Restriction Fragment Length Polymorphism Assay Research Articles

Study on the correlation between DPP9 rs2109069 and IFNAR2 rs2236757 polymorphisms with COVID-19 mortality

Understanding the complex mechanisms of the immune system in dealing with the COVID-19 infection, which is probably related to the polymorphism in cytokine and chemokine genes, can explain the pro-inflammatory condition of patients. Therefore, in this study, the relationship between the frequency of single nucleotide polymorphisms in the two pro-inflammatory genes dipeptidylpeptidase 9 (DPP9) and interferon alpha and beta receptor subunit 2 (IFNAR2) and the severity of COVID-19 was assessed. This study involved 954 COVID-19 patients, including 528 recovered and 426 deceased patients. To investigate the polymorphisms of IFNAR2 rs2236757 and DPP9 rs2109069, we used the polymerase chain reaction with the restriction fragment length polymorphism assay. The results showed that IFNAR2 rs2236757 A allele is related to the reduced severity of the disease, whereas the incidence of DPP9 rs2109069 A allele was higher among the deceased than recovered individuals. On the other hand, in people carrying the G allele in the DPP9 gene polymorphism and the allele A in the IFNR2 gene polymorphism, the improvement of the disease was significantly higher. In conclusion, the results showed that IFNAR2 rs2236757 A allele is related to the decrease in the severity of the disease, while the frequency of DPP9 rs2109069 A allele was higher in deceased people than in recovered people. This shows the important role of genes related to inflammatory responses as well as the role of genetic variants of these genes in the severity of COVID-19.

Associations of TNF-RII rs1061622 With Post-Traumatic Stress Disorder and Their Interplays on Serum Lipids Levels in Adolescents.

To verify effects of rs1061622 at tumor necrosis factor-α receptor II (TNF-RII) gene (TNF-RII) on post-traumatic stress disorder (PTSD) and its interactive effects with PTSD on serum lipids levels in adolescents. PTSD was measured by PTSD Checklist-Civilian Version (PCL-C) in 699 adolescent survivors at 6 months after Wenchuan earthquake in China. A polymerase chain reaction and restriction fragment length polymorphism assay were utilized for TNF-RII rs1061622 genotyping followed by verification using DNA sequencing. Serum triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol were tested using routine methods. G (deoxyguanine) allele carriers had higher PCL-C scores than TT (deoxythymidine) homozygotes in female subjects. Female adolescents had higher PCL-C scores than male subjects in TT homozygotes. Predictors of PTSD prevalence and severity were different between G allele carriers and TT homozygotes. Subjects with PTSD had lower TG, TG/HDL-C, TC/HDL-C, and higher HDL-C than adolescents without PTSD in male G allele carriers. G allele carriers had higher TG/HDL-C and TC/HDL-C than TT homozygotes in male adolescents without PTSD, and lower TG and TG/HDL-C in male PTSD patients. G allele carriers had higher TG than TT homozygotes only in female adolescents without PTSD. These results suggest reciprocal actions of TNF-RII rs1061622 with other factors on PTSD severity, interplays of TNF-RII rs1061622 with PTSD on serum lipid levels, and novel treatment strategies for PTSD and comorbidities of PTSD with hyperlipidemia among adolescents with different genetic backgrounds of TNF-RII rs1061622 after experiencing traumatic events.

Association of <i>NR3C1 Bcl1</i> gene polymorphism with impaired programmed cell death of lymphocytes in patients with atopic bronchial asthma

