Molecular Genetics and Genomics

Phosphorus Starvation Tolerance 1 in rice (OsPSTOL1, known as Phosphorus uptake 1, Pup1) is a receptor-like cytoplasmic protein kinase that confers tolerance to phosphorus deficiency. The OsPSTOL1 gene possesses a Ser/Thr kinase and shows high amino-acid sequence similarity with the leaf rust receptor-like kinase (OsLrK10). We hypothesize that the putative wheat TaPSTOL1 and TaLrK10 have a common ancestral origin and that putative TaPSTOL1 diverged recently acquiring new structural modifications and biological functions in the process. In this study, we identified all putative TaPSTOL1 homeologs and examine the evolutionary relationship between TaPSTOL1 and TaLrK10 in Triticum species. Our results indicate that the putative TaPSTOL1 diverged recently without possessing the amino-terminal domain, which is a typical characteristic of TaLrK10. We observed numerous conversions tracts between these two genes and the substitution pattern of randomly selected amino acids indicates that dynamic selection pressures acted on both genes. The putative TaPSTOL1 shows high nucleotide diversity compared to TaLrK10 within Triticum species. Further, a multiple-sequence analysis reveals that the third exon of TaLrK10 appears to have been duplicated and diverged as a putative single-exon based TaPSTOL1 in bread wheat. Overall, our comparative analysis indicates that both TaPSTOL1 and TaLrK10 appears to have diverged from a common ancestor, acquiring distinct structural organizations and biological functions.

The X chromosome (chrX) is the eighth largest human chromosome, harbouring an estimated total of 839 protein-coding genes. Historically, the chrX has been described as enriched for genes related to brain development, sexual differentiation and reproduction, earning the epithet of "smart and sexy chromosome". Many studies have confirmed that the chrX is indeed "smart", including a recent systematic analysis of human chrX genes which found an enrichment in genes relevant to brain functions. However, it is less clear whether the chrX being "sexy" still holds true. Here we reviewed the origins of this idea and we evaluated human X-linked genes in terms of their expression across several tissues, their annotated functions and their association with monogenic disorders related to sexual differentiation and reproduction (SDR). We found that sex-specific tissues show higher expression levels from chrX genes than from autosomal genes except in testis, but that X-linked genes are significantly enriched among the most highly expressed genes in testis, specifically within spermatogonia and Sertoli cells. Yet, we found no evidence for an enrichment of genes on the X with annotated functions related to male or female SDR. When analysing SDR-related monogenic disorders, we found a significant enrichment of genes on chrX associated with clinical terms related to male SDR but not with clinical terms related to female or general SDR. Overall, our results support the notion of a somewhat "sexy" X chromosome, shaped by X-linked expression patterns and clinical associations rather than current annotated gene functions.

BackgroundConventional models of human ribosomal DNA (rDNA) array organization have historically depended on transcription-centric boundaries, partitioning the unit into a [~]13 kb rDNA transcription region and a monolithic [~]31 kb intergenic spacer (IGS). While our previous identification of Duplication Segment Units (DSUs) mapped these arrays based on an intuitive analysis of the microsatellite density landscape of the complete reference human genome, our present deep mining of this landscape has revealed a more accurate rDNA Gene Unit Pattern. Methods & ResultsIn this study, we conducted a deep mining analysis of our previously established microsatellite density landscape of the T2T-CHM13 assembly, focusing specifically on nucleolar organizing regions (NORs). We suggest a more accurate rDNA Gene Unit Pattern containing a (CTTT)n microsatellite aggregation ahead of the rDNA gene and a (CT)n microsatellite aggregation behind the gene, rather than a pattern featuring an IGS region inserted between two rDNA genes. ConclusionsA correct rDNA gene pattern of the human genome probably includes a (CTTT)n microsatellite aggregation ahead of the gene and a (CT)n microsatellite aggregation behind it, which possibly constitute cis- and trans-regulating regions; the (CTTT)n and (CT)n microsatellite aggregations may provide two different local stable DNA structures for regulatory protein binding.

