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Article ; Online: Host-microbiome interactions: Gut-Liver axis and its connection with other organs.

Anand, Swadha / Mande, Sharmila S

2022 Volume 8, Issue 1, Page(s) 89

Abstract: An understanding of connections between gut microbiome and liver has provided important insights into the pathophysiology of liver diseases. Since gut microbial dysbiosis increases gut permeability, the metabolites biosynthesized by them can reach the ... ...

Abstract	An understanding of connections between gut microbiome and liver has provided important insights into the pathophysiology of liver diseases. Since gut microbial dysbiosis increases gut permeability, the metabolites biosynthesized by them can reach the liver through portal circulation and affect hepatic immunity and inflammation. The immune cells activated by these metabolites can also reach liver through lymphatic circulation. Liver influences immunity and metabolism in multiple organs in the body, including gut. It releases bile acids and other metabolites into biliary tract from where they enter the systemic circulation. In this review, the bidirectional communication between the gut and the liver and the molecular cross talk between the host and the microbiome has been discussed. This review also provides details into the intricate level of communication and the role of microbiome in Gut-Liver-Brain, Gut-Liver-Kidney, Gut-Liver-Lung, and Gut-Liver-Heart axes. These observations indicate a complex network of interactions between host organs influenced by gut microbiome.
MeSH term(s)	Humans ; Dysbiosis ; Gastrointestinal Microbiome/physiology ; Liver ; Bile Acids and Salts ; Inflammation
Chemical Substances	Bile Acids and Salts
Language	English
Publishing date	2022-11-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2817021-0
ISSN	2055-5008 ; 2055-5008
ISSN (online)	2055-5008
ISSN	2055-5008
DOI	10.1038/s41522-022-00352-6
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Article: Diet, Microbiota and Gut-Lung Connection.

Anand, Swadha / Mande, Sharmila S

Frontiers in microbiology

2018 Volume 9, Page(s) 2147

Abstract: The gut microbial community (Gut microbiota) is known to impact metabolic functions as well as immune responses in our body. Diet plays an important role in determining the composition of the gut microbiota. Gut microbes help in assimilating dietary ... ...

Abstract	The gut microbial community (Gut microbiota) is known to impact metabolic functions as well as immune responses in our body. Diet plays an important role in determining the composition of the gut microbiota. Gut microbes help in assimilating dietary nutrients which are indigestible by humans. The metabolites produced by them not only modulate gastro-intestinal immunity, but also impact distal organs like lung and brain. Micro-aspiration of gut bacteria or movement of sensitized immune cells through lymph or bloodstream can also influence immune response of other organs. Dysbiosis in gut microbiota has been implicated in several lung diseases, including allergy, asthma and cystic fibrosis. The bi-directional cross-talk between gut and lung (termed as Gut-Lung axis) is best exemplified by intestinal disturbances observed in lung diseases. Some of the existing probiotics show beneficial effects on lung health. A deeper understanding of the gut microbiome which comprises of all the genetic material within the gut microbiota and its role in respiratory disorders is likely to help in designing appropriate probiotic cocktails for therapeutic applications.
Language	English
Publishing date	2018-09-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2018.02147
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Article ; Online: 'GutFeel': an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome.

Anand, Swadha / Bose, Chandrani / Kaur, Harrisham / Mande, Sharmila S

FEBS letters

2021 Volume 595, Issue 13, Page(s) 1825–1843

Abstract: Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic ... ...

Abstract	Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic composition of the microbiomes is dependent on factors such as diet, lifestyle, and geography, these microbes perform a specific set of common functions in the gut. In this study, metabolic pathway-based markers (agnostic to above-mentioned factors) specific to commensals and those specific to pathogens are utilized as indicators of gut health. Furthermore, this gut health assessment requires only a small set of features rather than complete sequencing of metagenomes. The proposed scheme can also be used to design personalized biotherapeutics, depending on functional aspects observed in an individual.
MeSH term(s)	Bacteria/classification ; Bacteria/isolation & purification ; Computational Biology/methods ; Computer Simulation ; Dysbiosis/diagnosis ; Gastrointestinal Microbiome ; Health Status ; Humans ; Life Style ; Metabolic Networks and Pathways ; Metabolomics/methods ; Symbiosis
Language	English
Publishing date	2021-06-03
Publishing country	England
Document type	Journal Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14107
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Article: ‘GutFeel’: an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome

Anand, Swadha / Bose, Chandrani / Kaur, Harrisham / Mande, Sharmila S.

