bluuebunny/crossref_metadata_2025_split huggingface dataset:
The NmpRSTU multi-component signaling system of
Myxococcus xanthus
regulates expression of an oxygen utilization regulon
Authors: McAllister Colin T. , Ronk Allison M. , Stenzel Mason J. , Kirby John R. , Bretl Daniel J. 
Published: January 2025

ABSTRACT

Myxococcus xanthus
has numerous two-component signaling systems (TCSs), many of which regulate the complex social behaviors of this soil bacterium. A subset of TCSs consists of NtrC-like response regulators (RRs) and their cognate histidine sensor kinases (SKs). We have previously demonstrated that a multi-component, phosphorelay TCS named NmpRSTU plays a role in
M. xanthus
social motility. NmpRSTU was discovered through a screen that identified mutations in
nmp
genes that restored Type-IV pili-dependent motility to a nonmotile strain. The Nmp pathway begins with the SK NmpU, which is predicted to be active in the presence of oxygen. NmpU phosphorylates another SK, NmpS, a hybrid kinase containing an RR domain and a HisKA-CA domain. These two kinases work in a reciprocal fashion: when NmpU is active, NmpS is inactive, and vice versa. Finally, the phosphorelay culminates in NmpS phosphorylating the NtrC-like RR NmpR. To better understand the role of NmpRSTU in
M. xanthus
physiology, we determined the NmpR regulon by combining
in silico
predictions of the NmpR consensus binding sequence with
in vitro
electromobility shift assays (EMSAs) and
in vivo
transcriptional reporters. We identified several NmpR-dependent, upregulated genes likely to be important in oxygen utilization. Additionally, we demonstrate NmpRSTU plays a role in fruiting body development, suggesting a role for oxygen sensing in this behavior. We propose that NmpRSTU senses oxygen-limiting conditions, and NmpR upregulates genes associated with optimal utilization of that oxygen. This may be necessary for
M. xanthus
physiology and behaviors in the highly dynamic soil where oxygen concentrations vary dramatically.

IMPORTANCE

Bacteria use two-component signaling systems (TCSs) to respond to a multitude of environmental signals and subsequently regulate complex cellular physiology and behaviors.
Myxococcus xanthus
is a ubiquitous soil bacterium that encodes numerous two-component systems to respond to the conditions of its soil environment and coordinate multicellular behaviors such as coordinated motility, microbial predation, fruiting body development, and sporulation. To better understand how this bacterium uses a two-component system that has been linked to the sensing of oxygen concentrations, NmpRSTU, we determined the gene regulatory network of this system. We identified several genes regulated by NmpR that are likely important in oxygen utilization and for the
M. xanthus
response to varied oxygen concentrations in the dynamic soil environment.
Flow virometry: recent advancements, best practices, and future frontiers
Authors: Fernandes Claire , Persaud Arvin T. , Chaphekhar Deepa , Burnie Jonathan , Belanger Carolyn , Tang Vera A. , Guzzo Christina 
Published: January 2025

ABSTRACT

The imperative for developing robust tools to detect, analyze, and characterize viruses has become increasingly evident as they continue to threaten human health. In this review, we focus on recent advancements in studying human viruses with flow virometry (FV), an emerging technique that has gained considerable momentum over the past 5 years. These advancements include the application of FV in viral surface phenotyping, viral protein functionality, virus sorting, vaccine development, and diagnostics. With examples illustrated using primary data from our recent studies, we demonstrate that FV is a powerful yet underutilized methodology that, when employed with best practices and experimental rigor, can be highly valuable for studying individual virion heterogeneity, virus phenotypes, and virus-antibody interactions. In this review, we also address the current challenges when performing FV studies, propose strategies to overcome these obstacles, and outline best practices for both new and experienced researchers. Finally, we discuss the promising future prospects of FV within the broader context of virology research.
Extracellular vesicles in malaria: proteomics insights,
in vitro
and
in vivo
studies indicate the need for transitioning to natural human infections
Authors: Sima Núria , Ayllon-Hermida Alberto , Fernández-Becerra Carmen , del Portillo Hernando A. 
Published: January 2025

