bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of living cable bacteria with carbon electrodes in bioelectrochemical systems
Authors: Bonné Robin , Marshall Ian P. G. , Bjerg Jesper J. , Marzocchi Ugo , Manca Jean , Nielsen Lars Peter , Aiyer Kartik 
Published: July 2024

ABSTRACT

Cable bacteria are filamentous bacteria that couple the oxidation of sulfide in sediments to the reduction of oxygen via long-distance electron transport over centimeter distances through periplasmic wires. However, the capability of cable bacteria to perform extracellular electron transfer to acceptors, such as electrodes, has remained elusive. In this study, we demonstrate that living cable bacteria actively move toward electrodes in different bioelectrochemical systems. Carbon felt and carbon fiber electrodes poised at +200 mV attracted live cable bacteria from the sediment. When the applied potential was switched off, cable bacteria retracted from the electrode. qPCR and scanning electron microscopy corroborated this finding and revealed cable bacteria in higher abundance present on the electrode surface compared with unpoised controls. These experiments raise new possibilities to study metabolism of cable bacteria and cultivate them in bioelectrochemical devices for bioelectronic applications, such as biosensing and bioremediation.

IMPORTANCE
Extracellular electron transfer is a metabolic function associated with electroactive bacteria wherein electrons are exchanged with external electron acceptors or donors. This feature has enabled the development of several applications, such as biosensing, carbon capture, and energy recovery. Cable bacteria are a unique class of long, filamentous microbes that perform long-distance electron transport in freshwater and marine sediments. In this study, we demonstrate the attraction of cable bacteria toward carbon electrodes and demonstrate their potential electroactivity. This finding enables electronic control and monitoring of the metabolism of cable bacteria and may, in turn, aid in the development of bioelectronic applications.
Med3-mediated NADPH generation to help
Saccharomyces cerevisiae
tolerate hyperosmotic stress
Authors: Hou Shuo , Gao Cong , Liu Jia , Chen Xiulai , Wei Wanqing , Song Wei , Hu Guipeng , Li Xiaomin , Wu Jing , Liu Liming 
Published: July 2024

ABSTRACT

Hyperosmotic stress tolerance is crucial for
Saccharomyces cerevisiae
in producing value-added products from renewable feedstock. The limited understanding of its tolerance mechanism has impeded the application of these microbial cell factories. Previous studies have shown that Med3 plays a role in hyperosmotic stress in
S. cerevisiae
. However, the specific function of Med3 in hyperosmotic stress tolerance remains unclear. In this study, we showed that the deletion of the mediator Med3 impairs
S. cerevisiae
growth under hyperosmotic stress. Phenotypic analyses and yeast two-hybrid assays revealed that Med3 interacts with the transcription factor Stb5 to regulate the expression of the genes
gnd1
and
ald6
, which are involved in NADPH production under hyperosmotic stress conditions. The deletion of
med3
resulted in a decrease in intracellular NADPH content, leading to increased oxidative stress and elevated levels of intracellular reactive oxygen species under hyperosmotic stress, thereby impacting bud formation. These findings highlight the significant role of Med3 as a regulator in maintaining NADPH generation and redox homeostasis in
S. cerevisiae
during hyperosmotic stress.

IMPORTANCE

Hyperosmotic stress tolerance in the host strain is a significant challenge for fermentation performance in industrial production. In this study, we showed that the
S. cerevisiae
mediator Med3 is essential for yeast growth under hyperosmotic conditions. Med3 interacts with the transcription factor Stb5 to regulate the expression of genes involved in the NADPH-generation system during hyperosmotic stress. Adequate NADPH ensures the timely removal of excess reactive oxygen species and supports bud formation under these conditions. This work highlights the crucial role of Med3 as a regulator in maintaining NADPH generation and redox homeostasis in
S. cerevisiae
during hyperosmotic stress.
Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe
Veillonella dispar
in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate
Authors: Hung Jia-He , Zhang Shi-Min , Huang Shir-Ly 
Published: July 2024

ABSTRACT

Veillonella
spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal
Veillonella
reside in the human body site where lactate level is, however, limited for
Veillonella
growth. In this study, nitrate was shown to promote the anaerobic growth of
Veillonella
in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote
Veillonella dispar
growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled
V. dispar
to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways
via
reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal
V. dispar
utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.

