bluuebunny/crossref_metadata_2025_split huggingface dataset:
The dynamin-related protein PfDyn2 is essential for both apicoplast and mitochondrial fission in
Plasmodium falciparum
Authors: Morano Alexander A. , Xu Wei , Navarro Francesca M. , Shadija Neeta , Dvorin Jeffrey D. , Ke Hangjun 
Published: November 2024

ABSTRACT

Dynamins, or dynamin-related proteins (DRPs), are large mechano-sensitive GTPases that mediate membrane dynamics or organellar fission/fusion events.
Plasmodium falciparum
encodes three dynamin-like proteins whose functions are poorly understood. Here, we demonstrate that one of these dynamin-related proteins, PfDyn2, is required to divide both the apicoplast and the mitochondrion, a striking divergence from the biology of related parasites. Using super-resolution and ultrastructure expansion microscopy (U-ExM), we show that PfDyn2 is expressed in dividing schizonts, and that it localizes to both the apicoplast and the mitochondrion. Our use of long-term, live-cell microscopy allows for the visualization of apicoplast and mitochondrial division in live parasites at super resolution for the first time, and demonstrates that in PfDyn2-deficient parasites, while the apicoplast and mitochondrion increase in size and complexity, they do not undergo fission. We also show that these organellar fission defects prevent successful individualization of the schizont mass and the formation of new daughter cells, or merozoites because the basal complex, the cytokinetic ring of
Plasmodium
, cannot fully contract in PfDyn2-deficient parasites, a phenotype secondary to physical blockage by undivided organelles occluding the ring. PfDyn2’s singular role in mediating both apicoplast and mitochondrial fission has not been observed in other organisms possessing two endosymbiotic organelles, including other Apicomplexans, thus reflecting a unique, potentially exploitable method of organellar division in
P. falciparum
.

IMPORTANCE

Plasmodium falciparum
remains a significant global pathogen, causing over 200 million infections and over 600,000 deaths per year. One significant obstacle to the control of malaria is increasing resistance to first-line artemisinin-based antimalarials. Another is a lack of basic knowledge about the cell biology of the parasite. Along with the mitochondrion,
Plasmodium
contains a second organelle descended from an endosymbiotic event, the apicoplast. Both organelles are common targets for antimalarials, but because many proteins involved in organellar fission are not conserved in
Plasmodium
, until now, the mechanisms underlying apicoplast and mitochondrial division have been unknown. In this study, we demonstrate that PfDyn2, a dynamin-related protein (DRP), is required for the division of both organelles. We also show that defects in organellar division hinder segmentation of the schizont and formation of invasive merozoites by preventing full contraction of the basal complex. By demonstrating its necessity for the proper division of both the apicoplast and the mitochondria, this study highlights PfDyn2 as a potential target for new antimalarials.
Complete genome sequences of six coliphages isolated from local water systems in the Philippines
Authors: Sabban Emilia Andrea V. , Eclipse Adonis N. , Arcan Stephen Kyle C. , Esliza Dexter Bryan L. , Lanete Paul Jeremy C. , Susi Lindley C. , Sikat Gelito Joseph M. 
Published: November 2024

ABSTRACT

Complete genome sequences of six coliphages (genomic size: 87–347 Kbp; GC content: 35.10%–45.27%) belonging to the
Felixounavirus
,
Tequintavirus
, and
Asteriusvirus
genera were isolated from Philippine wastewater facilities and drainage systems. These phages offer potential for development as diagnostic and therapeutic tools for food and water safety.
Complete genome sequence of a methanotrophic bacterium,
Methylomicrobium lacus
strain 22M6SE5-12 isolated from a freshwater sediment environment
Authors: Kim Eui-Jin , Yim Kyung June , Bae Mi-Jung , Han Kook-IL 
Published: November 2024

ABSTRACT

We assembled the complete genome of
Methylomicrobium lacus
strain 22M6SE5-12 isolated from a freshwater sediment in South Korea. The genome consists of a 4.36-Mbp chromosome and two plasmids and has 3,961 coding sequences, 12 rRNA genes, and 55 tRNA genes. We identified a gene set encoding the particulate methane monooxygenase subunits.
Draft genome sequences of two multidrug-resistant
Enterobacter soli
strains isolated from wastewater in Spain
Authors: Lois Marta , Rodríguez Sergio , Romalde Jesús L. 
Published: November 2024

