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Papers by Syed Hassan Abbas

Research paper thumbnail of A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

BioMed Research International

Background. Next-generation sequencing methods have been developed and proposed to investigate an... more Background. Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective. The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end u...

Research paper thumbnail of Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene

PLOS ONE, 2020

Single Nucleotide Polymorphisms (SNPs) are the most common candidate mutations in human beings th... more Single Nucleotide Polymorphisms (SNPs) are the most common candidate mutations in human beings that play a vital role in the genetic basis of certain diseases. Previous studies revealed that Solute Carrier Family 26 Member 4 (SLC26A4) being an essential gene of the multi-faceted transporter family SLC26 facilitates reflexive movement of Iodide into follicular lumen through apical membrane of thyrocyte. SLC26A4 gene encodes Pendred protein, a membrane glycoprotein, highly hydrophobic in nature, present at the apical membrane of thyrocyte functioning as transporter of iodide for thyroid cells. A minor genetic variation in SLC26A4 can cause Pendred syndrome, a syndrome associated with thyroid glands and deafness. In this study, we performed in-silico analysis of 674 missense SNPs of SLC26A4 using different computational platforms. The bunch of tools including SNPNEXUS, SNAP-2, PhD-SNP, SNPs&GO, I-Mutant, ConSurf, and ModPred were used to predict 23 highly confident damaging and disease causing nsSNPs (G209V,

Research paper thumbnail of The Health Assessment of Vultures (Gyps bengalnesis) From Changa Manga, Lahore: A case Study

BioScientific Review, 2021

Vultures are considered as an important indicator of a healthy environment, and they play a vital... more Vultures are considered as an important indicator of a healthy environment, and they play a vital ecological role as scavengers. The present study was designed to estimate the health of critically endangered Gyps bengalensis in Changa Manga, Lahore, using a technique that does not require drawing blood. Fecal matter of seven pairs were examined and analyzed for protozoan or helminth infections. Gross examination involved checking consistency and color of feces, presence of blood in feces and gross parasites. Obtained samples had different colors and consistency but no blood was found in them. Pair 1 was infested with oocytes, but in pairs 5 and 6 only males were infested, while the female was infested in pair 7. Pair 2, 3, and 4 was completely healthy. Gram staining was also performed to assess the presence or absence of bacteria culture in digestive tracks of Gyps bengalensis. All pairs were infected with either gram positive or negative except Pair 5 which was negative for all gra...

Research paper thumbnail of Dietary Selenium reduces the toxic effect of Mercury on different organs (Brain, Gills, Kidney and Liver) of Rohu fish (Labeo rohita)

BioScientific Review

Because of improbably high partiality with antioxidant selenium to mercury, selenium isolates mer... more Because of improbably high partiality with antioxidant selenium to mercury, selenium isolates mercury and reduces its biological handiness to organisms. The present study investigates the effect of mercury (Hg) and selenium (Se) on the fingerling of Labeo rohita. The various sub-lethal concentrations of Hg i.e. 0.125µg/g, 0.250µg/g, and 0.500µg/g was used and incorporated in diet with a commercial diet (fish meal 40%, soya bean 33%, 3 % of vitamins premix, mineral premix and oil each and rice polish 18%). To understand how selenium reduces the toxic effect of mercury, fingerlings were exposed with 6ug/g Se singly and combined with doses of Hg. The effect of these heavy metals was observed after 24, 48, 72, and 96 hours in different organs of (Brain, Gills, Kidney and Liver) of Labeo rohita. The organs of exposed rohu showed significant changes in their microscopic anatomy in comparison to control. Prominent changes were observed in Hg treatments and found embody shrinkage of capilla...

Research paper thumbnail of In-silico analysis of Human miRNAs in SARS-CoV-2 Genome

BioScientific Review, 2021

Background: In Dec. 2019, a new virus (Coronavirus) was discovered in Wuhan city (China), indicat... more Background: In Dec. 2019, a new virus (Coronavirus) was discovered in Wuhan city (China), indicating its potential for rapid fatal outbreaks in confined and cross borders areas. Statistics showed the fatality rate as about 1.4 %. Till now, there is no successful therapy for SARS-CoV-2. Method: The miRNAs from genome (Coronavirus/SARS-CoV-2) were analyzed using various computational approaches in this study. The complete genome sequence was retrieved from NCBI. Results: We investigated potential antiviral treatment for the SARS-CoV-2 virus using host miRNAs, which could slow down the expression of viral genes to suppress viral replication. The result of our study highlighted that hsa-miR-3675-3p (MD19), hsa-miR-363-5p (MD220), hsa-miR-325 (MD306), hsa-miR-2114-5p (MD306), hsa-miR-744-3p (MR186) and hsa-miR-448 (MR186), can be used as anti-viral treatment to quell the replication of SARS-CoV-2 virus in human. Conclusion: The findings and observations of our study opened new possi...

