bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term tillage regime structures bacterial carbon assimilation
Authors: Schaedel Marie , Koechli Chantal , Buckley Daniel 
Published: January 2025

AbstractMicrobial growth dynamics are deterministic of the fate of carbon in soil, responsible for the transformation of new carbon inputs and their stabilization on soil surfaces. Bacterial life history strategies are predictive of C substrate assimilation and growth response. High disturbance management practices such as tillage alter microbial community structure but have a poorly described impact on life histories that are central to C metabolism. We conducted a DNA stable isotope probing experiment using soil from a long-term field experiment with a 42-year legacy of no-till or annual moldboard plowing. We predicted that divergent legacies of disturbance would result in bacterial communities with distinct life histories, altering C assimilation dynamics. We incubated soil from each tillage regime with13C-xylose and13C-cellulose, two substrates that are components of plant litter and which differ in bioavailability. We identified 730 bacterial taxa that incorporated the labeled substrates and tracked their abundance in bulk microcosm soil over a 30 day period. Carbon addition rapidly altered bacterial community structure and function, with tilled soils demonstrating lower mineralization rates of each substrate. Xylose-assimilating taxa exhibited significantly lagged growth in tilled soils relative to no-till. We also found a higher number and diversity of late (day 30) cellulose incorporators in no-till soil, suggesting that minimal disturbance resulted in a longer residence time of13C-cellulose in members of the bacterial community. We show that soil management practices shape the path of carbon through bacterial communities by altering dynamic growth responses and secondary incorporation of carbon.HighlightsDNA SIP identified divergent carbon dynamics resulting from tillage legaciesXylose assimilation in plow-till soils was late and decoupled from mineralizationCellulose-C was assimilated later in no-till soils relative to plow-tillGrowth responses of incorporator taxa differ by tillage and explain mineralization
Virus and Cell Specific HMGB1 Secretion and Subepithelial Infiltrate Formation in Adenovirus Keratitis
Authors: Saha Amrita , Islam Mohammad Mirazul , Kumar Rahul , Ismail Ashrafali Mohamed , Garcia Emanuel , Gullapali Rama R , Chodosh James , Rajaiya Jaya 
Published: January 2025

AbstractA highly contagious infection caused by human adenovirus species D (HAdV-D), epidemic keratoconjunctivitis (EKC) results in corneal subepithelial infiltration (SEI) by leukocytes, the hallmark of the infection. To date, the pathogenesis of corneal SEI formation in EKC is unresolved. HMGB1 (high-mobility group box 1 protein) is an alarmin expressed in response to infection and a marker of sepsis. Earlier studies using a different adenovirus species, HAdV-C, showed retention of HMGB1 in the infected cell nucleus by adenovirus protein VII, enabling immune evasion. Here, using HAdV-D we show cell-specific HMGB1 secretion by infected cells, and provide an HAdV-D specific mechanism for SEI formation in EKC. HMGB1 was secreted only upon infection of human corneal epithelial cells, not from other cell types, and only upon infection by HAdV-D types associated with EKC. Acetylated HMGB1 translocation from the nucleus to the cytoplasm, then to the extracellular milieu, was tightly controlled by CRM1 and LAMP1, respectively. Primary stromal cells when stimulated by rHMGB1 expressed proinflammatory chemokines. In a novel 3D culture system in tune with the architecture of the cornea, HMGB1 released by infected corneal epithelial cells induced leukocytic infiltrates either directly and/or indirectly via stimulated stromal cells, which together explains SEI formation in EKC.
Evaluating the Link Between Efflux Pump Expression and Motility Phenotypes inPseudomonas aeruginosaTreated with Virulence Inhibitors
Authors: Lembke Hannah K. , Nauta Kelsie. M. , Hunter Ryan C. , Carlson Erin E. 
Published: January 2025