Conventional gene annotation pipelines classify eukaryotic genes into protein-coding and non-coding. Alternative splicing may generate non-coding transcript variants from protein-coding genes, that are expressed in tissue- or disease-specific manner. We and others have described the genes which transcribe both coding and non-coding transcripts as bifunctional genes. Here we present a genome-wide analyses of bifunctional genes and reannotate the genes in the human genome reference assembly into coding, non-coding and bifunctional. We identify over 4000 "bifunctional genes" in the human genome, constituting approximately 10% of the transcribed genes, and present evidence that these genes are conserved in evolution and their number correlate well with genome size and complexity. These genes are enriched in gene sets involved in vesicular transport, autophagy, RNA/DNA binding, glycosylation and splicing. By monitoring the expression of non-coding exons in long-read sequencing datasets and by quantitative RT-qPCR, we provide evidence for the expression of non-coding variants from bifunctional genes. The ncRNA transcripts from these genes might have similar or different roles from their cognate mRNA counterparts. They may act as miRNA sponges or harbour non-canonical open-reading frames that encode microproteins, while also competing for binding with RNA-binding proteins. We present evidence for establishing potential biological functions of bifunctional genes and summarise the findings in a searchable database. Further studies and functional characterization focused on this special group of genes may reveal interesting gene regulatory mechanisms relevant to physiology and pathology.

Social stress is a risk factor for psychiatric disorders and also influences immune function. While it is known that acute social stress impacts the number of immune cells in circulation, the temporal dynamics of stress induced immune-related transcriptional changes in human blood remain unclear. To investigate changes in gene expression, we exposed 26 adults to the Trier Social Stress Test (TSST), and collected blood at baseline, as well as 5, 30, 60 and 90 min after stress. Whole-blood gene expression was profiled using a 5 targeted RNA-sequencing method (STRT). Differential expression was analyzed using linear and cubic models. We observed a total of 54 differentially expressed genes following stress. Fast responses, with a transient peak immediately following stress, were enriched for cytotoxic T cell, NK cell and dendritic cell functions (e.g., GZMB, GNLY, CCL4 and GZMA) and paralleled lymphocyte count changes. In contrast, gradual, linear responses without any evident peak were enriched for neutrophil related genes (e.g., FPR2, PLAUR, CXCR2, AQP9, and QPCT) and did not mirror neutrophil counts, indicating cell intrinsic transcriptional changes. From pathway and transcription factor enrichment analyses, IL-12 family mediated signaling is inferred as a central mechanism linking stress to immune gene regulation. Our results show that acute psychosocial stress induces both fast and slower changes in gene expression in different immune cell populations. The involvement of the IL-12-STAT4 axis and genes such as PLAUR and FPR2 suggests molecular mechanisms through which stress-related immune activation may contribute to vulnerability for anxiety and depressive disorders.

A method to measure telomere length in S. cerevisiae was developed based on bioluminescence resonance energy transfer (BRET). The system uses energy transfer between a luciferase-Rif2 fusion protein and fluorescently tagged Rap1. The study demonstrates that the BRET ratio correlates with the Rap1/Rif2 complex at the telomeres and thus the availability of telomeric Rap1 binding sites. This enables the measurement of telomere length in living cells. The system was able to reproduce reported deviations in telomere length in mutants lacking telomere length regulators, cells treated with telomere length modifying compounds and strains expressing inducible telomerase. The BRET ratio linearly correlated with the average number of telomeric nucleotides derived from long-read sequencing data using a novel algorithm for telomere length calculation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/711003v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1850c4dorg.highwire.dtl.DTLVardef@1ead295org.highwire.dtl.DTLVardef@1a76358org.highwire.dtl.DTLVardef@6b3183_HPS_FORMAT_FIGEXP M_FIG C_FIG

