Polymorphic DNA Research Articles

Association of DNA methylation, polymorphism and mRNA level of ALAS1 with antituberculosis drug-induced liver injury.

Aim: To investigate the association of DNA methylation, genetic polymorphisms and mRNA level of aminolevulinate synthase 1 (ALAS1) with antituberculosis drug-induced liver injury (AT-DILI) risk.Methods: Based on a 1:1 matched case-control study with 182 cases and 182 controls, one CpG island and three single nucleotide polymorphisms (SNPs) were detected. ALAS1 mRNA level was detected in 34 samples.Results: Patients with methylation status were at high risk of AT-DILI (odds ratio: 1.567, 95% CI: 1.015-2.421, p =0.043) and SNP rs352169 was associated with AT-DILI risk (GA vs. GG, odds ratio: 1.770, 95% CI: 1.101-2.847, p=0.019). ALAS1 mRNA level in the cases was significantly lower than that in the controls (0.75±0.34 vs. 1.00±0.42, p =0.021).Conclusion: The methylation status and SNP rs352169 of ALAS1 were associated with AT-DILI risk.

Association of rs2241766 and rs1501299 polymorphisms in the adiponectin gene with metabolic syndrome.

To investigate the influence of adiponectin (APN) rs2241766 and rs1501299 polymorphisms on adiponectin levels and their association with metabolic syndrome (MetS). Analyzed two polymorphisms (rs2241766 and rs1501299) of the adiponectin gene (ADIPOQ) in 210 MetS patients and 102 control patients using the polymerase chain reaction-restriction fragment length polymorphism method and DNA sequencing technology. The genotypes of the rs2241766 T/G and rs1501299 G/T polymorphism were significantly associated with serum APN levels in MetS patients. The ADIPOQ polymorphisms were associated with a risk of MetS when compared with that in healthy controls. TG and GG genotypes of rs2241766 were associated with a significantly elevated risk of MetS as compared with the TT genotype (OR = 1.32 and OR = 2.53). Subjects with the G allele appeared to have higher susceptibility to MetS than those with the T allele (OR = 2.21). In common with the findings for rs2241766, the rs1501299 GT and TT genotypes were associated with a significantly increased risk of MetS as compared with the GG genotype (OR = 1.51 and OR = 2.24). The susceptibility to MetS appeared to be higher in subjects with the T allele than in those with the G allele (OR = 1.88). The occurrence of MetS may be associated with genetic variations at the rs2241766 and rs1501299 loci, especially in individuals with T to G mutations (rs2241766) and G to T mutations (rs1501299). These mutations may lead to decreased APN levels and a higher risk of developing MetS.

Phenotypic and Molecular-Markers-Based Assessment of Jamun (Syzygium cumini) Genotypes from Pakistan

Jamun plant displays enormous diversity throughout Pakistan, which necessitates its screening, evaluation, and validation to document elite genotypes having better traits for the benefit of the fruit industry and farmers. Surveys were made in natural Jamun habitats across Punjab, Pakistan, and genotypes were marked based on visual diversity of trees and fruits. In total, 60 Jamun genotypes were selected for characterization based on phenotypic and genetic markers. Phenotypic characters related to trees, leaf, and flower along with fruit qualitative traits were assessed in situ. Results revealed significant diversity with high (>25%) coefficient of variance values and the first two components of correspondence analysis exhibited 41.71% variation among genotypes. A strong association was observed among traits like upright tree and round fruit shape (0.74), bluish-colored fruit and pinkish pulp (0.85), and elliptic-shaped fruit with low fruit waxiness (−0.72). Leaves of phenotypically characterized plants were brought to Wheat Biotechnology Lab., University of Agriculture, Faisalabad, Pakistan, where Jamun genotypes were investigated genetically using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 132 bands were scored, of which 108 were polymorphic, corresponding to almost 81% polymorphism among collected genotypes. High polymorphism information content values were observed against RAPD (0.389) and ISSR (0.457) markers. Genotypes were compared in relation to genetic markers, which exhibited that almost 86% of genetic variability was attributed to differences among accessions, while 14% of variation was due to differences between collections of different areas. Findings of this study confirmed wide phenotypic and genetic distinctness of Jamun in Pakistan that can aid breeders for marker-assisted selection and germplasm enhancement for future crop improvement programs.

