Accession ID Research Articles

Screening of differential gene expression patterns through survival analysis for diagnosis, prognosis and therapies of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of kidney cancer. Although there is increasing evidence linking ccRCC to genetic alterations, the exact molecular mechanism behind this relationship is not yet completely known to the researchers. Though drug therapies are the best choice after the metastasis, unfortunately, the majority of the patients progressively develop resistance against the therapeutic drugs after receiving it for almost 2 years. In this case, multi-targeted different variants of therapeutic drugs are essential for effective treatment against ccRCC. To understand molecular mechanisms of ccRCC development and progression, and explore multi-targeted different variants of therapeutic drugs, it is essential to identify ccRCC-causing key genes (KGs). In order to obtain ccRCC-causing KGs, at first, we detected 133 common differentially expressed genes (cDEGs) between ccRCC and control samples based on nine (9) microarray gene-expression datasets with NCBI accession IDs GSE16441, GSE53757, GSE66270, GSE66272, GSE16449, GSE76351, GSE66271, GSE71963, and GSE36895. Then, we filtered these cDEGs through survival analysis with the independent TCGA and GTEx database and obtained 54 scDEGs having significant prognostic power. Next, we used protein-protein interaction (PPI) network analysis with the reduced set of 54 scDEGs to identify ccRCC-causing top-ranked eight KGs (PLG, ENO2, ALDOB, UMOD, ALDH6A1, SLC12A3, SLC12A1, SERPINA5). The pan-cancer analysis with KGs based on TCGA database showed the significant association with different subtypes of kidney cancers including ccRCC. The gene regulatory network (GRN) analysis revealed some crucial transcriptional and post-transcriptional regulators of KGs. The scDEGs-set enrichment analysis significantly identified some crucial ccRCC-causing molecular functions, biological processes, cellular components, and pathways that are linked to the KGs. The results of DNA methylation study indicated the hypomethylation and hyper-methylation of KGs, which may lead the development of ccRCC. The immune infiltrating cell types (CD8+ T and CD4+ T cell, B cell, neutrophil, dendritic cell and macrophage) analysis with KGs indicated their significant association in ccRCC, where KGs are positively correlated with CD4+ T cells, but negatively correlated with the majority of other immune cells, which is supported by the literature review also. Then we detected 10 repurposable drug molecules (Irinotecan, Imatinib, Telaglenastat, Olaparib, RG-4733, Sorafenib, Sitravatinib, Cabozantinib, Abemaciclib, and Dovitinib.) by molecular docking with KGs-mediated receptor proteins. Their ADME/T analysis and cross-validation with the independent receptors, also supported their potent against ccRCC. Therefore, these outputs might be useful inputs/resources to the wet-lab researchers and clinicians for considering an effective treatment strategy against ccRCC.

Exploring genetic associations between metabolites and atopic dermatitis: insights from bidirectional Mendelian randomization analysis in European population.

There is growing evidence indicating a complex interaction between blood metabolites and atopic dermatitis (AD). The objective of this study was to investigate and quantify the potential influence of plasma metabolites on AD through Mendelian randomization (MR) analysis. Our procedures followed these steps: instrument variable selection, primary analysis, replication analysis, Meta-analysis of results, reverse MR analysis, and multivariate MR (MVMR) analysis. In our study, the exposure factors were derived from the Canadian Longitudinal Study on Aging (CLSA), encompassing 8,299 individuals of European descent and identifying 1,091 plasma metabolites and 309 metabolite ratios. In primary analysis, AD data, was sourced from the GWAS catalog (Accession ID: GCST90244787), comprising 60,653 cases and 804,329 controls. For replication, AD data from the Finnish R10 database included 15,208 cases and 367,046 controls. We primarily utilized the inverse variance weighting method to assess the causal relationship between blood metabolites and AD. Our study identified significant causal relationships between nine genetically predicted blood metabolites and AD. Specifically, 1-palmitoyl-2-stearoyl-GPC (16:0/18:0) (OR = 0.92, 95% CI 0.89-0.94), 1-methylnicotinamide (OR = 0.93, 95% CI 0.89-0.98), linoleoyl-arachidonoyl-glycerol (18:2/20:4) [1] (OR = 0.94, 95% CI 0.92-0.96), and 1-arachidonoyl-GPC (20:4n6) (OR = 0.94, 95% CI 0.92-0.96) were associated with a reduced risk of AD. Conversely, phosphate / linoleoyl-arachidonoyl-glycerol (18:2/20:4) [2] (OR = 1.07, 95% CI 1.04-1.10), docosatrienoate (22:3n3) (OR = 1.07, 95% CI 1.04-1.10), retinol (Vitamin A) / linoleoyl-arachidonoyl-glycerol (18:2/20:4) [2] (OR = 1.08, 95% CI 1.05-1.11), retinol (Vitamin A) / linoleoyl-arachidonoylglycerol (18:2/20:4) [1] (OR = 1.08, 95% CI 1.05-1.12), and phosphate / linoleoyl-arachidonoyl-glycerol (18:2/20:4) [1] (OR = 1.09, 95% CI 1.07-1.12 were associated with an increased risk of AD. No evidence of reverse causality was found in the previously significant results. MVMR analysis further confirmed that 1-palmitoyl-2-stearoyl-GPC (16:0/18:0) and 1-methylnicotinamide are independent and dominant contributors to the development of AD. Our study revealed a causal relationship between genetically predicted blood metabolites and AD. This discovery offers specific targets for drug development in the treatment of AD patients and provides valuable insights for investigating the underlying mechanisms of AD in future research.

