Restriction Fragment Length Polymorphism Research Articles

Association of a non-synonymous variant of MLH3 gene involved in meiotic recombination with conception rate of Japanese Black cattle

Context Conception rate, which is an important parameter to evaluate female fertility, has been gradually decreasing in Japanese Black cattle during the past decades. Meiosis is an essential biological process in gamete formation and meiotic failure could be a cause of infertility or reduced fertility in mammals. Of note, single nucleotide polymorphisms (SNPs) in the MLH3 gene involved in meiotic recombination were reported to affect the genome-wide recombination rate of meiosis in cattle. Aims The present study was conducted to investigate the association of SNPs in the MLH3 gene with conception rate in Japanese Black cattle. Methods On the basis of the reproductive data of 2045 Japanese Black cattle born from 1990 to 2009, we selected two groups of the reproductive females with high conception rate (n = 103) and low conception rate (n = 109). Then, we genotyped the SNPs in MLH3 gene in both reproductive groups by sequencing and polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP). The significant association of SNPs with conception rate in Japanese Black cattle was estimated by Fisher’s exact test, by using R commander. Key results We found the presence of five SNPs of MLH3 gene in Japanese Black cattle, including non-synonymous variants of MLH3 N408S that has been reported to be involved in meiotic recombination rate and MLH3 S591G newly identified in the present study. Comparison of genotype distributions and allele frequencies of the MLH3 N408S between high and low conception-rate groups indicated a significant difference between these groups, suggesting that this SNP is associated with conception rate. However, there is no significant difference between MLH3 S591G with conception rate in Japanese Black cattle. Conclusions We found a significant association between a non-synonymous variant of MLH3 N408S and conception rate, suggesting that this SNP can be a potential marker for selecting the Japanese Black cattle for improving fertility. We also identified a novel non-synonymous variant of MLH3 S591G in Japanese Black cattle. Implications These findings will be informative for future marker-assisted selection to improve the fertility of Japanese Black cattle. This is the first report of a genetic variant implicated in meiotic recombination being linked to female fertility in cattle.

Genotyping of human isolates from human toxoplasmosis outbreak: Restriction Fragment Length Polymorphism and Sanger Sequencing.

Toxoplasmosis is a parasitic disease caused by infection with Toxoplasma gondii, capable of infecting a wide range of hosts. The parasite exhibits a broad genetic diversity, necessitating genotypic characterization for genotype identification and associations with epidemiological information. Therefore, the Restriction Fragment Length Polymorphism (RFLP) technique is used for characterization. This study aimed to perform genotypic characterization of isolates from pregnant women infected during a human toxoplasmosis outbreak, comparing the RFLP and Sanger Sequencing methodologies. For this purpose, six human isolates were subjected to conventional PCR, Multiplex PCR, Nested PCR, Enzymatic Digestion, and Sanger Sequencing. Additionally, the standard strains GTI (Type I), PTG (Type II), and CTG (Type III) were also subjected to the same techniques described above. Subsequently, the amplified DNA products were compared with the standard strains. As a result, it was observed that Sanger Sequencing provides the same information as RFLP PCR, as well as the possibility of cost reduction for genotypic characterization, and providing greater agility in issuing results. Additionally, Sanger Sequencing of T. gondii isolates allows for detailed evaluation of nucleotide sequences, including the assessment of SNPs and enzymatic restriction sites, which the RFLP technique does not.

Potassium inwardly-rectifying channel subfamily J member 11 (KCNJ11) gene polymorphism in Egyptian type 2 diabetic patients: a single-center study.

