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Background: Ventricular septal defects (VSDs) are one of the leading causes of death due to cardiac anomalies during the first months of life. The prevalence of VSD in neonates is reported up to 4%. Despite the remarkable progress in medication, treatment and surgical procedure for VSDs, the genetic etiology of VSDs is still in infancy because of the complex genetic and environmental interactions. Methods: Three hundred fifty subjects (200 VSD children and 150 healthy controls) were recruited from different pediatric cardiac units. Pediatric clinical and demographic data were collected. A total of six variants, rs1017 (ISL1), rs7240256 (NFATc1), rs36208048 (VEGF), variant of HEY2, rs11067075 (TBX5) and rs1801133 (MTHFR) genes were genotyped by tetra-ARMS PCR and PCR–RFLP methods. Results: The results showed that in cases, the rs1017 (g.16138A > T) variant in the ISL1 gene has an allele frequency of 0.42 and 0.58 respectively for the T and A alleles, and 0.75 and 0.25 respectively in the controls. The frequencies of the AA, TA and TT genotypes were, 52%, 11% and 37% in cases versus 21%, 8% and 71% respectively in the controls. For the NFATc1 variant rs7240256, minor allele frequency (MAF) was 0.43 in cases while 0.23 in controls. For the variant in the VEGF gene, genotype frequencies were 0% (A), 32% (CA) and 68% (CC) in cases and 0.0%, 33% and 67% respectively in controls. The allele frequency of C and A were 0.84 and 0.16 in cases and 0.83 and 0.17 respectively in controls. The TBX5 polymorphism rs11067075 (g.51682G > T) had an allelic frequency of 0.44 and 0.56 respectively for T and G alleles in cases, versus 0.26 and 0.74 in the controls. We did not detect the presence of the HEY2 gene variant (g.126117350A > C) in our pediatric cohort. For the rs1801133 (g.14783C > T) variant in the MTHFR gene, the genotype frequencies were 25% (CC), 62% (CT) and 13% (TT) in cases, versus 88%, 10% and 2% in controls. The ISL1, NFATc1, TBX5 and MTHFR variants were found to be in association with VSD in the Pakistani pediatric cohort whilst the VEGF and HEY2 variants were completely absent in our cohort. Conclusion: We propose that a wider programme of genetic screening of the Pakistani population for genetic markers in heart development genes would be helpful in reducing the risk of VSDs. [ABSTRACT FROM AUTHOR]

Background: Ventricular septal defects (VSDs) are malformations in the septum separating the heart's ventricles. VSDs may present as a single anomaly (isolated/nonsyndromic VSD) or as part of a group of phenotypes (syndromic VSD). The exact location of the defect is crucial in linking the defect to the underlying genetic cause. The number of children visiting cardiac surgery units is constantly increasing. However, there are no representative data available on the genetics of VSDs in Pakistani children. Methods: Two hundred forty-two subjects (121 VSD children and 121 healthy controls) were recruited from pediatric cardiac units of Lahore. The clinical and demographic data of the subjects were collected. A total of four SNPs, one each from MTRR, GATA4, VEGF, and ISL1 genes were genotyped by PCR-RFLP. Results: The results showed that the minor allele (T) frequency (MAFs) for the MTRR gene variant rs1532268 (c.524C > T) was 0.20 and 0.41 in the controls and the cases, respectively, with the genotype frequencies 3, 35, 62% in the controls and 12, 59 and 29% in the cases for TT, CT, CC genotypes, respectively (allelic OR: 5.73, CI: 3.82–8.61, p-value: 5.11 × 10− 7). For the GATA4 variant rs104894073 (c.886G > A), the MAF for the controls and the cases was 0.16 and 0.37, respectively, the frequencies of AA, GA and GG genotypes were 2, 28, and 70% in the controls and 5, 64 and 31% of the cases (allelic OR: 3.08, CI: 2.00–4.74, p-value: 8.36 × 10− 8). The rs699947 (c.-2578C > A) of VEGF gene showed MAF 0.36 and 0.53 for the controls and cases, respectively, with the genotype frequencies 13, 42, and 45% in the controls and 22, 15, and 63% in the cases for the AA, CA, CC (allelic OR: 2.03, CI: 1.41–2.92, p-value: 0.0001). The ISL1 gene variant rs6867206 (g.51356860 T > C), the MAFs were 0.26 and 0.31 in the controls and cases, respectively. The genotype frequencies were 48, 52, 0% in the controls and 39, 61, 0% in the cases for TT, TC, CC genotypes (allelic OR: 0.27, CI: 0.85–1.89, p-value: 0.227). The MTRR, GATA4 and VEGF variants showed association while ISL1 variant did not appear to be associated with the VSD in the recruited cohort. Conclusion: This first report in Pakistani children demonstrates that single nucleotide polymorphisms in genes encoding transcription factors, signaling molecules and structural heart genes involved in fetal heart development are associated with developmental heart defects., however further work is needed to validate the results of the current investigation. [ABSTRACT FROM AUTHOR]

Background: Type 1 Diabetes Mellitus (T1DM) is the autoimmune disorder of destruction of β cells of pancreas, creating insulin deficiency condition, which leads to hyperglycemia, polyuria, polydipsia, ketoacidosis, and other metabolic disorder especially in children. Different genetic aspects and environmental factors are involved in pathophysiology of the disease. About 20 genes are associated with this disease in which the most common is the different combination of haplotype DRB1‐DQA1‐DQB1 present at HLA gene. At HLA‐DQB1, there are some SNPs which are associated with T1DM. In T1DM, there are number of biochemical, serological parameters which show some abnormalities leading to some complications. Methods: Samples were subjected to all biochemical and serological techniques to get the measurement of concentration of glucose, lipid profile (cholesterol, triglycerides, and HDL and LDL cholesterol), urea, creatinine, albumin, insulin, anti‐insulin antibodies, C‐peptides, and leptin. All these values were compared with controls values and statistical analysis was also done on these values. At molecular level, two primers set which were allele specific at HLA‐DQB1, were used to amplify the SNPs, homozygous and heterozygous conditions were stated. Results: PCR results for the studied population showed that most of samples have heterozygous condition for these SNPs of this allele specific region on HLA‐DQB1. Very few of them have homozygous state for it. Even in the control sample have the same conditions. Conclusion: In Pakistan, there is dire need of studies about SNPs and haplotypes related to HLA‐DQB1 which show association with T1DM. [ABSTRACT FROM AUTHOR]

