bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and characterization of an infectious cDNA clone of turtle grass virus X from a naturally infected
Thalassia testudinum
plant
Authors: Alvarado-Marchena Luis , Furman Bradley T. , Breitbart Mya 
Published: December 2024

ABSTRACT

Seagrasses are a polyphyletic group of marine flowering plants that play crucial roles in nearshore ecology, yet their interactions with viruses remain largely unexplored. This study presents the construction and characterization of an infectious cDNA clone of the potexvirus turtle grass virus X (TGVX). The complete genome of this positive-sense single-stranded RNA virus was amplified from field samples of
Thalassia testudinum
and assembled into a pLX-based mini binary vector using a multi-fragment directional cloning strategy, resulting in the infectious clone pLX-TGVX. Agroinfection assays of potexvirus-free
T. testudinum
plants resulted in systemic infections by TGVX, as confirmed by multiplex RT-PCR experiments and phenotypic changes reflecting virus-induced symptoms. Ultrastructural studies also demonstrated significant cytopathological changes resulting from TGVX infection, including chloroplast swelling, reduced thylakoid grana, and the presence of viral replication organelles and filamentous virus-like particles. The development of the TGVX infectious clone offers a novel tool for investigating the impact of this virus on seagrass health and productivity. This study demonstrates the first successful agroinfection of a marine plant with an infectious clone, creating a new avenue for studying viruses identified through sequence-based surveys and paving the way for exploring the ecological significance of viral infection in these critical marine ecosystems.

IMPORTANCE

This study pioneers the construction of an infectious clone of turtle grass virus X and describes its application in the natural marine plant host,
Thalassia testudinum
. The creation of this infectious clone not only provides a valuable tool for marine plant virology research but also opens new avenues for exploring the influence of viral infections on the health and productivity of seagrass meadows. Given that seagrasses play a crucial role in sediment stabilization, nutrient cycling, and habitat provisioning, understanding the impact of viruses on these ecosystems is essential for their effective conservation and management. This methodological advance enables detailed studies of viral replication, virus-host interactions, and the broader ecological implications of viral infections in marine plants.
Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization
Authors: Christel Stephan , Carrell Alyssa A. , Hochanadel Leah H. , Villalobos Solis Manuel I. , Abraham Paul E. , Jawdy Sara S. , Chaves Julie E. , Engle Nancy L. , Berhane Timkhite-Kulu , Yao Tao , Chen Jin-Gui , Muchero Wellington , Tschaplinski Timothy J. , Cregger Melissa A. , Michener Joshua K. 
Published: December 2024

ABSTRACT

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the
Pseudomonas
genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.

IMPORTANCE

Horizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition
in situ
by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.
Vibrio alginolyticus
is the pathogen of “Baotou” disease causing serious damage to
Gracilariopsis lemaneiformis
cultivation in China
Authors: Pang Tong , Wang Feng , Guo Qunqun , Zhang Mengjie , Sun Yuanyuan , Liu Jianguo 
Published: December 2024

ABSTRACT

In recent years, a disease called “Baotou” has been causing large-scale yield reductions of
Gracilariopsis lemaneiformis
in China. Interestingly,
Vibrio alginolyticus
, which once reported to be a probiotic or pathogen for multiple marine organisms, was strongly proved to be the pathogen causing “Baotou” disease in this study. Analysis of 16S rRNA gene profiling revealed that
V. alginolyticus
was the most abundant and dominant bacterium on the algal thalli suffering from “Baotou” disease, whereas its presence was scarcely detected on healthy thalli. Scanning electron microscope (SEM) analysis revealed that a large number of
V. alginolyticus
cells were found to be attached to the algal thalli with “Baotou” disease and the rotten thalli acquired by the lab infection treatment.
V. alginolyticus
could cause the rotten symptoms which were consistent with those of “Baotou” disease. According to Koch’s postulates,
V. alginolyticus
was identified as the pathogen causing “Baotou” disease.

