Polymorphism Patterns Research Articles

ISSR and RAPD primers selection for assessing genetic diversity of Enhalusacoroides (L.f.) Royle

Inter Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) are common PCR-based molecular markers used to study genetic diversity both between and within species. One of important steps in ISSR and RAPD analyses is primer selection to obtain bright PCR products. The aim of this study was to select ISSR and RAPD primers that produced scorable fragments of PCR product for genetic diversity evaluation of seagrass Enhalusacoroides (L.f.) Royle. The study also aimed to compare ISSR and RAPD technique in producing informative fragments. Enhalusacoroides is one seagrass species widely distributed in Indonesia. Seagrass samples were collected from Sanur Coastal Water and from Nusa Dua Coastal Water. DNA was extracted using CTAB method. Ten ISSR primers and eight RAPD primers were tested. Results showed that RAPD was more informative than ISSR. Among ten ISSR primers, only four primers resulted in scorable fragments in all samples, and only one among those primers gave polymorphic pattern. As many as 15 fragments have resulted from three ISSR primers and only 1 fragment was polymorphic. All RAPD primers produced scorable products, and three primers resulted in polymorphic fragments. A total of 42 RAPD fragments were produced and 4 from them were polymorphic fragments

Primary cutaneous methotrexate-associated B-cell lymphoproliferative disorders other than EBV-positive mucocutaneous ulcer: clinical, pathological, and immunophenotypic features

Methotrexate (MTX)-associated B-cell lymphoproliferative disorders (B-LPD) may first present in the skin. Epstein-Barr virus (EBV)-positive mucocutaneous ulcer (EBVMCU) is now a well known disease listed in the 2017 World Health Organization classification. However, primary cutaneous MTX-associated B-LPD (pcMTX B-LPD), other than EBVMCU, appear to be underestimated, and their distinctiveness remains unproven. This study aimed to document the clinicopathological characteristics of nine patients with pcMTX B-LPD that were not EBVMCU to extend our understanding of this peculiar disease. The cohort included three males and six females, with a median age of 74 years (range 54-83 years). All patients were treated with MTX for RA. Of nine patients, four presented with a solitary lesion, and five had multiple lesions. Histologically, five cases showed a polymorphic pattern, and four showed a monomorphic pattern. Immunohistochemically, four cases showed positive EBER staining, and one showed positive CD5 staining. In eight cases, once pcMTX B-LPD was diagnosed, methotrexate was immediately withdrawn. All eight of these patients experienced spontaneous regression and achieved complete remission (CR), without relapse. The patient with CD5 positivity received cytotoxic chemotherapy as the initial treatment. This patient achieved a CR after the initial treatment, but eventually experienced disease relapse resulting in death. We also revealed that pcMTX B-LPD and MTX-associated EBVMCU exhibited similar biological behaviours. We concluded that most pcMTX B-LPD cases could be cured by stopping MTX treatment. We also highlighted the fact that pcMTX B-LPD and MTX-EBVMCU had overlapping features. This finding suggested that pcMTX B-LPD and MTX-EBVMCU might share an underlying mechanism.

Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber

Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.

Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus.

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

Population Genomics Insights into the First Wave of COVID-19.

Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.

DILS: Demographic inferences with linked selection by using ABC.

We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.

Bovine subclinical mastitis-associated methicillin-resistant Staphylococcus aureus, selective genotyping and antimicrobial susceptibility profile of the isolates in Kurdistan province of Iran.

