Genomic Analysis Research Articles

Evaluation and characteristic analysis of SSRs from the transcriptomic sequences of Perilla crop (Perilla frutescens L.)

Perilla crop is a self-fertilizing annual plant, cultivated and used mainly in East Asia. Perilla frutescens var. frutescens seeds are rich in unsaturated fatty acids, which have health benefits, and Perilla frutescens var. crispa leaves are rich in anthocyanins. However, genomic analysis such as whole genome sequencing or genetic mapping has not been performed on Perilla crop. This current study confirms the abundance and diversity of 15,991 simple sequence repeats (SSRs) classified in previous studies in the Perilla genome, selects and designs 1,538 SSR primer sets, and confirms which SSR primer sets exhibit high polymorphism. Of the 15,991 SSRs classified, there were 9,910 (62%) dinucleotide repeats, 5,652 (35.3%) trinucleotide repeats, and 429 (2.7%) tetranucleotide repeats. Among these, the most identified was (CT)n with a total of 4,817. The 15,991 SSRs had 4 to 26 repeats. Four repeats were the most frequent with 11,084 (69.3%). A total of 1,538 SSR primers were selected and designed to confirm polymorphism, of which 157 showed persistent and clear polymorphism. Among these 157 SSR primer sets, 98 (62.4%) were dinucleotide repeats, 39 (24.8%) were trinucleotide repeats, and 20 (12.7%) were tetranucleotide repeats. Among 549 SSR primers that showed polymorphism, trinucleotide repeats showed persistent polymorphism at a high rate. Therefore, when developing SSR primer sets for Perilla crop in the future, it is recommended that trinucleotide repeats be selected first. These research results will be helpful in future genomic analysis and development of SSR primers in Perilla crop.

The OsNAC41-RoLe1-OsAGAP module promotes root development and drought tolerance in upland rice

Drought is a major environmental stress limiting crop yields worldwide. Upland rice (Oryza sativa) has evolved complex genetic mechanisms to adjust to drought stress. However, few genetic variants have been identified that mediate drought resistance in upland rice, and little is known about the evolution of this trait during domestication. Here, using a genome-wide association study in rice, we identified ROOT LENGTH 1 (RoLe1) controlling root length and drought resistance. We demonstrate that a G-to-T polymorphism in the RoLe1 promoter increases binding of the transcription factor OsNAC41 to activate its transcription. We also show that RoLe1 interacts with and interferes with the function of OsAGAP, an ARF-GTPase activating protein involved in auxin-dependent root development, to modulate root development. Furthermore, RoLe1 enhanced crop yield by increasing the seed setting rate under moderate drought conditions. Genomic evolution analysis showed that a newly arisen favorable allelic variant, proRoLe1-526T, originated from Region I (Midwest Asia) and was retained in upland rice during domestication. Our findings propose a OsNAC41-RoLe1-OsAGAP module, providing promising genetic targets for molecular breeding of drought-resistant varieties in rice.

Genomic and metabolomic analysis of Latilactobacillus sakei DCF0720 for black soybean yogurt fermentation

Lactic acid bacteria are commonly used in plant-based fermentation to reduce off-flavor and improve sensory characteristics. However, there have been few studies on Latilactobacillus sakei for plant-based yogurt fermentation and, particularly, its metabolic features at the genomic level remain unclear. This study aims to analyze the fermentation characteristics of the L. sakei DCF0720 strain and compare genetics and metabolic relations. For this, DCF0720 was used to ferment the black soybean milk and conduct the physicochemical analysis and sensory test. The genomic and metabolic analyses were performed by complete genome sequencing and 500 MHz 1H NMR, respectively. As a result, DCF0720 exhibited enhanced fermentation performance and sensory evaluations at 37 °C compared to 30 °C, which is generally recognized as the optimal growth temperature for most L. sakei strains. It also produced flavor enhancing volatile compounds such as acetoin and hydroxyacetone, possessing all three key genes for acetoin biosynthesis. DCF0720 lacks 2,3-butanediol dehydrogenase, which leads to the inhibition of acetoin production. DCF0720 possesses a complete pathway to utilize primary black soybean carbon sources such as sucrose, raffinose, and stachyose. DCF0720 also possesses genes for the GH28 family, including the key enzymes in the hydrolysis of pectin substances, which means eliminating the main soybean nonstarch polysaccharides. This study demonstrates that DCF0720 is a suitable starter for plant-based yogurt fermentation, providing a better understanding of fermentation conditions with genetic and metabolic features for black soybean yogurt. Various carbon source utilization abilities with depth metabolic pathway analysis provide that DCF0720 can be employed to develop enhanced starter cultures for black soybean yogurt and diverse plant-based yogurts.

