Sayan Paul is a Ph.D. graduate from Department of Biotechnology, Manonmaniam Sundaranar University, India. He is interested in the field of Genome sequencing, transcriptome sequencing and genome data analysis, annotation and creating the genome and transcriptome web resources illustrating the list of genes, their functions and associated pathways for the species having regeneration potential and clinical importance. Supervisors: Dr. Dhandapany Perundurai and Supervisor
Naunyn-Schmiedeberg's Archives of Pharmacology, 2022
Cancer is a complex disease affecting millions of people around the world. Despite advances in su... more Cancer is a complex disease affecting millions of people around the world. Despite advances in surgical and radiation therapy, chemotherapy continues to be an important therapeutic option for the treatment of cancer. The current treatment is expensive and has several side effects. Also, over time, cancer cells develop resistance to chemotherapy, due to which there is a demand for new drugs. Drug repurposing is a novel approach that focuses on finding new applications for the old clinically approved drugs. Current advances in the high-dimensional multiomics landscape, especially proteomics, genomics, and computational omics-data analysis, have facilitated drug repurposing. The drug repurposing approach provides cheaper, effective, and safe drugs with fewer side effects and fastens the process of drug development. The review further delineates each repurposed drug's original indication and mechanism of action in cancer. Along with this, the article also provides insight upon artificial intelligence and its application in drug repurposing. Clinical trials are vital for determining medication safety and effectiveness, and hence the clinical studies for each repurposed medicine in cancer, including their stages, status, and National Clinical Trial (NCT) identification, are reported in this review article. Various emerging evidences imply that repurposing drugs is critical for the faster and more affordable discovery of anti-cancerous drugs, and the advent of artificial intelligence-based computational tools can accelerate the translational cancer-targeting pipeline.
The cabbage butterfly, Pieris brassicae (L.) is an economically important cosmopolitan insect, th... more The cabbage butterfly, Pieris brassicae (L.) is an economically important cosmopolitan insect, that causes appreciable crop loss in cabbage, cauliflower and other cruciferous crops, especially during winter and early spring in India. To reduce its pest density, a granulovirus infecting Pieris brassicae (PibrGV) was found to be a promising eco-friendly pathogen in the present study. Our report describes the pathogenicity, structural details, genome sequence, and characterization of the PibrGV Manipur isolate. The median lethal concentration and survival time were calculated for the third instar larvae of P. brassicae and the bioassay revealed that LC 50 and LT 50 of the virus were found to be 4.8 x 10 4 OBs/ml and 120 hours, respectively. Post-purification of occlusion bodies, the viral DNA was extracted and subjected to genome sequencing and annotation. There were 128 Glimmer-predicted ORFs in the 106,469 bp long viral genome characterized by 33.7% GC content. The study further indicated that a total of 14 genes were involved in replication, 10 genes were associated with transcription and 24 genes were related to structure formation, respectively. The above database will help in understanding the molecular mechanisms and genetic makeup of the virus and assist in pest management strategies through recombinant DNA technology.
Public Health Review : International Journal of Public Health Research, 2020
In late 2019 the outbreak of a novel infectious coronavirus (SARS CoV2) which became globalpandem... more In late 2019 the outbreak of a novel infectious coronavirus (SARS CoV2) which became globalpandemic and named as Coronavirus disease (CoViD-19) World Health Organization (WHO). On 22March, 2020 the Prime Minister of India announced and 14 hours’ public curfew and from 24 March,2020 announced sudden complete lockdown. The sudden complete lockdown made changes in theliving habits and social behaviors of public. Web based survey was conducted among the Indianpopulation of different age groups to understand the impacts on dietary habits and health during thesudden complete lockdown in India.
Naunyn-Schmiedeberg's Archives of Pharmacology, 2022
Cancer is a complex disease affecting millions of people around the world. Despite advances in su... more Cancer is a complex disease affecting millions of people around the world. Despite advances in surgical and radiation therapy, chemotherapy continues to be an important therapeutic option for the treatment of cancer. The current treatment is expensive and has several side effects. Also, over time, cancer cells develop resistance to chemotherapy, due to which there is a demand for new drugs. Drug repurposing is a novel approach that focuses on finding new applications for the old clinically approved drugs. Current advances in the high-dimensional multiomics landscape, especially proteomics, genomics, and computational omics-data analysis, have facilitated drug repurposing. The drug repurposing approach provides cheaper, effective, and safe drugs with fewer side effects and fastens the process of drug development. The review further delineates each repurposed drug's original indication and mechanism of action in cancer. Along with this, the article also provides insight upon artificial intelligence and its application in drug repurposing. Clinical trials are vital for determining medication safety and effectiveness, and hence the clinical studies for each repurposed medicine in cancer, including their stages, status, and National Clinical Trial (NCT) identification, are reported in this review article. Various emerging evidences imply that repurposing drugs is critical for the faster and more affordable discovery of anti-cancerous drugs, and the advent of artificial intelligence-based computational tools can accelerate the translational cancer-targeting pipeline.
