Mutations Research Articles

City as a filter: urban density affects taxonomic and functional diversity of foliage dwelling spiders

ContextUrbanization affects landscape structure, functions and local environmental conditions, with major impacts on biodiversity. An evaluation of its effects on biodiversity, including both taxonomic and functional diversity, is thus compelling, with a specific focus on taxonomic groups providing fundamental ecosystem services. Spiders are ideal biological models for urban ecology studies because they are renowned bioindicators and can be found abundantly along urbanization gradients.ObjectivesIn this work, we aim at evaluating the filtering role exerted by urbanization at landscape scale on foliage-dwelling spider communities both at functional and taxonomic level.MethodsWe assessed the response of foliage-dwelling spiders to urbanization in Torino (NW-Italy), by sampling their communities in urban parks along an urbanization gradient and in a control area located in a nearby natural park. We tested their response in terms of taxonomic and functional diversity to urban density and six landscape metrics. Results of statistical models (GLMMs) were used to predict values of the current biodiversity in the city and its values under different future scenarios of urbanization (i.e. 2040, 2050).ResultsSpider abundance and species richness decreased in the city compared to the control area and along the urbanization gradient. Variation in the community composition was mostly due to species replacement (67%) within the control area, and to species loss in the urban area (62%). This pattern was mostly due to the loss of specialized foraging guilds, such as pollinator-feeding spiders. Functional dissimilarity among samples within the urban area was mostly explained by functional loss (69%), suggesting an environmental filter favoring species preadapted to urban conditions. By projecting biodiversity measures in two “greener city” scenarios, we identified 8 priority areas in the city where management actions should be implemented.ConclusionsOur findings underscore the role of urbanization in shaping spider communities, favoring generalist species and specific functional traits. The prediction on future scenarios proved to be useful to identify areas where increasing the surface of urban parks may contribute most effectively to spider biodiversity.

In vitro activity and genomic characterization of KPC-producing Klebsiella pneumoniae clinical blood culture isolates resistant to ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam: an Italian nationwide multicentre observational study (2022-23).

To evaluate the in vitro activity of ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam and comparators against KPC-producing Klebsiella pneumoniae (KPC-Kp) clinical isolates collected from a multicentre study in Italy (2022-23) and genomic characterization of the molecular mechanisms causing resistance. Consecutive KPC-Kp isolates from blood cultures (n = 264) were collected from 14 hospital centres in the period 2022-23. Antimicrobial susceptibility testing was performed using broth microdilution. WGS was used to investigate KPC-Kp strains resistant to the new approved β-lactam/β-lactam inhibitor combinations (BLICs). Overall, meropenem/vaborbactam (95.1% susceptible by EUCAST and 93.9% susceptible by CLSI; MIC50 = 0.5 mg/L; MIC90 = 4 mg/L) and imipenem/relebactam (97% susceptible by EUCAST and 92.8% susceptible by CLSI; MIC50 = 0.25 mg/L; MIC90 = 0.5 mg/L) showed similar activity, followed by ceftazidime/avibactam (93.9% susceptible by both EUCAST and CLSI; MIC50 = 2 mg/L; MIC90 = 8 mg/L). Ten out of 13 (76.9%) KPC-Kp resistant to ceftazidime/avibactam carried a blaKPC variant including blaKPC-31, blaKPC-205, blaKPC-203 and blaKPC-93. Among KPC-Kp resistant to meropenem/vaborbactam and imipenem/relebactam, 90.9% (10/11) and 80% (4/5) harboured a WT carbapenemase (i.e. blaKPC-2 or blaKPC-3), respectively. All strains resistant to meropenem/vaborbactam and/or imipenem/relebactam carried truncated OmpK35 and/or mutated (ins135GD) OmpK36. New BLICs were shown to be the most widely active therapeutic option against KPC-Kp clinical isolates collected in Italy. Ceftazidime/avibactam resistance is mainly driven by the expression of KPC variants, whereas the loss of function of the OmpK35 and OmpK36 porins appears to play a key but not exclusive role in the development of meropenem/vaborbactam and/or imipenem/relebactam resistance.