Screening of potential targets and small-molecule drugs related to lipid metabolism in ovarian cancer based on bioinformatics

Backgroundabout 70% of ovarian cancer (OC) patients with postoperative chemotherapy relapse within 2-3 years due to drug resistance and metastasis, and the 5-year survival rate is only about 30%. Lipid metabolism plays an important role in OC.We try to explore the potential targets and drugs related to lipid metabolism to provide clues for the treatment of OC. Methodsthe gene expression profiles of OC and normal ovarian tissue samples were obtained from the cancer genome atlas(TCGA) and genotype-tissue expression databases(GTEx).The differentially expressed genes(DEGs) were analyzed.Lipid metabolism related genes (LMRGs) were downloaded from MSigDB database.The DEGs related to lipid metabolism in OC was obtained by intersection.And gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses were performed. The protein-protein interaction(PPI) network of lipid metabolism related DEGs was constructed, and seven algorithms were used to screen core potential target genes.Its expression in OC and prognostic ability were analyzed by Univariate Cox.Cmap database mining OC lipid metabolism related potential small-molecular drugs and docking. CCK8, scratch assay, transwell test and free fatty acid(FFA) assay, fluorescence detection of cellular fatty acid uptake, and the reactivity assay of CPT1A were used to detect the biological effects of drugs on OC cell..Rreverse transcription PCR(RT-qPCR) and WesternBlot were performed to measure the expression of core targets. Results437 DEGs related to lipid metabolism of OC were screened. GO and KEGG analysis showed that these DEGs were lipid metabolism,fatty acid metabolism,sphingolipid metabolism,PPAR signal pathway and so on.The PPI network based on lipid metabolism DEGs consists of 301 nodes and 1107 interaction pairs,and 6 core target genes were screened. ROC curve analysis showed that all of the 6 genes could predict the prognosis of OC. Three small molecular drugs Cephaeline, AZD8055 and GSK-1059615 were found by cmap and molecular docking showed that they all had good binding ability to target gene.Cephaeline has the strongest inhibitory effect on SKOV3 cells of OC, and could significantly inhibit cell migration and invasion regulate the mRNA and protein expression of some targets,and inhibit lipid metabolism process in ovarian cancer cells. Conclusionsix OC potential genes related to lipid metabolism were identified and verified,which can be used as potential biomarkers and therapeutic targets to evaluate the prognostic risk of OC patients.In addition, three small-molecular drugs that may be effective in the treatment of OC were unearthed, among which Cephaeline has the most potential. We speculate that Cephaeline may target six genes to inhibit progression of OC by affecting lipid metabolism.

Developing Patient-Derived 3D-Bioprinting models of pancreatic cancer

IntroductionPancreatic cancer (PC) remains a challenging malignancy, and adjuvant chemotherapy is critical in improving patient survival post-surgery. However, the intrinsic heterogeneity of PC necessitates personalized treatment strategies, highlighting the need for reliable preclinical models. ObjectivesThis study aimed to develop novel patient-derived preclinical PC models using three-dimensional bioprinting (3DP) technology. MethodsPatient-derived PC models were established using 3DP technology. Genomic and histological analyses were performed to characterize these models and compare them with corresponding patient tissues. Chemotherapeutic drug sensitivity tests were conducted on the PC 3DP models, and correlations with clinical outcomes were analyzed. ResultsThe study successfully established PC 3DP models with a modeling success rate of 86.96%. These models preserved genomic and histological features consistent with patient tissues. Drug sensitivity testing revealed significant heterogeneity among PC 3DP models, mirroring clinical variability, and potential correlations with clinical outcomes. ConclusionThe PC 3DP models demonstrated their utility as reliable preclinical tools, retaining key genomic and histological characteristics. Importantly, drug sensitivity profiles in these models showed potential correlations with clinical outcomes, indicating their promise in customizing treatment strategies and predicting patient prognoses. Further validation with larger patient cohorts is warranted to confirm their potential clinical utility.

