Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome.

The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species.

Association between risk factors and migraine in Pakistani females.

BACKGROUND: Migraine is a typical cripple issue of the brain identified with cerebral pain which is an indication of numerous health conditions. About 18% of women (27 million) and 6% of men (10 million) are afflicted by migraine in the United States. Based on a case-control study, to explore the different risk factors, causing migraine in females and examine the association between risk factors and migraine. METHODS: A sample of 1055 individuals were selected in different areas of Lahore from September 2019 to March 2020. The information was obtained by using the direct interview method and questionnaire method. Descriptive analysis, bivariate analysis and binary logistic regression analysis were carried out in data analysis. RESULTS: Among 1055 individuals 740 cases and 315 controls were included. In a binary logistic regression model, physical activities, stress, summer season, menstruation and morning were the risk factors that cause migraine and these were found to be positively significant with the odds ratios and 95% confidence interval of odds ratios (1.399; 1.122-1.746), (1.510; 1.187-1.922), (1.595; 1.374-1.851), (1.513; 1.247-1.836) and (1.309; 1.028-1.665) respectively. Nausea, isolation and back head pain were caused by migraine and these were found positively significant with the odds ratios and 95% confidence interval of odds ratios(1.290; 1.122-1.484), (1.882; 1.617-2.190) and (1.285; 1.123-1.471) respectively. CONCLUSIONS: Stress, physical Activities and Menstruation increase the risk of migraine but weight loss, Breakfast, lunch, thirst, injury and Second trimester during pregnancy reduce the risk of migraine.

A bibliometric analysis of the top 100 most cited papers and research trends in breast cancer related BRCA1 and BRCA2 genes.

This study aimed to identify, characterize, and map the important attributes of the top 100 most cited papers on BRCA1 and BRCA2 genes. The scientific literature on BRCA1 and BRCA2 was searched in the Web of Science Core Collection database using the keywords "BRCA1" OR "BRCA2" (Title). The top 100 most cited papers were selected based on citations. The obtained data were exported into HistCiteTM, RStudio, and VOSviewer software for prerequisite analysis. The top 100 most cited papers on BRCA1 and BRCA2 were authored by 932 authors from 24 countries and published in 27 journals. These papers were cited 79,713 times, ranging from 441 to 4671 citations. The highly cited paper was cited 4671 times and published in Science (1994). The leading author, journal, publication year, institution, and country were Easton DF (n = 16), Nature Genetics (n = 11), 2002 (n = 11), University of Pennsylvania (n = 17), and the USA (n = 76), respectively. The results show that all the top 100 papers were produced in developed countries. The collaboration index among the authors was 9.49. The most frequently appeared keywords were ovarian-cancer, breast-cancer, mutations, gene, and familial breast. In recent times, the trend topics were patients, mutations, carriers, ovarian, and risk.

Some pathogenic SETX variants are partially conserved during evolution.

Variants in SETX have been implicated in recessively and dominantly inherited disorders, ataxia with oculomotor apraxia type 2 (AOA2 OMIM# 606002) and amyotrophic lateral sclerosis (ALS4, OMIM# 602433) respectively, in humans. We report two novel bi-allelic pathogenic variants in SETX in patients suffering from ataxia with oculomotor apraxia type 2, extending the allelic spectrum of the gene variants. We also discuss the pathogenicity of SETX variants in relation to the evolutionary conservation status of the affected amino acids. Our analyses suggest that variants of some amino acids which are not fully conserved in evolution, may cause a disorder in humans, provided the particular pathogenic variant is absent in other orthologues.

Metagenomic analysis of drinking water samples collected from treatment plants of Hyderabad City and Mehran University Employees Cooperative Housing Society.

The quality assessment of water, supplied to the end user, is an essential part to assess the physical, chemical, and biological status of water, which impacts on human health. For the quality assessment of drinking water treatment plants and distribution systems of Hyderabad City and Mehran University of Engineering and Technology, Jamshoro, Pakistan, 13 surface drinking water samples were collected from three treatment plants, two of Hyderabad City, including WASA treatment plant and its distribution system (n = 5), Hala Nakka treatment plant and its distribution system (n = 6), and Mehran University Employees Cooperative Housing Society (MUECHS) treatment plant and its distribution system (n = 2). Physicochemical parameters of all drinking water samples were in the range compared to EPA and WHO guidelines, except in L-12 sample. Notably, no free-chlorine was detected in all samples. In metagenomics analysis, targeting V3-V4 hypervariable region of 16S rRNA gene, in QIIME2 environment, high bacterial prevalence was observed in all samples. On average, 348 OTUs were observed per sample. Among all samples, treated water sample from the Hala Nakka Treatment Plant (HNTR) was the most diverse sample in bacterial composition (Shannon 7.51 and Simpsons reciprocal indices 0.98). Overall, Proteobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Actinobacteria were the five most abundant phyla (relative abundances of 43.6, 37.9, 8.5, 2.5, and 2.4 percent, respectively). Notably, Cyanobacteria are well-known toxin producers which effect the human, and animal health. At genus level, Flavobacterium (4.86%) and Aquirestis (3.77%) were the most abundant genera. Functional predictions, based on 16S rRNA gene by PICRUSt, predicted 6909 KEGG orthologies, relating to 245 KEGG pathways. Among the predicted pathways of KEGG orthologies, pathways to human infections were also found. In conclusion, this study gave a deep insight into bacterial contamination in drinking water samples of Hyderabad City and MUECHS treatment plants and water quality status in Hyderabad and Mehran University of Engineering and Technology.

