Differential Patterns Research Articles

Examining the integration of SDGs in a first-year methodology course: a case study in social education by admission pathway

Purpose This study aims to analyse how Sustainable Development Goals (SDGs) are incorporated into a first-year Social Education methodology course at a Spanish public university. It assesses the impact on students’ understanding of sustainability and its relevance to socio-educational research and future careers, considering different admission pathways. Design/methodology/approach A case study on integrating the SDGs into a methodology course, which involved 110 students. Students’ knowledge and perceptions were measured before and after the teaching experience using an online questionnaire. Differences based on admission pathways [Advances Vocational Training Programs (CFGS) and University Entrance Exam (PAU)] were explored. Findings Initially, students had a low understanding of sustainability and SDGs, with those entering through PAU having an even lower understanding. However, both groups showed significant improvement after the teaching experience. Interestingly, the pattern of differentiation was inverse, with PAU students showing a higher level of SDG knowledge compared to CFGS students by the end of the course. While students recognised the importance of SDGs in their careers, their personal involvement with them in daily life appeared moderate. Research limitations/implications The assessment tool, based on validated surveys, aims for better accuracy in measuring university students’ knowledge and perceptions of sustainability. Future research may broaden its scope to assess effectiveness in different courses and among diverse student groups. Practical implications The variations in student knowledge and perception about sustainability and the SDGs, before and after the teaching experience, and across different admission pathways, highlight the important role of higher education institutions in achieving equity and shaping future change agents’ perspectives. Originality/value These findings reveal how innovative educational experiences promote sustainability and social responsibility among university students, emphasising the crucial role of ongoing assessment in ensuring effective sustainability and equity education.

Comprehensive pathological evaluation of risk factors for metastasis after endoscopic resection of superficial esophageal squamous cell carcinoma.

Esophageal cancer is a major cause of cancer mortality worldwide. Endoscopic resection (ER) is a curative treatment for esophageal squamous cell carcinoma (ESCC). Predicting risk of metastasis is crucial for post-ER management. In this study, we aimed to identify predictors of metastasis by examining endoscopically resected specimens. The cohort of this retrospective multicenter study comprised 422 patients who had undergone ER for ESCC from 1994 to 2017. Inclusion required a histological diagnosis of pT1a-muscularis mucosa or pT1b-submucosa (SM) cancer. Central pathological review comprehensively evaluated depth of invasion, lymphovascular invasion (LVI), droplet infiltration (DI), infiltrative growth pattern, histological differentiation, intraductal and intraglandular involvement, solitary nest, resected margin, and other factors. Logistic regression was used to identify predictors of metastasis. Metastases were identified in 103 patients. Univariate analysis identified LVI, depth of invasion, and DI as significant predictive factors. Multivariate analysis identified LVI, depth of invasion pT1b-SM2 (odds ratio 2.72) and indeterminate (positive vertical margin) (odds ratio 3.63) compared with the reference category of pT1b-SM1 as independent predictors of metastasis. Conversely, there were no significant associations between metastasis and lesion size, differentiation, cytological atypia, or infiltration pattern. Subgroup analysis showed that both the number and layer of LVI were associated with metastasis risk. In addition, four or more foci of DI was an independent predictor of LVI. LVI and depth of invasion were significant predictors of metastasis in ESCC. Detailed pathological evaluation and standardized criteria are essential for accurately assessing risk of metastasis and guiding post-ER treatment strategies.

Ancient duplication and functional differentiation of phytochelatin synthases is conserved in plant genomes