Research paper thumbnail of A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

BioMed Research International

Background. Next-generation sequencing methods have been developed and proposed to investigate an... more Background. Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective. The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end u...

Research paper thumbnail of Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene

PLOS ONE, 2020

Single Nucleotide Polymorphisms (SNPs) are the most common candidate mutations in human beings th... more Single Nucleotide Polymorphisms (SNPs) are the most common candidate mutations in human beings that play a vital role in the genetic basis of certain diseases. Previous studies revealed that Solute Carrier Family 26 Member 4 (SLC26A4) being an essential gene of the multi-faceted transporter family SLC26 facilitates reflexive movement of Iodide into follicular lumen through apical membrane of thyrocyte. SLC26A4 gene encodes Pendred protein, a membrane glycoprotein, highly hydrophobic in nature, present at the apical membrane of thyrocyte functioning as transporter of iodide for thyroid cells. A minor genetic variation in SLC26A4 can cause Pendred syndrome, a syndrome associated with thyroid glands and deafness. In this study, we performed in-silico analysis of 674 missense SNPs of SLC26A4 using different computational platforms. The bunch of tools including SNPNEXUS, SNAP-2, PhD-SNP, SNPs&GO, I-Mutant, ConSurf, and ModPred were used to predict 23 highly confident damaging and disease causing nsSNPs (G209V,

Research paper thumbnail of The Health Assessment of Vultures (Gyps bengalnesis) From Changa Manga, Lahore: A case Study

BioScientific Review, 2021

Vultures are considered as an important indicator of a healthy environment, and they play a vital... more Vultures are considered as an important indicator of a healthy environment, and they play a vital ecological role as scavengers. The present study was designed to estimate the health of critically endangered Gyps bengalensis in Changa Manga, Lahore, using a technique that does not require drawing blood. Fecal matter of seven pairs were examined and analyzed for protozoan or helminth infections. Gross examination involved checking consistency and color of feces, presence of blood in feces and gross parasites. Obtained samples had different colors and consistency but no blood was found in them. Pair 1 was infested with oocytes, but in pairs 5 and 6 only males were infested, while the female was infested in pair 7. Pair 2, 3, and 4 was completely healthy. Gram staining was also performed to assess the presence or absence of bacteria culture in digestive tracks of Gyps bengalensis. All pairs were infected with either gram positive or negative except Pair 5 which was negative for all gra...

Research paper thumbnail of Dietary Selenium reduces the toxic effect of Mercury on different organs (Brain, Gills, Kidney and Liver) of Rohu fish (Labeo rohita)

BioScientific Review

Because of improbably high partiality with antioxidant selenium to mercury, selenium isolates mer... more Because of improbably high partiality with antioxidant selenium to mercury, selenium isolates mercury and reduces its biological handiness to organisms. The present study investigates the effect of mercury (Hg) and selenium (Se) on the fingerling of Labeo rohita. The various sub-lethal concentrations of Hg i.e. 0.125µg/g, 0.250µg/g, and 0.500µg/g was used and incorporated in diet with a commercial diet (fish meal 40%, soya bean 33%, 3 % of vitamins premix, mineral premix and oil each and rice polish 18%). To understand how selenium reduces the toxic effect of mercury, fingerlings were exposed with 6ug/g Se singly and combined with doses of Hg. The effect of these heavy metals was observed after 24, 48, 72, and 96 hours in different organs of (Brain, Gills, Kidney and Liver) of Labeo rohita. The organs of exposed rohu showed significant changes in their microscopic anatomy in comparison to control. Prominent changes were observed in Hg treatments and found embody shrinkage of capilla...

Research paper thumbnail of In-silico analysis of Human miRNAs in SARS-CoV-2 Genome

BioScientific Review, 2021

Background: In Dec. 2019, a new virus (Coronavirus) was discovered in Wuhan city (China), indicat... more Background: In Dec. 2019, a new virus (Coronavirus) was discovered in Wuhan city (China), indicating its potential for rapid fatal outbreaks in confined and cross borders areas. Statistics showed the fatality rate as about 1.4 %. Till now, there is no successful therapy for SARS-CoV-2. Method: The miRNAs from genome (Coronavirus/SARS-CoV-2) were analyzed using various computational approaches in this study. The complete genome sequence was retrieved from NCBI. Results: We investigated potential antiviral treatment for the SARS-CoV-2 virus using host miRNAs, which could slow down the expression of viral genes to suppress viral replication. The result of our study highlighted that hsa-miR-3675-3p (MD19), hsa-miR-363-5p (MD220), hsa-miR-325 (MD306), hsa-miR-2114-5p (MD306), hsa-miR-744-3p (MR186) and hsa-miR-448 (MR186), can be used as anti-viral treatment to quell the replication of SARS-CoV-2 virus in human. Conclusion: The findings and observations of our study opened new possi...