bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Daily Physical Activity With Motivation in Prefrail and Frail Older Adults Living in Retirement Communities
Authors: Rubin Daniel S. , Conroy David E. , Danilovich Margaret K. 
Published: August 2024

Older adults living in retirement communities are an understudied population, and the association between their motivation and daily physical activity is unknown. We recruited participants (n = 173) living in a retirement community who completed the Behavioral Regulation in Exercise Questionnaire-2 and wore an activPAL accelerometer to evaluate this relationship. Participants had a median age of 81 years and demonstrated low levels of daily activity with an average step count of 3,637 (±1,965) steps per day and 52 (±25) min of daily stepping time. External motivation was negatively associated with the square root of daily step count (β = −4.57; p < .001) and square root of daily stepping time (β = −0.49; p < .001). Older adults living in retirement communities demonstrated low levels of daily activity, with a negative association between external motivation and daily activity. Strategies are needed to make an active lifestyle supportive and enticing for older adults in these communities.
The
Toxoplasma gondii
mitochondrial transporter ABCB7L is essential for the biogenesis of cytosolic and nuclear iron-sulfur cluster proteins and cytosolic translation
Authors: Maclean Andrew E. , Sloan Megan A. , Renaud Eléa A. , Argyle Blythe E. , Lewis William H. , Ovciarikova Jana , Demolombe Vincent , Waller Ross F. , Besteiro Sébastien , Sheiner Lilach 
Published: August 2024

ABSTRACT

Iron-sulfur (Fe-S) clusters are ubiquitous inorganic cofactors required for numerous essential cellular pathways. Since they cannot be scavenged from the environment, Fe-S clusters are synthesized
de novo
in cellular compartments such as the apicoplast, mitochondrion, and cytosol. The cytosolic Fe-S cluster biosynthesis pathway relies on the transport of an intermediate from the mitochondrial pathway. An ATP-binding cassette (ABC) transporter called ABCB7 is responsible for this role in numerous commonly studied organisms, but its role in the medically important apicomplexan parasites has not yet been studied. Here we identify and characterize a
Toxoplasma gondii
ABCB7 homolog, which we name ABCB7-like (ABCB7L). Genetic depletion shows that it is essential for parasite growth and that its disruption triggers partial stage conversion. Characterization of the knock-down line highlights a defect in the biogenesis of cytosolic and nuclear Fe-S proteins leading to defects in protein translation and other pathways including DNA and RNA replication and metabolism. Our work provides support for a broad conservation of the connection between mitochondrial and cytosolic pathways in Fe-S cluster biosynthesis and reveals its importance for parasite survival.

IMPORTANCE

Iron-sulfur (Fe-S) clusters are inorganic cofactors of proteins that play key roles in numerous essential biological processes, for example, respiration and DNA replication. Cells possess dedicated biosynthetic pathways to assemble Fe-S clusters, including a pathway in the mitochondrion and cytosol. A single transporter, called ABCB7, connects these two pathways, allowing an essential intermediate generated by the mitochondrial pathway to be used in the cytosolic pathway. Cytosolic and nuclear Fe-S proteins are dependent on the mitochondrial pathway, mediated by ABCB7, in numerous organisms studied to date. Here, we study the role of a homolog of ABCB7, which we name ABCB7-like (ABCB7L), in the ubiquitous unicellular apicomplexan parasite
Toxoplasma gondii
. We generated a depletion mutant of
Toxoplasma
ABCB7L and showed its importance for parasite fitness. Using comparative quantitative proteomic analysis and experimental validation of the mutants, we show that ABCB7L is required for cytosolic and nuclear, but not mitochondrial, Fe-S protein biogenesis. Our study supports the conservation of a protein homologous to ABCB7 and which has a similar function in apicomplexan parasites and provides insight into an understudied aspect of parasite metabolism.
Discovery of GuaB inhibitors with efficacy against
Acinetobacter baumannii
infection
Authors: Kofoed Eric M. , Aliagas Ignacio , Crawford Terry , Mao Jialin , Harris Seth F. , Xu Min , Wang Shumei , Wu Ping , Ma Fang , Clark Kevin , Sims Jessica , Xu Yiming , Peng Yutian , Skippington Elizabeth , Yang Ying , Reeder Janina , Ubhayakar Savita , Baumgardner Matt , Yan Zhengyin , Chen Jacob , Park Summer , Zhang Hua , Yen Chun-Wan , Lorenzo Maria , Skelton Nicholas , Liang Xiaorong , Chen Liuxi , Hoag Bridget , Li Chun Sing , Liu Zhiguo , Wai John , Liu Xingrong , Liang Jun , Tan Man Wah 
Published: August 2024