AIMS. B-cell acute lymphoblastic leukemia (B-ALL) is amongst the most prevalent cancers of children in Pakistan. Genetic variations in FLT3 are associated with auto-phosphorylation of kinase domain that leads to increased proliferation of blast cells. Paired box family of transcription factor (PAX5) plays a critical role in commitment and differentiation of B-cells. Variations in PAX5 are associated with the risk of B-ALL. We aimed to analyze the association of FLT3 and PAX5 polymorphisms with B cell leukemia in Pakistani cohort. METHODS. We collected 155 B-ALL subject and 155 control blood samples. For analysis, genotyping was done by tetra ARMS-PCR. SPSS was used to check the association of demographic factors of SNPs present in the population with the risk of B-ALL. RESULTS. Risk allele frequencyAat locus 13q12.2 (rs35958982, FLT3) was conspicuous and showed positive association (OR D 2.30, CI [1.20-4.50], P D0:005) but genotype frequency (OR D 3.67, CI [0.75-18.10], P D0:088) failed to show any association with the disease. At locus 9p13.2 (rs3780135, PAX5), the risk allele frequency was significantly higher in B-ALL subjects than ancestral allele frequency (OR D 2.17, CI [1.37-3.43], P D 0:000). Genotype frequency analysis of rs3780135 polymorphism exhibited the protective effect (ORD0.55, CI [0.72-1.83], P D0:029). At locus 13q12.2 (rs12430881, FLT3), the minor allele frequency G (OR D 1.15, CI [1.37-3.43], P D 0:043) and genotype frequency (OR D 2.52, P D0:006) reached significance as showed p<0:05. CONCLUSION. In the present study, a strong risk of B-cell acute lymphoblastic leukemia was associated with rs35958982 and rs12430881 polymorphisms. However, rs3780135 polymorphism showed the protective effect. Additionally, other demo-graphic factors like family history, smoking and consanguinity were also found to be important in risk assessment. We anticipate that the information from genetic variations in this study can aid in therapeutic approach in the future. [ABSTRACT FROM AUTHOR]

Compromised quality of life (QoL) has been reported in individuals suffering from β-thalassemia major (β-TM) in Pakistan. However, insufficient data of its associated psychosocial, physical and other disease-related determinants is available. In an observational analytical study, 200 subjects aged between 5-25 years, were examined using a transfusion-dependent QoL (TranQoL) questionnaire. Clinical records and other related data were also gathered from transfusion center databases. The TranQoL mean score was 48.33 ± 5.6, ranging from 53.86 ± 13.6 for family functioning and support domain to 39.70 ± 18.4 for school and career functioning domain. Age, income, education, pre transfusion hemoglobin (Hb), serum ferritin level, pain, death due to β-thal, monetary issues and pain were significantly associated with TranQoL scores. It was not only the clinical conditions but life alterations, social relationship and psychological events also loomed in improvement of treatment outcomes. Therefore, a tetra-cone of patient, school representatives, family and physicians are needed for better patient prospective. [ABSTRACT FROM AUTHOR]

Coronary artery disease (CAD) is one of the leading public health problems associated with mortality and morbidity in the world. It is a complex disorder influenced by both genetic and environmental factors. Atherosclerosis and elevated levels of plasma cholesterol contribute to increased risk for CAD. Other risk factors include age, hypertension, obesity, diabetes, smoking, and family history. Previous genetic studies have identified multiple polymorphisms in various genes to be associated with the risk of CAD in different populations. We aimed to examine the association of MRAS/rs9818870 and C12orf43/rs2258287 polymorphisms with the risk of CAD in a Pakistani sample. A total of 200 samples (100 cases and 100 controls) was analyzed by Allele-specific PCR. Genotypes were determined by agarose gel electrophoresis. In the current study, locus C12orf43/rs2258287 was found to be associated with the risk of CAD in the studied Pakistani cohort (OR 0.18; CI 0.08-0.37; p = 0.0001) while no association was observed for MRAS/rs9818870 (OR 1.34; CI 0.65-2.76; p = 0.42). In conclusion, the rs2258287 SNP may play an important role in the progression of CAD in the Pakistani subjects. However, future studies should be done on a larger sample size to fully establish its exact role in CAD. [ABSTRACT FROM AUTHOR]

The prevalence of obesity has increased worldwide and it has been designated as a global epidemic by WHO. In Pakistan, recent decades have seen an explosion of obesity, but the research in the field of obesity genetics is limited. We aimed to determine the allele/genotype frequencies of Ala54Thr polymorphism of the FABP 2 gene that affects fatty acid metabolism and look for its association on serum biochemical parameters in the Pakistani population. A total of 569 obese and 446 non obese controls were genotyped by PCR-RFLP method. Serum parameters were determined by commercially available kits. Results showed a higher allele frequency of Thr54 allele in cases (0.424) as well as controls (0.331) than Caucasians (0.271). The risk allele was significantly associated with obesity (p = 0.002) and there was a significant difference in allele and genotype frequencies among cases and controls (p = 0.002). The risk allele is significantly associated with serum total cholesterol and LDL-c but not triglycerides, HDL-c, leptin, systolic/diastolic blood pressure and insulin. The Ala54Thr polymorphism has a high prevalence in the Pakistani population and may play a considerable role in the development of obesity. The effect on obesity may be in part mediated through changing serum cholesterol levels. We then performed a systematic search for any previous reports on the association of the variant with obesity. We identified 5 studies for Ala54Thr association with obesity in Asian subjects. The meta-analysis revealed a significant association of the variant with obesity (Thr allele: OR = 1.15, CI = 1.02–1.30 and p -value = 0.02). [ABSTRACT FROM AUTHOR]

