Pandemic influenza A (H1N1) 2009 virus was first
detected in India in May 2009 which subsequently... more Pandemic influenza A (H1N1) 2009 virus was first detected in India in May 2009 which subsequently became endemic in many parts of the country. Influenza A viruses have the ability to evade the immune response through its ability of antigenic variations. The study aims to characterize influenza A (H1N1) pdm 09 viruses circulating in Mumbai during the pandemic and post-pandemic period. Nasopharyngeal swabs positive for influenza A (H1N1) pdm 09 viruses were inoculated on Madin–Darby canine kidney cell line for virus isolation. Molecular and phylogenetic analysis of influenza A (H1N1) pdm 09 isolates was conducted to understand the evolution and genetic diversity of the strains. Nucleotide and amino acid sequences of the HA gene of Mumbai isolates when compared to A/California/07/2009- vaccine strain revealed 14 specific amino acid differences located at the antigenic sites. Amino acid variations in HA and NA gene resulted in changes in the N-linked glycosylation motif which may lead to immune evasion. Phylogenetic analysis of the isolates revealed their evolutionary position with vaccine strain A/California/07/2009 but had undergone changes gradually. The findings in the present study confirm genetic variability of influenza viruses and highlight the importance of continuous surveillance during influenza outbreaks
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bi... more The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution. " Nature's stern discipline enjoins mutual help at least as often as warfare. The fittest may also be the gentlest. " as proclaimed by Theodosius Dobzhansky on mankind evolution, like galaxy formations, the evolution of human remains the generation long grit of thinkers. Non-recombining loci, such as the maternally inherited mitochon-drial DNA have been known to provide a richer estimation insight into ancestral human genetic variations during evolution 1. Mitochondrial DNA is highly polymorphic, and its diverse nature in humans may contribute to individual differences in function 2,3. Sequence variations considered in human mtDNA are selectively neutral 4. Under this assumption, the pool of mutations that enter a population and are subsequently fixed by the selection or by the stochastic process of genetic drift will differ across populations 5,6. Conversely, mtDNA polymorphism might also have been shaped via positive selection because of mito-nuclear co-evolution 7. The evidence in support of mtDNA sequence polymorphism affecting phenotypic variation in metabolism, life-history traits and fitness is compelling 8. In retrospect, several studies were carried out that highlighted the role of natural selection and genetic drift on the diversity and divergence of mtDNA 2. The methods based on phylogenetics, distances among sequences and clustering have successfully classified various traits and migrational events in human population 9. Furthermore, genome wide studies and mapping techniques, such as quantitative trait loci and linkage disequilibrium have effectively sorted genes and alleles among the population as well as a linked group of single nucleotide polymor-phisms (SNPs), as a causing agent 8,10. With the above advent of techniques, various probabilistic and machine learning based efforts have been made to measure the rate at which different types of mutation occur. Besides that these efforts have helped not only to predict quantitatively subsequent fate of mutations in populations but also to assess the way mutations affect some properties of population 8. Mutation in mtDNA is attributed to its protein-coding part 11 because a large portion of non-coding mtDNA is directly known to co-evolve with coding mtDNA 6,12. Independent dispersal of evolutionary signatures in mtDNA and extent of their conservation in human sub-populations are critical to understand complex mitochondrial evolution and formation of genetic
Human influenza is a seasonal disease associated with significant morbidity and mortality. Anti-f... more Human influenza is a seasonal disease associated with significant morbidity and mortality. Anti-flu ayurvedic/herbal medicines have played a significant role in fighting the virus pandemic. Plumbagin and allicin are commonly used ingredients in many therapeutic remedies, either alone or in conjunction with other natural substances. Evidence suggests that these extracts are associated with a variety of pharmacological activities. To evaluate anti-influenza activity from Plumbago indica and Allium sativum extract against Influenza A (H1N1)pdm09. Different extraction procedures were used to isolate the active ingredient in the solvent system, and quantitative HPLTC confirms the presence of plumbagin and allicin. The cytotoxicity was