Purpose Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthwor... more Purpose Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result The FastqSifter sifted a total of 593,130 Ve...
The Escherichia coli phage CMSTMSU was isolated from shrimp farm effluent water in Ramanathapuram... more The Escherichia coli phage CMSTMSU was isolated from shrimp farm effluent water in Ramanathapuram, India. The phage exhibited lytic activity against both E. coli and the fish pathogen Pseudomonas aeruginosa. Here we report the draft genome sequence, assembly, and annotation of the isolated CMSTMSU phage. This genome resource can be used to utilize the phage as a crucial biocontrol agent in the fish aquaculture sector.
species 062011 msu is a harmful pathogenic strain responsible for causing abscessation in sheep a... more species 062011 msu is a harmful pathogenic strain responsible for causing abscessation in sheep and goat population studied by Mariappan et al. (2012) [1]. The organism specifically targets the female sheep and goat population and results in the reduction of milk and meat production. In the present study, we have performed the whole genome sequencing of the pathogenic isolate using the Ion Torrent sequencing platform and generated 458,944 raw reads with an average length of 198.2 bp. The genome sequence was assembled, annotated and analysed for the genetic islands, metabolic pathways, orthologous groups, virulence factors and antibiotic resistance genes associated with the pathogen. Simultaneously the 16S rRNA sequencing study and genome sequence comparison data confirmed that the strain belongs to the species and exhibits 99% sequence homo;logy with the genomes of ATCC 10987 and FRI-35. Hence, we have renamed the organism as 062011msu. The Whole Genome Shotgun (WGS) project has bee...
In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral ... more In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categ...
Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthwo... more Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods: We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result: The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search. Conclusion: The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.
Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost s... more Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost segments. The adult earthworm Eudrilus eugeniae contains 120 segments and the body segments of the earthworm are divided into pre-clitellar, clitellar and post-clitellar segments. The present study denoted that clitellum plays vital role in the successful regeneration of the species. We have performed histological studies to identify among the three skin layers of the earthworm, which cellular layer supports the blastema formation and regeneration of the species. The histological evidences denoted that the proliferation of the longitudinal cell layer at the amputation site is crucial for the successful regeneration of the earthworm and it takes place only in the presence of an intact clitellum. Besides we have performed clitellar transcriptome analysis of the earthworm Eudrilus eugeniae to monitor the key differentially expressed genes and their associated functions and pathways controlling the clitellar tissue changes during both anterior and posterior regeneration of the earthworm. A total of 4707 differentially expressed genes (DEGs) were identified between the control clitellum and clitellum of anterior regenerated earthworms and 4343 DEGs were detected between the control clitellum and clitellum of posterior regenerated earthworms. The functional enrichment analysis confirmed the genes regulating the muscle mass shape and structure were significantly downregulated and the genes associated with response to starvation and anterior-posterior axis specification were significantly upregulated in the clitellar tissue during both anterior and posterior regeneration of the earthworm. The RNA sequencing data of clitellum and the comparative transcriptomic analysis were helpful to understand the complex regeneration process of the earthworm.
Telomeres, the nucleoprotein structures, located at the end of the chromosomes are correlated wit... more Telomeres, the nucleoprotein structures, located at the end of the chromosomes are correlated with cancer and aging. The accelerated telomere attrition can accelerate human aging and leads to the progression of several cancers. Our work describes the finding of two novel telomeric repeats "CACAGA" and "TCTCTGCGCCTGCGCCGGCGCGGCGCGCC" and demonstrates their distribution in human chromosomes compare to the reported telomeric repeat TTAGGG. Simultaneously, the distance between the adjacent telomeric repeats (loop) was determined and the presence of shorter loops in the telomeric regions might address the correlation between the telomere attrition and senescence condition in human.