Objective: Leptin receptor gene (LEPR) encodes a receptor for leptin hormone expressed in hypothalamus and single nucleotide polymorphisms in LEPR may have a considerable effect on obesity phenotype. The aim of this study was to investigate an extensively studied LEPR polymorphism Gln223 Arg in a Pakistani study group and its association patterns with different serum biochemical parameters. Methods: The study included 250 obese and 225 nonobese subjects. Gln223 Arg polymorphism was genotyped by polymerase chain reaction restriction fragment-length polymorphism. Anthropometric parameters and plasma glucose, total cholesterol, triacylglycerols, high density lipoprotein cholesterol, low density lipoprotein cholesterol, leptin, and insulin were measured. Results: The Gln223 Arg polymorphism was found to be significantly associated with body mass index, systolic and diastolic blood pressure, and weight only in obese subjects, and with all lipid parameters in both obese and nonobese subjects when Gln/Gln or Gln/Arg genotypes were compared with Arg/Arg genotype. Conclusions: The LEPR Gln223 is associated with obesity, lipid parameters, and plasma glucose in all subjects, with weight, body mass index, and systolic and diastolic blood pressure only in obese subjects, but showed no association with leptin, insulin, and HOMA-IR in a Pakistani study group. [ABSTRACT FROM AUTHOR]

Occupational noise enhances the risk of several cardiovascular and non-cardiovascular diseases. The reason behind the drastic effects of noise exposure is the excessive generation of reactive oxygen species molecules. The present study investigates oxidative stress due to occupational noise exposure in 192 male smoking workers exposed to normal noise (sound level ≤80 dBA), low noise (sound level 81-94 dBA), and loud noise (sound level ≥95 dBA). University-aged volunteers were selected for the normal sound exposed group. Drivers and conductors were selected for the low-noise exposed group, and workers of power loom factories were chosen for the high-noise exposed group. Oxidative stress was estimated using 8 OHdG as a biomarker for oxidative DNA damage. Serum aldosterone and serum cortisol level was estimated using the enzyme immunoassay method. Results indicated that 8 OHdG level was significantly different in different exposure groups. It was highest in the low-noise exposed group (0.370±0.017 ng/ml) and lowest in the normal-sound exposed group (0.22±0.01 ng/ml). Level of 8 OHdG in the high-noise exposed group was 0.29±0.00. There was no significant variation of aldosterone levels among different groups. Cortisol levels of both noise groups was higher than that of the normal sound group. It can be concluded that noise exposure induces stress in the Pakistani population. This stress leads to oxidative DNA damage. [ABSTRACT FROM AUTHOR]

Absence of resistance/tolerance against bacterial leaf blight (BLB), incited by Xanthomonas oryzae pv. oryzae, in famous basmati varieties is one of the main reason for BLB epidemic in Punjab in 2007–2008. For developing resistance against BLB, the response of 26 IRBB lines of IRRI including 10 near isogenic lines (NILs) and 16 gene pyramids carrying two to five resistance genes (Xa series) was evaluated against 61 indigenous Xoo isolates under artificial inoculation field conditions. None of the NILs or gene pyramid provides complete protection against all the isolates. However, Xa21 and xa13 were found resistant against the majority of Xoo isolates, followed by Xa14 and Xa7. Of the 16 gene pyramids used in this study, IRBB-54 (Xa5 + Xa21), IRBB-55 (Xa13 + Xa21) followed by IRBB-58 (Xa4 + Xa13 + Xa21) were found effective against the majority of the Xoo isolates. These resistance genes (individually and in combinations) can be incorporated for the improvement of basmati rice cultivars cultivated in Punjab province of Pakistan. Effectiveness of gene combination supports the strategy of pyramiding appropriate resistance genes. Newly identified resistant genes may also be evaluated for achieving broad spectrum resistance against more Xoo isolates of the area. [ABSTRACT FROM PUBLISHER]

Chromium-resistant bacteria isolated from industrial wastes can be used to detoxify toxic chromium from contaminated sources. From effluent of Shafiq Tannery, Kasur, Pakistan, bacterial strain STCr-1 that could endure 40 mg mL of potassium chromate in nutrient agar medium was isolated. STCr-1, identified as Ochrobactrum anthropi by 16S rRNA gene sequence homology, demonstrated substantial Cr(VI) reduction at pH 7 and temperature 37°C. It completely reduced 250 μg mL of Cr(VI) and showed 71.2 % Cr(VI) reduction at Cr(VI) concentrations of 550 μg mL. Rate of Cr(VI) reduction increased with increase in cell and Cr(VI) concentration. The presence of Cu, Co and Mn significantly stimulated Cr(VI) reduction. Assay with cell free extracts clearly indicated that Cr(VI) reduction was solely associated with the soluble fraction of the cell. [ABSTRACT FROM AUTHOR]

Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. [ABSTRACT FROM AUTHOR]