We examined how thermal shifts influence development time and adult body size in Drosophila melanogaster. Individual flies were exposed to alternating temperatures of 25{degrees}C (optimal) and 17{degrees}C (cold), with shifts introduced at key developmental transitions: larval hatching and pupariation. We found while larval-stage temperature is the biggest determinant of thermal plasticity of development time and adult size, the egg-stage temperature also influences the pace of development and growth throughout pre-adult duration. The effect of low-to-high and high-to-low temperature shifts on development and growth may not be symmetric. When eggs are reared at 25{degrees}C and then shifted to 17{degrees}C, larval and pupal durations undergo reduction compared to constant 17{degrees}C, but it produces slightly larger adults. A higher egg-stage temperature thus seem to exert a carryover effect that accelerates subsequent development and growth when later stages experience colder temperatures. Surprisingly, flies whose egg stage is exposed to 17{degrees}C followed by a shift to 25{degrees}C also have reduced larval duration and larger size, relative to those developing at constant 25{degrees}C. We speculate this could be either because 17{degrees}C to 25{degrees}C represents a low-to-high temperature shift or a sub-optimal-to-optimal thermal shift that results in metabolic and/or hormonal changes accelerating differentiation and growth. While pupal duration is sensitive to current and to some extent prior thermal environments, it does not contribute substantially to thermal plasticity of size. Development time is longer in males than in females, and this difference seems to start from larval stage while the pupal duration plays a bigger role in creating this sex-specific difference. Overall, employing individual fly rearing, this study helped to unravel the effect of thermal shifts on growth and development in D. melanogaster with great precision.

BackgroundPolycystic ovary syndrome (PCOS) is a prevalent endocrine disorder and a leading cause of female infertility, with complex genetic, metabolic, and hormonal etiologies. Long non-coding RNAs (lncRNAs) have emerged as important regulators of diverse biological processes, yet their roles in PCOS remain underexplored. Here, we identified and characterized PCOS differentially expressed gene-associated lncRNAs (PDEGAL) with an integrative approach combining expression data, genetic association, and evolutionary analysis. MethodsThirty-three PCOS-associated protein-coding genes were obtained from our prior study, and all their nearby and overlapping lncRNAs were annotated. These candidates were analyzed using UCSC Genome Browser-mapped annotations and datasets, including NCBI RefSeq, GENCODE, GTEx, GWAS SNPs, and conservation, as well as the FANTOM5 cap analysis of gene expression (CAGE) promoter data, to assess their expression, regulatory potential, genetic variant overlaps, and evolutionary conservation. ResultsTwenty-three PDEGALs (18 antisense to, and 5 sharing bidirectional promoters with, known PCOS-associated protein-coding genes) were identified. 17 PDEGALs contained GWAS SNPs with statistically significant disease associations, 9 of which were associated with PCOS-related traits. 5 PDEGALs demonstrated expression in the KGN granulosa cell model of PCOS. Key gene structure element (KGSE) analysis revealed that most PDEGALs are primate-specific. Integrating four criteria--GTEx expression, GWAS SNPs, FANTOM promoterome, and KGSE conservation--highlighted HELLPAR as the only lncRNA fulfilling all four, while five others--PGR-AS1, MTOR-AS1, ENSG00000265179, ENSG00000256218, and LOC105377276--fulfilled three of the four criteria. ConclusionsWe have systematically identified candidate PCOS regulatory lncRNAs with convergent genetic, expression, and evolutionary evidence. These results provide a framework for functional validation and highlight lncRNAs as potential biomarkers and therapeutic targets in PCOS that function by regulating their nearby and overlapping protein-coding genes.