SiRNA silencing and hypoxia challenge indicate that the function of common carp (Cyprinus carpio) hif-1αb genes are tightly linked to hif-1αa and hif-3α genes

BackgroundFishes are susceptible to hypoxia stress, while the common carp is known for its high tolerance to hypoxia. The hypoxia-inducible factor (HIF) pathway directly regulates the cell’s response to hypoxia. Still, it is currently unknown which members of the hif-α genes are present in common carp and their specific functions.ResultsIn this study, we found that the hif-1α, hif-2α, and hif-3α genes of common carp all contained twice the number of copies of their orthologs in zebrafish. Common carp has four copies of the hif-1α gene, of which the two hif-1αa genes were expressed at low levels in the vast majority of tissues, while the two hif-1αb genes were expressed at high levels in multiple tissues. We silenced the two hif-1αb genes using chitosan nanoparticles (CSNPs) carrying siRNA and subjected two groups to hypoxic stress. Transcriptome sequencing results show that whether under normoxia or hypoxia, the number of differentially expressed genes (DEGs) caused by silencing the hif-1αb genes in the heart exceeds 1,000, far more than the number of DEGs in the gills or brain. GO enrichment and KEGG enrichment showed that DEGs in the heart were mainly related to immune function and myocardial contraction. DEGs in the gills and brain also enriched many immune-related terms, and some DEGs in the gills were related to iron metabolism and erythropoiesis. Among the paralogs, the two hif-1αa genes were most obviously up-regulated under normoxia, while the hif-3α genes were most obviously up-regulated under hypoxia. We did not find any downstream genes of the HIF pathway that were specifically regulated by the hif-1αb genes.ConclusionsThe main effect site of the common carp hif-1αb genes is the heart, and their main functions are to regulate immune response and myocardial contraction. Their functions are partially redundant with the hif-1αa genes and hif-3α genes. When their expressions are inhibited, the expression of hif-1αa genes or hif-3α genes would be up-regulated in specific contexts, thereby compensating for their loss of function. The downstream genes of the HIF pathway in common carp may be generally regulated by multiple hif-α genes.

Understanding Bacterial Resistance to Heavy Metals and Nanoparticles: Mechanisms, Implications, and Challenges.

Antimicrobial resistance is a global health problem as it contributes to high mortality rates in several infectious diseases. To address this issue, engineered nanoparticles/nano-formulations of antibiotics have emerged as a promising strategy. Nanoparticles are typically defined as materials with dimensions up to 100nm and are made of different materials such as inorganic particles, lipids, polymers, etc. They are widely dispersed in the environment through various consumer products, and their clinical applications are diverse, ranging from contrast agents in imaging to carriers for gene and drug delivery. Nanoparticles can also act as antimicrobial agents either on their own or in combination with traditional antibiotics to produce synergistic effects, earning them the label of "next-generation therapeutics." They have also shown great effectiveness against multidrug-resistant pathogens responsible for nosocomial infections. However, overexposure or prolonged exposure to sublethal doses of nanoparticles can promote the development of resistance in human pathogens. The resistance can arise from various factors such as genetic mutation, horizontal gene transfer, production of reactive oxygen species, changes in the outer membrane of bacteria, efflux-induced resistance, cross-resistance from intrinsic antibiotic resistance determinants, plasmid-mediated resistance, and many more. Continuous exposure to nanoparticles can also transform an antibiotic-susceptible bacterial pathogen into multidrug resistance. Considering all these, the current review focuses on the mode of action of different heavy metals and nanoparticles and possible mechanisms through which bacteria attain resistance towards these heavy metals and nanoparticles.

A chromosome-scale reference genome of the Banna miniature inbred pig

The Banna miniature inbred pig (BN) is an intensively inbred line for biomedical research and xenotransplantation due to its low individual variation and stable genetic background. Although it is originated from the Diannan miniature pig (DN), substantial genetic changes have actually occurred. However, the lack of a BN reference genome has limited studies on the complete genomic architecture and utilization as a biomedical model. Here, we present a high-quality genome for BN using PacBio HiFi and Hi-C sequencing technologies, with a total length of 2.66 Gb, a scaffold N50 of 143.60 Mb, and 97.59% of the sequences anchored to chromosomes. Its BUSCO score is 96.30%, higher than porcine reference assembly and DN. The genome contains 48.49% of repeats, 19,756 protein-coding genes, and 7,207 non-coding RNAs according to our annotation. The OMArk score shows a proteome completeness and consistency of 99.58% and 93.62%, respectively. These findings indicate that the chromosome-scale genome of BN provides a valuable resource for studying the genetic basis of inbreeding, facilitating further research and clinical applications.