Atopic asthma is a chronic disease characterized by airway obstruction, bronchial hyperresponsiveness, and inflammation. Patients show increased activation of immune cells in the airways, especially T-lymphocytes, leading to chronic inflammation. The lymphocytes of asthma patients are known to have an impairment of the type 1 and 2 programmed cell death, i.e., apoptosis and autophagy, thus contributing to prolongation and intensification of inflammatory process. As compared to apoptosis, autophagy may also contribute to cell survival under stress conditions. Its disruption and hyperactivation leads to exacerbation of allergic responses. Glucocorticoids are the main drugs for the treatment of atopic bronchial asthma by activating the glucocorticoid receptor, thus triggering anti-inflammatory response and apoptosis of the cells. However, some patients exhibit resistance to therapy due to various factors, including single nucleotide polymorphisms of NR3C1 glucocorticoid receptor gene. The highest association between asthma severity and resistance to therapy was found for the GG variant of the NR3C1 Bcl1 polymorphism. Common molecular pathways for glucocorticoid receptor activation and programmed cell death and mediating molecules suggest a significant role for the polymorphic receptor variant in cell death. The aim of our study was to evaluate the effect of a single nucleotide polymorphism (G allele, i.e., Bcl1 polymorphism of NR3C1 gene) of glucocorticoid receptor on expression levels of genes that regulate apoptosis (BCL2, CASP3) and autophagy (BECN1, LC3) in lymphocytes of patients with moderate and severe atopic bronchial asthma. The study was performed with peripheral blood samples of 24 patients aged 20 to 45 years with an established diagnosis of moderate to severe atopic bronchial asthma. Using PCR technique with restriction fragment length polymorphism (RFLP) assay, the patients were distributed according to the genotypes of the BclI polymorphism of the NR3C1 gene: 12 patients with CC genotype, 8 persons with GC genotype, and 4 cases with GG genotype. The lymphocytes were isolated in Ficoll density gradient and cultivated with dexamethasone under the conditions of nutrient depletion. The level of gene expression was determined by real-time PCR. When studying associations between various genotypes of Bcl1 polymorphism and expression of cell death marker genes, the anti-apoptotic reactions were detected in lymphocytes of patients with GG polymorphism under the influence of dexamethasone thus being a potential mechanism for development of resistance to glucocorticosteroid therapy in asthma. Impaired activation of BECN1 gene expression in patients with the GG genotype may suggest deregulation of the autophagy in this group of patients, as a mode of programmed cell death. Moreover, in patients with GC genotype during long-term cultivation, exposure to dexamethasone increases the expression of the LC3 gene, indicating a more pronounced activation of autophagy. Hence, this work demonstrates differences in response of lymphocytes to synthetic glucocorticoid therapy, and probable effect of G allele (Bcl1 polymorphism) on dysregulation of programmed cell death under the influence of dexamethasone.

Multiplex PCR-based RFLP assay for early identification of prevalent Mycobacterium leprae genotypes

Mycobacterium leprae is classified into four SNP genotypes and 16 subtypes (from 1A to 4P) that exhibit phylogeographical association reported from around the world. Among them, genotypes 1D and 3I represent more than 60% of M. leprae strains. Here, we report a new method for M. leprae genotyping which identifies the genotypes 1D and 3I by combining multiplex PCR amplification and restriction fragment length polymorphism (RFLP) of a M. leprae DNA amplicons using AgeI restriction enzyme. Agarose gel electrophoresis showed a deletion of 11 bp only among 3I genotypes by electrophoresis. When this multiplex PCR reaction is subjected to AgeI digestion, successful restriction digestion shows three bands for all the genotypes except 1D where only two bands were observed due to loss of restriction site. This method gives us the advantage of 1-step identification of the two most prevalent strains of M. leprae without using specialized equipments such as the Sanger sequencing system or quantitative PCR.

The Waist-Hip Ratio is a Mediator Between Serum Levels of Brain-Derived Neurotrophic Factor and Its Val66Met Polymorphism in Adolescents.