Non-invasive sampling has been used by the researchers to estimate the population density of several different carnivore species. This study was conducted to determine whether, noninvasive genetic analysis could be used to estimate the wild population of snowleopard in Soqterabad nullah. Of overall 20 randomly selected, best samples, only 8 could be amplified using species-specific DNA-markers. PCR success rate was 40%. Three different banding-patterns were obtained, which indicate their origin from three different individuals. The study showed that at least one individual was present in the surveyed area, and preliminary findings indicate that there may be three in Soqterabad, within an area of 20km. [ABSTRACT FROM AUTHOR]

Background: Congenital leptin deficiency is a rare human genetic condition clinically characterized by hyperphagia and acute weight gain usually during the first postnatal year. The worldwide data on this disorder includes only 14 cases and four pathogenic mutations have been reported in the leptin gene. Study objective: The objectives of this study were to measure serum leptin levels in obese children and to detect leptin gene mutations in those found to be leptin deficient. Patients and results: A total of 25 obese children were recruited for the study. Leptin deficiency was detected in nine of them. Leptin gene sequencing identified mutations in homozygous state in all the leptin deficient children. Two cases carried novel mutations (c.481_482delCT and c.104_106delTCA) and each of the remaining seven the previously reported frameshift mutation (c.398delG). Conclusion: The results suggest that leptin deficiency caused by mutations in the leptin gene may frequently be seen in obese Pakistani children from Central Punjab. [ABSTRACT FROM AUTHOR]

Purpose: To investigate the role of ACE ID and ACE G2350A polymorphism in increasing the blood pressure of persons exposed to different sound levels. Method: Persons exposed to normal sound level (≤80 dBA) and noise (>80 dBA) were divided in two categories on the basis of blood pressure. Category A was comprised of the individuals with blood pressure ranges equal or less than that for normotensive persons. Category B was composed of the workers with blood pressure above than that for category A. ACE ID and ACE G2350A polymorphism was detected for analysis of its association with the increased blood pressure considering noise as modifier. Results: Least homozygous allele model for ACE ID polymorphism indicates no association of DD allele with the increased blood pressure in persons exposed to normal sound (Odds ratio: 0.831; 95% Confidence interval: 0.340-2.030). Similar findings were noted in persons exposed to noise (Odds ratio: 0.992; 95% Confidence interval: 0.536-1.835). Combining all the samples did not change the results (Odds ratio: 0.948; 95% Confidence interval: 0.580-1.549). For ACE G2350A polymorphism, least common homozygote model revealed that AA allele did not affect the chances of increased blood pressure in normal sound exposed group (Odds ratio: 0.827; 95% Confidence interval: 0.169-4.042) and noise exposed group (Odds ratio: 1.416; 95% Confidence interval: 0.682-2.941). There was no prominent variation in the results on combining all the samples (Odds ratio: 1.529; 95% Confidence interval: 0.807-2.872). Conclusions: No association was observed between ACE ID/ACE G2350A polymorphism and the increased blood pressure in persons exposed to normal sound and noise in Pakistani population. [ABSTRACT FROM AUTHOR]

In the developing world, the vast majority of people rely on solid biomass fuels for cooking and heating which results in poor indoor air quality. The present study determined indoor air quality in some rural and urban areas of Pakistan. Measurements were made of particulate mass (PM10, PM2.5 and PM1), number concentration and bioaerosols in different micro environments. PM10 concentrations of up to 8,555 μg/m3 were observed inside the kitchens where biofuels were used as energy source. Cleaning and smoking was identified as a major source of indoor particulate pollution and concentrations of more than more than 2,000 μg/m3 were recorded in the living room during these activities. Indoor number concentrations in Lahore were typically greater than those observed outdoors in European cites. At a rural site the highest Colony Forming Units (CFUs) were in the 0.5 μm–2 μm size fraction, while at the urban location CFUs were dominant for 2 μm–16 μm. It was observed that CFUs(Colony Forming Units) counts were higher inside living rooms than kitchens. It is important to note that women and children were exposed to extremely high levels of particulates during cooking. Overall, indoor air quality in Pakistan was poor and there is a dire need to take a serious step to combat with it. [ABSTRACT FROM AUTHOR]

Summary Obesity has become a great health issue and socioeconomic burden globally in the past few decades and has afflicted Pakistan in the same way. However, there is limited research on obesity genetics in Pakistan. Proopiomelanocortin (POMC) neurons bear leptin receptor and act as anorectic targets of leptin in the brain. Leptin binding induces a series of processing events producing melanocortins which then bind to their respective signals. R236G is a mutation which disrupts such a normal processing event resulting in an overall weight gain and early onset obesity. A total of 475 subjects were genotyped to search for this mutation, and their serum traits were measured. We detected one obese subject heterozygous for R236G (0.4%) and no control subject with the mutation. We then systematically searched for previous reports of R236 substitution and combined the results of our study with the previous frequencies and found that the mutation has an overall prevalence of 0.704% in obese cases and 0.18% in non-obese controls. In conclusion, such mutations involving a prohormone processing site are very rare in nature and may not contribute a significant proportion of common forms of obesity observed currently. Such mutations may exert their effect by affecting other pathways and are more prominent in the early stages of life only. [ABSTRACT FROM AUTHOR]

