Single Cell Omics (SCO) is an evolving field in biomedical research which offers prime application in neurosciences. The human nervous system is complex and shows variability in cell types. It includes neurons (functional components), glial cells (supporting cells), astrocytes (provide nourishment), oligodendrocytes (synthesize myelin sheath), and microglia (defense mechanism). To understand the functional and disease states of the nervous system, it is essential to investigate them at the single-cell level. It has been estimated that every 1 in 9 people is affected by mental or neurological disorders, including psychological disorders (generally referred to as mental disorders), psychotic disorders (involving psychosis), and neurological disorders (involving neurological factors), globally. These disorders have multifactorial etiology and are caused by genetic and environmental factors. Every disorder has distinct pathophysiology affecting multiple brain regions. SCO has excellent potential to provide insight regarding the diagnosis, pathophysiology, and treatment of neurological disorders. The stringent well directed SCO methods enhance the understanding of complex nervous system disorders, such as meningitis, stroke, schizophrenia, Parkinson’s disease, and Alzheimer’s disease, which paves the way for future research.
{"title":"Prospects of Single Cell Omics (SCO) Analysis for Investigating Nervous System Disorders","authors":"M. Khan, S. Bakhtiar","doi":"10.32350/cto.21.03","DOIUrl":"https://doi.org/10.32350/cto.21.03","url":null,"abstract":"Single Cell Omics (SCO) is an evolving field in biomedical research which offers prime application in neurosciences. The human nervous system is complex and shows variability in cell types. It includes neurons (functional components), glial cells (supporting cells), astrocytes (provide nourishment), oligodendrocytes (synthesize myelin sheath), and microglia (defense mechanism). To understand the functional and disease states of the nervous system, it is essential to investigate them at the single-cell level. It has been estimated that every 1 in 9 people is affected by mental or neurological disorders, including psychological disorders (generally referred to as mental disorders), psychotic disorders (involving psychosis), and neurological disorders (involving neurological factors), globally. These disorders have multifactorial etiology and are caused by genetic and environmental factors. Every disorder has distinct pathophysiology affecting multiple brain regions. SCO has excellent potential to provide insight regarding the diagnosis, pathophysiology, and treatment of neurological disorders. The stringent well directed SCO methods enhance the understanding of complex nervous system disorders, such as meningitis, stroke, schizophrenia, Parkinson’s disease, and Alzheimer’s disease, which paves the way for future research.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126792631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Yousafzai, F. Nawaz, M. Luqman, N. Ahmed, Muneeza Arbab, J. Tabassum, Jamil Ahmad, S. Daud
Thalassemia is a hereditary blood disorder. It occurs due to two mutations in the HBB gene located on chromosome 11. This gene has 1606 base pairs and contains three exons. Moreover, HBB gene codes for β globin protein have been identified to posses 868 mutations, which comprise point mutation, insertion, deletion, and gene arrangement. In β thalassemia major, both alleles are mutated and no β chain is synthesized. In this study, three human families with thalassemia were selectedfrom different areas of Balochistan. For DNA extraction and estimation, 5 ml blood samples were extracted intravenously from the affected individuals, their normal siblings, and parents in 15ml falcon tubes containing 200μl EDTA. Primer sequences were designed on primer 3 for the mutational analysis of the HBB gene. Since the gene has a total of three exons and two introns, three primers, namely HBBX1, HBBX2 and HBBX3, were designed. These primers were used to amplify the HBB gene responsible for β thalassemia in all family samples. The amplified product was sequenced through an automated 3100 ABI Prism DNA sequence. The sequencing results were analyzed by the SaqMan software. This was done to determine if any genetic variable in the selected families showed mutations. In Family 1, 1 bp substitution mutation (c.9T>C) (p.his3his) and 1bp insertion (c.111T>G) (p.Ser10 val) in exon 1 of HBB gene were identified in thalassemia locus, while in in Family 2, 1bp substitution mutation (c.9T>C) (p.His3His) in exon 1 of HBB gene was identified in thalassemia locus. No mutation was observed in Family 03after sequencing.