Antagonistic potential of Trichoderma strains isolated from Musa paradisiaca cv. Malnad Rasbale grown farmyards against Foc race 4 pathogen

Foc race 4 is a causative pathogen for Panama wilt disease of Musa Paradisiaca cv. Malnad Rasbale. The cost-effective measure to control rather than the usage of agrochemicals is still not available for this cultivar. Trichoderma strains act as an antagonistic agent against different phytopathogenic fungi including many pathogenic races of Panama wilt-causing pathogens. An attempt has been made to recognize the mode of action of this antagonistic agent in in vitro conditions and interaction between six Trichoderma strains. Foc race 4 was first investigated by dual plate culture method on PDA medium. This study revealed the potential of native strain KUVKU-TH02 for the biological control of Foc race 4 pathogen affecting Malnad Rasbale cultivar in in vivo conditions rather than native isolates KUVKU-TH01, KUVKU-TV01 and KUVKU-TV02. Observations revealed the lysis of hyphal ending in inhibited colonies of the fungal pathogen. Pure culture of isolated fungal strains incubated on potato dextrose broth made a path to isolate DNA for identification and molecular characterization studies. Upon DNA sequencing, native isolates sequences were deposited to NCBI genebank to gain accession IDs. The phylogenetic tree built showed the evolutionary relationship between the isolates and also the potency of native biocontrol isolates against procured isolates.

Whole genome sequence of Lactiplantibacillus plantarum strain HA9 isolated from conventional Iraqi cheese: First report

Background: Lactiplantibacillus plantarum is a renowned probiotic known for its ability to enhance health when ingested in sufficient quantities. While L. plantarum typically exhibits unique characteristics, variations in strains and environments can occur. Therefore, it is crucial to conduct genetic identification of the strain before incorporating it into products or administering it for health benefits.Methods: After being isolated from classic artisanal milk cheeses, the bacterial DNA extraction kit from GENEAID, Korea, was used, and strain HA9's genomic DNA was isolated. Then, the highly conserved section of ribosomal RNA was amplified with universal primers. The results were confirmed by a blast analysis of the NCBI database. The genome of HA9 was sequenced using the Illumina and PacBio Sequel II technologies (HN00194138; Psomagen/USA). The Prokaryotic Dynamic Programming Gene-Finding Algorithm software was applied to forecast coding genes. The Pathosystems Resource Integration Center constructed the L. plantarum genome.Result: According to the findings, the genome of the L. plantarum HA9 strain has a length of 3,321,986 bp and a GC percentage of 44.40. This assembled genome contained a total of 1,420 coding proteins and 82 contigs, as discovered by the Comprehensive Genome Analysis. The isolate had been submitted to the NCBI and received the HA9 genome sequence (accession ID: JAUTDL000000000.1).Conclusion Microbes' whole-genome sequencing plays a crucial role in clarifying their probiotic properties and enables accurate identification down to the strain level. The authors argue that further research should be done on probiotics' whole genomes, with a special emphasis on second-generation strains.Keywords: Lactiplantibacillus plantarum; Probiotics; Whole genome sequencing

