This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using ...next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (
n
= 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains.
Dendritic spines represent the major site of neuronal activity in the brain; they serve as the receiving point for neurotransmitters and undergo rapid activity-dependent morphological changes that ...correlate with learning and memory. Using a combination of homozygosity mapping and next-generation sequencing in two consanguineous families affected by nonsyndromic autosomal-recessive intellectual disability, we identified truncating mutations in formin 2 (FMN2), encoding a protein that belongs to the formin family of actin cytoskeleton nucleation factors and is highly expressed in the maturing brain. We found that FMN2 localizes to punctae along dendrites and that germline inactivation of mouse Fmn2 resulted in animals with decreased spine density; such mice were previously demonstrated to have a conditioned fear-learning defect. Furthermore, patient neural cells derived from induced pluripotent stem cells showed correlated decreased synaptic density. Thus, FMN2 mutations link intellectual disability either directly or indirectly to the regulation of actin-mediated synaptic spine density.
Intellectual disability (ID) is a phenotypically and genetically heterogeneous disorder.
In this study, genome wide SNP microarray and whole exome sequencing are used for the variant identification ...in eight Pakistani families with ID. Beside ID, most of the affected individuals had speech delay, facial dysmorphism and impaired cognitive abilities. Repetitive behavior was observed in MRID143, while seizures were reported in affected individuals belonging to MRID137 and MRID175.
In two families (MRID137b and MRID175), we identified variants in the genes CCS and ELFN1, which have not previously been reported to cause ID. In four families, variants were identified in ARX, C5orf42, GNE and METTL4. A copy number variation (CNV) was identified in IL1RAPL1 gene in MRID165.
These findings expand the existing knowledge of variants and genes implicated in autosomal recessive and X linked ID.
Purpose
ß-thalassemia is a hereditary disorder due to mutation in the ß-globin gene on chromosome 11. Out of 200 known ß-globin gene chain mutations recognized, it is better to identify the most ...common mutation in specific regions and ethnicity for cost-effective molecular diagnosis of this disorder. Therefore, this study aims to practice multiplex-amplification refractory mutation system (ARMS) PCR on patients with thalassemia in Khyber Pakhtunkhwa (KP) to investigate the most common mutations in the ß-globin chain gene.
Design/methodology/approach
Twenty-two individuals (patients, their parents and non-affected siblings) with signed consent were studied from six consanguineous families of ß-thalassemia. Blood samples were collected for DNA isolation. For the detection of mutations in the ß-globin gene, ARMS-PCR was used. The amplicon was visualized through 2% Agarose Gel.
Findings
The most common mutations among different ethnic groups in the study area residents were Fr 8-9 (+G) and IVS 1-5 (G> C). The prominent enhancing factors for ß-thalassemia are inter-family marriages and lack of awareness.
Practical implications
Multiplex ARMS_PCR is the most valuable technique for assessing multiple mutations in a single reaction tube.
Social implications
Due to extensively found ethnic and regional variations and a high rate of consanguinity, the Pashtun population has a great risk of mutations in their genome. Therefore, ARMS-PCR is a cost-effective mutational diagnostic strategy that can help to control disease burden.
Originality/value
Limited studies using ARMS-PCR for mutational analysis in the ß-globin gene are conducted. This study is unique as it targeted consanguineous families of KP Pakistan.
Identification of Mendelian genes for neurodevelopmental disorders using exome sequencing to study autosomal recessive (AR) consanguineous pedigrees has been highly successful. To identify causal ...variants for syndromic and non-syndromic intellectual disability (ID), exome sequencing was performed using DNA samples from 22 consanguineous Pakistani families with ARID, of which 21 have additional phenotypes including microcephaly. To aid in variant identification, homozygosity mapping and linkage analysis were performed. DNA samples from affected family member(s) from every pedigree underwent exome sequencing. Identified rare damaging exome variants were tested for co-segregation with ID using Sanger sequencing. For seven ARID families, variants were identified in genes not previously associated with ID, including:
EI24, FXR1
and
TET3
for which knockout mouse models have brain defects; and
CACNG7
and
TRAPPC10
where cell studies suggest roles in important neural pathways. For two families, the novel ARID genes
CARNMT1
and
GARNL3
lie within previously reported ID microdeletion regions. We also observed homozygous variants in two ID candidate genes,
GRAMD1B
and
TBRG1
, for which each has been previously reported in a single family. An additional 14 families have homozygous variants in established ID genes, of which 11 variants are novel. All ARID genes have increased expression in specific structures of the developing and adult human brain and 91% of the genes are differentially expressed
in utero
or during early childhood. The identification of novel ARID candidate genes and variants adds to the knowledge base that is required to further understand human brain function and development.