A hybrid epithelial-mesenchymal transition program enables basal epithelial cells to bypass stress-induced stasis and contributes to a metaplastic breast cancer progenitor state

BackgroundHuman mammary epithelial cell (HMEC) cultures encounter a stress-associated barrier termed stasis, during which most cells adopt a senescence-like phenotype. From these cultures, rare variants emerge from the basal epithelial population, re-initiating growth. Variants exhibit pre-malignant properties, including an aberrant epigenetic program that enables continued proliferation and acquisition of genetic changes. Following oncogenic transformation, variants produce tumors that recapitulate the histopathological characteristics of metaplastic breast cancer (MBC), a rare and aggressive subtype marked by the differentiation of neoplastic epithelium into squamous and mesenchymal elements.MethodsUsing a serum-free HMEC culture system, we probed the capacity for phenotypic plasticity inherent to basal epithelial cell populations from human breast tissue as they navigated stasis and emerged as variant populations.ResultsWe observed robust activation of a TGF-β-dependent epithelial-mesenchymal transition (EMT) program in basal epithelial cells during stasis, followed by subsequent attenuation of this program in emerging variants. Inhibition of the TGF-β pathway or depleting the EMT regulators Snail or Slug allowed basal epithelial cells to collectively bypass stasis, demonstrating that cellular dysfunction and arrest resulting from TGF-β and EMT activation are central to this in vitro barrier. The spontaneous emergence of variants from stasis cultures was associated with a restricted EMT trajectory, characterized by the stabilization of hybrid EMT states associated with greater proliferative capacity, rather than progressing to a complete mesenchymal state characterized by irreversible growth arrest. Epigenetic mechanisms, which contributed to the dysregulated growth control characteristic of the variant phenotype, also contributed to the stability of the hybrid EMT program in variants. By overcoming the cellular dysfunction and growth arrest resulting from TGF-β and complete EMT, variants exhibited a higher oncogenic transformation efficiency compared to pre-stasis basal epithelial cells. Inhibiting the TGF-β pathway prior to stasis significantly reduced EMT in the basal epithelial population, alleviated selective pressure driving variant emergence, and also enhanced oncogenic transformation efficiency, resulting in tumors with markedly diminished metaplastic differentiation.ConclusionsThis study reveals how an epigenetic program governs basal epithelial cell fate decisions and contributes to the development of MBC progenitors by restricting access to terminal mesenchymal states that induce growth arrest and, instead, favoring hybrid EMT states with enhanced tumorigenic potential.

Effect of Preoperative Body Composition on Postoperative Anastomotic Leakage in Oncological Ivor Lewis Esophagectomy—A Retrospective Cohort Study

Background: Surgery for esophageal cancer has an associated high rate of postoperative complications such as anastomotic leakage (AL) and fistulas. Pre-operative sarcopenia as a loss of skeletal muscle mass and function is identified as a potential prognostic factor in determining the outcomes of oncological surgical resections for esophageal cancers. In this study, we evaluated the impact of body composition on postoperative complications in esophageal cancer surgery. Methods: In this cohort study, we analyzed patients’ body composition at the level of the third lumbar vertebra on CT scans before Ivor Lewis resections for esophageal cancers between January 2015 and December 2022. Patients with a skeletal muscle index (SMI) ≤ 38.5 cm2/m2 in women and ≤52.4 cm2/m2 in men were classified as sarcopenic. Postoperative complications were categorized following the Dindo–Clavien classification and included AL, postoperative pneumonia, length of hospital stay, and failure-to-rescue which were compared between the sarcopenic and non-sarcopenic patients. Results: From a group of 111 patients with Ivor Lewis esophagectomy, 70 patients (63.1%) were classified as sarcopenic based on the SMI and the previously published gender-specific cut-off values. AL occurred at 12.6% (5.6% in adenocarcinoma). Within the whole cohort, patients with AL had a significantly low SMI of 43.487 ± 8.088 vs. 48.668 ± 7.514; p = 0.012. Additionally, the SMI showed a negative correlation to the length of postoperative hospital stay (r = −0.204; p = 0.032; N = 111). The failure-to-rescue rate was higher in the group of sarcopenic patients (12.8% vs. 8%). Conclusions: Our data showed a correlation between SMI and AL. This effect could not be seen in gender-specific SMI. This study showed a lower failure-to-rescue rate in non-sarcopenic patients after Ivor Lewis esophagectomy. These findings underscore the crucial role of determining the preoperative nutritional and body composition status as measured by the preoperative CT scans.