Indian Journal of Pharmaceutical Education and Research, 2021
Background: The advancement of plant biotechnology improved crop production by revolutionizing pl... more Background: The advancement of plant biotechnology improved crop production by revolutionizing plant science. Humans were commonly infected by Helicobacter pylori, and it was closely linked to stomach ulcers and cancer. In addition to traditional vaccines for H. pylori, transgenic plants have also been produced to produce its antigens as well as edible and non-edible parts that can produce an immune response after consumption. The protein present in H. pylori associated with virulence (iceA1) is believed to predispose to stomach cancer. Objectives: The current study was aimed to evaluate the iceA1 gene expression within brinjal plant to produce novel transgenic lines LC420461-B7,-B10,-B15,-B22 and-B27. Materials and Methods: In the present study, amplified iceA1 gene from H. pylori strain 26695 was transformed into callus of brinjal (from leaf explants) through Agrobacterium tumefacians (EHA105). pBI121 vector was used in constructing the plant expression vector, and the transgenics generated were further evaluated by quantitative Real-Time PCR and western blot analysis. Results: Out of the 46 plants obtained five of them were found to be positive for the iceA1 expression. Both real time and western blot confirmed of the presence of expressed gene iceA1 within the plant sample leaves. By studying transgenic brinjal, the study may result in an H. pylori vaccine candidate. As well, the data can be used by researchers to get valid scientific information.
Cardiac glycosides are natural sterols and constitute a group of secondary metabolites isolated f... more Cardiac glycosides are natural sterols and constitute a group of secondary metabolites isolated from plants and animals. These cardiotonic agents are well recognized and accepted in the treatment of various cardiac diseases as they can increase the rate of cardiac contractions by acting on the cellular sodium potassium ATPase pump. However, a growing number of recent efforts were focused on exploring the antitumor and antiviral potential of these compounds. Several reports suggest their antitumor properties and hence, today cardiac glycosides (CG) represent the most diversified naturally derived compounds strongly recommended for the treatment of various cancers. Mutated or dysregulated transcription factors have also gained prominence as potential therapeutic targets that can be selectively targeted. Thus, we have explored the recent advances in CGs mediated cancer scope and have considered various signaling pathways, molecular aberration, transcription factors (TFs), and oncogenic...
Bulletin of Environmental Contamination and Toxicology, 2021
In this study, pot-culture experiments were conducted to investigate the single effect of Cd, PCB... more In this study, pot-culture experiments were conducted to investigate the single effect of Cd, PCBs, and the combined effect of Cd-PCBs with Tagetes patula L. The study highlights that the minimum concentration of PCBs (100 µg kg −1) could enable the growth of the plant with an increase in biomass by 27.76% when compared with the control. In all the experiments performed, the Cd concentrations over the surface parts were found to be above 100 mg kg −1. Significant positive correlations were observed between the Cd and PCBs concentrations accumulated in tissues of the soil and plants (p < 0.05). T. patula exhibited high tolerance to Cd and PCBs, and the plant promoted the removal rate of PCBs. The removal rates of PCB18 and PCB28 were up to 42.72 and 42.29%, respectively. The study highlights the potential and suitability of T. patula for phytoremediation of Cd and PCBs in contaminated soils.
International Journal of Pharmaceutical Investigation, 2021
Background: Plant biotechnology revolutionized the branch of plant sciences contributing to impro... more Background: Plant biotechnology revolutionized the branch of plant sciences contributing to improving crop production. Helicobacter pylori was predominantly seen among all the sectors of the human population, closely stuck to stomach ulcers and cancer. Even though traditional vaccines are effective in preventing H. pylori, edible and non-edible parts of special transgenic plants were also being generated to express its antigens which could elicit an immune response after consuming. The induce by contact with epithelium (iceA1) protein of H. pylori is associated with virulence and stated as predisposing factor to stomach cancer. Objectives: This study intends to study the expression levels of iceA1 gene in the brinjal plant. Materials and Methods: The present study, magnified the iceA1 gene from H. pylori strain 26695 and transformed it into callus of brinjal (from leaf explants) through Agrobacterium tumefacians (EHA105). pBI121 vector was used to construct the plant expression vector, and the transgenic plants generated were further validated through gene amplification and protein expression studies. Results: Out of the 46 plants obtained from this study, five of them were found to be positive for the iceA1 expression as seen on validation assays like gene amplification and protein expression studies. Conclusion: The study could beneficially produce a vaccine candidate against H. pylori from transgenic brinjal. In Addition, it could provide, valid scientific data which can further be used by researchers.