ABSTRACT

We report the draft genome sequences of two
Enterobacter soli
strains isolated from wastewater in Galicia (NW Spain). Genomic analysis revealed that both
E. soli
strains harbor multiple genes associated with resistance to sulfonamides, fluoroquinolones, β-latamics, and other drugs.
Virulence is not directly related to strain success
in planta
in
Clavibacter nebraskensis
Authors: Veregge Molly , Hirsch Cory D. , Moscou Matthew J. , Burghardt Liana , Tiffin Peter , Khokhani Devanshi 
Published: November 2024

ABSTRACT

Goss’s wilt and leaf blight of maize is an economically important disease caused by the Gram-positive bacterium,
Clavibacter nebraskensis
(
Cn
). Little is known about the ecology and pathogenesis of this bacterium. Here, we used phenotypic assays and a high-throughput whole-genome sequencing approach to explore among-strain variation in virulence and multistrain reproductive success
in planta
. Our survey of 41 strains revealed that more recently sampled strains tended to have higher virulence than strains sampled before 2010 and tended to be more genetically divergent from the reference strain, isolated in 1971. More detailed assays with a representative sample of 13 of these strains revealed that host genotype (resistant or susceptible) did not strongly affect strain success and that strain success
in planta
in multi-strain communities was not closely associated with virulence in single-strain assays. Two weakly virulent strains, CIC354 and CIC370, had the greatest reproductive success, whereas the most highly virulent strains did not significantly change in frequency in any host genotype. A genomic analysis revealed candidate genes, including putative virulence factors (i.e., a secreted cellulase), responsible for among-strain variation in reproductive success.

IMPORTANCE
Non-pathogenic strains of many bacterial pathogens are reported to coexist with pathogenic strains in symptomatic plants. To understand the ecology and pathogenesis of the pathogen population, it is essential to study strain dynamics in the context of the host. We created a community of 13 strains exhibiting diverse virulence phenotypes and used this community to infect the host plant. We compared the strain frequency of these strains before and after the host infection. Contrary to our hypothesis of highly virulent strains being selected by the susceptible host, we found that weakly virulent strains were selected by both resistant and susceptible host lines. We identified several genes associated with strain frequency shifts suggesting their role in strain colonization, virulence, and fitness.
Multi-omics mechanical analysis of gut microbiota, carboxylic acids, and cardiac gene expression interaction triggering diabetic cardiomyopathy
Authors: Shi Meixin , Zhao Bingbing , Cai Wenjie , Yuan Hui , Liang Xiao , Li Zhitao , Liu Xinyu , Jin Ye , Liu Xi , Wei Can 
Published: November 2024

ABSTRACT

It is well known that gut microbial imbalance is a potential factor for the occurrence and development of diabetes mellitus (DM) and its complications. Moreover, the heart and gut microbiota can regulate each other through the gut–metabolite–heart axis. In this study, metagenomics, metabolomics, and transcriptomics were chosen to sequence the changes in gut microbiota, serum metabolite levels, and differentially expressed genes (DEGs) in leptin receptor-deficient db/db mice and analyze the correlation between serum metabolites and gut microbiota or DEGs. According to the results, there were significant differences in the 1,029 cardiac genes and 353 serum metabolites in diabetic mice of the db/db group, including DEGs enriched in the PPAR signaling pathway and increased short-chain carboxylic acids (CAs), when compared with the normal db/m group. According to metagenomics, the gut microbiota of mice in the db/db group were disrupted, and particularly Lachnospiraceae bacteria and Oscillospiraceae bacteria significantly decreased. Also, according to the Pearson correlation analysis, a significant positive correlation was found between CAs and PPAR signaling pathway-related DEGs, and a negative correlation was found between CAs and the abundance of the above-mentioned species. To sum up, type 2 diabetes mellitus (T2DM) can upregulate the expression of partial cardiac genes through the levels of serum short-chain CAs affected by gut microbiota, thus playing a role in the occurrence and development of diabetic cardiomyopathy (DCM).

