Genome-wide CNV analysis uncovers novel pathogenic regions in cohort of five multiplex families with neurodevelopmental disorders.

Structural reorganization of chromosomes by genomic duplications and/or deletions are known as copy number variations (CNVs). Pathogenic and disease susceptible CNVs alter gene dosage and its phenotypic expression that often leads to human genetic diseases including Neurological disorders. CNVs affecting same common genes in multiple neurodevelopmental disorders can better explain the shared clinical and genetic aetiology across brain diseases. Our study presents the novel copy number variations in a cohort of five multiplex consanguineous families with intellectual disability, microcephaly, ASD, epilepsy, and neurological syndromic features. Cytoscan HD microarray suite has revealed genome wide deletions, duplications and LOH regions which are co-segregating in the family members for the rare neurodevelopmental syndromic phenotypes. This study identifies 1q21.1 microduplication, 16p11.2 microduplication, Xp11.22 microduplication, 4p12 microdeletion and Xq21.1 microdeletion that significantly contribute to primary disease onset and its progression for the first time in Pakistani families. Our study has potential impact on the understanding of pathogenic genetic predisposition for appearance of complex and heterogeneous neurodevelopmental disorders with otherwise unexplained syndromic features. Identification of altered gene dosage across the genome is helpful in improved diagnosis, better disease management in day-to-day life activities of patients with cognitive impairment and genetic counselling of families where consanguinity is a tradition. Our study will contribute to expand the knowledge of genotype-phenotype expression and future gateways in therapeutics and precision medicine research will be open in Pakistan.

Mechanism of the antidiabetic action of Nigella sativa and Thymoquinone: a review.

Introduction: Long used in traditional medicine, Nigella sativa (NS; Ranunculaceae) has shown significant efficacy as an adjuvant therapy for diabetes mellitus (DM) management by improving glucose tolerance, decreasing hepatic gluconeogenesis, normalizing blood sugar and lipid imbalance, and stimulating insulin secretion from pancreatic cells. In this review, the pharmacological and pharmacokinetic properties of NS as a herbal diabetes medication are examined in depth, demonstrating how it counteracts oxidative stress and the onset and progression of DM. Methods: This literature review drew on databases such as Google Scholar and PubMed and various gray literature sources using search terms like the etiology of diabetes, conventional versus herbal therapy, subclinical pharmacology, pharmacokinetics, physiology, behavior, and clinical outcomes. Results: The efficiency and safety of NS in diabetes, notably its thymoquinone (TQ) rich volatile oil, have drawn great attention from researchers in recent years; the specific therapeutic dose has eluded determination so far. TQ has anti-diabetic, anti-inflammatory, antioxidant, and immunomodulatory properties but has not proved druggable. DM's intimate link with oxidative stress, makes NS therapy relevant since it is a potent antioxidant that energizes the cell's endogenous arsenal of antioxidant enzymes. NS attenuates insulin resistance, enhances insulin signaling, suppresses cyclooxygenase-2, upregulates insulin-like growth factor-1, and prevents endothelial dysfunction in DM. Conclusion: The interaction of NS with mainstream drugs, gut microbiota, and probiotics opens new possibilities for innovative therapies. Despite its strong potential to treat DM, NS and TQ must be examined in more inclusive clinical studies targeting underrepresented patient populations.

Natural regulatory T cells increase significantly in pediatric patients with parasitic infections: Flow cytometry study.