FEBS letters. 2021 July, v. 595, no. 13

2021

Abstract	Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic composition of the microbiomes is dependent on factors such as diet, lifestyle, and geography, these microbes perform a specific set of common functions in the gut. In this study, metabolic pathway‐based markers (agnostic to above‐mentioned factors) specific to commensals and those specific to pathogens are utilized as indicators of gut health. Furthermore, this gut health assessment requires only a small set of features rather than complete sequencing of metagenomes. The proposed scheme can also be used to design personalized biotherapeutics, depending on functional aspects observed in an individual.
Keywords	computer simulation ; diet ; digestive system ; dysbiosis ; geography ; health effects assessments ; health status ; humans ; intestinal microorganisms ; lifestyle ; metagenomics ; microbiome ; taxonomy
Language	English
Dates of publication	2021-07
Size	p. 1825-1843.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14107
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Article ; Online: Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases

Anand Swadha / Mohanty Debasisa

BMC Structural Biology, Vol 12, Iss 1, p

a docking and molecular dynamics study

2012 Volume 10

Abstract: Abstract Background Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the ... ...

Abstract	Abstract Background Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant) group of the holo-Acyl Carrier Protein (holo-ACP) domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. Results We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS . In case of KR domain, the substrate binding site identified by our simulations was in proximity of the known stereo-specificity determining residues. Conclusions We have modeled the holo-ACP:DH and holo-ACP:KR complexes and identified the specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. Analysis of the conservation profile of binding pocket residues in homologous sequences of DH and KR domains indicated that, these results can also be extrapolated to reductive domains of other modular PKS clusters.
Keywords	Molecular dynamics ; Protein-ligand docking ; Protein-protein interaction ; Substrate binding site ; Evolutionary conservation ; Modular polyketide synthase ; Dehydratase domain ; Ketoreductase domain ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2012-05-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
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Article: Corrigendum: FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways.

Bhatt, Vineet / Mohapatra, Anwesha / Anand, Swadha / Kuntal, Bhusan K / Mande, Sharmila S

Frontiers in microbiology

2020 Volume 11, Page(s) 605419

Abstract: This corrects the article DOI: 10.3389/fmicb.2018.02183.]. ...

Abstract	[This corrects the article DOI: 10.3389/fmicb.2018.02183.].
Language	English
Publishing date	2020-10-29
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.605419
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Article: In silico

Khater, Shradha / Anand, Swadha / Mohanty, Debasisa

Synthetic and systems biotechnology

2016 Volume 1, Issue 2, Page(s) 80–88

Abstract: ... In ... ...

Abstract	In silico
Language	English
Publishing date	2016-04-01
Publishing country	China
Document type	Journal Article
ISSN	2405-805X
ISSN	2405-805X
DOI	10.1016/j.synbio.2016.03.001
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Article: Comparative

Anand, Swadha / Kaur, Harrisham / Mande, Sharmila S

Frontiers in microbiology

2016 Volume 7, Page(s) 1945

Abstract: Biosynthesis of butyrate by commensal bacteria plays a crucial role in maintenance of human gut health while dysbiosis in gut microbiome has been linked to several enteric disorders. Contrastingly, butyrate shows cytotoxic effects in patients with oral ... ...

