LIVIVO - Search results -

Search results

Result 1 - 10 of total 434

Search options

Article: Whole genome sequencing of

Chhettri, Saroja / Sevigny, Joseph / Pesce, Céline / Sarkar, Indrani / Thomas, W Kelley / Nouioui, Imen / Sen, Gargi / Tisa, Louis S / Sen, Arnab

Journal of genomics

2024 Volume 12, Page(s) 6–13

Abstract: ... ...

Abstract	Streptomyces
Language	English
Publishing date	2024-01-01
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2692697-0
ISSN	1839-9940
ISSN	1839-9940
DOI	10.7150/jgen.87156
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article: Niche adaptation of Frankia do not drastically influence their metabolic profiling

Sarkar, Indrani / Sen, Arnab

Journal of forest research. 2022 Mar. 04, v. 27, no. 2

2022

Abstract: Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. ... ...

Abstract	Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. Information regarding the metabolomics of Frankia is elusive. In this study, we analyzed 48 Frankia whole-genome sequences. Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG Automatic Annotation Server (KAAS) were used for the prediction and functional annotation of genes associated with diverse metabolic pathways. Comprehensive codon and amino-acid usage analyses along with tRNA adaptation index and dN/dS-based evolutionary inquest were performed. We have used the Database-of-Essential-Genes (DEG) server to predict the essentiality of the metabolic pathway-related-genes. We found a strong effect of compositional constraints on the metabolic pathway genes of Frankia. The evolutionary analysis revealed the conserved nature of the studied genes. Since the metabolic pathway-related genes were found to be housekeeping genes, they are conserved and less evolved. This was further validated with a dN/dS value of less than 1. Moreover, the number of synonymous changes was more than non-synonymous changes so that the amino acid sequence remains identical. The cluster of orthologs (COG) analysis revealed “metabolism” as the main functional category of the studied gene set. The core metabolic pathway-related genes among considered Frankia strains accumulated 115 genes. This study for the first time reveals the genomic characteristics of the metabolic pathway-related genes among Frankia. From all the analysis, we could hypothesize that in spite of their host specificity and differential taxonomical distribution, Frankia maintain a core metabolic proficiency among them.
Keywords	Frankia ; amino acid sequences ; amino acids ; biochemical pathways ; databases ; forests ; genomics ; host specificity ; metabolites ; metabolomics ; prediction ; research
Language	English
Dates of publication	2022-0304
Size	p. 100-105.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2104467-3
ISSN	1610-7403 ; 1341-6979
ISSN (online)	1610-7403
ISSN	1341-6979
DOI	10.1080/13416979.2022.2028707
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article ; Online: Correction to: Comprehensive profiling of functional attributes, virulence potential and evolutionary dynamics in mycobacterial secretomes.

Roy, Ayan / Sen, Arnab / Chakraborty, Sourav / Sarkar, Indrani

World journal of microbiology & biotechnology

2021 Volume 37, Issue 1, Page(s) 10

Language	English
Publishing date	2021-01-04
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	1499109-3
ISSN	1573-0972 ; 0959-3993
ISSN (online)	1573-0972
ISSN	0959-3993
DOI	10.1007/s11274-020-02969-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Details ▾
- Full text online
- Order with fees

Article ; Online: Phytocompounds from

Datta, Sutapa / Sarkar, Indrani / Goswami, Nabajyoti / Mahanta, Saurov / Borah, Probodh / Sen, Arnab

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–18

Abstract: Monkeypox is a communicable disease similar to smallpox, primarily occurring in African countries. However, recently it has spread to countries outside Africa and may arise as the next threat after COVID-pandemic. The causative organism, i.e. Monkeypox ... ...

Abstract	Monkeypox is a communicable disease similar to smallpox, primarily occurring in African countries. However, recently it has spread to countries outside Africa and may arise as the next threat after COVID-pandemic. The causative organism, i.e. Monkeypox Virus (MPV) spreads from one individual to another primarily through inhalation of respiratory droplets or through contact with skin lesions of infected individuals. No known drugs are available specifically for MPV. Due to its similarity with smallpox, treatment of monkeypox is being attempted through the administration of the smallpox vaccine. Therefore, we evaluated the efficacy of the plant
Language	English
Publishing date	2023-12-11
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2291166
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2093: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Neem and Turmeric in the management of Covid Associated Mucormycosis (CAM) derived through network pharmacology.

Datta, Sutapa / Sarkar, Indrani / Sen, Gargi / Sen, Arnab

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 8, Page(s) 3281–3294

Abstract: Mucormycosis or 'Black Fungus' has been known to target immunocompromised individuals even before the emergence of COVID-19. Nevertheless, the present circumstances provide the best opening for Covid Associated Mucormycosis (CAM), as the global pandemic ... ...