Background: The most accepted definition of regulatory T cells (Tregs) relies on the expression of several biomarkers, including CD4, CD25, and transcription factor, Foxp3. The Tregs maintain tolerance to self-antigens and prevent autoimmune diseases. Aim: The purpose of this study was to determine the difference in natural Treg levels in Entamoeba histolytica, Schistosoma mansoni, Giardia lamblia, Enterobius vermicularis, and Hymenolepis nana infected patients. Setting and Design: Fifty-one pediatric subjects (29 males and 22 females) were recruited from a tertiary care hospital, and were divided into infected and non-infected (control) groups. The mean age of the subjects was 8.7 years. Materials and Methods: Blood samples were collected from infected and non-infected groups, and change in the level of Tregs in these subjects was investigated by flow cytometry. Statistical Analysis Used: The statistical analysis of data was performed by SPSS software. Quantitative data used in this study included mean and standard deviation. Data from the two groups were compared by the Student's t-test. The age of the patient and infection status were used for multivariate logistic regression analysis. Odds ratios (ORs) were estimated within a 95% confidence interval, and a P value of <0.05 was considered significant. Results and Conclusions: The levels of natural regulatory T cells, indicated by the biomarkers, CD4+, CD25+, and Foxp3+, increase significantly in patients infected by Entamoeba histolytica, Schistosoma mansoni, Giardia lamblia, Enterobius vermicularis, and Hymenolepis nana as compared to controls. They also increase in cases of mixed infection as compared to infection by a single parasite.

Acute Intermittent Porphyria's Symptoms and Management: A Narrative Review.

Acute intermittent porphyria (AIP) is an autosomal dominant disorder of heme biosynthesis in the liver that is caused by the accumulation of toxic heme metabolites aminolevulinic acid (ALA) and porphobilinogen (PBG) due to a deficiency in the enzyme hydroxymethylbilane synthase (HMBS). The prevalence of AIP is found to commonly affect females of reproductive age (ages 15-50) and people of Northern European descent. The clinical manifestations of AIP include acute and chronic symptoms that can be outlined into three phases: the prodromal phase, the visceral symptom phase, and the neurological phase. Major clinical symptoms involve severe abdominal pain, peripheral neuropathy, autonomic neuropathies, and psychiatric manifestations. Symptoms are often heterogeneous and vague, which can lead to life-threatening signs if not treated and managed appropriately. Whether treating AIP in its acute or chronic form, the cornerstone of treatment consists of the suppression of the production of ALA and PBG. The mainstay of managing acute attacks continues to comprise discontinuing porphyrogenic agents, adequate caloric support, heme treatment, and the treatment of symptoms. In recurrent attacks and chronic management, prevention is key with the consideration of liver transplantation and/or renal transplantation. In recent years, there has been great interest in emerging treatments that focus on a molecular level such as enzyme replacement therapy, ALAS1 gene inhibition, and even liver gene therapy (GT), which has changed the way of traditionally managing this disease and will pave the way for innovative therapies to come.

Reduced Graphene Oxide-Zinc Sulfide Nanocomposite Decorated with Silver Nanoparticles for Wastewater Treatment by Adsorption, Photocatalysis and Antimicrobial Action.

Reduced graphene oxide nanosheets decorated with ZnS and ZnS-Ag nanoparticles are successfully prepared via a facile one-step chemical approach consisting of reducing the metal precursors on a rGO surface. Prepared rGO-ZnS nanocomposite is employed as an adsorbent material against two model dyes: malachite green (MG) and ethyl violet (EV). The adsorptive behavior of the nanocomposite was tuned by monitoring some parameters, such as the time of contact between the dye and the adsorbent, and the adsorbent dose. Experimental data were also simulated with kinetic models to evaluate the adsorption behavior, and the results confirmed that the adsorption of both dyes followed a pseudo 2nd order kinetic mode. Moreover, the adsorbent was also regenerated in a suitable media for both dyes (HCl for MG and ethanol for EV), without any significant loss in removal efficiency. Ag doped rGO-ZnS nanocomposite was also utilized as a photocatalyst for the degradation of the selected organic contaminant, resorcinol. The complete degradation of the phenolic compound was achieved after 60 min with 200 mg of rGO-ZnS-Ag nanocomposite under natural sunlight irradiation. The photocatalytic activity was studied considering some parameters, such as the initial phenol concentration, the photocatalyst loading, and the pH of the solution. The degradation kinetics of resorcinol was carefully studied and found to follow a linear Langmuir-Hinshelwood model. An additional advantage of rGO-ZnS and rGO-ZnS-Ag nanocomposites was antibacterial activity against Gram-negative bacterium, E. coli, and the results confirmed the significant performance of the nanocomposites in destroying harmful pathogens.