IntroductionIndigenous groups across the world have been underrepresented in the ongoing efforts to map human microbiome diversity. This study investigates the gut microbiome and resistome diversities of three indigenous Malaysian (Orang Asli, OA) communities with different lifestyles and degree of urbanisation. We included an urban Malay group as a comparison. MethodsHealthy participants over 18 years old gave were recruited from three indigenous communities, namely Temuan (urban, n=12), Temiar (semi-urban, n=9) and Jahai (rural, hunter-gatherer, n=12), and Malay (urban, non-indigenous, n=9). Stools were collected on dry ice and sequenced using shotgun metagenomics. ResultsApproximately 65% of the reads were classified across the dataset. Microbial alpha diversity (Shannon) decreased but antibiotic resistance genes (ARGs) diversity increased as the degree of urbanisation in the groups increased (P < 0.05). The groups contributed to 13% of the variation observed in the microbial composition (PERMANOVA, P = 0.001), and 14.5% in resistome composition (PERMANOVA, P = 0.001). Romboutsia timonensis was significantly depleted in Jahai compared to Malay (FDR = 0.04). Shared ARGs conferring resistance to beta-lactams (cfxA), tetracyclines (tet), and macrolides (erm) were observed across all groups, irrespective of geographical location, ethnicity and lifestyle. ConclusionThis study provides initial characterisation of the gut microbiome and resistome of three underrepresented indigenous OA communities in Malaysia. Our findings offer foundational evidence of antimicrobial resistance patterns and underscores the need for broader inclusion of underrepresented populations in national surveillance and stewardship efforts.

Agriculture has modified the soil structure due to the influence of external factors and processes that affect microbial biodiversity. Metagenomics is a fundamental tool for the study of soil microbial diversity because it provides information about the ecosystem diversity, including both the microorganisms that cannot be isolated in culture media and those that are no longer viable in the analyzed sample. In this work, six soil samples obtained from agroecosystems of central and northern Argentina were subjected to a preliminary 16S metagenomic analysis. Copiotrophic bacteria (Proteobacteria and Actinobacteria) were dominant and one of the samples had a dominance of an oligotrophic Phylum (Acidobacteria). Our findings support previous evidence from traditionally managed agroecosystems and provide new insights into the diversity of soil microbiomes in Argentine regions outside the Pampas. Finally, we analyzed the most common genera with relevant species to agronomy, both beneficial and pathogenic, and their abundance and diversity in the sequenced samples.

Purine moieties are essential for many functions within the eukaryotic cell, including energy, signaling and nucleic acid synthesis. While purine starvation is known to induce stress resistance in eukaryotic model organism budding yeast Saccharomyces cerevisiae, it remains unclear whether the physiological response is related to disruption of synthesis pathway in particular position or it is uniform across all genetic deficiencies within the de novo adenine biosynthesis pathway. It is also not known how purine starved cells perceive purine shortage - weather they share the same signaling elements with nitrogen starvation or not. MethodsWe characterised physiology of strains with deletions in adenine biosynthesis pathway when cultivated in full or purine deficient and compared to cell physiological parameters when cultivated in nitrogen deficient media. We tested stress tolerance, carbon flux, cell cycle arrest and did transcription profiling (RNA-seq). ResultsOur findings demonstrate that purine starvation-induced stress resistance is significantly modulated by the specific step at which the pathway is interrupted. Transcriptional analysis revealed that purine starvation in many aspects phenocopies nitrogen starvation, particularly - in both starvations strong downregulation of ribosome related genes occurs. In the same time several metabolic features which differ from N- and ade- starvations: pentose phosphate pathway is specifically upregulated within ade4{Delta}-ade2{Delta} and downregulated in N-cells. Notably, the expression of stress-responsive genes such as HSP12, HSP26, and GRE1 varied between mutants, suggesting that the accumulation of pathway intermediates (e.g., AIR in ade2{Delta}) or the absence of downstream precursors (AICAR) alters the perception of starvation especially in the case of ade16{Delta}ade17{Delta} strain. ConclusionsMetabolic and stress-tolerance phenotypes of purine auxotrophs are not merely a result of purine depletion but seems that the response is signalled via the same pathways, like TOR1. The results suggest that strains having mutations within various positions of the purine pathway "perceive" purine limitation a bit differently - especially when we compare the end of the pathway with the other mutants. Different phenotypic outcomes of the occasional purine depletion might give preferences for organisms which have mutations in the beginning rather at the end of the pathway. Besides, our findings might have implications in the design of synthetic pathways and the use of auxotrophic markers in yeast research.

