Chlorophytum borivilianum is a very popular herb in traditional Indian medicine and used as a pot... more Chlorophytum borivilianum is a very popular herb in traditional Indian medicine and used as a potent "Rasayana" drug in "Ayurveda" as a rejuvenator. Currently, a large body of evidence supports the key role of free radicals in diverse pathological conditions such as aging and atherosclerosis. The present investigation essentially focuses on the comprehensive account of in vitro antioxidant activity exerted by C.borivilianum root extracts (i.e., aqueous and ethanolic), to clarify the pharmacological antagonism of chemicals/metals-mediated oxidation. Graded-dose (25 to 1000 microg/ml) of aqueous extract exhibited higher antioxidant potency as evidenced by powerful nitric oxide, superoxide, hydroxyl, DPPH and ABTS(*+) radicals scavenging activity along with reducing capacity (Fe(3+)/ferricyanide complex and FRAP assays), metal chelating ability, as well as markedly suppressed the lipid peroxidation in mitochondrial fractions as compared to ethanolic extract. Further, aqueous extract significantly decreased (P < 0.05) copper-mediated human serum and kinetics of LDL oxidation, as demonstrated by prolongation of lag phase time with decline of oxidation rate, conjugated dienes, lipid hydroperoxides and thiobarbituric acid reactive substances. In addition, the total polyphenol and flavonoid contents of aqueous extract were higher than that of ethanolic extract, which indicated a positive correlation between antioxidant activity and contents of total phenols. The IC(50) values of both extracts were also compared with appropriate antioxidant standards. Overall, aqueous extract of C.borivilianum root has significant powerful antioxidant activity and may favorably affect atherosclerosis risk status by reducing LDL oxidation susceptibility.
Cyanobacteria trap light energy by arrays of pigment molecules termed "phycobilisomes (PBSs)", or... more Cyanobacteria trap light energy by arrays of pigment molecules termed "phycobilisomes (PBSs)", organized proximal to "reaction centers" at which chlorophyll perform the energy transduction steps with highest quantum efficiency. PBSs, composed of sequential assembly of various chromophorylated phycobiliproteins (PBPs), as well as nonchromophoric, basic and hydrophobic polypeptides called linkers. Atomic resolution structure of PBP is a heterodimer of two structurally related polypeptides but distinct specialised polypeptides- a and ß, made up of seven alpha-helices each which played a crucial step in evolution of PBPs. PBPs carry out various light dependent responses such as complementary chromatic adaptation. The aim of this review is to summarize and discuss the recent progress in this field and to highlight the new and the questions that remain unresolved.
Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds due to their high hydro... more Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds due to their high hydrophobicity and tendency to partition in organic phase of soils. Pyrene is a high-molecular weight PAH, which has human health concerns. In the present study, a bacterial consortium, PBR, was developed from a long-term polluted site, viz., Amlakhadi, Ankleshwar, Gujarat, for effective degradation of pyrene. The consortium effectively metabolized pyrene as a sole source of carbon and energy. The consortium comprised three bacterial species, Pseudomonas sp. ASDP1, Burkholderia sp. ASDP2, and Rhodococcus sp. ASDP3. The maximum growth rate of consortium was 0.060/h and the maximum pyrene degradation rate was 16 mg/l/day. The organic and inorganic nutrients along with different surfactants did not affect pyrene degradation, but degradation rate moderately increased in the presence of sodium succinate. The significant characteristic of the consortium was that it possessed an ability to degrade six other hydrocarbons, both independently and simultaneously at 37°C, in BHM (pH 7.0) under shaking conditions (150 rpm) and it showed resistance towards mercury at 10 mM concentration. Phthalic acid as one of the intermediates during pyrene degradation was detected through high-performance liquid chromatography (HPLC). The efficiency of consortium for pyrene degradation was validated in simulated microcosms' study, which indicated that 99% of pyrene was metabolized by the consortium under ambient conditions.
