bluuebunny/crossref_metadata_2025_split huggingface dataset:
Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms
Authors: Cui Han , Wang Shuaitao , Fan Shen , Long Hongan , Lin Jinshui , Ding Wei , Zhang Weipeng 
Published: February 2025

ABSTRACT

Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (
Leisingera aquaemixtae
M597,
Roseibium aggregatum
S1616,
Alloyangia pacifica
T6124, and
Sulfitobacter indolifex
W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616–M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.

IMPORTANCE
Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.
A novel regulation on the developmental checkpoint protein Sda that controls sporulation and biofilm formation in
Bacillus subtilis
Authors: He Yinghao , Qin Yuxuan , Greenwich Jennifer , Balaban Samantha , Darcera Migue Van Louis , Gozzi Kevin , Chai Yunrong 
Published: February 2025

ABSTRACT

Biofilm formation by
Bacillus subtilis
is triggered by an unusually simple environmental sensing mechanism. Certain serine codons, the four TCN codons (N for A, T, C, or G), in the gene for the biofilm repressor SinR caused lowered SinR translation and subsequent biofilm induction during transition from exponential to stationary growth. Global ribosome profiling showed that ribosomes pause when translating the four UCN (U for T on the mRNA) serine codons on mRNA, but not the two AGC/AGU serine codons. We proposed a serine codon hierarchy (AGC/AGT vs TCN) in that genes enriched in the TCN serine codons may experience reduced translation efficiency when serine is limited. In this study, we designed an algorithm to score all protein-coding genes in
B. subtilis
NCIB3610 based on the serine codon hierarchy. We generated a short list of 50 genes that could be subject to regulation by this novel mechanism. We further investigated one such gene from the list,
sda
, which encodes a developmental checkpoint protein regulating both sporulation and biofilm formation. We showed that synonymously switching the TCN serine codons to AGC in
sda
led to delayed biofilm formation and sporulation. This engineered strain also outgrew strains with other synonymously substituted
sda
alleles (TCN) in competition assays for biofilm formation and sporulation. Finally, we showed that the AGC serine codon substitutions in
sda
elevated the Sda protein levels. This serine codon hierarchy-based novel signaling mechanism could be exploited by bacteria in adapting to stationary phase and regulating important biological processes.

IMPORTANCE

Genome-wide ribosome profiling in
Bacillus subtilis
shows that under serine limitation, ribosomes pause on the four TCN (N for A, C, G, and T), but not AGC/AGT serine codons, during translation at a global scale. This serine codon hierarchy (AGC/T vs TCN) differentially influences the translation efficiency of genes enriched in certain serine codons. In this study, we designed an algorithm to score all 4,000+ genes in the
B. subtilis
genome and generated a list of 50 genes that could be subject to this novel serine codon hierarchy-mediated regulation. We further investigated one such gene,
sda
, encoding a developmental checkpoint protein. We show that
sda
and cell developments controlled by Sda are also regulated by this novel mechanism.
Evaluating stool microbiome integrity after domestic freezer storage using whole-metagenome sequencing, genome assembly, and antimicrobial resistance gene analysis
Authors: Momo Cabrera Paula , Bokulich Nicholas A. , Zimmermann Petra 
Published: February 2025

ABSTRACT

The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with −80°C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples obtained from 20 children under 4 years of age with the use of shotgun metagenome sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4°C and analyzed within 24 hours, while others were frozen in domestic freezers (below −18°C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition.

IMPORTANCE
Most prior studies on sample storage have relied on amplicon sequencing, which is less applicable to metagenome sequencing—given considerations of contig quality and functional gene detection—and less reliable in representing microbial composition. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been previously investigated. Our findings suggest that stool samples stored in domestic freezers for up to 6 months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.
Mutations leading to ceftolozane/tazobactam and imipenem/cilastatin/relebactam resistance during
in vivo
exposure to ceftazidime/avibactam in
Pseudomonas aeruginosa
Authors: Rapsinski Glenn J. , Rokes Alecia B. , Van Tyne Daria , Cooper Vaughn S. 
Published: February 2025

ABSTRACT

Identifying resistance mechanisms to novel antimicrobials informs treatment strategies during infection and antimicrobial development. Studying resistance that develops during the treatment of an infection can provide the most clinically relevant mutations conferring resistance, but cross-sectional studies frequently identify multiple candidate resistance mutations without resolving the driver mutation. We performed whole-genome sequencing of longitudinal
Pseudomonas aeruginosa
from a patient whose
P. aeruginosa
developed imipenem/cilastatin/relebactam and ceftolozane/tazobactam resistance during ceftazidime/avibactam treatment. This analysis determined new mutations that arose in isolates resistant to both imipenem/cilastatin/relebactam and ceftolozane/tazobactam. Mutations in penicillin-binding protein 3
ftsI,
the MexAB-OprM repressor
nalD
, and a virulence regulator
pvdS
were found in resistant isolates. Importantly, drug efflux was not increased in the resistant isolate compared to the most closely related susceptible isolates. We conclude that mutations in peptidoglycan synthesis genes can alter the efficacy of multiple antimicrobials.