Identification of Molecular Correlations of GSDMD with Pyroptosis inAlzheimer's Disease.

An analysis of bioinformatics and cell experiments was performed to verify the relationship between gasdermin D (GSDMD), an executive protein of pyroptosis, and Alzheimer's disease (AD). The training set GSE33000 was utilized to identify differentially expressed genes (DEGs) in both the AD group and control group, as well as in the GSDMD protein high/low expression group. Subsequently, the weighted gene co-expression network analysis (WGCNA) and the least absolute shrinkage and selection operator (LASSO) regression analysis were conducted, followed by the selection of the key genes for the subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The association between GSDMD and AD was assessed and confirmed in the training set GSE33000, as well as in the validation sets GSE5281 and GSE48350. Immunofluorescence (IF) was employed to detect the myelin basic protein (MBP), a distinctive protein found in the rat oligodendrocytes (OLN-93 cells). A range of concentrations (1-15 μmol/L) of β-amyloid 1-42 (Aβ1-42) were exposed to the cells, and the subsequent observations were made regarding cell morphology. Additionally, the assessments were conducted to evaluate the cell viability, the lactate dehydrogenase (LDH) release, the cell membrane permeability, and the GSDMD protein expression. A total of 7,492 DEGs were screened using GSE33000. Subsequently, WGCNA analysis identified 19 genes that exhibited the strongest correlation with clinical traits in AD. Additionally, LASSO regression analysis identified 13 key genes, including GSDMD, AFF1, and ATOH8. Furthermore, the investigation revealed that the key genes were associated with cellular inflammation based on GO and KEGG analyses. Moreover, the area under the curve (AUC) values for the key genes in the training and validation sets were determined to be 0.95 and 0.70, respectively. Significantly, GSDMD demonstrated elevated levels of expression in AD across both datasets. The positivity of MBP expression in cells exceeded 95%. As the concentration of Aβ1-42 action gradually escalated, the detrimental effects on cells progressively intensified, resulting in a gradual decline in cell survival rate, accompanied by an increase in lactate dehydrogenase release, cell membrane permeability, and GSDMD protein expression. The association between GSDMD and AD has been observed, and it has been found that Aβ1-42 can induce a significant upregulation of GSDMD in OLN-93 cells. This suggests that Aβ1-42 has the potential to induce cellular pyroptosis and can serve as a valuable cellular pyroptosis model for the study of AD.

The key monooxygenase involved in phenanthrene degradation of Ruegeria sp. PrR005

As a typical polycyclic aromatic hydrocarbon (PAH), phenanthrene is often present in diverse environments, leading to severe environmental contamination. However, bacterial degradation plays a crucial role in remediating phenanthrene contamination and has been widely adopted. The widely distributed marine Roseobacter-clade bacteria are frequently found in phenanthrene-contaminated environments, but their catalyzing ability and related molecular mechanism have been rarely elucidated. Our previous work showed Ruegeria sp. PrR005 isolated from the Pearl River Estuary sediment could degrade phenanthrene and other PAHs. Integrated approaches including multi-omics and biochemical analysis were applied here to explore its catabolism mechanism. The genomic and transcriptomic analysis indicated that six new P450 monooxygenase proteins could be closely associated with phenanthrene degradation. Heterologous expression of P450 monooxygenase candidates revealed that PrR005_00615, PrR005_04282, PrR005_04577 have considerable activity in phenanthrene removal, with PrR005_00615 being the primary contributor. Further, the biochemical and metabolic analysis revealed that PrR005_00615 could catalyze phenanthrene to phenanthrene-9,10-epoxide by introducing an oxygen atom at 9,10-carbon positions, which functioned as a monooxygenase. The present study provides compelling evidences of a novel enzyme responsible for catalyzing the initial step of phenanthrene transformation in PrR005. These findings hold significant importance in unraveling the mechanism behind phenanthrene degradation by Roseobacter-clade bacteria.