Antioxidant, Antimicrobial, Cytotoxic, and Protein Kinase Inhibition Potential in Aloe vera L.

Aloe vera is a multifunctional plant that has gained acceptance as an excellent home remedy source in Asia and the world. The present study was intended to evaluate the phytochemical contents and in vitro antioxidant, antimicrobial, antileishmanial, and protein kinase inhibition activities in different fractions of A. vera leaf. Methanolic extract of A. vera leaves was fractionated using column chromatography and ten fractions (AV1-AV10) were obtained. Phenolics composition, antioxidant, antimicrobial, antileishmanial, and protein kinase inhibition activities were evaluated using standard protocols. Well-known compounds of A. vera were used for in silico study against enzymes involved in brine shrimp and antileishmanial and hyphae formation inhibition assay on the basis of results. Five fractions (AV3 to AV7) possess potential total phenolics and flavonoids contents along with significant biological activities. AV4 fraction exhibited the highest total phenolics content 332.4 ± 32.6µg GAE/mg and total antioxidant activity 150.4 ± 25.815µg AAE/mg determined by phosphomolybdenum complex assay. Fraction AV6 showed 95% antileishmanial effect as well as the lowest LD50 value of 0.5305µg/mL in brine shrimp lethality assay. The Protein Kinase inhibition potential in A. vera leaves was determined for the first time and three fractions AV1, AV6, and AV7 depicted activity with the highest zone of inhibition up to 21±0.5mm (AV7). Docking analysis showed that A. vera contains anthraquinones, anthrones, chromones, and polysaccharides responsible for synergistic cytotoxic, antileishmanial, antibacterial, and antioxidant potential of this plant. Therefore, with more studies, A. vera could probably have the potential to be used for drug development against leishmaniasis.

AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders.

AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by GRIA1-4 genes. GluA2 has an especially important role because, following post-transcriptional editing at the Q607 site, it renders heteromultimeric AMPARs Ca2+-impermeable, with a linear relationship between current and trans-membrane voltage. Here, we report heterozygous de novo GRIA2 mutations in 28 unrelated patients with intellectual disability (ID) and neurodevelopmental abnormalities including autism spectrum disorder (ASD), Rett syndrome-like features, and seizures or developmental epileptic encephalopathy (DEE). In functional expression studies, mutations lead to a decrease in agonist-evoked current mediated by mutant subunits compared to wild-type channels. When GluA2 subunits are co-expressed with GluA1, most GRIA2 mutations cause a decreased current amplitude and some also affect voltage rectification. Our results show that de-novo variants in GRIA2 can cause neurodevelopmental disorders, complementing evidence that other genetic causes of ID, ASD and DEE also disrupt glutamatergic synaptic transmission.

Author Correction: Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia.

In the version of this article initially published, the name of author Wai Yan Yau was misspelled. The error has been corrected in the HTML and PDF versions of the article.

Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia.

Late-onset ataxia is common, often idiopathic, and can result from cerebellar, proprioceptive, or vestibular impairment; when in combination, it is also termed cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS). We used non-parametric linkage analysis and genome sequencing to identify a biallelic intronic AAGGG repeat expansion in the replication factor C subunit 1 (RFC1) gene as the cause of familial CANVAS and a frequent cause of late-onset ataxia, particularly if sensory neuronopathy and bilateral vestibular areflexia coexist. The expansion, which occurs in the poly(A) tail of an AluSx3 element and differs in both size and nucleotide sequence from the reference (AAAAG)11 allele, does not affect RFC1 expression in patient peripheral and brain tissue, suggesting no overt loss of function. These data, along with an expansion carrier frequency of 0.7% in Europeans, implies that biallelic AAGGG expansion in RFC1 is a frequent cause of late-onset ataxia.

A Novel Homozygous Variant of SETX Causes Ataxia with Oculomotor Apraxia Type 2.

