bluuebunny/crossref_metadata_2025_split huggingface dataset:
XopM, An FFAT Motif‐Containing Type III Effector Protein From Xanthomonas, Suppresses MTI Responses at the Plant Plasma Membrane
Authors: Brinkmann Charlotte , Bortlik Jennifer , Raffeiner Margot , González‐Fuente Manuel , Börnke Linus F. , Üstün Suayib , Börnke Frederik 
Published: December 2024

ABSTRACTMany gram‐negative pathogenic bacteria use type III effector proteins (T3Es) as essential virulence factors to suppress host immunity and to cause disease. However, in many cases the molecular function of T3Es remains unknown. The plant pathogen Xanthomonas campestris pv. vesicatoria (Xcv) is the causal agent of bacterial spot disease on tomato and pepper plants and is known to translocate around 36 T3Es into its host cell, which collectively suppress plant defence and promote infection. XopM is an Xcv core T3E with unknown function that has no similarity to any other known protein. We found that XopM interacts with vesicle‐associated membrane protein (VAMP)‐associated proteins (VAPs) in an isoform‐specific manner. The endoplasmic reticulum (ER) integral membrane protein VAP is a common component of membrane contact sites involved in both tethering and lipid transfer by binding directly to proteins containing an FFAT (two phenylalanines [FF] in an acidic tract [AT]) motif. Sequence analyses revealed that XopM displays two FFAT motifs that cooperatively mediated the interaction of XopM with VAP. When expressed in plants, XopM supported growth of a nonpathogenic bacterial strain and dampened the production of reactive oxygen species, indicating its ability to suppress plant immunity. Further analyses revealed that the interaction with VAP and the ability to suppress microbe‐associated molecular pattern‐triggered immunity (MTI) are structurally and functionally separable, although XopM requires localisation to the host membrane system for full MTI suppression activity. We discuss a working model in which XopM uses FFAT motifs to target the membrane to interfere with early MTI responses.
Knowledge About Sexually Transmitted Infections and Associated Factors Among Brazilian Riverside People
Authors: Pinho Ellen Christiane Correa , Galvão José Jorge Da Silva , Martins Wenderson Melo , Goncalves Flavine Evangelista , Aben‐Athar Cintia Yolette Urbano Pauxis , da Silva Richardson Augusto Rosendo , Botelho Eliã Pinheiro , Cunha Carlos Leonardo Figueirdo , Ferreira Glenda Roberta Oliveira Naiff 
Published: December 2024

ABSTRACTRiverside populations in the Amazon are considered vulnerable due to their living conditions, social aspects, and access to health services; therefore, they may be more exposed to sexually transmitted infections. The objective of this study is to analyze knowledge about STI and associated factors in the riverside population of a metropolis from the Brazilian Amazon. A cross‐sectional study carried out in the Combú environmental protection area. The participants were individuals aged at least 18 years old living in the study area. A questionnaire on knowledge about STI was applied, in addition to another one on associated factors. Multiple binary logistic regression was performed in Minitab 22. A total of 325 riverside dwellers participated in the study. Participants with low schooling levels, incomes below one minimum wage and who had never taken any rapid HIV tests are twice as likely to having low knowledge about STI. Those who live with more people in the same household are more likely to presenting low knowledge levels. The social factors exerted a greater impact on low knowledge about STI.
Colder Climates and Dementia: An Ecological Analysis of Climate‐Patterned Temperature's Influence on Neurological Health
Authors: You Wenpeng 
Published: December 2024