Wellbeing is commonly defined as the combination of feeling good and functioning well and typically conceptualized as two related but distinct components. Hedonic wellbeing emphasizes pleasure, happiness, and life satisfaction, while eudaimonic wellbeing focuses on meaning, personal growth, flourishing, and the realization of ones potential. The Mental Health Continuum-Short Form was developed as a comprehensive measure of wellbeing and includes three subscales assessing emotional, social, and psychological wellbeing. Although the Mental Health Continuum total score is often interpreted as an indicator of overall wellbeing, the underlying genetic structure of its three subscales and its genetic overlap with other commonly used wellbeing measures remains unclear. Using data from 5,212 individuals from the Netherlands Twin Register (72% female, mean age 36.4), we fitted multivariate twin models to examine the genetic architecture of the Mental Health Continuum and its associations with other wellbeing measures (quality of life, life satisfaction, subjective happiness, and flourishing). Results indicate that, at the genetic level, the Mental Health Continuum is best explained by its three distinct subscales rather than by a latent factor. When considering the Mental Health Continuum together with the other wellbeing measures, we found moderate to high genetic correlations (r = 0.52 - 0.83), indicating substantial overlap in the genetics underlying the wellbeing constructs. However, we did not find evidence for a single common genetic factor underlying all constructs. These findings highlight the multidimensional structure of wellbeing, but the moderate to high genetic correlations across measures suggest that it is important to align the level of measurement (phenotypic vs genetic) with the research question.

Psychosocial stress is a significant risk factor for mental and physical illness, and emerging evidence suggests that altered oral microRNAs (miRNAs) and microbiome may act as biomarkers or mediators of stress responses. This study investigated stress-associated molecular changes in saliva from 113 male police officers. Based on repeated administrations of the Karasek Demand/Control and Effort/Reward Imbalance questionnaires, subjects were stratified by perceived stress response (SR) to homogeneous occupational stressors into low, intermediate, or high responders. Salivary miRNA profiles were analyzed using small RNA sequencing, and microbiome composition was assessed through shotgun metagenomics. Eighteen miRNAs were significantly differentially expressed between high- and low-SR groups, with four miRNAs with increasing (miR-10400-5p, miR-1290, miR-6074-5p, and miR-9902) and fourteen with decreasing (including miR-21-5p and mirR-142-3p) levels in the high SR group (adj.p<0.05). The identified salivary miRNAs showed a progressive alteration from low- to high-SR groups. Functional enrichment analysis indicated that dysregulated miRNA targets are involved in apoptosis, cellular stress responses, and metabolic regulation. Distinct salivary microbial communities were also observed across SR groups. Several taxa displayed progressive abundance shifts, with Prevotella baroniae and Schaalia odontolytica increasing and Actinomyces naeslundii and Capnocytophaga ochracea decreasing in the high SR group. Functional predictions revealed, in this group, a significant enrichment of inositol degradation pathways, paralleled by a reduction in bacteria involved in L-tryptophan and thiamine biosynthesis. These findings suggest that salivary miRNAs and microbiota profiles may serve as non-invasive biomarkers of psychosocial stress and provide insight into molecular mechanisms linking chronic stress to physiological and behavioral outcomes.

Torpor is a hypometabolic state employed by many mammalian and non-mammalian species to cope with harsh environments. When exposed to a short photoperiod, Djungarian hamsters (Phodopus sungorus) enter daily torpor with body temperatures dropping to as low as 15{degrees}C. Despite the widely-held notion that torpor is a form of deep sleep, torpid animals are not completely inactive but exhibit occasional movements reflected in an increase in EMG tone. Little is known about these EMG events during torpor and whether they have a functional role during the torpid state. We here analysed EEG, EMG, and brain temperature data from Djungarian hamsters, and used an automatic detection algorithm to identify periods of EMG activation during spontaneous daily torpor. The hamsters exhibited regular periods of motility that were invariably initiated during a decline in brain temperature and were followed by a brain temperature increase. The frequency of EMG events exhibited a negative correlation with brain temperature, such that lower brain temperature was associated with a higher frequency of EMG events. In addition, EMG events were associated with a pronounced increase in EEG power, especially between 9.5-15.5 Hz, which often started with an EEG pattern similar to an evoked potential preceding the increase in the EMG activity. On the contrary, micro-arousals during normothermic NREM sleep were associated with a decrease in EEG power, a decrease in brain temperature and were of shorter duration than torpor EMG events, indicating that the two phenomena may serve different purposes. We speculate that periodic motility associated with increased brain activity during torpor may play a role in thermoregulation, and help retain vigilance to potentially mitigate predation risk during this hypometabolic state.