In silico approach for the identification of tRNA-derived small non-coding RNAs in SARS-CoV infection.

tsRNAs (tRNA-derived small non-coding RNAs), including tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been implicated in some viral infections, such as respiratory viral infections. However, their involvement in SARS-CoV infection is completely unknown. A comprehensive analysis was performed to determine tsRNA populations in a mouse model of SARS-CoV-infected samples containing the wild-type and attenuated viruses. Data from the Gene Expression Omnibus (GEO) dataset at NCBI (accession ID GSE90624 ) was used for this study. A count matrix was generated for the tRNAs. Differentially expressed tRNAs, followed by tsRNAs derived from each significant tRNAs at different conditions and time points between the two groups WT(SARS-CoV-MA15-WT) vs Mock and ΔE (SARS-CoV-MA15-ΔE) vs Mock were identified. Notably, significantly differentially expressed tRNAs at 2dpi but not at 4dpi. The tsRNAs originating from differentially expressed tRNAs across all the samples belonging to each condition (WT, ΔE, and Mock) were identified. Intriguingly, tRFs (tRNA-derived RNA fragments) exhibited higher levels compared to tiRNAs (tRNA-derived stress-induced RNAs) across all samples associated with WT SARS-CoV strain compared to ΔE and mock-infected samples. This discrepancy suggests a non-random formation of tsRNAs, hinting at a possible involvement of tsRNAs in SARS-CoV viral infection.

Identification of the SIRT1 gene's most harmful non-synonymous SNPs and their effects on functional and structural features-an in silico analysis.

The sirtuin (Silent mating type information regulation 2 homolog)1(SIRT1) protein plays a vital role in many disorders such as diabetes, cancer, obesity, inflammation, and neurodegenerative and cardiovascular diseases. The objective of this in silico analysis of SIRT1's functional single nucleotide polymorphisms (SNPs) was to gain valuable insight into the harmful effects of non-synonymous SNPs (nsSNPs) on the protein. The objective of the study was to use bioinformatics methods to investigate the genetic variations and modifications that may have an impact on the SIRT1 gene's expression and function. nsSNPs of SIRT1 protein were collected from the dbSNP site, from its three (3) different protein accession IDs. These were then fed to various bioinformatic tools such as SIFT, Provean, and I- Mutant to find the most deleterious ones. Functional and structural effects were examined using the HOPE server and I-Tasser. Gene interactions were predicted by STRING software. The SIFT, Provean, and I-Mutant tools detected the most deleterious three nsSNPs (rs769519031, rs778184510, and rs199983221). Out of 252 nsSNPs, SIFT analysis showed that 94 were deleterious, Provean listed 67 dangerous, and I-Mutant found 58 nsSNPs resulting in lowered stability of proteins. HOPE modelling of rs199983221 and rs769519031 suggested reduced hydrophobicity due to Ile 4Thr and Ile223Ser resulting in decreased hydrophobic interactions. In contrast, on modelling rs778184510, the mutant protein had a higher hydrophobicity than the wild type. Our study reports that three nsSNPs (D357A, I223S, I4T) are the most damaging mutations of the SIRT1 gene. Mutations may result in altered protein structure and functions. Such altered protein may be the basis for various disorders. Our findings may be a crucial guide in establishing the pathogenesis of various disorders.

First microphological and molecular parasitological survey of Benedenia in humpback grouper (Cromileptes altivelis) of Lampung and Situbondo, Indonesia

Abstract. Amiin MK, Subekti S, Masithah ED, Nirmala D, Yunus M, Santanumurti MB, Rivaie AR. 2023. First microphological and molecular parasitological survey of Benedenia in humpback grouper (Cromileptes altivelis) of Lampung and Situbondo, Indonesia. Biodiversitas 24: 6858-6867. Capsalid monogenean infections, such as Benedenia, affect grouper aquaculture production. Benedenia will cause lesions and skin damage which will cause fish prices to drop. Secondary infection from bacteria, viruses, and fungi by Benedenia triggers a slow growth rate and even mortality. Benedenia infection on grouper has been conducted in Indonesia, specifically in this study in Lampung and Situbondo. However, molecular identification of this parasite is still lacking. This study aims to determine the microscopic and molecular characteristics of Benedenia from the Hurun Bay waters of Lampung and the North Coast of the Java Sea, Situbondo. The main parameters observed in this study were DNA base sequence, morphology, and phylogenetic tree. Benedenia from Lampung (637 bp) and Situbondo (741 bp) in this study was confirmed by the morphological and molecular close as Benedenia sargocentron with nucleotides. Interestingly, the similarity was less than 98% with B. sargocentron with accession ID JN797597.1 (similarity of 97.15% from Lampung and 86.33% from Situbondo). It could be indicated as a new species of Benedenia. The prevalence of Benedenia in Lampung was 90%, while Situbondo showed 80% with 3 parasite/fish intensity for each location. The outcome of this study is the characteristics of Benedenia from Lampung and Situbondo were similar to B. sargocentron according to morphological and molecular identification. This is the first report of B. sargocentron from Lampung and Situbondo since no molecular identification has been done in those places to confirm their species. Further research by another molecular target apart from 28S rRNA should be needed to identify this parasite more accurately.