Summary Despite the paramount importance in metal(loid) detoxification by phytochelatin synthase (PCS) genes, no comprehensive analysis of their evolutionary patterns has been carried out in land plants in general and in crops in particular. A phylogenetic large-scale analysis of gene duplication in angiosperms was carried out followed by in vitro recombinant protein assays as well as complementation analysis (growth, thiol-peptides, elements) of Arabidopsis cad1-3 mutant with four representative PCS genes from two model crop species, Malus domestica and Medicago truncatula. We uncovered a so far undetected ancient tandem duplication (D duplication) spanning the whole core eudicotyledon radiation. Complementation with PCS genes from both D-subclades from M. domestica and M. truncatula displayed clear in vivo conservation of the differences between D1 and D2 paralogous proteins in plant growth, phytochelatin and glutathione pools, as well as element contents under heavy metal(loid) stress. In vitro recombinant PCS analysis identified analogous patterns of differentiation, showing a higher activity of D2 PCS genes, so far largely overlooked, compared to their paralogs from the D1 clade. This suggests that in many other crop species where the duplication is present, the D2 copy might play a significant role in metal(loid) detoxification. The retention of both PCS paralogs and of their functional features for such long divergence time suggests that PCS copy number could be constrained by functional specialization and/or gene dosage sensitivity. These results uncover the patterns of PCS evolution in plant genomes and of functional specialization of their paralogs in the genomes of two important model crops.

Sensory processing subtypes relate to distinct emotional and behavioral phenotypes in a mixed neurodevelopmental cohort.

Children with autism and other neurodevelopmental concerns (NDC) frequently exhibit an array of sensory processing dysfunction phenotypes, posing a significant challenge their adaptive development. Additionally, these children often encounter difficulties with self-regulation, including emotion dysregulation, anxiety, and symptoms associated with attention and hyperactivity. However, further research is required to comprehend how patterns of sensory processing differences across neurodevelopmental conditions may contribute to regulatory control problems. Adopting a transdiagnostic perspective within the Research Domain Criteria (RDoC) framework, this study examined the relationship between clusters of sensory processing phenotypes and differential patterns of self-regulation behaviors. We recruited a sample of 117 participants (8-12 years) with a diverse range of neurodevelopmental concerns including autism, ADHD, anxiety, and sensory processing differences. This study aimed to (1) establish the prevalence of self-regulation problems in a community-recruited cohort of children with diverse NDCs; (2) construct data-driven sensory processing latent subtypes; (3) investigate group differences in emotion dysregulation, anxiety, and ADHD symptoms. Results showed that 39% of NDC children met clinically concerning thresholds for emotion dysregulation, 19% for anxiety, and 62% for ADHD. Second, latent profile analysis identified five sensory processing subtypes categorized by modality: Typical Processing, Intermediate/Mixed, Sensory Over-Responsive, Sensory Seeking, and Sensory Under-Responsive. Notably, the Sensory Over-Responsive group exhibited distinctively elevated anxiety scores, while the Sensory Seeking and Sensory Under-Responsive groups showed heightened ADHD scores. Intriguingly, the Sensory Over-Responsive, Sensory Under-Responsive, and Sensory Seeking subgroups all demonstrated elevated emotion dysregulation scores, suggesting a potential shared mechanism of emotion dysregulation that might elucidate the connection between sensory processing differences and increased anxiety and ADHD behaviors in children with autism and other NDCs.

Divergent Population Structure in Five Common Rockfish Species of Puget Sound, WA Suggests the Need for Species-Specific Management.

Quantifying connectivity between endangered or threatened marine populations is critical information for management and conservation, especially where abundance and productivity differ among such populations. Spatial patterns of such connectivity depend not only on extrinsic factors such as oceanography and bathymetry but also on intrinsic species-specific factors such as life history, demography and the location of glacial refugia. Nevertheless, population structure is often inferred from related or ecologically similar species. For example, the population structure in most rockfish species (Sebastes spp.) in the Salish Sea and the US West Coast is currently inferred from genetic data of three species that are known to hybridise in Puget Sound. Here, we determined the population structure and connectivity in five Puget Sound Rockfish species (Black [Sebastes melanops], Yellowtail [S. flavidus], Redstripe [S. proriger], Greenstriped [S. elongatus], and Puget Sound Rockfish [S. emphaeus]) from over 12,000 restriction-site associated DNA sequencing (RADseq) loci. We found species-specific patterns of genetic differentiation, attributable to both extrinsic and intrinsic factors. Specifically, Black and Puget Sound rockfishes showed no genetic differentiation; Yellowtail and Greenstriped rockfishes were structured according to known geographic barriers; and Redstripe Rockfish revealed evidence for temporal genetic differentiation, suggesting irregular recruitment influences population structure. Only Yellowtail Rockfish followed the federal DPS boundaries generally assumed for rockfish, further emphasizing the importance of species-specific management for the effective recovery and management of these rockfish populations and of marine species in general.