Background: Cardiac morphogenesis is a dynamic and complex process that involves a complex interaction of many genetic and environmental factors. Ventricular septal defects (VSDs) are the commonest congenital heart defects (CHDs), accounting for ~ 40% of all cardiac malformations. In Pakistan, the prevalence of VSD is increasing (4–6 in 1000 live births). In the current study, we aimed to determine the pattern of different hematological parameters and various risk factors in VSDs in local pediatric patients. We recruited the clinically diagnosed VSD children (n = 125) from various hospitals. The diagnosis was made based on echocardiography, size, number, and exact location of the defect. Hematological parameters, chemical pathological assays, and liver function analysis were performed. The blood group distribution and various risk factors were also assessed. The statistical analysis was done using the SPSS (IBM statistics version 22) software. Results: The results showed that for RBCs, 20% of patients in category of 0 to 3 months are above normal range; for WBCs, 33.3% of patients are above normal range in category of 4–5 years and 12–14 years. For hemoglobin, highest percentage of patients was observed below normal range; 30% of patients in category of 0 to 3 months, 40% of patients in category 4–9 months, 35.2% of patients in category of 10 months–3 years, and 33.3% of patients in category of 12–14 years were below normal range. For platelet count, 5.66% patients were below normal range and 16.9% were above normal range. For prothrombin time (PT) and activated partial thromboplastin time (APTT) more than 90% patients were in normal range value. Elevated ALP level and significantly lower albumin levels were observed. In age range of 13–14 years, 50% patients were below range for both calcium and serum creatinine. The prevalence of cousin marriages was 62.3%, about 60% mothers used antibiotics during pregnancy, B + ve and O + ve had the highest frequencies, and most of the patients were seen in age group of 2–35 months. Conclusion: All tested parameters show divergence from normal values their predictive capabilities of VSDs. To the best of our knowledge, the present study is the first to report data on hematological parameters and demographic risk factor associated with VSDs, in the Pakistani children. This data may have implication on the characterization and diagnosis of VSDs as well as on the assessment of related risk factors. [ABSTRACT FROM AUTHOR]

• First study from Pakistan to signify importance of DISC locus in association with schizophrenia. • Minor allele of rs1417584 is found associated with onset of disease. • 325 Kb region on DISC locus is found to be important prognostic marker for diagnosis of schizophrenia. Schizophrenia is a stressful, chronic and in many cases incorrigible psychological disorder. Till now no biomarker is available for diagnosis of this condition and diagnosis is done purely on psychiatric bases. A strong genetic association of human genome region 1q24.1 is implicated with onset of schizophrenia in many studies. Present study is first from Pakistan to report effect of this locus in transmission and liaison of schizophrenia in Pakistani population. For this analysis 300 samples were genotyped of four SNPs, rs1417584, rs1954175, rs821616 and rs113012343 that were selected on basis of minor allele frequency and effects on schizophrenia. Haplotype and transmission disequilibrium analysis was also performed on data. Association of SNPs revealed a significant relation between MAF of rs1417584 and schizophrenia in given samples (χ2 5.57; p 0.02). Haplotype association led to formation of three significant blocks TCAG (OR 20.06), TTAG (OR 4.65) and CCTG (OR 26.17) for rs1417584, rs1954175, rs821616 and rs113012343 that were expected to cause schizophrenia in said combinations. rs1417584, rs1954175 and rs821616 were found to be in a linkage block based on D' value (p < 0.0001) with 22% co inheritance alongside disease onset. This block was represented by 325 kb on chromosome 1. It is concluded from this study that this 325 Kb region can be considered prognostic marker for schizophrenia development in Pakistani population. [ABSTRACT FROM AUTHOR]

Background: With prevalence up to 4%, Ventricular Septal Defect (VSD) is one of the leading causes of neonatal deaths. VSD is a common complex genetic disorder that has been associated with many genetic determinants. Variants from genes for the transcription factors including T-Box TBX5 and NFATc1 (nuclear factor of activated T cells, cytoplasmic 1), Vascular endothelial growth factor (VEGF), ISLET1 (encoded by the ISL1 gene) and enzyme MTHFR, a methylene tetrahydrofolate reductase were selected. Genetic risk score (GRS) is a widely accepted approach used to convert the genetic data into prediction and assessment tool for disease susceptibility., Methods: A total of 200 participants were recruited for the current study, 100 VSD patients and 100 controls. Genotyping of the ISL1: rs1017, NFATc1: rs7240256, VEGF: rs36208048, TBX5: rs11067075, and MTHFR: rs1801133 variants was performed using tetra primer ARMS PCR and PCR-RFLP. For the statistical analysis, the software SPSS version 23 was used. Genotypic frequencies of cases and controls were calculated using chi-square (χ²) whereas allelic frequencies were calculated by using the SNPStats tool. The association of GRS quartiles with VSD was examined using binary logistic regression. Adjusted p-value 0.01 was used as significance threshold for all analyses., Results: The ISL1 (OD: 0.242, CI: 0.158-0.37, p-value: 2.15 × 10 - 4 :), NFATc1 (OD: 2.53, CI: 1.64-3.89, p-value: 2.11 × 10 - 5 ), TBX5 (OD: 2.24, CI: 1.47-3.41, p-value:1.6 × 10 - 4 ) and MTHFR (OD: 10.46, CI: 5.68-19.26, p-value: 2.09 × 10 - 9 :) variants were found to be in association with VSD. In contrast, the VEGF (OD: 0.952, CI: 0.56-1.62, p-value: 0.8921) variant did not show significance association with the VSD. For cases, the mean GRS score was 3.78 ± 1.285 while in controls it was 2.95 ± 1.290 (p-value: 0.479, CI: 0.474-1.190). Comparison of GRS between cases and control showed that mean GRS of cases was 1.90 ± 0.480 while in controls it was 1.68 ± 0.490 (p-value: 0.001, CI: 0.086-0.354). Higher quartiles were more prevalent in cases whereas lower quartiles were more prevalent in controls., Conclusion: GRS of these five loci was strongly associated with VSD. Moreover, genetic risk score can provide better information for the association between variants and disease as compared to a single SNP. We also illustrated that the cumulative power of GRS is greater over the single SNP effect. This is a pilot scale study with a relatively small sample size whose findings should be replicated in a larger sample size for the unique local Pakistani population., (© 2023. The Author(s).)