IMPORTANCE

Nitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects
via
microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health.
Veillonella
are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by
V. dispar
to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of
V. dispar
further suggested the potential roles of nitrate and
Veillonella
in the promotion of human health.
Bacttle: a microbiology educational board game for lay public and schools
Authors: Trabajo Tania Miguel , Dorcey Eavan , van der Meer Jan Roelof 
Published: July 2024

ABSTRACT

Inspired by the positive impact of serious games on science understanding and motivated by personal interests in scientific outreach, we developed “Bacttle,” an easy-to-play microbiology board game with adaptive difficulty, targeting any player from 7 years old onward. Bacttle addresses both the lay public and teachers for use in classrooms as a way of introducing microbiology concepts. The layout of the game and its mechanism are the result of multiple rounds of trial, feedback, and re-design. The final version consists of a deck of cards, a 3D-printed board, and tokens (with a paper-based alternative), with all digital content open source. Players in Bacttle take on the character of a bacterial species. The aim for each species is to proliferate under the environmental conditions of the board and the interactions with the board and with other players, which vary as the play evolves. Players start with a given number of lives that will increase or decrease based on the traits they play for different environmental scenarios. Such bacterial traits come in the form of cards that can be deployed strategically. To assess the impact of the game on microbiological knowledge, we scored differences in the understanding of general concepts before and after playing the game. We assessed a total of 169 visitors at two different university open-day science fairs. Players were asked to fill out a brief survey before and after the game with questions targeting conceptual advances. Results show that Bacttle increases general microbiology knowledge on players as young as 5 years old and with the highest impact on those who have no
a priori
microbiology comprehension.
CRISPR screens identify genes essential for
in vivo
virulence among proteins of hyperLOPIT-unassigned subcellular localization in
Toxoplasma
Authors: Tachibana Yuta , Sasai Miwa , Yamamoto Masahiro 
Published: July 2024

ABSTRACT

The research field to identify and characterize genes essential for
in vivo
virulence in
Toxoplasma gondii
has been dramatically advanced by a series of
in vivo
clustered regularly interspaced short palindromic repeats (CRISPR) screens. Although subcellular localizations of thousands of proteins were predicted by the spatial proteomic method called hyperLOPIT, those of more than 1,000 proteins remained unassigned, and their essentiality in virulence was also unknown. In this study, we generated two small-scale gRNA libraries targeting approximately 600 hyperLOPIT-unassigned proteins and performed
in vivo
CRISPR screens. As a result, we identified several genes essential for
in vivo
virulence that were previously unreported. We further characterized two candidates, TgGTPase and TgRimM, which are localized in the cytoplasm and the apicoplast, respectively. Both genes are essential for parasite virulence and widely conserved in the phylum Apicomplexa. Collectively, our current study provides a resource for estimating the
in vivo
essentiality of
Toxoplasma
proteins with previously unknown localizations.

IMPORTANCE

Toxoplasma gondii
is a protozoan parasite that causes severe infection in immunocompromised patients or newborns.
Toxoplasma
possesses more than 8,000 genes; however, the genes essential for
in vivo
virulence were not fully identified. The apicomplexan parasites, including
Toxoplasma
, developed unique organelles that do not exist in other model organisms; thus, determining the subcellular location of parasite proteins is important for understanding their functions. Here, we used
in vivo
genetic screens that enabled us to investigate hundreds of genes in
Toxoplasma
during mouse infection. We screened approximately 600 parasite proteins with previously unknown subcellular localizations. We identified many novel genes that confer parasite virulence in mice. Among the top hits, we characterized two genes essential for
in vivo
virulence, TgGTPase and TgRimM, which are widely conserved in the phylum Apicomplexa. Our findings will contribute to understanding how apicomplexans adapt to the host environment and cause disease.
Draft genome sequence of
Ruoffia tabacinasalis
isolated from a bovine nasal swab: a novel member of the bovine nasal microbiota
Authors: Howe Samantha , Wei Xiaoyuan , Kovac Jasna , Zhao Jiangchao 
Published: July 2024

