Safdar Abbas - Academia.edu (original) (raw)

Papers by Safdar Abbas

Dynamic nature of beta tubulin (β-tubulin) gene is unleashed by recent studies reporting that apa... more Dynamic nature of beta tubulin (β-tubulin) gene is unleashed by recent studies reporting that apart from being a reliable reference gene serving for normalization purposes in gene expression analysis, β-tubulin encodes for structural proteins playing important role in cell cytoskeleton, microtubules and regulation of cell networking. This study is focused on the identification, isolation and characterization of 6 novel β-tubulin genes isolated from diverse range of 6 medicinal plants including Ficus carica, Pisum sativum, Capsicum annum, Capparis decidua, Maytenus royleana and Eruca sativa. The genomic sequences of newly isolated β-tubulin genes were analyzed and confirmed by using different bioinformatics tools followed by submission to genebank. We used ClustalW for pairwise alignment of these novel sequences with other known 18S rRNA sequences to find out their phylogenetic relationships. Our results have shown conserved nature of β-tubulin with some variable regions might be landmarks of some historical signals. Being housekeeping gene, β-tubulin can be used as good marker and internal control for several types of molecular analysis followed by validations of their consistent expression in the several plant species in future. This study will provide a platform for the molecular biologist interested in studying novel mechanisms of different medicinal plants.

Increasing population is facing the challenge for food security. Researchers are searching the co... more Increasing population is facing the challenge for food security. Researchers are searching the convenient and fast ways for improving crop production. Basic research provides us with genetic mechanism of plants. Tools have been discovered to manipulate and alter these mechanisms to get the new and desirable products and to incorporate innovative characteristics in plants. Synthetically made promoters, enhancers and repressors for native or transgene expression regulation are some of these tools. Some tools like, transformation of plant with artificially synthesized chromosomes and linked multiple genes are gaining importance. The most advanced one is CRISPR-Cas genome editing system. To assess their implicational potential in addressing agro-environmental problems, such genomic tools should be integrated.

Mostly organisms do not have the ability to cope with the high temperatures and this is one of th... more Mostly organisms do not have the ability to cope with the high temperatures and this is one of the contributing environmental factors which can significantly affect the growth and lipid production capacity of that particular organism. In this study, we have tried to increase the growth and total lipid production of green microalgae, Chlamydomonas reinhardtii at high temperature because we know that they can be potentially utilized as novel raw materials for the production of biodiesel. We examined closely the effects of two different cultivation temperatures i.e., 25˚C (control) and 33˚C (high temperature). We have determined the biomass and lipid productivity of these strains. We also have done the biochemical analysis using carbohydrate, protein, chlorophyll and carotenoids content. Detailed fatty acid methyl ester (FAME) analysis of these strains has also been done using the GC-MS. Our results revealed that there is a strong negative correlation between biomass accumulation and lipid contents of the three selected mutant strains. Interestingly we found a differential preference of temperature among these algal strains, like CC-4033 grew faster at 25˚C but CC-1171 showed high growth at 33˚C. Our results showed that CC-1173 strain performed equally well at both selected temperature points. Similarly lipid contents were also changed at given temperatures in the order CC-4033 >CC-1171 >CC-1173 at 33˚C. In all three mutant strains FAMEs were identified which are considered as the suitable biodiesel components. Antioxidant enzymes like catalase and ascorbate peroxidases were found to be low at 33˚C in all the studied strains. Here we suggest that CC-4033 strain can be considered as a potential mutant among all three mutants strains studied for the exploration of new renewable energy.

Bioinformatics plays an important role in agriculture science. As the data amount grows exponenti... more Bioinformatics plays an important role in agriculture science. As the data amount grows exponentially, there is a parallel growth in tools and methods demand in visualization, integration, analysis, prediction and management of data. At the same time, many researchers in the field of plant sciences are unfamiliar with available methods, databases, and tools of bioinformatics which could lead to missed information opportunities or misinterpretation. Some key concepts of software packages, methods, and databases used in bioinformatics are described in this review. In this review, we have discussed some problems related to biological databases and biological sequence analyses. Gene findings, genome annotation, type of biological database, how to data represent and store was deliberated. Future perspective of bioinformatics tools was also discussed in this review.

Ribosomal RNAs (rRNAs) are universally distributed and known for their functional equivalence amo... more Ribosomal RNAs (rRNAs) are universally distributed and known for their functional equivalence among all the known organisms. Analysis of small-subunit rRNAs (16-18S rRNAs) can permit the accurate statistical measurement of a broad range of phylogenetic relationships due to highly conserved sequences. Therefore, we identified and partially sequenced novel isoforms of 18S rRNA gene from 7 wild, medicinal plants (Ferocactus glaucescens, Capparis decidua, Calatropis procera, Maytenus royleana, Prosopis Juliflora, Ficus carica and Mentha spicata) and three cultivated plants (Cyamopsis tetragonoloba, Eruca sativa and Solanum lycopersicum). The genomic sequences of 18S rRNA from all of these diverse plants were analyzed and confirmed by using bioinformatics tools and submitted to genebank. We used ClustalW for pairwise alignment of these novel sequences with other known 18S rRNA sequences to find out their phylogenetic relationships. Our results have shown highly conserved nature of 18S rRNA with variable regions might be indications of some historical signals. Secondary structure constrains of rRNA can affect their phylogenetic interpretations rarely. These novel 18S rRNA sequences can also be used as internal controls for several types of molecular analysis after accurate validations of their consistent expression in the given plant species in future studies, as less is known about these housekeeping genes of wild plants.

Pathogens get entry into host cell, reproduce there and use biological machinery of host plants w... more Pathogens get entry into host cell, reproduce there and use biological machinery of host plants which is threat to global crop production. Integrated management strategies based upon minimizing population and use of resistant cultivars can address this potential problem. In developing world farmers are less likely to adopt these approaches instead they prefer the use of chemical pesticides. Reckless use of chemical pesticides is destroying our ecosystem. That's why it is required to explore ecofriendly alternatives, like plant based metabolites to control pathogens. Studies conducted on different plant-metabolites reported that these metabolite can potentially combat plant pathogens. In this study we have also discussed some of plant secondary metabolites including alkaloids, flavonoids and phenolics. In this review we tried to highlight the new trends in utilizing secondary metabolites for controlling bacterial, viral and fungal pathogens with the hope that upcoming drugs will be human and ecosystem friendly.

Peripheral blood samples were obtained from 2 affected (IV-2, IV-5) and 3 unaffected individuals ... more Peripheral blood samples were obtained from 2 affected (IV-2, IV-5) and 3 unaffected individuals (III-1, IV-3, IV-4) (Figure 1A). Genomic DNA was extracted and quantified using standard procedures.

Shaheen et al. Medicinal Plants for Children Diseases knowledge related to children diseases. In ... more Shaheen et al. Medicinal Plants for Children Diseases knowledge related to children diseases. In conclusion we recommend giving priority for further phytochemical investigation to plants that scored highest FIC, UV values, as such values could be considered as good indicator of prospective plants for discovering new drugs and attract future generations toward traditional healing practices.

Discussion and Conclusion: This is the first report of LGMD2F caused by an SGCD variant in a Paki... more Discussion and Conclusion: This is the first report of LGMD2F caused by an SGCD variant in a Pakistani population. The mutation identified in the present investigation extends the body of evidence implicating the gene SGCD in causing LGMD2F and might help in genetic counseling, which is more important to deliver the risk of carrier or affected in the future pregnancies.