{"title":"Mutational Studies of Gene HBB in β-Thalassemia Patients from Balochistan, Pakistan","authors":"A. Yousafzai, F. Nawaz, M. Luqman, N. Ahmed, Muneeza Arbab, J. Tabassum, Jamil Ahmad, S. Daud","doi":"10.32350/cto.12.05","DOIUrl":"https://doi.org/10.32350/cto.12.05","url":null,"abstract":"Thalassemia is a hereditary blood disorder. It occurs due to two mutations in the HBB gene located on chromosome 11. This gene has 1606 base pairs and contains three exons. Moreover, HBB gene codes for β globin protein have been identified to posses 868 mutations, which comprise point mutation, insertion, deletion, and gene arrangement. In β thalassemia major, both alleles are mutated and no β chain is synthesized. In this study, three human families with thalassemia were selectedfrom different areas of Balochistan. For DNA extraction and estimation, 5 ml blood samples were extracted intravenously from the affected individuals, their normal siblings, and parents in 15ml falcon tubes containing 200μl EDTA. Primer sequences were designed on primer 3 for the mutational analysis of the HBB gene. Since the gene has a total of three exons and two introns, three primers, namely HBBX1, HBBX2 and HBBX3, were designed. These primers were used to amplify the HBB gene responsible for β thalassemia in all family samples. The amplified product was sequenced through an automated 3100 ABI Prism DNA sequence. The sequencing results were analyzed by the SaqMan software. This was done to determine if any genetic variable in the selected families showed mutations. In Family 1, 1 bp substitution mutation (c.9T>C) (p.his3his) and 1bp insertion (c.111T>G) (p.Ser10 val) in exon 1 of HBB gene were identified in thalassemia locus, while in in Family 2, 1bp substitution mutation (c.9T>C) (p.His3His) in exon 1 of HBB gene was identified in thalassemia locus. No mutation was observed in Family 03after sequencing.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134184234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meningioma is the most common benign intracranial tumour that develops in the meningeal protective covering of the central nervous system (CNS). Globally, every nine individuals out of 100,000 are diagnosed with this cancer. Basic risk factors of meningioma comprise ionizing radiation, hormonal imbalance, and genetic aberrations. In this study, various bioinformatics tools, specialized for consensus-based identification, sequence-homology, and supervised learning, were employed to analyze and screen the deleterious mutational landscape of commonly associated genes of meningioma/genes commonly associated with meningioma. This study employed an in-silico approach aimed to utilize thirteen different tools to benchmark pathogenic single nucleotide polymorphisms (SNPs) in SMARCB1, AKT1, SMO, SUFU, NF2 and MTHFR genes related to meningioma. We identified six highly pathogenic SNPs related to meningioma: SMARCB1 (rs387906812, rs387906811, rs267607072), AKT1 (rs121434592), SMO (rs121918347), and SUFU (rs202247756). Additionally, several deleterious missense variants of NF2 and MTHFR genes were also identified. Hence, this study is a gateway for research on SNPs since they can be utilized to conduct a type-based diagnosis of meningioma for its early prognosis. They can also be utilized as genomic targets for a targeted therapy by developing inhibitors against mutated proteins. For this purpose, further wet-lab experiments and genome-wide association studies are required to genotype these SNPs in a large number of samples, collected from different populations belonging to various ethnicities, for the development of SNP(s) gene panels.