To explore anthropometric, metabolic and dietary factors associated with and their interplays with the Val66Met polymorphism at brain-derived neurotrophic factor (BDNF) gene (Bdnf) on serum BDNF levels in adolescents. Serum BDNF levels were quantified using an enzyme-linked immunosorbent assay in 644 high school students (278 males/366 females). A polymerase chain reaction and restriction fragment length polymorphism assay were utilized for Bdnf Val66Met genotyping followed by verification using DNA sequencing. Serum levels of metabolic characteristics were assayed by routine methods. The intake of macro and micronutrients was collected by a three-day food record. Serum BDNF levels were found to be significantly different in the subjects with different genotypes of Bdnf Val66Met (Val/Val homozygotes, 60.05 ± 28.07 ng/mL vs Val/Met heterozygotes, 56.37 ± 29.34 ng/mL vs Met/Met homozygotes, 51.32 ± 24.54 ng/mL, p = 0.022). Among the 36 tested variables, waist-hip ratio (WHR) (β = -0.163, p < 0.001), iodine intake (β = 0.132, p = 0.001), heart rate (β = 0.108, p = 0.005), high-density lipoprotein cholesterol (HDL-C) (β = 0.098, p = 0.011) and dietary fiber intake (β = 0.082, p = 0.084) were the predictor of serum BDNF levels, while SBP (β = 0.097, p = 0.013) and WHR (β = 0.091, p = 0.021) were related with Bdnf Val66Met. Moreover, WHR was observed to play a partial mediating role in the relationship between Bdnf Val66Met and serum BDNF levels (95% CI [-1.161, -0.087]) and contribute 13.05% of its total effect on serum BDNF levels. There are interplays between WHR and Bdnf Val66Met on serum BDNF levels, which may be among the explanations for the previous heterogeneous reports and provide novel insights into the regulation of serum BDNF levels.

Screening of natural Wolbachia infection in mosquitoes (Diptera: Culicidae) from the Cape Verde islands

BackgroundWolbachia pipientis is an endosymbiont bacterium that induces cytoplasmic incompatibility and inhibits arboviral replication in mosquitoes. This study aimed to assess Wolbachia prevalence and genetic diversity in different mosquito species from Cape Verde.MethodsMosquitoes were collected on six islands of Cape Verde and identified to species using morphological keys and PCR-based assays. Wolbachia was detected by amplifying a fragment of the surface protein gene (wsp). Multilocus sequence typing (MLST) was performed with five housekeeping genes (coxA, gatB, ftsZ, hcpA, and fbpA) and the wsp hypervariable region (HVR) for strain identification. Identification of wPip groups (wPip-I to wPip-V) was performed using PCR–restriction fragment length polymorphism (RFLP) assay on the ankyrin domain gene pk1.ResultsNine mosquito species were collected, including the major vectors Aedes aegypti, Anopheles arabiensis, Culex pipiens sensu stricto, and Culex quinquefasciatus. Wolbachia was only detected in Cx. pipiens s.s. (100% prevalence), Cx. quinquefasciatus (98.3%), Cx. pipiens/quinquefasciatus hybrids (100%), and Culex tigripes (100%). Based on the results of MLST and wsp hypervariable region typing, Wolbachia from the Cx. pipiens complex was assigned to sequence type 9, wPip clade, and supergroup B. PCR/RFLP analysis revealed three wPip groups in Cape Verde, namely wPip-II, wPip-III, and wPip-IV. wPip-IV was the most prevalent, while wPip-II and wPip-III were found only on Maio and Fogo islands. Wolbachia detected in Cx. tigripes belongs to supergroup B, with no attributed MLST profile, indicating a new strain of Wolbachia in this mosquito species.ConclusionsA high prevalence and diversity of Wolbachia was found in species from the Cx. pipiens complex. This diversity may be related to the mosquito's colonization history on the Cape Verde islands. To the best of our knowledge, this is the first study to detect Wolbachia in Cx. tigripes, which may provide an additional opportunity for biocontrol initiatives.Graphical

Co-Selection of Bacterial Metal and Antibiotic Resistance in Soil Laboratory Microcosms.

Accumulation of heavy metals (HMs) in agricultural soil following the application of superphosphate fertilisers seems to induce resistance of soil bacteria to HMs and appears to co-select for resistance to antibiotics (Ab). This study aimed to investigate the selection of co-resistance of soil bacteria to HMs and Ab in uncontaminated soil incubated for 6 weeks at 25 °C in laboratory microcosms spiked with ranges of concentrations of cadmium (Cd), zinc (Zn) and mercury (Hg). Co-selection of HM and Ab resistance was assessed using plate culture on media with a range of HM and Ab concentrations, and pollution-induced community tolerance (PICT) assays. Bacterial diversity was profiled via terminal restriction fragment length polymorphism (TRFLP) assay and 16S rDNA sequencing of genomic DNA isolated from selected microcosms. Based on sequence data, the microbial communities exposed to HMs were found to differ significantly compared to control microcosms with no added HM across a range of taxonomic levels.