Genome-Wide Identification of the CAT Genes and Molecular Characterization of Their Transcriptional Responses to Various Nutrient Stresses in Allotetraploid Rapeseed

Brassica napus is an important oil crop in China and has a great demand for nitrogen nutrients. Cationic amino acid transporters (CAT) play a key role in amino acid absorption and transport in plants. However, the CATs family has not been reported in B. napus so far. In this study, genome-wide analysis identified 22 CAT members in the B. napus genome. Based on phylogenetic and synteny analysis, BnaCATs were classified into four groups (Group I–Group IV). The members in the same subgroups showed similar physiochemical characteristics and intron/exon and motif patterns. By evaluating cis-elements in the promoter regions, we identified some cis-elements related to hormones, stress and plant development. Darwin’s evolutionary analysis indicated that BnaCATs might have experienced strong purifying selection pressure. The BnaCAT family may have undergone gene expansion; the chromosomal location of BnaCATs indicated that whole-genome replication or segmental replication may play a major driving role. Differential expression patterns of BnaCATs under nitrate limitation, phosphate shortage, potassium shortage, cadmium toxicity, ammonium excess and salt stress conditions indicated that they were responsive to different nutrient stresses. In summary, these findings provide a comprehensive survey of the BnaCAT family and lay a foundation for the further functional analysis of family members.

A multi-class support vector machine classification model based on 14 microRNAs for forensic body fluid identification

MicroRNAs (miRNAs) are promising biomarkers for forensic body fluid identification owing to their small size, stability against degradation, and differential expression patterns. However, the expression of most body fluid-miRNAs is relative (differentially expressed in certain body fluids) rather than absolute (exclusively expressed in a specific body fluid). Moreover, different body fluids contain heterogeneous cell types, complicating their identification. Therefore, appropriate normalization strategies to eliminate non-biological variations and robust models to interpret expression levels accurately are necessary prerequisites for applying miRNAs in body fluid identification. In this study, the expression stability of six candidate reference genes (RGs) across five body fluids was validated using geNorm, NormFinder, BestKeeper and RankAggreg, and the most suitable combination of RGs (hsa-miR-484 and hsa-miR-191–5p) was identified under our experimental conditions. Subsequently, we systematically evaluated the expression patterns of the 28 most promising body fluid-specific miRNA markers using TaqMan RT-qPCR and selected the optimal combination of markers (12 miRNAs) to establish a multi-class support vector machine (MSVM) classification model. An independent test set (60 samples) was used to validate the accuracy of the proposed classification model, while an additional 30 casework samples were used to assess its robustness. The MSVM model accurately predicted the body fluid origin for almost all (59/60) single-source samples. Moreover, this model demonstrated the capability to identify aged forensic samples and to predict the primary components of mixed stains to a certain extent. In summary, this study presented a miRNA-based MSVM classification model for forensic body fluid identification using the qPCR platform. However, extensive validation, especially inter-laboratory collaborative exercises, is necessary before miRNA can be routinely applied in forensic identification practice.