ABSTRACT

Guanine nucleotides are required for growth and viability of cells due to their structural role in DNA and RNA, and their regulatory roles in translation, signal transduction, and cell division. The natural antibiotic mycophenolic acid (MPA) targets the rate-limiting step in
de novo
guanine nucleotide biosynthesis executed by inosine-5´-monophosphate dehydrogenase (IMPDH). MPA is used clinically as an immunosuppressant, but whether
in vivo
inhibition of bacterial IMPDH (GuaB) is a valid antibacterial strategy is controversial. Here, we describe the discovery of extremely potent small molecule GuaB inhibitors (GuaBi) specific to pathogenic bacteria with a low frequency of on-target spontaneous resistance and bactericidal efficacy
in vivo
against
Acinetobacter baumannii
mouse models of infection. The spectrum of GuaBi activity includes multidrug-resistant pathogens that are a critical priority of new antibiotic development. Co-crystal structures of
A. baumannii, Staphylococcus aureus
, and
Escherichia coli
GuaB proteins bound to inhibitors show comparable binding modes of GuaBi across species and identifies key binding site residues that are predictive of whole-cell activity across both Gram-positive and Gram-negative clades of Bacteria. The clear
in vivo
efficacy of these small molecule GuaB inhibitors in a model of
A. baumannii
infection validates GuaB as an essential antibiotic target.

IMPORTANCE

The emergence of multidrug-resistant bacteria worldwide has renewed interest in discovering antibiotics with novel mechanism of action. For the first time ever, we demonstrate that pharmacological inhibition of
de novo
guanine biosynthesis is bactericidal in a mouse model of
Acinetobacter baumannii
infection. Structural analyses of novel inhibitors explain differences in biochemical and whole-cell activity across bacterial clades and underscore why this discovery may have broad translational impact on treatment of the most recalcitrant bacterial infections.
Critical roles of Dpb3-Dpb4 sub-complex of DNA polymerase epsilon in DNA replication, genome stability, and pathogenesis of
Candida albicans
Authors: Utkalaja Bhabasha Gyanadeep , Patel Shraddheya Kumar , Sahu Satya Ranjan , Dutta Abinash , Acharya Narottam 
Published: August 2024

ABSTRACT

DNA polymerase ε (Polε) is an essential replicative polymerase consisting of Pol2, Dpb2, Dpb3, and Dpb4 subunits and has not been explored in the pathogenic yeast
Candida albicans. C. albicans
is accountable for >40% of deaths due to systemic candidiasis per year worldwide. Genome plasticity is one of the adaptive mechanisms associated with virulence, and as it is associated with DNA polymerase function, this study explored the role of Polε in genome stability and pathogenesis of
C. albicans. POL2
and
DPB2
are haploinsufficient, but
DPB3
and
DPB4
are dispensable for cell survival in diploid
C. albicans
. However, unlike in
Saccharomyces cerevisiae
, loss of any or both of the nonessential subunits or defective interaction between the two resulted in slow growth and temperature-sensitive phenotypes. Knockout strains of
C. albicans (dpb3
ΔΔ and
dpb4
ΔΔ and
dpb3
ΔΔ
dpb4
ΔΔ) also exhibited sensitivity to genotoxic agents and delayed cell cycle progression. Reduced processive DNA synthesis and increased rate of mutagenesis were observed in
dpb3
and
dpb4
null strains. Whole-genome sequencing further confirmed the accumulation of indels and SNPs majorly in the intergenic repeat regions of the chromosomes of
dpb3
ΔΔ
dpb4
ΔΔ. Polε-defective strains were constitutively filamentous and non-pathogenic in mice models of systemic candidiasis. Altogether, this study showed that the function of the Dpb3-Dpb4 subcomplex is critical for fungal morphogenesis and virulence besides its role as a structural component of Polε in DNA replication and genome stability; thus, their interacting interface may be targeted to develop antifungal drugs.