AbstractAntibiotic resistance continues to rise as a global health threat. Novel anti-virulence strategies diminish the drive for evolutionary pressure, but still hinder a pathogen’s ability to infect a host. Treatment of the highly virulentPseudomonas aeruginosastrain PA14 with virulence inhibitors (R-2 and R-6) elicited widely varying transcriptional profiles. Of interest, expression of a family of resistance-nodulation-division (RND) efflux pumps implicated in the intrinsic drug resistance ofP. aeruginosa, was significantly altered by R-2 and R-6 treatment. While structurally similar, these inhibitors caused differential expression of various RND efflux pumps within the Mex family—R-2 treatment stimulated expression ofmexEF-oprNwhile R-6 treatment led to increasedmexAB-oprMexpression. Further expansion into a small library of virulence inhibitors revealed chemical motifs that trigger increases in RND efflux pump expression. Additionally, activation of these efflux pumps suggests low accumulation of virulence inhibitors in WT PA14. Treatment of an efflux pump-deficient strain with R-2 or R-6 resulted in inhibition of several virulence factors, for example R-2 was found to abolish swimming motility. Collectively, treatment with either R-2 or R-6 gives rise to a convoluted transcriptomic response, confounded by the impact of efflux pump expression on the system. However, understanding the moieties that lead to high expression of the efflux pumps enables further rational design of novel virulence inhibitors that do not cause RND efflux pump activation.SummaryAntibiotic resistance continues to rise across the world. The continued failure of antibiotics to treat infectious disease clearly demonstrates the need for new therapeutics. Small molecule inhibitors of virulence, or the ability of a bacteria to establish and maintain an infection, have showed promise in this area. By reducing virulence, the host immune system can clear the infection on its own and there is less selective pressure on the bacteria, reducing the emergence of resistance.Our work demonstrates a clear link between virulence inhibitors and efflux pump expression. Efflux pumps are critical for bacteria to extrude toxic compounds from their interior. Interestingly, the changes in efflux pump expression can be quite large even with similar molecular structures. Additionally, the repression of efflux expression caused by our virulence inhibitors results in synergy with current antibiotics. This work will allow the future design of virulence inhibitors that do not activate efflux pump expression and therefore, enable high intracellular concentrations.
Isolation of phages infecting the zoonotic pathogenStreptococcus suisreveals novel structural and genomic characteristics
Authors: Osei Emmanuel Kuffour , O’Hea Reuben , Cambillau Christian , Athalye Ankita , Hille Frank , Franz Charles M.A.P. , O’Doherty Áine , Wilson Margaret , Murray Gemma G. R , Weinert Lucy A. , Manzanilla Edgar Garcia , Mahony Jennifer , Kenny John G 
Published: January 2025

AbstractBacteriophage research has experienced a renaissance in recent years, owing to their therapeutic potential and versatility in biotechnology, particularly in combating antibiotic resistant-bacteria along the farm-to-fork continuum. However, certain pathogens remain underexplored as targets for phage therapy, including the zoonotic pathogenStreptococcus suiswhich causes infections in pigs and humans. Despite global efforts, the genome of only one infectiveS. suisphage has been described. Here, we report the isolation of two phages that infectS. suis: Bonnie and Clyde. The phages infect 58% of 100S. suisstrains tested, including representatives of seven different serotypes and thirteen known sequence types from diverse geographical origins. Clyde suppressed bacterial growthin vitrowithin two multi-strain mixes designed to simulate a polyclonalS. suisinfection. Both phages demonstrated stability across various temperatures and pH levels, highlighting their potential to withstand storage conditions and maintain viability in delivery formulations. Genome comparisons revealed that neither phage shares significant nucleotide identity with any cultivated phages in the NCBI database and thereby represent novel species belonging to two distinct novel genera. This study is the first to investigate the adhesion devices ofS. suisinfecting phages. Structure prediction and analysis of adhesion devices with AlphaFold2 revealed two distinct lineages ofS. suisphages:Streptococcus thermophilus-like (Bonnie) andS. suis-like (Clyde). The structural similarities between the adhesion devices of Bonnie andS. thermophilusphages, despite the lack of nucleotide similarity and differing ecological niches, suggest a common ancestor or convergent evolution, highlighting evolutionary links between pathogenic and non-pathogenic streptococcal species. These findings provide valuable insights into the genetic and phenotypic characteristics of phages that can infectS. suis, providing new data for the therapeutic application of phages in a One Health context.
Pluripotency factors enhance the firing efficiency of late DNA replication origins in mouse embryonic stem cells
Authors: Rodriguez-Carballo Eddie , Dionellis Vasilis S. , Ntallis Sotirios G. , Bernasconi Lilia , Keskin Ezgi , Halazonetis Thanos D. 
Published: January 2025