ABSTRACT

We report the isolation and draft genome sequence of
Ruoffia tabacinasalis,
a novel member of the bovine nasal microbiota. The genome, which is estimated to be 90.5% complete, is composed of one contig comprising 2,363,349 bp with a GC content of 36.66%.
Draft genome sequences of
Brucella melitensis
from human and animal sources in India
Authors: Ayoub Haris , Kumar M. Suman , Mehta Rishabh , Thomas Prasad , Dhanze Himani , Bhilegaonkar K. N. , Singh Vibha , Salih Harith M. , Amachawadi Raghavendra G. 
Published: July 2024

ABSTRACT

We present the draft genome sequences of 23
Brucella melitensis
isolates derived from human and animal sources across India with genome size predominantly at 3.207 M and uniform GC content (57.24%) across isolates. The accession numbers and detailed sequencing data enhance the utility of this resource for further genomic studies.
Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data
Authors: Myers Kevin S. , Place Michael , Gasch Audrey P. , Noguera Daniel R. , Donohue Timothy J. 
Published: July 2024

ABSTRACT

Multiplex, randomized CRISPR interference sequencing (MuRCiS) allows for the simultaneous identification of multiple gene knockouts that together influence microbial processes. Here, we report on an updated analysis tool called Auto-MuRCiS that utilizes Docker to make the analysis of these data rapid and more user-friendly.
Complete genome sequences of
Klebsiella pneumoniae
bacteriophages YMR1 and YMR2 isolated from sewage
Authors: Kwon Miri , Lee Yonghyun , Kim Minsik 
Published: July 2024

ABSTRACT

Two
Klebsiella pneumoniae
bacteriophages, YMR1 and YMR2, which form plaques with halos, were isolated from sewage in Seoul, South Korea. YMR1 and YMR2 have double-stranded DNA genomes of 40,338 bp and 40,756 bp with 49 and 52 predicted protein-coding genes, respectively. Both are predicted to be members of the family
Autographiviridae
.
Acupuncture for fatigue in breast cancer survivors: a study protocol for a pragmatic, mixed method, randomised controlled trial
Authors: Alræk Terje , Skjerve Hilde , Sørensen Anette , Lie S A , Presterud Ødegård Hilde , Lu Weidong , Mao Jun , Deng G , Lee Myeong Soo , Birch Stephen , Lamu Admassu Nadew , Kim Tae-hun , MacPherson Hugh 
Published: July 2024