IMPORTANCE

This study explored the role of DNA polymerase epsilon, especially its non-essential structural subunits in
Candida albicans
biology. Apart from their role in DNA replication and genome stability, the Dpb3-Dpb4 subcomplex regulates morphological switching and virulence. Since the defective strain is locked in filamentous form and is avirulent, the complex may be targeted for anti-fungal drug development.
A multistage
Plasmodium
CRL4
WIG1
ubiquitin ligase is critical for the formation of functional microtubule organization centers in microgametocytes
Authors: Rashpa Ravish , Smith Cameron , Artavanis-Tsakonas Katerina , Brochet Mathieu 
Published: August 2024

ABSTRACT

Malaria is a mosquito-borne infectious disease caused by unicellular eukaryotic parasites of the
Plasmodium
genus. Protein ubiquitination by E3 ligases is a critical post-translational modification required for various cellular processes during the lifecycle of
Plasmodium
parasites. However, little is known about the repertoire and function of these enzymes in
Plasmodium
. Here, we show that
Plasmodium
expresses a conserved cullin RING E3 ligase (CRL) complex that is functionally related to CRL4 in other eukaryotes. In
P. falciparum
asexual blood stages, a cullin-4 scaffold interacts with the RING protein RBX1, the adaptor protein DDB1, and a set of putative receptor proteins that may determine substrate specificity for ubiquitination. These receptor proteins contain WD40-repeat domains and include
W
D-repeat protein
i
mportant for
g
ametogenesis 1 (WIG1). This CRL4-related complex is also expressed in
P. berghei
gametocytes, with WIG1 being the only putative receptor detected in both the schizont and gametocyte stages.
WIG1
disruption leads to a complete block in microgamete formation. Proteomic analyses indicate that
WIG1
disruption alters proteostasis of ciliary proteins and components of the DNA replication machinery during gametocytogenesis. Further analysis by ultrastructure expansion microscopy (U-ExM) indicates that WIG1-dependent depletion of ciliary proteins is associated with impaired the formation of the microtubule organization centers that coordinate mitosis with axoneme formation and altered DNA replication during microgametogenesis. This work identifies a CRL4-related ubiquitin ligase in
Plasmodium
that is critical for the formation of microgametes by regulating proteostasis of ciliary and DNA replication proteins.

IMPORTANCE

Plasmodium
parasites undergo fascinating lifecycles with multiple developmental steps, converting into morphologically distinct forms in both their mammalian and mosquito hosts. Protein ubiquitination by ubiquitin ligases emerges as an important post-translational modification required to control multiple developmental stages in
Plasmodium
. Here, we identify a cullin RING E3 ubiquitin ligase (CRL) complex expressed in the replicating asexual blood stages and in the gametocyte stages that mediate transmission to the mosquito. WIG1, a putative substrate recognition protein of this ligase complex, is essential for the maturation of microgametocytes into microgametes upon ingestion by a mosquito. More specifically, WIG1 is required for proteostasis of ciliary proteins and components of the DNA replication machinery during gametocytogenesis. This requirement is linked to DNA replication and microtubule organization center formation, both critical to the development of flagellated microgametes.
Metagenomic discovery of microbial eukaryotes in stool microbiomes
Authors: Crouch Audra L. , Monsey Laine , Rambeau Molly , Ramos Cameron , Yracheta Joseph M. , Anderson Matthew Z. 
Published: August 2024

ABSTRACT

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa,
de novo
assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.