PDLIM1, a novel miR-3940-5p target, regulates the malignant progression of diffuse large B-cell lymphoma

ABSTRACT Background PDZ And LIM domain protein 1 (PDLIM1), a protein-coding gene, has been widely reported to exhibit differential expression patterns across various human cancers, including hematological malignancies. This study aimed to investigate PDLIM1 expression pattern and its functional role in diffuse large B-cell lymphoma (DLBCL) both in vitro and in vivo. Methods PDLIM1 expression patterns were reanalyzed using data from the Gene Expression Omnibus, and the results were subsequently validated in patient tissue samples and a panel of four DLBCL cell lines. MicroRNA-3940-5p (miR-3940-5p) was identified as an upstream regulator of PDLIM1. The interaction between PDLIM1 and miR-3940-5p and its effects on DLBCL cellular activities and cancer development were further explored using a DLBCL mouse model. Results Elevated PDLIM1 expression was observed in DLBCL cells and tissues. Reduced cell proliferation and increased DLBCL cell apoptosis were observed following the knockdown of this gene. Furthermore, short hairpin RNA (shRNA)-mediated PDLIM1 knockdown diminished tumorigenesis of DLBCL cells in nude mice. miR-3940-5p was identified as an upstream regulator of PDLIM1. PDLIM1 expression and function were negatively modulated by the upregulation of miR-3940-5p, consequently affecting the malignant phenotype of DLBCL cells. Conclusion These findings suggest that the miR-3940-5p/PDLIM1 axis may play a crucial role in DLBCL pathogenesis and could potentially be exploited for therapeutic interventions.

Analyzing longitudinal trait trajectories using GWAS identifies genetic variants for kidney function decline

Understanding the genetics of kidney function decline, or trait change in general, is hampered by scarce longitudinal data for GWAS (longGWAS) and uncertainty about how to analyze such data. We use longitudinal UK Biobank data for creatinine-based estimated glomerular filtration rate from 348,275 individuals to search for genetic variants associated with eGFR-decline. This search was performed both among 595 variants previously associated with eGFR in cross-sectional GWAS and genome-wide. We use seven statistical approaches to analyze the UK Biobank data and simulated data, finding that a linear mixed model is a powerful approach with unbiased effect estimates which is viable for longGWAS. The linear mixed model identifies 13 independent genetic variants associated with eGFR-decline, including 6 novel variants, and links them to age-dependent eGFR-genetics. We demonstrate that age-dependent and age-independent eGFR-genetics exhibit a differential pattern regarding clinical progression traits and kidney-specific gene expression regulation. Overall, our results provide insights into kidney aging and linear mixed model-based longGWAS generally.

The facilitated osteogenic differentiation by extracellular proline treatment in in vitro cell cultivation using MC3T3E1 and hPDLF.

Proline is a major substrate in collagen biosynthesis and is required for collagen molecule formations. However, detailed explanations of the molecular basis through which proline functions in collagen biosynthesis have yet to be provided. Thus, genome-wide screening was employed to elucidate these in the pre-osteoblastic MC3T3-E1 and human periodontal ligament fibroblast (hPDLF) cell lines. Indeed, both cell lines represent important sources for collagen biosynthesis and tissue regeneration in the dental region, specifically treating extracellular proline during cultivations. The altered gene expression patterns were identified, and the precise expression patterns were confirmed by microarray. Cell viability and osteogenic differentiation patterns were examined using a range of experimental methods, such as the MTS assay, ALP staining, ARS staining, and collagen (COL)-type1A ELISA. Overall, we revealed a cell line-specific function of exogenous proline in collagen biosynthesis during osteogenic differentiation conditions with the candidate signaling pathways. These putative signaling networks could represent plausible answers to understanding collagen biosynthesis for regenerating connective tissues such as skin, muscle, and bone.

Multi-omic analyses of a twin pair with mirror image cleft lip identifies pathogenic variant in FGF20 modified by differential methylation upstream of ZFP57.