Inter and intra population genetic variability in ducks under conservation programs

This study focuses on estimation of the inter and intra population genetic variability of 6 duck populations. Microsatellite loci were used to assess the genetic variation and population structure of 6 duck populations under a conservation program in Poland. DNA polymorphism was assessed using 24 microsatellite markers and 50 individuals from each population. Polymorphism information content (PIC), heterozygosity with 2 estimators of genetic differentiation (FST and GST), and Nei's standard genetic distance were calculated. The results showed that these 6 endangered duck populations showed high genetic polymorphism. Observed heterozygosity within populations ranged from 0.14 to 0.83, with the average value of 0.58. PIC within populations ranged from 0.038 (P-8 and P-9 lines) to 0.89 (LsA line). Average number of alleles in the studied populations ranged from 4.5 (KhO-1 line) to 7.3 (LsA line). Based on the results, the pairs of lines LsA: P-33 and P-8: P-9 were found to be the most related; and the most genetically distant group was KhO-1 line, which originated as a cross between Khaki Campbell with Orpington duck.

Single Nucleotide Polymorphisms in APE1, hOGG1, RAD51 Genes and their Association with Radiotherapy Induced Toxicity among Head and Neck Cancer Patients.

Radiotherapy (RT) is a crucial treatment for head and neck cancer however, it causes adverse reactions to the normal tissue and organs adjacent to target tumor. The present study was carried out to investigate possible association of single nucleotide polymorphism in DNA repair genes with toxicity effects of radiotherapy on normal tissue. Three hundred and fifty head and neck cancer patients receiving radiotherapy treatment were enrolled in this study. The adverse after effects of radiotherapy on the normal tissue in the form of skin reactions were recorded. Single nucleotide polymorphisms of APE1 (rs1130409), hOGG1 (rs1052133) and Rad51 (rs1801320, rs1801321) genes were studied by polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) and direct DNA sequencing methods and their association with development of severe radio-toxicity effects was evaluated logistic regression analysis. The 172G/T polymorphism of Rad51 was 2.85 times higher and significantly associated with skin reactions (OR=2.85, 95% CI: 1.50-5.41; p=0.001) and severe oral mucositis (OR=4.96, 95% CI: 2.40-10.25; p<0.0001). These results suggested that the polymorphic nature of Rad51 is responsible for risk of radiotherapy adverse effects in HNC patients. The variant 326Cys and heterozygous 326Ser/Cys genotype of hOGG1 was significantly associated with high tumor grade (OR=3.16 95% CI: 1.66-5.99; p=0.0004, and OR=3.97 95% CI: 2.15-7.34; p=<0.0001 respectively). The homozygous variant 172TT genotype of Rad51 showed positive association with poor response of both tumor and nodes towards radiotherapy treatment (p=0.007 and p=0.022). Interpretation of our results revealed significant association of rs1801321 SNP of Rad51 with development of adverse toxicity reactions in normal tissue of head and neck cancer patients treated with radiotherapy.

Phenotypic and genotypic assessment of fluoroquinolones and aminoglycosides resistances in Pseudomonas aeruginosa collected from Minia hospitals, Egypt during COVID-19 pandemic

BackgroundOne of the most prevalent bacteria that cause nosocomial infections is Pseudomonas aeruginosa. Fluoroquinolones (FQ) and aminoglycosides are vital antipseudomonal drugs, but resistance is increasingly prevalent. The study sought to investigate the diverse mechanisms underlying FQ and aminoglycoside resistance in various P. aeruginosa strains particularly during the COVID-19 crisis.MethodsFrom various clinical and environmental samples, 110 P. aeruginosa isolates were identified and their susceptibility to several antibiotic classes was evaluated. Molecular techniques were used to track target gene mutations, the presence of genes encoding for quinolone resistance, modifying enzymes for aminoglycosides and resistance methyltransferase (RMT). Efflux pump role was assessed phenotypically and genotypically. Random amplified polymorphic DNA (RAPD) analysis was used to measure clonal diversity.ResultsQnrS was the most frequently encountered quinolone resistance gene (37.5%) followed by qnrA (31.2%) and qnrD (25%). Among aminoglycoside resistant isolates, 94.1% harbored modifying enzymes genes, while RMT genes were found in 55.9% of isolates. The aac(6')-Ib and rmtB were the most prevalent genes (79.4% and 32.3%, respectively). Most FQ resistant isolates overexpressed mexA (87.5%). RAPD fingerprinting showed 63.2% polymorphism.ConclusionsAminoglycosides and FQ resistance observed in this study was attributed to several mechanisms with the potential for cross-contamination existence so, strict infection control practices are crucial.