ABSTRACTDNA replication initiates at genomic loci known as origins, which fire according to a spatiotemporal program, still not yet well-defined in mammals. Here, we investigated whether pluripotent mouse embryonic stem cells (mESCs), which proliferate rapidly and have very short G1 phases, have a different spatiotemporal origin firing program than differentiated cells. Using EdU-seq combined with various cell cycle synchronization methods, we identified DNA replication initiation zones (IZs) in mESCs, mesenchymal stem cells and mouse embryo fibroblasts (MEFs). Similar profiles of IZs were present in the early-replicating genomic domains in all cell types. Uniquely in mESCs, we observed, within 1-2 hours of entry into S phase, origin firing at IZs that mapped to the mid and late-replicating genomic domains. This change in the replication timing program, which did not lead to shortening of the length of S phase, was driven by pluripotency transcription factors, notably OCT4, as documented by examining mESCs in which OCT4 expression was transiently suppressed. We propose that pluripotency factors in mESCs bind to IZs at mid and late-replicating genomic domains to enhance chromatin accessibility, which in turn leads to changes in the replication timing program. These results provide an example of how transcription factors control DNA replication in a cell type-specific manner.
Regionalized regulation of actomyosin organization influences cardiomyocyte cell shape changes during chamber curvature formation
Authors: Leerberg Dena M. , Avillion Gabriel B. , Priya Rashmi , Stainier Didier Y.R. , Yelon Deborah 
Published: January 2025

AbstractCardiac chambers emerge from a heart tube that balloons and bends to create expanded ventricular and atrial structures, each containing a convex outer curvature (OC) and a recessed inner curvature (IC). A comprehensive understanding of the cellular and molecular mechanisms underlying the formation of these characteristic curvatures remains lacking. Here, we demonstrate in zebrafish that the initially similar populations of OC and IC ventricular cardiomyocytes diverge in the organization of their actomyosin cytoskeleton and subsequently acquire distinct OC and IC cell shapes. Altering actomyosin dynamics hinders cell shape changes in the OC, and mosaic analyses indicate that actomyosin regulates cardiomyocyte shape in a cell-autonomous manner. Additionally, both blood flow and the transcription factor Tbx5a influence the basal enrichment of actomyosin and squamous cell morphologies in the OC. Together, our findings demonstrate that intrinsic and extrinsic factors intersect to control actomyosin organization in OC cardiomyocytes, which in turn promotes the cell shape changes that drive curvature morphogenesis.
Identification of Dehydrogenase, Hydratase, and Aldolase Required for C17 Propionyl Residue Removal in Steroid Degradation byComamonas testosteroniTA441: Structural and Functional Insights into the (ChsE1-ChsE2)2and (ChsH1-ChsH2MaoC)2-(Ltp2-ChsH2DUF35)2Complexes
Authors: Horinouchi Masae 
Published: January 2025