{"title":"Analysis of Functional Polymorphisms in Meningioma associated Genes","authors":"Anum Javaid, Binyamin Wattoo, R. Abid, S. Sadaf","doi":"10.32350/cto.12.01","DOIUrl":"https://doi.org/10.32350/cto.12.01","url":null,"abstract":"Meningioma is the most common benign intracranial tumour that develops in the meningeal protective covering of the central nervous system (CNS). Globally, every nine individuals out of 100,000 are diagnosed with this cancer. Basic risk factors of meningioma comprise ionizing radiation, hormonal imbalance, and genetic aberrations. In this study, various bioinformatics tools, specialized for consensus-based identification, sequence-homology, and supervised learning, were employed to analyze and screen the deleterious mutational landscape of commonly associated genes of meningioma/genes commonly associated with meningioma. This study employed an in-silico approach aimed to utilize thirteen different tools to benchmark pathogenic single nucleotide polymorphisms (SNPs) in SMARCB1, AKT1, SMO, SUFU, NF2 and MTHFR genes related to meningioma. We identified six highly pathogenic SNPs related to meningioma: SMARCB1 (rs387906812, rs387906811, rs267607072), AKT1 (rs121434592), SMO (rs121918347), and SUFU (rs202247756). Additionally, several deleterious missense variants of NF2 and MTHFR genes were also identified. Hence, this study is a gateway for research on SNPs since they can be utilized to conduct a type-based diagnosis of meningioma for its early prognosis. They can also be utilized as genomic targets for a targeted therapy by developing inhibitors against mutated proteins. For this purpose, further wet-lab experiments and genome-wide association studies are required to genotype these SNPs in a large number of samples, collected from different populations belonging to various ethnicities, for the development of SNP(s) gene panels.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"289 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133631268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Erum Dilshad, A. Asif, Hina Arooj, S. Khan, S. Bakhtiar
The potato (Solanum tuberosum L.) plant is grown in about 150 countries of the world and is considered an important food crop. However, this crop is susceptible to different biotic and abiotic factors, which can affect its crop yield. This vulnerability can be reduced or eliminated by growing potatoes under sterilized conditions. Cytokinins, such as 6-Benzylaminopurine, are proven to show a significant role in the in vitro regulation of plants. In the current study, explants of Kuroda variety were/potato cv. Kuroda were grown using diverse concentrations of 6-Benzylaminopurine (BAP), which displayed varied results. BAP concentration of 0.01 mg/l showed a 10 cm shoot length with 41 shoots having 66.66% regeneration efficiency. Meanwhile, the explant grown in 0.25 mg/l BAP concentration showed 16 cm shoot length with 65 shoots having 83.33% regeneration efficiency. On the other hand, the explants that were grown using 0.05 mg/l and 1 mg/l BAP concentration showed 7 cm and 10 cm shoot length with 35 and 52 shoots having 63.33% and 76.66% regeneration efficiency, respectively. Therefore, it was concluded that 0.25 mg/L of BAP showed the best results with the highest number of shoots and shoot length as well as maximum regeneration efficiency among all the tested concentrations.