Background and Objectives:Staphylococcus aureus is frequently involved in bovine subclinical mastitis worldwide. Besides, the methicillin-resistant S. aureus (MRSA) carrier state of animals is a matter of worrisome. This study aimed to evaluate the frequency of MRSA, discriminatory geno-analysis and antibiotic resistance scheme of the strains isolated from bovine subclinical mastitis in Kurdistan province of Iran.Materials and Methods:A total of 283 samples were collected and analyzed for S. aureus phenotypically and molecularly. SCCmec and coa types, and pvl gene were evaluated using polymerase chain reaction (PCR). Finally, the restriction fragment length polymorphism (RFLP) patterns of coa types and the antimicrobial susceptibility profile of the isolates were assessed.Results:Among the 95 isolates of S. aureus, 11 (11.57%) strains were recognized as MRSA. Six, one, and four SCCmec types represented for IVa, IVc, and V were determined, respectively, among which an individual IVa and V determinant harboured pvl gene. Restriction digestion products of 490 bp, 680 bp, and 730 bp of coa bands were generated. Tobramycin, mupirocin, fusidic acid, clindamycin, and chloramphenicol were the most effective drugs against the MRSA isolates.Conclusion:The detrimental involvement of S. aureus in bovine subclinical mastitis is proved herein. Besides, the contribution of MRSA and potential contamination of milk and dairy products with the bacterium may impose a serious public health risk. This demands serious and long-lasting efforts to control the infection. The results may be effective in the implementation of accurate controlling strategies.

Genetic Characterization of the Central Javanese Duck using Microsatellite Markers

Duck conservation strategy based on genetic characteristics has been undertaken to preserve indigenous breeds and produce high quality offspring. In addition, the genetic characteristic analysis provides further information for studying avian influenza viruses. The aim of this research was to study the genetic characterisation of indigenous Central Javanese duck in Indonesia using microsatellite markers. Microsatellite or simple sequence repeats (SSR) or short tandem repeats (STR) of various breeds of Central Javanese duck were analysed on 35 local ducks which consisted of seven variants of Javanese ducks in Central Java. Ten pairs of duck microsatellite primers were used to amplify the DNA from feathers. Nine out of 10 microsatellite loci (90%) demonstrated polymorphic patterns containing 50 alleles. The number of alelles varied from two to 10 alleles at various polymorphic microsatellite loci with an average of 5.56 alelles per locus. From the study, CAUD013 locus was determined as the highest heterozygosity with 0.882 score while CAUD030 locus was the lowest one with 0.034 score.Similarly, CAUD030 locus had the lowest PIC score (0.30) whereas the CAUD013 locus had the highest PIC value (0.869). Hence, it was showed that microsatellite markers were highly polymorphic in several loci for the Central Javanese duck and may be useful for genetic description of other native duck in terms of species conservation.

Keragaman genetik Anggrek Grammatophyllum scriptum asal biji dari hasil Kultur In Vitro berdasarkan penanda RAPD

Propagation through tissue culture by using orchid seed as explants will produce a lot of orchid plants. This study aims to measure the genetic character of orchid plantlets that were regenerated from seeds which have been resulted from in vitro culture. The genetic character of the original orchid plants produced from in vitro culture was determined using Random Amplified Polymorphic DNA (RAPD) molecular markers. The results showed that the primers used in the RAPD analysis showed a polymorphic band pattern of 14 DNA bands, with sizes between 500 bp - 8000 bp. The genetic distance of Grammatophyllum scriptum orchids that was regenerated from seeds is between 0.229 and 0.649. The progenis produced from in vitro culture were clustered into seven groups at a dissimilarity coefficient of 45%.

Identifying Clinical and Genomic Features Associated With Chronic Kidney Disease.

We apply a pattern-based classification method to identify clinical and genomic features associated with the progression of Chronic Kidney disease (CKD). We analyze the African-American Study of Chronic Kidney disease with Hypertension dataset and construct a decision-tree classification model, consisting 15 combinatorial patterns of clinical features and single nucleotide polymorphisms (SNPs), seven of which are associated with slow progression and eight with rapid progression of renal disease among African-American Study of Chronic Kidney patients. We identify four clinical features and two SNPs that can accurately predict CKD progression. Clinical and genomic features identified in our experiments may be used in a future study to develop new therapeutic interventions for CKD patients.

Human leucocyte antigen association of patients with Stevens-Johnson syndrome/toxic epidermal necrolysis with severe ocular complications in Han Chinese

Background/aimsStevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) induced by cold medicine (CM) may result in severe ocular complications (SOCs). The purpose of this study was to investigate the human leucocyte antigen (HLA)...