Highly recurrent BRAF p.V595E mutation in canine papillary oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is the most common oral epithelial malignancy in dogs. It exhibits locally aggressive biological behaviour with the potential to metastasize, and a reported 1-year survival rate of 0% when left untreated. Expression studies suggest that aberrant MAPK signalling plays a key role in canine OSCC tumorigenesis, which is consistent with BRAF and HRAS MAPK-activating mutations reported in some tumours. Several morphological subtypes of canine OSCC have been described, with papillary, conventional, and basaloid as the most common patterns. We hypothesized that mutational differences may underlie these phenotypic variations. In this study, targeted Sanger sequencing and restriction fragment length polymorphism assays demonstrate that up to 85.7% of canine papillary OSCC (n=14) harbour a BRAF p.V595E mutation. Assessment of neoplastic epithelial cell proliferation using Ki67 immunolabelling (n=10) confirmed a relatively high proliferation activity, consistent with their known aggressive clinical behaviour. These findings underscore a consistent genetic feature of canine papillary OSCC and provide a basis for the development of novel diagnostic and targeted therapeutic approaches that can improve the quality of veterinary care.

CC Genotype of GNAS c.393C>T (rs7121) Polymorphism Has a Protective Effect against Development of BK Viremia and BKV-Associated Nephropathy after Renal Transplant

The GNAS gene encodes the alpha-subunit of the stimulatory G-protein (Gαs) in humans and mice. The single-nucleotide polymorphism of GNAS, c.393C>T, is associated with an elevated production of Gαs and an increased formation of cyclic adenosine monophosphate (cAMP). In the present study, we analyzed the effect of this GNAS polymorphism on a renal allograft outcome. We screened a cohort of 436 renal allograft recipients, who were retrospectively followed up for up to 5 years after transplant. GNAS genotypes were determined with polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assays. The 393T allele was detected in 319 (73%) recipients (113 recipients with TT and 206 with CT genotype) and the CC genotype in 117 (27%). The CC genotype was associated with a significantly lower frequency of BK viremia (CC, 17 recipients (15%); T 84 (26%)); p = 0.01; TT, 27 vs. CC, 17, p = 0.07; TT, 27 vs. CT, 57, p = 0. 46; CT, 57 vs. CC, 17, p = 0.01) and BKV-associated nephropathy (CC, 3 recipients (3%); T, 27 (8%); p = 0.03; TT,10 vs. CC, 3, p = 0.04; TT, 10 vs. CT,17, p = 0.85; CT, 17 vs. CC,3, p = 0.04) after transplant. BKV-associated nephropathy-free survival was significantly better among CC genotype carriers than among T allele carriers (p = 0.043; TT vs. CC, p = 0.03; CT vs. CC, p = 0.04; TT vs. CT, p = 0.83). Multivariate analysis indicated an independent protective effect of the CC genotype against the development of both BK viremia (relative risk. 0.54; p = 0.04) and BKV-associated nephropathy after renal transplant (relative risk. 0.27; p = 0.036). The GNAS 393 CC genotype seems to protect renal allograft recipients against the development of BK viremia and BKV-associated nephropathy.

Prevalence of polycystic kidney disease in Persian and Persian-related cats in western Mexico.