ObjectiveThe objective of this study is to provide a concise overview of the various molecular problems and possible treatment targets that have been linked and associated with the onset of certain psychiatric diseases. MethodsObtaining the data from NCBI, we applied GREIN to analyze our datasets. The protein-protein interaction, gene regulatory network, protein-drug-chemical, gene ontology, and pathway network were constructed using STRING, Funrich and DAVID libraries. In order to display our suggested network, we utilized Cytoscape and R studio, verifying our hub gene using roc analysis. ResultsWe discovered a number of strong candidate hub proteins in significant pathways, namely out of 32 (HLA-DRA, HLA-A, HLA-B, HLA-DOB and BRD2) common genes. We also identified a number of TFs (FOXC1, NFYA, RELA, GATA2, FOXL1, SRF and NFIC); miRNA (hsa-mir-129-2-3p, hsa-mir-148b-3p, hsa-mir-196a-5p, hsa-mir-26a-5p, hsa-mir-27a-3p, hsa-mir-23b-3p, hsa-mir-500a-3p, hsa-mir-423-5p, hsa-miR-142-5p, and hsa-miR-671-5p) and chemicals (Estradiol, Antirheumatic Agents, Valproic Acid, Selenium, Vitamin E, ICG 001, Ifosfamide, Tetrachlorodibenzodioxin, arsenic trioxide, entinostat, sodium arsenite and Hydralazine) may control DEGs in transcription as well as post-transcriptional expression levels. ConclusionIn summary, our computational methods have identified distinct potential biomarkers that demonstrate the impact of PTSD, Schizophrenia, and BD on autoimmune inflammation and infectious diseases. Additionally, we have identified pathways and gene regulators through which these psychiatric disorders may affect biological processes. Graphical AbstractThe graphical abstract demonstrates the thorough strategy of combining systems biology and computational technologies to identify significant markers and pathways in blood tissues impacted by post-traumatic stress disorder, Schizophrenia, and Bipolar disorder. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/708243v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1cd13bforg.highwire.dtl.DTLVardef@cb6392org.highwire.dtl.DTLVardef@f634cforg.highwire.dtl.DTLVardef@532bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological advances, researchers can sequence genomes in the thousands and probe numerous genomic activities of many species and conditions. Such studies have identified thousands of potential proteins, RNAs and associated activities. However there are conflicting interpretations of the results and therefore which regions of the genome are "functional". Here we investigate the relative strengths of associations between coding and non-coding gene functionality and genomic features, by comparing reliably annotated functional genes to non-genic regions of the genome. We find that the strongest and most consistent association between functional genes and genomic features are transcriptional activity and evolutionary conservation. We also evaluated sequence-based statistics, genomic repeats, epigenetic and population variation data. Other features strongly associated with function include histone marks, chromatin accessibility, genomic copy-number, and sequence alignment statistics such as coding potential and covariation. We also identify potential issues with SNP annotations in short non-coding RNAs, as some highly conserved ncRNAs have significantly higher than expected SNP densities. Our results demonstrate the importance of evolutionary conservation and transcription activity for indicating protein-coding and non-coding gene function. Both should be taken into consideration when differentiating between functional sequences and biological or experimental noise.