IMPORTANCE
Microbial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.
Classical swine fever virus inhibits serine metabolism-mediated antiviral immunity by deacetylating modified PHGDH
Authors: Li Xiaowen , Huang Yaoyao , Liu Xueyi , Zhang Lihong , Wang Xinyan , Zhao Feifan , Zou Linke , Wu Keke , Chen Wenxian , Qin Yuwei , Zeng Sen , Li Bingke , He Yintao , Song Yiwan , Li Zhaoyao , Fan Jindai , Zhao Mingqiu , Yi Lin , Ding Hongxing , Fan Shuangqi , Chen Jinding 
Published: August 2024

ABSTRACT

Classical swine fever virus (CSFV), an obligate intracellular pathogen, hijacks cellular metabolism to evade immune surveillance and facilitate its replication. The precise mechanisms by which CSFV modulates immune metabolism remain largely unknown. Our study reveals that CSFV infection disrupts serine metabolism, which plays a crucial role in antiviral immunity. Notably, we discovered that CSFV infection leads to the deacetylation of PHGDH, a key enzyme in serine metabolism, resulting in autophagic degradation. This deacetylation impairs PHGDH’s enzymatic activity, reduces serine biosynthesis, weakens innate immunity, and promotes viral proliferation. Molecularly, CSFV infection induces the association of HDAC3 with PHGDH, leading to deacetylation at the K364 site. This modification attracts the E3 ubiquitin ligase RNF125, which facilitates the addition of K63-linked ubiquitin chains to PHGDH-K364R. Subsequently, PHGDH is targeted for lysosomal degradation by p62 and NDP52. Furthermore, the deacetylation of PHGDH disrupts its interaction with the NAD
+
substrate, destabilizing the PHGDH-NAD complex, impeding the active site, and thereby inhibiting
de novo
serine synthesis. Additionally, our research indicates that deacetylated PHGDH suppresses the mitochondria-MAVS-IRF3 pathway through its regulatory effect on serine metabolism, leading to decreased IFN-β production and enhanced viral replication. Overall, our findings elucidate the complex interplay between CSFV and serine metabolism, revealing a novel aspect of viral immune evasion through the lens of immune metabolism.

IMPORTANCE
Classical swine fever (CSF) seriously restricts the healthy development of China’s aquaculture industry, and the unclear pathogenic mechanism and pathogenesis of classical swine fever virus (CSFV) are the main obstacle to CSF prevention, control, and purification. Therefore, it is of great significance to explore the molecular mechanism of CSFV and host interplay, to search for the key signaling pathways and target molecules in the host that regulate the replication of CSFV infection, and to elucidate the mechanism of action of host immune dysfunction and immune escape due to CSFV infection for the development of novel CSFV vaccines and drugs. This study reveals the mechanism of serine metabolizing enzyme post-translational modifications and antiviral signaling proteins in the replication of CSFV and enriches the knowledge of CSFV infection and immune metabolism.
Complete genome sequence of
Pseudomonas fluorescens
IMGN2 isolated from undisturbed soil
Authors: Ryu Hyeonmin , Kim Soomin , Kim Yeongjun , Han Jeong A. , Kim Eun Yu , Lee Ho-Seok 
Published: August 2024

ABSTRACT

Here, we report the complete genome sequence of
Pseudomonas fluorescens
IMGN2, highlighting its biocontrol and plant growth-promoting capabilities. The genome analysis reveals genetic features that contribute to its potential in agricultural biotechnology, including genes related to secondary metabolite synthesis and plant-microbe interactions.
The Tectonic Inversion Prediction in Fold-and-Thrust Belts by Using Numerical Modeling
Authors: Zaidi S. F. A. , Ahsan N. 
Published: August 2024