Autosomal dominant polycystic kidney disease (ADPKD), the most frequently diagnosed hereditary disease affecting Persian cats, is caused by a cytosine-to-adenine transversion (10063C>A) in PKD1, the gene that codes for polycystin-1. The objective of this study was to provide a preliminary estimate of the frequency of the pathogenic 10063C>A single nucleotide polymorphism (SNP) of PKD1 in Persian and Persian-related cat breeds in western Mexico. Blood samples were collected from 104 cats (89 Persian, seven Persian crossbreed, five Siamese and three Himalayan cats). Genotyping was performed with our proposed PCR restriction fragment length polymorphism (RFLP) assay, as well as a previously established PCR-RFLP method for validation. The genotypes of control cats were corroborated by a commercial veterinary genetics laboratory. Our proposed PCR-RFLP assay and the validated PCR-RFLP methodology indicated that 24/104 (23.1%) cats in this study were heterozygous carriers of the 10063C>A SNP, including 23/89 Persian cats (25.8%) and 1/7 Persian crossbreed cats (14.3%). No Siamese or Himalayan cats were carriers. There were no discrepancies between the results obtained with our proposed assay and those obtained with the validation method or with commercial laboratory results. The carrier frequency of the PKD1 10063C>A SNP in Persian and Persian-related cat breeds in western Mexico was found to be 23.1%. ADPKD frequencies among cat populations in Mexico have not been published previously. Genotyping assays can be used to facilitate the selection of breeding stocks by local breeders and veterinarians to avoid propagation of ADPKD.

MTHFR-c 677C>T polymorphism and male infertility: An analysis in a cohort of Pakistani men

ObjectiveTo analyze existence of an association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism with male infertility. Materials and methodsA case–control study was conducted from June 2017 to August 2018 in which 88 infertile and 40 fertile were recruited. Polymerase chain reaction (PCR) – restriction fragment length polymorphism (RFLP) assay was carried out to study the allelic frequency of C677T polymorphism. The differences in allelic and genotypic frequencies of C677T locus between fertile and infertile groups were evaluated by the Pearson chisquare test. A logistic regression model was used to calculate Odds ratios and 95% confidence intervals, p value<0.05 was considered significant. The Hardy–Weinberg equilibrium was tested using HWE software. ResultsIn infertile subjects, frequency distribution of CC allele was (60.2%), the CT allele was (30.7%) the TT allele was (9.1%) and in the fertile controls the frequency was CC allele (75%), CT allele (20%) and TT allele (5%) respectively. Analysis revealed MTHFR 677 CC genotype associated significantly with male infertility (p<.046, OR=2.385; 95% CI=1.014–5.608); Frequency of CT (30.7%) and TT (9.1) genotypes were higher in infertile men as compared to CT (20%) TT (5%) in fertile controls but statistically these were not significantly different (p=0.097; OR=0.455; CI=0.179–1.153 and p=0.431; OR=0.526; CI=0.107–2.599 respectively). Significant association of age and BMI with MTHFR genotypes and infertility was observed. ConclusionOur results showed that MTHFR C677T polymorphism is not a risk factor for male infertility in our Pakistani population.

Early Detection and Identification of Parasitoid Wasps Trichogramma Westwood (Hymenoptera: Trichogrammatidae) in Their Host Eggs Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism.

Parasitoid wasps are invaluable agents in pest biological control. Early detection and identification of parasitoid immatures are vital in characterizing parasitoid-host interactions and for evaluating parasitism rates accurately in the field. Trichogramma is the most widely used parasitoid wasp, and several studies have been performed for its molecular identification. However, those studies were mainly focused on Trichogramma adults and rarely on immatures. Here, we report a method to detect and identify Trichogramma larvae in their host eggs. We designed a pair of Trichogramma-specific primers that amplified Trichogramma mtCOI sequences from Corcyra cephalonica (Stainton) eggs parasitized by any of eight Trichogramma species tested but not from nonparasitized eggs of four lepidopteran hosts. This PCR method reliably detected Trichogramma immatures in parasitized eggs as early as 1 h after parasitism. We further developed an RFLP (restriction fragment length polymorphism) assay using restriction enzymes SspI and VspI to differentiate eight Trichogramma species at their immature stage. Overall, we developed a sensitive and reliable PCR-RFLP method to detect and identify immature-stage Trichogramma in their lepidopteran hosts. This method shows promise for conveniently identifying Trichogramma in insectaries and accurately evaluating parasitism rates in the field.

Genetic Polymorphisms in the 3'-Untranslated Regions of SMAD5, FN3KRP, and RUNX-1 Are Associated with Recurrent Pregnancy Loss.