The highly evolutionarily conserved transport protein particle (TRAPP) complexes (TRAPP II and III) perform fundamental roles in subcellular trafficking pathways. Here we identified biallelic ...variants in TRAPPC10, a component of the TRAPP II complex, in individuals with a severe microcephalic neurodevelopmental disorder. Molecular studies revealed a weakened interaction between mutant TRAPPC10 and its putative adaptor protein TRAPPC2L. Studies of patient lymphoblastoid cells revealed an absence of TRAPPC10 alongside a concomitant absence of TRAPPC9, another key TRAPP II complex component associated with a clinically overlapping neurodevelopmental disorder. The TRAPPC9/10 reduction phenotype was recapitulated in TRAPPC10-/- knockout cells, which also displayed a membrane trafficking defect. Notably, both the reduction in TRAPPC9 levels and the trafficking defect in these cells could be rescued by wild type but not mutant TRAPPC10 gene constructs. Moreover, studies of Trappc10-/- knockout mice revealed neuroanatomical brain defects and microcephaly, paralleling findings seen in the human condition as well as in a Trappc9-/- mouse model. Together these studies confirm autosomal recessive TRAPPC10 variants as a cause of human disease and define TRAPP-mediated pathomolecular outcomes of importance to TRAPPC9 and TRAPPC10 mediated neurodevelopmental disorders in humans and mice.
Assessing forest carbon and its fluctuations in mountainous areas is especially important for carbon budgeting, wildlife protection, assessing ecosystem vulnerability, and a variety of other ...ecological and environmental purposes. Conservation and maintaining carbon stocks in forests are widely recognized as a relatively low-cost option for mitigating climate risks. The present research was carried out to evaluate the C stocks in the forests of Zabarwan mountain range of Kashmir Himalaya. We carried out random sampling of tree vegetation in the five (5) major forest types in the study area. The carbon stock was calculated and analyzed using hierarchical cluster analysis. The data were subjected to hierarchical cluster analysis via, using PAST software ver.3.14. We recorded 20 forest tree species taxonomically distributed among 15 genera. The total carbon stock in the study area was 872.45 Mg C ha
−1
and could store an average of 174.49 Mg C ha
−1
. Highest total carbon stock (258.46 ± 47.53 Mg C ha
−1
) was observed for
Pinus wallichiana
forest, followed by Broad-leaved forest (230.84 ± 84.04 Mg C ha
−1
), whereas the least value (56.68 ± 16.19 Mg C ha
−1
) was observed for Scrub forest type. The decreasing trend in total carbon stock was
P. wallichiana
forest > Broad-leaved forest >
Acacia
forest > Oak forest > Scrub forest. The most significant tree species in terms of carbon stock was
P. wallichiana, Quercus robur, Celtis australis,
and
Robinia pseudoacacia.
The results indicated that the forests of the Zabarwan range show a good signal toward an opportunity in effectively conserving the carbon storage of Kashmir Himalayas by checking destruction of lush green woody forests.
Wilson's disease is arare inherited disorder of copper met abolism. If le f t untre ated, i t can turn into a multi systemic disease with copper deposition in the liver, brain, a nd other tissues. ...Diagnosi s of Wilson's is delayed in Pak ist an by many ye a rs on average due to va riabl e presen tations. In ad olescents, the initial s igns a re more likely to b e neuropsychiatric. Here we present a case of Wilso n's disease that pre sented initially with he patic symptoms and did not have signs specific to the di sea s e such as Kayser-Fleischer rings. Our case was diagnosed to be Wilson's Disease on ly on further investigat ions and s ubsequently the patient was treated with chela tion therapy using D-Penicillamine.Wilson's Disease should be kept in mind as a differential diagno sis in adolesce nt patients that present with unexplained acute liver failure and cytopenias without any neurological symptoms, as a missed diagnosis can prove to be fatal.
Background. There is clinical importance to investigate the disease progression through potential biomarkers of SARS-CoV-2 infection. In the present study, we aim to evaluate the significance of ...inflammatory markers in different categories of COVID-19 in admitted patients. Methods. In a single-center, observational study of 50 in-hospital patients who were diagnosed with COVID-19 and admitted to the intensive care unit of a tertiary care hospital in Peshawar, infection biomarkers, including hs-CRP, serum ferritin, serum creatinine, ALT, ALP, cardiac troponin-I, and IL-6 were analyzed. Results. The median age was 61.3 years. 70% (35) were male while 30% (15) were female. We noted significantly increased hs-CRP (9.32 mg/dL ± 10.03) and ferritin levels (982.3 ng/ml ± 601.9). A noteworthy increase was observed in neutrophil count (11.05 × 109/L) and a decrease was observed in lymphocyte count (0.27 × 109/L) (P<0.05), and the platelet count was borderline decreased (244.1 × 109/L). IL-6 levels were markedly increased in all admitted patients (100.2 pg/ml ± 122.2 pg/ml). Conclusion. The serum levels of CRP, troponin-I, ALP, ALT, serum creatinine, and ferritin are markedly increased in COVID-19 patients. Increased CRP and ferritin levels were also associated with secondary bacterial infection and poor clinical outcomes.
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