Loss of function mutations in RP1 are responsible for retinitis pigmentosa in consanguineous familial cases.

PurposeThis study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families.MethodsLarge consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon-intron boundaries of RP1 were sequenced to identify the causal mutation.ResultsThe ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G>A (p.I263Nfs8*), a 2 bp duplication in exon 2: c.551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples.ConclusionsThese results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families

Pathogenic mutations in TULP1 responsible for retinitis pigmentosa identified in consanguineous familial cases.

PurposeTo identify pathogenic mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous familial cases.MethodsSeven large familial cases with multiple individuals diagnosed with retinitis pigmentosa were included in the study. Affected individuals in these families underwent ophthalmic examinations to document the symptoms and confirm the initial diagnosis. Blood samples were collected from all participating members, and genomic DNA was extracted. An exclusion analysis with microsatellite markers spanning the TULP1 locus on chromosome 6p was performed, and two-point logarithm of odds (LOD) scores were calculated. All coding exons along with the exon-intron boundaries of TULP1 were sequenced bidirectionally. We constructed a single nucleotide polymorphism (SNP) haplotype for the four familial cases harboring the K489R allele and estimated the likelihood of a founder effect.ResultsThe ophthalmic examinations of the affected individuals in these familial cases were suggestive of RP. Exclusion analyses confirmed linkage to chromosome 6p harboring TULP1 with positive two-point LOD scores. Subsequent Sanger sequencing identified the single base pair substitution in exon14, c.1466A>G (p.K489R), in four families. Additionally, we identified a two-base deletion in exon 4, c.286_287delGA (p.E96Gfs77*); a homozygous splice site variant in intron 14, c.1495+4A>C; and a novel missense variation in exon 15, c.1561C>T (p.P521S). All mutations segregated with the disease phenotype in the respective families and were absent in ethnically matched control chromosomes. Haplotype analysis suggested (p<10(-6)) that affected individuals inherited the causal mutation from a common ancestor.ConclusionsPathogenic mutations in TULP1 are responsible for the RP phenotype in seven familial cases with a common ancestral mutation responsible for the disease phenotype in four of the seven families

Concurrent dengue and malaria infection in Lahore, Pakistan during the 2012 dengue outbreak

SummaryIntroductionWe conducted this study to determine the frequency of malaria and dengue–malaria co-infection in patients admitted to our hospital as ‘probable’ cases of dengue fever during the 2012 outbreak of dengue, and to ascertain whether dengue–malaria co-infection was more severe than either infection alone.MethodsThis cross-sectional observational study was conducted at Jinnah Hospital Lahore, Pakistan between August and November 2012. Patients with 2–10 days of fever and with two or more of the following: myalgia, arthralgia, retro-orbital pain, headache, skin rash, and hemorrhagic manifestations plus thrombocytopenia and leukopenia, were classified as probable cases of dengue fever and were subjected to reverse transcriptase (RT)-PCR and/or dengue-specific IgM by ELISA. The diagnosis of malaria was established on thick and thin blood film microscopy. Severe disease was defined by the presence of an altered level of consciousness, World Health Organization grade ≥2 bleeding, jaundice, circulatory shock, hemoglobin <50g/l, platelet count <50×109/l, serum creatinine >265μmol/l, or death.ResultsThere were 85 probable cases of dengue fever. Sixty-four (75%) were male and the median age was 22 years (range 12–90 years). Of 52 patients for whom results of diagnostic tests for both dengue and malaria were available, five (10%) had isolated dengue infection, 18 (35%) isolated Plasmodium infection, and 17 (33%) dengue–malaria co-infection. Thirty-five out of 52 (67%) probable cases had malaria and 17 out of 22 (77%) dengue-specific IgM reactive patients had concurrent malaria. Patients with isolated malaria had significantly lower median hemoglobin concentrations (124.5g/l vs. 144.0 g/l, p = 0.04) and median hematocrit (36.0 vs. 41.7, p=0.02) at presentation than cases of isolated dengue. Patients with dengue–malaria co-infection had a significantly lower rate of jaundice than those with isolated dengue (0% vs. 40%, p = 0.04). The frequency of severe disease was comparable amongst the three groups; this was seen in five (100%) cases of isolated dengue, 17 (94%) cases of isolated malaria, and 16 (94%) cases of dengue–malaria co-infection.ConclusionsThe rate of isolated malaria and dengue–malaria co-infection was high in probable cases of dengue fever in our study. Except for jaundice, we could not find any significant between-group differences in the severity of the disease