Preparation of stimuli responsive microgel with silver nanoparticles for biosensing and catalytic reduction of water pollutants.

Herein, we report poly(N-isopropylacrylamide/2-acrylamido-2-methylpropane sulfonic acid) microgel fabricated with silver nanoparticles. The identification of copolymerization and functional groups in the bare microgel and those fabricated with silver nanoparticles was examined by Fourier transform infrared spectroscopy. The pH and temperature sensitivity of microgels was studied using dynamic light scattering. Thermogravimetric analysis was carried out to study the thermal stability. X-Ray diffraction patterns indicated the amorphous nature of bare microgel and crystalline nature of those containing silver nanoparticles. A bathochromic shift was found in the surface plasmon resonance of silver nanoparticles present in microgel with increase in pH of the medium. Moreover, the microgel containing silver nanoparticles served as an effective catalyst for reducing the toxic nitroaromatic pollutants and carcinogenic dyes. The microgel containing silver nanoparticles also showed good capability to serve as biosensor for the detection of hydrogen peroxide.

Impact of interpregnancy intervals on perinatal and neonatal outcomes in a multiethnic Pakistani population.

BACKGROUND: Short birth intervals (SBIs) and long birth intervals (LBIs) have been shown to have serious implications for health of both mothers and their children. This study was aimed to investigate the determinants and reproductive outcome of SBI and LBI in a multiethnic Pakistani population. METHODS: In a cross-sectional prospective study design, 2798 women admitted in a tertiary-care hospital in Islamabad for delivery were recruited and data on second or higher birth order deliveries were collected. Birth intervals were defined as short (<24 months) and long (>36 months). The reproductive outcome was defined in terms of perinatal and neonatal mortalities, and neonatal complications. Univariate and multivariate logistic regression analyses were performed. RESULTS: Pregnancies with SBI and LBI were observed in 20% and 24% of 2798 women, respectively. Women with SBI had increased odds of perinatal death [adjusted odd ratio (AOR): 1.50] and neonatal death (AOR: 1.47) as compared to women with optimal birth intervals, while women with LBI had slightly lower odds of perinatal deaths (AOR: 0.96), but increased odds of neonatal deaths (AOR: 1.12). Further, the pregnancies with both SBI and LBI were associated with increased odds of short body length, low birth weight, small head circumference and low APGAR score. CONCLUSION: Nearly half of all pregnancies do not have optimal birth spacing albeit there is wide heterogeneity in the distribution of BI in various Pakistani ethnicities. Pregnancies with SBI and LBI had high risk of adverse reproductive outcome. Intervention programs for maternal and child health need to emphasize optimal birth spacing.

Birth interval (BI) or interpregnancy interval is the length of time between a birth and conception of the next pregnancy. Short birth intervals (SBIs) as well as long birth intervals (LBIs) have been shown to have serious implications for health of both mothers and their children. WHO recommendation for optimal spacing between 3 and 5 years. In this study, we aimed to investigate the effect of SBI and LBI on pregnancy outcome in the Pakistani population. A total of 2798 pregnant women admitted in a tertiary-care hospital in Islamabad for delivery were recruited and data on BI and pregnancy outcomes, i.e. perinatal and neonatal mortalities, and neonatal complications, were obtained. Results revealed that pregnancies with SBI and LBI were 20% and 24% of the total pregnancies, respectively. Women with SBI had higher likelihood of perinatal and neonatal death as compared to women with optimal birth intervals. Similarly, the women with LBI had higher likelihood of neonatal deaths. Furthermore, the pregnancies with both SBI and LBI were associated neonatal complications like short body length, low birth weight, small head circumference and low APGAR score. In conclusion, nearly half of all pregnancies do not have optimal birth spacing. Intervention programs for maternal and child health need to emphasize optimal birth spacing.

Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an outbreak of a pandemic worldwide. The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. The S1 subunit contains a receptor-binding domain that recognizes and binds to the host receptor angiotensin-converting enzyme 2 (ACE2), while the S2 subunit mediates viral cell membrane fusion with the cell membrane and subsequent entry into cells. Mutations in the spike protein (S) are of particular interest due to their potential for reduced susceptibility to neutralizing antibodies or increasing the viral transmissibility and infectivity. Recently, many mutations in the spike protein released new variants, including the Delta and Kappa ones (known as the Indian variants). The variants Delta and Kappa are now of most recent concern because of their well-increased infectivity, both a spin-off of the B.1.617 lineage, which was first identified in India in October 2020. This study employed homology modeling to probe the potential structural effects of the mutations. It was found that the mutations, Leu452Arg, Thr478Lys, and Glu484Gln in the spike protein increase the affinity for the hACE2 receptor, which explains the greater infectivity of the SARS-Cov-2 B.1.617 (Indian Variant).

Enteric parasites can disturb leptin and adiponectin levels in children.

INTRODUCTION: Infection by intestinal parasites in childhood may be the main cause of many health-related problems in developed countries such as anemia, anorexia, loss of appetite, retarded growth and development. The aim of the present study was to assess the effect of different intestinal parasites on white adipose tissue hormones. MATERIAL AND METHODS: Eighty-one children infected by different parasites and 35 apparently healthy children were enrolled in this study. All patients and controls were subjected to clinical examination, measurement of body mass index (BMI) and laboratory examination. RESULTS: For BMI percentiles, there was a significant increase in serum leptin level (p = 0.042) and a significant decrease in serum adiponectin level (p = 0.039) in uninfected children, whereas there were no significant changes in the infected group (p = 0.068 and 0.082 respectively). A significant increase in leptin and decrease in adiponectin levels were observed for E. histolytica, Strongyloides and E. histolytica and Giardia infections compared to the control group (p = 0.047, 0.035 and 0.019 for leptin, and p = 0.025, 0.038 and 0.041 for adiponectin, respectively). CONCLUSIONS: The infection by some intestinal parasites may deregulate the secretion of leptin and adiponectin and also affect the absorption of some nutrients which can disturb the BMI and cause anorexia.

Increase in activity of Na+, K+-ATPase by Porphyrin compounds as treatment for Dysnatremias caused by Diabetes Mellitus.

OBJECTIVE: The aim of this study was to test the action of Porphyrin compounds, Tetraphenylporphine sulfonate (TPPS), 5,10,15,20-Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) Chloride (FeTPPS) and 5,10,15,20-Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) nitrosyl Chloride (FeNOTPPS), on Na+, K+ -ATPase of cell membrane of erythrocytes. METHODS: Enzymatic assays, measuring the amount of inorganic phosphate produced, were used to estimate the activity of Na+, K+-ATPase. RESULTS: The results show that Porphyrin compounds exert an insulin-like effect on Na+, K+-ATPase. They act by increasing the activity of the membrane-bound enzyme. CONCLUSION: All the three Porphyrin compounds increased the activity of erythrocyte Na+, K+-ATPase. The exact mechanism of action of these compounds is not clear.

Differences in structural elements of Bcr-Abl oncoprotein isoforms in Chronic Myelogenous Leukemia.

in silico modeling, using Psipred and ExPASy servers was employed to determine the structural elements of Bcr-Abl oncoprotein (p210(BCR-ABL)) isoforms, b2a2 and b3a2, expressed in Chronic Myelogenous Leukemia (CML). Both these proteins are tyrosine kinases having masses of 210-kDa and differing only by 25 amino acids coded by the b3 exonand an amino acidsubstitution (Glu903Asp). The secondary structure elements of the two proteins show differences in five α-helices and nine ß-strands which relates to differences in the SH3, SH2, SH1 and DNA-binding domains. These differences can result in different roles played by the two isoforms in mediating signal transduction during the course of CML.