{"title":"Impact of BAP on in Vitro Regeneration of Potato (Solanum Tuberosum L.)","authors":"Erum Dilshad, A. Asif, Hina Arooj, S. Khan, S. Bakhtiar","doi":"10.32350/cto.12.04","DOIUrl":"https://doi.org/10.32350/cto.12.04","url":null,"abstract":"The potato (Solanum tuberosum L.) plant is grown in about 150 countries of the world and is considered an important food crop. However, this crop is susceptible to different biotic and abiotic factors, which can affect its crop yield. This vulnerability can be reduced or eliminated by growing potatoes under sterilized conditions. Cytokinins, such as 6-Benzylaminopurine, are proven to show a significant role in the in vitro regulation of plants. In the current study, explants of Kuroda variety were/potato cv. Kuroda were grown using diverse concentrations of 6-Benzylaminopurine (BAP), which displayed varied results. BAP concentration of 0.01 mg/l showed a 10 cm shoot length with 41 shoots having 66.66% regeneration efficiency. Meanwhile, the explant grown in 0.25 mg/l BAP concentration showed 16 cm shoot length with 65 shoots having 83.33% regeneration efficiency. On the other hand, the explants that were grown using 0.05 mg/l and 1 mg/l BAP concentration showed 7 cm and 10 cm shoot length with 35 and 52 shoots having 63.33% and 76.66% regeneration efficiency, respectively. Therefore, it was concluded that 0.25 mg/L of BAP showed the best results with the highest number of shoots and shoot length as well as maximum regeneration efficiency among all the tested concentrations.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128514412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Misbah Saleem, Anum Javaid, S. Shahid, Hammad Arshad
The history of coronaviruses dates back to the 1960s. There have been several coronaviruses induced epidemics such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) in the recent past. More recently, another coronavirus-induced disease, namely COVID-19 emerged as an epidemic and rapidly developed into a pandemic due to the high transmissibility of SARS-CoV-2. It emerged as an epidemic novel COVID-19, in late 2019, instigated by SARS-CoV2. This review analyses the different aspects of SARS-CoV-2 including its genomic structure, protein composition, transmission mode, and life cycle. SARS-CoV-2 is an RNA virus, which codes four structural proteins along with various accessory proteins. A unique property of COVID-19 is that it incorporates a polybasic cleavage site, which increases its pathogenicity. The genomic variation of COVID-19/SARS-CoV-2 is assumed to be the reason behind its high transmissibility. It was identified that this genomic variation hinders the development of treatment against this disease. This review aims to facilitate the prevention of this infectious disease as well as suggest possible treatment regimens.
{"title":"Coronaviruses: A Review of the Genetics and Proteins Associated with the Life Cycle of SARS-CoV-2","authors":"Misbah Saleem, Anum Javaid, S. Shahid, Hammad Arshad","doi":"10.32350/cto.12.03","DOIUrl":"https://doi.org/10.32350/cto.12.03","url":null,"abstract":"The history of coronaviruses dates back to the 1960s. There have been several coronaviruses induced epidemics such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) in the recent past. More recently, another coronavirus-induced disease, namely COVID-19 emerged as an epidemic and rapidly developed into a pandemic due to the high transmissibility of SARS-CoV-2. It emerged as an epidemic novel COVID-19, in late 2019, instigated by SARS-CoV2. This review analyses the different aspects of SARS-CoV-2 including its genomic structure, protein composition, transmission mode, and life cycle. SARS-CoV-2 is an RNA virus, which codes four structural proteins along with various accessory proteins. A unique property of COVID-19 is that it incorporates a polybasic cleavage site, which increases its pathogenicity. The genomic variation of COVID-19/SARS-CoV-2 is assumed to be the reason behind its high transmissibility. It was identified that this genomic variation hinders the development of treatment against this disease. This review aims to facilitate the prevention of this infectious disease as well as suggest possible treatment regimens.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115158378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ayesha Safdar, Sobia Khurshid, U. Farwa, S. Bakhtiar
Autism spectrum disorder (ASD) is a complex group of neurodevelopmental disorders encompassing perturbations in verbal and non-verbal communication, social skills, as well as repetitive and restricted behaviour, activity, or response. The pathogenesis of the disorder is still unknown, yet several studies have documented the involvement of both genetic and environmental factors in its onset. Intense efforts have been made to identify reliable biomarkers to aid in early diagnosis. MicroRNAs (miRNAs) are the regulatory noncoding regions of ribonucleic acid (RNA) that can alter the expression of a gene through posttranscriptional mechanisms. In this study, an in-silico technique was used to identify two novel biomarkers, namely miR-106b-5p and miR-93-5p. The analysis identified that these diagnostic biomarkers are associated with ASD and can aid in its early treatment since miRNAs play a significant role in the development and function of the central nervous system (CNS).