The Biology of Polymorphic Melanic Side-Spotting Patterns in Poeciliid Fishes

Melanin-based color patterns are an emerging model for studying molecular and evolutionary mechanisms driving phenotypic correlations. Extensive literature exists on color patterns and their correlated traits in the family Poeciliidae, indicating that these fishes are tractable models. We review the biology of polymorphic melanic side-spotting patterns characterized by macromelanophores forming irregular spotted patterns across fishes’ flanks. These patterns are present in the generaGambusia, Limia, Phalloceros, Poecilia, andXiphophorus. Their presence is controlled by dominant genes on autosomes or sex chromosomes. Variation in expression is under polygenic control; however, these genes’ identities are still largely unknown. In someGambusia holbrookiandPoecilia latipinna, expression is dependent on low temperature exposure, but underlying molecular mechanisms are unknown. Spotted fish develop melanoma in rare cases and are a well-developed model for melanoma research. Little is known about other physiological correlates except that spottedG. holbrookimales exhibit higher basal cortisol levels than unspotted males and that metabolic rate does not differ between morphs in someXiphophorusspecies. Behavioral differences between morphs are widespread, but specific to population, species, and social context. SpottedG. holbrookimales appear to be more social and more dominant. Juvenile spottedG. holbrookihave lower behavioral flexibility, and spottedX. variatusexhibit greater stress resistance. Findings conflict on whether morphs differ in sexual behavior and in sexual selection by females. Melanic side-spotting patterns are uncommon (<30%) in populations, although extreme high-frequency populations exist. This low frequency is surprising for dominant genes, indicating that a variety of selective pressures influence both these patterns and their correlated traits. Little is known about reproductive life history traits. SpottedG. holbrookiare larger and have higher survival when uncommon, but underlying mechanisms remain unknown. Spotted morphs appear to have a strong selective advantage during predation. Predators prefer to attack and consume unspotted morphs; however, this preference disappears when spottedG. holbrookimales are common, indicating negative frequency-dependent selection. Spotted morphs are preferred socially under turbid conditions, but other environmental factors that shape phenotypic correlations and morph fitness have not been studied. Finally, we present questions for future studies on melanic side-spotting patterns.

Comparitive Genome Sequence Analysis of Bovine Lymphocyte Antigen BoLA DRB3.2 Alleles in Deoni and Ongole (Bos indicus) Cattle Breeds of India

Background: India, a major livestock region of the Asian countries is rich in animal genetic resources having special qualities of hardy nature, resistance to many diseases and adopted to adverse climatic conditions. The cattle MHC, Bovine Lymphocyte Antigen DRB3 (BoLA-DRB3) is considered to be a major gene linked with disease resistance traits of Indian cattle. Methods: The present study was carried out to sequence the BoLA-DRB3.2 alleles in Deoni and Ongole breeds of Indian cattle. PCR RFLP analysis of the BoLA-DRB3.2 alleles in Deoni (n=51) and Ongole (n=60) cattle using three different restriction enzymes RsaI, BstYI and HaeIII to find out the possible restriction pattern. Based on the combined allelic patterns, each sample was further analyzed by PCR- SBT technique to detect the SNP variations present in BoLA-DRB3.2 alleles.Result: The PCR RFLP analysis revealed that the highest frequent alleles are *6 (0.216) and *15 (0.225) in Deoni and Ongole breeds of cattle, respectively. The second-highest frequency was observed for BoLA alleles *11 and *6 which were present at a frequency of 0.167 and 0.200 in Deoni and Ongole breeds of cattle, respectively. To get the complete picture of polymorphic pattern of BoLA-DRB3.2 allele direct sequencing was carried out for each plymorphic pattern. The interesting feature noticed in the Ongole breed was that at position 91 and 133 of the sequence, it had both A and G nucleotides in contrast to Bos taurus breed, which had only TT nucleotides. The sequence analysis of BoLA-DRB3 exon 2 between two breeds revealed that there are numerous variations in exon 2, whatever variation, that lead to different mobility shift and band pattern in gels. Deoni and Ongole breeds of cattle had similar variations at positions 94, 134, 211, 235 and 258noticed due to the unique nature of native breeds.