ABSTRACT

Globally, an estimated 2.1 billion malaria cases and 11.7 million malaria deaths were averted in the period 2000–2022. Noticeably, despite effective control measurements, in 2022 there were an estimated 249 million malaria cases in 85 malaria-endemic countries and an increase of 5 million cases compared with 2021. Further understanding the biology, epidemiology, and pathogenesis of human malaria is therefore essential for achieving malaria elimination. Extracellular vesicles (EVs) are membrane-enclosed nanoparticles pivotal in intercellular communication and secreted by all cell types. Here, we will review what is currently known about EVs in malaria, from biogenesis and cargo to molecular insights of pathophysiology. Of relevance, a meta-analysis of proteomics cargo, and comparisons between
in vitro
and
in vivo
human studies revealed striking differences with those few studies reported from patients. Thus, indicating the need for rigor standardization of methodologies and for transitioning to human infections to elucidate their physiological role. We conclude with a focus on translational aspects in diagnosis and vaccine development and highlight key gaps in the knowledge of EVs in malaria research.
Coding-complete genome sequence of a GI-13 infectious bronchitis virus from commercial chicken in India
Authors: Kariithi Henry M. , Volkening Jeremy D. , Afonso Claudio L. , Helmy Mohamed , Chaudhari Pushparaj P. , Decanini Eduardo L. 
Published: January 2025

ABSTRACT

Infectious bronchitis virus (IBV) causes a highly contagious, acute upper respiratory disease in chickens characterized by nasal discharge, coughing, and rales. Here, the complete genome sequence of a recombinant GI-13 IBV strain ck/IN/A2332039-001/24 was sequenced from a choanal sample of a commercial broiler chicken in India using nontargeted next-generation sequencing.
Bioenergetic trade-offs can reveal the path to superior microbial CO
2
fixation pathways
Authors: Taha Ahmed , Patón Mauricio , Rodríguez Jorge 
Published: January 2025

ABSTRACT

A comprehensive optimization of known prokaryotic autotrophic carbon dioxide (CO
2
) fixation pathways is presented that evaluates all their possible variants under different environmental conditions. This was achieved through a computational methodology recently developed that considers the trade-offs between energy efficiency (yield) and growth rate, allowing us to evaluate candidate metabolic modifications
in silico
for microbial conversions. The results revealed the superior configurations in terms of both yield (efficiency) and rate (driving force). The pathways from anaerobic organisms appear to fix carbon at lower net ATP cost than those found in aerobic organisms, and the reverse TCA cycle pathway shows the lowest overall energy cost and maximum adaptability across a broad range of CO
2
and electron donor (H
2
) concentrations. The reverse tricarboxylic acid cycle and Wood-Ljungdahl pathways appear highly efficient under a broad range of conditions, while the 3-hydroxypropionate 4-hydroxybutyrate cycle and the 3-hydroxypropionate bicycle appear capable of generating large thermodynamic driving forces at only moderate ATP yield losses.

IMPORTANCE
Biotechnology can lead to cost-effective processes for capturing carbon dioxide using the natural or genetically engineered metabolic capabilities of microorganisms. However, introducing desirable genetic modifications into microbial strains without compromising their fitness (growth yield and rate) during industrial-scale cultivation remains a challenge. The approach and results presented can guide optimal pathway configurations for enhanced prokaryotic carbon fixation through metabolic engineering. By aligning strain modifications with these theoretically revealed near-optimal pathway configurations, we can optimally engineer strains of good fitness under open culture industrial-scale conditions.
Rapid, sensitive, and visible RPA-LFD assay for BoHV-1 and BoHV-5
Authors: Wu Yue , Zhang Wenci , Yi Chenyang , He Kuijing , Hu Changmin , Ye Guishan , Zhang Anding 
Published: January 2025

ABSTRACT

Bovine herpesvirus (BoHV) infection poses a significant threat to the healthy development of the cattle industry. BoHV-1 primarily causes infectious bovine rhinotracheitis, while BoHV-5 is associated with bovine necrotic meningoencephalitis. These two pathogens not only exhibit a high correlation in antigenicity and genetic background but, more importantly, can establish latent infections within the bovine ganglion. Therefore, establishing a rapid and convenient pathogen detection method for BoHV-1 and BoHV-5 is crucial for early diagnosis, epidemic monitoring, and minimizing economic losses. In this study, utilizing the conserved sequences of BoHV-1 and BoHV-5 as targets, we developed a rapid and visually accessible recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) assay suitable for on-site detection. This method enables visual detection within 30 min for clinical samples containing as little as 1 tissue culture infectious dose 50 (TCID
50
) and performs comparably to qPCR, with slightly lower sensitivity. The findings of this research offer new insights for early clinical detection and the control of BoHV-1 and BoHV-5 infections.