IMPORTANCE

A highly contagious disease known as “Baotou” disease has persistently triggered significant yield reductions in
G. lemaneiformis
throughout China. The pathogen of “Baotou” disease was isolated and identified as
V. alginolyticus
in this study. Interestingly,
V. alginolyticus
was once reported to be a probiotic to
Saccharina japonica
, and pathogen to
Haliotis diversicolor
,
Paleopneustes cristatus
,
Ruditapes decussatus,
and
Litopenaeus vannamei
. The study indicates that
V. alginolyticus
play a significant role in the competition or co-existence between
G. lemaneiformis
,
S. japonica
, abalone, sea urchin, bivalve, and shrimp.
Geographically widespread and novel hemotropic mycoplasmas and bartonellae in Mexican free-tailed bats and sympatric North American bat species
Authors: Becker Daniel J. , Dyer Kristin E. , Lock Lauren R. , Olbrys Beckett L. , Pladas Shawn A. , Sukhadia Anushka A. , Demory Bret , Nunes Batista Juliana Maria , Pineda Micaela , Simmons Nancy B. , Adams Amanda M. , Frick Winifred F. , O'Mara M. Teague , Volokhov Dmitriy V. 
Published: December 2024

ABSTRACT

Bacterial pathogens remain poorly characterized in bats, especially in North America. We describe novel (and in some cases panmictic) hemoplasmas (10.1% positivity) and bartonellae (25.6% positivity) across three colonies of Mexican free-tailed bats (
Tadarida brasiliensis
), a partially migratory species that can seasonally travel hundreds of kilometers. Molecular analyses identified three novel
Candidatus
hemoplasma species most similar to another novel
Candidatus
species in Neotropical molossid bats. We also detected novel hemoplasmas in sympatric cave myotis (
Myotis velifer
) and pallid bats (
Antrozous pallidus
), with sequences in the latter 96.5% related to
Candidatus
Mycoplasma haematohominis. We identified nine
Bartonella
genogroups, including those in cave myotis with 96.1% similarity to
Candidatus
Bartonella mayotimonensis. We also detected
Bartonella rochalimae
in migratory Mexican free-tailed bats, representing the first report of this human pathogen in the Chiroptera. Monthly sampling of migratory Mexican free-tailed bats during their North American occupancy period also revealed significant seasonality in infection for both bacterial pathogens, with prevalence increasing following spring migration, peaking in the maternity season, and declining into fall migration. The substantial diversity and seasonality of hemoplasmas and bartonellae observed here suggest that additional longitudinal, genomic, and immunological studies in bats are warranted to inform One Health approaches.

IMPORTANCE

Bats have been intensively sampled for viruses but remain mostly understudied for bacterial pathogens. However, bacterial pathogens can have significant impacts on both human health and bat morbidity and even mortality. Hemoplasmas and bartonellae are facultative intracellular bacteria of special interest in bats, given their high prevalence and substantial genetic diversity. Surveys have also supported plausible zoonotic transmission of these bacteria from bats to humans, including
Candidatus
Mycoplasma haematohominis and
Candidatus
Bartonella mayotimonensis. Greater characterization of these bacteria across global bat diversity (over 1,480 species) is therefore warranted to inform infection risks for both bats and humans, although little surveillance has thus far been conducted in North American bats. We here describe novel (and in some cases panmictic) hemoplasmas and bartonellae across three colonies of Mexican free-tailed bats and sympatric bat species. We find high genetic diversity and seasonality of these pathogens, including lineages closely related to human pathogens, such as
Bartonella rochalimae
.
Advancing dental biofilm models: the integral role of pH in predicting
S. mutans
colonization
Authors: Sangha Jay S. , Gogulancea Valentina , Curtis Thomas P. , Jakubovics Nicholas S. , Barrett Paul , Metris Aline , Ofiţeru Irina D. 
Published: December 2024

ABSTRACT

Mathematical models can provide insights into complex interactions and dynamics within microbial communities to complement and extend experimental laboratory approaches. For dental biofilms, they can give a basis for evaluating biofilm growth or the transition from health to disease. We have developed mathematical models to simulate the transition toward a cariogenic microbial biofilm, modeled as the overgrowth of
Streptococcus mutans
within a five-species dental community. This work builds on experimental data from a continuous flow reactor with hydroxyapatite coupons for biofilm growth, in a chemically defined medium with varying concentrations of glucose and lactic acid. The biofilms formed on the coupons were simulated using individual-based models (IbMs), with bacterial growth modeled using experimentally measured kinetic parameters. The IbM assumes that the maximum theoretical growth yield for biomass is dependent on the local concentration of reactants and products, while the growth rates were described using traditional Monod equations. We have simulated all the conditions studied experimentally, considering different initial relative abundance of the five species, and also different initial clustering in the biofilm. The simulation results only reproduced the experimental dominance of
S. mutans
at high glucose concentration after we considered the species-specific effect of pH on growth rates. This highlights the significance of the aciduric property of
S. mutans
in the development of caries. Our study demonstrates the potential of combining
in vitro
and
in silico
studies to gain a new understanding of the factors that influence dental biofilm dynamics.