ABSTRACTBacterial steroid degradation is gaining attention for its diverse roles, such asMycobacterium tuberculosis’s reliance on the degradation of the C17 side chain of cholesterol for survival in host environments. ORF40 to ORF44 ofComamonas testosteroniTA441, previously characterized for its A-, B-, C-, and D-ring cleavage pathways, were hypothesized to correspond to theigroperon ofM. tuberculosis, encoding the dehydrogenase ChsE1E2, hydratase ChsH1H2maoC, and aldolase Ltp2 ChsH2DUF35, responsible for propionyl residue removal in C17 side-chain degradation. However, low amino acid identity between the corresponding enzymes precluded functional assignment without experimental evidence.In this study, we generated gene-disrupted mutants of ORF40–44 and demonstrated that ORF41/44, ORF40/42, and ORF43 encode the dehydrogenase, hydratase, and aldolase, respectively. ORF40 encodes a bifunctional protein comprising MaoC and DUF35 domains. The MaoC domain of ORF40 and the ORF42-encoded protein form the hydratase, while the DUF35 domain is essential for aldolase activity. A mutant expressing ORF40MaoCand ORF40DUF35separately exhibited both hydratase and aldolase activities, suggesting these activities do not require a strictly formed complex of hydratase and aldolase. However, efficient propionyl residue removal appears to depend on the proper formation of each enzymatic complex, including ChsE1E2, ChsH1H2MaoC, and Ltp2ChsH2DUF35; although (ChsE1-ChsE2)2does not form a stable complex with (ChsH1-ChsH2MaoC)2-(Ltp2-ChsH2DUF35)2, some degree of interaction was suggested. AlphaFold-predicted 3D structures of the TA441 enzymes and their complexes revealed striking similarities to those ofM. tuberculosis, despite low amino acid identities. These findings shed light on the structural and functional conservation of bacterial steroid-degrading enzymes.IMPORTANCEResearch on bacterial steroid degradation began over 50 years ago, primarily to produce substrates for steroid drugs. Recently, the role of steroid-degrading bacteria in human health has garnered increasing attention.Comamonas testosteroniTA441 is a prominent model organism for studying aerobic steroid degradation, with its overall pathways for A-, B-, C-, and D-ring cleavage already elucidated. In this study, we identified the mechanism for removing the propionyl residue at C17, a crucial step in degrading steroids with a C17 side chain, such as cholic acid, cholesterol, and other biologically significant compounds in animals and plants. The functions and structures of the identified enzymes show remarkable similarity to those inMycobacterium tuberculosis. These findings suggest that insights gained from TA441 could provide valuable clues for understandingM. tuberculosissteroid metabolism and the broader ecological and health-related implications of bacterial steroid degradation.
Measurement and interpretation of the Harare HIV combination prevention cascade in priority populations: A population survey of adolescent girls and young women and young men in Zimbabwe
Authors: Moorhouse Louisa , Imai-Eaton Jeffrey W. , Dadirai Tawanda , Maswera Rufurwokuda , Museka Tafadzwa , Mandizvidza Phyllis , Dzamatira Freedom , Tsenesa Blessing , Hallett Timothy B , Nyamukapa Constance , Gregson Simon 
Published: January 2025

AbstractIntroductionHIV-negative adolescent girls and young women (AGYW), and male partners, have disproportionately high HIV incidence in many African countries. We used a new HIV Prevention Cascade (HPC) approach to quantify levels of, and barriers to, prevention method use to guide interventions to increase effective uptake of primary HIV prevention.MethodsData from the Manicaland HPC pilot study (2018-19; N=9803) in Zimbabwe were used to measure levels of sexual risk behaviour and construct HPCs for male condom, PrEP (females), VMMC (males) and combination prevention use by HIV-negative sexually-active AGYW (15-24-years) and male partners (15-29-years).Results19% of AGYW (N=1140) and 37% of young men (N=955) who had started sex reported one or more HIV risk behaviour and met the definition of the priority populations for HIV prevention. Of these, 63% of females and 87% of males were motivated to use an HIV prevention method, 28% and 63% had access to a method, and 16% and 53% used a method. Male condoms were the most commonly used prevention method, accounting for 97% of use in females and 55% in males. Barriers to motivation, access and capacity to use were reported for all priority populations and methods. Some barriers were common across HPCs (e.g. lack of risk perception, social unacceptability, and lack of acceptable provision); others were specific to particular prevention methods or priority populations (e.g. lack of availability).ConclusionHIV risk behaviours were commonly reported, but use of prevention methods is low in young people in Manicaland. Population survey measurements of HPCs revealed large gaps in all steps in the cascade (lack of motivation, lack of access and lack of capacity to use prevention) but also provided information on the reasons for these gaps that can aid in designing interventions that reduce new infections.
A Microphysiological Model of Progressive Human Hepatic Insulin Resistance
Authors: Hellen Dominick J. , Ungerleider Jessica , Tevonian Erin , Sphabmixay Pierre , Roy Priyatanu , Lewis Caroline , Jeppesen Jacob , Demozay Damien , Griffith Linda G. 
Published: January 2025