BACKGROUND AND PURPOSE: Autosomal recessive cerebellar ataxias constitute a highly heterogeneous group of neurodegenerative disorders. This study was carried out to determine the clinical and genetic causes of ataxia in two families from Pakistan. METHODS: Detailed clinical investigations were carried out on probands in two consanguineous families. Magnetic resonance imaging was performed. Exome sequencing data were examined for likely pathogenic variants. Candidate variants were checked for cosegregation with the phenotype using Sanger sequencing. Public databases including ExAC, GnomAD, dbSNP, and the 1,000 Genome Project as well as ethnically matched controls were checked to determine the frequencies of the alleles. Conservation of missense variants was ensured by aligning orthologous protein sequences from diverse vertebrate species. RESULTS: Reverse phenotyping identified spinocerebellar ataxia, autosomal recessive 1 [OMIM 606002, also referred to as ataxia oculomotor apraxia type 2 (AOA2)] and ataxia telangiectasia (OMIM 208900) in the two families. A novel homozygous missense mutation c.202 C>T (p.Arg68Cys) was identified within senataxin, SETX in the DNA of both patients in one of the families with AOA2. The patients in the second family were homozygous for a known variant in ataxia-telangiectasia mutated (ATM) gene: c.7327 C>T (p.Arg2443Ter). Both variants were absent from 100 ethnically matched control chromosomes and were either absent or present at very low frequencies in the public databases. CONCLUSIONS: This report extends the allelic heterogeneity of SETX mutations causing AOA2 and also presents an asymptomatic patient with a pathogenic ATM variant.

Frequency of non-motor symptoms in Parkinson's disease presenting to tertiary care centre in Pakistan: an observational, cross-sectional study.

OBJECTIVE: To determine the frequency of non-motor symptoms (NMS) in patients of Parkinson's disease (PD) presenting to a movement disorder clinic at a tertiary care centre in Pakistan, and how frequency of NMS is different in male and female patients. STUDY DESIGN: Observational, cross-sectional study. SETTING: Tertiary care centre. PARTICIPANTS: Out of 102 patients, 85 were included. Inclusion criteria were patients with PD diagnosed according to the UK Parkinson's Disease Society Brain Bank Clinical Diagnostic Criteria, age ≥18 years, able to give consent and have no difficulty in answering questions. Exclusion criteria were diseases that resemble PD, stroke, dementia, patients unable to provide information and history of antipsychotic use. RESULTS: The NMSQuest revealed a mean of nearly seven different NMS per patient. Autonomic problems such as constipation (56%) and nocturia (49%) were the most common NMS, while urinary urgency was reported by 35% of patients. Low mood and feeling sad were reported by 47%, whereas feeling anxious/panicky was reported by 36%. Problem with memory was reported by 45% of patients. Feeling of light-headedness and dizziness was reported by 40% of patients. Problems with sexual relationship were reported by 30% of patients. The most common sleep problem was difficulty falling sleep (29%). Pain not related to the musculoskeletal system was reported by 30% of patients. Loss or change in the ability to taste or smell was reported by 29% of patients. The rest of NMS were less than 25% in frequency. Feeling sad or blue, feeling light-headed/dizzy, unexplained pain, unpleasant sensations in the legs, difficulty in swallowing and faecal incontinence were more common in female participants, while problems with sex were more common in male participants. CONCLUSION: NMS are quite prevalent in PD in our population. Certain NMS are more common in women as compared with men. There is a need for a large-scale study to look for the association of different NMS with sex.

A novel mutation in ALS2 associated with severe and progressive infantile onset of spastic paralysis.

Infantile onset ascending spastic paralysis (IAHSP) is a type of recessively inherited spastic paraplegia. We investigated the clinical and genetic cause of a recessively inherited disorder in two siblings manifesting severe spasticity in the lower limbs which hindered their gait. A novel homozygous nonsense mutation c.1918 C > T (p.Arg640*) was identified after whole-exome sequencing within ALS2 in the DNA of both patients. The obligate carriers were heterozygous for the mutation and other unaffected members were homozygous for the wild type allele. The variant was absent from 100 control chromosomes and all public databases. This report extends the allelic heterogeneity of ALS2 mutations and emphasizes the importance of genetic testing for diagnosis of pediatric disorders.

TFG associated hereditary spastic paraplegia: an addition to the phenotypic spectrum.

Hereditary spastic paraplegias (HSPs) constitute movement disorders with extreme lower limb spasticity caused by axonopathies of the upper motor neurons. We describe two siblings affected with a recessive form of movement disorder. Whole-exome sequencing revealed a homozygous missense mutation c.64 C>T (p.Arg22Trp) in TFG as cause of the disorder. Comparison of the phenotype of the patients of this study, with that reported previously, revealed differences in the severity of the disorder as well as new clinical findings. These include presence of clonus, undeveloped speech, and sleep disturbances. Our findings extend the phenotypic spectrum associated with the TFG mutations in HSP.