carried out on Madin-Darby Canine kidney cells, and the 50% cytotoxic concentration (CC50) values were below 20 mg/mL for both plant extracts. To assess the anti-influenza activity, two assays were employed, simultaneous and posttreatment assay. A. sativum methanolic and ethanolic extracts showed only 14% reduction in hemagglutination in contrast to P. indica which exhibited 100% reduction in both simultaneous and posttreatment assay at concentrations of 10 mg/mL, 5 mg/mL, and 1 mg/mL. Our results suggest that P. indica extracts are good candidates for anti-influenza therapy and should be used in medical treatment after further research. The search for natural antiviral compounds from plants is a promising approach in the development of new therapeutic agents. In the past century, several scientific efforts have been directed toward identifying phytochemicals capable of inhibiting virus. Knowledge of ethnopharmacology can lead to new bioactive plant compounds suitable for drug discovery and development. Macromolecular docking studies provides most detailed possible view of drug-receptor interaction where the structure of drug is designed based on its fit to three dimensional structures of receptor site rather than by analogy to other active structures or random leads. Our previous studies indicate that Allicin sand Plumbagin could be used as the potent multi drug targets against the Neuraminidase, Hemagglutinin and M2 protein channel of influenza A (H1N1) pdm09. This in-vittro study has shown that P. indica L. and A. sativum extracts can inhibit influenza A (H1N1)pdm09 virus by inhibiting viral nucleoprotein synthesis and polymerase activity.
Molecular networks act as the backbone of cellular activities, providing an excellent
opportunit... more Molecular networks act as the backbone of cellular activities, providing an excellent
opportunity to understand the developmental changes in an organism. While network data usually
constitute only stationary network graphs, constructing a multilayer PPI network may provide
clues to the particular developmental role at each stage of life and may unravel the importance
of these developmental changes. The developmental biology model of Caenorhabditis elegans
analyzed here provides a ripe platform to understand the patterns of evolution during the life
stages of an organism. In the present study, the widely studied network properties exhibit overall
similar statistics for all the PPI layers. Further, the analysis of the degree-degree correlation
and spectral properties not only reveals crucial differences in each PPI layer but also indicates
the presence of the varying complexity among them. The PPI layer of the nematode life stage
exhibits various network properties different to the rest of the PPI layers, indicating the specific
role of cellular diversity and developmental transitions at this stage. The framework presented
here provides a direction to explore and understand the developmental changes occurring in the
different life stages of an organism.
The global rise in dengue cases is a major public health concern in terms of morbidity and mortal... more The global rise in dengue cases is a major public health concern in terms of morbidity and mortality. The recent study reports 390 million dengue infections annually of which 96 million infections becomes clinically or subclinically severe. Therefore, development of an effective tetravalent vaccine against dengue is a top priority. Dengue envelope domain III is a surface exposed protein; involved in host cell binding and containing multiple, serotype-specific and subcomplex-specific neutralizing epitopes, thus becomes an ideal target for vaccine development. The rapid growth in bioinformatics or immunoinformatics area in terms of development of sophisticated tools assists researchers to predict immunodominant epitopes and study various characteristics of the predicted vaccine model. The combination of computer-aided or in silico methods and experimental methods are useful tools to address complex problems such as deciphering immune responses and vaccine design. In the present study ...
More than 300 000 new cases worldwide are being diagnosed with oral cancer annually. Complexity
... more More than 300 000 new cases worldwide are being diagnosed with oral cancer annually. Complexity
of oral cancer renders designing drug targets very difficult. We analyse protein-protein interaction
network for the normal and oral cancer tissue and detect crucial changes in the structural properties of
the networks in terms of the interactions of the hub proteins and the degree-degree correlations. Further
analysis of the spectra of both the networks, while exhibiting universal statistical behaviour, manifest
distinction in terms of the zero degeneracy, providing insight to the complexity of the underlying system.