IntroductionFatigue is a common symptom observed in post-cancer treatment, yet its underlying mechanisms remain poorly understood. Acupuncture has been employed to alleviate cancer-related fatigue (CRF); however, its effectiveness in addressing associated comorbidities that may influence fatigue is also poorly understood. This study represents the first investigation to use acupuncture as an intervention for fatigue in breast cancer survivors within a Norwegian cohort. The study will employ questionnaires to evaluate various facets of fatigue. As a pragmatic trial, it statistically assesses its clinical relevance, documents adverse events and evaluates the cost-effectiveness of the acupuncture treatment.Methods and analysisThis assessor-blinded, pragmatic, randomised, mixed method, controlled trial with two parallel arms aims to evaluate the effectiveness, safety and cost-effectiveness of acupuncture. It will recruit 250 participants presented with CRF for 6 months or longer. Patients will be randomly allocated either to acupuncture and usual care (n=125) or to usual care alone (n=125). Acupuncture treatments (12 in total) are to be given within 12 weeks. The statistician who will analyse the data will be blinded to group allocation. The primary outcome will be changes in CRF measured by the Chalder fatigue scale. Measurements will be taken 12 weeks and 6 months after randomisation. The secondary outcomes include patient-reported outcomes of pain, anxiety, depression, hot flashes, insomnia and sleepiness. Health-related quality of life and economic evaluation will also be conducted 12 weeks and 6 months after randomisation. Nested within this randomised controlled trial are two qualitative studies and one sub-study measuring biomarkers (C-reactive protein, interleukin (IL)-1, IL-6, tumour necrosis factor alpha (TNF-α) and aPL in addition to the current genotype genes TNF-308 and IL-6–174) from blood samples (n=80). Such biomarkers can potentially address changes in CRF.Ethics and disseminationEthical approval of this study has been granted by the Regional Committees for Medical and Health Research Ethics (REC southeast ID number: 112285). Written informed consent will be obtained from all participants. The outcomes of the trial will be disseminated through peer-reviewed publications.Trial registration numberNCT04418115.
PT-IN-MIND: study protocol for a multisite randomised feasibility trial investigating physical therapy with integrated mindfulness (PT-IN-MIND) for patients with chronic musculoskeletal pain and long-term opioid treatment who attend outpatient physical therapy
Authors: Magel John S , Beneciuk Jason M. , Siantz Elizabeth , Fritz Julie , Garland Eric L. , Hanley Adam , Shen Jincheng , Blosser Priscilla , Matev Taisiya , Gordon Adam J 
Published: July 2024

IntroductionMany individuals receiving outpatient physical therapy have musculoskeletal pain and up to one-third use prescription opioids. The impact of physical therapist-led mindfulness-based interventions integrated with evidence-based physical therapy (I-EPT) to manage patients with chronic musculoskeletal pain and long-term opioid treatment has not been elucidated. This project evaluates the feasibility of conducting a cluster randomised trial to test the effectiveness of I-EPT.Methods and analysisStudy 1 aim: Refine and manualise the I-EPT treatment protocol. Our approach will use semistructured interviews of patients and physical therapists to refine an I-EPT training manual. Study 2 aim: Evaluate different intensities of physical therapist training programmes for the refined I-EPT treatment protocol. Physical therapists will be randomised 1:1:1 to high-intensity training (HighIT), low-IT (LowIT) training and no training arms. Following training, competency in the provision of I-EPT (LowIT and HighIT groups) will be assessed using standardised patient simulations. Study 3 aim: Evaluate the feasibility of the I-EPT intervention across domains of the Reach, Effectiveness, Adoption, Implementation, Maintenance implementation framework. The refined I-EPT treatment protocol will be tested in two different health systems with 90 patients managed by the randomised physical therapists. The coprimary endpoints for study 3 are the proportions of the Pain, Enjoyment of Life and General Activity Scale and the Timeline Followback for opioid use/dose collected at 12 weeks.Ethics and disseminationEthics approval for the study was obtained from the University of Utah, University of Florida and Florida State University Institutional Review Boards. Informed consent is required for participant enrolment in all phases of this project. On completion, study data will be made available in compliance with NIH data sharing policies.Trial registration numberNCT05875207.
Urban–rural health disparity among patients with chronic kidney disease: a cross-sectional community-based study from 2012 to 2019
Authors: Wu Yi-Lien , Wu Yun-Chun , Akhmetzhanov Andrei R , Wu Mei-Yi , Lin Yuh-Feng , Lin Chia-Chin 
Published: July 2024