AbstractBackground & AimsHepatic insulin resistance is a fundamental phenomenon observed in both Type 2 diabetes (T2D) and metabolic (dysfunction) associated fatty liver disease (MAFLD). The relative contributions of nutrients, hyperinsulinemia, hormones, inflammation, and other cues are difficult to parsein vivoas they are convoluted by interplay between the local and systemic events. Here, we used a well-established human liver microphysiological system (MPS) to establish a physiologically-relevant insulin-responsive metabolic baseline and probe how primary human hepatocytes respond to controlled perturbations in insulin, glucose, and free fatty acids (FFAs).MethodsReplicate liver MPS were maintained in media with either 200 pM (normal) or 800 pM (T2D) insulin for up to 3 weeks. Conditions of standard glucose (5.5 mM), hyperglycemia (11 mM glucose), normal (20µM) and elevated FFA (100 µM), alone and in combination were used at each insulin concentration, either continuously or reversing back to standard media after 2 weeks of simulated T2D conditions. Hepatic glucose production, activation of signaling pathways, insulin clearance, transcriptome analysis, and intracellular lipid and bile acid accumulation were assessed.ResultsHyperinsulinemia alone induces insulin resistance after one week of exposure, while hyperglycemia and increased FFAs significantly exacerbate this phenotype. Hyperinsulinemia, along with elevated glucose and FFAs, transcriptionally predisposes hepatocytes to insulin resistance through altered metabolic and immune signaling pathways. The phenotypes observed in hyperinsulinemia and nutrient overload are partially reversible upon return to normophysiologic conditions.ConclusionsOur enhancedin vitromodel, replicating multiple aspects of the insulin-resistant condition, offers improved insights into disease mechanisms with relevance to human physiology.Lay SummaryThe many nutritional, hormonal, and systemic inflammatory factors that contribute to the loss of sensitivity to insulin in Type 2 Diabetes and other metabolic disorders are difficult to parse in human patients, and animal models fail to capture all the human dimensions of the relevant biology. We, therefore, developed a microphysiological systems model, involving a microfluidic platform that cultures a simulated human liver for weeks at a time, under controlled nutrient and hormone concentrations, to analyze how the effects of nutrition (glucose and free fatty acids) together with increased insulin cause pathological features seen in human liverin vivo. We found that continually high levels of insulin predispose the liver to some of these features, along with reversal when the nutritional and insulin levels were restored to healthy values.
Re-imagining client learning and knowledge sharing of architectural services through a multi-layered journey map tool
Authors: Yönder Çiğdem , Mertens Audrey , Hamarat Yaprak , Elsen Catherine 
Published: January 2025

PurposeIn this paper, we investigate the current conditions as well as possibilities of a better interaction between architects and user–clients in the Belgian single-family housing context. We specifically focus on issues around client learning and knowledge sharing of architectural services.Design/methodology/approachFollowing the research through design methodology, we report on a co-design process converging towards a multi-layered journey map tool. We analyze the discussions held between architects and user-clients during “Ideation & Design” workshops that led to this specific tool idea, within a broader co-design process context.FindingsIn terms of client learning and knowledge sharing, there is a need for (1) sharing the process knowledge, (2) clarifying responsibilities and missions of both parties and (3) considering different levels of engagement of user-clients. Current ways of interaction around these issues are mostly based on verbal exchanges during meetings and written explanations in contracts. In terms of future expectations, it has been revealed that both parties are in favor of (1) keeping the relationship trustworthy but informal, (2) using visual ways of representing the architectural journey and (3) providing additional “pedagogical” support when needed.Originality/valueOur work not only discusses current practices regarding client learning and knowledge sharing of architectural services but also highlights the future-oriented aspirations of architects and user-clients. It proposes actionable design criteria and a multi-layered journey map tool to support the relationship between architects and user-clients, both transferable to architectural education.