Asymptomatic cytomegalovirus gastritis in an immunocompetent COVID-19 patient: A case report.

A number of complications are associated with COVID-19 due to reduced immunity. Of these, opportunistic infections are of great significance because of their atypical presentation and low detection rates. Co-infection of various parts of the gastrointestinal system with cytomegalovirus (CMV) is a common occurrence in COVID- 19 patients. Dysphagia and odynophagia are the main complaints of oesophagitis caused by CMV. Colitis due to CMV presents with melena, diarrhoea, or constipation. However, gastritis due to the same agent can be asymptomatic or associated with atypical symptoms like fever and epigastric pain. Cytomegalovirus gastritis can be fatal if not detected early. Hence, continued monitoring of routine baseline investigations is imperative until the complete resolution of COVID-19, as prompt diagnosis improves the outcomes.

Concurrent Obsessive-Compulsive Symptoms in Patients With Schizophrenia: A Retrospective Study From a Tertiary Care Centre in Sindh, Pakistan.

INTRODUCTION: The present study aimed to evaluate the proportion of concurrent symptoms of obsessive-compulsive symptoms (OCSs) among patients with schizophrenia. METHODS: A retrospective study was undertaken at the Department of Psychiatry, Jinnah Postgraduate Medical Center, Sindh, Pakistan between 1st March 2019 and 1st April 2020. All cases with diagnosed schizophrenia irrespective of gender, age, or ethnicity were eligible for the study. We excluded patients with acute psychosis due to isolated substance use disorder or any organic brain disease. The medical records for each patient were retrieved from the departmental database. Sociodemographic factors including age, gender, ethnicity, and presence of OCSs and other psychiatric comorbidities were recorded in a predefined pro forma. The presence of OCSs was noted by the attending psychiatrist during history taking as positive or negative. RESULTS: A total of 139 patients were included. A predominance of the male gender was noted. There were 63 (45.3%) patients with concurrent OCSs. Out of the total patients, 42 (66.67%) males and 21 (33.33%) females had OCSs. A total of 28 (44.44%) patients between 31 and 45 years of age had OCSs. Out of the 63 patients with OCSs, 36 (57.14%) had a history of substance abuse (p = 0.471). In the study, 17 (26.98%) Balochi and 19 (30.16%) Pashtuns had OCSs. However, the difference was statistically insignificant. CONCLUSION: In conclusion, OCSs were frequent in patients with schizophrenia, according to the current study. We discovered that males, individuals between the ages of 18 and 30 years, Balochis, Pashtuns, and those with a history of substance abuse were more likely to have OCSs. However, the difference was not statistically significant.

A homozygous frame-shift variant in PROSER1 is associated with developmental delay, hypotonia, genitourinary malformations, and distinctive facial features.

We report four children from three related families who presented with a similar phenotype characterized by developmental delay, hypotonia, seizures, failure-to-thrive, strabismus, drooling, recurrent otitis media, hearing impairment, and genitourinary malformations. They also shared common facial features including arched eyebrows, prominent eyes, broad nasal bridge, low-hanging columella, open mouth, thick lower lip, protruding tongue, large low-set ears, and parietal bossing. Exome sequencing for affected individuals revealed a homozygous frame-shift variant, c.1833del; p.(Thr612Glnfs*22), in PROSER1 which encodes the proline and serine rich protein 1 (PROSER1). PROSER1 has recently been found to be part of the histone methyltransferases KMT2C/KMT2D complexes. PROSER1 stabilizes TET2, a member of the TET family of DNA demethylases which is involved in recruiting the enhancer-associated KMT2C/KMT2D complexes and mediating DNA demethylation, activating gene expression. Therefore, PROSER1 may play vital and potentially general roles in gene regulation, consistent with the wide phenotypic spectrum observed in the individuals presented here. The consistent phenotype, the loss-of-function predicted from the frame-shift, the co-segregation of the phenotype in our large pedigree, the vital role of PROSER1 in gene regulation, and the association of related genes with neurodevelopmental disorders argue for the loss of PROSER1 to be the cause for a novel recognizable syndrome.