Dengue has become endemic in Pakistan with annual recurrence. A sudden increase in the dengue cases was reported from Rawalpindi in 2016, while an outbreak occurred for the first time in Peshawar in 2017. Therefore, a multi-center study was carried out to determine the circulating dengue virus (DENV) serotypes and Chikungunya virus (CHIKV) co-infection in Lahore, Rawalpindi, and Peshawar cities in 2016-18. A hospital-based cross-sectional study was carried out in Lahore and Rawalpindi in 2016-18, while a community-based study was carried out in Peshawar in 2017. The study participants were tested for dengue NS1 antigen using an immunochromatographic device while anti-dengue IgM/IgG antibodies were detected by indirect ELISA. All NS1 positive samples were used for DENV serotyping using multiplex real-time PCR assay. Additionally, dengue samples were tested for CHIKV co-infection using IgM/IgG ELISA. A total of 6291 samples were collected among which 8.11% were NS1 positive while 2.5% were PCR positive. DENV-2 was the most common serotype (75.5%) detected, followed by DENV-1 in 16.1%, DENV-3 in 3.9% and DENV-4 in 0.7% while DENV-1 and DENV-4 concurrent infections were detected in 3.9% samples. DENV-1 was the predominant serotype (62.5%) detected from Lahore and Rawalpindi, while DENV-2 was the only serotype detected from Peshawar. Comorbidities resulted in a significant increase (p-value<0.001) in the duration of hospital stay of the patients. Type 2 diabetes mellitus substantially (p-value = 0.004) contributed to the severity of the disease. Among a total of 590 dengue positive samples, 11.8% were also positive for CHIKV co-infection. Co-circulation of multiple DENV serotypes and CHIKV infection in Pakistan is a worrisome situation demanding the urgent attention of the public health experts to strengthen vector surveillance., Competing Interests: The authors have declared that no competing interests exist.

Background: Human behavioral traits are known to be significantly heritable. Certain individuals have a greater tendency of negative behavioral aspects including aggression. The quest to identify tunderlying genetic causes has led to identification of a number of genetic markers, one of them is the monoamine oxidase-A (MAO-A) gene., Objective: We aimed to genotype a variable number of tandem repeats (VNTRs) in the promoter region and a functional SNP within this gene (T941G, dbSNP ID: rs6323) in the recruited cohort of 482 subjects., Methods: After DNA isolation, genotyping was done by PCR-RFLP and the results were confirmed by sequencing., Results: For VNTRs, the results showed, highest frequency of 3.5 repeats in males and 4 repeats in females in the promoter region. The genotype frequencies for the SNP in cases were GG=16.3%, TG=20.6% and TT=63.1%, while in controls, the frequencies were GG=12.7%, TG=6.3%, and TT=81.0%. The allele frequencies were significantly different between cases and controls (p=0.015; OR=1.51; CI=1.085-2.102)., Conclusion: The selected VNTR and SNP appeared to be significantly associated with aggression. These VNTRs and SNP have not been studied previously in the Pakistani population, hence they represent a unique ethnic group. These results, however, would have to be replicated in larger cohorts., (© 2021 Sarwar S et al.)

The serotonin transporter (SLC6A4), 5-HT 2A (HTR2A) and 5-HT 2B (HTR2B) recepter genes, express proteins that are important regulators of serotonin reuptake and signaling, and thereby may contribute to the pathogenesis of aggressive criminal behavior. 370 sentenced murderers in Pakistani prisons and 359 men without any history of violence or criminal delinquency were genotyped for six candidate polymorphisms in SLC6A4, HTR2A and HTR2B genes. An association of higher expressing L/L and L A /L A variants of the 5-HTTLPR polymorphism was observed with homicidal behavior (bi-allelic: OR = 1.29, p = 0.016, tri-allelic: OR = 1.32, p = 0.015) and in the murderer group only with response to verbal abuse (OR = 2.11, p = 0.015), but not with other measures of self-reported aggression. L/L and L A /L A genotypes of the 5-HTTLPR polymorphism were associated with higher aggression scores on STAX1 scale of aggression compared to lower expressing genotypes (S/S, S/L G , L G /L G ) in prison inmates. No associations were apparent for other serotonergic gene polymorphisms analyzed. Using the Braineac and GTEx databases, we demonstrated significant eQTL based functional effects for rs25531 in HTTLPR and other serotonergic polymorphisms analyzed in different brain regions and peripheral tissues. In conclusion, these findings implicate SLC6A4* HTTLPR as a major genetic determinant associated with criminal aggression. Future studies are needed to replicate this finding and establish the biologic intermediate phenotypes mediating this relationship.

We aimed to identify the genetic causes of common forms of obesity in the Pakistani people and find out the mechanistic link by observing the relationship of genes and serum lipid traits. Four hundred and seventy-five subjects were genotyped for two mutations in (leptin:N103K and proopiomelanocortin:R236G) and ten common variants in different genes. Serum lipids were also measured. The prevalence of mutations was very low (one heterozygous subject each for both mutations), but fairly high minor/risk allele frequency (M/RAF) was observed for all SNPs. MAF of G2548A was 42.8% in obese and 30.1% in controls ( P =5.7 × 10 -5 ), it showed association with weight, body mass index (BMI), waist circumference (WC), high density lipoprotein cholesterol (HDL-c) and leptin, Gln223Arg had MAF 32% in obese and 18.7% in controls ( P =5.4 × 10 -6 ), it showed association with fasting plasma glucose (FPG) and all lipid traits, Ala54Thr had MAF 42.4% in obese and 33.1% ( P =0.002), it showed association with none of the tested parameters. rs9939609 MAF was 26.6%, and showed association with none of the tested parameters. rs1802295 ( P =0.002); rs7178572 ( P =0.007); rs2028299 ( P =0.04); rs4812829 ( P =0.02) showed significant while rs3923113 and rs16861329 did not show a significant association ( P =0.20 and P =0.3, respectively) with obesity. Major genetic contribution to common forms of obesity in Pakistan is from low/modest effect size common variants that act additively to affect body weight quantitatively and mechanism may involve modulating serum lipids., (© 2018 The Author(s).)