{"title":"The Analyzing miR-106b-5p and miR-93-5p as Promising Diagnostic Markers for Autism Spectrum Disorder","authors":"Ayesha Safdar, Sobia Khurshid, U. Farwa, S. Bakhtiar","doi":"10.32350/cto.12.02","DOIUrl":"https://doi.org/10.32350/cto.12.02","url":null,"abstract":"Autism spectrum disorder (ASD) is a complex group of neurodevelopmental disorders encompassing perturbations in verbal and non-verbal communication, social skills, as well as repetitive and restricted behaviour, activity, or response. The pathogenesis of the disorder is still unknown, yet several studies have documented the involvement of both genetic and environmental factors in its onset. Intense efforts have been made to identify reliable biomarkers to aid in early diagnosis. MicroRNAs (miRNAs) are the regulatory noncoding regions of ribonucleic acid (RNA) that can alter the expression of a gene through posttranscriptional mechanisms. In this study, an in-silico technique was used to identify two novel biomarkers, namely miR-106b-5p and miR-93-5p. The analysis identified that these diagnostic biomarkers are associated with ASD and can aid in its early treatment since miRNAs play a significant role in the development and function of the central nervous system (CNS).","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"116 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128031266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The publication of the first draft of human genome, has led to the explosion of high throughput technologies including genomics, epigenomics, transcriptomic, proteomics, and metabolomics aiming to characterize the various biological molecules (DNA, RNA, proteins, and metabolites). These high throughput technologies collectively called as omics revolutionized medical research in the last two decades. The advent of next generation sequencing (NGS) reduced the time and economic cost of traditional sequencing and has led to the emergence of genomics as the first discipline of omics. Following the emergence of genomics, a number of projects such as The Cancer Genome Atlas (TCGA), 1000 Genome Project (1KGP), and the International Cancer Genome Consortium have been accomplished. These projects contributed significantly to the understanding of genetic variations in different cancers, for instance, TCGA produced over 2.5 petabytes of big data. Furthermore, the big data produced by these mega projects has been made publicly available to the clinicians and researchers to fast-track the diagnosis and prognosis of complex rare diseases. In developed countries, a multi-omics approach has been applied holistically to the clinical practice for the diagnosis and prognosis of various cancers and rare Mendelian diseases.
人类基因组初稿的发表，导致了高通量技术的爆发，包括基因组学、表观基因组学、转录组学、蛋白质组学和代谢组学，旨在表征各种生物分子(DNA、RNA、蛋白质和代谢物)。这些高通量技术被统称为组学，在过去的二十年里彻底改变了医学研究。下一代测序(NGS)的出现减少了传统测序的时间和经济成本，并导致基因组学作为组学的第一学科的出现。随着基因组学的出现，癌症基因组图谱(TCGA)、1000基因组计划(1KGP)、国际癌症基因组联盟(International Cancer Genome Consortium)等一系列项目相继完成。这些项目对了解不同癌症的遗传变异做出了重大贡献，例如，TCGA产生了超过2.5 pb的大数据。此外，这些大型项目产生的大数据已公开提供给临床医生和研究人员，以快速跟踪复杂罕见疾病的诊断和预后。在发达国家，多组学方法已全面应用于各种癌症和罕见孟德尔病的诊断和预后的临床实践。
{"title":"Omic or Multi-omics Approach Can Save The Mankind","authors":"Johar Ali, Ome Kalsoom Afridi","doi":"10.32350/cto.11.01","DOIUrl":"https://doi.org/10.32350/cto.11.01","url":null,"abstract":"The publication of the first draft of human genome, has led to the explosion of high throughput technologies including genomics, epigenomics, transcriptomic, proteomics, and metabolomics aiming to characterize the various biological molecules (DNA, RNA, proteins, and metabolites). These high throughput technologies collectively called as omics revolutionized medical research in the last two decades. The advent of next generation sequencing (NGS) reduced the time and economic cost of traditional sequencing and has led to the emergence of genomics as the first discipline of omics. Following the emergence of genomics, a number of projects such as The Cancer Genome Atlas (TCGA), 