IN-SILICO CHARACTERIZATION OF HUMAN HER2 GENE TO PREDICT THE BREAST CANCER ASSOCIATED BIOMARKERS

HER2 gene hyperactivation is responsible for the incidence of invasive breast cancer (BC). It leads to over expression of HER2 receptors in breast cells resulting in abnormal receptor dimerization and signal transduction cascade initiation. It ultimately causes uncontrolled proliferation of breast cells. Therefore, this is the most susceptible target gene for BC treatment. HER2 gene transcript with accession ID ENST00000269571.10 was selected for association analysis in present study. A total of ten single nucleotide polymorphisms (SNPs) of gene were analyzed using in-silico tools like CELLO, PROTPARAM, SOPMA, and SWISSMODEL. These tools helped in determining the effect of variants on sub-cellular localization, physiochemical properties, and secondary (2D) and tertiary (3D) structures of mutated proteins. Variants rs1249755832, rs769703068, rs1567913219, and rs1213602748 altered the localization of mutated proteins. SNPs rs1213602748, rs769703068, and rs1249755832 considerably changed the isoelectric point (pI), extinction coefficient, instability index, aliphatic index, and GRAVY. Variant rs769703068 caused a change in all four properties of the 2D structure, i.e., alpha helix, extended strand, beta-turn, and random coil. Polymorphisms that caused a significant deviation in 3D configuration were rs769703068, rs144434331, and rs146177313. These variants can be recommended as biomarkers for HER2+ BC cell diagnosis.

Racial disparities in Clostridioides difficile testing in three southeastern US hospitals.

To analyze Clostridioides difficile testing in 3 hospitals in central North Carolina to validate previous racial health-disparity findings. We completed a retrospective analysis of inpatient C. difficile tests from 2015 to 2021 at 3 university-affiliated hospitals in North Carolina. We calculated the number of C. difficile tests per 1,000 patient days stratified by race: White, Black, and non-White, non-Black (NWNB). We defined a unique C. difficile test as one that occurred in an inpatient unit with a matching laboratory accession ID and on differing calendar days. Tests were evaluated overall, by hospital, by year, and by positivity rate. In total, 35,160 C. difficile tests and 2,571,850 patient days across all 3 hospitals from 2015 to 2021 were analyzed. The median number of C. difficile tests per 1,000 patient days was 13.85 (interquartile range [IQR], 9.88-16.07). Among all C. difficile tests, 5,225 (15%) were positive. White patients were administered more C. difficile tests (14.46 per 1,000 patient days) than Black patients (12.96; P < .0001) or NWNB race patients (10.27; P < .0001). Black patients were administered more tests than NWNB patients (P < .0001). White patients tested positive at a similar rate to Black patients (15% vs 15%; P = .3655) and higher than NWNB individuals (12%; P = .0061), and Black patients tested positive at a higher rate than NWNB patients (P = .0024). White patients received more C. difficile tests than Black and NWNB patient groups when controlling for race patient days. Future studies should control for comorbidities and investigate community onset of C. difficile by race and ethnicity.

Identification and characterization of Azotobacter sp. screened from different agro-climatic zones in Telangana.