Abstract
This research investigates tectonic inversion in rifted continental margins, specifically focusing on the interaction between foreland sediment deposits and fold-and-thrust belts during orogeny. Using numerical modeling with ANSYS-2023 R1 software and a Maxwell-type viscoelastic rheology, the study explores positive inversion in petroleum basins, revealing insights into the evolution of inverted basins. The research emphasizes the role of pre-existing extensional fault systems in controlling thrust faults, delving into the reactivation of faults and uplift of the hanging wall during tectonic compression. The study highlights diverse structural patterns associated with tectonic inversion in sub-thrust regions of fold-and-thrust belts, including anticlines, back-thrusts, fault propagation folds, pop-up, and an inversion-related fracture pattern. Results demonstrate the critical influence of rheological properties in fault reactivation and deformational styles during tectonic inversion. Comparisons with natural case studies, like the Helvetic nappes in Switzerland, validate the predictive capability of numerical models for tectonic inversion structures in different geological settings, including the Kohat-Potwar Fold and Thrust Belt in Pakistan. We find important of understanding interplay between geological structures and rheological properties for accuracy of predicting evolution of inverted basins. The deeply study of tectonic inversion are extending to optimizing exploration efforts and interpreting structural complexities in petroleum exploration, providing valuable insights for reservoir prediction and fold-and-thrust belt structural evolution.
Transport of critically ill children to paediatric intensive care units in the UK and Ireland: 2013–2022
Authors: Ramnarayan Padmanabhan , Wood Dora , Draper Elizabeth , Palmer Lyn , Feltbower Richard , Buckley Hannah L , Griksaitis Michael J , Lutman Daniel Henry , Kanaris Constantinos , O’Shea Deirdre , Seaton Sarah E 
Published: August 2024

ObjectiveTo explore the trends and changes in the transport of children to paediatric intensive care units (PICUs) between 2013 and 2022.DesignRetrospective analysis of routinely collected data.PatientsChildren transported for care in a PICU in the UK and Ireland aged<16 years.InterventionsNone.Measurements and main resultsThere were 43 058 transports to a PICU involving 36 438 children from 2013 to 2022 with the majority of children requiring only one transport. The number of transports increased from 4131 (2013) to 4792 (2022). Over the study period the percentage of children aged under 1 year who were transported decreased from 50.2% to 45.2% and similarly, the percentage who were invasively ventilated also decreased from 81.1% to 70.2%. Conversely, the use of non-invasive ventilation during transports increased slightly from 4.0% to 7.0%. The percentage of transports where a parent was able to accompany the child increased over time (2013: 66.2% to 2019: 74.9%), although there were reductions due to the COVID-19 pandemic and requirements for social distancing (2020: 52.4%).ConclusionsWe have demonstrated an increased use of specialist paediatric transport services and changes in the PICU population over time. Routine data collection from the transport services provide a means to measure improvements and changes over time in the service provided to critically ill children and young people who need transport to the PICU.
Health And Performance Promotion in Youth (HAPPY) hybrid effectiveness-implementation cluster randomised trial: comparison of two strategies to implement an injury prevention exercise programme in Danish youth handball
Authors: Møller Merete , Nygaard Andersen Lotte , Möller Sören , Kongsted Alice , Juhl Carsten B , Roos Ewa M 
Published: August 2024

ObjectiveTo investigate if a combination of an online and onsite implementation strategy was superior to an online-only strategy in enhancing the use of an injury prevention exercise programme (IPEP) and in reducing the risk of shoulder, knee and ankle injuries in youth community handball players (age 11–17) over a handball season.MethodsIn this 30-week hybrid effectiveness-implementation cluster randomised type 3 study, 20 youth handball clubs were randomly assigned 1:1 to either a combined online and onsite implementation strategy (coach workshop using the health action process approach behaviour change model and health service provider (HSP) support) or an online-only strategy (control group). The primary implementation outcome was coach-reported adherence, measured as the average IPEP exercise usage by the team over 30 weeks. The primary effectiveness outcome was player-reported handball playing time to any new handball-related shoulder, knee and ankle injuries, reported weekly using the Oslo Sports Trauma Research Centre Questionnaire on Health Problems.ResultsWe enrolled 63 coaches (27% women) and 945 players (mean age 14.5 years, 55% girls). Intention-to-treat analyses showed no statistically significant difference between implementation strategies in adherence (between-group difference 1.4, 95% CI −0.5 to 3.4) or in cumulative injury risk (between-group difference 5.5% points, 95% CI −2.2 to 13.1).ConclusionOur findings demonstrate that in youth community handball, a combined online and onsite implementation strategy, including a coach workshop and HSP support, was not superior to an online-only strategy regarding adherence to an IPEP or in reducing shoulder, knee and ankle injury risk.Trial registration numberNCT05294237.