Whole-genome sequencing and variant discovery of Citrus reticulata "Kinnow" from Pakistan.

Citrus is a source of nutritional and medicinal advantages, cultivated worldwide with major groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars Feutral's Early, Dancy, Honey, and Kinnow. The present study designed to understand the genetic architecture of this unique variety of Citrus reticulata 'Kinnow.' The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seedlessness, juice content, thickness of peel, and shelf-life. A total of 139,436,350 raw sequence reads were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, 3,503,033 SNPs, 176,949 MNPs, 323,287 INS, and 333,083 DEL were identified using the GATK4 variant calling pipeline against Citrus clementina. Furthermore, g:Profiler was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts in cellular components. In a nutshell, 18,153 high impact variants and 216 genic variants found in the current study, which may be used after its functional validation for marker-assisted breeding programs of "Kinnow" to propagate its valued traits for the improvement of contemporary citrus varieties in the region.

Genetic susceptibility of vitamin D receptor gene polymorphisms on autosomal recessive primary microcephaly patients in Pakistani population: a case-control and in-silico study.

BACKGROUND: Autosomal recessive primary microcephaly (MCPH) is a rare genetic disorder that leads to reduced cerebral cortex caused by a mutation in corticogenesis. The expression of the Vitamin D receptor (VDR) gene is involved in the proliferation and differentiation of neural stem cells, and VDR polymorphisms have been associated with various neurological disorders. However, their relationship with MCPH has not been explored. This study aimed to investigate the association of VDR polymorphisms with MCPH due to its role in Wnt signaling pathway and its In-silico analysis. METHODS: Blood samples of 64 MCPH patients and 52 controls were collected to genotype VDR SNPs (TaqI (rs731236), FokI (rs2228570) and BsmI (rs1544410). In-silico tools were also used to assess the effects of exonic SNPs on mRNA and protein structure and pathogenicity of exonic and intronic SNPs. RESULTS: The study found that serum 25-OH vitamin D3 levels were significantly different in MCPH patients and healthy controls (P = 0.000). The genetic analysis showed that VDR polymorphisms of FokI and BsmI were seven times more frequent in MCPH patients than in controls (P < 0.05) and the recessive model for TaqI and dominant model for BsmI polymorphisms were also associated with the pathogenesis of MCPH. In-silico analysis showed that the pathogenicity effects of rs2228570 and rs1544410 are neutral while rs731236 causes a silent mutation which has no effect on VDR protein. CONCLUSION: VDR polymorphisms of FokI and BsmI are associated with the risk of MCPH. These findings suggest that VDR polymorphisms play a role in MCPH, which could provide important insights for understanding the molecular mechanisms of the disease.

Evaluation of antimicrobial activity of extracts of in vivo and in vitro grown Vinca rosea L. (Catharanthus roseus) against pathogens.

The antimicrobial activity of Vinca rosea was evaluated against pathogenic bacterial strains (Bacillus subtilis, B. licheniformis and Azotobacter sp.) and fungal strains (Asprgillus niger, Alternaria solani and Rhizopus oryzae) using agar well diffusion method. Methanolic extracts of in vivo leaf, in vitro leaf, in vitro calluses of leaf, nodal and fruit explants were used and exhibited antimicrobial activity as indicated by minimum inhibitory concentration (MIC). In vitro extracts showed better results as compared to the in vivo extracts for both the antibacterial as well as the antifungal activity. Among all the extracts, maximum zone of inhibition (30.3 mm ± 0.58(a)) was formed by in vitro leaf callus extract concentration of 2.0mg/ml against B. licheniformis. Similarly in case of antifungal activity, maximum zone of inhibition (34.6mm ± 0.57(a)) was formed by in vitro leaf callus extract and MIC value is 6.0mg/ml against A. niger. Hence these results clearly depicts that V. rosea possess a great strength to fight against the microbial activity and can be used against various infections.

Efficient detoxification of textile wastewater by applying Chenopodium album nanoparticles and its application in simulated metal-bearing effluents removal.

Large-scale pollution of water and soils bodies is associated with the discharge of the untreated textile industry effluents. Halophytes grows on saline lands and accumulate secondary metabolites and other stress protective compounds. Utilization of Chenopodium album (halophytes) to synthesize zinc oxide (ZnO) and their efficiency to treat different concentrations of textile industry waste water is proposed in this study. Potential of nanoparticles textile industry waste water effluents was also analyzed by exposing different concentrations of nanoparticles (0 (control), 0.2, 0.5, 1 mg) and time intervals of 5, 10, and 15 days. The absorption peaks by UV region, FTIR and SEM analysis were used characterized on ZnO NPs for the first time. FTIR analysis showed the preens of various functional groups and vital phytochemicals that can play its role in the formation of nanoparticles that can be used for trace elements removal and bioremediation. SEM analysis indicated that the pure ZnO NPs synthesis ranged from 30 to 57 nm. Results shows that the green synthesis of halophytic nanoparticles presents maximum removal capacity after 15 days exposure to 1 mg of ZnO NPs. Hence, the prepared ZnO Nps from halophytes can be a viable solution for treating the textile industry effluents before they are discharged into water bodies for sustainable environmental growth and environmental safety.