Turmeric use is associated with reduced goitrogenesis: Thyroid disorder prevalence in Pakistan (THYPAK) study

Introduction: South Asian population has a particularly high prevalence of thyroid disorders mainly due to iodine deficiency and goitrogen use. There is no data available for prevalence of thyroid disorders in the general population living in nonmountainous regions of Pakistan. Materials and Methods: A total of 2335 residents of Pak Pattan, Punjab, Pakistan were interviewed about demographic, dietary, medical and environmental history as well as screened for goiter. Individuals of all ages and either gender were included. Results: Median age was 34 (10-88) years and 1164 (49.9%) were males. Median monthly income was 49 (3.9-137) USD. Six hundred and sixty-nine (28.7%) subjects had palpable goiter. 77.5% (n = 462) and 22.5% (n = 133) had World Health Organization Grade I and Grade II goiters respectively, further screened by measuring thyroid-stimulating hormone (TSH). In subjects with TSH <0.4 mg/dL, free T3 and free T4 levels were measured. In 185 goiter subjects when TSH was measured, 50% (n = 93) were euthyroid, 48% (n = 89) were hyperthyroid, and one subject each was hypothyroid and subclinically hyperthyroid. 29/89 hyperthyroid subjects underwent radionuclide scanning. Twelve subjects had heterogeneous uptake consistent with multinodular goiter, 12 subjects had diffuse uptake, two had cold nodules and two had hyperfunctioning single nodules. Goiter was significantly more common among females, unmarried individuals and individuals drinking tube well (subterranean) water. Goiter was less common among those who consumed daily milk, daily ghee (hydrogenated oil), spices, chilies, and turmeric. Discussion: In our study population, goiter was endemic with very high prevalence of hyperthyroidism. Turmeric use was association with reduced goitrogenesis. Further studies to assess iodine sufficiency, thiocyanate exposure and autoimmunity need to be conducted. Masses consuming high goitrogen diets should be educated to incorporate turmeric, spices and green chilies in their cooking recipes, to reduce the risk of goiter development. In addition, use of iodized salt in their daily diet cannot be overemphasized

High prevalence of preobesity and obesity among medical students of Lahore and its relation with dietary habits and physical activity

Objective: The objective of this study was to determine the prevalence of obesity among students of medical colleges of Lahore and to study its correlation with high-caloric diet intake and physical inactivity. Study Design: A cross-sectional survey was conducted at four medical colleges of Lahore, Pakistan between March and June 2012. Methods: A total of 244 medical students (85 males, 159 females) of the median age of 20 years (range: 18–25) were randomly included in the study. Anthropometric measures were obtained. High-caloric diet intake and physical profile were assessed through a self-reported questionnaire. The relationships between obesity indices (body mass index [BMI], waist-to-hip ratio) were investigated and correlated with the studied dietary and physical activity factors. Results: Approximately, 30.5% males and 16% females had BMI ≥25.0 kg/m2 overall affecting 21% of total medical students. Central obesity was found in 46% of male and 31.4% of female students. Central obesity was associated with a higher total daily caloric intake, studying at private medical college and male gender. Overall, 197 of 244 (80.7%) students played no sports in college. Median time to watch television or work on the computer was 120 min a day (range: 30–420). Only 70 (28.7%) students had regular walk or jogging. Conclusion: A substantial proportion of Pakistani medical students were overweight or obese. Higher total daily caloric intake was associated with central obesity but not a BMI >25. Physical activity parameters favored an overall sedentary aptitude for medical students

Utility of teleconsultation in accessing eye care in a developing country during COVID-19 pandemic.