UGT1A6 and UGT2B7 Gene Polymorphism and its Effect in Pediatric Epileptic Patients on Sodium Valproate Monotherapy

To evaluate the pattern of UGT1A6 and UGT2B7 gene polymorphism in pediatric epileptic patients and to compare the sodium valproate concentration in different patterns of UGT gene polymorphism. In this cross-sectional study, 99 pediatric epileptic patients aged 2-18 y receiving Sodium valproate monotherapy for the past one month were included from JusticeK S Hegde Charitable hospital, Mangalore after obtaining informed consent. Genetic polymorphism patterns were evaluated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Trough level serum valproate concentration was estimated by high-performance liquid chromatography (HPLC). Sodium valproate concentration in different UGT genotypes was compared by Analysis of Variance (ANOVA). P value <0.05 was considered significant. In the present study population, the predominant mutant allele pattern was observed in UGT1A6 (T19G, A541G, A552C) gene. In UGT2B7 (A268G, C161T) showed predominant mutant allele pattern while (G211T) showed predominant wild type. Mean steady-state sodium valproate concentration was 105.40 ± 49.9μg/ml and adjusted sodium valproate concentration was 5.5± 3.2mg/kg/L. It was found that there was no statistical difference in sodium valproate concentration in different UGT1A6 and UGT2B7 gene polymorphism. The present study concluded that though there was a difference in pattern of gene polymorphism with concerning UGT1A6 and UGT2B7, however, it has not contributed to variation in serum concentration of sodium valproate in the present study population.

Genetic Polymorphism of Tumor Necrosis Factor-Alpha, Interferon-Gamma and Interleukin-10 and Association With Risk of Mycobacterium Tuberculosis Infection.

Background. Mycobacterium tuberculosis has become the leading cause of morbidity and death in humans worldwide. Thus, genetic variability of the host plays a major role in human susceptibility to the pathogen, among others. Therefore, the objective of this finding was to assess the association of genetic polymorphisms of cytokines with tuberculosis infection.Method.A cross-sectional study was conducted between January and May 2018. Five ml of whole blood was collected and extracted the genomic DNA through simple salting out method. The patterns of genetic polymorphism were determined by amplification refractory method PCR using specific primers. Finally, the PCR run on electrophoresis of agarose gel and the band was visualized under UV light. A logistical regression model has been adapted to assess the association of genetic polymorphisms with tubercular infection. In order to determine the association between the explanatory and outcome variable, the odds ratio with 95% CI was calculated. P < 0.05 is a statistically significant value.Result.In present study, the frequency of TNF-α -308 G allele and GG genotype OR (95% CI)= 0.20 (0.11-0.37), and OR (95% CI)= 0.29 (0.18-0.46)), respectively) and IFN-γ +874 A allele and AA genotype OR (95% CI)= 3.80 (2.11-6.86) and (OR (95% CI)= 1.61(1.13-2.28), respectively) were significantly associated with tuberculosis incidence. In contrast, there is no significant correlation between IL-10 -1082 A and AA of allele and genotype, respectively in tuberculosis patients (p > 0.05) was evident.Conclusion.From our finding, the genetic variability of TNF-α -308 A and IFN-γ +874 alleles are the potent host genetic risk factors associated with tuberculosis infection.

Association of UGT1A6 gene polymorphism with clinical outcome in pediatric epileptic patients on sodium valproate monotherapy.