IMPORTANCE

Bovine herpesvirus (BoHV), a significant respiratory pathogen in cattle, is widely prevalent worldwide, posing a substantial economic threat to the cattle industry. In this study, we have developed a rapid on-site detection method for BoHV, termed RPA-LFD, which can carry out pathogen detection with a sensitivity of no less than 1 TCID
50
within 30 min. When combined with screening, isolation, and culling measures, this approach can effectively eliminate the sources of BoHV infection, providing a scientifically feasible solution for BoHV prevention and control.
Approaches to the Formation of the Key 2-Oxabicyclo[3.3.0]octan-3-one Precursor of Galiellalactone
Authors: Gimazetdinov A. M. , Zagitov V. V. , Makaev Z. R. 
Published: January 2025

Abstract
New vicinal all-cis-trisubstituted derivatives of cyclopentane- and cyclopentenetriols were synthesized.
Topical brinzolamide-induced ciliary body effusion with secondary angle closure and myopic shift
Authors: Guymer Chelsea , Galanopoulos Anna 
Published: January 2025

Here, we describe a rare case of drug-induced unilateral ciliary body effusion precipitated by topical brinzolamide, presenting acutely with pain, angle closure and myopic shift.Ciliary body effusion was suspected clinically and confirmed by ultrasound biomicroscopy. Brinzolamide was ceased, atropine instilled and the ciliary body effusion promptly resolved without need for further treatment. Brinzolamide is a sulfonamide-derived carbonic anhydrase inhibitor (CAI) commonly used in the treatment of glaucoma. Sulfite derivates can rarely cause ciliary and suprachoroidal effusions, so if ocular pain or visual changes develop, these need to be promptly assessed.
Age- and sex-specific incidence rates and future projections for hip fractures in Zimbabwe
Authors: Wilson Hannah , Manyanga Tadios , Burton Anya , Mushayavanhu Prudance , Chipanga Joseph , Hawley Samuel , Ward Kate A , Graham Simon , Masters James , Bandason Tsitsi , Costa Matthew L , Ndekwere Munyaradzi , Ferrand Rashida A , Gregson Celia L 
Published: January 2025

IntroductionPopulation ageing in Africa is increasing healthcare demands. Hip fractures require multidisciplinary care and are considered an indicator condition for age-related health services. We aimed to estimate current hip fracture incidence in Zimbabwe, compare rates against other regional estimates and estimate future fracture numbers.MethodsAll hip fracture cases in adults aged ≥40 years, presenting to any hospital in Harare over 2 years, were identified. From this, age- and sex-specific hip fracture incidence rates per 100 000 person-years were estimated using 2022 Zimbabwean Census data and compared with South African and Botswanan estimates. Furthermore, using the United Nations population projections, future hip fracture numbers were estimated to 2052 for Zimbabwe.ResultsIn 2022, 1 83 312 women and 1 79 212 men aged ≥40 years were living in Harare (14.9% of the city’s population). Over 2 years 243 hip fracture cases, 133 (54.7%) female, mean (SD) age 71.2 (15.9) years, were identified. Most presented to public hospitals (202 [83.1%]) and were fragility hip fractures (211 [86.8%]); high-impact trauma (eg, traffic accidents) was more common in younger men. Presentation delays of >2 weeks were common (37.4%). Incidence rates for adults aged ≥40 years in Harare (observed) and Zimbabwe (estimated) were 33.5 and 53.8/100 000 person-years, respectively. Over age 50, rates increased with age, with the highest rates seen in women aged ≥85 years (704/100 000 person-years). Age-standardised hip fracture incidence rates are broadly comparable between Zimbabwe, Botswana and Black South Africans in those aged 40–69 years; thereafter, rates in Zimbabwean women and men exceed those in Botswana and South Africa. Across Zimbabwe, the number of hip fractures occurring annually is expected to increase more than 2.5-fold from 1709 in 2022 to 4414 by 2052.ConclusionIn Zimbabwe, most hip fractures in adults ≥50 years are fragility fractures, consistent with age-associated osteoporosis; incidence rates exceed those previously reported regionally. Demands on already challenged healthcare systems will increase.
Adverse childhood experiences and perceived body size across the life course: a longitudinal study using data from the Canadian Longitudinal Study on Aging (CLSA)
Authors: De Rubeis Vanessa , Gonzalez Andrea , Griffith Lauren , Tarride Jean-Eric , Anderson Laura N 
Published: January 2025