Abstract	Biosynthesis of butyrate by commensal bacteria plays a crucial role in maintenance of human gut health while dysbiosis in gut microbiome has been linked to several enteric disorders. Contrastingly, butyrate shows cytotoxic effects in patients with oral diseases like periodontal infections and oral cancer. In addition to these host associations, few syntrophic bacteria couple butyrate degradation with sulfate reduction and methane production. Thus, it becomes imperative to understand the distribution of butyrate metabolism pathways and delineate differences in substrate utilization between pathogens and commensals. The bacteria utilize four pathways for butyrate production with different initial substrates (Pyruvate, 4-aminobutyrate, Glutarate and Lysine) which follow a polyphyletic distribution. A comprehensive mining of complete/draft bacterial genomes indicated conserved juxtaposed genomic arrangement in all these pathways. This gene context information was utilized for an accurate annotation of butyrate production pathways in bacterial genomes. Interestingly, our analysis showed that inspite of a beneficial impact of butyrate in gut, not only commensals, but a few gut pathogens also possess butyrogenic pathways. The results further illustrated that all the gut commensal bacteria (
Language	English
Publishing date	2016-12-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.01945
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Article ; Online: FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information.

Anand, Swadha / Kuntal, Bhusan K / Mohapatra, Anwesha / Bhatt, Vineet / Mande, Sharmila S

Bioinformatics (Oxford, England)

2019 Volume 36, Issue 8, Page(s) 2575–2577

Abstract: Motivation: Functional potential of genomes and metagenomes which are inferred using homology-based methods are often subjected to certain limitations, especially for proteins with homologs which function in multiple pathways. Augmenting the homology ... ...

Abstract	Motivation: Functional potential of genomes and metagenomes which are inferred using homology-based methods are often subjected to certain limitations, especially for proteins with homologs which function in multiple pathways. Augmenting the homology information with genomic location of the constituent genes can significantly improve the accuracy of estimated functions. This can help in distinguishing cognate homolog belonging to a candidate pathway from its other homologs functional in different pathways. Results: In this article, we present a web-based analysis platform 'FunGeCo' to enable gene-context-based functional inference for microbial genomes and metagenomes. It is expected to be a valuable resource and complement the existing tools for understanding the functional potential of microbes which reside in an environment. Availability and implementation: https://web.rniapps.net/fungeco [Freely available for academic use]. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Genome, Bacterial/genetics ; Internet ; Metagenome ; Microbiota/genetics ; Software
Language	English
Publishing date	2019-12-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz957
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Article ; Online: Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study.

Anand, Swadha / Mohanty, Debasisa

BMC structural biology

2012 Volume 12, Page(s) 10

Abstract: Background: Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the catalysis ... ...

Abstract	Background: Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant) group of the holo-Acyl Carrier Protein (holo-ACP) domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. Results: We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS. In case of KR domain, the substrate binding site identified by our simulations was in proximity of the known stereo-specificity determining residues. Conclusions: We have modeled the holo-ACP:DH and holo-ACP:KR complexes and identified the specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. Analysis of the conservation profile of binding pocket residues in homologous sequences of DH and KR domains indicated that, these results can also be extrapolated to reductive domains of other modular PKS clusters.
MeSH term(s)	Acyl Carrier Protein/chemistry ; Alcohol Oxidoreductases/chemistry ; Bacterial Proteins/chemistry ; Biocatalysis ; Holoenzymes/chemistry ; Hydro-Lyases/chemistry ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Polyketide Synthases/chemistry ; Protein Binding ; Protein Structure, Tertiary ; Spinacia oleracea ; Substrate Specificity ; Time Factors
Chemical Substances	Acyl Carrier Protein ; Bacterial Proteins ; Holoenzymes ; Polyketide Synthases (79956-01-7) ; Alcohol Oxidoreductases (EC 1.1.-) ; polyketide synthase ketoreductase (EC 1.1.-) ; Hydro-Lyases (EC 4.2.1.-)
Language	English
Publishing date	2012-05-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2050440-8
ISSN	1472-6807 ; 1472-6807
ISSN (online)	1472-6807
ISSN	1472-6807
DOI	10.1186/1472-6807-12-10
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