GALNTL5, which is restricted to mouse spermatids, impairs endoplasmic reticulum (ER) function through direct interaction with ER chaperone proteins

Polypeptide N-acetylgalactosaminyltransferase-like protein 5 (GALNTL5) was identified as a pp-GalNAc-T family gene. Nevertheless, GALNTL5 has no glycosyltransferase activity. In mice, Galntl5 expression is restricted to differentiating spermatids, and haploinsufficiency leads to immotile spermatozoa with an aberrant protein composition. Moreover, heterozygotic deletions of human GALNTL5 have been detected in patients diagnosed with asthenozoospermia (low sperm motility). Although these findings indicate that GALNTL5 is a functional molecule essential for mature sperm formation in mammals, the exact function of GALNTL5 in spermiogenesis remains unknown. To clarify this role, we established the mouse spermatocyte cell line GC-2spd(ts), which exhibits drug-inducible GALNTL5 expression. Interestingly, continuous GALNTL5 expression in the resultant cell lines caused apoptosis with cell shrinkage, and GALNTL5 was localized in the endoplasmic reticulum (ER) and was associated with two ER-resident chaperone proteins, calnexin and BiP (GRP78). Calnexin recognized and strongly bound to the N-glycans on GALNTL5 molecules modified in the ER. In contrast, ER-resident BiP likely attached to GALNL5 regardless of its glycosylation. GALNTL5 expression abolished the binding between calnexin and misfolded substrate proteins, indicating that GALNTL5 directly blocks calnexin function. Furthermore, the interaction between GALNTL5 and calnexin decreased the level of BiP protein, and consequently also the expression levels of proteins that are resident in the ER, Golgi apparatus, and cytoplasm. These reduced protein levels were confirmed by loss of calnexin or BiP function in the GC-2spd(ts) cell line using siRNA knockdown. Further, sustained expression of GALNTL5 resulted in cell structure changes, including the position of the cis-Golgi apparatus and alterations in the ER network. These results strongly suggest that GALNTL5 contributes to alteration of the cell structure specific to differentiating spermatids by blocking ER function.

Double mutant DNMT3A AML: a unique subtype experiencing increased DNA damage and poor prognosis.

Mutation of DNMT3A, encoding a de novo methyltransferase essential for cytosine methylation, is a common early event in clonal hematopoiesis (CH) and adult acute myeloid leukemia (AML). Spontaneous deamination of methylated cytosines damages DNA, which is repaired by the base excision repair (BER) enzymes MBD4 and TDG. Congenital MBD4-deficiency has been linked to early-onset CH and AML, and is marked by exceedingly high levels of DNA damage and mutation of DNMT3A. Strikingly, wildtype (WT) DNMT3A binds TDG, thereby potentiating its repair activity. Since TDG is the only remaining BER enzyme in MBD4-deficient AML patients capable of repairing methylation damage, we investigated whether mutant DNMT3A negatively affects the repair function of TDG. We found that, whereas WT DNMT3A stimulates TDG function, mutant DNMT3A impairs TDG-mediated repair of DNA damage in vitro. In light of this finding and to extrapolate our observations to the broader AML patient population, we investigate here the genetic profiles and survival outcomes of AML patients with single (SM) versus double mutant (DM) DNMT3A. DM DNMT3A AML patients show a characteristic driver mutation landscape and reduced overall survival when compared to SM DNMT3A AML patients. Importantly, whole-genome sequencing showed a trend for increased DNA damage in primary DM DNMT3A AML samples, especially when DNMT3A mutations are located at the DNMT3A-TDG interaction interface.