Patients with HbE/{beta}-thalassemia inheriting the same {beta}-globin mutations display varied clinical manifestations, the mechanism of which is only partially known. The study aimed to decipher the heterogenous basis of HbE/{beta}-thalassemia patients in more details by focusing on both hematological and genetic modifiers influencing the disease severity, which included-(i) HbF and HbE levels using Hb electrophoresis, (ii) {beta}-thalassemia mutations, (iii) anti3.7triplication using Gap-PCR, (iv) individual and cumulative effects of HbF-inducing SNPs in 4 major modifier genes, namely HBG2, BCL11A, HBSB1L_MYB intergenic-region, and HBBP1 which were genotyped using DNA sequencing and Real-time PCR-HRM methods. Accordingly, 130 diagnosed Bangladeshi patients with HbE/{beta}-thalassemia were enrolled and categorized as mild, moderate, and severe as per Mahidol scoring system. c.79G>A+IVS1_5G>C was the most predominant (73.8% of total) mutation pair across all the 3 severity groups, indicating secondary modifiers might influence the severity. Our study found both HbF and HbE protective to HbE/{beta}-thalassemia, as both were inversely related to the severity score (HbF: p<0.0001/r=-0.55; HbE: p<0.0001/r=-0.56). Four SNPs-XmnI-G{gamma}, rs2071348 (HBBP1), rs489544 and rs28384513 (HBS1L_MYB) showed significant association with the elevated HbF levels (p=0.005, 0.0001, 0.0001, 0.004 respectively). The multivariate analysis showed that the risk genotypes with single or combination of 2, 3,and 4 SNPs showed gradually increased risk [Odd Ratio (95%CI)= 2.51, 5.47, 19.5, 39.0, respectively] of less severe phenotype, suggesting that these linked SNP variants had a cumulative effect on both HbF level and clinical severity score. However, low HbE level and copresence of anti3.7triplication were found to nullify the ameliorating effect of multiple SNPs.

Osteoporosis affects millions of women globally. In this study, we applied bioinformatics methods to screen for novel diagnostic biomarkers of osteoporosis in women using the GSE62402 and GSE56814 datasets. PCSK5, ZNF225, and H1FX were used to construct a diagnostic model. ROC, calibration, and decision curve analyses were performed to assess the diagnostic performance on the training (GSE56814) and external (GSE56815) datasets. The expression level of model genes was validated in GEO datasets. Furthermore, five transcription factors (ETS1, NOTCH1, MAZ, ERG, and FLI1) were identified as common upstream regulators of model genes. PCSK5, ZNF225, and H1FX serve as novel diagnostic biomarkers, providing new insights into the pathogenesis of and treatment strategies for osteoporosis in women.

As cannabis use continues to rise among people with HIV (PWH), understanding its impact on immune function in this population is becoming increasingly important. To provide new insights on how cannabis modulates immune function, we analyzed single-nucleus multi-omic profiles of peripheral blood mononuclear cells (PBMCs) from PWH to characterize the changes in gene expression and chromatin accessibility associated with chronic cannabis exposure. We identified numerous differentially expressed genes (DEGs) between cannabis users and non-users in each cell type, approximately half of which were unique to individual cell types. Changes in pro- and anti-inflammatory gene expression associated with cannabis use are dependent on cell lineage and type. We identified hundreds of differential chromatin accessibility regions in each cell type, including cis-regulatory elements correlated with cell-type-dependent DEGs (e.g. NFKBIA in CD4+ T cells and CCL3L1 in classical monocytes). Multiple cannabis-associated transcription factors (e.g., NFKB1, FOS, and TCF7) emerge as regulators of the differentially expressed inflammatory genes. Furthermore, cannabis altered the communication between classical monocytes and lymphocytes. These findings indicate that cannabis-induced immunomodulatory effects are profound, dynamic and complex among cell types and that transcriptional changes are regulated at least in part by epigenetic mechanisms.

ObjectivesThe fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social elite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall. Material and MethodsWe analysed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries dated to I-III century CE (Lucus Feroniae and Isola Sacra) and one post-Classical cemetery dated to IV-VIII century CE (Selvicciola), all located in proximity to the city of Rome, Italy. ResultsWe detect significant differences in the oral microbiome taxonomic and functional composition across time periods and social classes, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible. DiscussionThe distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices. The rural position of this community may have mitigated the cyclical food crises that, instead, affected the contemporary Isola Sacra and the later community of Selvicciola, thereby buffering against the nutritional stress observed in these two locations.