Antarctic Spore-Forming Microorganisms from Deception Island Inhibit the Growth of Various Bacterial Strains

Antarctic microbes have evolved and adapted unique strategies to survive in the harsh polar environment. Apart from the ability to adapt to the low nutrient soil content and extremely dry and cold polar environment, a particular strategy used by Antarctic bacteria is the production of antimicrobial compounds that can eliminate rivals in the same niche, giving them a competitive edge over other microbes. In contrast, it is unclear whether spore-forming microbes possess similar antimicrobial properties as one of their survival strategies, especially those from the Antarctic volcanic Deception island in the West Antarctic. Hence, this study aims to isolate and characterize the spore-forming microbes in Deception Island, Antarctica, as well as to identify the ones that are equipped with the ability to inhibit other microorganisms. Microbes were isolated using various growth media and were segregated into clusters based on their random amplified polymorphic DNA (RAPD) fingerprints. A total of 90 strains were isolated and clustered into 30 groups at a similarity of 60%. Representative strains from each cluster were assayed for antimicrobial activities against 13 Gram-positive and Gram-negative test bacteria comprising human pathogens. Twenty-five strains exhibited the ability to inhibit at least one test bacterium. The four strains, A60, Im31, Im32 and Im33 that showed the strongest inhibitory activities were subjected to 16S or 18S rDNA sequencing and analysis to identify them. They were identified as Pseudogymnoascus, Bacillus, Leohumicola, and Talaromyces spp. The ability of the aforementioned microbes to thrive in harsh environments and compete with fierce competitors for scarce nutrients is probably due to their ability to produce antimicrobial compounds that target and kill their rivals.

Intrabreed variability of Landrace animals based on microsatellite DNA polymorphism

Intrabreed variability of Landrace animals based on microsatellite DNA polymorphism

Exploring genetic diversity of yellow-berried night shade (Solanum virginianum L.) using genetic divergence and molecular markers

The rationale of this research was to explore the genetic divergence of 54 kantakari accessions (Solanum virginianum L. syn. S. surattense Burm. f.), to identify their significant traits, and unravel their genetic variations. Kantakari is a widely used medicinal plant in traditional medicine worldwide and is also known for its allopathic properties. The morphological descriptors and molecular markers (Random Amplified Polymorphic DNA) used to characterize these samples revealed significant within-accession heterogeneity, indicating the possibility of future selection. Twenty-three morphological and biochemical features were examined to assess taxonomic traits. Accessions were classified into six clusters based on Mahalanobis D2 statistics of 23 quantitative traits. Clusters V and VI had the largest intercluster distance (1183.81), whereas Cluster IV had the largest intracluster distance (D2 = 275.67) (Cluster V and VI). Random Amplified Polymorphic DNA marker amplification using 10 polymorphic primers revealed 79 alleles with an overall mean of 7.90 alleles per marker, with Polymorphism Information Content values varying from 0.11 to 0.37 (Mean = 0.30). Cluster assessment produced three distinct groups. In conclusion, the investigation underscores that substantial diversity was observed among the surveyed kantakari accessions. Using molecular markers in tandem with morphological characterization, presents a robust approach for elucidating the intricacies of species-specific genetic variation with greater accuracy and depth.

Molecular characterization and multifunctional evaluation of lactic acid bacteria isolated from traditional sourdough

The primary objective of this study was to characterize lactic acid bacteria (LAB) strains derived from sourdough for possible utilization as functional starters to produce sourdough and various cereal-based fermented foods. A total of 350 autochthonous LAB strains were isolated from 65 Type I sourdough samples and characterized using six random amplified polymorphic DNA (RAPD) primers at intra- and interspecific levels. Species identification of selected strains representing distinct clusters from RAPD analysis was performed based on the 16S rRNA region. The LAB strains were identified as Companilactobacillus crustorum (n = 135), Levilactobacillus brevis (n = 125), Latilactobacillus curvatus (n = 40), Companilactobacillus paralimentarius (n = 32), and Lactiplantibacillus plantarum (n = 18). A total of 66 LAB strains were selected for technological characterization along with two commercial strains. The characterization involved acidity development, EPS production potential, leavening activity, and growth abilities under harsh conditions. Principle component analysis (PCA) identified 2 Lp. plantarum and 14 Lev. brevis strains as the most relevant technologically. Among them, Lp. plantarum L35.1 and Lev. brevis L37.1 were resistant to tetracycline. Evaluation of probiotic characteristics (survival in pH 2.5 and bile presence, auto aggregation capacity, hydrophobic activity, antioxidant activity, antimicrobial activity) by PCA identified four strains with relevance to Lactobacillus rhamnosus GG (LGG), which were further selected for in vitro digestion assays. Lactiplantibacillus plantarum L7.8, Lev. brevis L55.1, and L62.2 demonstrated similar viability indices to LGG, along with increased auto aggregation capacity and antioxidant activity. These strains are promising as candidate starters for producing sourdough and sourdough-related fermented food products.

Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses.

Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.

Genetic polymorphism in waxweed (Red Book of the Russian Federation) in North-West Russia

BACKGROUND: Waxweed (Myrica gale L.) is a protected plant species found in the Russian Federation only in the Leningrad Region and Karelia. It is almost not studied from the genetic point of view. This species is presumably hexaploid; it propagates mainly vegetatively, and the role of sexual reproduction in the life cycle of waxweed is unclear. All waxweed populations in the Russian Federation are small and belong to the edge ones (occupy the easternmost positions in the range). AIM: The aim of the study is to investigate genomic DNA polymorphism in waxweed populations in the Russian Federation, and to evaluate the role of sexual reproduction in propagation and dispersal of this species. MATERIALS AND METHODS: AFLP-analysis of waxweed genomic DNA in 6 natural populations (5 populations in the Leningrad Region, 1 in Karelia). Using 3 pairs of primers, we studied waxweed genomic polymorphism for 22 DNA fragments. RESULTS: Each of the studied waxweed populations is genetically polymorphic. Among 182 analyzed plants we distinguished 27 different AFLP-genotypes, two of which were common in all populations studied. Most of others AFLP genotypes (20) were represented just by a single plant or a couple of plants. Some of these rare AFLP genotypes are likely the results of mutation and/or recombination processes affecting the common AFLP genotypes. CONCLUSIONS: The role of sexual reproduction in waxweed propagation, although minor, is noticeable.

Investigating Safety and Technological Traits of a Leading Probiotic Species: Lacticaseibacillus paracasei.

Lacticaseibacillus spp. are genetically close lactic acid bacteria species widely used in fermented products for their technological properties as well as their proven beneficial effects on human and animal health. This study, the first to include such a large collection of heterogeneous isolates (121) obtained from international collections belonging to Lacticaseibacillus paracasei, aimed to characterize the safety traits and technological properties of this important probiotic species, also making comparisons with other genetically related species, such as Lacticaseibacillus casei and Lacticaseibacillus zeae. These strains were isolated from a variety of heterogeneous sources, including dairy products, sourdoughs, wine, must, and human body excreta. After a preliminary molecular characterization using repetitive element palindromic PCR (Rep-PCR), Random Amplification of Polymorphic DNA (RAPD), and Sau-PCR, particular attention was paid to safety traits, evaluating antibiotic resistance profiles, biogenic amine (BA) production, the presence of genes related to the production of ethyl carbamate and diaminobenzidine (DAB), and multicopper oxidase activity (MCO). The technological characteristics of the strains, such as the capability to grow at different NaCl and ethanol concentrations and different pH values, were also investigated, as well as the production of bacteriocins. From the obtained results, it was observed that strains isolated from the same type of matrix often shared similar genetic characteristics. However, phenotypic traits were strain-specific. This underscored the vast potential of the different strains to be used for various purposes, from probiotics to bioprotective and starter cultures for food and feed production, highlighting the importance of conducting comprehensive evaluations to identify the most suitable strain for each purpose with the final aim of promoting human health.

Study of the Karachay Population Based on the Analysis of Ten Polymorphic DNA Loci

Genetic structure of Karachai population has been studied based on analysis of 10 autosomal DNA markers (diallelicand multiallelic): CCR5∆32, ACE, D7S23(KM19) STR/THOI, STR/FABP, STR/IVS6a, VNTR/PAH, VNTR/DAT1, VNTR/eNOS VNTR/APOB. The total number of sample makes up 485 individuals who are residents of five Karachai regions: Karachaevsky, Prikubansky, Malokarachayevsky, Ust-Dzhegutinsky and the city of Cherkessk, the capital of the Republic of Karachaevo-Cherkessia. Analysis of allele’s frequency of autosomal DNA markers in Karachay geographic subgroups shows considerable genetic differentiation between them. The highest level of genetic diversity for Karachay people on dialle system is set at the locus ID/ACE, Hobs = 0.513, on multi-allele system isat the locus STR/THOI, Hobs = 0.792. The average value of the observed heterozygosity per locus is 0.466, varying from 0.441 in Ust-Dzhegutinsky to 0.503 in Cherkessk. The level of genetic differences between Karachai groups (FST = 0.007) is inside the variance defined in the previously studied peoples, Mari (FST = 0.0024), Udmurt (FST = 0.0048), Chuvash (FST = 0.006), Tatars (FST = 0.0075) and Bashkir (FST = 0.008).