BackgroundEarly life adversity has long-term effects; however, the influence on changes in body size across the life course is not well understood. Objectives of this study were to define trajectories of body size across the life course and to evaluate the association between adverse childhood experiences (ACEs) and perceived life course body size trajectories.MethodsA longitudinal study using data from the Canadian Longitudinal Study on Aging (CLSA) was conducted (n=11 830). Adults aged 49–93 were asked to recall eight ACEs and their perceived body size at ages 25, 45, 55, 65 and current using pictograms. Body size trajectories were identified using latent class growth mixture modelling. Multinomial logistic regression was used to estimate ORs and 95% CIs for the association between ACEs and perceived body size trajectories. Effect modification by sex was explored.ResultsSix distinct life course body size trajectories were identified: consistently low (9.7%), consistently mid-size (24.7%), moderate increase (37.4%), strong increase (14.7%), decline (4.9%) and consistently high (8.6%). High ACE exposure, compared with none, was associated with increased odds of the strong increase (OR: 1.49; 95% CI: 1.21 to 1.83) and consistently high (OR: 1.36; 95% CI: 1.08 to 1.73) body size trajectories, compared with the moderate-increase trajectory. For females, there was a strong association for those who reported 4–8 ACEs with the consistently high trajectory (OR: 1.70; 95% CI: 1.24 to 2.34) but no association for males (OR: 0.99; 95% CI: 0.69 to 1.41).DiscussionDistinct patterns of body size throughout the life course exist. ACEs are associated with trajectories that are characterised by obesity incidence in both early and later life.
Fasting-mimicking diet-enrichedBifidobacterium pseudolongumsuppresses colorectal cancer by inducing memory CD8+T cells
Authors: Nan Ke , Zhong Ziwen , Yue Ying , Shen Yang , Zhang Hao , Wang Zhiqiang , Zhuma Kameina , Yu Baichao , Fu Ying , Wang Luman , Sun Xingfeng , Qu Mengdi , Chen Zhaoyuan , Guo Miaomiao , Zhang Jie , Chu Yiwei , Liu Ronghua , Miao Changhong 
Published: January 2025

BackgroundFasting-mimicking diet (FMD) boosts the antitumour immune response in patients with colorectal cancer (CRC). The gut microbiota is a key host immunity regulator, affecting physiological homeostasis and disease pathogenesis.ObjectiveWe aimed to investigate how FMD protects against CRC via gut microbiota modulation.DesignWe assessed probiotic species enrichment in FMD-treated CRC mice using faecal metagenomic sequencing. The candidate species were verified in antibiotic-treated conventional and germ-free mouse models. Immune landscape alterations were evaluated using single-cell RNA sequencing and multicolour flow cytometry. The microbiota-derived antitumour metabolites were identified using metabolomic profiling.ResultsFaecal metagenomic profiling revealedBifidobacterium pseudolongumenrichment in FMD-treated CRC mice.B. pseudolongummediates the FMD antitumour effects by increasing the tissue-resident memory CD8+T-cell (TRM) population in CRC mice. The level of L-arginine, aB. pseudolongumfunctional metabolite, increased in FMD-treated CRC mice; furthermore, L-arginine induced the TRM phenotype in vivo and in vitro. Mechanistically, L-arginine is transported by the solute carrier family 7-member 1 (SLC7A1) receptor in CD8+T cells. Both FMD andB. pseudolongumimproved anti-CTLA-4 efficacy in the orthotopic mouse CRC model. In FMD-treated patients with CRC, the CD8+TRM cell number increased asB. pseudolongumand L-arginine accumulated. The abundance of CD8+TRM cells andB. pseudolongumwas associated with a better prognosis in patients with CRC.ConclusionB. pseudolongumcontributes to the FMD antitumour effects in CRC by producing L-arginine. This promotes CD8+T-cell differentiation into memory cells.B. pseudolongumadministration is a potential CRC therapeutic strategy.
Measuring Chern–Simons level k by braiding $$SU(2)_k$$ anyons
Authors: Belov Artem , Morozov Andrey 
Published: January 2025