Declining soil quality due to overexploited used of chemical-based fertilizers, pesticides and insecticides have deleterious effect on soil health. This has resulted in decreased productivity. The use of azotobacter sp. as an alternative to the chemical based Agri-practice can be a remedial step to increase soil healthiness and in turn productivity. For the proposed research, soil sample from rhizosphere of Pigeon pea cultivated at Mahabubnagar and Medchal agroclimatic zone of Telangana. The Azotobacter sp. were isolated and maintained on Ashby’s mannitol agar medium. The Azotobacter sp. were evaluated by morphological, biochemical and molecular attributes. Biochemical tests and 16s rRNA sequencing revealed identification of strains as Azotobacter beijerinckii strain (BKPOU06TS) and Azotobacter tropicalis strain (BKPOU08TS). The 16s rRNA sequences of Azotobacter beijerinckii strain (BKPOU06TS) and Azotobacter tropicalis strain (BKPOU08TS) were submitted to GenBank with accession ID- OP536202 and OP536206 respectively

Molecular Characterization of spa, hld, fmhA, and lukD Genes and Computational Modeling the Multidrug Resistance of Staphylococcus Species through Callindra harrisii Silver Nanoparticles.

The problem of multidrug resistance in bacterial pathogens is significant and is related to the high morbidity and death rates of living things due to increased levels of beta-lactamases. Plant-derived nanoparticles have gained a great significance in the field of science and technology to combat bacterial diseases, especially multidrug-resistant bacteria. This study examines the multidrug resistance and virulent genes of identified pathogenic Staphylococcus species obtained from Molecular Biotechnology and Bioinformatics Laboratory (MBBL), culture collection. The polymerase chain reaction-based characterization of Staphylococcus aureus and Staphylococcus argenteus having ON875315.1 and ON876003.1 accession IDs revealed the presence of the spa, LukD, fmhA, and hld genes. The green synthesis of silver nanoparticles (AgNPs) was carried out by utilizing the leaf extract of Calliandra harrisii, of which metabolites act as capping and reducing agents for the precursor of nano-synthesis, i.e., AgNO3 of 0.25 M. The synthesized AgNPs were characterized via UV-vis spectroscopy, Fourier transform infrared spectroscopy, scanning electron microscopy, and energy-dispersive X-ray analysis which inferred the bead-like shape of our nanoparticles with the size of 2.21 nm with the existence of aromatic and hydroxyl functional groups at surface plasmon resonance of 477 nm. The antimicrobial activity by AgNPs showed 20 mm inhibition of Staphylococcus species as compared to the vancomycin and cefoxitin antibiotics along with crude plant extract, which showed a minimum zone of inhibition. The synthesized AgNPs were also analyzed for various biological activities like anti-inflammatory with 99.15% inhibition in protein denaturation, antioxidant with 99.8% inhibition in free radical scavenging, antidiabetic with 90.56% inhibition of alpha amylase assay, and anti-haemolytic with 89.9% inhibition in cell lysis which shows good bioavailability and biocompatibility of the nanoparticles with the biological system of the living being. The amplified genes (spa, LukD, fmhA, and hld) were also analyzed for their interaction with AgNPs computationally at the molecular level. The 3-D structure of AgNP and amplified genes was retrieved from ChemSpider (ID: 22394) and Phyre2 online server, respectively. The binding affinities of AgNP with spa, LukD, fmhA, and hld were -7.16, -6.5, -6.45, and -3.3 kJ/mol, respectively, which infers a good docking score except of hld which is -3.3 kJ/mol due to its small size. The salient features of biosynthesized AgNPs proved to be an effective approach in combating the multidrug-resistant Staphylococcus species in the future.

Genome-wide association analysis identifies ancestry-specific genetic variation associated with acute response to metformin and glipizide in SUGAR-MGH.