Naunyn-Schmiedeberg's Archives of Pharmacology, 2022
Cancer is a complex disease affecting millions of people around the world. Despite advances in su... more Cancer is a complex disease affecting millions of people around the world. Despite advances in surgical and radiation therapy, chemotherapy continues to be an important therapeutic option for the treatment of cancer. The current treatment is expensive and has several side effects. Also, over time, cancer cells develop resistance to chemotherapy, due to which there is a demand for new drugs. Drug repurposing is a novel approach that focuses on finding new applications for the old clinically approved drugs. Current advances in the high-dimensional multiomics landscape, especially proteomics, genomics, and computational omics-data analysis, have facilitated drug repurposing. The drug repurposing approach provides cheaper, effective, and safe drugs with fewer side effects and fastens the process of drug development. The review further delineates each repurposed drug's original indication and mechanism of action in cancer. Along with this, the article also provides insight upon artificial intelligence and its application in drug repurposing. Clinical trials are vital for determining medication safety and effectiveness, and hence the clinical studies for each repurposed medicine in cancer, including their stages, status, and National Clinical Trial (NCT) identification, are reported in this review article. Various emerging evidences imply that repurposing drugs is critical for the faster and more affordable discovery of anti-cancerous drugs, and the advent of artificial intelligence-based computational tools can accelerate the translational cancer-targeting pipeline.
The cabbage butterfly, Pieris brassicae (L.) is an economically important cosmopolitan insect, th... more The cabbage butterfly, Pieris brassicae (L.) is an economically important cosmopolitan insect, that causes appreciable crop loss in cabbage, cauliflower and other cruciferous crops, especially during winter and early spring in India. To reduce its pest density, a granulovirus infecting Pieris brassicae (PibrGV) was found to be a promising eco-friendly pathogen in the present study. Our report describes the pathogenicity, structural details, genome sequence, and characterization of the PibrGV Manipur isolate. The median lethal concentration and survival time were calculated for the third instar larvae of P. brassicae and the bioassay revealed that LC 50 and LT 50 of the virus were found to be 4.8 x 10 4 OBs/ml and 120 hours, respectively. Post-purification of occlusion bodies, the viral DNA was extracted and subjected to genome sequencing and annotation. There were 128 Glimmer-predicted ORFs in the 106,469 bp long viral genome characterized by 33.7% GC content. The study further indicated that a total of 14 genes were involved in replication, 10 genes were associated with transcription and 24 genes were related to structure formation, respectively. The above database will help in understanding the molecular mechanisms and genetic makeup of the virus and assist in pest management strategies through recombinant DNA technology.
Public Health Review : International Journal of Public Health Research, 2020
In late 2019 the outbreak of a novel infectious coronavirus (SARS CoV2) which became globalpandem... more In late 2019 the outbreak of a novel infectious coronavirus (SARS CoV2) which became globalpandemic and named as Coronavirus disease (CoViD-19) World Health Organization (WHO). On 22March, 2020 the Prime Minister of India announced and 14 hours’ public curfew and from 24 March,2020 announced sudden complete lockdown. The sudden complete lockdown made changes in theliving habits and social behaviors of public. Web based survey was conducted among the Indianpopulation of different age groups to understand the impacts on dietary habits and health during thesudden complete lockdown in India.
Naunyn-Schmiedeberg's Archives of Pharmacology, 2022
Cancer is a complex disease affecting millions of people around the world. Despite advances in su... more Cancer is a complex disease affecting millions of people around the world. Despite advances in surgical and radiation therapy, chemotherapy continues to be an important therapeutic option for the treatment of cancer. The current treatment is expensive and has several side effects. Also, over time, cancer cells develop resistance to chemotherapy, due to which there is a demand for new drugs. Drug repurposing is a novel approach that focuses on finding new applications for the old clinically approved drugs. Current advances in the high-dimensional multiomics landscape, especially proteomics, genomics, and computational omics-data analysis, have facilitated drug repurposing. The drug repurposing approach provides cheaper, effective, and safe drugs with fewer side effects and fastens the process of drug development. The review further delineates each repurposed drug's original indication and mechanism of action in cancer. Along with this, the article also provides insight upon artificial intelligence and its application in drug repurposing. Clinical trials are vital for determining medication safety and effectiveness, and hence the clinical studies for each repurposed medicine in cancer, including their stages, status, and National Clinical Trial (NCT) identification, are reported in this review article. Various emerging evidences imply that repurposing drugs is critical for the faster and more affordable discovery of anti-cancerous drugs, and the advent of artificial intelligence-based computational tools can accelerate the translational cancer-targeting pipeline.