Background: Oseltamivir is an important antiviral agent for controlling the transmission and diss... more Background: Oseltamivir is an important antiviral agent for controlling the transmission and dissemination of influenza viruses. The emergence and widespread occurrence of oseltamivir-resistant A (H1N1) viruses are of major concern. Information on drug susceptibility of seasonal influenza A viruses in India is limited. To understand the genetic background of antiviral drug-resistance, we performed sequence analysis of seasonal influenza A viruses circulating during 2009 pandemic influenza in Mumbai. Methods: Nasopharyngealswabs positive for seasonal influenza A virus by real time reverse transcriptase polymerase chain reaction were inoculated on Madin-Darby canine kidney (MDCK) cell line for virus isolation. Molecular analysis of hemagglutinin (HA), neuraminidase (NA) and matrix (M2) genes was used to detect known mutations contributing to resistance. Resistance to neuraminidase was assayed using a commercially available chemiluminescence based NA-Star Influenza Neuraminidase Inhibi...
Recent studies and the analysis of sequenced proteome have been providing important insights into... more Recent studies and the analysis of sequenced proteome have been providing important insights into the Streptococcus suis. The current study based on complete proteome information of S. suis available in biological databases to identify putative protein targets. In this study, subtraction of S. suis and human proteome provided essential proteins which are unique to pathogen and absent in the host hence can be safely used as target in the drug development process. Total proteome of S. suis contain 482 proteins of which 37 proteins are unique in the pathogen and among these 16 proteins play an important role in the cellular pathways and membrane associated works. All the non-homologous essential proteins were characterized for differential metabolic pathways. We also suggested 7 novel protein targets in the S. suis having crucial role in the cellular pathways.
Journal of Computational Intelligence in Bioinformatics, Sep 10, 2013
Biological data is growing in dramatic way. Human genome project and
bioinformatics algorithms l... more Biological data is growing in dramatic way. Human genome project and
bioinformatics algorithms lead to the development in the computational
biology tools and databases. Research in computational biology depends
critically on access to biological sequences, databases and outputs of various
bioinformatics tools. Various bioprogramming modules are constructed to
speed up the bioinformatics tool development. Bioprogramming tools are
available for windows, Linux, UNIX and macOS platforms. These modules
are easy to use by anyone and can effectively be amalgamated with the tools
for the versatile use. These packages still need of continuous development and
modification to compete with the expansion of data.
The present study deals with the screening of antimicrobial principles of mangroves species, Rhiz... more The present study deals with the screening of antimicrobial principles of mangroves species, Rhizophora mucronata and Rhizophora apiculata
occurring along Mumbai coast. The cold and hot extracts of these mangrove species were prepared in different solvents i.e. methanol, ethanol and
tested against gram positive and gram negative bacteria and one fungi, C.albicans. The minimum inhibitory concentration (MIC) and
characterization of bioactive compounds were carried out. Overall results suggested that R.apiculata contain both thermolabile and thermostable
bioactive principles of broad spectrum activity while R.mucronata contains only antibacterial compounds of moderate to mild potency. Highly
potent antimicrobial were observed in cold stem extracts of R.mucronata active against E.coli , S.aureus and S.typhi as MIC was 0.5 mg/ml against
this microorganism in this part of the plants .