A Homozygous AKNA Frameshift Variant Is Associated with Microcephaly in a Pakistani Family.

Primary microcephaly (MCPH) is a prenatal condition of small brain size with a varying degree of intellectual disability. It is a heterogeneous genetic disorder with 28 associated genes reported so far. Most of these genes encode centrosomal proteins. Recently, AKNA was recognized as a novel centrosomal protein that regulates neurogenesis via microtubule organization, making AKNA a likely candidate gene for MCPH. Using linkage analysis and whole-exome sequencing, we found a frameshift variant in exon 12 of AKNA (NM_030767.4: c.2737delG) that cosegregates with microcephaly, mild intellectual disability and speech impairment in a consanguineous family from Pakistan. This variant is predicted to result in a protein with a truncated C-terminus (p.(Glu913Argfs*42)), which has been shown to be indispensable to AKNA's localization to the centrosome and a normal brain development. Moreover, the amino acid sequence is altered from the beginning of the second of the two PEST domains, which are rich in proline (P), glutamic acid (E), serine (S), and threonine (T) and common to rapidly degraded proteins. An impaired function of the PEST domains may affect the intracellular half-life of the protein. Our genetic findings compellingly substantiate the predicted candidacy, based on its newly ascribed functional features, of the multifaceted protein AKNA for association with MCPH.

Biallelic variants in PCDHGC4 cause a novel neurodevelopmental syndrome with progressive microcephaly, seizures, and joint anomalies.

PURPOSE: We aimed to define a novel autosomal recessive neurodevelopmental disorder, characterize its clinical features, and identify the underlying genetic cause for this condition. METHODS: We performed a detailed clinical characterization of 19 individuals from nine unrelated, consanguineous families with a neurodevelopmental disorder. We used genome/exome sequencing approaches, linkage and cosegregation analyses to identify disease-causing variants, and we performed three-dimensional molecular in silico analysis to predict causality of variants where applicable. RESULTS: In all affected individuals who presented with a neurodevelopmental syndrome with progressive microcephaly, seizures, and intellectual disability we identified biallelic disease-causing variants in Protocadherin-gamma-C4 (PCDHGC4). Five variants were predicted to induce premature protein truncation leading to a loss of PCDHGC4 function. The three detected missense variants were located in extracellular cadherin (EC) domains EC5 and EC6 of PCDHGC4, and in silico analysis of the affected residues showed that two of these substitutions were predicted to influence the Ca2+-binding affinity, which is essential for multimerization of the protein, whereas the third missense variant directly influenced the cis-dimerization interface of PCDHGC4. CONCLUSION: We show that biallelic variants in PCDHGC4 are causing a novel autosomal recessive neurodevelopmental disorder and link PCDHGC4 as a member of the clustered PCDH family to a Mendelian disorder in humans.

A 24-generation-old founder mutation impairs splicing of RBBP8 in Pakistani families affected with Jawad syndrome.

Jawad syndrome is a multiple congenital anomaly and intellectual disability syndrome with mutation in RBBP8 reported only in two families. Here, we report on two new families from Pakistan and identified a previously reported variant in RBBP8, NM_002894.3:c.1808-1809delTA. We could show that this mutation impairs splicing resulting in two different abnormal transcripts. Finally, we could verify a shared haplotype among all four families and estimate the founder event to have occurred some 24 generations ago.

Modifier Genes in Microcephaly: A Report on WDR62, CEP63, RAD50 and PCNT Variants Exacerbating Disease Caused by Biallelic Mutations of ASPM and CENPJ.