The KCNJ11 gene belongs to the potassium channel gene family. It has a major role inthe secretion of insulin. Genetic variations in KCNJ11 are possibly responsible for the progression of type 2 diabetes mellitus (T2DM). In this study, we investigated the possible correlation between KCNJ11 (rs5210) gene polymorphism and T2DM. This study included 92 individuals divided into two groups. Group 1 included 46 type 2 diabetic patients. Group 2 (control group) included 46 healthy participants. A complete history was taken and a full physical examination was performed. Anthropometric data were measured. Laboratory investigations included fasting blood glucose (FBG), two hours post-prandial blood glucose (2HPPBG), glycated hemoglobin (HbA1c), and fasting lipid profile. KCNJ11 (rs5210) single nucleotide polymorphism was detected by polymerase chain reaction restriction-fragment length polymorphism (PCR-RFLP). Both AG and GG genotypes were associated with increased risk for T2DM (OR 5.2, 95% CI 1.32-20.5, P = 0.01 for AG; and OR 18.2, 95% CI 2.99-31.7, P = 0.002 for GG). Also, the frequency of the G allele was significantly higher in type 2 diabetic patients compared to healthy controls (50% versus 23.9%, respectively). The G allele of rs5210 in KCNJ11 contributed to an increased risk of T2DM (OR 3.18, 95% CI 1.31-7.75, P = 0.01). There was a statistically significant association between increased 2HPPBG and HbA1c levels and the carrier of AG and GG genotypes (P = 0.01 and 0.007, respectively). There was a statistically significant association between total cholesterol(TC), low-density lipoprotein-cholesterol (LDL-c), and high-density lipoprotein-cholesterol (HDL-c) levels and the carrier of AG and GG genotypes (P < 0.001, 0.02, and 0.007, respectively). Regression analysis detected that body mass index (BMI), 2HPPBG, TC, triglycerides (TG), and the G allele of rs5210 in KCNJ11 gene showed a significant association with T2DM (P = 0.004, 0.042, 0.003, 0.006, and 0.01, respectively) while no association was observed with FBG, HbA1c, LDL-c or HDL-c (P = 0.099, 0.123, 0.522, and 0.765, respectively). KCNJ11 rs5210 genetic polymorphism may raise the risk for the occurrence ofT2DM among Egyptians.

Diagnostic Implications of CD63 and CD64 Expression Levels and FcγRIIIA 158 V/F Gene Polymorphism in Primary Immune Thrombocytopenia Adult Patients.

Immune thrombocytopenic purpura (ITP) is an acquired autoimmune disease characterized by reduced platelet counts due to immune system dysregulation caused by many factors, including genetics, autoimmune diseases, infections, and inflammations. Therefore, the current study aimed to evaluate immunological markers such as the expression level of lysosomal associated membrane protein 3 (LAMP-3), also known as CD63, and the expression level of Fc-gamma receptor I (FcγRI), also known as CD64 and also investigate the association of Fc-gamma receptor IIIA (FcγRIIIA) 158 V/F polymorphism to the risk of ITP. A total of 180 subjects; 60 ITP patients, 60 patients with thrombocytopenia of other causes and 60 controls were enrolled into our study. The expression level of CD63 was done using reverse transcription quantitative PCR (RTqPCR), while CD64 expression level was done by flow cytometry. The polymorphism of FcγRIIIA 158 V/F gene was analyzed by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) analysis. Finally, CD63 and CD64 protein-protein interactions were done by using the STRING online database. The expression of CD63 was significantly elevated in ITP patients than thrombocytopenia patients and healthy control. Also there was high expression level of CD64 on granulocytes and monocytes from ITP patients than other groups. Receiver operating characteristic curve (ROC curve) analysis of CD63 showed an area under the curve (AUC) revealed of 1.00, sensitivity of 100% and specificity of 100%; while for CD64 on granulocytes, AUC of 0.998 as well as a sensitivity of 96.66% and specificity of 93.33%. Regarding FcγRIIIa 158 V/F polymorphism, all patients and healthy volunteers included in this study showed the wild FF genotype. The expression of both CD63 and CD64 were significantly increased in ITP patients and could be good biomarkers to diagnose ITP. Additionally, there is no association between FcγRIIIa 158 V/F polymorphism and the risk of ITP disease.

Molecular analysis of vector-borne pathogens in Eurasian badgers (Meles meles) from continental Europe