IMPORTANCE

Antibiotic resistance is a significant challenge for physicians trying to treat infections. The development of novel antibiotics to treat resistant infections has not been prioritized for decades, limiting treatment options for infections caused by many high-priority pathogens. Cross-resistance, when one mutation provides resistance to multiple antibiotics, is most problematic. Mutations that cause cross-resistance need to be considered when developing new antibiotics to guide developers toward drugs with different targets, and thus a better likelihood of efficacy. This work was undertaken to determine the mutation that caused resistance to three antibiotics for highly resistant
Pseudomonas aeruginosa
infection treatment while the bacteria were exposed to only one of these agents. The findings provide evidence that drug developers should endeavor to find effective antibiotics with new targets and that medical providers should utilize medications with different mechanisms of action in bacteria that have become resistant to even one of these three agents.
Multiple Self-Healing Squamous Epithelioma and Loeys-Dietz syndrome: a singleTGFBR1variant, two phenotypes in one patient
Authors: Moeris Emilie , Battisti Gladys , Lenne Antoine , Cambier Nicolas 
Published: February 2025

Multiple Self-Healing Squamous Epithelioma of Ferguson-Smith (OMIM 132800) is a syndrome increasing the risk of developing keratoacanthomas, which are locally aggressive skin tumours. Loeys-Dietz syndrome is a connective tissue disease characterised by arterial fragility. There is no increased risk of skin tumours classically described.Both phenotypes have been associated with a different pathogenic variant of theTGFBR1gene involved in the TGFbeta signalling pathway. We present the case of a patient with both phenotypes. This appears to be caused by a single likely pathogenic variant withinTGFBR1: c.1421G>A (p.Cyst474Tyr) in the protein domain of the serine-threonine protein kinase.This is the fourth reported case exhibiting this dual clinical presentation with a single genetic variant in this same region.
Woven EndoBridge (WEB) device used for vertebral artery sacrifice
Authors: Sims Jason J , Khattar Nicolas , Mulpur Bhageeradh , Arthur Adam S 
Published: February 2025

In this case study, we presented a challenging neurovascular intervention where a Woven EndoBridge (WEB) intrasaccular device was used to treat a 4.5 mm ruptured vertebral artery fusiform aneurysm by sacrificing the vessel with great precision. The patient had a dissection of the left vertebral artery at the posterior inferior cerebellar artery (PICA) origin. The WEB device was deployed immediately proximal to the origin of the PICA. After WEB deployment, further stasis and occlusion were achieved with coils. This combination of the WEB device and coils allowed for a precise and controlled sacrifice, ensuring continued filling of the PICA from the contralateral vertebral artery. The outcome of the procedure was successful, as the patient experienced complete vessel occlusion with no adverse effects.This case demonstrates a non-standard use of the WEB device in tandem with coils to treat a ruptured fusiform vertebral artery aneurysm.
Public satisfaction with Healthy China Action Plan implementation: a web-based cross-sectional survey in southwest China
Authors: Chen Wuzhao , Bai Xinyu , Liu Dongyang , Pan Li , Chongsuvivatwong Virasakdi , Chen Yi 
Published: February 2025

ObjectiveThe Healthy China (Guangxi) Action Plan has been in effect for approximately 4 years, with its primary goals being to improve public health and prevent diseases. However, there is limited information available on the community-level public satisfaction with the outcomes of its implementation. Therefore, we intend to conduct an assessment based in southwest China.DesignA population-based, cross-sectional survey was performed between 1 June 2023 and 31 July 2023.SettingCommunity members of all 14 prefecture-level cities within Guangxi, China, during June 2023 to July 2023.ParticipantsA total of 62 4016 participants were included for analysis based on exclusion criteria, with 44.4% aged 18–35 and a male to female ratio of 3:2.Primary outcome measure‘Public satisfaction with the Healthy China (Guangxi) Action Plan implementation’ was measured by the combination of ‘Willingness to join health promotion’ and ‘Satisfaction to overall medical implementation measures and services’ using a structural equation model with a multiple-indicator, multiple-cause approach in R software.ResultsThe study proposed a comprehensive five-factor model to evaluate the public satisfaction with Healthy China (Guangxi) Action Plan implementation. With the mediator of ‘awareness of Healthy China (Guangxi) Action Plan’, health education/promotion demonstrated important effect on overall public satisfaction with Healthy China (Guangxi) Action Plan implementation. Mental health had small but positive effect on the outcomes. High socio-characteristic variables showed negative effects on all latent variables except for the mental health status. All of the effects were statistically significant.ConclusionsUnderstanding the impact of background variables on public satisfaction with Healthy China (Guangxi) Action Plan implementation was crucial, along with considering the sociodemographic traits of participants. This knowledge helped policymakers to develop tailored interventions and strategies.
Assessing the impact of antimicrobial resistance policies on antibiotic use and antimicrobial resistance-associated mortality in children and adults in low and middle-income countries: a global analysis
Authors: Zay Ya Kyaw , Patel Jay , Fink Günther 
Published: February 2025