Congenital microcephaly is the clinical presentation of significantly reduced head circumference at birth. It manifests as both non-syndromic-microcephaly primary hereditary (MCPH)-and syndromic forms and shows considerable inter- and intrafamilial variability. It has been hypothesized that additional genetic variants may be responsible for this variability, but data are sparse. We have conducted deep phenotyping and genotyping of five Pakistani multiplex families with either MCPH (n = 3) or Seckel syndrome (n = 2). In addition to homozygous causal variants in ASPM or CENPJ, we discovered additional heterozygous modifier variants in WDR62, CEP63, RAD50 and PCNT-genes already known to be associated with neurological disorders. MCPH patients carrying an additional heterozygous modifier variant showed more severe phenotypic features. Likewise, the phenotype of Seckel syndrome caused by a novel CENPJ variant was aggravated to microcephalic osteodysplastic primordial dwarfism type II (MOPDII) in conjunction with an additional PCNT variant. We show that the CENPJ missense variant impairs splicing and decreases protein expression. We also observed centrosome amplification errors in patient cells, which were twofold higher in MOPDII as compared to Seckel cells. Taken together, these observations advocate for consideration of additional variants in related genes for their role in modifying the expressivity of the phenotype and need to be considered in genetic counseling and risk assessment.

Effect of alkaline and chemically engineered biochar on soil properties and phosphorus bioavailability in maize.

Phosphorous (P) fixation in alkaline calcareous soils is a serious concern worldwide and acidified-biochar application has been proposed to improve the agronomic benefits of applied P. The present study aims to improve understanding of P transformation process in an alkaline soil following different biochar amendments (rice-husk biochar (RHB), sugarcane-bagasse biochar (SWB) and wheat-straw biochar (WSB)), chemically engineered (acidification with 1 N HCl or washing with distilled water (pristine biochar)) along with or without P at 60 mg kg-1. A pot experiment was conducted with three biochars (RHB, SWB, WSB) and control, two chemical modifications (acidic and pristine), and two P-levels (without or with P). A pot study by growing spring maize and a parallel incubation study were done to test the treatment effects on P transformation. Results demonstrated that acidified SBC and WSB increased the plant P uptake and dry-matter yield by 40% and 29.7%, respectively, with P-supply. Both pristine or acidified RHB produced 80.5% and 110.7%, more root dry-matter, respectively, compared to respective controls without P. Non-acidified WSB along with P showed significantly higher Olson's P in incubation study. While in case of acidification along with P addition, RHB exhibited greater P availability, but it was inconsistent at different times during incubation. It can be concluded that acidified biochar amendments have potential to improve P management with inconsistent results. It is difficult to rule out that acidification of biochars is a pre-requisite for alkaline soils for P improvement. Further research is needed to explore site-specific P management for sustainable crop production.

An update of pathogenic variants in ASPM, WDR62, CDK5RAP2, STIL, CENPJ, and CEP135 underlying autosomal recessive primary microcephaly in 32 consanguineous families from Pakistan.

BACKGROUND: Primary microcephaly (MCPH) is a congenital neurodevelopmental disorder manifesting as small brain and intellectual disability. It underlies isolated reduction of the cerebral cortex that is reminiscent of early hominids which makes it suitable model disease to study the hominin-specific volumetric expansion of brain. Mutations in 25 genes have been reported to cause this disorder. Although majority of these genes were discovered in the Pakistani population, still a significant proportion of these families remains uninvestigated. METHODS: We studied a cohort of 32 MCPH families from different regions of Pakistan. For disease gene identification, genome-wide linkage analysis, Sanger sequencing, gene panel, and whole-exome sequencing were performed. RESULTS: By employing these techniques individually or in combination, we were able to discern relevant disease-causing DNA variants. Collectively, 15 novel mutations were observed in five different MCPH genes; ASPM (10), WDR62 (1), CDK5RAP2 (1), STIL (2), and CEP135 (1). In addition, 16 known mutations were also verified. We reviewed the literature and documented the published mutations in six MCPH genes. Intriguingly, our cohort also revealed a recurrent mutation, c.7782_7783delGA;p.(Lys2595Serfs*6), of ASPM reported worldwide. Drawing from this collective data, we propose two founder mutations, ASPM:c.9557C>G;p.(Ser3186*) and CENPJ:c.18delC;p.(Ser7Profs*2), in the Pakistani population. CONCLUSIONS: We discovered novel DNA variants, impairing the function of genes indispensable to build a proper functioning brain. Our study expands the mutational spectra of known MCPH genes and also provides supporting evidence to the pathogenicity of previously reported mutations. These novel DNA variants will be helpful for the clinicians and geneticists for establishing reliable diagnostic strategies for MCPH families.