BackgroundVector-borne pathogens (VBPs) are increasing in significance in veterinary medicine and public health settings, with wildlife playing a potentially crucial role in their transmission. Eurasian badgers (Meles meles) are widely distributed across Europe. However, information currently available on the prevalence of VBPs in badgers is limited. The objective of the current study was to investigate the occurrence of Anaplasmataceae, Bartonella spp., Mycoplasma spp., Rickettsia spp., Piroplasmida, Trypanosomatida and Filarioidea in badgers and subsequently, based on the results, assess the potential risk to domestic animals, other wildlife and humans.MethodsBetween 2017 and 2021, blood or spleen samples from 220 badgers were collected in nine continental European countries: Austria (n = 7), Bosnia and Herzegovina (n = 2), Croatia (n = 22), France (n = 44), Germany (n = 16), Hungary (n = 7), Italy (n = 16), Romania (n = 80) and Serbia (n = 26). VBPs were identified by performing PCR analysis on the samples, followed by Sanger sequencing. Additionally, to distinguish between different Babesia lineages we performed restriction fragment length polymorphism (RFLP) analysis on piroplasm-positive samples, using HinfI as restriction enzyme. A phylogenetic analysis was performed on Mycoplasma spp.ResultsThe pathogens identified were Babesia sp. badger type A (54%), B (23%), and C (37%); Trypanosoma pestanai (56%); Mycoplasma sp. (34%); Candidatus Mycoplasma haematomelis (8%); Candidatus Mycoplasma haematominutum (0.5%); and Ehrlichia spp. (2%). Rickettsia spp., Bartonella spp. and filarioid nematodes were not detected among the tested samples.ConclusionsThe large sample size and diverse study populations in this study provide valuable insights into the distribution and epidemiology of the analyzed pathogens. Some of the VBPs identified in our study show high similarity to those found in domestic animals, such as dogs. This finding suggests that badgers, as potential reservoirs for these pathogens, may pose a threat not only to other wildlife but also to domestic animals in close vicinity. Continuous surveillance is essential to monitor VBPs in wildlife as a means to enable the assessment of their impact on other wildlife species, domestic animals and human health.Graphical

Cleaved Amplified Polymorphic Sequence Markers in Horticultural Crops: Current Status and Future Perspectives

DNA markers have broad applications, including marker-assisted selection (MAS) for breeding new cultivars. Currently, single nucleotide polymorphisms (SNPs) have become a preferred choice of markers for molecular geneticists and breeders. They offer many advantages, such as high abundance and coverage in the genome, codominant inheritance, locus specificity, and flexibility for high-throughput genotyping/detection formats, and they are relatively inexpensive. The availability of reference genome sequences enables precise identification of candidate genes and SNPs associated with a trait of interest through quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS). Such SNPs can be converted into markers for their application in MAS in crop breeding programs. Cleaved amplified polymorphic sequence (CAPS) markers amplify short genomic sequences around the polymorphic endonuclease restriction site. This review provides insight into the recent advancements made in the development and application of CAPS markers in several horticultural plants. We discussed many new tools that aid faster and more accurate design of CAPS markers from the whole genome resequencing (WGRS) data. The developed CAPS markers offer immense application in germplasm screening and field trials, genomic loci mapping, identifying candidate genes, and MAS of important horticultural traits such as disease resistance, fruit quality and morphology, and genetic purity.

Molecular identification of two phytoplasma strains associated with the gladiolus virescence disease in Iran

Severe symptoms of virescence in gladiolus flowers were observed in the Chaharmahal-Bakhtiari province of Iran in 2023. In the areas surveyed the disease incidence ranged from 5% to 40% and has a substantial economic impact, posing a serious threat to gladiolus cut flower production. Given that these disease symptoms have been reported to be associated with the presence of phytoplasmas, verifying the presence and identity of these bacteria is essential for focused disease management. Sequence analyses of the 16S rRNA, ribosomal protein (rp), and tuf genes confirmed the presence of `Candidatus Phytoplasma asteris' and `Ca. P. tritici' strains in the symptomatic plants. Restriction fragment length polymorphism indicated that the phytoplasmas in the 30 symptomatic gladiolus plant samples examined belong to subgroups 16SrI-F and 16SrI-R. These results were also confirmed through phylogenetic analysis on the three studied genes in which the two strains resulted closely related to phytoplasmas in the 16SrI-R and 16SrI-F subgroups, respectively. This is the first report of 16SrI-R and 16SrI-F phytoplasmas associated with the virescence disease in gladiolus plants.