Recurrent pregnancy loss (RPL) is typically defined as two or more consecutive pregnancy losses prior to 20 weeks of gestation. Although the causes of idiopathic RPL are not completely understood, vascular development and glucose concentration were reported to correlate with the pregnancy loss. The TGF-β signaling pathway which plays a significant role in pregnancy is activated by the interaction between high glucose and SMAD signaling and affects the vascular cells. SMAD5 and RUNX-1 are involved in the TGF-β signaling pathway and contribute to advanced glycation end products (AGEs) production and vascular development. FN3KRP, a newly described gene, is also associated with vascular diseases and suggested to relate to AGEs. Therefore, in the present study, we investigated associations between RPL risk and genetic polymorphisms of SMAD5, FN3KRP, and RUNX-1 in 388 women with RPL and 280 healthy control women of Korean ethnicity. Participants were genotyped using real-time polymerase chain reaction and restriction fragment length polymorphism assay to determine the frequency of SMAD5 rs10515478 C>G, FN3KRP rs1046875 G>A, and RUNX-1 rs15285 G>A polymorphisms. We found that women with RPL had lower likelihoods of the FN3KRP rs1046875 AA genotype (adjusted odds ratio (AOR), 0.553; p = 0.010) and recessive model (AOR, 0.631; p = 0.017). Furthermore, combination analysis showed that SMAD5 rs10515478 C>G and FN3KRP rs1046875 G>A mutant alleles were together associated with reduced RPL risk. These findings suggest that the FN3KRP rs1046875 G>A polymorphism has a significant role on the prevalence of RPL in Korean women. Considering that it is the first study indicating a significant association between FN3KRP and pregnancy disease, RPL, our results suggest the need for further investigation of the role of FN3KRP in pregnancy loss.

Methylene-tetrahydrofolate reductase gene C677T and A1298C polymorphisms as a risk factor for Crimean-Congo hemorrhagic fever

Crimean-Congo hemorrhagic fever (CCHF) is a deadly viral disease. Methylene-tetrahydrofolate reductase (MTHFR) has an important role in folate metabolism, and also in the formation of new cells, DNA synthesis, repair and methylation. We aimed to examine the relationship between MTHFR gene C677T (Ala222Val, rs1801133) and A1298C (Glu429Ala, rs1801131) polymorphisms with CCHF in a Turkish population. Totally 273 participants were included in the current study. One hundred forty-one participants were CCHF patients and one hundred thirty-two participants were healthy controls. The polymerase chain reaction (PCR) and further restriction fragment length polymorphism (RFLP) assays were applied to determine the genotypes of MTHFR polymorphisms. We did not find any differences between the CCHF patients and healthy controls in terms of allele and genotype distributions of both the C677T and A1298C polymorphisms. In composite genotype analysis between different groups, the frequency of CT-AA composite genotype, which is formed by C677T-A1298C polymorphisms, was found to be significantly higher in Mild CCHF patients compared to both Severe CCHF patients and controls (p = 0.036 and p = 0.008, respectively). In conclusion, in this study, we found a relationship between CCHF and MTHFR gene polymorphisms. CT-AA composite genotype of MTHFR gene C677T and A1298C polymorphisms showed a predisposition to Mild CCHF.

A Combinatorial Q-Locus and Tubulin-Based Polymorphism (TBP) Approach Helps in Discriminating Triticum Species.

The simple and straightforward recognition of Triticum species is not an easy task due to their complex genetic origins. To provide a recommendation, we have compared the performance of different PCR-based methods relying on the discrimination ability of the Q- and γ-gliadin (GAG56D) genes, as well as TBP (Tubulin-Based Polymorphism), a method based on the multiple amplification of genes of the β-tubulin family. Among these approaches, the PCR-RFLP (Restriction Fragment Length Polymorphism) assay based on a single-nucleotide polymorphism (SNP) present in the Q gene is the only one capable of fully discerning hexaploid spelt and common wheat species, while both γ-gliadin and TBP fail with similar error frequencies. The Q-locus assay results in the attainment of either a single fragment or a doublet, depending on the presence of a suitable restriction site, which is affected by the mutation. This dual pattern of resolution limits both the diagnostic effectiveness, when additional Triticum species are assayed and compared to each other, and its usefulness, when commercially available flours are analyzed. These limitations are overtaken by flanking the Q-locus assay with the TBP analysis. In this way, almost all of the Triticum species can be accurately identified.