Insights into pathogenicity mechanisms of Phytophthora meadii, the abnormal leaf fall pathogen in rubber tree, through whole genome sequencing and analysis

Insights into pathogenicity mechanisms of Phytophthora meadii, the abnormal leaf fall pathogen in rubber tree, through whole genome sequencing and analysis

The S341P mutant MYOC renders the trabecular meshwork sensitive to cyclic mechanical stretch

The trabecular meshwork (TM) plays an essential role in the circulation of aqueous humor by sensing mechanical stretch. The balance between the outflow and inflow of aqueous humor is critical in regulating intraocular pressure (IOP). A dysfunctional TM leads to resistance to the outflow of aqueous humor, resulting in an elevated IOP, a major risk factor for glaucoma. It is widely accepted that mutant myocilin (MYOC) can cause damage to the TM. However, few studies have investigated how TM cells carrying mutant MYOC respond to cyclic mechanical stretch (CMS) and whether these cells are more sensitive to CMS under this genetic background. In this study, we applied mechanical stretch to TM cells using the Flexcell system to mimic physiological stress. In addition, we performed genome-wide transcriptome analysis and oxidized lipidomics to systematically compare the gene expression and oxylipin profiles of non-stretched control human primary TM cells, human primary TM cells under CMS (TM-CMS), and human primary TM cells overexpressing MYOCS341P under CMS (S341P-CMS). We found that TM cells that overexpressed MYOCS341P were more sensitive to mechanical stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that downregulated genes were most enriched in oxidative phosphorylation, indicating mitochondria dysfunction and the likelihood of oxidative stress. Oxidized lipidomics analysis revealed significant changes in oxylipin profiles between the S341P-CMS and TM-CMS groups. Through further genome-wide transcriptomic analysis, we identified several genes that may be involved in the sensitivity of TM cells that overexpressed MYOCS341P to mechanical stress, including SARM1, AHNAK2, NT5C, and SOX8. The importance of these genes was validated by quantitative real-time PCR. Collectively, our findings indicate that mitochondrial dysfunction may contribute to the damage that occurs to TM cells with a MYOCS341P background under mechanical stretch.

Pseudohoeflea coraliihabitans sp. nov., a poly-β-hydroxybutyrate-producing, halotolerant bacterium isolated from coral sediment in the Dapeng peninsula (Guangdong, China).

A Gram-stain-negative, strictly aerobic, motile, flagellated, rod-shaped, halotolerant, and poly-β-hydroxyalkanoate-producing bacterium, designated DP4N28-3T, was isolated from offshore sediment surrounding hard coral in the Dapeng peninsula (Guangdong, PR China). Growth occurred at 15-35 °C (optimal at 30 °C), pH 6.0-9.5 (optimal at 6.0-7.0), and 0.0-30.0 % NaCl concentration (w/v, optimal at 0.0-2.0 %), showing halotolerance. Phylogeny based on 16S rRNA gene sequences, five housekeeping genes, and genome sequences identified Pseudohoeflea suaedae DSM 23348T (98.1 %, 16S rRNA gene sequence similarity) as the most related species to strain DP4N28-3T. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain DP4N28-3T and P. suaedae DSM 23348T were all below the threshold of species demarcation. Major phenotypic differences were the flagella type and the limited sources of single carbon utilization by strain DP4N28-3T, which only included acetic acid, acetoacetic acid, d-glucuronic acid, and glucuronamide. Strain DP4N28-3T harboured the class I poly-β-hydroxyalkanoate synthase gene (phaC) and produced poly-β-hydroxybutyrate. The fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c, 49.4 %) and C16 : 0 (13.4 %). The major cellular polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, and sulfoquinovosyl diacylglycerol. The respiratory quinone was Q-10. The results of the phylogenetic, genomic, phenotypic, and chemotaxonomic analysis indicated that the isolated strain represents the type strain of a novel species. Based on these results, strain DP4N28-3T (=MCCC 1K05639T=KCTC 82803T) is proposed as the type strain of the novel species Pseudohoeflea coraliihabitans sp. nov.