1000 Genome Project (1KGP), and the International Cancer Genome Consortium have been accomplished. These projects contributed significantly to the understanding of genetic variations in different cancers, for instance, TCGA produced over 2.5 petabytes of big data. Furthermore, the big data produced by these mega projects has been made publicly available to the clinicians and researchers to fast-track the diagnosis and prognosis of complex rare diseases. In developed countries, a multi-omics approach has been applied holistically to the clinical practice for the diagnosis and prognosis of various cancers and rare Mendelian diseases.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130072497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Misbah Saleem, S. Alam, Iqra Kainat, Ramsha Iftikhar, Aqsa Ijaz
Single-cell sequencing investigates the differences in proteomic and genetic information about individual cells by using next-generation sequencing technologies. Sequencing of the whole genome, epigenome, and transcriptome involves the heterogeneous process of diagnosis, progression, and treatment of disease. Previous studies show that only a few selected proteins and RNAs can be measured but recent molecular studies explore that advances in next-generation sequencing and whole genome amplification enabled us to examine the differences among a variety of transcriptomic cells, gene expression, and phenotypic expressions. In our study, we try to summarize different technologies and their applications at single-cell level in diverse fields such as embryology, oncology, immunology, neurology, microbiology, tissue and organ development, antibody screening, and stem cell research.
{"title":"Single Cell Sequencing, Its Application and Future Challenges","authors":"Misbah Saleem, S. Alam, Iqra Kainat, Ramsha Iftikhar, Aqsa Ijaz","doi":"10.32350/cto.11.05","DOIUrl":"https://doi.org/10.32350/cto.11.05","url":null,"abstract":"Single-cell sequencing investigates the differences in proteomic and genetic information about individual cells by using next-generation sequencing technologies. Sequencing of the whole genome, epigenome, and transcriptome involves the heterogeneous process of diagnosis, progression, and treatment of disease. Previous studies show that only a few selected proteins and RNAs can be measured but recent molecular studies explore that advances in next-generation sequencing and whole genome amplification enabled us to examine the differences among a variety of transcriptomic cells, gene expression, and phenotypic expressions. In our study, we try to summarize different technologies and their applications at single-cell level in diverse fields such as embryology, oncology, immunology, neurology, microbiology, tissue and organ development, antibody screening, and stem cell research. \u0000 ","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129395146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tayyba Kousar, Noor Fatima, Syeda Saleha Hassan, S. Sadaf
Acute lymphoblastic leukemia (ALL) is a hematologic condition with more than a quarter of pediatric cancers. Aberrant promoter methylation of Notch pathway genes causes the deactivation of TSGs. The pathway is also considered a crucial factor in the pathogenesis of ALL due to its active involvement in B and T cell development. Hypermethylation of Notch pathway genes has been reported previously. In this study, the promoter methylation frequency of genes DLL4 and Hes5 of the Notch pathway were studied using methylation-specific PCR in 30 pediatric ALL blood samples against 10 healthy controls. The objective of the study was to find the subtype-specific diagnostic biomarker for ALL. Hypermethylation frequency of DLL4 in pre-B ALL and T-ALL samples was found to be 84.21% and 100%, respectively. Whereas, Hes5 showed 100% mixed methylation in both diseased and control samples. The results predicted the possible epigenetic changes of Notch pathway and the possible role of DLL4 as a diagnostic biomarker of ALL.