Cardiocutaneous syndrome is caused by aggregation of iASPP mutants

The ASPP (apoptosis-stimulating protein of p53) family of proteins is involved in many cellular interactions and is starting to emerge as a major scaffolding hub for numerous proteins involved in cancer biology, inflammation and cellular integrity. It consists of the three members ASPP1, ASPP2 and iASPP which are best known for modulating the apoptotic function of p53, thereby directing cell fate decision. Germline mutations in iASPP have been shown to cause cardiocutaneous syndromes, a combination of heart and skin defects usually leading to death before the age of five. Mutations in iASPP causing these syndromes do not cluster in hot spots but are distributed throughout the protein. To understand the molecular mechanism(s) of how mutations in iASPP cause the development of cardiocutaneous syndromes we analysed the stability and solubility of iASPP mutants, characterized their interaction with chaperones and investigated their influence on NF-ĸB activity. Here we show that three different mechanisms are responsible for loss of function of iASPP: loss of the complete C-terminal domain, mutations resulting in increased auto-inhibition and aggregation due to destabilization of the C-terminal domain. In contrast to these germline mutations causing cardiocutaneous syndromes, missense mutations found in cancer do not result in aggregation.

Interplay between Netrin-1 and Norrin controls arteriovenous zonation of blood–retina barrier integrity

The integrity of the blood-retina barrier (BRB) is crucial for phototransduction and vision, by tightly restricting transport of molecules between the blood and surrounding neuronal cells. Breakdown of the BRB leads to the development of retinal diseases. Here, we show that Netrin-1/Unc5b and Norrin/Lrp5 signaling establish a zonated endothelial cell gene expression program that controls BRB integrity. Using single-cell RNA sequencing (scRNA-seq) of postnatal BRB-competent mouse retina endothelial cells (ECs), we identify >100 BRB genes encoding Wnt signaling components, tight junction proteins, and ion and nutrient transporters. We find that BRB gene expression is zonated across arteries, capillaries, and veins and regulated by opposing gradients of the Netrin-1 receptor Unc5b and Lrp5-β-catenin signaling between retinal arterioles and venules. Mice deficient for Ntn1 or Unc5b display more BRB leakage at the arterial end of the vasculature, while Lrp5 loss of function causes predominantly venular BRB leakage. ScRNA-seq of Ntn1 and Unc5b mutant ECs reveals down-regulated β-catenin signaling and BRB gene expression that is rescued by Ctnnb1 overactivation, along with BRB integrity. Mechanistically, we demonstrate that Netrin-1 and Norrin additively enhance β-catenin transcriptional activity and Lrp5 phosphorylation via the Discs large homologue 1 (Dlg1) scaffolding protein, and endothelial Lrp5-Unc5b function converges in protection of capillary BRB integrity. These findings explain how arteriovenous zonation is established and maintained in the BRB and reveal that BRB gene expression is regulated at the level of endothelial subtypes.

Clinical and genetic characterization of a progressive RBL2-associated neurodevelopmental disorder.

Retinoblastoma (RB) proteins are highly conserved transcriptional regulators that play important roles during development by regulating cell-cycle gene expression. RBL2 dysfunction has been linked to a severe neurodevelopmental disorder. However, to date, clinical features have only been described in six individuals carrying five biallelic predicted loss of function (pLOF) variants. To define the phenotypic effects of RBL2 mutations in detail, we identified and clinically characterized a cohort of 35 patients from 20 families carrying pLOF variants in RBL2, including fifteen new variants that substantially broaden the molecular spectrum. The clinical presentation of affected individuals is characterized by a range of neurological and developmental abnormalities. Global developmental delay and intellectual disability were uniformly observed, ranging from moderate to profound and involving lack of acquisition of key motor and speech milestones in most patients. Disrupted sleep was also evident in some patients. Frequent features included postnatal microcephaly, infantile hypotonia, aggressive behaviour, stereotypic movements, seizures, and non-specific dysmorphic features. Neuroimaging features included cerebral atrophy, white matter volume loss, corpus callosum hypoplasia and cerebellar atrophy. In parallel, we used the fruit fly, Drosophila melanogaster, to investigate how disruption of the conserved RBL2 orthologue Rbf impacts nervous system function and development. We found that Drosophila Rbf LOF mutants recapitulate several features of patients harbouring RBL2 variants, including developmental delay, alterations in head and brain morphology, locomotor defects, and perturbed sleep. Surprisingly, in addition to its known role in controlling tissue growth during development, we found that continued Rbf expression is also required in fully differentiated post-mitotic neurons for normal locomotion in Drosophila, and that adult-stage neuronal re-expression of Rbf is sufficient to rescue Rbf mutant locomotor defects. Taken together, our study provides a clinical and experimental basis to understand genotype-phenotype correlations in an RBL2-linked neurodevelopmental disorder, and suggests that restoring RBL2 expression through gene therapy approaches may ameliorate some symptoms caused by RBL2 pLOF.