ObjectiveTo evaluate the utility of teleconsultation in the provision of eye care services during the COVID-19 lockdown. Disparities in the consultation burden of sub-specialities and socio-demographic differences in teleconsultation utilization were also assessed.MethodsAl-Shifa Trust Eye Hospital Rawalpindi began audio and video teleconsultation using broadband telecommunication services during the lockdown. Patients' and consultations' data gathered during the first three weeks after the commencement of this programme were compared with data from the four weeks prior to lockdown. The weekly consultation ratio and overall consultation burden of sub-specialities were measured. Chi-Square tests of association determined the relationship between different variables (socioeconomic status and consultation characteristics) and consultation modality (on-site vs online).ResultsIn total, 17507 on-site consultations (4377/week) were conducted compared to 1431 teleconsultations (477/week), which maintained 10.89% of the weekly pre-lockdown eye care services. The post-lockdown teleconsultation programme saw a relatively higher percentage of service utility among female (47.09% vs 44.71%), younger-age (31.33±19.45 vs 41.25±23.32 years) and higher-socioeconomic-status (32.21% vs 0.30%) patients compared to pre-lockdown on-site consultations. The most common indication for teleconsultation was red-eye (16.70%). While cornea and glaucoma clinics maintained most of the pre-lockdown services (30.42% and 29% respectively), the highest dropout was seen in optometric and vitreoretinal services supporting only 5.54% and 8.28% of pre-lockdown services, respectively.ConclusionDigital initiatives could partially maintain eye care services during the lockdown. Focused strategies to improve teleconsultation utilization are required during the pandemic and beyond

Combined Deep Learning and Molecular Docking Simulations Approach Identifies Potentially Effective FDA Approved Drugs for Repurposing Against SARS-CoV-2

The ongoing pandemic of Coronavirus Disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a serious threat to global public health. Currently no approved drug or vaccine exists against SARS-CoV-2. Drug repurposing, represented as an effective drug discovery strategy from existing drugs, is a time efficient approach to find effective drugs against SARS-CoV-2 in this emergency situation. Both experimental and computational approaches are being employed in drug repurposing with computational approaches becoming increasingly popular and efficient. In this study, we present a robust experimental design combining deep learning with molecular docking experiments to identify most promising candidates from the list of FDA approved drugs that can be repurposed to treat COVID-19. We have employed a deep learning based Drug Target Interaction (DTI) model, called DeepDTA, with few improvements to predict drug-protein binding affinities, represented as KIBA scores, for 2,440 FDA approved and 8,168 investigational drugs against 24 SARS-CoV-2 viral proteins. FDA approved drugs with the highest KIBA scores were selected for molecular docking simulations. We ran docking simulations for 168 selected drugs against 285 total predicted and/or experimentally proven active sites of all 24 SARS-CoV-2 viral proteins. We used a recently published open source AutoDock based high throughput screening platform virtualflow to reduce the time required to run around 50,000 docking simulations. A list of 49 most promising FDA approved drugs with best consensus KIBA scores and AutoDock vina binding affinity values against selected SARS-CoV-2 viral proteins is generated. Most importantly, anidulafungin, velpatasvir, glecaprevir, rifabutin, procaine penicillin G, tadalafil, riboflavin 5’-monophosphate, flavin adenine dinucleotide, terlipressin, desmopressin, elbasvir, oxatomide, enasidenib, edoxaban and selinexor demonstrate highest predicted inhibitory potential against key SARS-CoV-2 viral proteins.</p

Mutations in CERKL and RP1 cause retinitis pigmentosa in Pakistani families

This study was conducted to identify the genetic basis of retinal dystrophies in consanguineous Pakistani families. We recruited two families with retinitis pigmentosa (RP) displaying visual difficulties, including nyctalopia and constricted visual fields. Linkage analysis and Sanger sequencing resulted in the identification of a previously reported nonsense mutation, c.847C &gt; T, in exon 5 of CERKL in one family and a novel four-base pair deletion in exon 4 of RP1, c.delAGAA4218_4221, leading to premature protein termination in the second family. Here, we report two RP-causing mutations extending the genetic heterogeneity of the disease