Pediatric epilepsy comprises chronic neurological disorders characterized by recurrent seizures. Sodium valproate is one of the common antiseizure medications used for treatment. Glucuronide conjugation is the major metabolic pathway of sodium valproate, carried out by the enzyme uridine 5′-diphosphate (UDP) glucuronosyl transferase (UGT) whose gene polymorphisms may alter the clinical outcome. The objective of this study was to assess the association between UGT1A6 genetic polymorphism and clinical outcome in terms of efficacy and tolerability in pediatric epileptic patients on sodium valproate monotherapy. Pediatric epileptic patients (n=65) aged 2-18 years receiving sodium valproate monotherapy for the past one month were included. Genetic polymorphism patterns of UGT1A6 (T19G, A541G, A552C) were evaluated by PCR-RFLP. Clinical outcome was seizure control during the 6 months observation period. Tolerability was measured by estimating the hepatic, renal, and other lab parameters. Out of 65 patients, TT (40%), TG (57%), and GG (3%) patterns were observed in UGT1A6 (T19G) gene, AA (51%), AG (40%), and GG (9%) in (A541G) gene, and AA (43%), AC (43%), and CC (14%) in (A552C) gene. No statistical difference in clinical outcome was found for different UGT1A6 genetic polymorphism patterns. We concluded that different patterns of UGT1A6 genetic polymorphism were not associated with the clinical outcome of sodium valproate in terms of efficacy and tolerability. Sodium valproate was well-tolerated among pediatric patients with epilepsy and can be used as an effective antiseizure medication.

Single Nucleotide Polymorphism of Insulin Receptor Gene rs2059806 in Polycystic Ovary Syndrome- A Case-control Study

Introduction: One of the most common endocrinopathies faced in clinical practice is Polycystic Ovary Syndrome (PCOS). Furthermore, it is one of the major causative factors of anovulatory infertility affecting a large number of female population worldwide. They are also at a greater risk for developing impaired glucose tolerance, type 2 diabetes mellitus and cardiovascular disease. Decreased sensitivity to insulin is a common feature observed in women with this syndrome. Aim: To assess whether polymorphism of insulin receptor gene has a significant role to develop the PCOS. Materials and Methods: This was a case-control, observational, hospital-based study, conducted at Department of Biochemistry, Calcutta National Medical College, Kolkata from January 2018 to September 2018. Total 123 patients with PCOS cases and 111 normo-ovulatory normal control female subjects were selected. Blood samples were collected for estimation of serum testosterone and Deoxyribonucleic Acid (DNA) extraction. Polymerase Chain Reaction (PCR) followed by Restriction Fragment Length Polymorphism (RFLP) pattern of PCR fragments of DNA samples were determined. The study analysed and compared the genotyping and allele frequencies of rs2059806 polymorphism in control and case group. For comparison, chi-square test was performed (Odds ratio, p&lt;0.05). Results: Amongst the 123 PCOS cases and 111 normal female subjects of the study, mean age of PCOS patients were 22.59±4.7 years and that of control subjects was 21.9±5.1 years. The present study observed an increase in mutant G allele in PCOS subjects (Odds ratio-2.18, p=0.0035). Conclusion: The polymorphism of insulin receptor gene rs2059806 may have a probable role in the development of PCOS.

Molecular Characterization of Alternaria porri (Ellis) Cif., The Causal Agent of Purple Blotch Disease of Onion, With the Help of Simple Sequence Repeat Markers

Purple blotch disease of onion, caused by Alternaria porri (Ellis) Cif., causes extensive damage to the bulb and seed crops. The present study was aimed to assess the morpho-cultural variations and genetic diversity in 14 isolates of A. porri by simple sequence repeat (SSR) markers (selected on the basis of polymorphism pattern). Most isolates showed white fluffy colony growth and yellow to light orange pigmentation with circular, irregular and smooth margin along with clear-cut zonation. During the study period, 36 loci were obtained and the average expected gene diversity was found in the range of 0.0531-0.3707. Shan cluster analysis and unweighted pair-group method with arithmetic averages (UPGMA) analysis revealed that the isolates ‘A.p.B4’ and ‘A.p.B1' had maximum similarity coefficient (0.9166667), while isolates ‘A.p.B12’ and ‘A.p.B13’ had distant similarity coefficient (0.6111111). The SSR primers D.N.alt4 (200-720 bp) and D.N.alt10 (300-600 bp) represented unique bands for all isolates which were used for the identification of isolates. The polymorphic information content (PIC) value for primer D.N.alt-4 and D.N.alt-10 was 0.0, with maximum and minimum PIC value for D.N.alt14 (0.2978) and D.N.alt-5 (0.0495), respectively, thus represented the discriminatory power of a locus. The study revealed that the nine SSR markers tested were helpful in the isolation and molecular characterization of A. porri on the basis of polymorphism or genetic diversity.