Disturbances in the intricate processes that control craniofacial morphogenesis can result in birth defects, most common of which are orofacial clefts (OFCs). Nonsyndromic cleft lip (nsCL), one of the phenotypic forms amongst OFCs, has a non-random laterality presentation with the left side being affected twice as often compared to the right side. This study investigates the etiology of nsCL and the factors contributing to its laterality using a pair of monozygotic twins with mirror-image cleft lip. We conducted whole-genome sequencing (WGS) analyses in a female twin pair with mirror image nsCL, their affected mother and unaffected father to identify etiopathogenic variants. Additionally, to identify possible cleft lip laterality modifiers, DNA-methylome analysis was conducted to test for differential methylation patterns between the mirror twins. Lastly, DNA methylation patterns were also analyzed on an independent cohort of female cases with unilateral cleft lip (left=22; right=17) for replication purposes. We identified a protein-altering variant in FGF20 (p.Ile79Val) within the fibroblast growth factor interacting family domain segregating with the nsCL in this family. Concurrently, DNA-methylome analysis identified differential methylation regions (DMRs) upstream of Zinc-finger transcription factor ZFP57 (Δβ > 5%). Replication of these results on an independent cohort, confirmed these DMRs, emphasizing their biological significance (p<0.05). Enrichment analysis indicated that these DMRs are involved in DNA methylation during early embryo development (FDR adjusted p-value = 1.3241E-13). Further bioinformatics analyses showed one of these DMRs acting as a binding site for transcription factor AP2A ( TFAP2A ), a key player in craniofacial development. Interactome analysis also suggested a potential role for ZFP57 in left/right axis specification, thus emphasizing its significance in cleft laterality. This study provides novel insights into the etiology of nsCL and its laterality, suggesting an interplay between etiopathogenic variants and DNA methylation in cleft laterality. Our findings elucidate the intricate mechanisms underlying OFCs development. Understanding these factors may offer new tools for prevention and management of OFCs, alleviating the burden on affected individuals, their families and global health.

Unveiling differential interaction pattern for iminium and alkanolamine forms of Sanguinarine with β-Lactoglobulin protein

A comparative study on the interaction of two tautomeric forms of sanguinarine (SANG), an alkaloid with therapeutic properties, with β-lactoglobulin (β-LG) protein was explored using spectroscopic and computational methods. The spectroscopic study reveals a high binding affinity for alkanolamine to monomeric β-LG (at pH = 9) as compared to iminium to dimeric β-LG (at pH = 6.2). Temperature dependent fluorescence study provides thermodynamic parameters for the binding process. Circular dichroism spectra showed changes in the secondary structure of the protein with major conformational transition from α-helix to β-sheets. Molecular docking and MD simulation validate the stable protein-drug complex during a 200 ns simulation period. All results clearly depict the differential interactions of two forms of SANG with β-LG protein. Overall, the characterization of SANG binding interactions with the whey milk protein provides valuable insights for pharmacological research and design of novel drug carriers based on β-LG protein.

Envenomation with Snake Venoms as a Cause of Death: A Forensic Investigation of the Decomposition Stages and the Impact on Differential Succession Pattern of Carcass-Attracted Coleopteran Beetles.

Coleoptera is the second-most significant insect group associated with decomposing carcasses, yet its role in the decomposition process and postmortem colonization following envenomation is poorly understood. This study aimed to investigate the effects of the venoms from Cerastes cerastes and Naja haje on the decomposition of rabbit carcasses while evaluating the main beetle taxa attracted to these decaying remains. Three groups of rabbits, each with five individuals, were utilized. The first group was injected with the venom of Cerastes cerastes, the second with Naja haje venom, and the control group received 0.85% physiological saline before euthanasia with CO2. Four decomposition stages (fresh, bloating, decay, and dry) with durations varying based on venom type and carcass condition were observed. A total of 647 individual beetles of six species (Necrobia rufipes, Attagenus sp., Dermestes frischii, D. maculatus, Bledius sp., and Apentanodes sp.) belonging to four families (Cleridae, Dermestidae, Staphylinidae, and Tenebrionidae) were collected and identified. D. maculatus was the most abundant species. Fewer beetles were attracted to carcasses envenomed with N. haje compared to the other groups. Envenomation by snake venom influences the attraction and succession rate of necrophilous coleopterans to carcasses, which is important for forensic investigations.