ABSTRACTCountries with lower climate‐patterned temperatures (Tcp), typically colder, have not been consistently correlated with higher dementia risk in population studies. This study explores Tcp's influence on global and regional dementia rates. Country‐specific Tcp data was analyzed alongside dementia incidence using bivariate analysis, partial correlation, and multiple linear regression. Factors like life expectancy (Life e(0)), economic affluence, genetic predisposition (Biological State Index), and urbanization were considered. Both Pearson's r and nonparametric tests revealed a significant inverse correlation between Tcp and dementia incidence, holding true even after adjusting for life expectancy, affluence, genetic predisposition, and urbanization. Multiple linear regression identified Tcp as a key predictor of dementia incidence, ranking second after life expectancy. Affluence, genetic predisposition, and urbanization did not significantly predict dementia rates. Tcp's predictive power was consistent across different country groups, with minor correlation variations between developing versus developed countries and LMICs versus high‐income nations. Countries with colder climate (lower Tcp) may experience higher dementia rates, a correlation robust across major risk factors. Including Tcp in dementia studies is crucial for understanding its public health implications.
Disguised Blessings: A Mechanistic Understanding of the Beneficial Outcomes Triggered by Partial K Replacement With Na in Two Eucalyptus Species Under Drought Stress
Authors: Mateus Nikolas Souza , Florentino Antonio Leite , Moreira Gabriel Luis Lima Soares , Nogueira Marina Lima , Ferreira Maria Eduarda Pena , Rossi Monica Lanzoni , Linhares Francisco Scaglia , Lavres Jose 
Published: December 2024

ABSTRACTWhile not essential for most plants, sodium (Na+) can partially substitute for potassium (K+) in some metabolic functions. Thus, understanding the mechanisms underlying K+ and Na+ uptake, transport, utilization, and ion replacement is crucial to sustain forest production. A pot experiment was designed with 6 K/Na ratios (100/0, 85/15, 70/30, 55/45, 40/60, and 0/0%) and two water conditions (well‐watered, W+; and water‐stressed, W−) on two Eucalyptus species with contrasting drought tolerance. In a multi‐level analysis, we measured morphological, nutritional, physiological, biochemical, molecular, and anatomical traits. Low to moderate K replacement with Na (85/15%–55/45%) provided partial and faster stomatal closure (lower δ13C), thereby enhancing plants' water status (WUE, RLWC, ΨPD, ΨMD), photosynthetic capacity (gs, E, A, Ci/Ca), photoprotection (NPQ, qP, ETR, Fv/FM, ΦPSII), and growth (height, collar diameter, LA, TDM) relative to exclusive K supply. The 70/30% K/Na replacement was defined as the ideal ratio, upregulating K+ and water uptake (overexpression of AKT1, PIP2;5, PIP2;7 and TIP1;3), maximizing enzymatic antioxidant performance and biomass production, and reducing oxidative stress. High K replacement with Na (40/60%) and K deficiency (0/0%) led to incomplete stomatal closure reduced water status, photosynthetic capacity, photoprotection, and growth, especially in the species with low drought tolerance.
MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi‐Omics Data
Authors: Xu Chaoqun , Song Ling‐Yu , Li Jing , Zhang Lu‐Dan , Guo Ze‐Jun , Ma Dong‐Na , Dai Ming‐Jin , Li Qing‐Hua , Liu Jin‐Yu , Zheng Hai‐Lei 
Published: December 2024

ABSTRACTMangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi‐omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole‐genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web‐based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue‐specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.
Does the implementation status of gender provisions affect the implementation of a peace agreement? Evidence from Colombia's 2016 peace agreement implementation process
Authors: Joshi Madhav 
Published: December 2024

AbstractIn 2016, the Colombian government and the leftist insurgency group FARC (Fuerzas Armadas Revolucionarias de Colombia – Ejército del Pueblo) signed an agreement that ensures women's greater participation in the peace implementation process, their access to benefits from the programs, and their ability to reform initiatives in the agreement. While applauded for adhering to the UNSCR 1325 normative commitments on women's roles in peace processes, it's unclear how adopting a gender perspective affects the entire agreement's implementation success. This article analyzes monthly data on the implementation of 578 stipulations and 70 subthemes (reforms or programs) and evaluates peace implementation from a gender perspective. The findings from the stipulation level analysis reveal an implementation gap between gender and gender‐neutral or non‐gender provisions. The subtheme level analyses further confirm this finding that gender provisions alone do not contribute to the overall peace implementation success; rather, implementing those provisions is foundational for advancing the overall peace implementation.
Intramuscular blood flow and muscle oxygenation of the vastus lateralis response to intermittent incremental muscle contractions
Authors: Izumi Kazuma , Yamamori Keisuke , Katayama Keisho , Kano Yutaka , Tanaka Noriko , Akima Hiroshi 
Published: December 2024