Rann of Kachchh (RoK) is a unique geoformation, which is exposed to dynamic environmental changes... more Rann of Kachchh (RoK) is a unique geoformation, which is exposed to dynamic environmental changes such as salinity, temperature, and nutrients throughout the year. In this study, the pooled mat sample was examined for the cyanobacterial community structure using culture-dependent and culture-independent approaches. Taxonomic profiling was studied using amplicon sequencing that revealed the enrichment of Pseudanabaenales and Oscillatoriales by QIIME and MG-RAST, respectively. Other abundant orders were represented by Chroococcales, Nostocales, and unclassified cyanobacteria by both approaches. Nine cyanobacterial cultures were isolated from mat samples showing 90–98% similarities with available sequences in GenBank. The culture-dependent study suggested that mat was dominated by cyanobacterial orders such as Oscillatoriales—filamentous and Chroococcales—unicellular. Our results from the culture-dependent approach also indicated that despite high similarities in gene sequences, six cyanobacteria fall into the separate clade in the phylogenetic analysis that could be signs of evolution due to an extreme environment. Cultured isolates are correlated well with abundant taxa from amplicon sequencing. Further, protein profiling was done specifically for phycobiliproteins which will be helpful to elucidate their roles in light harvesting and energy transfer mechanism in the unique environment of RoK.Electronic supplementary materialThe online version of this article (10.1007/s13205-019-1837-y) contains supplementary material, which is available to authorized users.
Mixed cultures BDN (BDN) proficient in decolourizing diazo dye-reactive blue 160 (RB160) consist ... more Mixed cultures BDN (BDN) proficient in decolourizing diazo dye-reactive blue 160 (RB160) consist of eight bacterial strains, was developed through culture enrichment method from soil samples contaminated with anthropogenic activities. The synthrophic interactions of BDN have led to complete decolourization and degradation of RB160 (100mg/L) within 4h along with co-metabolism of yeast extract (0.5%) in minimal medium. BDN microaerophilicaly decolourized even 1500mg/L of RB160 under high saline conditions (20g/L NaCl) at 37°C and pH 7.0. BDN exhibited broad substrate specificity and decolourized 27 structurally different dyes. The reductase enzymes symmetrically cleaved RB160 and oxidative enzymes further metabolised the degraded products and five different intermediates were identified using FTIR, (1)HNMR and GC-MS. The phytotoxicity assay confirmed that intact RB160 was more toxic than dye degraded intermediates. The BDN was able to colonize and decolourized RB160 in soil model system in presence of indigenous miocroflora as well as in sterile soil without any amendment of additional nutrients, which signifies it useful and potential application in bioremediation.
Abstract At the dawn of this millennium microbiologists unfurled the new era in genomics and it i... more Abstract At the dawn of this millennium microbiologists unfurled the new era in genomics and it is now perceived as “metagenomics.” Over the years workers in metagenomics have made astonishing discoveries in microbial taxonomy; concurrently functional capabilities have revealed new aspects of various biomes. Conventionally, metagenomics researchers have revealed various novel bioactive compounds by constructing libraries of environmental DNA of variable inserts in suitable vectors. Although it has been a good alternative to trap the potentiality of uncultivable microbes, one of the mammoth tasks is the screening of millions of clones. Functional metagenomics has supplied another innovative breakthrough in high-throughput sequencing. Through massive parallel direct sequencing of the collective genome from a particular biome, we have gained significant insight into the potential functions of microbial communities of individual niches. By integrating other “omics” technologies (metatranscriptomics, metaproteomics, metabolomics, interactomics) with bioinformatics tools, functional metagenomics can identify the individual traits employed by microbes that vary across time and space for their survival.
