Eurasian Journal of Applied Biotechnology

DEVELOPMENT AND EVALUATION OF OFFLINE SOFTWARE FOR WORKING WITH THE MLVA MtbC15 9 NOMENCLATURE USING MIRU-VNTR TYPING AND WHOLE-GENOME SEQUENCING DATA OF MYCOBACTERIUM TUBERCULOSIS

2026-10-27T12:02:12+05:00

Molecular epidemiology of tuberculosis is moving from typing by variable-number tandem repeats to whole-genome sequencing (WGS), yet the record of how Mycobacterium tuberculosis genotypes spread over past decades is written in the MLVA MtbC15‑9 nomenclature, and short sequencing reads do not resolve MIRU-VNTR profiles reliably. The codes were assigned by a single web service, MIRU-VNTRplus (https://www.miru-vntrplus.org), whose interactive functions became unavailable in 2026. This work moved the service functions to the laboratory to keep new data linked to that record. Offline software for Windows, MTBC Lab Toolkit, was developed that assigns codes by the exact-match rule of the 15-locus and 9-locus panels, processes sets of profiles, reports the nearest registered types and links MIRU-VNTR profiles with whole-genome sequencing results. Its reference data comprise 3 906 coded profiles from 152 publications and 23 560 MtbC15 types from the service's official table. Of 400 published codes, the software reproduced all 392 agreeing with the official table; the other 8 were publication errors, and no wrong code was returned. A missing locus is not guessed: the software searches known profiles matching the other 23 loci and returns the nearest code only if a single such profile exists. A profile with one locus changed never received its previous code. TB-Profiler and Mykrobe import was verified on their output files; a batch of 3 293 profiles is processed in 7.3 s. The software compares new data, including profiles inferred from long reads, with accumulated and published MIRU-VNTR typing results without an external server.

PROTEOMIC ANALYSIS OF EXTRACELLULAR MEMBRANE VESICLES OF BACTEROIDES FRAGILIS UNDER ANTIBIOTIC STRESS

2026-01-08T15:34:01+05:00

The high antibiotic resistance of Bacteroides fragilis and its ability to combine symbiosis with pathogenicity in the human body make this species a key model for studying the bacterial stress response. Outer membrane vesicles (OMVs), secreted by Gram-negative bacteria, play a key role in intercellular communication, pathogenesis, and adaptation to antibiotics. In this study, we performed a proteomic analysis of B. fragilis OMVs exposed to meropenem using LC-MS/MS and label-free quantification (LFQ). Nineteen differentially expressed proteins were identified, belonging to the main functional groups: enzymes of amino acid and carbohydrate metabolism, antioxidant defense proteins, replication and translation factors, and methyltransferases. Taken together, these changes reflect a redistribution of metabolic fluxes toward maintaining energy balance and antioxidant defense under antibiotic stress. Thus, the proteomic profile of B. fragilis OMVs demonstrates their significant role in the mechanisms of bacterial survival and resistance, and also highlights their potential involvement in pathogenesis.

DEVELOPMENT OF THE CROPPOPSTRUCTURE GENOMIC PLATFORM FOR GENETIC DIVERSITY ANALYSIS AND SUPPORT OF BREEDING DECISIONS

2026-10-29T09:30:16+05:00

Understanding genetic diversity and population structure is essential for efficiently using crop germplasm collections in breeding, yet a complete analysis requires many separate programs and command-line skills. This study aimed to develop CropPopStructure, a web-based genomic platform that performs a full population genetic analysis of a germplasm collection from a VCF file and a population list, and to validate it on data with a known structure. The platform combines a Nextflow pipeline based on PLINK, VCFtools, and R packages with an R Shiny web interface accessible from a browser. It validates the input data and runs eleven analysis modules: genetic diversity indices, principal component analysis (PCA), discriminant analysis of principal components (DAPC), sNMF ancestry estimation, genomic kinship, a neighbor-joining tree, analysis of molecular variance (AMOVA), pairwise F_ST, private SNPs, SNP density, and linkage disequilibrium (LD) decay. HapMap files can be converted to VCF with TASSEL within the platform. The platform was tested on a simulated collection of 98 homozygous lines from four populations genotyped with 35,000 SNPs and generated under a hierarchical coalescent model. PCA separated all four populations (PC1 = 6.32%, PC2 = 1.96% of variance), and the BIC criterion indicated two main genetic groups corresponding to the model's two lineages. AMOVA attributed 21.9 % of molecular variance to differences among populations (Φ_PT = 0.219; p < 0.001). Pairwise F_ST values were 0.037–0.039 between sister populations and 0.124–0.125 between lineages, reproducing the simulated hierarchy. CropPopStructure allows breeders and geneticists without bioinformatics training to obtain reproducible results that support forming core collections, selecting genetically distant parents, and controlling population structure in association studies.