Purpose Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthwor... more Purpose Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result The FastqSifter sifted a total of 593,130 Ve...
The Escherichia coli phage CMSTMSU was isolated from shrimp farm effluent water in Ramanathapuram... more The Escherichia coli phage CMSTMSU was isolated from shrimp farm effluent water in Ramanathapuram, India. The phage exhibited lytic activity against both E. coli and the fish pathogen Pseudomonas aeruginosa. Here we report the draft genome sequence, assembly, and annotation of the isolated CMSTMSU phage. This genome resource can be used to utilize the phage as a crucial biocontrol agent in the fish aquaculture sector.
species 062011 msu is a harmful pathogenic strain responsible for causing abscessation in sheep a... more species 062011 msu is a harmful pathogenic strain responsible for causing abscessation in sheep and goat population studied by Mariappan et al. (2012) [1]. The organism specifically targets the female sheep and goat population and results in the reduction of milk and meat production. In the present study, we have performed the whole genome sequencing of the pathogenic isolate using the Ion Torrent sequencing platform and generated 458,944 raw reads with an average length of 198.2 bp. The genome sequence was assembled, annotated and analysed for the genetic islands, metabolic pathways, orthologous groups, virulence factors and antibiotic resistance genes associated with the pathogen. Simultaneously the 16S rRNA sequencing study and genome sequence comparison data confirmed that the strain belongs to the species and exhibits 99% sequence homo;logy with the genomes of ATCC 10987 and FRI-35. Hence, we have renamed the organism as 062011msu. The Whole Genome Shotgun (WGS) project has bee...
In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral ... more In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categ...
Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthwo... more Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods: We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result: The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search. Conclusion: The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.
Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost s... more Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost segments. The adult earthworm Eudrilus eugeniae contains 120 segments and the body segments of the earthworm are divided into pre-clitellar, clitellar and post-clitellar segments. The present study denoted that clitellum plays vital role in the successful regeneration of the species. We have performed histological studies to identify among the three skin layers of the earthworm, which cellular layer supports the blastema formation and regeneration of the species. The histological evidences denoted that the proliferation of the longitudinal cell layer at the amputation site is crucial for the successful regeneration of the earthworm and it takes place only in the presence of an intact clitellum. Besides we have performed clitellar transcriptome analysis of the earthworm Eudrilus eugeniae to monitor the key differentially expressed genes and their associated functions and pathways controlling the clitellar tissue changes during both anterior and posterior regeneration of the earthworm. A total of 4707 differentially expressed genes (DEGs) were identified between the control clitellum and clitellum of anterior regenerated earthworms and 4343 DEGs were detected between the control clitellum and clitellum of posterior regenerated earthworms. The functional enrichment analysis confirmed the genes regulating the muscle mass shape and structure were significantly downregulated and the genes associated with response to starvation and anterior-posterior axis specification were significantly upregulated in the clitellar tissue during both anterior and posterior regeneration of the earthworm. The RNA sequencing data of clitellum and the comparative transcriptomic analysis were helpful to understand the complex regeneration process of the earthworm.
Telomeres, the nucleoprotein structures, located at the end of the chromosomes are correlated wit... more Telomeres, the nucleoprotein structures, located at the end of the chromosomes are correlated with cancer and aging. The accelerated telomere attrition can accelerate human aging and leads to the progression of several cancers. Our work describes the finding of two novel telomeric repeats "CACAGA" and "TCTCTGCGCCTGCGCCGGCGCGGCGCGCC" and demonstrates their distribution in human chromosomes compare to the reported telomeric repeat TTAGGG. Simultaneously, the distance between the adjacent telomeric repeats (loop) was determined and the presence of shorter loops in the telomeric regions might address the correlation between the telomere attrition and senescence condition in human.