{"title":"Epigenetic Alterations of DLL4 and Hes5 in Acute Lymphoblastic Leukemia (ALL)","authors":"Tayyba Kousar, Noor Fatima, Syeda Saleha Hassan, S. Sadaf","doi":"10.32350/cto.11.04","DOIUrl":"https://doi.org/10.32350/cto.11.04","url":null,"abstract":"Acute lymphoblastic leukemia (ALL) is a hematologic condition with more than a quarter of pediatric cancers. Aberrant promoter methylation of Notch pathway genes causes the deactivation of TSGs. The pathway is also considered a crucial factor in the pathogenesis of ALL due to its active involvement in B and T cell development. Hypermethylation of Notch pathway genes has been reported previously. In this study, the promoter methylation frequency of genes DLL4 and Hes5 of the Notch pathway were studied using methylation-specific PCR in 30 pediatric ALL blood samples against 10 healthy controls. The objective of the study was to find the subtype-specific diagnostic biomarker for ALL. Hypermethylation frequency of DLL4 in pre-B ALL and T-ALL samples was found to be 84.21% and 100%, respectively. Whereas, Hes5 showed 100% mixed methylation in both diseased and control samples. The results predicted the possible epigenetic changes of Notch pathway and the possible role of DLL4 as a diagnostic biomarker of ALL.","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129092481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Waqar Hanif, Hijab Fatima, Muhammad Qasim, R. M. Atif, M. Javed
For any sequence analysis procedure, a single or multiple sequence must be retrieved, stored, organized. One of the most common public databases used for biological sequence retrieval is GenBank which is a comprehensive public database of nucleotide sequences. However, as the length of the sequence to be retrieved increases such as a chromosome, entire genome, scaffold, etc., the elapsed time to download the file gets even elongated due to slower bandwidth to download/retrieve the sequence.[8] In most cases, during sequence analysis, the researcher requires messenger RNA (mRNA), RNA, DNA, protein sequences of the same sequence-of-interest to work with, which consumes a substantial amount of the researcher in finding and retrieving the sequence files. An access to GenBank through JAVA HTTPS protocols is established to request and receive the sequence files associated with the input accessions. SeqDown was shown to be much efficient in terms of retrieval time of the sequences as compared to the other internet browsers and was found to be 15.27% faster than Mozilla Firefox. SeqDown also provides the feature to retrieve coding DNA sequences & protein sequences present in a single chromosome. Sequence retrieval from the most biological databases don’t have proper naming of their files and the user has to deal with the redundantly named sequence files which leads to incorrect and time-consuming analysis and can be solved with SeqDown. SeqDown is available as a free-to-download software at https://bit.ly/3cUwchz
{"title":"SeqDown: An Efficient Sequence Retrieval Software and Comparative Sequence Retrieval Analysis","authors":"Waqar Hanif, Hijab Fatima, Muhammad Qasim, R. M. Atif, M. Javed","doi":"10.32350/cto.11.03","DOIUrl":"https://doi.org/10.32350/cto.11.03","url":null,"abstract":"For any sequence analysis procedure, a single or multiple sequence must be retrieved, stored, organized. One of the most common public databases used for biological sequence retrieval is GenBank which is a comprehensive public database of nucleotide sequences. However, as the length of the sequence to be retrieved increases such as a chromosome, entire genome, scaffold, etc., the elapsed time to download the file gets even elongated due to slower bandwidth to download/retrieve the sequence.[8] In most cases, during sequence analysis, the researcher requires messenger RNA (mRNA), RNA, DNA, protein sequences of the same sequence-of-interest to work with, which consumes a substantial amount of the researcher in finding and retrieving the sequence files. An access to GenBank through JAVA HTTPS protocols is established to request and receive the sequence files associated with the input accessions. SeqDown was shown to be much efficient in terms of retrieval time of the sequences as compared to the other internet browsers and was found to be 15.27% faster than Mozilla Firefox. SeqDown also provides the feature to retrieve coding DNA sequences & protein sequences present in a single chromosome. Sequence retrieval from the most biological databases don’t have proper naming of their files and the user has to deal with the redundantly named sequence files which leads to incorrect and time-consuming analysis and can be solved with SeqDown. SeqDown is available as a free-to-download software at https://bit.ly/3cUwchz","PeriodicalId":271898,"journal":{"name":"Current Trends in OMICS","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125288957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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