AbstractPower Doppler ultrasonography is used to measure blood flow within a given muscle, otherwise known as intramuscular blood flow. However, it is not fully understood how intramuscular blood flow and muscle oxygenation change with repetitive muscle contraction. The present study was conducted to assess changes in intramuscular blood flow and muscle oxygenation of the vastus lateralis (VL) during intermittent and incremental contractions. Fifteen healthy male subjects (21.7 ± 2.6 years) performed intermittent (5 s contraction, 5 s relaxation) and incremental isometric knee extensions at 30%, 40%, 50%, 60% and 70% of maximal voluntary contraction (MVC) until task failure. Intramuscular blood flow and muscle oxygen saturation () were simultaneously measured using power Doppler ultrasonography and near‐infrared spectroscopy, respectively, from the right VL of the mid‐thigh. Intramuscular blood flow was increased from 0.5 ± 0.5% at rest to 13.9 ± 9.5% at task failure. Intramuscular blood flow significantly increased from rest to 30% and 40% MVC (P = 0.001), and significantly decreased from 30% to 70% MVC (P = 0.004). These results indicate that intramuscular blood flow and show different patterns of change, suggesting that the contribution of intramuscular blood flow to oxygen supply decreases within the VL at moderate and higher exercise intensities.
Influence of Prematch Perceived Wellness on High-Intensity Locomotor Activities of Professional Soccer Players During in-Season Matches
Authors: Marqués-Jiménez Diego , Quílez-Larrayad Pablo , Izquierdo José M. 
Published: December 2024

Purpose: The aim of this study was to determine the influence of prematch perceived wellness on high-intensity locomotor activities of professional soccer players during in-season matches. Methods: Twenty male soccer players (26.74 [3.27] y; 179.77 [6.06] cm; 76.72 [9.33] kg), members of a professional soccer team, participated in this longitudinal study. Data collection was conducted during the competitive period of 1 season and involved the 34 league official matches. Perceived wellness was assessed individually 3 hours before each match using a 5-point Likert questionnaire, and external loads during matches were monitored using global navigation satellite system devices. Each wellness item (ie, fatigue, delayed-onset muscle soreness [DOMS], sleep, and stress) was considered as an individual wellness component and analyzed as raw score, team z score, and individualized z score. Different random forest regression models and linear mixed models were carried out for statistical analysis. Results: Individualized z scores should be considered the most important variables to estimate the proportion of external-load variation during match play, but the proportion of the variance that may be explained from the prematch perceived wellness suggests a limited capacity in relation to external-load measures. Only individualized z scores of DOMS showed significant effects on sprint running distance (>24.0 km·h−1) and number of sprints (>24.0 km·h−1) during matches (P < .05). Conclusions: Sprint performance of professional soccer players during in-season matches may be slightly influenced by the players’ day-to-day variation of prematch perceived DOMS.
Assembly and engineering of BioBricks to develop an efficient NADH regeneration system
Authors: Cheng Feng , Wang Cheng-Jiao , Gong Xiao-Xiao , Sun Ke-Xiang , Liang Xi-Hang , Xue Ya-Ping , Zheng Yu-Guo 
Published: December 2024