CONSTITUTIVE OVEREXPRESSION OF THE DELLA-LIKE GENE ZPR31 FROM ZYGOPHYLLUM POTANINII MAXIM SUPPRESSES THE ANTIOXIDANT RESPONSE OF ARABIDOPSIS THALIANA UNDER MANNITOL-INDUCED OSMOTIC STRESS

2026-10-14T15:24:51+05:00

ZpR31, a DELLA-like transcript whose deduced protein shares sequence similarity with GAI1, was previously identified by suppression subtractive hybridization (SSH) as downregulated in mannitol-stressed Zygophyllum potaninii. To characterise its function, transgenic Arabidopsis thaliana lines constitutively overexpressing ZpR31 (ZpR31-OE) were generated and, together with wild-type (WT) Col-0 plants, exposed to 200 mM mannitol. After 15 days of treatment, malondialdehyde (MDA) content was markedly higher in two independent ZpR31-OE lines (approximately 23–32 nmol g^‑1) than in WT (approximately 16.5 nmol g^‑1), indicating more extensive membrane lipid peroxidation. Superoxide dismutase (SOD) activity increased markedly in stressed WT (from approximately 410 to 515 U g^‑1), whereas it declined to approximately 210 U g^‑1 in both ZpR31-OE lines. Stem-loop RT-qPCR of six stress-associated microRNAs in ZpR31-OE plants relative to WT revealed transient induction of miR156, miR165, miR398 and miR827 at 24 h, a delayed miR393 peak at 48 h, and sustained miR171 repression. Because miR398 is normally downregulated under oxidative stress to permit induction of Cu/Zn-SOD genes, its induction here suggests a plausible mechanism by which ZpR31 suppresses the SOD response. These results indicate that ZpR31 acts as a negative regulator of osmotic-stress tolerance in Arabidopsis, consistent with its identification as a stress-downregulated transcript in native Z. potaninii.

MICROSATELLITE INSTABILITY PROFILING WITH MSISENSOR2 IN WHOLE-EXOME SEQUENCING DATA FROM HEALTHY CONTROLS AND COLORECTAL CANCER PATIENTS

2026-10-22T11:29:10+05:00

Microsatellite instability (MSI) is a molecular phenotype linked to defects in DNA mismatch repair (MMR) and serves as a biomarker in colorectal cancer (CRC). Computational MSI assessment using next-generation sequencing data enables characterisation of microsatellite instability without a dedicated MSI assay. This study evaluated MSIsensor2 scores in blood-derived whole-exome sequencing (WES) data from healthy individuals and two CRC patients.

Whole-exome sequencing (WES) data from peripheral blood samples of 235 healthy Kazakh individuals were obtained from the DNA Biobank of the Laboratory of Genomic and Personalised Medicine, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan. Blood-derived WES data from two patients with CRC, designated BR110 and BR114, were also analysed. Sequencing libraries were prepared using Illumina workflows and sequenced on the NovaSeq 6000 platform. MSIsensor2 was employed to assess MSI scores and quantify the number of unstable microsatellite loci detected. Relationships among MSI scores, locus coverage, and sequencing data volume were examined descriptively.

Of the 235 healthy individuals, 205 samples (87.2%) had MSI scores below 10%, while 30 samples (12.8%) had scores between 10% and 40% per study-specific classification. No sample exceeded 40%. The CRC-associated blood samples BR110 and BR114 demonstrated MSI scores of 5.43% and 7.81%, respectively. BR110 exhibited 10 unstable microsatellite sites among 184 covered sites, whereas BR114 had 26 among 333 covered sites. The higher score in BR114 corresponded with increased sequencing coverage and a greater number of evaluable loci. These findings indicate variability in computational MSI measurements across blood-derived WES datasets but do not establish tumour MSI status.

MSIsensor2 produced MSI-associated measurements from blood-derived WES data in both healthy individuals and patients with CRC. However, MSI scores from blood sequencing do not necessarily reflect tumour status; therefore, determining the clinical relevance of these findings requires investigation using tumour-derived material, established MSI reference assays, and a larger clinical cohort.