The Influence of Blood Titanium Levels on DNA Damage in Brazilian Workers Occupationally Exposed to Different Chemical Agents.

Occupational exposure to pollutants may cause health-damaging effects in humans. Genotoxicity assays can be used to detect the toxic effects of pollutants. In the present study, we evaluated genetic damage in three populations occupationally exposed to benzene, pyrenes, and agrochemicals and assessed the possible influence of titanium (Ti) co-exposure. A total of 275 subjects were enrolled in this study. The occupationally exposed population was composed of 201 male individuals, divided into three different groups: gas station attendants (GSA group) (n = 76), taxi drivers (TD group) (n = 97), farmers (farmers group) (n = 28), and control (n = 74). Biomarkers of exposure and effect were investigated such as AChe, BuChE, t,t-muconic acid (t,t-MA), and 1-hydroxypyrene (1-OHP). Ti levels in blood were higher in all the workers compared with the control group. DNA damage evaluated by comet assay was higher in the taxi drivers and farmers than in the controls, and the frequency of micronucleate buccal cells was higher in the gas station attendants and taxi drivers than in the controls. Correlations were found among occupational exposure time and biomarkers of exposure, genotoxicity biomarkers, and blood Ti levels. Our results demonstrated Ti co-exposure in the gas station attendants, taxi drivers, and farmers, and blood Ti levels were linked with the respective biomarkers of exposure. Additionally, tools through machine learning corroborated these findings, and Ti was the factor that contributed to DNA damage. Thus, the present study indicates the role of Ti in occupational settings and interactions with already known major xenobiotics present in the occupational environment contributing to genotoxicity.

Boswellia serrate Gum Resin Mitigates Renal Toxicity: Role of TNF-α, Interleukins, TGF-β, and Lipid Peroxidation

Background and aim: Being a central organ in homeostasis and maintaining the health of the biological system, kidneys are exposed to variable toxicants. Long-term exposure to nephrotoxic molecules causes chronic renal damage that causes fibrosis and loss of function. Such damage can be initiated by oxidative stress which provokes inflammation. We aim at investigating the potential therapeutic effects of Boswellia serrata (BS) gum resin extract in managing CCl4-induced renal toxicity. Methods: Male Wistar albino rats were assigned to groups: healthy control; CCl4-treated (CCl4, twice/week, for 6 weeks); CCl4 + BS-treated: CCl4 for 6 weeks followed by BS (150 mg/kg/day) for 2 weeks; and CCl4 + Silymarin-treated: CCl4 for 6 weeks followed by Silymarin (100 mg/kg/day) for 2 weeks. Blood and kidney tissue were utilized to assess oxidative stress status, inflammatory cytokines, and histopathological changes. Results: BS treatment ameliorated signs of renal damage and fibrosis as it improved renal antioxidant status and renal function markers and significantly reduced the levels of inflammatory cytokines TNF-α, IL-1β, IL-6, and IL-8 along with the fibrogenic marker TGF-β. Kidney tissues showed improved histological features after BS treatment. Conclusions: BS gum resin extract has significant therapeutic potential against CCl4-induced renal damage and fibrosis. These effects could be mediated via its previously reported antioxidant, free radical scavenging, and anti-inflammatory effects.

How to Keep Doing What You Like Doing: A Qualitative Study of Active Older Adults’ Insights on the Facilitators and Barriers to Maintenance of Physical Activity (From the MOVEAGE-Act Project)