Engineered FnCas9 mediated mutation profiling for clarithromycin resistance in Helicobacter pylori strains isolated from Indian patients with gastrointestinal disorders

Helicobacter pylori is a highly prevalent gut pathogen with reported implications in a wide range of gastrointestinal disorders. Antibiotic based therapy, especially with clarithromycin is one of most effective treatment strategies against H. pylori. However, rising global prevalence of clarithromycin resistance in certain H. pylori strains, primarily attributed to point mutations in the 23 s ribosomal RNA coding gene, pose a major challenge in the effective eradication of this pathogen. There are a number of established methodologies devised for H. pylori mutation detection, so as to provide a tailored treatment plan to the patients and resist further transmissions of antibiotic resistant strains. However, there is no ‘gold standard’ method available to detect mutation status in clinical isolates of H. pylori from infected patients. CRISPR-Cas9 based technologies have revolutionized the field of mutation detection in biological samples, particularly during the recent COVID-19 pandemic. Although multiple assays have been reported for detection of H. pylori in clinical samples including CRISPR diagnostics (CRISPRDx) platforms, there is no such assay reported till date to detect specific mutations that confer antibiotic resistance to this pathogen. In this study, we have developed an assay using engineered FnCas9 (en31-FnCas9) protein to effectively detect the A2142G and A2143G mutations in the 23 s rDNA of H. pylori strains isolated from gastric biopsy samples. The data from in vitro cleavage assays and strip-based lateral flow tests using en31-FnCas9 and guide RNAs targeting the conserved and mutated loci of H. pylori 23 s rDNA are in perfect congruence with the data from Sanger sequencing and restriction fragment length polymorphism (RFLP) analysis. Our results indicate that en31-FnCas9 based mutation analysis can be deployed as an efficient diagnostic methodology to detect clarithromycin susceptibility in patients with suspected H. pylori infections.

Contribution of ERCC2 rs13181 (Lys751Gln) and rs1799793 (Asp312Asn) polymorphisms to the risk of bladder cancer in Bangladesh

BackgroundHuman Excision Repair Cross-Complementation Group 2 (ERCC2) proteins play a vital role in the nucleotide excision repair pathway through ATP-dependent helicase activity. Several studies found that polymorphisms in the ERCC2 gene are associated with susceptibility to different cancers, although the outcomes were confusing. ObjectiveAs a result, in this retrospective study, we investigated the relationship between genetic polymorphisms of the ERCC2 gene at codons 312 (rs1799793) and 751 (rs13181) and bladder cancer susceptibility in Bangladesh, as well as the disease's aggressiveness. MethodsGenetic polymorphisms of ERCC2 were assayed by the polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) method with 121 bladder cancer patients and 130 healthy controls. ResultsPatients who had the Gln/Gln polymorphism of ERCC2 at codon 751 (OR=3.27; 95% CI=1.19-8.67; p<0.05) and Asp/Asn at codon 312 (OR=2.14; 95% CI=1.03-4.29; p<0.05) were significantly associated with a higher risk of developing bladder cancer. Again, Gln/Gln polymorphisms in bladder cancer (p<0.05) were more likely to be present in individuals with cancer in the family. ConclusionsThis study reveals that susceptibility and bladder cancer aggressiveness are associated with polymorphisms at codon 751 and Asp/Asn at codon 312 of the ERCC2 gene.

Association of 25(OH)-Vitamin D3 Serum Concentrations and Vitamin D Receptor Gene Variants with the Risk of Idiopathic Spontaneous Preterm Birth in the Croatian Population.

Preterm birth (PTB) forms a heterogeneous group with possible genetic predisposition. 25(OH)-vitamin D3 plays a significant role during implantation, placentation, and the maintenance of normal pregnancy. The aim of our research was to examine whether FokI, Cdx2, and ApaI VDR gene variants, as well as serum concentrations of 25-hydroxy25(OH)-vitamin D3 in women and their newborns, might be predisposing factors for idiopathic spontaneous preterm birth. The patient group consisted of 44 pairs of women with ISPTB and their children, and the control group consisted of 44 pairs of women who delivered at term and their children. At the time of delivery, peripheral blood was collected from every woman, and after newborn delivery, umbilical cord blood was collected. For genotyping of the rs2228570 C/T, rs11568820 G/A, and rs7975232 T/G SNPs, a combination of polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) was used. Serum concentrations of 25(OH)-vitamin D3 were determined using high-performance liquid chromatography (HPLC). There were no statistically significant differences in the frequencies of VDR genotypes and alleles between women with ISPTB and control women. There was a statistically significant difference in the distribution of VDR Cdx-2 (rs11568820) genotypes between preterm-born children and controls, with the GG genotype and G allele being more prevalent among patients than controls (p < 0.001). There were no statistically significant differences in mean values between women with ISPTB and control women, nor between preterm and full-term newborns, although the 25(OH)-vitamin D3 concentrations in preterm-born children were lower than in controls. Furthermore, there was a statistically significant correlation in 25(OH)-vitamin D3 concentrations between mothers and children both in the patient and in the control groups (b = 0.771, p < 0.001). The results of our study demonstrate a notable association between the VDR Cdx2 gene polymorphism and idiopathic spontaneous preterm birth (ISPTB) in a Caucasian population, but because of the small number of participants, further research is needed.