Characterisation of genetic variation that influences the response to glucose-lowering medications is instrumental to precision medicine for treatment of type 2 diabetes. The Study to Understand the Genetics of the Acute Response to Metformin and Glipizide in Humans (SUGAR-MGH) examined the acute response to metformin and glipizide in order to identify new pharmacogenetic associations for the response to common glucose-lowering medications in individuals at risk of type 2 diabetes. One thousand participants at risk for type 2 diabetes from diverse ancestries underwent sequential glipizide and metformin challenges. A genome-wide association study was performed using the Illumina Multi-Ethnic Genotyping Array. Imputation was performed with the TOPMed reference panel. Multiple linear regression using an additive model tested for association between genetic variants and primary endpoints of drug response. In a more focused analysis, we evaluated the influence of 804 unique type 2 diabetes- and glycaemic trait-associated variants on SUGAR-MGH outcomes and performed colocalisation analyses to identify shared genetic signals. Five genome-wide significant variants were associated with metformin or glipizide response. The strongest association was between an African ancestry-specific variant (minor allele frequency [MAFAfr]=0.0283) at rs149403252 and lower fasting glucose at Visit 2 following metformin (p=1.9×10-9); carriers were found to have a 0.94 mmol/l larger decrease in fasting glucose. rs111770298, another African ancestry-specific variant (MAFAfr=0.0536), was associated with a reduced response to metformin (p=2.4×10-8), where carriers had a 0.29 mmol/l increase in fasting glucose compared with non-carriers, who experienced a 0.15 mmol/l decrease. This finding was validated in the Diabetes Prevention Program, where rs111770298 was associated with a worse glycaemic response to metformin: heterozygous carriers had an increase in HbA1c of 0.08% and non-carriers had an HbA1c increase of 0.01% after 1 year of treatment (p=3.3×10-3). We also identified associations between type 2 diabetes-associated variants and glycaemic response, including the type 2 diabetes-protective C allele of rs703972 near ZMIZ1 and increased levels of active glucagon-like peptide 1 (GLP-1) (p=1.6×10-5), supporting the role of alterations in incretin levels in type 2 diabetes pathophysiology. We present a well-phenotyped, densely genotyped, multi-ancestry resource to study gene-drug interactions, uncover novel variation associated with response to common glucose-lowering medications and provide insight into mechanisms of action of type 2 diabetes-related variation. The complete summary statistics from this study are available at the Common Metabolic Diseases Knowledge Portal ( https://hugeamp.org ) and the GWAS Catalog ( www.ebi.ac.uk/gwas/ , accession IDs: GCST90269867 to GCST90269899).

The power of TOPMed imputation for the discovery of Latino-enriched rare variants associated with type 2 diabetes

Aims/hypothesisThe Latino population has been systematically underrepresented in large-scale genetic analyses, and previous studies have relied on the imputation of ungenotyped variants based on the 1000 Genomes (1000G) imputation panel, which results in suboptimal capture of low-frequency or Latino-enriched variants. The National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) released the largest multi-ancestry genotype reference panel representing a unique opportunity to analyse rare genetic variations in the Latino population. We hypothesise that a more comprehensive analysis of low/rare variation using the TOPMed panel would improve our knowledge of the genetics of type 2 diabetes in the Latino population.MethodsWe evaluated the TOPMed imputation performance using genotyping array and whole-exome sequence data in six Latino cohorts. To evaluate the ability of TOPMed imputation to increase the number of identified loci, we performed a Latino type 2 diabetes genome-wide association study (GWAS) meta-analysis in 8150 individuals with type 2 diabetes and 10,735 control individuals and replicated the results in six additional cohorts including whole-genome sequence data from the All of Us cohort.ResultsCompared with imputation with 1000G, the TOPMed panel improved the identification of rare and low-frequency variants. We identified 26 genome-wide significant signals including a novel variant (minor allele frequency 1.7%; OR 1.37, p=3.4 × 10−9). A Latino-tailored polygenic score constructed from our data and GWAS data from East Asian and European populations improved the prediction accuracy in a Latino target dataset, explaining up to 7.6% of the type 2 diabetes risk variance.Conclusions/interpretationOur results demonstrate the utility of TOPMed imputation for identifying low-frequency variants in understudied populations, leading to the discovery of novel disease associations and the improvement of polygenic scores.Data availabilityFull summary statistics are available through the Common Metabolic Diseases Knowledge Portal (https://t2d.hugeamp.org/downloads.html) and through the GWAS catalog (https://www.ebi.ac.uk/gwas/, accession ID: GCST90255648). Polygenic score (PS) weights for each ancestry are available via the PGS catalog (https://www.pgscatalog.org, publication ID: PGP000445, scores IDs: PGS003443, PGS003444 and PGS003445).Graphical abstract

EPS-mediated biosynthesis of nanoparticles by Bacillus stratosphericus A07, their characterization and potential application in azo dye degradation.