Scholars research library, European Journal of zoological Research
The principal objective of the present research work was to determine the antibacterial potential... more The principal objective of the present research work was to determine the antibacterial potential of A. marmelos
against four standard pathogenic bacterial strains. To evaluate antibacterial activity the agar-well diffusion assay
was used. All the four extracts showed the highest and significant antibacterial activity against both Gram negative
and Gram-positive bacteria. It is the strain Bacillus subtilis that is almost resistant to the four extracts of A.
marmelos
Pandemic influenza A (H1N1) 2009 virus was first
detected in India in May 2009 which subsequently... more Pandemic influenza A (H1N1) 2009 virus was first detected in India in May 2009 which subsequently became endemic in many parts of the country. Influenza A viruses have the ability to evade the immune response through its ability of antigenic variations. The study aims to characterize influenza A (H1N1) pdm 09 viruses circulating in Mumbai during the pandemic and post-pandemic period. Nasopharyngeal swabs positive for influenza A (H1N1) pdm 09 viruses were inoculated on Madin–Darby canine kidney cell line for virus isolation. Molecular and phylogenetic analysis of influenza A (H1N1) pdm 09 isolates was conducted to understand the evolution and genetic diversity of the strains. Nucleotide and amino acid sequences of the HA gene of Mumbai isolates when compared to A/California/07/2009- vaccine strain revealed 14 specific amino acid differences located at the antigenic sites. Amino acid variations in HA and NA gene resulted in changes in the N-linked glycosylation motif which may lead to immune evasion. Phylogenetic analysis of the isolates revealed their evolutionary position with vaccine strain A/California/07/2009 but had undergone changes gradually. The findings in the present study confirm genetic variability of influenza viruses and highlight the importance of continuous surveillance during influenza outbreaks
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bi... more The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution. " Nature's stern discipline enjoins mutual help at least as often as warfare. The fittest may also be the gentlest. " as proclaimed by Theodosius Dobzhansky on mankind evolution, like galaxy formations, the evolution of human remains the generation long grit of thinkers. Non-recombining loci, such as the maternally inherited mitochon-drial DNA have been known to provide a richer estimation insight into ancestral human genetic variations during evolution 1. Mitochondrial DNA is highly polymorphic, and its diverse nature in humans may contribute to individual differences in function 2,3. Sequence variations considered in human mtDNA are selectively neutral 4. Under this assumption, the pool of mutations that enter a population and are subsequently fixed by the selection or by the stochastic process of genetic drift will differ across populations 5,6. Conversely, mtDNA polymorphism might also have been shaped via positive selection because of mito-nuclear co-evolution 7. The evidence in support of mtDNA sequence polymorphism affecting phenotypic variation in metabolism, life-history traits and fitness is compelling 8. In retrospect, several studies were carried out that highlighted the role of natural selection and genetic drift on the diversity and divergence of mtDNA 2. The methods based on phylogenetics, distances among sequences and clustering have successfully classified various traits and migrational events in human population 9. Furthermore, genome wide studies and mapping techniques, such as quantitative trait loci and linkage disequilibrium have effectively sorted genes and alleles among the population as well as a linked group of single nucleotide polymor-phisms (SNPs), as a causing agent 8,10. With the above advent of techniques, various probabilistic and machine learning based efforts have been made to measure the rate at which different types of mutation occur. Besides that these efforts have helped not only to predict quantitatively subsequent fate of mutations in populations but also to assess the way mutations affect some properties of population 8. Mutation in mtDNA is attributed to its protein-coding part 11 because a large portion of non-coding mtDNA is directly known to co-evolve with coding mtDNA 6,12. Independent dispersal of evolutionary signatures in mtDNA and extent of their conservation in human sub-populations are critical to understand complex mitochondrial evolution and formation of genetic