ABSTRACT

The cofactor regeneration system plays a crucial role in redox biocatalysis for organic synthesis and the pharmaceutical industry. The alcohol dehydrogenase (ADH)-based regeneration system offers a promising solution for the
in situ
regeneration of NAD(P)H. However, its widespread use is hindered by low activity and poor expression of ADH in
Escherichia coli
. Herein, the BioBricks (promoter, ribosome binding site [RBS], functional gene, and terminator) were assembled and engineered to constitute an efficient NADH regeneration system. The semi-rational design was employed to enhance the catalytic efficiency of
Gst
ADH (an ADH from
Geobacillus stearothermophilus
), resulting in a beneficial
Gst
ADH variant with a 2.1-fold increase in catalytic efficiency. Furthermore, the RBS optimization was used to increase the expression of ADH genes, leading to the identification of an RBS with a 3.2-fold increased translation rate. Using this developed system, the NADH generating velocity reached more than 2 s
−1
even toward 0.1 mM NAD
+
, indicating that it is the most promising NADH regeneration so far. Finally, the engineered system was utilized for the asymmetric biosynthesis of
l-
phosphinothricin (a chiral herbicide), with a high yield (>95%).

IMPORTANCE

The alcohol dehydrogenase (ADH)-based coenzyme regeneration system serves as a useful tool in redox biocatalysis. This system effectively replenishes NAD(P)H by utilizing isopropanol as a substrate, with the added advantage of easily separable acetone as a by-product. Previous studies focused on discovering new
adh
genes and engineering the ADH protein for higher catalytic efficiency, neglecting the optimization of other gene components. In this study, a remarkably efficient NADH regeneration system was developed using BioBricks assembly for system initialization. The ADH engineering was used to enhance catalytic efficiency, and RBS optimization for elevated ADH expression, which resulted in not only a 2.1-fold increase in catalytic efficiency but also a 3.2-fold increase in translation rate. Together, these improvements resulted in an overall 6.7-fold enhancement in performance. This system finds application in a wide range of NADH-dependent biocatalysis processes and is particularly advantageous for the biosynthesis of fine chemicals.
A new target of multiple lysine methylation in bacteria
Authors: Inoue Shori , Yoshimoto Shogo , Hori Katsutoshi 
Published: December 2024

ABSTRACT

The methylation of ε-amino groups in protein lysine residues is an important posttranslational modification in eukaryotes. This modification plays a pivotal role in the regulation of diverse biological processes, including epigenetics, transcriptional control, and cellular signaling. Recent research has begun to reveal the potential role of methylation in modulating bacterial immune evasion and adherence to host cells. In this study, we analyzed the cell surface proteins of the toluene-degrading bacterium
Acinetobacter
sp. Tol 5 by label-free liquid chromatography‒mass spectrometry and found multiple lysine methylation in its trimeric autotransporter adhesin (TAA), AtaA. Over 130 lysine residues of AtaA, consisting of 3,630 amino acids and containing 234 lysine residues, were methylated. We identified that the outer membrane protein lysine methyltransferase (OM PKMT) of Tol 5, KmtA, specifically methylates the lysine residues of AtaA. In the KmtA-deficient mutant, most lysine methylations on AtaA were absent, indicating that KmtA is responsible for the methylation of multiple lysine residues throughout AtaA. Bioinformatic analysis revealed that the OM PKMT genes were widely distributed among Gram-negative bacteria, including pathogens with TAAs that promote infectivity, such as
Burkholderia mallei
and
Haemophilus influenzae
. Although KmtA has sequence similarities to the OM PKMTs of
Rickettsia
involved in infectivity, KmtA-like PKMTs formed a distinct cluster from those of the
Rickettsia
type according to the clustering analysis, suggesting that they are new types of OM PKMTs. Furthermore, the deletion of Tol 5 KmtA led to an increase in AtaA on the cell surface and enhanced bacterial adhesion, resulting in slower growth.