Background/objective: Obesity has become a global epidemic due to an increase in the number of obese individuals worldwide. There is little research in the field of obesity genetics in Pakistan. The aim of the current study was to analyze the association of common variants in Fat Mass and Obesity associated (FTO) gene with obesity in Pakistan, to find out the effect of the selected SNPs on anthropometric and biochemical traits, and to observe whether these variants act synergistically., Methods: Samples from 631 subjects were taken after informed consent and were used for serum parameters and genetic analysis. Lipid profile was determined, tetra-ARMS PCR was used for genotyping, and allele/genotype frequencies and genescore were calculated., Results: All FTO variants were associated with obesity, and some biochemical and anthropometric measures and had higher minor allele frequencies than those reported for Asian populations previously. The risk allele of each single nucleotide polymorphism resulted in an increase in BMI in a quantitative manner., Conclusion: Common forms of obesity are due to a combined net effect of many variants presented in same or different genes. The more the number of risk alleles present, the higher the risk and severity of obesity resulting from an increase in BMI.

This cross-sectional study was carried out to explore the epidemiological and clinical features of dengue fever in Faisalabad, Pakistan during 2011 and 2012. During the study period, anti-dengue IgM positive cases were reported in the post-monsoon period during the months of August-December. Certain hotspots for the dengue infection were identified in the city that coincide with the clusters of densely populated urban regions of the city. Out of total 299 IgM positive patients (male 218 and female 81); there were 239 dengue fever (DF) and 60 dengue hemorrhagic fever (DHF) patients. There was decrease in the median age of dengue patients from 31 years in 2011 to 21.5 years in 2012 (p<0.001). Abdominal pain was seen in 35% DHF patients followed by nausea in 28.3%, epistaxis in 25% and rash in 20% patients (p<0.05). Patients reported to be suffering from high-grade fever for an average of 8.83 days in DHF as compared to 5.82 days in DF before being hospitalized. Co-morbidities were found to be risk factor for the development of DHF in dengue patients. Clinical and laboratory features of dengue cases studied could be used for the early identification of patients at risk of severe dengue fever.

Pakistan is blessed with plants of Asteraceae family with known medicinal background used for centuries by Hakims (traditional physicians). Keeping in mind the background of their anti-larval potential, a total of 21 endophytic actinomycetes were isolated from four Asteraceae plants and screened against the first and fourth instar stages of Culex quinquefasciatus Say mosquito larvae. Of the 21 isolates, 6 of them gave strong larvicidal activity (80-100% mortality) in the screening results and 4 isolates gave a potent larvicidal activity (100% mortality) at the fourth instar stage. These isolates belonged to different species within the actinomycetes group, namely Streptomyces albovinaceus and Streptomyces badius. This communication reports the larvicidal potential of endophytic actinomycetes residing within the native Asteraceae plants in Pakistan. The study suggests further exploration through large-scale productions leading to the identification of the larvicidal compounds.

Introduction: This study investigates the effect of angiotensin converting enzyme (ACE) polymorphisms on the association between noise and hypertension., Subjects and Methods: A cross sectional study was conducted involving 385 male volunteers. In the control group 156 participants were exposed to a sound level of ≤ 80 dB; in the exposed group 229 individuals were exposed to a sound level ≥ 80 dB. Both groups were subdivided into categories on the basis of blood pressure. A polymerase chain reaction (PCR)-based strategy was used to differentiate the various genotypes of ACE ID and ACE G2350A. Association of noise with genotypes as modifiers was estimated after adjustment of data for age and body mass index., Results: These showed the following odds ratios (OR) with 95% confidence interval (CI) indicating that noise is associated with hypertension in a Pakistani population (OR: 3.196; CI: 1.803-5.666). ACE ID and ACE G2350A polymorphism affects this association. ID (OR: 2.844: CI: 1.32-6.110) and DD allele carriers (OR: 4.487; CI: 1.549-12.99) were at increased risk of hypertension. GG (OR: 3.970; CI: 1.628-9.681) and GA (OR: 3.705; CI: 1.407-9.758) carriers were also at increased risk of hypertension associated with noise. However II and AA allele carriers were not found to be at increased risk of hypertension., Conclusion: ACE ID polymorphism and ACE G2350A polymorphism modulates the effects of noise on blood pressure.

Selenium concentrations in the blood of 112 (56 females and 56 males) normal subjects, from different regions of the Punjab (Pakistan), have been determined using the technique of inductively coupled plasma-mass spectrometry. The whole blood selenium concentrations were found to be 452 ± 12 ppb (parts per billion or nano-gram of Se per gram freeze-dried blood or 96 ± 3 μg/L ), with 470 ± 16 ppb (or 100 ± 4 μg/L) in female and 435 ± 16 ppb (or 92 ± 4 μg/L) in male population. Compared with other populations of the world [corrected] these levels are similar with the exception of the low-selenium-region of China. [corrected].