While the facilitators/barriers for the initiation of physical activity (PA) are well documented, there is less known about these facilitators/barriers for maintenance of PA in the older population in general and not following an intervention. This study aimed to explore older adults’ perspectives on the facilitators/barriers to maintaining PA. The study used a descriptive qualitative design, with three focus groups, one in Ireland and two in France. Participants were community-dwelling older adults (≥60 years) 66% were female, recruited through older adult websites. Findings were analyzed thematically using a Socio-Ecological Model as a framework. Thirty-three older adults participated, and 88% met the international physical activity guidelines of 150 minutes of moderate activity per week. From intrapersonal and interpersonal perspectives, enjoyment, social engagement, adapting physical activity for their age, establishing routines/habits, and combining PA with other activities and interests were all key facilitators in PA maintenance. From the policy, environmental and organizational perspectives, limited policies or their implementation, activity-related factors (insufficient information on activities, age appropriateness and availability of suitable activities, accessibility, inadequate support), and social connectedness were identified. Multiple interrelationships across the different social-ecological perspectives emerged. It was evident for PA maintenance that a balance is needed between having activities that are enjoyable and yet challenging and being able to adapt them to age-related changes such as loss of function and confidence. In addition, it was apparent that older adults were more likely to engage in PA if it had a social element and if they had access to relevant information and safe, age-appropriate activities and support. These factors should be further incorporated into PA promotion, activities, and policies to maximize PA maintenance. Barriers may lead to non-maintenance of healthy aging targets, with implications for health service economies and older adults’ health.

Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming.

Repeated antigen exposure leads to T-cell exhaustion, a transcriptionally and epigenetically distinct cellular state marked by loss of effector functions (e.g., cytotoxicity, cytokine production/release), up-regulation of inhibitory receptors (e.g., PD-1), and reduced proliferative capacity. Molecular pathways underlying T-cell exhaustion have been defined for CD8+ cytotoxic T cells, but which factors drive exhaustion in CD4+ T cells, that are also required for an effective immune response against a tumor or infection, remains unclear. Here, we utilize quantitative proteomic, phosphoproteomic, and metabolomic analyses to characterize the molecular basis of the dysfunctional cell state induced by chronic stimulation of CD4+ memory T cells. We identified a dynamic response encompassing both known and novel up-regulated cell surface receptors, as well as dozens of unexpected transcriptional regulators. Integrated causal network analysis of our combined data predicts the histone acetyltransferase p300 as a driver of aspects of this phenotype following chronic stimulation, which we confirmed via targeted small molecule inhibition. While our integrative analysis also revealed large-scale metabolic reprogramming, our independent investigation confirmed a global remodeling away from glycolysis to a dysfunctional fatty acid oxidation-based metabolism coincident with oxidative stress. Overall, these data provide both insights into the mechanistic basis of CD4+ T-cell exhaustion and serve as a valuable resource for future interventional studies aimed at modulating T-cell dysfunction.

Genetic Structural Changes While Maintaining Effective Population Size of Bighead Catfish in Nong Han Lake: Implications of Metapopulation Dynamics or Release Activities

ABSTRACTThe Bighead Catfish (Clarias macrocephalus) plays crucial roles in the ecosystem and as a protein source for humans in Nong Han Lake, Thailand, but their ecological and population dynamics, along with their genetic diversity and structure, are poorly understood. Therefore, the dynamics of genetic diversity and differentiation of bighead catfish populations in Nong Han Lake were investigated during 2018–2023 to provide essential insights into preserving biodiversity and maintaining ecological balance. Microsatellite genotyping was used to assess the genetic diversity of one bighead catfish population in 2018, two populations in 2023, and one hatchery population. Potentially stable, effective population sizes and distinct genetic clusters of these populations were identified, which represented the resilience of populations and the complexity of their genetic dynamics. Genetic differentiation between sample dates and among populations suggested that limited recent and historical genetic exchanges could potentially influence genetic structure. The impact of ecological factors, including flooding, metapopulation dynamics, and human interventions, was indicated by unique and shared gene pools among populations and subpopulations in different years. Ongoing assessment of genetic diversity and structure of bighead populations is essential for developing conservation strategies and ensuring sustainable management.

Loss in Pluripotency Markers in Mesenchymal Stem Cells upon Infection with Chlamydia trachomatis.