<p>Residues from α-subunit (shown as XXXnnn(A)) and from β-subunit (shown as XXXnnn(B)) wit... more <p>Residues from α-subunit (shown as XXXnnn(A)) and from β-subunit (shown as XXXnnn(B)) within a distance of 3.9Å from the chromophore atoms are displayed. Non-chromophore residues involved in hydrophobic contact(s) are shown with residue labels. Side chains of residues forming covalent and H-bonds with the chromophore atoms are shown as sticks. H-bonds are shown in green dashed lines. Chromophore bonds are shown in purple. <b>A)</b> Microenvironment around the α-chromophore (labeled Cyc181(A) in the figure). <b>B</b>) Microenvironment around chromophore (Cyc181(B)) covalently bound to Cys-81 of β-subunit. The figure was prepared using LigPlus suite [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124580#pone.0124580.ref041" target="_blank">41</a>].</p
Chlorophytum borivilianum is a very popular herb in traditional Indian medicine and used as a pot... more Chlorophytum borivilianum is a very popular herb in traditional Indian medicine and used as a potent &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;Rasayana&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; drug in &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;Ayurveda&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; as a rejuvenator. Currently, a large body of evidence supports the key role of free radicals in diverse pathological conditions such as aging and atherosclerosis. The present investigation essentially focuses on the comprehensive account of in vitro antioxidant activity exerted by C.borivilianum root extracts (i.e., aqueous and ethanolic), to clarify the pharmacological antagonism of chemicals/metals-mediated oxidation. Graded-dose (25 to 1000 microg/ml) of aqueous extract exhibited higher antioxidant potency as evidenced by powerful nitric oxide, superoxide, hydroxyl, DPPH and ABTS(*+) radicals scavenging activity along with reducing capacity (Fe(3+)/ferricyanide complex and FRAP assays), metal chelating ability, as well as markedly suppressed the lipid peroxidation in mitochondrial fractions as compared to ethanolic extract. Further, aqueous extract significantly decreased (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05) copper-mediated human serum and kinetics of LDL oxidation, as demonstrated by prolongation of lag phase time with decline of oxidation rate, conjugated dienes, lipid hydroperoxides and thiobarbituric acid reactive substances. In addition, the total polyphenol and flavonoid contents of aqueous extract were higher than that of ethanolic extract, which indicated a positive correlation between antioxidant activity and contents of total phenols. The IC(50) values of both extracts were also compared with appropriate antioxidant standards. Overall, aqueous extract of C.borivilianum root has significant powerful antioxidant activity and may favorably affect atherosclerosis risk status by reducing LDL oxidation susceptibility.
Cyanobacteria trap light energy by arrays of pigment molecules termed "phycobilisomes (PBSs)", or... more Cyanobacteria trap light energy by arrays of pigment molecules termed "phycobilisomes (PBSs)", organized proximal to "reaction centers" at which chlorophyll perform the energy transduction steps with highest quantum efficiency. PBSs, composed of sequential assembly of various chromophorylated phycobiliproteins (PBPs), as well as nonchromophoric, basic and hydrophobic polypeptides called linkers. Atomic resolution structure of PBP is a heterodimer of two structurally related polypeptides but distinct specialised polypeptides- a and ß, made up of seven alpha-helices each which played a crucial step in evolution of PBPs. PBPs carry out various light dependent responses such as complementary chromatic adaptation. The aim of this review is to summarize and discuss the recent progress in this field and to highlight the new and the questions that remain unresolved.
Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds due to their high hydro... more Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds due to their high hydrophobicity and tendency to partition in organic phase of soils. Pyrene is a high-molecular weight PAH, which has human health concerns. In the present study, a bacterial consortium, PBR, was developed from a long-term polluted site, viz., Amlakhadi, Ankleshwar, Gujarat, for effective degradation of pyrene. The consortium effectively metabolized pyrene as a sole source of carbon and energy. The consortium comprised three bacterial species, Pseudomonas sp. ASDP1, Burkholderia sp. ASDP2, and Rhodococcus sp. ASDP3. The maximum growth rate of consortium was 0.060/h and the maximum pyrene degradation rate was 16 mg/l/day. The organic and inorganic nutrients along with different surfactants did not affect pyrene degradation, but degradation rate moderately increased in the presence of sodium succinate. The significant characteristic of the consortium was that it possessed an ability to degrade six other hydrocarbons, both independently and simultaneously at 37°C, in BHM (pH 7.0) under shaking conditions (150 rpm) and it showed resistance towards mercury at 10 mM concentration. Phthalic acid as one of the intermediates during pyrene degradation was detected through high-performance liquid chromatography (HPLC). The efficiency of consortium for pyrene degradation was validated in simulated microcosms' study, which indicated that 99% of pyrene was metabolized by the consortium under ambient conditions.