Using Data From Ontario's Episode-Based Funding Model to Assess Quality of Chemotherapy.

INTRODUCTION: A new episode-based funding model for ambulatory systemic therapy was implemented in Ontario, Canada on April 1, 2014, after a comprehensive knowledge transfer and exchange strategy with providers and administrators. An analysis of the data from the first year of the new funding model provided an opportunity to assess the quality of chemotherapy, which was not possible under the old funding model. MATERIALS AND METHODS: Options for chemotherapy regimens given with adjuvant/curative intent or palliative intent were informed by input from disease site groups. Bundles were developed and priced to enable evidence-informed best practice. Analysis of systemic therapy utilization after model implementation was performed to assess the concordance rate of the treatments chosen with recommended practice. The actual number of cycles of treatment delivered was also compared with expert recommendations. RESULTS: Significant improvement compared with baseline was seen in the proportion of adjuvant/curative regimens that aligned with disease site group-recommended options (98% v 90%). Similar improvement was seen for palliative regimens (94% v 89%). However, overall, the number of cycles of adjuvant/curative therapy delivered was lower than recommended best practice in 57.5% of patients. There was significant variation by disease site and between facilities. CONCLUSION: Linking funding to quality, supported by knowledge transfer and exchange, resulted in a rapid improvement in the quality of systemic treatment in Ontario. This analysis has also identified further opportunities for improvement and the need for model refinement.

Phylogenetic analysis of Torque Teno Virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients.

BACKGROUND: Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the present study compiles the first indigenous report to comprehensively illustrate the incidence of the virus in uninfected and hepatitis infected population from Pakistan. Another aim of the study was to present the sequence of full length TTV genome from a local isolate and compare it with the already reported genome sequences from other parts of the world. METHODS: TTV DNA was screened in the serum of 116, 100 and 40 HBV infected, HCV infected and uninfected individuals respectively. Nearly full length genome of TTV was cloned from a HBV patient. The genome sequence was subjected to in-silico analysis using CLC Workbench, ClustalW, ClustalX and TreeView. Statistical analysis was carried out in SPSS v17.0. RESULTS: Our results report that 89.7%, 90.0% and 92.5% of HBV, HCV patients and healthy control population were positive for TTV infection. TTV genome of 3603 bp was also cloned from a local isolate and given the identity of TPK01. The TTV genome sequence mentioned in this paper is submitted in the GenBank/EMBL/DDBJ under the accession number JN980171. Phylogenetic analysis of TPK01 revealed that the Pakistani isolate has sequence similarities with genotype 23 and 22 (Genogroup 2). CONCLUSION: The results of the current study indicate that the high frequency of TTV viremia in Pakistan conforms to the reports from other areas of the world, wherever screening of TTV DNA was performed against 5'-UTR of the genome. The high sequence diversity among TTV genome sequences and the high frequency of prevalence makes it harder to study this virus in cellular systems.

An overview: in vitro models of HCV replication in different cell cultures.

Although much of productive research has been conducted in the field of molecular virology of Hepatitis C virus (HCV) regarding its genes, gene functions and proteins, development of an efficient cell culture model for its replication remained a focused area. Focus has been directed to establish HCV in vitro replication system. This replication system should mimic its intrahepatic pathogenesis so that antivirals should be screened and in vitro gene profiling of HCV induced pathogenesis should be worked out. Since 1990 various experimental approaches and strategies have been utilized in phase of development of a robust replication model for HCV, and success has been reported for a few genotypes. Still the work is going on to have more success in availing such robust replication models for all the genotypes. This will help to have a common antiviral strategy against HCV induced pathogenesis involving any genotype or subtype.

Hepatitis C virus infection: molecular pathways to insulin resistance.

Chronic Hepatitis C virus has the potential of inducing insulin resistance and type 2 Diabetes Mellitus in vitro as well as in vivo . Structural and non-structural proteins of HCV modulate cellular gene expression in such a way that insulin signaling is hampered, concomitantly leads toward diabetes mellitus. A number of mechanisms have been proposed in regard to the HCV induced insulin resistance involving the upregulation of Inflammatory cytokine TNF-α, hypophosphorylation of IRS-1 and IRS-2, phosphorylation of Akt, up-regulation of gluconeogenic genes, accumulation of lipids and targeting lipid storage organelles. This review provides an insight of molecular mechanisms by which HCV structural and non-structural proteins can induce insulin resistance.