The intracellular pathogen Chlamydia trachomatis can inflict substantial damage on the host. Notably, Chlamydia infection is acknowledged for its precise modulation of diverse host signaling pathways to ensure cell survival, a phenomenon intricately connected to genetic regulatory changes in host cells. To monitor shifts in gene regulation within Chlamydia-infected cells, we employed mesenchymal stem cells (MSCs) as a naïve, primary cell model. Utilizing biochemical methods and imaging, our study discloses that acute Chlamydia infection in human MSCs leads to the downregulation of transcription factors Oct4, Sox2, and Nanog, suggesting a loss of pluripotency markers. Conversely, pluripotency markers in MSCs were sustained through treatment with conditioned medium from infected MSCs. Additionally, there is an augmentation in alkaline phosphatase activity, along with elevated Sox9 and CD44 mRNA expression levels observed during acute infection. A comprehensive screening for specific cell markers using touchdown PCR indicates an upregulation of mRNA for the early chondrogenesis gene Sox9 and a decrease in mRNA for the MSC marker vimentin. Real-time PCR quantification further corroborates alterations in gene expression, encompassing increased Sox9 and CD44 mRNA levels, alongside heightened alkaline phosphatase activity. In summary, the infection of MSCs with C. trachomatis induces numerous genetic deregulations, implying a potential trend towards differentiation into chondrocytes. These findings collectively underscore a targeted impact of Chlamydia on the gene regulations of host cells, carrying significant implications for the final fate and differentiation of these cells.

Kidney Function and Body Composition in Adult Survivors of Unilateral, Non-Syndromic Wilms Tumor: A Report From the St. Jude Lifetime Cohort Study.

The relationships among treatment exposures, body composition, and estimated glomerular filtration rate (eGFR) in adult survivors of Wilms tumor have not been well studied. We evaluated body composition with dual-energy x-ray absorptiometry (DXA) and eGFR with the updated Chronic Kidney Disease Epidemiology Collaboration equations (creatinine only-eGFRCr, cystatin C only-eGFRCysC, creatinine and cystatin C-eGFRCr+CysC) without race in 134 adults previously treated for unilateral, non-syndromic Wilms tumor at St. Jude Children's Research Hospital between 1964 and 2004 with chemotherapy and with (hemiabdomen [HA] or whole abdomen [WA]) or without radiation therapy (RT). Z-scores for DXA variables were calculated using data from the National Health and Nutrition Examination Survey. WART was associated with a lower relative total (p = 0.004) and trunk (p < 0.001) lean mass, eGFRCr (p = 0.008), eGFRCysC, (p < 0.001), and eGFRCr+CysC (p < 0.001), and higher values of cystatin C (p < 0.001). Linear regression demonstrated that relative total lean mass (p = 0.009) and relative trunk lean mass (p < 0.001) Z-scores, and eGFRCr (p = 0.013) were lower among those who received WART compared to No RT patients. WART is associated with lower relative total and trunk lean mass Z-scores and eGFR, regardless of the equation used, and is lower in survivors treated with WART compared to unirradiated survivors of unilateral, non-syndromic WT. Assessments using other GFR measures may provide greater insight into the mechanism and magnitude of kidney function loss among WART-treated WT survivors.

Whole exome sequencing reveals heparan sulfate proteoglycan 2 (HSPG2) as a potential causative gene for kidney stone disease in a Thai family

Kidney stone disease (KSD) is a prevalent and complex condition, with an incidence of 85 cases per 100,000 individuals in Thailand. Notably, over 40% of cases are concentrated in the northeastern region, indicating a potential genetic influence, which is supported by genetic mutations reported in several families by our research group. Despite this, the genetic basis of KSD remains largely unknown for many Thai families. This study aimed to identify the genetic mutation responsible for KSD in a specific Thai family, the UBRS131 family, which includes four affected individuals. Whole exome sequencing was performed, and variant filtering using the VarCards2 program identified 10 potentially causative mutations across 9 genes. These mutations were subjected to segregation analysis among family members and screened in 180 control and 179 case samples using real-time PCR-HRM or PCR-RFLP techniques. Prioritization of these variants using GeneDistiller identified the p.Asp775Glu mutation in the heparan sulfate proteoglycan 2 (HSPG2) gene as the likely causative mutation for KSD in this family. The Asp775 residue is highly conserved across vertebrates, and structural analysis suggests that the Glu775 substitution may disrupt the formation of two crucial hydrogen bonds, potentially altering the mutant protein’s configuration. Immunohistochemistry confirmed the presence of perlecan (HSPG2 protein) in the proximal tubules in nephrons. These findings highlight the significant role of the HSPG2 gene in familial KSD within this study family.