Diagnosis and Molecular Characterization of Dermatophytosis: An Observational Study

Dermatophytes are the keratinophilic fungi which infect humans and is the most recurring type of disease. The high level of transmissibility creates an epidemiological risk and emphasises the significance of these illnesses. However, a growing number of reports describing dermatophytes can cause deep infections in diabetic and immunocompromised patients, by invading deep layers like the dermis and hypodermis. Despite the prevalence and significance of dermatophytes in clinical mycology, it is not always possible to accurately diagnose this specific infection due to its overlapping structures among species of dermatophytes. Since it is difficult to identify species that exhibit weak characteristics in the morphological highlights, identification of the dermatophyte is often relied on its morphological analysis, which is a laborious process and demands skill. The massive shift in genetic variation, the source of infection, and epidemiological research can be discovered using molecular approaches. Therefore, the development of an accurate laboratory test for dermatophyte species identification is essential for the prevention and efficient management of dermatophytoses. One such methodology allows use of PCR technology which has many methods for molecular level characterization which is rapid, efficient, and capable of producing DNA polymorphisms specific to various dermatophyte species based on distinctive band patterns seen by agarose gel electrophoresis. The RAPD-PCR approach will be used in this study protocol to molecularly characterize the dermatophytes for precise speciation of the sample. In addition to improving knowledge of fungal biology and pathology with a focus on adaptive mechanisms to combat difficult conditions from host counteractions, there is a need to improve awareness of the importance of these diseases through accurate epidemiological data. The advantages of molecular approaches for characterizing objects over traditional methods are their sensitivity and specificity.

Genetic analysis: Therapeutic drug monitoring of metformin and glimepiride on diabetic patients' plasma including genetic polymorphism.

Diabetes is a widespread disease that needs to be controlled. Therapeutic monitoring of drugs is very helpful in maintaining desirable doses. To study a correlation between the blood level of metformin (to a lesser extent, glimepiride) and genotyping (mainly the SULT1A1 genotype). Determine drug levels using a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) tool. A validated LC-MS/MS method was developed to determine metformin and glimepiride levels in human plasma. DNA extraction was performed using Jena Bioscience's Blood DNA preparation, in which a column kit was used to extract DNA for genetic polymorphism. The investigation was carried out using both medications in type 2 diabetes patients alongside the genetic polymorphism. One hundred and six patients were assessed. The prevalence of homozygosity for SULT1A1 and wild-type CYP2D6 * 4 were 72.6% and 73.6%, respectively. After adjustment for daily intake of metformin, three patients out of five with the highest levels of metformin had no homozygosity (SULT1A1 genotype). Statistically, variables that demonstrated an insignificant correlation with the level of metformin were body mass index (rs (87) = 0.32, P = 0.011) and age (rs (87) =0.26, P = 0.017). The homozygous (SULT1A1 genotype) correlation was moderate (rs (87) =0.21, P = 0.052). According to the findings, patients with the wt/wt CYP2D6 genotype had considerably greater levels of endoxifen than those with the v/v CYP2D6 genotype. The study's results reported a probable correlation between the blood level of metformin (to a lesser extent, glimepiride) and genotyping (mainly the SULT1A1 genotype). Genotype-guided drug therapy may provide a novel contribution to maximize drug efficacy and/or minimize toxicity.

Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model

BackgroundVariable number tandem repeats (VNTRs) are highly polymorphic DNA regions harboring many potentially disease-causing variants. However, VNTRs often appear unresolved (“dark”) in variation databases due to their repetitive nature. One particularly complex and medically relevant VNTR is the KIV-2 VNTR located in the cardiovascular disease gene LPA which encompasses up to 70% of the coding sequence.ResultsUsing the highly complex LPA gene as a model, we develop a computational approach to resolve intra-repeat variation in VNTRs from largely available short-read sequencing data. We apply the approach to six protein-coding VNTRs in 2504 samples from the 1000 Genomes Project and developed an optimized method for the LPA KIV-2 VNTR that discriminates the confounding KIV-2 subtypes upfront. This results in an F1-score improvement of up to 2.1-fold compared to previously published strategies. Finally, we analyze the LPA VNTR in > 199,000 UK Biobank samples, detecting > 700 KIV-2 mutations. This approach successfully reveals new strong Lp(a)-lowering effects for KIV-2 variants, with protective effect against coronary artery disease, and also validated previous findings based on tagging SNPs.ConclusionsOur approach paves the way for reliable variant detection in VNTRs at scale and we show that it is transferable to other dark regions, which will help unlock medical information hidden in VNTRs.

