The L-2-hydroxyglutarate dehydrogenase (L2HGDH) gene encodes an important mitochondrial enzyme. However, its altered activity results in excessive levels of L-2-hydroxyglutarate, which results in diverse psychiatric features of intellectual disability. In the current study, we executed an in-silico analysis of all reported L2HGDH missense and nonsense variants in order to investigate their biological significance. Among the superimposed 3D models, the highest similarity index for a wild-type structure was shown by the mutant Glu336Lys (87.26%), while the lowest similarity index value was shown by Arg70* (10.00%). Three large active site pockets were determined using protein active site prediction, in which the 2nd largest pocket was shown to encompass the substrate L-2-hydroxyglutarate (L2HG) binding residues, i.e., 89Gln, 195Tyr, 402Ala, 403Gly and 404Val. Moreover, interactions of wild-type and mutant L2HGDH variants with the close functional interactor D2HGDH protein resulted in alterations in the position, number and nature of networking residues. We observed that the binding of L2HG with the L2HGDH enzyme is affected by the nature of the amino acid substitution, as well as the number and nature of bonds between the substrate and protein molecule, which are able to affect its biological activity.

Polydactyly is a rare autosomal dominant or recessive appendicular patterning defect of the hands and feet, phenotypically characterized by the duplication of digits. Postaxial polydactyly (PAP) is the most common form and includes two main types: PAP type A (PAPA) and PAP type B (PAPB). Type A involves a well-established extra digit articulated with the fifth or sixth metacarpal, while type B presents a rudimentary or poorly developed superfluous digit. Pathogenic variants in several genes have been identified in isolated and syndromic forms of polydactyly. The current study presents two Pakistani families with autosomal recessive PAPA with intra- and inter-familial phenotype variability. Whole-exome sequencing and Sanger analysis revealed a novel missense variant in KIAA0825 (c.3572C>T: p.Pro1191Leu) in family A and a known nonsense variant in GLI1 (c.337C>T: p.Arg113*) in family B. In silico studies of mutant KIAA0825 and GLI1 proteins revealed considerable structural and interactional modifications that suggest an abnormal function of the proteins leading to the disease phenotype. The present study broadens the mutational spectrum of KIAA0825 and demonstrates the second case of a previously identified GLI1 variant with variable phenotypes. These findings facilitate genetic counseling in Pakistani families with a polydactyly-related phenotype.

Intellectual disability (ID) is a neuro-developmental condition that affects a person’s cognitive ability and results in a learning defect. It affects 1–3% of the general population; however, the ratio may be expected to be more in a consanguineous population. Herein in the present study, we identified a nuclear family from Dera Ismail Khan City in Pakistan. Whole exome sequencing was performed to map the pathogenic variant. Protein structural modeling and interaction studies were carried out to validate the variant with disease association. Molecular modeling of normal and mutated proteins was performed through I-TASSER and Chimera tools, while docking and interaction analysis was carried out using Cluspro. Clinical analysis of the patient determined mild intellectual disability and gait problem. Candidate gene analysis in this family found a homozygous missense mutation NM_002508:c.C2512T (p.Arg838Cys) in the 12th exon of NID1 gene. Molecular modeling of wild-type and mutant NID1 proteins determined a significant effect on the protein’s secondary and tertiary structure. Hence, based on the exome sequence analysis, NID1 is proposed to be a strong novel candidate ID gene in this family. The genetic mapping of the present family led us to determine a novel candidate gene to be associated with intellectual disability. Linkage of additional ID families with genes would confirm its validity and strengthen our notion. Furthermore, expression studies and pathway analysis will help in exploring the biological mechanism of learning and memory.

The current study aims to produce stable liposomes from total lipid extracts from bacteria. Liposomes are the small vesicles that are made up of lipids. On their structural basis, they can be considered as simplified cell structure of cell membrane. Structure of liposomes depends on the pH of preparation buffer, method of preparation and the environmental condition in which they are prepared. Liposomes have importance in the field of medicines for diagnostic and therapeutic purposes. They mainly work as a vehicle for drug delivery. The objective of the current study was to make stable liposomes from two types of bacterial samples i.e., a Gram-positive and a Gram-negative strain. E. coli and Bacillus sp. were selected as representative of Gram-negative and Gram-positive bacteria, respectively. Lipid extraction was performed by various methods, out of which the modified Bligh and Dyer method gave most effective results. Liposomes were prepared by extrusion and their stability and efficiency was tested by fluorescence spectrophotometer using OxanolVI. Our results showed that liposomes formed by lipids extracted from E. coli were more stable than the liposomes formed by lipids extracted from Bacillus sp. Keywords: liposomes, Lipids, diagnostic, therapeutic, purposes, fluorescence, Bacillus sp.

Bardet-Biedl syndrome (BBS) is a rare ciliopathic disorder that segregates in an autosomal recessive manner. Genetic studies have so far identified 26 BBS-associated genes worldwide. This study analyzed a multiplex consanguineous Pakistani family with Bardet-Biedl syndrome. Genetic analysis was performed using whole-exome sequencing and Sanger sequencing. Additionally, in silico predictions were performed for functional characterization of the identified mutation. Whole exome analysis of this family identified a novel nonsense mutation [(NM_144596: exon11:c.C1047G: p.(Tyr349*)] in the 11th exon of TTC8 gene. The identified mutation presumably leads to removal of four TPR domains and C-terminus portion. Structural analyses of mutant TTC8 protein showed substantial morphologic and interactional variations, suggesting a defective role of the TTC8 protein in BBSome complex and thus its involvement in disease progression. Identification of novel mutation has expanded the mutational spectrum of TTC8. Moreover, these findings will help in genotype-phenotype association, prenatal diagnosis and genetic counseling of families at risk of BBS syndrome.