Human influenza is a seasonal disease associated with significant morbidity and mortality. Anti-f... more Human influenza is a seasonal disease associated with significant morbidity and mortality. Anti-flu ayurvedic/herbal medicines have played a significant role in fighting the virus pandemic. Plumbagin and allicin are commonly used ingredients in many therapeutic remedies, either alone or in conjunction with other natural substances. Evidence suggests that these extracts are associated with a variety of pharmacological activities. To evaluate anti-influenza activity from Plumbago indica and Allium sativum extract against Influenza A (H1N1)pdm09. Different extraction procedures were used to isolate the active ingredient in the solvent system, and quantitative HPLTC confirms the presence of plumbagin and allicin. The cytotoxicity was carried out on Madin-Darby Canine kidney cells, and the 50% cytotoxic concentration (CC50) values were below 20 mg/mL for both plant extracts. To assess the anti-influenza activity, two assays were employed, simultaneous and posttreatment assay. A. sativum methanolic and ethanolic extracts showed only 14% reduction in hemagglutination in contrast to P. indica which exhibited 100% reduction in both simultaneous and posttreatment assay at concentrations of 10 mg/mL, 5 mg/mL, and 1 mg/mL. Our results suggest that P. indica extracts are good candidates for anti-influenza therapy and should be used in medical treatment after further research. The search for natural antiviral compounds from plants is a promising approach in the development of new therapeutic agents. In the past century, several scientific efforts have been directed toward identifying phytochemicals capable of inhibiting virus. Knowledge of ethnopharmacology can lead to new bioactive plant compounds suitable for drug discovery and development. Macromolecular docking studies provides most detailed possible view of drug-receptor interaction where the structure of drug is designed based on its fit to three dimensional structures of receptor site rather than by analogy to other active structures or random leads. Our previous studies indicate that Allicin sand Plumbagin could be used as the potent multi drug targets against the Neuraminidase, Hemagglutinin and M2 protein channel of influenza A (H1N1) pdm09. This in-vittro study has shown that P. indica L. and A. sativum extracts can inhibit influenza A (H1N1)pdm09 virus by inhibiting viral nucleoprotein synthesis and polymerase activity.
Molecular networks act as the backbone of cellular activities, providing an excellent
opportunit... more Molecular networks act as the backbone of cellular activities, providing an excellent
opportunity to understand the developmental changes in an organism. While network data usually
constitute only stationary network graphs, constructing a multilayer PPI network may provide
clues to the particular developmental role at each stage of life and may unravel the importance
of these developmental changes. The developmental biology model of Caenorhabditis elegans
analyzed here provides a ripe platform to understand the patterns of evolution during the life
stages of an organism. In the present study, the widely studied network properties exhibit overall
similar statistics for all the PPI layers. Further, the analysis of the degree-degree correlation
and spectral properties not only reveals crucial differences in each PPI layer but also indicates
the presence of the varying complexity among them. The PPI layer of the nematode life stage
exhibits various network properties different to the rest of the PPI layers, indicating the specific
role of cellular diversity and developmental transitions at this stage. The framework presented
here provides a direction to explore and understand the developmental changes occurring in the
different life stages of an organism.
The global rise in dengue cases is a major public health concern in terms of morbidity and mortal... more The global rise in dengue cases is a major public health concern in terms of morbidity and mortality. The recent study reports 390 million dengue infections annually of which 96 million infections becomes clinically or subclinically severe. Therefore, development of an effective tetravalent vaccine against dengue is a top priority. Dengue envelope domain III is a surface exposed protein; involved in host cell binding and containing multiple, serotype-specific and subcomplex-specific neutralizing epitopes, thus becomes an ideal target for vaccine development. The rapid growth in bioinformatics or immunoinformatics area in terms of development of sophisticated tools assists researchers to predict immunodominant epitopes and study various characteristics of the predicted vaccine model. The combination of computer-aided or in silico methods and experimental methods are useful tools to address complex problems such as deciphering immune responses and vaccine design. In the present study ...
More than 300 000 new cases worldwide are being diagnosed with oral cancer annually. Complexity
... more More than 300 000 new cases worldwide are being diagnosed with oral cancer annually. Complexity
of oral cancer renders designing drug targets very difficult. We analyse protein-protein interaction
network for the normal and oral cancer tissue and detect crucial changes in the structural properties of
the networks in terms of the interactions of the hub proteins and the degree-degree correlations. Further
analysis of the spectra of both the networks, while exhibiting universal statistical behaviour, manifest
distinction in terms of the zero degeneracy, providing insight to the complexity of the underlying system.