Abstract C025: Identification of cell-cell signaling programs across the tumor-tumor microenvironment ecosystem and associated with clinical status in neoadjuvant osimertinib treated patient samples revealed by spatial profiling

Abstract Lung cancer is the leading cause of cancer mortality, and despite improvements in treatment, tumors typically respond incompletely and resume growth after acquisition of drug resistance. Recent completion of a neoadjuvant osimertinib Phase II trial treating patients with surgically resectable stage I-IIIA EGFR-mutated non-small cell lung cancer (EGFRm NSCLC) (NCT03433469) (Blakely et. Al, JCO 2024) has highlighted the importance of further identifying non-genomic mechanisms of persistence and resistance to targeted therapy. Here we analyzed these patient samples to identify transcriptionally regulated signaling patterns enriched at Residual Disease (RD) after neoadjuvant osimertinib treatment compared to treatment naïve samples (TN), as well as signaling patterns enriched at RD in patients who ultimately develop disease recurrence after surgical resection compared to those who remain disease-free. Spatially resolved transcriptomic sequencing was performed, using the 10X Genomics Visium platform, on 36 tissue sections (n=9 TN, n=19 RD, n=4 Progressive Disease (PD), n=4 Tumor Adjacent Normal), from 25 patients. TN and PD samples were from standard-of-care surgical resections. 18 of 19 RD samples were from NCT03433469. The Visium array spots that tile the sequencing capture area are 55 µm in diameter, and thus can contain an estimated 1-10 cells within each array spot. After quality control, 91,582 array spots remained for downstream analysis. We identified high confidence tumor array spots annotated both as “Cancer” by a board-certified pathologist and with tumor characteristic copy number variations. Through dimensionality reduction clustering, we identified 10 major array spot clusters, including the high confidence tumor array spot cluster. These clusters were further subset into 44 high resolution clusters of array spot niches, 32 of which were shared across at least nine patients. Because array spots are not single-cell resolution, these niches represent spots with similar mixed cell type composition and transcriptional signatures. We identified significant increases in the CCL14+ Endothelial Cell Niche, CXCL2+ Endothelial Cell Niche, Lymphocytes + Endothelial Niche, and CXCL12+ Fibroblast Niche in RD samples compared to TN. We identified a cell signaling program defined by spatially co-expressed ligand-receptor pairs associated with focal adhesion, enriched in PD samples. This same pattern was enriched in RD samples from patients who had recurrent disease after surgical resection compared to RD samples from patients who remained disease free. These data describe an increase in immune trafficking in RD samples, as well as identify an EGFR- alternative signaling pathway correlating with osimertinib resistance. Identification of spatially resolved, differential architectural organization and signaling patterns in RD and PD states will expand our understanding of targeted therapy resistance in EGFRm NSCLC, with the potential to identify additional clinically actionable targets. Citation Format: Whitney Tamaki, Daniel L. Kerr, Wei Wu, Grant Eilers, Anatoly Urisman, Yu-Ting Chou, Philippe Gui, Shigeki Nanjo, Johannes R. Kratz, David M. Jablons, Trever G. Bivona, Collin M. Blakely. Identification of cell-cell signaling programs across the tumor-tumor microenvironment ecosystem and associated with clinical status in neoadjuvant osimertinib treated patient samples revealed by spatial profiling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C025.

Plasma metabolomic characteristics of atrial fibrillation patients with spontaneous echo contrast

BackgroundThe spontaneous echo contrast (SEC) in patients with atrial fibrillation (AF) indicates a prethrombic state that ultimately progresses into thrombus formation. A comprehensive understanding of specific plasma metabolomics characteristics may protect AF patients from thrombus, particularly in the early stage.ObjectivesThrough the investigation of metabolic pathways, we endeavor to uncover the metabolomic characteristics associated with SEC states, and to examine the differential metabolites by which may exert their influence on thrombotic states.MethodsPatients with AF were enrolled, and the participants were divided into three groups based on the results of the echocardiogram: non-SEC, low-SEC and high-SEC group. Samples were collected and subjected to non-targeted metabolomics analysis. The analytical process included data quality control, metabolite difference analysis, component analysis, Kegg cluster analysis, etc.ResultsOur metabolic phenotype revealed a clear differential metabolic pattern between the SEC and non-SEC. Specifically, we identified 35 and 142 significantly differential metabolites in venous and atrial plasma, respectively, suggesting that SEC may be involved in pervasive metabolic dysregulation and that the degree of metabolic dysregulation in atrial plasma is more severe than that in venous blood.ConclusionPatients with SEC have a significantly different metabolic pattern compared to those without SEC. Our work promoted the understanding of mechanism of the occurrence and development of SEC, facilitated the screening of the target metabolites for its therapeutic intervention, and provided evidence for the prevention and treatment of SEC or thrombosis in AF. Our work also provided new directions for subsequent research in related fields. In conclusion, our study not only provides a theoretical basis for understanding the occurrence and development of SEC in AF, but also provides recommendations for the daily diet of AF patients with SEC, such as a balanced intake of essential amino acids, avoiding excessive intake of benzoic acid, and intake of appropriate inositol.Clinical trial numberNot applicable.