The effect of VEGF and KDR gene variants on Crimean-Congo hemorrhagic fever

Background Crimean-Congo hemorrhagic fever (CCHF), an acute viral hemorrhagic fever disease, has a high mortality rate among humans. Hemorrhagic propensity is caused by coagulation malfunction and increased capillary permeability brought on by the resultant vascular injury. Vascular endothelial growth factor (VEGF) and VEGF receptor-2, or KDR (kinase insert domain containing receptor), are effective in vasculogenesis and angiogenesis. CCHF was stated to have endothelial dysfunction. This study aimed to evaluate whether the VEGF and KDR gene variants contribute to the development of CCHF in the Turkish population. Methods A total of 101 subjects, including 51 CCHF patients and 50 healthy controls, were included in the study. The polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method was used to genotype VEGF 936 C > T (rs3025039) and KDR − 604 T > C (rs2071559) variants. The results were statistically analyzed. Results The VEGF 936 C > T genotype and allele distributions did differ significantly between the patients and the controls. The subjects carrying the C/C genotype and C allele had a higher risk of developing CCHF than the control group (p˂0.05). There was a statistically significant association between the controls and the patients in terms of VEGF 936 C > T C/C versus C/T + T/T (p˂0.05, OR:3.273, 95%Cl: 1.44–7.63). The KDR − 604 T > C variant’s allele and genotype distribution were not significantly different between the patients and controls. Conclusion This study suggests the VEGF 936 C > T variant is a genetic marker of sensitivity to CCHF among the Turkish population and may help protect against the disease.

The impact of LEP gene polymorphisms located at exon 2 (LEP-HinfI) and intron 2 (LEP-Sau3AI) on growth and reproductive traits in Saanen goats

Abstract. Leptin (LEP), alternatively recognized as the obesity gene, influences food consumption, energy balance, and lipid metabolism. Additionally, it plays a crucial role in energy metabolism, and variations in the LEP gene have been studied extensively among various livestock species. These investigations have unveiled correlations with traits such as meat quality, milk yield and composition, and growth characteristics. Nevertheless, the existing knowledge regarding its correlation with growth and reproductive traits in goats is comparatively limited, particularly when juxtaposed with studies of cattle. Hence, the objective of the current study was to investigate the relationship between polymorphisms in the intron 2 (Sau3AI) and exon 2 (HinfI) regions of the LEP gene and growth and reproductive traits in Saanen goats. The study comprised 185 Saanen goats in total. The PCR-RFLP (polymerase chain reaction restriction fragment length polymorphism) technique was employed to genotype these polymorphisms. Population genetic analysis included the number of effective alleles, heterozygosity, polymorphism information content, and compatibility with the Hardy–Weinberg equilibrium. The general linear model procedure's least-squares methods were used for the statistical analysis. The SNP (single-nucleotide polymorphism) located in exon 2 (LEP-HinfI) was monomorphic. Remarkably, the SNP located in intron 2 (LEP-Sau3AI) was associated with birth weight (p&lt;0.05) and average daily weight gain (p&lt;0.05). In this context, the AA genotype demonstrated higher birth weight and daily live weight gain means compared to other genotypes. No significant differences were observed in litter size, total weight gain, or morphometric measurements. The caprine LEP-Sau3AI polymorphism situated within intron 2 proved influential in traits critical for the profitability and sustainability of goat breeding. The findings of this study provide novel and valuable information for future research on the LEP gene in goats.