Rann of Kachchh (RoK) is a unique geoformation, which is exposed to dynamic environmental changes... more Rann of Kachchh (RoK) is a unique geoformation, which is exposed to dynamic environmental changes such as salinity, temperature, and nutrients throughout the year. In this study, the pooled mat sample was examined for the cyanobacterial community structure using culture-dependent and culture-independent approaches. Taxonomic profiling was studied using amplicon sequencing that revealed the enrichment of Pseudanabaenales and Oscillatoriales by QIIME and MG-RAST, respectively. Other abundant orders were represented by Chroococcales, Nostocales, and unclassified cyanobacteria by both approaches. Nine cyanobacterial cultures were isolated from mat samples showing 90–98% similarities with available sequences in GenBank. The culture-dependent study suggested that mat was dominated by cyanobacterial orders such as Oscillatoriales—filamentous and Chroococcales—unicellular. Our results from the culture-dependent approach also indicated that despite high similarities in gene sequences, six cyanobacteria fall into the separate clade in the phylogenetic analysis that could be signs of evolution due to an extreme environment. Cultured isolates are correlated well with abundant taxa from amplicon sequencing. Further, protein profiling was done specifically for phycobiliproteins which will be helpful to elucidate their roles in light harvesting and energy transfer mechanism in the unique environment of RoK.Electronic supplementary materialThe online version of this article (10.1007/s13205-019-1837-y) contains supplementary material, which is available to authorized users.
Mixed cultures BDN (BDN) proficient in decolourizing diazo dye-reactive blue 160 (RB160) consist ... more Mixed cultures BDN (BDN) proficient in decolourizing diazo dye-reactive blue 160 (RB160) consist of eight bacterial strains, was developed through culture enrichment method from soil samples contaminated with anthropogenic activities. The synthrophic interactions of BDN have led to complete decolourization and degradation of RB160 (100mg/L) within 4h along with co-metabolism of yeast extract (0.5%) in minimal medium. BDN microaerophilicaly decolourized even 1500mg/L of RB160 under high saline conditions (20g/L NaCl) at 37°C and pH 7.0. BDN exhibited broad substrate specificity and decolourized 27 structurally different dyes. The reductase enzymes symmetrically cleaved RB160 and oxidative enzymes further metabolised the degraded products and five different intermediates were identified using FTIR, (1)HNMR and GC-MS. The phytotoxicity assay confirmed that intact RB160 was more toxic than dye degraded intermediates. The BDN was able to colonize and decolourized RB160 in soil model system in presence of indigenous miocroflora as well as in sterile soil without any amendment of additional nutrients, which signifies it useful and potential application in bioremediation.
Abstract At the dawn of this millennium microbiologists unfurled the new era in genomics and it i... more Abstract At the dawn of this millennium microbiologists unfurled the new era in genomics and it is now perceived as “metagenomics.” Over the years workers in metagenomics have made astonishing discoveries in microbial taxonomy; concurrently functional capabilities have revealed new aspects of various biomes. Conventionally, metagenomics researchers have revealed various novel bioactive compounds by constructing libraries of environmental DNA of variable inserts in suitable vectors. Although it has been a good alternative to trap the potentiality of uncultivable microbes, one of the mammoth tasks is the screening of millions of clones. Functional metagenomics has supplied another innovative breakthrough in high-throughput sequencing. Through massive parallel direct sequencing of the collective genome from a particular biome, we have gained significant insight into the potential functions of microbial communities of individual niches. By integrating other “omics” technologies (metatranscriptomics, metaproteomics, metabolomics, interactomics) with bioinformatics tools, functional metagenomics can identify the individual traits employed by microbes that vary across time and space for their survival.
<p>Residues from α-subunit (shown as XXXnnn(A)) and from β-subunit (shown as XXXnnn(B)) wit... more <p>Residues from α-subunit (shown as XXXnnn(A)) and from β-subunit (shown as XXXnnn(B)) within a distance of 3.9Å from the chromophore atoms are displayed. Non-chromophore residues involved in hydrophobic contact(s) are shown with residue labels. Side chains of residues forming covalent and H-bonds with the chromophore atoms are shown as sticks. H-bonds are shown in green dashed lines. Chromophore bonds are shown in purple. <b>A)</b> Microenvironment around the α-chromophore (labeled Cyc181(A) in the figure). <b>B</b>) Microenvironment around chromophore (Cyc181(B)) covalently bound to Cys-81 of β-subunit. The figure was prepared using LigPlus suite [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124580#pone.0124580.ref041" target="_blank">41</a>].</p
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