IMPORTANCE

We have developed
in silico
models able to reproduce the relative abundance measured
in vitro
in the synthetic dental biofilm communities growing in a chemically defined medium. The advantage of this combination of
in vitro
and
in silico
models is that we can study the influence of one parameter at a time and aim for direct validation. Our work demonstrates the utility of individual-based models for simulating diverse conditions affecting dental biofilm scenarios, such as the frequency of glucose intake, sucrose pulsing, or integration of pathogenic or probiotic species. Although
in silico
models are reductionist approaches, they have the advantage of not being limited in the scenarios they can test by the ethical consideration of an
in vivo
system, thus significantly contributing to dental biofilm research.
PhoU homologs from
Staphylococcus aureus
dimerization and protein interactions
Authors: Matthews Clayton T. , Mahmud Sakib , Gardner Stewart G. 
Published: December 2024

ABSTRACT

PhoU proteins are negative regulators of the phosphate response, regulate virulence, and contribute to antibiotic resistance.
Staphylococcus aureus
has multiple genes encoding PhoU homologs that regulate persister formation and potentially virulence, but the molecular mechanisms of this regulation are not fully understood. We used a bacterial adenylate cyclase two-hybrid system to assess interactions between PhoU homologs and other proteins known to interact with PhoU from
Escherichia coli. S. aureus
PhoU (also referred to as PhoU1) interacted with PhoU itself; PitR (also referred to as PhoU2) interacted with PitR itself. We identified potential structural and dimerization models for
S. aureus
PhoU homologs. Dimerization was confirmed using size exclusion chromatography of purified proteins. These results highlight the complex nature of PhoU proteins. Further analysis may elucidate the potential mechanisms for regulating gene expression, persister formation, and virulence in
S. aureus
.

IMPORTANCE

PhoU proteins affect pathogenesis and persister formation in many bacterial species. This protein is essential for signaling environmental phosphate levels in
Escherichia coli
but is still not well characterized in many other pathogenic bacterial strains. This work identifies some similarities and key differences in
Staphylococcus aureus
PhoU homologs compared to
E. coli
PhoU, specifically, PhoU and PitR from
S. aureus
form homodimers but do not appear to interact with PhoR or phosphate transporter proteins.
Gut mycobiome alterations and network interactions with the bacteriome in patients with atherosclerotic cardiovascular disease
Authors: Su Guangming , Huang Ping , Liu Dan , Xing Guorui , Guo Ruochun , Li Shenghui , Fan Shao , Cheng Lin , Yan Qiulong , Yang Wei 
Published: December 2024

ABSTRACT

The connection between the gut mycobiome and atherosclerotic cardiovascular disease (ACVD) is largely uncharted. In our study, we compared the gut fungal communities of 214 ACVD patients with those of 171 healthy controls using shotgun metagenomic sequencing and examined their interactions with gut bacterial communities and network key taxa. The gut mycobiome composition in ACVD patients is significantly different, showing a rise in opportunistic pathogens like
Candida albicans
,
Exophiala spinifera
, and
Malassezia restricta
, with
Exophiala
and
Malassezia
showing the most significant changes (Wilcoxon rank-sum test,
P
< 0.001, fold change >10). Network analysis revealed a less interconnected and more uneven gut microbial network in ACVD patients. Network key taxa identified in the ACVD gut microbiome network include
Malassezia globosa
c182,
Nakaseomyces glabratus
c88,
Malassezia arunalokei
c192, and
Penicillium sumatraense
c22. Predictive models that integrated both bacterial and fungal taxa enhanced prediction accuracy, underscoring the critical role of gut fungi in ACVD. Our findings offer a thorough understanding of the link between the gut mycobiome and ACVD progression, which is vital for directing future therapeutic research.