FSHB and FSHR genes variants in combination with hormones levels predict low and high ovarian response to controlled ovarian stimulation: a logistic regressive model

BackgroundPredicting the number of follicles obtained after controlled ovarian stimulation (COS) is challenging, especially considering individual variability. Since FSH is a fundamental hormone that controls growing follicle activity, genetic variants are predicted to affect ovarian response to stimulation.The aim of the studyThe purpose of this study was to analyze whether FSHB rs10835638 and FSHR rs6166 genetic variants in combination with clinical parameters might be considered as potential precise predictors of ovarian response during COS.Materials and methodsThe present study included 144 women from infertile couples who underwent assisted reproductive technologies. Women with reduced FSH and/or AMH serum levels were excluded from the study. Genotyping was carried out applying restriction fragment length polymorphism analysis.ResultsGenotypes frequencies for FSHB rs10835638 and FSHR rs6166 were GG (73%), GT (24%), TT (3%) and AA (42%), AG (39%), GG (19%), respectively. FSHR rs6166 GG genotype was shown as associated with higher early follicular phase serum FSH, LH and progesterone levels, compared to AA and AG genotypes. Logistic regressive models that simultaneously use the patient’s genetic and clinical characteristics to calculate the probability of low or high ovarian response have been developed.ConclusionThe present study suggests that rs10835638 and rs6166 genetic variants affect hypothalamic-pituitary–gonadal hormones serum levels, and together may provide an improved model for predicting an ovarian response during COS.

Gene Sequencing Study of Mitochondrial Cytochrome Oxidase Subunit I (COI) in Aedes aegypti Mosquito

Aedes aegypti is an important vector from the public health point of view. It transmits pathogens of Dengue and various other diseases. Controlling vector populations is key to reducing disease transmission and it is possible by understanding the taxonomic characteristics of the vectors and their genetic analysis helps in the identification of the genetic variations in species of different geographical areas. The main aim of the present study is the screening of the Aedes mosquito genome of local species as genetic studies give some insights into the vaccine for the treatment of the diseases caused by mosquito species. In the present study, the adult Ae. aegypti collected from Suryapet town where Dengue fever is endemic, used for the mitochondrial Cytochrome Oxidase subunit I (COI) gene sequencing using the techniques of polymerase chain reaction, Electrophoretic separation, spectrophotometric analysis, and BLAST. The mitochondrial COI sequence of 583 bps is published in the National Centre for Biotechnology Information (NCBI) with accession number ON413769. The sequence data was matched with the database available in the NCBI to identify variation in the gene as this gene keeps changing in the organisms and may contribute to the species establishing itself in a particular region due to congenial environmental conditions. One match with the protein called haem copper oxidase subunit I. The transmission of different pathogens in different areas can be ascertained by comparing similar sequence studies documented. Genomic studies involving genetic markers are of immense help in developing the vaccine. The mitochondrial COI gene is the marker often used for evolutionary research. The single nucleotide polymorphisms (SNP) or Restricted fragment length polymorphisms (RFLPs) that occur in DNA also contribute to the vector's adaptability to the different geographical areas and also the survival benefit which are the basis for understanding the vectors thoroughly and their role in disease transmission.

Exploring the association between SLC11A1 and CARD15 gene polymorphisms and tuberculosis susceptibility in Holstein cattle

Abstract. Bovine tuberculosis (bTB) is a contagious disease that has a socio-economic impact on familial and industrial farms. Genetic selection can improve resistance against bTB. This study aimed to characterize the links between SLC11A1 and CARD15 gene polymorphisms and tuberculosis (TB) susceptibility. In total 200 animals were used (50 cases and 150 controls). Polymorphisms in the SLC11A1 and CARD15 genes were identified and analyzed with the restriction fragment length polymorphism (PCR-RFLP) method. Our results report the PstI PCR-RFLP marker for the SLC11A1-SNP1 site and the StyI PCR-RFLP marker for the CARD51-SNP1 site in Tunisian Holstein cows. Statistical analysis showed a significant association between SLC11A1-SNP1, CARD15-SNP1 and susceptibility/resistance to TB (P &lt; 0.05). Two SLC11A1-SNP1 genotypes were susceptible to tuberculosis, i.e., the heterozygote CG and the homozygote CC, while one SLC11A1-SNP1 genotype, i.e., the GG mutated homozygote, was less susceptible to infection. Concerning the CARD15 gene, two genotypes are highly sensitive to the incidence of bovine tuberculosis, i.e., AA and AG, while the GG genotype is more beneficial and more tolerant of Mycobacterium bovis. SLC11A1 and CARD15 are two useful candidate genes associated with tuberculosis, and this information can be used to improve the health status of domestic cattle and humans.