Qualitative analysis of Fasciola gigantica excretory and secretory products coimmunoprecipitated with buffalo secondary infection sera shows dissimilar components from primary infection sera

Buffaloes cannot mount a robust adaptive immune response to secondary infection by Fasciola gigantica. Even if excretory and secretory products (ESPs) exhibit potent immunoregulatory effects during primary infection, research on ESPs in secondary infection is lacking, even though the ESP components that are excreted/secreted during secondary infection are unknown. Therefore, qualitative analysis of ESP during secondary infection was performed and compared with that of primary infection to deepen the recognition of secondary infection and facilitate immunoregulatory molecules screening. Buffaloes were divided into three groups: A (n = 3, noninfected), B (n = 3, primary infection) and C (n = 3, secondary infection). Buffaloes in the primary (0 weeks post infection; wpi) and secondary (-4 and 0 wpi) infection groups were infected with 250 metacercariae by oral administration. Then, sera were collected from groups at different wpi, and interacting proteins were precipitated by coimmunoprecipitation (Co-IP), qualitatively analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to infer their potential functions. In group C, 324 proteins were identified, of which 76 proteins were consistently identified across 7 time points (1, 3, 6, 8, 10, 13, and 16 wpi). Compared with 87 proteins consistently identified in group B, 22 proteins were identified in group C. Meanwhile, 34 proteins were only identified in group C compared to 200 proteins identified in group B. Protein pathway analysis indicated that these proteins were mainly involved in the cellular processes and metabolism of F. gigantica. Among them, 14-3-3θ was consistently identified in group C and may be involved in various cellular processes and innate immune signalling pathways. Members of the HSP family were identified in both groups B and C and may function in both primary and secondary infection processes. The proteins discovered in the present study will help to deepen the understanding of the molecular interactions between F. gigantica and buffalo during secondary infection and facilitate the identification of new potential immunoregulatory molecules.

Epidemiology and molecular evolution of GI.1 sapovirus in the recent era.

Sapovirus (SaV) infection is increasing worldwide. Herein, we provided evidence of a significant increase in SaV infection in Japan during 2010-2022, primarily due to the considerable (p = 0.0003) rise of the GI.1 genotype. Furthermore, we found that all major and minor SaV outbreaks in Japan, including the largest SaV outbreak in 2021-2022, were caused by the GI.1 genotype. Therefore, to get insight into the underlying molecular mechanism behind this rising trend of the SaV GI.1 type, we selected 15 SaV GI.1 outbreak strains for complete genome analysis through next-generation sequencing. Phylogenetically, our strains remained clustered in different branches in lineages I and II among the GI.1 genotype. We showed all amino acid (aa) substitutions in different open reading frames (ORFs) in these strains. Importantly, we have demonstrated that the strains involved in the largest SaV outbreak in Japan in 2021-2022 belonged to lineage II and possessed the third ORF. We have identified some unique aa mutations in these major outbreak strains in the NS1 and NS6-NS7 regions that are thought to be associated with viral pathogenicity, cell tropism, and epidemiological competence. Thus, in addition to enriching the database of SaV's complete sequences, this study provides insights into its important mutations.

Pesticides and winemaking: A comprehensive review of conventional and emerging approaches.

The use of pesticides in viticulture may play a crucial role in ensuring the health and quality of grapes. This review analyzes the most common pesticides used, illustrating their classification and toxicity, and their variations throughout the winemaking process. Fungicides are generally harmless or mildly toxic, whereas insecticides are classified as either highly or moderately hazardous. Potential alternatives to synthetic pesticides in wine production are also reviewed, thereby including biopesticides and biological agents. Analytical methods for detecting and quantifying pesticide residues in wine are then described, including liquid chromatography and gas chromatography coupled with mass spectrometry. This review also discusses the impact of the winemaking process on pesticide content. Pesticides with strong hydrophobicity were more likely to accumulate in solid byproducts, whereas hydrophilic pesticides were distributed more in the liquid phase. Grape's skin contains lipids, so hydrophobic pesticides adsorb strongly on grape surfaces and the clarification has been shown to be effective in the reduction of hydrophobic compounds. Therefore, the final wine could have more quantities of hydrophilic pesticides. Alcoholic fermentation has been shown to be crucial in pesticide dissipation. However, pesticide residues in wine have been shown an antagonistic effect on yeasts, affecting the safety and quality of wine products. Therefore, proteomic and genomic analyses of yeast growth are reviewed to understand the effects of pesticides on yeast during fermentation. The last section describes new effective methods used in removing pesticides from grapes and wine, thereby improving product quality and reducing harmful effects.