Background: Oseltamivir is an important antiviral agent for controlling the transmission and diss... more Background: Oseltamivir is an important antiviral agent for controlling the transmission and dissemination of influenza viruses. The emergence and widespread occurrence of oseltamivir-resistant A (H1N1) viruses are of major concern. Information on drug susceptibility of seasonal influenza A viruses in India is limited. To understand the genetic background of antiviral drug-resistance, we performed sequence analysis of seasonal influenza A viruses circulating during 2009 pandemic influenza in Mumbai. Methods: Nasopharyngealswabs positive for seasonal influenza A virus by real time reverse transcriptase polymerase chain reaction were inoculated on Madin-Darby canine kidney (MDCK) cell line for virus isolation. Molecular analysis of hemagglutinin (HA), neuraminidase (NA) and matrix (M2) genes was used to detect known mutations contributing to resistance. Resistance to neuraminidase was assayed using a commercially available chemiluminescence based NA-Star Influenza Neuraminidase Inhibi...
Recent studies and the analysis of sequenced proteome have been providing important insights into... more Recent studies and the analysis of sequenced proteome have been providing important insights into the Streptococcus suis. The current study based on complete proteome information of S. suis available in biological databases to identify putative protein targets. In this study, subtraction of S. suis and human proteome provided essential proteins which are unique to pathogen and absent in the host hence can be safely used as target in the drug development process. Total proteome of S. suis contain 482 proteins of which 37 proteins are unique in the pathogen and among these 16 proteins play an important role in the cellular pathways and membrane associated works. All the non-homologous essential proteins were characterized for differential metabolic pathways. We also suggested 7 novel protein targets in the S. suis having crucial role in the cellular pathways.
Journal of Computational Intelligence in Bioinformatics, Sep 10, 2013
Biological data is growing in dramatic way. Human genome project and
bioinformatics algorithms l... more Biological data is growing in dramatic way. Human genome project and
bioinformatics algorithms lead to the development in the computational
biology tools and databases. Research in computational biology depends
critically on access to biological sequences, databases and outputs of various
bioinformatics tools. Various bioprogramming modules are constructed to
speed up the bioinformatics tool development. Bioprogramming tools are
available for windows, Linux, UNIX and macOS platforms. These modules
are easy to use by anyone and can effectively be amalgamated with the tools
for the versatile use. These packages still need of continuous development and
modification to compete with the expansion of data.
The present study deals with the screening of antimicrobial principles of mangroves species, Rhiz... more The present study deals with the screening of antimicrobial principles of mangroves species, Rhizophora mucronata and Rhizophora apiculata
occurring along Mumbai coast. The cold and hot extracts of these mangrove species were prepared in different solvents i.e. methanol, ethanol and
tested against gram positive and gram negative bacteria and one fungi, C.albicans. The minimum inhibitory concentration (MIC) and
characterization of bioactive compounds were carried out. Overall results suggested that R.apiculata contain both thermolabile and thermostable
bioactive principles of broad spectrum activity while R.mucronata contains only antibacterial compounds of moderate to mild potency. Highly
potent antimicrobial were observed in cold stem extracts of R.mucronata active against E.coli , S.aureus and S.typhi as MIC was 0.5 mg/ml against
this microorganism in this part of the plants .