IMPORTANCE

Lysine methylation has been underexplored in prokaryotes, and information on it is limited to some pathogens. Our finding is the second case of multiple lysine methylation of bacterial outer membrane (OM) proteins, following that of OmpB of
Rickettsia
. The newly found target of methylation, AtaA, a trimeric autotransporter adhesin family protein of
Acinetobacter
sp. Tol 5 isolated from activated sludge, extends our understanding of OM protein methylation to non-pathogenic environmental strains. The newly identified enzyme KmtA shows higher specificity than rickettsial lysin methylases, protein lysine methyltransferases, and methylates more lysine residues of the target, which raises interest in the mechanism underlying its biological specificity. The widespread presence of KmtA-like PKMTs throughout Gram-negative bacteria suggests that lysine methylation functions more extensively in bacterial physiology than previously recognized.
Pulmonary thromboembolism masquerading as bronchial asthma in a remote medical setup at extreme high altitude
Authors: Singh Arashdeep , Ramamurthy Ravi H , Goyal Rahul , Rajpal Drishti 
Published: December 2024

Pulmonary thromboembolism (PTE) is a life-threatening illness. It is a great masquerader that mimics many respiratory illnesses, warranting a high index of suspicion for diagnosis. It should be suspected when respiratory illnesses do not respond to the expected course of treatment. At this point, additional imaging modalities such as echocardiography and CT scans can assist with the diagnosis; however, these facilities are usually not available in remote medical setups such as mountainous regions in the Himalayas. The definitive diagnosis is delayed until the patient is brought down to a well-equipped hospital at a lower altitude. Making an early provisional diagnosis is hence crucial for timely evacuation and optimal first-line management to circumvent associated morbidity and mortality.We present a case of PTE in a remote medical establishment whose initial evaluation pointed towards an episode of severe asthma. The poor response to standard management prompted us to undertake bedside echocardiography to diagnose features of PTE.
Integrating accelerometry, GPS, GIS and molecular data to investigate mechanistic pathways of the urban environmental exposome and cognitive outcomes in older adults: a longitudinal study protocol
Authors: Hunter Ruth F , Cleland Claire , Trott Mike , O’Neill Sean , Küçükali Hüseyin , Mullineaux Shay , Kee Frank , McKinley Jennifer M , Neville Charlotte , O'Hara Leeanne , Marr Calum , McAlinden Michael , Ellis Geraint , McKnight Amy , Schipperijn Jasper , McHugh Power Joanna , Duong Trung , McGuinness Bernadette 
Published: December 2024

IntroductionMaintaining cognitive health in later life is a global priority. Encouraging individuals to make health behaviour changes, such as regular physical activity, and providing supportive urban environments can help maintain cognitive health, thereby preventing or delaying the progress of dementia and cognitive decline. However, the mechanistic pathways by which the urban environmental exposome influences cognitive health outcomes are poorly understood. The aim of this study is to use granular measures of the urban environment exposome (encompassing the built, natural and social environment) and physical activity to explore how these interact with a person’s biology to ultimately influence cognitive health outcomes.Methods and analysisThis ongoing study uses a cohort design, recruiting participants from the Northern Ireland Cohort for the Longitudinal study of Ageing and the Harmonised Cognitive Assessment Protocol study. Participants (n=400 at each wave) will be aged ≥65 years and have the capacity to provide written informed consent. Measures include device-measured physical activity (Actigraph wGT3XP-BT), environmental location data (Global Positioning System, Qstarz BT-Q1000XT), linked to a battery of neuropsychological tests, including the Mini Mental State Examination and the Centre for Epidemiological Studies Depression Scale. Blood-derived biochemical, genetic and epigenetic data will be included in multimodal analyses. These data will be integrated with urban environment Geographic Information System data and analysed using causal inference and mediation methods to investigate plausible mechanistic pathways.Ethics and disseminationThis study has been approved by the Queen’s University Belfast, Faculty of Medicine, Health and Life Sciences Research Ethics Committee (MHLS 21_72). Alongside peer-reviewed publications in high-ranking international journals, dissemination activities include conference presentations, project videos, working papers, policy briefing papers, newsletters, summaries and case study stories.