Benefits and limitations of a new genome-based PCR-RFLP genotyping assay (GB-RFLP): A SNP-based detection method for identification of species in extremely young adaptive radiations.

High‐throughput DNA sequencing technologies make it possible now to sequence entire genomes relatively easily. Complete genomic information obtained by whole‐genome resequencing (WGS) can aid in identifying and delineating species even if they are extremely young, cryptic, or morphologically difficult to discern and closely related. Yet, for taxonomic or conservation biology purposes, WGS can remain cost‐prohibitive, too time‐consuming, and often constitute a “data overkill.” Rapid and reliable identification of species (and populations) that is also cost‐effective is made possible by species‐specific markers that can be discovered by WGS. Based on WGS data, we designed a PCR restriction fragment length polymorphism (PCR‐RFLP) assay for 19 Neotropical Midas cichlid populations (Amphilophus cf. citrinellus), that includes all 13 described species of this species complex. Our work illustrates that identification of species and populations (i.e., fish from different lakes) can be greatly improved by designing genetic markers using available “high resolution” genomic information. Yet, our work also shows that even in the best‐case scenario, when whole‐genome resequencing information is available, unequivocal assignments remain challenging when species or populations diverged very recently, or gene flow persists. In summary, we provide a comprehensive workflow on how to design RFPL markers based on genome resequencing data, how to test and evaluate their reliability, and discuss the benefits and pitfalls of our approach.

Molecular-based detection of Leishmania tropica isolates among sensitive, resistant, and relapsed patients treated with Meglumine Antimoniate.

The appearance of resistance to pentavalent antimony, as the mainline of treatment for Cutaneous Leishmaniasis (CL) has been reported from Iran. According to the patients' laboratory and clinical history, 96 archived slides of patients infected with Leishmania tropica (L. tropica) treated with Meglumine Antimoniate (Glucantime®) were selected. After microscopic examination, Nested Polymerase Chain Reaction (Nested-PCR) and Restriction Fragment Length Polymorphism (RFLP) assays were done for each sample. In Nested-PCR, all positive samples were characterized as L. tropica. Additionally, some positive products of sensitive, resistant, and recidivans cases were selected to check their differentiations by sequencing software. In RFLP, various patterns of schizodemes were detected according to the reference patterns. Most sensitive cases of L. tropica (treated with Glucantime®) were categorized as schizodeme B, and most resistant cases were identified as schizodeme B and D. In recidivans cases, 91% of specimens categorized as schizodeme A and B. However, study on the type of L. tropica isolates that are resistant or sensitive to Glucantime® could be helpful before drug therapy.

Characterization of genetic polymorphisms in oral cancer-related genes pertaining to oxidative stress, carcinogen detoxifying, and DNA repair: A case-control study.

The genetic polymorphism in the DNA repair and maintenance genes leads to mutations and deregulated growth hormones which have implications in cancer. Apart from identified carcinogens such as tobacco, specific genetic polymorphisms correspond to an individual's risk of oral cancer. The current study aims at identification of differences in genetic polymorphisms in subjects with and without oral cancer in Karad, India. The aim of the study was to characterize genetic polymorphisms in oral cancer-related genes pertaining to oxidative stress, carcinogen detoxifying, and DNA repair. A hospital-based case-control was conducted with 150 subjects sorted into cases (n = 75) and controls (n = 75). The polymerase chain reaction-based restriction fragment length polymorphism assay was used to genotype the polymorphisms of selected DNA repair, detoxifying, and oxidative stress-related genes. In the cases group, among the DNA repair set, Gene-1 (XRCC1), Gene-3 (XRCC3), Xeroderma Pigmentosum Group-D gene (XPD), and human 8-oxoguanine DNA glycosylase (hOGG1) showed significant genetic polymorphism. Similarly, the genetic polymorphism in the carcinogen detoxifying genes-n-acetyl transferase, GSTP1, and oxidative stress-related gene catalase were noted. The Cramer's V/odds ratio was applied to estimate the association of genetic risk factors with oral cancer. The polymorphisms of XRCC1, XRCC3, XPD, and hOGG1 genes were associated with a higher susceptibility to oral cancer as compared to controls. This information may be a useful novel marker in oral oncology for primary prevention and intervention.

PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan.

Plasmodium vivax is the most common human malaria parasite in Asian countries including Pakistan. Present study was designed to explore the genetic diversity of plasmodium vivax genotypes based on Pvmsp-3α and Pvmsp-3βgenes using allelic specific nested PCR and RFLP assays markers from field isolates in district Mardan, Pakistan. Blood samples of 200 P. vivax malarial patients were collected after taking their written informed consent. Genetic diversity in nested PCR products was determined by Restriction Fragment Length Polymorphism (RFLP) utilizing Alu1 and PstI restriction enzymes for alpha and beta gene products digestion, respectively. For analysis the genetic diversity of the sub allelic variants of Pvmsp3α and Pvmsp3β genes, Chi-Square test was performed by utilizing Minitab programming software 18. The P value 0.05 was considered as statistically significant. For Pvmsp-3α genes after gel electrophoresis of digested products, four distinct genotypes were obtained from total of 50 samples; type A: 35 (70%) (1.5-2.0 kb), 12 of type B (24%) (1.5-1.7 kb), 2 of type C (4%) (0.5-1.5) and one for type D (2%) (0.5-0.65 kb) which could be characterized into 9 allelic pattern (A1-A4, B1-B3, C1, D), in which A3 remained the most predominant. For Pvmsp-3βgenes, three distinct genotypes were obtained from 50 samples; 40(80%) of type A (1.5-2.5 kb), 9 (18%) of type B (1.0-1.5kb) and 1(2%) of type C (0.65 kb) which could be characterized into 6 allelic patterns (A1-A3, B1-B2, and C1). Most dominant one in Type A was A1 alleles which were noted (46%), while in Type B, the most dominant were B1 (10%).This study is the first ever report of molecular epidemiology and genetic variation in Pvmsp-3α and Pvmsp-3β genes of P. vivax isolates by using PCR/RFLP from District Mardan and showed a remarkable level of genetic diversity in the studied genes of circulating parasites in the study area. The results of this study will contribute in future studies about the genetic structure of parasite and vaccine development against the malaria.

Increased diversity, fungal burden, and virulence of oral Candida spp. in patients undergoing anti-tuberculosis treatment

Some studies have demonstrated a high prevalence of Candida species in patients with tuberculosis (TB). This is most likely due to long-term antimicrobial therapy. To date, no longitudinal studies addressed the effects of anti-TB treatment on the fungal burden and virulence of Candida spp. This study investigated the prevalence and virulence of Candida spp. in the oral cavity of 30 TB patients at different stages of treatment through a cohort study. These results were compared with those of 60 systemically healthy individuals in a cross-sectional study.Oral rinse samples from TB patients were collected before 45 and after 120 days of treatment. In the control group, the biological samples were collected only once. Candida spp. were identified by restriction fragment length polymorphism (RFLP) assays, and the following virulence factors were studied: phospholipase C and proteinase production, as well as Candida spp. biofilm and hyphae formation.The clinical diagnosis of TB and its treatment time were associated with the greater fungal burden (p < 0.0001), presence of non-albicans Candida (NAC) species (p = 0.0003), and increased virulence factors when compared with the Candida spp. isolated from systemically healthy individuals. The results showed that anti-TB treatment time was responsible for the increased fungal burden and isolation of NAC in TB patients (p = 0.0233).The increased prevalence, quantification, and virulence of Candida spp. isolated from the oral cavity of TB patients highlight the greater risk of oral lesions and cases of systemic dissemination in these patients.