Scholars research library, European Journal of zoological Research
The principal objective of the present research work was to determine the antibacterial potential... more The principal objective of the present research work was to determine the antibacterial potential of A. marmelos
against four standard pathogenic bacterial strains. To evaluate antibacterial activity the agar-well diffusion assay
was used. All the four extracts showed the highest and significant antibacterial activity against both Gram negative
and Gram-positive bacteria. It is the strain Bacillus subtilis that is almost resistant to the four extracts of A.
marmelos
Uploads
Papers by Pramod Shinde
detected in India in May 2009 which subsequently became
endemic in many parts of the country. Influenza A viruses
have the ability to evade the immune response through its
ability of antigenic variations. The study aims to characterize
influenza A (H1N1) pdm 09 viruses circulating in Mumbai
during the pandemic and post-pandemic period. Nasopharyngeal swabs positive for influenza A (H1N1) pdm 09
viruses were inoculated on Madin–Darby canine kidney cell
line for virus isolation. Molecular and phylogenetic analysis
of influenza A (H1N1) pdm 09 isolates was conducted to
understand the evolution and genetic diversity of the strains.
Nucleotide and amino acid sequences of the HA gene of
Mumbai isolates when compared to A/California/07/2009-
vaccine strain revealed 14 specific amino acid differences
located at the antigenic sites. Amino acid variations in HA
and NA gene resulted in changes in the N-linked glycosylation motif which may lead to immune evasion. Phylogenetic analysis of the isolates revealed their evolutionary
position with vaccine strain A/California/07/2009 but had
undergone changes gradually. The findings in the present
study confirm genetic variability of influenza viruses and
highlight the importance of continuous surveillance during
influenza outbreaks
opportunity to understand the developmental changes in an organism. While network data usually
constitute only stationary network graphs, constructing a multilayer PPI network may provide
clues to the particular developmental role at each stage of life and may unravel the importance
of these developmental changes. The developmental biology model of Caenorhabditis elegans
analyzed here provides a ripe platform to understand the patterns of evolution during the life
stages of an organism. In the present study, the widely studied network properties exhibit overall
similar statistics for all the PPI layers. Further, the analysis of the degree-degree correlation
and spectral properties not only reveals crucial differences in each PPI layer but also indicates
the presence of the varying complexity among them. The PPI layer of the nematode life stage
exhibits various network properties different to the rest of the PPI layers, indicating the specific
role of cellular diversity and developmental transitions at this stage. The framework presented
here provides a direction to explore and understand the developmental changes occurring in the
different life stages of an organism.
of oral cancer renders designing drug targets very difficult. We analyse protein-protein interaction
network for the normal and oral cancer tissue and detect crucial changes in the structural properties of
the networks in terms of the interactions of the hub proteins and the degree-degree correlations. Further
analysis of the spectra of both the networks, while exhibiting universal statistical behaviour, manifest
distinction in terms of the zero degeneracy, providing insight to the complexity of the underlying system.
bioinformatics algorithms lead to the development in the computational
biology tools and databases. Research in computational biology depends
critically on access to biological sequences, databases and outputs of various
bioinformatics tools. Various bioprogramming modules are constructed to
speed up the bioinformatics tool development. Bioprogramming tools are
available for windows, Linux, UNIX and macOS platforms. These modules
are easy to use by anyone and can effectively be amalgamated with the tools
for the versatile use. These packages still need of continuous development and
modification to compete with the expansion of data.
occurring along Mumbai coast. The cold and hot extracts of these mangrove species were prepared in different solvents i.e. methanol, ethanol and
tested against gram positive and gram negative bacteria and one fungi, C.albicans. The minimum inhibitory concentration (MIC) and
characterization of bioactive compounds were carried out. Overall results suggested that R.apiculata contain both thermolabile and thermostable
bioactive principles of broad spectrum activity while R.mucronata contains only antibacterial compounds of moderate to mild potency. Highly
potent antimicrobial were observed in cold stem extracts of R.mucronata active against E.coli , S.aureus and S.typhi as MIC was 0.5 mg/ml against
this microorganism in this part of the plants .
against four standard pathogenic bacterial strains. To evaluate antibacterial activity the agar-well diffusion assay
was used. All the four extracts showed the highest and significant antibacterial activity against both Gram negative
and Gram-positive bacteria. It is the strain Bacillus subtilis that is almost resistant to the four extracts of A.