Indian Journal of Pharmaceutical Education and Research, 2021
Background: The advancement of plant biotechnology improved crop production by revolutionizing pl... more Background: The advancement of plant biotechnology improved crop production by revolutionizing plant science. Humans were commonly infected by Helicobacter pylori, and it was closely linked to stomach ulcers and cancer. In addition to traditional vaccines for H. pylori, transgenic plants have also been produced to produce its antigens as well as edible and non-edible parts that can produce an immune response after consumption. The protein present in H. pylori associated with virulence (iceA1) is believed to predispose to stomach cancer. Objectives: The current study was aimed to evaluate the iceA1 gene expression within brinjal plant to produce novel transgenic lines LC420461-B7,-B10,-B15,-B22 and-B27. Materials and Methods: In the present study, amplified iceA1 gene from H. pylori strain 26695 was transformed into callus of brinjal (from leaf explants) through Agrobacterium tumefacians (EHA105). pBI121 vector was used in constructing the plant expression vector, and the transgenics generated were further evaluated by quantitative Real-Time PCR and western blot analysis. Results: Out of the 46 plants obtained five of them were found to be positive for the iceA1 expression. Both real time and western blot confirmed of the presence of expressed gene iceA1 within the plant sample leaves. By studying transgenic brinjal, the study may result in an H. pylori vaccine candidate. As well, the data can be used by researchers to get valid scientific information.
Cardiac glycosides are natural sterols and constitute a group of secondary metabolites isolated f... more Cardiac glycosides are natural sterols and constitute a group of secondary metabolites isolated from plants and animals. These cardiotonic agents are well recognized and accepted in the treatment of various cardiac diseases as they can increase the rate of cardiac contractions by acting on the cellular sodium potassium ATPase pump. However, a growing number of recent efforts were focused on exploring the antitumor and antiviral potential of these compounds. Several reports suggest their antitumor properties and hence, today cardiac glycosides (CG) represent the most diversified naturally derived compounds strongly recommended for the treatment of various cancers. Mutated or dysregulated transcription factors have also gained prominence as potential therapeutic targets that can be selectively targeted. Thus, we have explored the recent advances in CGs mediated cancer scope and have considered various signaling pathways, molecular aberration, transcription factors (TFs), and oncogenic...
Bulletin of Environmental Contamination and Toxicology, 2021
In this study, pot-culture experiments were conducted to investigate the single effect of Cd, PCB... more In this study, pot-culture experiments were conducted to investigate the single effect of Cd, PCBs, and the combined effect of Cd-PCBs with Tagetes patula L. The study highlights that the minimum concentration of PCBs (100 µg kg −1) could enable the growth of the plant with an increase in biomass by 27.76% when compared with the control. In all the experiments performed, the Cd concentrations over the surface parts were found to be above 100 mg kg −1. Significant positive correlations were observed between the Cd and PCBs concentrations accumulated in tissues of the soil and plants (p < 0.05). T. patula exhibited high tolerance to Cd and PCBs, and the plant promoted the removal rate of PCBs. The removal rates of PCB18 and PCB28 were up to 42.72 and 42.29%, respectively. The study highlights the potential and suitability of T. patula for phytoremediation of Cd and PCBs in contaminated soils.
International Journal of Pharmaceutical Investigation, 2021
Background: Plant biotechnology revolutionized the branch of plant sciences contributing to impro... more Background: Plant biotechnology revolutionized the branch of plant sciences contributing to improving crop production. Helicobacter pylori was predominantly seen among all the sectors of the human population, closely stuck to stomach ulcers and cancer. Even though traditional vaccines are effective in preventing H. pylori, edible and non-edible parts of special transgenic plants were also being generated to express its antigens which could elicit an immune response after consuming. The induce by contact with epithelium (iceA1) protein of H. pylori is associated with virulence and stated as predisposing factor to stomach cancer. Objectives: This study intends to study the expression levels of iceA1 gene in the brinjal plant. Materials and Methods: The present study, magnified the iceA1 gene from H. pylori strain 26695 and transformed it into callus of brinjal (from leaf explants) through Agrobacterium tumefacians (EHA105). pBI121 vector was used to construct the plant expression vector, and the transgenic plants generated were further validated through gene amplification and protein expression studies. Results: Out of the 46 plants obtained from this study, five of them were found to be positive for the iceA1 expression as seen on validation assays like gene amplification and protein expression studies. Conclusion: The study could beneficially produce a vaccine candidate against H. pylori from transgenic brinjal. In Addition, it could provide, valid scientific data which can further be used by researchers.
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Papers by Dr. Sayan Paul