DISTRIBUTION OF PLASMODIUM FALCIPARUM CHLOROQUINE RESISTANCE TRANSPORTER (PFCRT) AND PLASMODIUM FALCIPARUM MULTIDRUG RESISTANCE 1(PFMDR-1) GENES IN ILORIN NORTH-CENTRAL NIGERIA

Globally, malaria is a peculiar health challenge particularly in continent of Africa. The ease of developing resistance to anti-malaria drugs by Plasmodium falciparum is a serious impediment towards programs aim at control and elimination of malaria. Consequently, drug efficacy surveillance is desirable to institute adequate and effective treatment policies. In this study, distribution of these genes in Plasmodium falciparum isolates in Ilorin metropolis were investigated. One hundred and three samples collected randomly from 5 hospitals in Ilorin metropolis. The samples were amplified at codon 76 and 86 for Pfcrt and Pfmdr-1 respectively using PCR / Restricted Fragment Length Polymorphism (RFLP). The most prevalent alleles were drug susceptible alleles in the study area (K76 and N86) with 31% and 40% respectively, while drug resistance alleles (86Y) have 13% and the least prevalence 2% was the mixed alleles K76T. UITH has the highest number of susceptible alleles followed by CSC 38% and 46% for K76 and N86 respectively. There are significant differences in the distribution of these alleles and the study sites (P&lt; 0.05). The prevalence of resistance alleles in the area is a welcome development that can be employed for possibility of re-introduction of CQ for the treatment of malaria in the study area which will serve as an advantage over expensive ACT due to fact that it is safe cheap and readily affordable.

The Relationship Between miR-196a2 Polymorphism and Colorectal Cancer Risk

ABSTRACT Objective MicroRNAs are small endogenous, non-coding, single-stranded posttranscriptional RNA molecules. The discovery of microRNAs has made new contributions to cancer diagnosis and treatment. These microRNAs reported as a responsible for colorectal cancer development with several epigenetic changes. In this study, it was aimed to evaluate the relationship between the polymorphism of miR-196a-2 polymorphism rs11614913 and colorectal cancer in Turkish population. Methods Two hundred colorectal cancer patient (124 colon cancer and 76 rectal cancer) and 240 health control individuals were included in our study, which was planned as a hospital based retrospective cohort study. MiR-196a2 polymorphism in peripheral blood samples has been determined by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) method. Significance of the results has been evaluated by using SPSS (20.0 SPSS Inc., Chicago, IL, USA.) statistical program. Results miR-196a2 C / C + C / T genotypes was found to be associated with the risk of colorectal cancer development (p: 0.001; OR: 2.04, 95% CI: 1.293-3.236). The subgroup analysis, showed that the C / C + C / T genotype increased the risk of colon cancer development 2.11 times (p: 0.016; 95% CI: 1.136-3.918) and rectal cancer 2.86 times (p: 0.011; 95% CI:1.242-6.592). The relationship between any clinicopathological features of colorectal cancer and the frequency of the C / C + C / T genotype of miR196a2 was not statistically significant (p&gt; 0.05). Conclusion This study supports that miR-196a2's C / C + C / T genotypes is related with increased colorectal cancer development risk.

Effects of APOE isoforms in diabetic nephropathy patients of South India.

Diabetic nephropathy (DN) is a grave complication and the most common renal dysfunction of diabetes mellitus. Genetic factors, including Apolipoprotein E (APOE) isoforms, have been implicated in the pathogenesis of DN. A total of 577 type 2 Diabetes mellitus subjects were categorized into diabetes non-nephropathic (Controls: n = 321), diabetes nephropathic (DN: n = 256) groups. Demographic, clinical, and biochemical parameters including age, BMI, lipid profiles (TC, LDL-C, HDL-C, TG), glucose metabolism (plasma glucose, HbA1c, serum insulin), renal function (UACR, PCR), and blood pressure (SBP, DBP) were assessed. APOE variant frequencies were determined using restriction fragment length polymorphism (RFLP) analysis, validated against Hardy-Weinberg equilibrium (HWE), and statistically correlated with each clinical and biochemical parameter. The DN group had an increased prevalence of hypertension, fatty liver, and dyslipidemia compared to the Control group. Biochemical analyses revealed elevated levels of TC (213.41mg/dL vs. 189.32mg/dL), LDL-C (134.46mg/dL vs. 107.56mg/dL), and reduced HDL-C (58.13mg/dL vs. 65.32mg/dL) in DN cases compared to Controls (all p < 0.0001). The APOE variants distribution showed a significant increase in E2 allele frequency (69.1% vs. 15.3%) and corresponding homozygous genotype (E2/2: 42.2% vs. 5.6%) in DN cohorts. The study found a higher frequency of E2 allele in the DN group compared to Controls, though no statistically significant risk of DN was linked to this allele. The results suggest a potential association for APOE polymorphisms, requiring broader studies to clarify the role of APOE polymorphisms in DN susceptibility.