IntroductionAntimicrobial resistance (AMR) poses a major threat to global health security today. In recent years, many low and middle-income countries (LMICs) have implemented policies to optimise antibiotic use in both formal and informal healthcare settings. However, there is limited evidence on the effectiveness of these national efforts in LMICs.MethodsWe investigated the empirical relationship between national policies aimed at restricting antibiotic use and actual antibiotic consumption in 138 LMICs. Data on national policies were obtained from the Tripartite AMR Country Self-Assessment Survey (TrACSS) as well as from the Global Survey of Experts on AMR (GSEAR). Seven independent variables relating to AMR policies were evaluated. Outcomes included the proportion of children receiving antibiotics for lower respiratory tract infections and diarrhoea (specific to paediatric populations), along with total antibiotic consumption and AMR-associated mortality in general populations.ResultsOur analysis of 138 LMICs found wide variation in antibiotic use between countries and regions. We observed strong evidence of negative association (mean difference MD=−0.150, 95% CI (−0.2593 to –0.0407)) between the presence of regulatory or legislative policies that ban over-the-counter sales of antibiotics and the proportion of children receiving antibiotic drugs for lower respiratory tract infection. Furthermore, stronger AMR governance was associated with reduced total antibiotic consumption at the country level (MD=−1.259, 95% CI (−2.297 to –0.2216)). No associations were found between other policy variables and antibiotic use or mortality.ConclusionThe results presented here suggest that there is some evidence of an empirical relationship between national policies aimed at limiting over-the-counter antibiotic sales and actual antibiotic usage practices. Further policy effectiveness research will be needed to better understand the true impact of government measures. In general, a multifaceted approach will likely be needed to fight AMR and preserve antibiotics’ effectiveness, including evidence-based policies, targeted education and research.
4-1BB agonist targeted to fibroblast activation protein α synergizes with radiotherapy to treat murine breast tumor models
Authors: Garate-Soraluze Eneko , Serrano-Mendioroz Irantzu , Fernández-Rubio Leticia , De Andrea Carlos E , Barrio-Alonso Celia , Herrero Claudia del Pilar , Teijeira Alvaro , Luri-Rey Carlos , Claus Christina , Tanos Tamara , Klein Christian , Umana Pablo , Rullan Antonio , Simón Jon Ander , Collantes María , Sánchez-Mateos Paloma , Melero Ignacio , Rodriguez-Ruiz Maria E 
Published: February 2025

BackgroundIonizing radiation (IR) is a double-edged sword for immunotherapy as it may have both immunosuppressive and immunostimulatory effects. The biological effects of IR on the tumor microenvironment (TME) are a key factor for this balance. Fibroblast activation protein (FAP) is expressed on the surface of cancer-associated fibroblasts (CAF) in many cancer types and its abundance is associated with the poor immune response to immune-checkpoint-blockade in patients. We hypothesized that IR increases FAP expression in CAFs, therefore the combination of IR with targeted immunomodulators such as an agonistic anti-FAP-4-1BBL fusion protein could enhance the immune-mediated antitumoral effects of these treatments.MethodsThe murine transplantable TS/A tumor-cell-line co-engrafted with CAFs was used to investigate increases in FAP expression in tumors following irradiation using immunohistochemistry, real-time polymerase chain reaction (RT-PCR) and multiplex tissue immunofluorescence. One lesion of bilateral tumor-bearing mice was only locally irradiated or combined with weekly injections of the bispecific muFAP-4-1BBL fusion protein (a mouse surrogate for RG7826). Tumor sizes were followed over time and TME was assessed by flow cytometry. Selective monoclonal antibody (mAb)-mediated depletions of immune cell populations, neutralizing interferon alpha/beta receptor 1 (IFNAR-I) IFNAR and interferon (IFN)-γ mAbs and gene-modified mice (4-1BB−/−) were used to delineate the immune cell subsets and mechanisms required for efficacy.67Ga labeled muFAP-4-1BBL tracked by SPECT-CT was used to study biodistribution. In human colorectal carcinoma samples, the inducibility of FAP expression following radiotherapy was explored by multiplex immunofluorescence.ResultsIrradiation of TS/A+CAF tumors in mice showed an increase in FAP levels after local irradiation. A suboptimal radiotherapy regimen in combination with muFAP-4-1BBL attained primary tumor control and measurable abscopal effects. Immune TME landscape analyses showed post-treatment increased infiltration of activated immune cells associated with the combined radioimmunotherapy treatment. Efficacy depended on CD8+T cells, type I IFN, IFN-γ and ability to express 4-1BB. Biodistribution studies of muFAP-4-1BBL indicated enriched tumor targeting to irradiated tumors. Human colorectal cancer samples pre and post irradiation showed enhanced FAP expression after radiotherapy.ConclusionIncreased FAP expression in the TME as a result of radiotherapy can be exploited to target agonist 4-1BB immunotherapy to malignant tumor lesions using an FAP-4-1BBL antibody fusion protein.
Global, regional and national burdens of cardiovascular disease attributable to secondhand smoke from 1990–2019: an age-period-cohort analysis
Authors: Jiang Hong , Liu Zeye , Wei Peijian , Zhang Fengwen , Wang Shouzheng , Ou-yang Wen-Bin , Li Xiaofei , Pan Xiang-Bin 
Published: February 2025