Comparative histopathological characterization of prostate cancer in Saudi patients by conventional and 2005 ISUP modified gleason systems.

BACKGROUND: The aim of this study was to compare the characterization of prostate cancer using the conventional and 2005 ISUP modified Gleason systems. MATERIALS AND METHODS: The study employed samples from 40 prostate cancer patients with resection, biopsy and RP materials. The majority of cases (95%) comprised adenocarcinoma of the prostate with a modified combined Gleason score of 7 in 20 of the cases (50%). RESULTS: Upgrading of Gleason scores to a score of 7 occurred in more than 45% of the cases. CONCLUSION: The study successfully showed that by the use of the 2005 ISUP modified Gleason system, score 6 cancers decreased from 25% to 17.5% of cases, whereas score 7 cancers increased from 45% to 50%.

A Structured-based Model for the Decreased Activity of Ala222Val and Glu429Ala Methylenetetrahydrofolate Reductase (MTHFR) Mutants.

The structure of human Methylenetetrahydrofolate Reductase (MTHFR) is not known either by NMR or by X-ray methods. Phosphorylation seems to play an important role in the functioning of this flavoprotein. MTHFR catalyzes an irreversible reaction in homocysteine metabolism. Phosphorylation decreases the activity of MTHFR by enhancing the sensitivity of the enzyme to SAdenosylmethione. Two common polymorphisms in MTHFR, Ala222Val and Glu429Ala, can result in a number of vascular diseases. Effects of the Glu429Ala polymorphism on the structure of human MTHFR remain undetermined due to limited structural information. Hence, structural models of the MTHFR mutants were constructed using I-TASSER and assessed by PROCHECK, DFIRE and Verify3D tools. A mechanism is further suggested for the decreased activity of the Ala222Val and Glu429Ala mutants due to a decrease in number of serine phosphorylation sites using information gleaned from the molecular models. This provides insights for the understanding of structure-function relationship for MTHFR.

Porphyrin derivatives as inhibitors for acetylcholinesterase from Drosophila melanogaster.

The cure for Alzheimer's disease (AD) is still unknown. According to Cholinergic hypothesis, Alzheimer's disease is caused by the reduced synthesis of the neurotransmitter, Acetylcholine. Regional cerebral blood flow can be increased in patients with Alzheimer's disease by Acetylcholinesterase (AChE) inhibitors. In this regard, Tetraphenylporphinesulfonate (TPPS), 5,10,15,20- Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) Chloride (FeTPPS) and 5,10,15,20-Tetrakis (4-sulfonatophenyl) porphyrinatoIron(III) nitrosyl Chloride (FeNOTPPS) were investigated as candidate compounds for inhibition of Acteylcholinesterase of Drosophila melanogaster (DmAChE) by use of Molecular Docking. The results show that FeNOTPPS forms the most stable complex with DmAChE.

Insight from γC1 protein model for implication in cotton leaf curl disease.

DNA γ is approximately half of the size of Begomovirus DNA. It encodes a γC1 gene that is conserved in position and size. This gene has the capacity to encode a 13 to 14 kDa protein comprising 118 amino acid residues. It has been shown earlier that γC1 protein is necessary for inducing symptoms of cotton leaf curl disease. The structure for γC1 (CLCuDγ01-Pakistan) is still unknown. Therefore, a model of γC1 (CLCuDγ01-Pakistan) was developed using DoBo and I-TASSER servers followed by validation by PROCHECK and VERIFY 3D servers. The developed model provides an insight in a role for this multifunctional protein in causing Cotton Leaf Curl Disease (CLCuD). A possible function of this protein might be the suppression of RNAsilencing in cotton plants.

Binding interactions of porphyrin derivatives with Ca(2+) ATPase of sarcoplasmic reticulum (SERCA1a).