marmelos
detected in India in May 2009 which subsequently became
endemic in many parts of the country. Influenza A viruses
have the ability to evade the immune response through its
ability of antigenic variations. The study aims to characterize
influenza A (H1N1) pdm 09 viruses circulating in Mumbai
during the pandemic and post-pandemic period. Nasopharyngeal swabs positive for influenza A (H1N1) pdm 09
viruses were inoculated on Madin–Darby canine kidney cell
line for virus isolation. Molecular and phylogenetic analysis
of influenza A (H1N1) pdm 09 isolates was conducted to
understand the evolution and genetic diversity of the strains.
Nucleotide and amino acid sequences of the HA gene of
Mumbai isolates when compared to A/California/07/2009-
vaccine strain revealed 14 specific amino acid differences
located at the antigenic sites. Amino acid variations in HA
and NA gene resulted in changes in the N-linked glycosylation motif which may lead to immune evasion. Phylogenetic analysis of the isolates revealed their evolutionary
position with vaccine strain A/California/07/2009 but had
undergone changes gradually. The findings in the present
study confirm genetic variability of influenza viruses and
highlight the importance of continuous surveillance during
influenza outbreaks
opportunity to understand the developmental changes in an organism. While network data usually
constitute only stationary network graphs, constructing a multilayer PPI network may provide
clues to the particular developmental role at each stage of life and may unravel the importance
of these developmental changes. The developmental biology model of Caenorhabditis elegans
analyzed here provides a ripe platform to understand the patterns of evolution during the life
stages of an organism. In the present study, the widely studied network properties exhibit overall
similar statistics for all the PPI layers. Further, the analysis of the degree-degree correlation
and spectral properties not only reveals crucial differences in each PPI layer but also indicates
the presence of the varying complexity among them. The PPI layer of the nematode life stage
exhibits various network properties different to the rest of the PPI layers, indicating the specific
role of cellular diversity and developmental transitions at this stage. The framework presented
here provides a direction to explore and understand the developmental changes occurring in the
different life stages of an organism.
of oral cancer renders designing drug targets very difficult. We analyse protein-protein interaction
network for the normal and oral cancer tissue and detect crucial changes in the structural properties of
the networks in terms of the interactions of the hub proteins and the degree-degree correlations. Further
analysis of the spectra of both the networks, while exhibiting universal statistical behaviour, manifest
distinction in terms of the zero degeneracy, providing insight to the complexity of the underlying system.
bioinformatics algorithms lead to the development in the computational
biology tools and databases. Research in computational biology depends
critically on access to biological sequences, databases and outputs of various
bioinformatics tools. Various bioprogramming modules are constructed to
speed up the bioinformatics tool development. Bioprogramming tools are
available for windows, Linux, UNIX and macOS platforms. These modules
are easy to use by anyone and can effectively be amalgamated with the tools
for the versatile use. These packages still need of continuous development and
modification to compete with the expansion of data.
occurring along Mumbai coast. The cold and hot extracts of these mangrove species were prepared in different solvents i.e. methanol, ethanol and
tested against gram positive and gram negative bacteria and one fungi, C.albicans. The minimum inhibitory concentration (MIC) and
characterization of bioactive compounds were carried out. Overall results suggested that R.apiculata contain both thermolabile and thermostable
bioactive principles of broad spectrum activity while R.mucronata contains only antibacterial compounds of moderate to mild potency. Highly
potent antimicrobial were observed in cold stem extracts of R.mucronata active against E.coli , S.aureus and S.typhi as MIC was 0.5 mg/ml against
this microorganism in this part of the plants .
against four standard pathogenic bacterial strains. To evaluate antibacterial activity the agar-well diffusion assay
was used. All the four extracts showed the highest and significant antibacterial activity against both Gram negative
and Gram-positive bacteria. It is the strain Bacillus subtilis that is almost resistant to the four extracts of A.
marmelos