The first genetic factors to be identified as important in the pathogenesis of Systemic lupus erythematosus (SLE) were those of the major histocompatibility complex (MHC) on chromosome 6. It is now widely accepted that MHC genes constitute a part of the genetic susceptibility to SLE. The study population comprised 61 SLE patients fulfilling at least four of the American college of Rheumatology criteria for SLE and 61 healthy blood donors as controls. SLE female versus male ratio was approximately 9:1. Mean age at diagnosis was 30.35 ± 1.687 (12-68 years). DNA-based HLA Typing for HLA-A, HLA-B, and HLA-DRB1 was carried out by Polymerase chain reaction with sequence specific primers using genomic DNA obtained from blood samples. A total of 22 alleles have been studied at locus A, 37 alleles at locus B and 17 DRB1 alleles. The allelic frequencies of HLA-A, HLA-B, and HLA-DRB1 antigens in SLE patients from Pakistan were compared with the controls. A significant increase was observed in the frequency of HLA-A*01, A*03, A*11, A*23, A*26 A*69, HLA-B*27, B*40, B*49, B*51, B*52, B*53, B*54, B*95, HLA-DRBI*01, DRBI*03, DRBI*11, DRBI*14 among SLE patients indicating a positive association of these alleles with SLE. HLA-A*24, A*29, A*31, A*34, A*68, A*92, HLA-B*18, HLA-DRB1*12, were found to be decreased in the patient group as compared to controls indicating a negative association of these alleles with SLE. Thus from this study we can conclude that SLE is associated with certain MHC alleles in Pakistani population.

The present study is aimed at assessing the ability of metal-resistant yeast, Candida tropicalis CBL-1, to uptake metal from liquid medium. The minimum inhibitory concentration of Cd(II) against Candida tropicalis CBL-1 was 2,800 mg/L. The yeast could also tolerate Zn(II) (3,100 mg/L), Hg(II) (2,400 mg/L), Ni(II) (2,200 mg/L), Cr(VI) (2,000 mg/L), Pb(II) (1,100 mg/L), and Cu(II) (2,200 mg/L). The yeast isolate showed typical growth curves but lag and log phases extended in the presence of cadmium. The yeast isolate showed optimum growth at 30ºC and pH 7. The metal processing ability of the isolate was determined in a medium containing 100 mg/L of Cd(II). Candida tropicalis CBL-1, could reduce Cd(II) 59%, 64% and 70% from the medium after 48, 96 and 144 h, respectively. C. tropicalis CBL-1 was also able to remove Cd(II) 46% and 60% from the wastewater after 6 and 12 days, respectively. Cd produced an increase in glutathione and non-protein thiols level by 37% (17.50±0.8-24.0±1.2) and 18% (3.30±0.7- 3.90±0.8) at 100 mg/L concentration, respectively. Metal tolerance and accumulation together with changes in the GSH status and non-protein thiols under Cd exposure were studied in C. tropicalis.

The present study investigates the relationship of different sound levels with hypertension and prehypertension in Pakistani population. A cross sectional study was conducted to determine the prevalence of hypertension and prehypertension due to exposure of sound level ≤80 dBA (A weighted sound pressure level), 81-94 dBA and ≥95 dBA in November 11, 2005 to January 30, 2007. Sites were selected with stable sound ranges according to the above mentioned criteria. After selecting sampling sites, workers living in that area for at least 8 hours per day were categorized on the basis of blood pressure in groups called as normotensive, prehypertensive and hypertensive. Persons with diabetes, chronic bacterial or viral infections, alcohol addiction, kidney problems were excluded from the study. For getting homogenous groups, age range of 30-50 years was selected. Out of 566 samples, 90 excluded samples were consisted of 8% diabetic patients, 5% hepatitis C patients, 3% hepatitis B patients and 0% AIDS patients. Out of 476 participants, 389 samples were found with age 40±10 years. High noise increased the risks of hypertension (Odds ratio: 4.41; Confidence interval: 2,123-9,196) and prehypertension (Odds ratio: 3,809; Confidence Interval: 1,804-8,042) as compared to the normal sound level. However increased chances of hypertension (Odds ratio: 2,271; Confidence interval: 1,043-4,946) and prehypertension (Odds ratio: 3,028; Confidence Interval: 1,440-6,367) were observed on median noise exposure also. These findings suggest that sound level more than 81 dBA increases the chances for development of hypertension and prehypertension in Pakistani population.

Several studies in different populations have shown mixed association of hypertension with ACE I/D and G2350A polymorphisms. To assess the link of these two polymorphisms with hypertension in population of Punjab--most populated province of Pakistan--we carried out this retrospective case control study in a mixed sample of 344 hypertensive and normotensive controls. Genotype of the ACE I/D was determined by nested PCR and G2350A. polymorphism was determined by amplification of a small fragment containing SNP and digesting it with the restriction enzyme. Statistical analysis revealed that I/D polymorphism is not associated with hypertension in the Punjabi population chi(2) (df = 2) = 5.611, P

Background: The renin-angiotensin-aldosterone system (RAAS) plays a key role in blood pressure (BP) regulation. Among the components of the RAAS, the gene for the angiotensinogen (AGT) has been extensively studied. Several studies in different populations link Threonine instead of methionine at position 235 (M235T) and Methinine instead of threonine at position 174 (T174M) polymorphisms with essential hypertension. We were unable to study these polymorphisms in the Punjab population of Pakistan through routine Restriction Fragment Length Polymorphism (RFLP) method. Considering the importance of this region we decided to further investigate the 300 bp region harbouring these two single nucleotide polymorphisms., Methods: Samples were derived from a larger study group. Polymerase chain reaction amplified fragments were subjected to either RFLP or Single Strand Conformation Polymorphism. Single stranded DNA showing mobility shift on denaturing gel were sequenced., Results: Sequencing confirmed the presence of M235T and T174M polymorphisms in the local population. In addition to these polymorphisms one additional base was found at an identical position in two of the samples. We found a substitution of G with C just adjacent to T174M polymorphism in all seven of our samples studied., Conclusions: We report two additional bases and one substitution in the angiotensinogen gene of Punjab population. We also suggest that SsmI can be used for the investigation of T174M polymorphism.