IMPORTANCE
ACVD is a leading cause of death and morbidity worldwide. While the role of the gut microbiome in ACVD development is recognized, the contribution of the gut mycobiome remains largely unexplored. Our study reveals significant alterations in the gut mycobiome of ACVD patients and identifies key fungal taxa associated with the disease. These findings underscore the importance of the gut mycobiome in the pathogenesis of ACVD and offer new avenues for developing preventive and therapeutic strategies targeting the gut fungal community. Our results provide valuable insights into the complex interplay between gut fungi and bacteria in ACVD, paving the way for novel therapeutic approaches.
Cardiorespiratory fitness is associated with cognitive function in late adulthood: baseline findings from the IGNITE study
Authors: Oberlin Lauren E , Wan Lu , Kang Chaeryon , Romano Allison , Aghjayan Sarah , Lesnovskaya Alina , Ripperger Hayley S , Drake Jermon , Harrison Rae , Collins Audrey M , Molina-Hidalgo Cristina , Grove George , Huang Haiqing , Kramer Arthur , Hillman Charles H , Burns Jeffrey M , Vidoni Eric D , McAuley Edward , Kamboh M Ilyas , Jakicic John M , Erickson Kirk I 
Published: December 2024

ObjectivesTo evaluate the association between cardiorespiratory fitness (CRF) and cognition in a large sample of older adults, and to examine clinical and demographic factors that might moderate these associations.MethodsCRF was measured with a graded exercise test performed on a motorised treadmill. A confirmatory factor analysis was conducted using data from a comprehensive neuropsychological battery to obtain latent factors reflecting core cognitive domains. Linear regression models evaluated the association between CRF and each of the cognitive composites, and potential moderators including demographic factors (age, sex, education), apolipoprotein E ε4 (APOE4) carriage, beta-blocker use and components of maximal effort criteria during CRF testing.ResultsThe sample consisted of 648 adults (mean (SD) age 69.88 (3.75)), including 461 women (71.1%). The highest oxygen consumption obtained during testing (VO2max) was mean (SD) = 21.68 (5.06) mL/kg/min. We derived a five-factor model composed of episodic memory, processing speed, working memory, executive function/attentional control and visuospatial function. Higher CRF was associated with better performance across all five cognitive domains after controlling for covariates. Age andAPOE4carriage did not moderate observed associations. The relationship between CRF and cognitive performance was greater in women, those with fewer years of education and those taking beta-blockers in the domains of processing speed (sex: β=−0.447; p=0.015; education: β=−0.863; p=0.018) and executive function/attentional control (sex: β=−0.417; p=0.022; education β=−0.759; p=0.034; beta-blocker use: β=0.305; p=0.047).ConclusionHigher CRF in older adulthood is associated with better cognitive performance across multiple domains susceptible to age-related cognitive decline. Sex, education and use of beta-blockers moderated observed associations within select cognitive domains.
Efficacy of combining aspirin with hydroxychloroquine in pregnancies at high risk for pre-eclampsia: a prospective, multicentre, open-label, single-arm clinical trial, investigator-initiated study (HUGS study)
Authors: Kim Yoo-Min , Seong Jisu , Kim Ji Hoi , Nam Gina , Kim Gwang jun , Cha Hyun-Hwa , Seong Won Joon , Sung Ji-Hee , Choi Suk-Joo , Oh Soo-Young , Roh Cheong-Rae 
Published: December 2024

IntroductionThe use of hydroxychloroquine (HCQ) during pregnancies complicated by systemic lupus erythematosus or refractory antiphospholipid antibody syndrome has demonstrated a significant ability to prevent pre-eclampsia (PE). As such, the potential for the administration of HCQ to prevent PE in other high-risk pregnancies is an important clinical research agenda among maternal and fetal medicine specialists. Mechanistically, the anti-inflammatory and immunomodulatory effects of HCQ can offer vascular protection and inhibit the placental dysfunction-associated thrombotic changes underlying the pathophysiology of PE, fetal growth restriction (FGR) and fetal death in utero (FDIU). Placenta-mediated complications exhibit a distinctive overlapping syndrome between pregnancies, and low-dose aspirin is the only prevention method currently in use. This study investigated the effects of improvements in outcomes with HCQ administration in high-risk pregnancies complicated by a previous experience of PE, FGR or FDIU.Methods and analysisThis multicentre, open-label, single-arm trial commenced on 31 May 2022, in three tertiary hospitals in Korea. Pregnant women with a prior history of PE, FGR or FDIU are eligible to participate. This single-arm study set the previous study with the most similar inclusion criteria, aspirin dose and drug administration period as the comparison group. The required sample size was determined to be 58, with an expected dropout rate of 10%.Ethics and disseminationThis study protocol was approved by the following institutions and committees: Institutional Review Boards of Chung-Ang University Gwangmyeong Hospital (2304-082-056), Samsung Medical Center (2021-11-087-003) and Kyungpook National University Chilgok Hospital (2021-06-005-006) and the Ministry of Food and Drug Safety. The results will be disseminated to the general public, grant funder, maternal–fetal medicine specialists and other researchers.Trial registration numberNCT05287321.