Methyl-Sensitive Amplification Polymorphism (MSAP) Analysis Provides Insights into the DNA Methylation Changes Underlying Adaptation to Low Temperature of Brassica rapa L.

DNA methylation can change rapidly to regulate the expression of stress-responsive genes. Previous studies have shown that there are significant differences in the cold resistance of winter rapeseed (Brassica rapa L.) after being domesticated in different selection environments; however, little is known about the epigenetic regulatory mechanisms of its cold resistance formation. Four winter rapeseed materials ('CT-2360', 'MXW-1', '2018-FJT', and 'DT-7') domesticated in different environments were selected to analyze the DNA methylation level and pattern changes under low temperature using methylation-sensitive amplified polymorphism technology with 60 primer pairs. A total of 18 pairs of primers with good polymorphism were screened, and 1426 clear bands were amplified, with 594 methylation sites, accounting for 41.65% of the total amplified bands. The total methylation ratios of the four materials were reduced after low-temperature treatment, in which the DNA methylation level of 'CT-2360' was higher than that of the other three materials; the analysis of methylation patterns revealed that the degree of demethylation was higher than that of methylation in 'MXW-1', '2018-FJT', and 'DT-7', which were 22.99%, 19.77%, and 24.35%, respectively, and that the methylation events in 'CT-2360' were predominantly dominant at 22.95%. Fifty-three polymorphic methylated DNA fragments were randomly selected and further analyzed, and twenty-nine of the cloned fragments were homologous to genes with known functions. The candidate genes VQ22 and LOC103871127 verified the existence of different expressive patterns before and after low-temperature treatment. Our work implies the critical role of DNA methylation in the formation of cold resistance in winter rapeseed. These results provide a comprehensive insight into the adaptation epigenetic regulatory mechanism of Brassica rapa L. to low temperature, and the identified differentially methylated genes can also be used as important genetic resources for the multilateral breeding of winter-resistant varieties.

DNA polymorphisms detected in MT-ATP6 and MT-ATP8 genes in the residents of Sarajevo Canton

DNA polymorphisms detected in MT-ATP6 and MT-ATP8 genes in the residents of Sarajevo Canton

Antibiotyping, RAPD- and ERIC-PCR fingerprinting of Klebsiella pneumoniae clinical isolates at a tertiary reference hospital in Denpasar, Bali, Indonesia.

Klebsiella pneumoniae is a healthcare-associated infections agent and could be an extended spectrum β-lactamase (ESBL) producer. Understanding the transmission of this bacterium in a hospital setting needs accurate typing methods. An antibiogram is used to detect the resistance pattern of the isolates. Random Amplified Polymorphic DNA (RAPD) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR are rapid, technically simple, and easy-to-interpret DNA typing methods. This study aimed to evaluate the use of antibiotyping, RAPD-, and ERIC-PCR to investigate the heterogeneity of K. pneumoniae isolated from clinical specimens. The antibiograms of 46 K. pneumoniae clinical isolates were determined by Vitek® 2 Compact. All isolates underwent RAPD-PCR using AP4 primer and ERIC-PCR using ERIC-2 primer. The dendrogram was generated using the GelJ software and analyzed to determine its similarity. The analysis of antibiogram and the molecular typing diversity index was calculated using the formula of the Simpson's diversity index. About 71.7% of the isolates were ESBL-producers, and more than 80% of isolates were susceptible to amikacin, ertapenem, and meropenem. The antibiotyping produced 32 diverse types with DI = 0.964. In addition, the RAPD-PCR produced 47 different types with DI = 1, while ERIC-PCR was 46 (DI=0.999). Antibiotyping, RAPD- and ERIC-PCR showed powerful discrimination power among the isolates, supported the diversity of K. pneumoniae isolates in current study. These combination could be promising tools for clonal relationship determination, including in tracking the transmission of the outbreak's agent in hospital setting.