ObjectivesThe incidence of chronic kidney disease (CKD) is increasing owing to the ageing population, resulting in an increased demand for dialysis and kidney transplantation, which can be costly. Current research lacks clarity regarding the relationship between residence setting and CKD prevalence or its related risk factors. This study explored the urban–rural disparities in CKD prevalence and risk factors in Taiwan. Our findings will aid the understanding of the distribution of CKD and the design of more effective prevention programmes.DesignThis cross-sectional community-based study used the Renal Value Evaluation Awareness and Lift programme, which involves early screening and health education for CKD diagnosis and treatment. CKD prevalence and risk factors including alcohol consumption, smoking and betel nut chewing were compared between urban and rural areas.SettingUrbanisation levels were determined based on population density, education, age, agricultural population and medical resources.ParticipantsA total of 7786 participants from 26 urban and 15 rural townships were included.ResultsThe prevalence of CKD was significantly higher in rural (29.2%) than urban (10.8%) areas, representing a 2.7-fold difference (p<0.0001). Risk factors including diabetes (rural vs urban: 21.7% and 11.0%), hypertension (59.0% vs 39.9%), hyperuricaemia (36.7% vs 18.6%), alcohol consumption (29.0% vs 19.5%), smoking (15.9% vs 12.0%), betel nut chewing (12.6% vs 2.8%) and obesity (33.6% vs 19.4%) were significantly higher (p<0.0001) in rural areas.ConclusionsThe prevalence of CKD is three times higher in rural versus urban areas. Despite >99% National Health Insurance coverage, disparities in CKD prevalence persist between residential areas. Targeted interventions and further studies are crucial for addressing these disparities and enhancing CKD management across different settings.
Designing a single-arm phase 2 clinical trial of mitapivat for adult patients with erythrocyte membranopathies (SATISFY): a framework for interventional trials in rare anaemias – pilot study protocol
Authors: Glenthøj Andreas , van Beers Eduard J , van Wijk Richard , Rab Minke A E , Groot Evelyn , Vejlstrup Niels , Toft Nina , Bendtsen Selma Kofoed , Petersen Jesper , Helby Jens , Chermat Fatiha , Fenaux Pierre , Kuo Kevin H M 
Published: July 2024

IntroductionMembranopathies encompass haemolytic disorders arising from genetic variants in erythrocyte membrane proteins, including hereditary spherocytosis and stomatocytosis. Congenital dyserythropoietic anaemia type II (CDA II) is associated with theSEC23Bgene and can exhibit phenotypic similarities to membranopathies. Current treatment options for these conditions, apart from splenectomy, are primarily supportive. Mitapivat, a novel pyruvate kinase (PK) activator, has demonstrated efficacy in increasing haemoglobin levels and reducing haemolysis in patients with PK deficiency, thalassemia, sickle cell disease and a mouse model of hereditary spherocytosis.Methods and analysesSafety and efficacy of mitapivatsulfate in adult patients with erythrocyte membranopathies (SATISFY) is a prospective, multicentre, single-arm phase two trial involving approximately 25 adult patients (≥18 years) diagnosed with a membranopathy or CDA II. During the 8-week dose escalation period, subjects will receive an initial dose of 50 mg mitapivat two times per day and may increase to 100 mg two times per day at week 4 based on the safety and changes in haemoglobin levels. Patients tolerating mitapivat well may be eligible to continue in two consecutive 24-week fixed dose periods.The primary objective of this study is to evaluate the safety of mitapivat, assessed through the occurrence of treatment-emergent adverse events. Secondary objectives include assessing the effects of mitapivat on haemoglobin levels, haemolysis, erythropoiesis, patient-reported outcome measures and spleen size.SATISFY aims to assess the safety and efficacy of mitapivat in adult patients with red blood cell membranopathies and CDA II, with the aim of establishing proof-of-concept in patients living with these rare conditions.Ethics and disseminationNCT05935202/CTIS:2023-503271-24-01. Findings will be published in peer-reviewed journals.Trial registration numberClinicaltrials.gov,NCT05935202. CTIS:2023-503271-24-01. Registered 07-July-2023. Protocol number: 2.1.https://clinicaltrials.gov/study/NCT05935202.