An Investigation of Polymorphism on the FASN, SCD1, and SLC27A3 Genes in Sheep

Milk traits of sheep are affected by many environmental and genetic factors. These traits are quantitative traits and are determined by many genes. This study aimed to investigate polymorphisms of milk-related Fatty-acid synthase (FASN), Stearoyl-CoA desaturase (SCD1), and solute carrier 27A3 (SLC27A3) genes in cross-bred Hamdani sheep. Blood samples were collected from 100 healthy cross-bred Hamdani ewes from the jugular vein into K3-EDTA-containing tubes. Genomic DNA was extracted using a commercial DNA isolation kit. PCR products of FASN (275 bp), SCD1 (225 bp), SLC27A3-P1 (341 bp), and SLC27A3-P2 (319 bp) were subjected to restriction fragment length polymorphism (RFLP) analysis using SSil (AciI), Cfr13I, AluI, and Hpy188III the restriction enzyme, respectively. However, all gene regions were found to be monomorphic. In the study, only TT, AA, AA, and GG genotypes were detected for FASN, SCD1, SLC27A3-P1, and SLC27A3-P2, respectively. Allele and genotype frequencies were 1.00 for all genotypes and alleles. Although this study did not reveal favorable genotypes in FASN, SCD1, and SLC27A3 genes that can be used for milk traits, more comprehensive studies with larger sample sizes should be conducted to investigate polymorphisms in cross-bred Hamdani sheep.

Genetic characterization of Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease in Lithuania.

Neisseria meningitidis is a gram-negative bacterium responsible for life-threatening invasive infections known as invasive meningococcal disease and is associated with high fatality rates and serious lifelong disabilities among survivors. This study aimed to characterize N. meningitidis isolates cultured from blood and cerebrospinal fluid collected between 2009 and 2021 in Lithuania, assess their genomic relationships with European strains, and evaluate the possibility of using a cost-effective method for strain characterization, thus improving the national molecular surveillance of invasive meningococcal disease. In total, 321 N. meningitidis isolates were collected and analyzed using multilocus restriction typing (MLRT). Amplification of the penA gene and restriction fragment length polymorphism analysis were performed to identify the modified penA genes. Based on the MLRT genotyping results, we selected 10 strains for additional analysis using whole-genome sequencing. The sequenced genomes were incorporated into a dataset of publicly available N. meningitidis genomes to evaluate genomic diversity and establish phylogenetic relationships within the Lithuanian and European circulating strains. We identified 83 different strains using MLRT genotyping. Genomic diversity of N. meningitidis genomes analysed revealed 21 different sequence types (STs) circulating in Lithuania. Among these, ST34 was the most prevalent. Notably, three isolates displayed unique combinations of seven housekeeping genes and were identified as novel STs: ST16969, ST16901, and ST16959. The analyzed strains were found to possess virulence factors not commonly found in N. meningitidis. Six distinct penA profiles were identified, each with different frequencies. In the present study, we also identified N. meningitidis strains with new penA, NEIS0123, NEIS1320, NEIS1525, NEIS1600, and NEIS1753 loci variants. In our study, using the cgMLST scheme, Minimum Spanning Tree (MST) analysis did not identify significant geographic relationships between Lithuanian N.meningitidis isolates and strains from Europe. Discussion: To our knowledge, this is the first study to employ whole genome sequencing (WGS) method for a comprehensive genetic characterization of invasive N. meningitidis isolates from Lithuania. This approach provides a more detailed and precise analysis of genomic relationships and diversity compared to prior studies relying on traditional molecular typing methods and antigen analysis.