BackgroundOver the past three decades, significant disparities in the global burden of cardiovascular disease (CVD) have been observed, particularly CVD attributed to secondhand smoke. However, a comprehensive understanding of global trends and their interaction with secondhand smoke remains inadequate.MethodsUsing Global Burden of Disease data (1990–2019), an age-period-cohort analysis examined temporal trends in CVD mortality among secondhand smoke-exposed populations, considering age, period and cohort interactions.ResultsOver the 30-year period, the global number of CVD deaths attributed to secondhand smoke increased substantially, from 432.6 thousand in 1990 (95% UI: 357.4–508.3) to 598.5 thousand in 2019 (95% UI: 489.7–713.5), representing a 38.4% increase (95% UI: 26.8%–49.5%). In 2019, CVD accounted for 45.9% of all deaths attributable to secondhand smoke among both sexes globally. Among these CVD deaths, ischaemic heart disease predominated, accounting for 66.4% of cases, compared with stroke. The distribution by sex revealed a slightly lower percentage of males (46.5%) than females (53.5%). Age-period-cohort models show overall global decline in CVD mortality due to secondhand smoke over 30 years, with regional, sex and subtype variations. Notably, a higher Sociodemographic Index (SDI) correlated with a greater reduction in mortality, exhibiting a significant 39.1% decrease in high SDI areas (95% UI: 35.6%–42.3%), in stark contrast to the minimal change observed in low SDI areas (0.1%, 95% UI: −52.4%–62.2%).ConclusionsThis study highlights the importance of considering secondhand smoke as a modifiable CVD risk. Further research is needed to understand disparities in CVD burden across development levels, sexes and subtypes.
Frequency and treatment of venous thromboembolic events in patients with space-occupying brain infarction and decompressive craniectomy
Authors: Dabbagh Alhuda , Mielke Janine , Mühlberg Katja S , Hoffmann Karl Titus , Lindner Dirk , Huber Charlotte , Michalski Dominik , Pelz Johann Otto 
Published: February 2025

IntroductionVenous thromboembolic events (VTEs) like deep vein thrombosis or pulmonary embolism are frequent complications in (neuro) critical ill patients. Anticoagulation for VTE after space-occupying brain infarction is a therapeutic dilemma. The aim of this retrospective study was to investigate the frequency of clinically apparent VTE in patients with acute ischaemic stroke (AIS) due to large vessel occlusion (LVO), its treatment, and the rate of complications.MethodsPatients with first AIS due to LVO were assigned to one of the following groups: space-occupying brain infarction with (1) or without (2) decompressive craniectomy (DC), AIS comprising more than 2/3 (3) or less than 2/3 (4) of the middle cerebral artery territory. Clinically obtained parameters included risk factors for VTE, type of thromboprophylaxis, treatment of VTE and treatment-associated complications.Results15 of 173 (8.7%) patients had a VTE, which was diagnosed 10.9 ± 7.2 days after admission. Patients with a space-occupying brain infarction and DC had significantly more VTE (n=11/63; 17.5%) than patients with a space-occupying brain infarction without DC (0/26; p =0.023) or patients without DC (4/110; 3.6%; p = 0.004). Younger age, DC and cumulative duration of central venous catheter were identified as risk factors for VTE. Only three patients had major bleeding events while being anticoagulated (one asymptomatic cerebral and two extracranial bleedings).DiscussionPatients with space-occupying brain infarction and DC hold a high risk for VTE. Despite extensive infarct size and DC, therapeutic anticoagulation required for VTE appeared to be safe regarding intracranial bleeding complications.