Abstract
Chern–Simons theory in application to the quantum computing is actively developing at the present. However, most discussed are the questions of using materials with known parameters and building corresponding quantum gates and algorithms. In this paper we discuss opposite problem of finding Chern–Simons level k in the unknown material. For this purpose, we use the previously derived braiding rules for Chern–Simons

$$SU(2)_k$$

S
U

(
2
)

k

anyons. Using certain operations (turnarounds) on three anyons, one can measure probabilities of annihilation of pairs of anyons, which depend on the parameter of the theory. Therefore, Chern–Simons level k can be found from such an experiment. It is implied that anyons additionally possess certain properties which are required for topological quantum computations.
A comprehensive analysis of stable configurations of nonrotating BTZ-ModMax thin-shell wormholes
Authors: Javed Faisal , Waseem Arfa , Sadiq Sobia , Mustafa G. 
Published: January 2025

Abstract
This paper investigates the characteristics and stability of nonrotating BTZ-ModMax thin-shell wormholes, emphasizing the interaction between spacetime structure and black hole parameters. The locality of the event horizon is substantially affected by the ModMax parameter

$$\xi $$

ξ

and the horizon shifting inward by increasing the ModMax parameter. We examine that enhancing the charge of a black hole results in an extension of the horizon radius which shows the intricate interplay between charge and geometry. Here, we use different types of matter distribution characterized by distinct equations of state. It is noted that the thin-shell wormhole configurations containing quintessence-like matter have more stability, whereas configurations with phantom energy demonstrate unstable behavior. Our stability analysis reveals that thin-shell wormholes exhibit increased stability with higher values of charge, whereas larger cosmological constants diminish stability regions. Moreover, the generalized Chaplygin gas results in unstable configurations, underscoring the significance of the matter type in ascertaining wormhole stability. These findings deepen our comprehension of thin-shell wormholes and create new possibilities for future inquiry in theoretical physics.
VAX014 Activates Tumor-Intrinsic STING and RIG-I to Promote the Development of Antitumor Immunity
Authors: Nelson Kinsey L. , Reil Katherine A. , Tsuji Shingo , Parikh Amanda M. , Robinson Mikella , House Carrie D. , McGuire Kathleen L. , Giacalone Matthew J. 
Published: January 2025

Abstract
In situ immunization (ISI) has emerged as a promising approach to bolster early phases of the cancer immunity cycle through improved T-cell priming. One class of ISI agents, oncolytic viruses (OV), has demonstrated clinical activity, but overall benefit remains limited. Mounting evidence suggests that due to their inherent vulnerability to antiviral effects of type I IFN, OVs have limited activity in solid tumors expressing stimulator of interferon genes (STING) and/or retinoic acid–inducible gene I (RIG-I). Here, using a combination of pharmacologic, genetic, and in vivo approaches, we demonstrate that VAX014, a bacterial minicell–based oncolytic ISI agent, activates both STING and RIG-I and leverages this activity to work best in STING-positive and/or RIG-I–positive tumors. Intratumoral treatment of established syngeneic tumors expressing STING and RIG-I with VAX014 resulted in 100% tumor clearance in two mouse models. Antitumor activity of VAX014 was shown to be dependent on both tumor-intrinsic STING and RIG-I with additive activity stemming from host-intrinsic STING. Analysis of human solid tumor datasets demonstrated STING and RIG-I co-expression is prevalent in solid tumors and associates with clinical benefit in many indications, particularly those most amenable to intratumoral administration. These collective findings differentiate VAX014 from OVs by elucidating the ability of this agent to elicit antitumor activity in STING-positive and/or RIG-I–positive solid tumors and provide evidence that STING/RIG-I agonism is part of VAX014’s mechanism of action. Taken together, this work supports the ongoing clinical investigation of VAX014 treatment as an alternative to OV therapy in patients with solid tumors.