The use of Porphyrin derivatives as photosensitizers in Photodynamic Therapy (PDT) was investigated by means of a molecular docking study. These molecules can bind to intracellular targets such as P-type CaCa(2+) ATPase of sarcoplasmic reticulum (SERCA1a). CAChe software was successfully employed for conducting the docking of Tetraphenylporphinesulfonate(TPPS), 5,10,15,20- Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) Chloride (FeTPPS) and 5,10,15,20-Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) nitrosyl Chloride (FeNOTPPS) with CaCa(2+) ATPase from sarcoplasmic reticulum of rabbit. The results show that FeNOTPPS forms the most stable complex with CaCa(2+) ATPase.

α(2)-µ-Globulin fragment (a2-f) from kidneys of male rats.

The structure of α(2)-µ-Globulin fragment (A2-f) is not known.α(2)-µ-Globulin fragment (A2-f) is a 15.5 kDa protein that binds equimolar amount of fatty acids in male rat kidneys. The expression of this protein has been shown to change in response to druginduced and genetic hypertension which suggests that it plays an important role in renal fatty acid metabolism under pathological conditions as well as normal conditions. A2-f has sequence homology with amino acid 28-178 of α(2)-µ-Globulin (A2U) that is synthesized pre-dominantly in the male rat liver and is present in the urine. It is believed that unusual structural features permit A2-f to be targeted to the proximal tubule cell; to escape lysosomal degradation in liver and to enter the cytosol of proximal tubule cells of the kidneys. Homology modeling has been employed to determine the structural elements of this protein and they have been compared with the published structure of A2U. Results suggest differences between the structure of A2-f and its precursor protein A2U.

Model of ß-Sheet of Muscle Fatty Acid Binding Protein of Locusta migratoria Displays Characteristic Topology.

The ß-sheet of muscle fatty acid binding protein of Locusta migratoria (Lm-FABP) was modeled by employing 2-D NMR data and the Rigid Body Assembly method. The model shows the ß-sheet to comprise ten ß-strands arranged anti-parallel to each other. There is a ß-bulge between Ser 13 and Gln 14 which is a difference from the published structure of ß-sheet of bovine heart Fatty Acid Binding Protein. Also, a hydrophobic patch consisting of Ile 45, Phe 51, Phe 64 and Phe 66 is present on the surface which is characteristic of most Fatty Acid Binding Proteins. A "gap" is present between ßD and ßE that provides evidence for the presence of a portal or opening between the polypeptide chains which allows ligand fatty acids to enter the protein cavity and bind to the protein.

Sulfonylureas rapidly cross phospholipid bilayer membranes by a free-diffusion mechanism.

Because sulfonylureas directly activate the exocytotic machinery, we were interested in the extent to which these compounds penetrate the beta-cell plasma membrane and the underlying molecular mechanism(s). We now provide evidence that sulfonylureas cross phospholipid bilayer membranes rapidly and effectively by a free-diffusion mechanism. Two sulfonylurea compounds investigated by 1H nuclear magnetic resonance spectroscopy, glibenclamide and tolbutamide, were found to incorporate into phospholipid bilayers, with the ionizable sulfonamide exposed to the aqueous interface and its apparent dissociation constant (pKa) increased to approximately 7.0. Diffusion of weak amphiphilic acids across membranes is associated with a measurable change in pH. Thus, by using a fluorescence-based pH assay, we could investigate the diffusion of sulfonylurea compounds across phospholipid bilayer membranes. A fluorescent pH indicator (pyranin or [2',7'-bis (2-carboxyethyl)-5(6)-carboxyfluorescein] [BCECF]) was trapped in egg phosphatidylcholine vesicles. Addition of glibenclamide decreased internal pH (pHin), and addition of albumin reversed this drop by 50%. With the same amount of tolbutamide, the decrease in pHin was much smaller, primarily because of the lower partitioning of tolbutamide into phospholipid bilayers. Using similar protocols, we also demonstrated diffusion by the same mechanism across the beta-cell plasma membrane. Thus, we now provide a molecular mechanism by which sulfonylureas can penetrate the plasma membrane and reach intracellular sites regulating exocytosis.