Embracing the informative missingness and silent gene in analyzing biologically diverse samples

Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel. We developed the ABDS tool suite specifically for analyzing biologically diverse samples. Collectively, a mechanism-integrated group-wise pre-imputation scheme is proposed to retain informative missingness associated with signature genes, a cosine-based one-sample test is extended to detect group-silenced signature genes, and a unified heatmap is designed to display multiple sample groups. We describe the methodological principles and demonstrate the effectiveness of three analytics tools under targeted scenarios, supported by comparative evaluations and biomedical showcases. As an open-source R package, ABDS tool suite complements rather than replaces existing tools and will allow biologists to more accurately detect interpretable molecular signals among phenotypically diverse sample groups.

Characterization and evaluation of antioxidant potential of onion peel extract of eight differentially pigmented short-day onion (Allium cepa L.) varieties

Outer papery peel of onion bulb is an inevitable bio-waste generated in the course of postharvest handling and processing. Onion peels are rich source of nutraceutically important polyphenolic compounds having many therapeutic potentials. In this study, we characterized onion peel extract (OPE) of eight differentially pigmented short-day onion varieties through ultra-high-performance liquid chromatography coupled with high-resolution single stage Orbitrap spectrometry and evaluated the antioxidant potential. A total of 49 phenolic compounds were identified in this study which include 33 anthocyanin, 8 flavanol, 4 flavones, and 1 each of pyranoanthocyanin, chalcone, phenolic acid, and ellagitannins. Anthocyanin was the most abundant polyphenolic compound followed by flavanol in all the varieties. Among anthocyanin, 10 cyanidin, 10 delphinidin, 4 peonidin, 4 petunidin, 3 pelargonidin, and 2 malvidin were identified. Cyanidin-3-(6-malonylglucoside), delphinidin, and delphinidin-3-galactoside were the predominant pigment in dark red varieties (BDR and BRJ), and its abundance suggests a key role in the differential pigmentation pattern of onion peel. Total phenol content (TPC) in peels ranged from 1738.21 to 1757.76 mg GAE/100 g DW in dark red onion, 1306.58 to 1646.73 mg GAE/100 g DW in red onion, and 78.77 to 85.5 mg GAE/100 g DW in white onion varieties. The mean total anthocyanin content was maximum (28.23 mg/100 g DW) in dark red varieties (BDR) and minimum (0.11 mg/100 g DW) in white variety (BSW). Total antioxidant activity ranged from 4.71 to 79.80 μmol/g DW, 22.71 to 286.7 μmol/g DW, and 8.72 to 156.89 μmol/g DW estimated through FRAP, ABTS, and DPPH methods, respectively. In all three methods, it was maximum in dark red var. BDR and minimum in white var. BSU.

Life Course Stressors, Latent Coping Strategies, Alcohol Use, and Latent Coping Strategies Among People with HIV.