Longitudinal two-years comparative genomic analysis of respiratory Staphylococcus aureus isolates from ICU mechanically ventilated patients

Longitudinal two-years comparative genomic analysis of respiratory Staphylococcus aureus isolates from ICU mechanically ventilated patients

Acidic proteomes are linked to microbial alkaline preference in African lakes

Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphile isolates. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies to environmental adaptation.

Photoprotective sulfated mannogalactan from heterotrophic Bacillus velezensis blocks UV-A mediated matrix metalloproteinase expression and nuclear DNA damage in human dermal fibroblast

Prolonged exposure of human dermal fibroblasts (HDF) to ultraviolet (UV) radiation triggers the production of reactive oxygen species by upregulating the expression of matrix metalloproteinases (MMP), causing type-I collagen degradation and photoaging. A sulfated (1 → 3)/(1 → 4) mannogalactan exopolysaccharide (BVP-2) characterized as [→3)-α-Galp-{(1 → 4)-α-6-O-SO3-Manp}-(1 → 3)-α-6-O-SO3-Galp-(1→] was isolated from seaweed-associated heterotrophic bacterium Bacillus velezensis MTCC13097. Whole genome analysis of B. velezensis MTCC13097 (Accession number JAKYLL000000000) revealed saccharine biosynthetic gene clusters for exopolysaccharide production. BVP-2 administrated cells showed noteworthy reduction in mitochondrial superoxide (~85 %, p < 0.05) and ROS production (62 %) than those exhibited by UV-A irradiated HDF cells. Oxidative imbalance in HDF cells (after UV-A exposure) was recovered with BVP-2 treatment by significantly downregulating nitric oxide (NO) production (98.6 μM/mL, 1.9-fold) and DNA damage (⁓67 %) in comparison with UV-A induced cells (191.8 μM/mL and 98.7 %, respectively). UV-irradiated HDF cells resulted ~56 % downregulation expression of MMPs (1, 2, and 9) after treatment with BVP-2. Considerable amount of sulfation (18 %) along with (1 → 3)/(1 → 4) glycosidic linkages in BVP-2 could be pivotal factors for down-regulation of the intracellular MMP-1, which was further supported by molecular docking and structure-activity studies. The (1 → 3)/(1 → 4)-linked bacterial exopolysaccharide (BVP-2) might be used as prospective natural lead to attenuate and mitigate UV-A-induced photoaging.

Genome-guided bioprospecting for industrially important enzyme from a thermophilic Bacillus subtilis strain SR-7, an isolate from hot spring of Madhya Pradesh, India

The study focused on isolating thermophilic bacteria from the hot springs of Madhya Pradesh, India, with the aim of identifying strains capable of producing industrially valuable enzymes. Among the 15 isolated strains, SR-7 identified as Bacillus subtilis exhibited significant enzyme activity, leading to its selection for further investigation. Genomic analysis revealed key characteristics of SR-7, including a 3,593,163 base pair chromosome with a GC content of 44.14 %. The genome was found to contain 55 tRNA genes, four rRNA clusters, and 3744 protein-coding genes. These genes encompass essential metabolic pathways and genes responsible for thermophilic adaptation, highlighting the potential for industrial applications. Further experimentation demonstrated SR-7 have the ability to produce various enzymes of industrial significance, such as amylase, lipase, cellulase, protease, lecithinase, gelatinase, and pectinase. Importantly, enzyme production was observed across a broad pH range (6.5 to 10) and temperature spectrum, indicating the versatility and adaptability of SR-7 to different environmental conditions. The findings suggest that SR-7 holds promise as a valuable resource for the pharmaceutical and industrial sectors. Its capacity to produce thermostable enzymes suitable for a range of applications underscores its potential contribution to biotechnological processes. By harnessing the enzymatic capabilities of thermophilic bacteria like SR-7, industries can pursue more sustainable and efficient production methods, reducing reliance on traditional chemical processes and enhancing overall productivity. Further research into the enzymatic properties and genetic mechanisms of SR-7 may unveil additional avenues for its utilization in various industrial processes.

Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.).

A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: gtex-1), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34mm; FS = 32.73gtex-1; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.

Comprehensive Genomic Analysis of Puerarin in Inhibiting Bladder Urothelial Carcinoma Cell Proliferation and Migration.

Bladder urothelial carcinoma (BUC) ranks second in the incidence of urogenital system tumors, and the treatment of BUC needs to be improved. Puerarin, a traditional Chinese medicine (TCM), has been shown to have various effects such as anti-cancer effects, the promotion of angiogenesis, and anti-inflammation. This study investigates the effects of puerarin on BUC and its molecular mechanisms. Through GeneChip experiments, we obtained differentially expressed genes (DEGs) and analyzed these DEGs using the Ingenuity® Pathway Analysis (IPA®), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analyses. The Cell Counting Kit 8 (CCK8) assay was used to verify the inhibitory effect of puerarin on the proliferation of BUC T24 cells. String combined with Cytoscape® was used to create the Protein-Protein Interaction (PPI) network, and the MCC algorithm in cytoHubba plugin was used to screen key genes. Gene Set Enrichment Analysis (GSEA®) was used to verify the correlation between key genes and cell proliferation. A total of 1617 DEGs were obtained by GeneChip. Based on the DEGs, the IPA® and pathway enrichment analysis showed they were mainly enriched in cancer cell proliferation and migration. CCK8 experiments proved that puerarin inhibited the proliferation of BUC T24 cells, and its IC50 at 48 hours was 218μmol/L. Through PPI and related algorithms, 7 key genes were obtained: ITGA1, LAMA3, LAMB3, LAMA4, PAK2, DMD, and UTRN. GSEA showed that these key genes were highly correlated with BUC cell proliferation. Survival curves showed that ITGA1 upregulation was associated with poor prognosis of BUC patients. Our findings support the potential antitumor activity of puerarin in BUC. To the best of our knowledge, bioinformatics investigation suggests that puerarin demonstrates anticancer mechanisms via the upregulation of ITGA1, LAMA3 and 4, LAMB3, PAK2, DMD, and UTRN, all of which are involved in the proliferation and migration of bladder urothelial cancer cells.

Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics.

As genomics technologies advance, there is a growing demand for computational biologists trained for genomics analysis but instructors face significant hurdles in providing formal training in computer programming, statistics, and genomics to biology students. Fully online learners represent a significant and growing community that can contribute to meet this need, but they are frequently excluded from valuable research opportunities which mostly do not offer the flexibility they need. To address these opportunity gaps, we developed an asynchronous course-based undergraduate research experience (CURE) for computational genomics specifically for fully online biology students. We generated custom learning materials and leveraged remotely accessible computational tools to address 2 novel research questions over 2 iterations of the genomics CURE, one testing bioinformatics approaches and one mining cancer genomics data. Here, we present how the instructional team distributed analysis needed to address these questions between students over a 7.5-week CURE and provided concurrent training in biology and statistics, computer programming, and professional development. Scores from identical learning assessments administered before and after completion of each CURE showed significant learning gains across biology and coding course objectives. Open-response progress reports were submitted weekly and identified self-reported adaptive coping strategies for challenges encountered throughout the course. Progress reports identified problems that could be resolved through collaboration with instructors and peers via messaging platforms and virtual meetings. We implemented asynchronous communication using the Slack messaging platform and an asynchronous journal club where students discussed relevant publications using the Perusall social annotation platform. The online genomics CURE resulted in unanticipated positive outcomes, including students voluntarily discussing plans to continue research after the course. These outcomes underscore the effectiveness of this genomics CURE for scientific training, recruitment and student-mentor relationships, and student successes. Asynchronous genomics CUREs can contribute to a more skilled, diverse, and inclusive workforce for the advancement of biomedical science.