Mediating the Fate of Cancer Cell Uptake: Dual-Targeted Magnetic Nanovectors with Biotin and Folate Surface Ligands.

Recognition of folate and biotin surface receptors by dual-functionalized nanoparticles (NPs) is key for site-selective receptor-mediated transport of anticancer drugs to cancer cells. We present here dopamine-capped iron oxide nanoprobes (Fe3O4, 10 ± 2 nm) containing two surface-grafted biologically relevant ligands, namely, folic acid (FA) and biotin (BT). The covalent attachment of both FA and BT on Fe3O4 nanoparticles was achieved by following carbodiimide coupling and click-chemistry protocols. The dual-function Fe3O4 probes were delivered into E-G7 and human HeLa cancer cell lines and tested toward their cellular uptake by immunofluorescence and flow cytometry analysis. Owing to receptor-mediated endocytosis, enhanced accumulation of nanoprobes in cancer cells was successfully monitored by confocal laser microscopy. When compared to dual-function probes, single-functionalized nanoparticles possessing either FA or BT ligands showed significantly reduced uptake in the tested cell lines, underlining the superior interaction potential of dual-purpose probes. A time-dependent receptor-mediated endocytosis of FA-Fe3O4-BT nanovectors was demonstrated by flow cytometry analysis, whereas the unfunctionalized NPs did not show any specificity in terms of uptake. Besides their specific uptake, the surface-functionalized nanoparticles exhibited promising cytotoxicity profiles by demonstrating good viability of more than 95% with analogous cancer cell lines. Our results demonstrate that dual and/or multivariate conjugation of receptor-specific ligands on NPs is highly effective in molecular recognition of surface biomarkers that enhances their potential in anticancer treatment for pretargeting-radio strategies based on biotin/avidin interactions.

Deleterious Variants in WNT10A, EDAR, and EDA Causing Isolated and Syndromic Tooth Agenesis: A Structural Perspective from Molecular Dynamics Simulations.

The dental abnormalities are the typical features of many ectodermal dysplasias along with congenital malformations of nails, skin, hair, and sweat glands. However, several reports of non-syndromic/isolated tooth agenesis have also been found in the literature. The characteristic features of hypohidrotic ectodermal dysplasia (HED) comprise of hypodontia/oligodontia, along with hypohidrosis/anhidrosis, and hypotrichosis. Pathogenic variants in EDA, EDAR, EDARADD, and TRAF6, cause the phenotypic expression of HED. Genetic alterations in EDA and WNT10A cause particularly non-syndromic/isolated oligodontia. In the current project, we recruited 57 patients of 17 genetic pedigrees (A-Q) from different geographic regions of the world, including Pakistan, Egypt, Saudi Arabia, and Syria. The molecular investigation of different syndromic and non-syndromic dental conditions, including hypodontia, oligodontia, generalized odontodysplasia, and dental crowding was carried out by using exome and Sanger sequencing. We have identified a novel missense variant (c.311G>A; p.Arg104His) in WNT10A in three oligodontia patients of family A, two novel sequence variants (c.207delinsTT, p.Gly70Trpfs*25 and c.1300T>G; p.Try434Gly) in EDAR in three patients of family B and four patients of family C, respectively. To better understand the structural and functional consequences of missense variants in WNT10A and EDAR on the stability of the proteins, we have performed extensive molecular dynamic (MD) simulations. We have also identified three previously reported pathogenic variants (c.1076T>C; p.Met359Thr), (c.1133C>T; p.Thr378Met) and (c.594_595insC; Gly201Argfs*39) in EDA in family D (four patients), E (two patients) and F (one patient), correspondingly. Presently, our data explain the genetic cause of 18 syndromic and non-syndromic tooth agenesis patients in six autosomal recessive and X-linked pedigrees (A-F), which expand the mutational spectrum of these unique clinical manifestations.