Toll-Like Receptor Gene Polymorphisms in Indian Patients with Inflammatory Bowel Disease

Background: Defective innate immune recognition of gut microbes may be one reason for the genesis of inflammatory bowel disease (IBD). Genetic defects in IBD show considerable variation between populations. This study evaluated three single-nucleotide polymorphisms (SNP) in the toll-like receptor (TLR) genes in patients with IBD and healthy controls. Methods: DNA isolated from peripheral blood of 200 IBD patients (100 Crohn's disease and 100 ulcerative colitis) and 100 healthy controls were subjected to polymerase chain reaction and restriction enzyme digestion for three SNPs in TLR4 (D299G, rs4986790), TLR5 (392 stop codon, rs5744168) and TLR9 (-1486 T/C, rs187084) genes, and genotypes assigned according to the restriction fragment length polymorphism pattern. Results: Minor allele frequencies for the 3 polymorphisms were not significantly different between IBD patients and healthy controls. The TLR4 rs4986790 minor allele (G) frequency was 27/200 in controls compared to 48/400 in IBD (odds ratio [OR] 0.87, 95% confidence interval [CI] 0.52–1.44, P = 0.6007). The TLR5 rs5744168 minor allele (T) frequency was 19/200 in controls compared to 45/400 in IBD (OR 1.20, 95% CI 0.63–2.12, P = 0.5132). The TLR9 rs187084 minor allele (C) frequency was 71/200 in controls compared to 129/400 in IBD (OR 0.88, 95% CI 0.61–1.26, P = 0.4261). Conclusion: These three polymorphisms in the TLR genes were not associated with IBD in the Indian population.

Cytokine Levels and Polymorphisms in Childhood Asthma Among the Iranian Population

Context: Chronic airway inflammation in asthma is affected by a complex network of interacting cytokines. The exact role of each cytokine in childhood asthma development has remained poorly understood. In this study, we aimed to review articles investigating cytokine levels and polymorphisms in childhood asthma among the Iranian population to assess susceptible cytokines related to childhood asthma. Evidence Acquisition: We performed a literature search in PubMed, Scopus, Science direct, and Embase databases to find articles that have evaluated the cytokine levels and gene polymorphisms in childhood asthma among the Iranian population until March 2, 2020. The terms used to search included “cytokine”, “interleukin”, “polymorphism”, “Asthma”, and “Iran” in the international databases. Only case-control studies with a healthy control group that investigated cytokine levels and polymorphism in childhood asthma among the Iranian population have been included. Results: Considering these criteria, we extracted 7 articles from international databases and included them in the current review. We investigated 4 cytokine levels and 4 cytokine polymorphism patterns in asthmatic and non-asthmatic subjects in Iran. Interleukin (IL)-23, IL-17, and IL-33 levels were statistically higher in asthmatic children, and also IL-33, IL-17 levels were associated with asthma severity. There were no significant differences between healthy and asthmatic subjects regarding IL-35 levels. Polymorphisms in cytokine IL-4, IL-10, tumor necrosis factor (TNF)-α, and IL-2 were susceptible to childhood asthma in the Iranian population. Conclusions: Increased IL-33 and IL-17 levels were related to disease severity in childhood asthma. Four cytokine polymorphisms (IL-4, IL-10, IL-2, and TNF-α) were associated with the risk of pediatric asthma in the Iranian population.