IMPORTANCE
Our research results clearly link the changes in heart genes of T2DM and normal mice with changes in serum metabolites and gut microbiota, indicating that some genes in biological processes are closely related to the reduction of protective microbiota in the gut microbiota. This study provides a theoretical basis for investigating the mechanism of DCM and may provide preliminary evidence for the future use of gut microbiota therapy for DCM.
Effects of temporal, spatial, and environmental factors on ciliates community in northeastern South China Sea, with notes on co-occurrence patterns of environment, phytoplankton, and ciliate
Authors: Liu Weiwei , Cheng Zijun , Wen Shaowei , Li Gang , Ke Zhixin , Li Daning , Tan Yehui 
Published: November 2024

ABSTRACT

Little is known about temp-spatial variations and determining mechanism of microplankton community from continental shelf to deep basin. Here, the distribution and determinants of ciliates in the northeastern South China Sea were investigated in summer and winter. We found that the alpha diversity were generally similar, but community composition showed clear difference in summer and winter. For spatial dimension, the alpha diversity significantly decreased from neritic water to deep, and the variations of community composition were only detected between upper and deep water. The determinants of community varied depending on the research scale. For entire community, the variations were higher explained by environmental factors than by temp-spatial factors. Specially, physical factors were the main determinants, which may attribute to the effects of physical processes occurred in the research area. For the three spatial subareas, season showed more significant influences on communities than other factors. Network analyses revealed that the ciliate exhibited more relationships with phytoplankton than with environment factors. Diatom and physical factors accounted for most of the ciliate-phytoplankton-environment co-occurrence relationships, suggesting their significant influences to the community stability of the microbial food web. This study improves our understanding for the mechanisms of community structuring of microzooplankton in the open sea across both space and time.

IMPORTANCE
Ciliates are important components of microplanktons and play a crucial role in global nutrient cycling. There is still large knowledge gap on their structuring mechanisms from continental shelf to deep basin. We revealed the distribution patterns of ciliate community in neSCS and assessed the relative contribution of temporal, spatial, and environmental factors for their community structuring. Compared with temp-spatial factors, environmental factors take more responsibilities for the ciliate distribution. Among the environmental factors, physical factors showed the largest contribution to community variation. Moreover, the ciliate-environment co-occurrence pattern showed that physical factors contributed more for their relationships. These findings suggested that the physical processes play key roles in temp-spatial dynamics of ciliate community in open ocean.
Comparison of the STANDARD M10
C
.
difficile
, Xpert
C
.
difficile
, and BD MAX Cdiff assays as confirmatory tests in a two-step algorithm for diagnosing
Clostridioides difficile
infection
Authors: Choi Hyunseul , Kang Minhee , Yun Sun Ae , Yu Hui-Jin , Suh Eunsang , Kim Tae Yeul , Huh Hee Jae , Lee Nam Yong 
Published: November 2024

ABSTRACT

Current guidelines recommend a two-step algorithm rather than relying solely on a single test for diagnosing
Clostridioides difficile
infection. This algorithm starts with enzyme immunoassay (EIA) for detecting glutamate dehydrogenase (GDH) and toxins A/B, followed by nucleic acid amplification test (NAAT) for GDH-positive but toxin-negative cases. This study compared the performance of three commercial NAATs: the STANDARD M10
C. difficile
, Xpert
C. difficile
, and BD MAX Cdiff assays, utilized as confirmatory testing of the two-step algorithm. Two hundred archived stool specimens, previously tested GDH-positive but toxin-negative by EIA, were analyzed in parallel with these NAATs and toxigenic culture, which served as the reference standard. Sensitivity, specificity, positive predictive value, and negative predictive value were 89.1%, 92.6%, 94.6%, and 85.2%, respectively, for the M10 assay; 95.8%, 86.4%, 91.2%, and 93.3%, respectively, for the Xpert assay; and 89.8%, 91.4%, 93.8%, and 86.0%, respectively, for the BD MAX assay. The rates of invalid results were 1.0%, 0.5%, and 1.0% for the M10, Xpert, and BD MAX assays, respectively. In conclusion, the M10 assay is a reliable diagnostic tool, performing comparably to the Xpert and BD MAX assays when used as confirmatory testing in the two-step algorithm.

IMPORTANCE

While numerous studies have assessed nucleic acid amplification tests (NAATs) as stand-alone tests for diagnosing
Clostridioides difficile
infection, limited research has compared their performance as confirmatory tests in a two-step algorithm. This study evaluated the performance of three commercial NAATs (M10, Xpert, and BD MAX assays) using 200 archived stool specimens initially tested as glutamate dehydrogenase (GDH)-positive but toxin-negative by GDH/toxin A/B enzyme immunoassay, the first step in the two-step algorithm. All three assays demonstrated high sensitivity (89.1% to 95.8%) and specificity (86.4% to 92.6%), with low rates of invalid results (≤1%). Our findings suggest that the M10 assay performs comparably to the Xpert and BD MAX assays when used as confirmatory testing in the two-step algorithm. Offering similar performance and turnaround time to these widely used assays at a slightly lower cost, the M10 assay serves as a practical alternative in this setting.
Transcriptome analysis reveals that PRV XJ delgE/gI/TK protects against intestinal damage in nose-dropping-infected mice by regulating ECM-ITGA/ITGB-P-FAK
Authors: Xu Tong , Zhang Yang , Tao Qian , Xu Lei , Lai Si-Yuan , Ai Yan-Ru , Huang Jian-Bo , Yang Ben-Lu , Zhu Ling , Xu Zhi-Wen 
Published: November 2024