Mycobacterium tuberculosis infection and resistance to rifampicin with GeneXpert®MTB/RIF: a single-center experience on bronchoalveolar lavage samples in renal failure patients.

Patients with end-stage renal disease (ESRD) are immunocompromised and are more at risk to develop and acquire Mycobacterium tuberculosis (MTB) infection. However, risk assessment is uncertain. The objective of current research was to study the frequency of MTB infection in ESRD patients . For this purpose, bronchoalveolar lavage (BAL) samples were evaluated for the presence of MTB by using GeneXpert®MTB/RIF test. We analysed 350 clinical samples of BAL collected from a tertiary care hospital in Pakistan, from September, 2015 to July, 2016. We performed the GeneXpert®test on each sample. According to our results prevalence of MTB was observed in 1.7% of bronchoalveolar lavage (BAL) samples taken from patients with chronic kidney diseases. All the positive samples were susceptible to rifampicin. There is a low prevalence of MTB infec tion (pulmonar y tuberculosis) in patients with chronic kidney disease in our setup. Suspected patients can be diagnosed by using GeneXpert®MTB/RIF testing on bronchoalveolar lavage samples.

Body Mass Index versus Other Adiposity Traits: Best Predictor of Cardiometabolic Risk.

BACKGROUND: A number of anthropometric indices have been used in different world populations as markers to estimate obesity and its related health risks. The present study is large population based study dealing with five anthropometric obesity scales; Body mass index (BMI), waist circumference (WC), waist to hip ratio (WHR), basal adiposity index (BAI), and Visceral adiposity index (VAI) to identify common adiposity trait(s) that best predict obesity and associated health complication(s). METHODS: A total of 4000 subjects including 1000 in each category of BMI from four provinces (Punjab, Sindh, Kahyber pakhtoonkha and Balochistan) of Pakistan from 2012-2017 were collected. Complete anthropometric measurementswere obtained and blood samples were collected and Biochemical profiling was performed. Descriptive statistics, linear regression, binary and multiple regression analysis was done. RESULTS: Our data analysis explored the relationships of obesity five indices; BMI, WC, WHR, BAI, and VAI with common metabolic health complications. Effect size analysis clearly indicates that a unit increase in BMI significant raised all anthropometric and clinical parameters. General and sex specific association analysis of adiposity traits with risk phenotypes (hypertension, hyperglycemia and dyslipidemia) indicated significant associations of WC with all three metabolic risks. Varying degrees of correlations of other adiposity traits with metabolic risks were observed. Frequency of different obesity classes among obese population group were as follows; 55.7% class I, 28.50% Class II and 15.80% Class III. CONCLUSION: WC is the strong predictor of obesity associated metabolic health issues in Pakistani populations. While BMI has significant increasing effect on other obesity indices like WHR, VAI and BAI.

A missense variant in ITPR1 provides evidence for autosomal recessive SCA29 with asymptomatic cerebellar hypoplasia in carriers.

Spinocerebellar ataxias (SCA) comprise a heterogeneous group of inherited neurological disorders characterized by a range of symptoms from both cerebellar and extra cerebellar structures. We investigated the cause of autosomal recessive, congenital SCA in six affected family members from a large consanguineous family. Using whole-exome sequencing, we identified a homozygous ITPR1 missense variant [c.5360T>C; p.(L1787P)] segregating in all affected individuals. Heterozygous carriers were asymptomatic despite cerebellar hypoplasia. Variants in the ITPTR1 gene have previously been associated exclusively with autosomal dominant SCA15 and SCA29 with slow or no progression. The L1787 residue is highly conserved and the leucine to proline substitution has a predicted destabilizing effect on the protein structure. Additionally, the L1787P variant is located in a domain separated from previously described and dominant-acting missense variants consistent with a distinct effect on IP3R1 tetramer structure and function. Taken together, we show for the first time that a biallelic ITPR1 missense variant may cause an autosomal recessive and infantile onset SCA29, albeit with subclinical cerebellar hypoplasia in carriers. Our findings add to the genetic complexity of SCA29 and broaden the correlations between ITPR1 variants and their clinical expression.