in their metabolism. The evolved variants exhibited alterations in colony morphology, biofilm formation, and metabolism, including changes in the preferred use of carbon, nitrogen, phosphorous, and sulfur substrates. These changes were accompanied by various genetic modifications, notably in genes encoding second messenger molecules that regulate multiple biochemical pathways implicated in stress survival and increased pathogenic potential. Our results suggest a continuous evolution of
V. cholerae
strains toward variants displaying increased survival under environmental stress conditions that may also be encountered in the human host.