ABSTRACT

Pseudorabies virus (PRV) is an ideal model for mechanistic investigations into α-herpesvirus. The neurotropism and latent infection of PRV have been extensively studied. Apart from neurological symptoms, diarrhea caused by PRV infection is also an essential cause of mortality in newborn and weaned piglets. However, little research has been done on PRV invasion of the gut. To fill this gap, a nasal drip PRV-infection mouse model was developed, consisting of three groups: the challenged group (Group A), the immunization-challenged group (Group B), and a mock group (Group C). The results showed that immunization with PRV XJ delgE/gI/TK successfully prevented intestinal damage caused by PRV drop-nose infection. Subsequently, intestines were collected for transcriptional analysis. Differentially expressed genes analysis revealed that PRV XJ delgE/gI/TK was effective in reducing the organismal intestinal transcriptional activity caused by PRV. The Group A vs Group C and Group A vs Group B had similar Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched signaling pathways and the differentially expressed genes were primarily enriched in pathways, such as cell adhesion molecules, focal adhesion kinase, and actin cytoskeleton regulation. Notably, transcriptome analysis indicated that genes associated with the focal adhesion kinase (FAK) signaling pathway (ECM-ITGA/ITGB-p-FAK) were significantly more highly expressed in Group A than in Group B and Group C. The results of quantitative real-time PCR (RT-qPCR) and western blotting were consistent with KEGG analysis. Therefore, we hypothesized that PRV promotes self-infection through activation of the ECM-ITGA/ITGB-p-FAK signaling pathway and that PRV XJ delgE/gI/TK immunization could attenuate the intestinal damage caused by PRV by inhibiting the activation of this pathway.

IMPORTANCE
Pseudorabies virus (PRV) poses a significant threat to the swine industry and public health due to its ability to infect multiple species, including humans, leading to substantial economic losses and potential health risks. This study addresses a critical gap in understanding the impact of PRV infection on the gut, which has been less explored compared to its neurological effects. By developing a drip-nose PRV-infection mouse model, the research indicated that PRV might promote self-infection through activation of the ECM-ITGA/ITGB-p-FAK signaling pathway, and PRV XJ delgE/gI/TK immunization effectively prevents intestinal damage by significantly reducing the expression of genes in the ECM-ITGA/ITGB-p-FAK signaling pathway. The research has important implications for the swine industry and public health by contributing to the development of better vaccines and treatments, ultimately helping to control PRV and prevent its cross-species transmission.
Comparative evaluation of BacT/ALERT VIRTUO and BACTEC FX400 blood culture systems for the detection of bloodstream infections
Authors: Qin Yurong , Liao Yiwen , Zhou Jingfang , Liu Weijiang , Chen Huimin , Chen Xiaoli , Wang Weisha , Zhang Ni , Zhao Yunhu , Wang Liang , Gu Bing , Liu Suling 
Published: November 2024

ABSTRACT

Bloodstream infections (BSI) pose significant threats to patient health, necessitating timely and accurate diagnostics to reduce mortality and morbidity. This study aimed to evaluate the clinical performance of the BacT/ALERT VIRTUO blood culture system with FANPlus bottles compared to the BACTEC FX400 system in detecting bloodstream pathogens. A total of 1,772 blood specimens were collected from various hospital wards. Specimen selection criteria were based on clinical suspicion of bloodstream infections, ensuring the inclusion of relevant and representative patient samples. These blood samples, collected from the same suspected sepsis patients, were cultured in parallel using both the BacT/ALERT VIRTUO and BACTEC FX400 systems. The diagnostic efficiency of both systems, including detection rates, time to detection (TTD), and sensitivity across different bacterial species, was assessed. In various application scenarios, the VIRTUO system demonstrates a higher positive detection rate, whether in the intensive care unit (ICU) (8.5% vs 6.4%,
P
= 0.028) or in general wards. Additionally, for different types of bacteria, the TVIRTUO system exhibits superior detection rates for anaerobic bacteria (5.9% vs 3.2%,
P
< 0.001) and aerobic bacteria (9.1% vs 7.2%,
P
= 0.043). Furthermore, it boasts a shorter median TTD of 14 hours compared to 16 hours, and a higher sensitivity for Gram-positive bacteria (2.8% vs 1.6%,
P
< 0.001). These findings emphasize VIRTUO’s effectiveness in enhancing diagnostic accuracy, achieving faster time to detection, and expanding the spectrum of detected organisms, thereby facilitating the quicker initiation of appropriate therapies, supporting precise clinical decision-making, and ultimately improving patient outcomes.