Microbial exopolysaccharides (EPS) are biocompatible, biodegradable, and less toxic substances secreted outside the cell. They adsorb metal cations to its surface, making it another captivating property, which helps in stabilizing and biosynthesizing metal nanoparticles. Owing to these properties, we adopted bacterial EPS toward the green synthesis of nanoparticles and its application in the removal of azo dyes. Extracted EPS weighed 2.6mg/mL from the most potential isolate A07 with 385μg/mg of the carbohydrate content. The top three isolates were subjected to nanoparticle synthesis via the intracellular method and, by their extracted EPS, silver nanoparticles (AgNP) with the size around 87nm were successfully produced by both methods mediated by the most potent isolate. The nanoparticles were characterized by UV-Vis spectroscopy, X-ray diffraction studies, atomic force microscopy, and FT-IR analysis. The nanoparticles were employed for dye degradation of azo dyes, namely, Methyl Orange (MO) and Congo Red (CO). EPS-Ag NPs showed fair degradation capability determined by UV-Vis kinetic studies. The work suggests electron transfer from reducing agent to dye molecule mediated by nanoparticles, destroying the dye chromophore. This makes EPS-Ag NPs a suitable, cheap, and environment-friendly candidate for biodegradation of harmful azo dyes. The most potential isolate was identified as Bacillus stratosphericus by 16S rRNA sequencing and submitted to GenBank under the accession id MK968439.

Cloning and Overexpression of Staphylococcal Enterotoxin B gene synthetic (SEBsyn) in pET-28a: Pre-development bacterial-toxin therapy for cancer

Staphylococcal enterotoxin B (SEB) from Staphylococcus aureus is a potential therapeutic agent for cancer. SEB can activate the immune response, which could induce apoptosis of various cancer cells. This study aimed to design and produce a recombinant SEB protein using Escherichia coli BL21(DE3) expression system. We designed and optimized the codon of the inserted gene for E. coli and then transformed it into E. coli BL21(DE3). The transformants were verified by selective media containing kanamycin followed by colony PCR with T7 promoter and T7 terminator primers and DNA sequencing. The results showed that the SEBsyn encoding gene could be synthesized and cloned into pET-28a(+) expression plasmid. This recombinant plasmid that carried the SEB encoding gene (pET-28a_SEBsyn) was successfully transformed into E. coli BL21(DE3). The amplicons of colony PCR visualized in 2% agarose gel showed that transformants carrying the recombinant plasmid had an inserted gene length of about 1 kb. Gene inserts sequence verification by DNA sequencing resulted in 1,148 bp sequence consensus. The blastx analysis showed that it had the best hit with enterotoxin B in the NCBI database accession id CAC6284025.1. The recombinant SEB protein was also successfully overexpressed in E.coli BL21(DE3) with 0.1 mM IPTG. Our recombinant SEB protein was dominantly insoluble in the inclusion body; however, some SEB protein was expressed as soluble. The molecular weight of the target protein is about 29 kDa.

Identification of the SIRT1 gene's most harmful non-synonymous SNPs and their effects on functional and structural features-an in silico analysis

Introduction: The sirtuin (Silent mating type information regulation 2 homolog)1(SIRT1) protein plays a vital role in many disorders such as diabetes, cancer, obesity, inflammation, and neurodegenerative and cardiovascular diseases. The objective of this in silico analysis of SIRT1's functional single nucleotide polymorphisms (SNPs) was to gain valuable insight into the harmful effects of non-synonymous SNPs (nsSNPs) on the protein. The objective of the study was to use bioinformatics methods to investigate the genetic variations and modifications that may have an impact on the SIRT1 gene's expression and function. Methods: nsSNPs of SIRT1 protein were collected from the dbSNP site, from its three (3) different protein accession IDs. These were then fed to various bioinformatic tools such as SIFT, Provean, and I- Mutant to find the most deleterious ones. Functional and structural effects were examined using the HOPE server and I-Tasser. Gene interactions were predicted by STRING software. The SIFT, Provean, and I-Mutant tools detected the most deleterious three nsSNPs (rs769519031, rs778184510, and rs199983221). Results: Out of 252 nsSNPs, SIFT analysis showed that 94 were deleterious, Provean listed 76 dangerous, and I-Mutant found 66 nsSNPs resulting in lowered stability of proteins. HOPE modelling of rs199983221 and rs769519031 suggested reduced hydrophobicity due to Ile 4Thr and Ile223Ser resulting in decreased hydrophobic interactions. In contrast, on modelling rs778184510, the mutant protein had a higher hydrophobicity than the wild type. Conclusions: Our study reports that three nsSNPs (D357A, I223S, I4T) are the most damaging mutations of the SIRT1 gene. Mutations may result in altered protein structure and functions. Such altered protein may be the basis for various disorders. Our findings may be a crucial guide in establishing the pathogenesis of various disorders.