People with HIV (PWH) have often experienced chronic stressors across their lifespan, including adverse childhood experiences (ACES), lifetime economic hardship (LEH), and concurrent stressors associated with living in urban areas (urban stress). Prolonged exposure to stressors might result in differential coping patterns among PWH that can impact care trajectories. We utilized a life course-informed approach to examine chronic stressors as antecedents of latent coping strategies among PWH in care. High-risk alcohol use and non-adherence to anti-retroviral therapy (ART) were examined as consequences of latent coping strategies. Data were utilized from the baseline and interim follow-up visit of the New Orleans Alcohol Use in HIV (NOAH) study. Three latent classes of coping strategies were identified: avoidance coping (31%), low-frequency coping (43%), and problem-solving coping (25%). Exposure to ACES was associated with greater use of avoidance versus low-frequency coping class at wave II. Urban stress was associated with greater use of avoidance coping compared to problem-solving or low-frequency coping classes at wave II. LEH was associated with greater use of low-frequency coping at wave II. Those utilizing low-frequency coping had a two-fold increase in ART non-adherence compared to problem-solving coping. PWH utilizing avoidance and low-frequency coping had a nearly two-fold increase in high-risk alcohol use versus problem-solving coping. These findings reveal important coping classifications that are linked to stressors across the life course of PWH. An understanding of coping styles and stressors may aid in improving the continuum of care among PWH by reducing alcohol use and improving medication adherence.

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration.

Antler is the only organ that can fully regenerate annually in mammals. However, the regulatory pattern and mechanism of gene expression and cell differentiation during this process remain largely unknown. Here, we obtain comprehensive assembly and gene annotation of the sika deer (Cervus nippon) genome. Together with large-scale chromatin accessibility and gene expression data, we construct gene regulatory networks involved in antler regeneration, identifying four transcription factors, MYC, KLF4, NFE2L2, and JDP2 with high regulatory activity across whole regeneration process. Comparative studies and luciferase reporter assay suggest the MYC expression driven by a cervid-specific regulatory element might be important for antler regenerative ability. We further develop a model called cTOP which integrates single-cell data with bulk regulatory networks and find PRDM1, FOSL1, BACH1, and NFATC1 as potential pivotal factors in antler stem cell activation and osteogenic differentiation. Additionally, we uncover interactions within and between cell programs and pathways during the regeneration process. These findings provide insights into the gene and cell regulatory mechanisms of antler regeneration, particularly in stem cell activation and differentiation.

Physiological, transcriptomic, and metabolomic analyses of the chilling stress response in two melon (Cucumis melo L.) genotypes

BackgroundChilling stress is a key abiotic stress that severely restricts the growth and quality of melon (Cucumis melo L.). Few studies have investigated the mechanism of response to chilling stress in melon.ResultsWe characterized the physiological, transcriptomic, and metabolomic response of melon to chilling stress using two genotypes with different chilling sensitivity (“162” and “13-5A”). “162” showed higher osmotic regulation ability and antioxidant capacity to withstand chilling stress. Transcriptome analysis identified 4395 and 4957 differentially expressed genes (DEGs) in “162” and “13-5A” under chilling stress, respectively. Metabolome analysis identified 615 and 489 differential enriched metabolites (DEMs) were identified in “162” and “13-5A” under chilling stress condition, respectively. Integrated transcriptomic and metabolomic analysis showed enrichment of glutathione metabolism, and arginine (Arg) and proline (Pro) metabolism, with differential expression patterns in the two genotypes. Under chilling stress, glutathione metabolism-related DEGs, 6-phosphogluconate dehydrogenase (G6PDH), glutathione peroxidase (GPX), and glutathione s-transferase (GST) were upregulated in “162,” and GSH conjugates (L-gamma-glutamyl-L-amino acid and L-glutamate) were accumulated. Additionally, “162” showed upregulation of DEGs encoding ornithine decarboxylase, Pro dehydrogenase, aspartate aminotransferase, pyrroline-5-carboxylate reductase, and spermidine synthase and increased Arg, ornithine, and Pro. Furthermore, the transcription factors (TFs), MYB, ERF, MADS-box, and bZIP were significantly upregulated, suggesting their crucial role in chilling tolerance of melon.ConclusionsThese findings elucidate the molecular response mechanism to chilling stress in melon and provide insights for breeding chilling-tolerant melon.