IMPORTANCE
Our study conducted a critical evaluation of advanced blood culture technologies for managing bloodstream infections (BSI). A distinctive strength of our research is the large sample size and the concurrent testing of the same patients with two systems, a methodology rarely achieved in other studies. BSIs present severe health threats, necessitating prompt and accurate diagnostics to mitigate morbidity and mortality. The BacT/ALERT VIRTUO system, in comparison to the BACTEC FX400 system, demonstrated superior detection capabilities, emphasizing the critical role of advanced diagnostics in clinical settings.
Predictors of upper limb motor recovery in stroke survivors: a pre–post test study design
Authors: Sikuka Hope Muwanei , Lupenga Joseph , Nkhata Loveness 
Published: November 2024

ObjectivesThe study aimed to assess the predictors of upper limb motor recovery in stroke survivors.DesignPre–post test study design.SettingConducted in two centres (First Level Hospital and University Teaching Hospital in Lusaka).ParticipantsPatients living with stroke accessing physiotherapy services at the two public hospitals. A total of 52 patients were recruited at the start of the study, 6 were lost to follow-up and 46 completed the study.InterventionConventional physiotherapy for 8 weeks (5 September 2022–28 October 2022).Primary outcomeMotor function measured using a Fugl-Meyer assessment of the upper extremity.ResultsAnalysis was conducted on 46 participants. A significant difference was observed between the level of motor function at baseline and after 8 weeks of treatment (p=0.0183). At baseline, 50% of participants had mild motor function, which improved after 8 weeks, with 69.6% having mild motor function. Stroke patients with severe motor function impairment at baseline were associated with 0.01 times likelihood of having mild motor function impairment after 8 weeks of physiotherapy treatment (AOR 0.01; 95 % CI 0.00 to 0.16; p=0.002).ConclusionThe motor function of stroke patients continues to improve over time. This study demonstrated that initial upper limb motor function impairment could be used as a predictor for upper limb motor function.
Development, validation and economic evaluation of a machine learning algorithm for predicting the probability of kidney damage in patients with hyperuricaemia: protocol for a retrospective study
Authors: Hou Zhengyao , Yang Yong , Deng Bo , Gao Guangjie , Li Mengting , Liu Xinyu , Chang Huan , Shen Hao , Zou Linke , Li Jinqi , Wu Xingwei 
Published: November 2024

IntroductionAccurate identification of the risk factors is essential for the effective prevention of hyperuricaemia (HUA)-related kidney damage. Previous studies have established the efficacy of machine learning (ML) methodologies in predicting kidney damage due to other chronic diseases. Nevertheless, a scarcity of precise and clinically applicable prediction models exists for assessing the risk of HUA-related kidney damage. This study aims to accurately predict the risk of developing HUA-related kidney damage using a ML algorithm, which is based on a retrospective database.Methods and analysisThis retrospective study aims to collect clinical data on outpatients and inpatients from the Sichuan Provincial People’s Hospital, China, covering the period from 1 January 2018 to 31 December 2021 with a focus on patients diagnosed with ‘hyperuricaemia’ or ‘gout’. Predictive models will be constructed using techniques such as data imputation, sampling, feature selection and ML algorithms. This research will evaluate the predictive accuracy, interpretability and fairness of the developed models to determine their clinical applicability. The net benefit and net saving will be calculated to gauge the economic value of the model. The most effective model will then undergo external validation and be made available as an online predictive tool to facilitate user access.Ethics and disseminationThe Ethics Review Committee at Sichuan Provincial People’s Hospital granted approval for the ethical review of this study without requiring informed consent. The findings of the study will be disseminated in a peer-reviewed journal.