Spectrum of Rare and Novel Indel Mutations Responsible for β Thalassemia in Eastern India.

The online version contains supplementary material available at 10.1007/s12291-022-01098-w.

ScFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction.

MotivationWith the recent surge of large-cohort scale single cell research, it is of critical importance that analytical methods can fully utilize the comprehensive characterization of cellular systems that single cell technologies produce to provide insights into samples from individuals. Currently, there is little consensus on the best ways to compress information from the complex data structures of these technologies to summary statistics that represent each sample (e.g. individuals).ResultsHere, we present scFeatures, an approach that creates interpretable cellular and molecular representations of single-cell and spatial data at the sample level. We demonstrate that summarizing a broad collection of features at the sample level is both important for understanding underlying disease mechanisms in different experimental studies and for accurately classifying disease status of individuals.Availability and implementationscFeatures is publicly available as an R package at https://github.com/SydneyBioX/scFeatures. All data used in this study are publicly available with accession ID reported in the Section 2.Supplementary information Supplementary data are available at Bioinformatics online.

BoMiProt 2.0: An update of the bovine milk protein database

Milk is a biofluid with various functions, containing carbohydrates, lipids, proteins, vitamins, and minerals. Owing to its importance and availability of vast proteomics information, our research group designed a database for bovine milk proteins (N = 3159) containing the primary and secondary information called BoMiProt. Due to the gaining interest and intensively published literature in the last three years, BoMiProt has been upgraded with newer identified proteins (N = 7459) from peer-reviewed journals, significantly expanding the database from different milk fractions (e.g., whey, fat globule membranes, and exosomes). Additionally, class, architecture, topology, and homology, structural classification of proteins, known and predicted disorder, predicted transmembrane helices, and structures have been included. Each protein entry in the database is thoroughly cross-referenced, including 1392 BoMiProt defined proteins provided with secondary information, such as protein function, biochemical properties, post-translational modifications, significance in milk, domains, fold, AlphaFold predicted models and crystal structures. The proteome data in the database can be retrieved using several search parameters using protein name, accession IDs, and FASTA sequence. Overall, BoMiProt represents an extensive compilation of newer proteins, including structural, functional, and hierarchical information, to help researchers better understand mammary gland pathophysiology, including their potential application in improving the nutritional quality of dairy products.

Valorization of frying oil waste for biodetergent production using Serratia marcescens N2 and gamma irradiation assisted biorecovery

BackgroundThe complexity, toxicity and abundance of frying oil waste (FOW) render it difficult to be degraded biologically. The aim of the present work was to valorize FOW and investigate the potential use of the produced biosurfactant by Serratia marcescens N2 (Whole Genome sequencing accession ID SPSG00000000) as a biodetergent.ResultsSerratia marcescens N2 demonstrated efficient valorization of FOW, using 1% peptone, 20% FOW and 8% inoculum size. Gene annotation showed the presence of serrawettin synthetase indicating that the produced biosurfactant was serrawettin. Zeta potential and Fourier Transform Infrared (FTIR) spectroscopy indicate that the biosurfactant produced was a negatively charged lipopeptide. The biosurfactant reduced the surface tension of water from 72 to 25.7 mN/m; its emulsification index was 90%. The valorization started after 1 h of incubation and reached a maximum of 83.3%. Gamma radiation was used to increase the biosurfactant yield from 9.4 to 19.2 g/L for non-irradiated and 1000 Gy irradiated cultures, respectively. It was noted that the biorecovery took place immediately as opposed to overnight storage required in conventional biosurfactant recovery. Both chemical and functional characteristics of the radiation induced biosurfactant did not change at low doses. The produced biosurfactant was used to wash oil stain; the highest detergency reached was 87% at 60 °C under stirring conditions for 500 Gy gamma assisted biorecovery. Skin irritation tests performed on experimental mice showed no inflammation.ConclusionThis study was able to obtain a skin friendly effective biodetergent from low worth FOW using Serratia marcescens N2 with 83% efficient valorization using only peptone in the growth media unlike previous studies using complex media. Gamma radiation was for the first time experimented to assist biosurfactant recovery and doubling the yield without affecting the efficiency.