Abstract	Mucormycosis or 'Black Fungus' has been known to target immunocompromised individuals even before the emergence of COVID-19. Nevertheless, the present circumstances provide the best opening for Covid Associated Mucormycosis (CAM), as the global pandemic is engulfing a large part of human population making them immunocompromised. This drastic increase in Mucormycosis infections has to be addressed as early as possible. There is a growing tendency of relying upon herbal drugs that have minimal side effects and does not compromise our immune system. Recently, the concept of network pharmacology has grabbed the attention of modern science, especially advanced medical sciences. This is a new discipline that can use computational power to systematically catalogue the molecular interactions between botanical formulations and the human body. In this study, Neem and Turmeric was considered as the target plants and an attempt was made to reveal various aspects through which phytocompounds derived from them may effectively manage CAM menace. We have taken a step-by-step approach for identifying the target proteins and ligands associated with Mucormycosis treatment. Functional network analysis and Molecular docking approaches were applied to validate our findings. Quercetin derived from both Neem and Turmeric was found to be one of the main phytocompounds working against Mucormycosis. Along with that, Caffeic acid, Curcumin, Kaempferol, Tetrahydrocurcumin and Myricetin also play a pivotal role in fighting against Black-Fungus. A thorough analysis of our result suggested a triple-front attack on the fungal pathogens and the approaches are necrosis inhibition, iron chelation and immuno-boosting.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Mucormycosis/drug therapy ; Curcuma ; Network Pharmacology ; Molecular Docking Simulation ; COVID-19
Language	English
Publishing date	2022-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2048077
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2093: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: In silico

Sarkar, Indrani / Sen, Arnab

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 8, Page(s) 3706–3710

Abstract: The ongoing outbreak of Coronavirus disease 2019 (COVID-19) is a matter of great concern. Although the mortality rate caused by this virus is less than that of SARS and MERS, it is showing higher efficacy in terms of human-to-human transmission. Several ... ...

Abstract	The ongoing outbreak of Coronavirus disease 2019 (COVID-19) is a matter of great concern. Although the mortality rate caused by this virus is less than that of SARS and MERS, it is showing higher efficacy in terms of human-to-human transmission. Several strategies have been taken by scientists and researchers worldwide to combat this virus. Numerous phytochemicals and synthesized chemicals are under incessant inspection to obtain a potent anti-covid drug. Since, till now no precise therapy is available for covid patients, researchers are trying to categorize all possible anti-covid substances. Repurposing of drugs and combined drug therapy are becoming popular in treating such viral diseases. In this study, we are proposing the repurposing of three chemicals
MeSH term(s)	COVID-19/drug therapy ; Common Cold ; Dexamethasone/pharmacology ; Dextromethorphan ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Prednisolone/pharmacology ; Protease Inhibitors ; SARS-CoV-2
Chemical Substances	Protease Inhibitors ; Dextromethorphan (7355X3ROTS) ; Dexamethasone (7S5I7G3JQL) ; Prednisolone (9PHQ9Y1OLM) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2020-11-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1850528
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2093: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Rate of occult metastasis in lip squamous cell carcinoma: A systematic review and meta-analysis.

Kansara, Sagar / Oral, Evrim / Sarkar, Indrani / Sandulache, Vlad / Mualla, Rula / Walvekar, Rohan R / Ryan, William / Ha, Patrick

Head & neck

2024

Abstract: Objectives: The rate of occult metastasis in lip cancer is poorly studied. Management of the regional nodal basin in lip cancer is thus controversial. This study sought to understand the true rate of micrometastasis in lip cancer.: Materials and ... ...

Abstract	Objectives: The rate of occult metastasis in lip cancer is poorly studied. Management of the regional nodal basin in lip cancer is thus controversial. This study sought to understand the true rate of micrometastasis in lip cancer. Materials and methods: Systematic review and meta-analysis was conducted of English language studies reporting lip cancer sentinel node biopsy results. Studies were obtained from the PubMed database between the years 2000 and 2023 using the search terms "sentinel node biopsy" and "squamous cell carcinoma." Random effect and fixed effect meta-analyses were performed. Results: Thirteen studies met inclusion criteria. Low heterogeneity was noted among the studies, as indicated by the I Conclusion: The rate of occult metastasis in lip cancer approaches the threshold for elective management of the regional nodal basin. Sentinel node biopsy is optimally suited for management of high-risk early T stage lip cancer.
Language	English
Publishing date	2024-03-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	645165-2
ISSN	1097-0347 ; 0148-6403 ; 1043-3074
ISSN (online)	1097-0347
ISSN	0148-6403 ; 1043-3074
DOI	10.1002/hed.27747
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1493: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Retraction Note: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family.

Sarkar, Indrani / Dey, Prateek / Sharma, Sanjeev Kumar / Ray, Swapna Devi / Kochiganti, Venkata Hanumat Sastry / Singh, Renu / Pramod, Padmanabhan / Singh, Ram Pratap

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18144

Language	English
Publishing date	2023-10-24
Publishing country	England
Document type	Retraction of Publication
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-45261-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: In-silico

Lala, Mousikha / Bhattacharjee, Soumita / Ghosh, Chandra / Sen, Arnab / Sarkar, Indrani

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 8, Page(s) 3511–3523

Abstract: One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 ... ...

Abstract	One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 aftermath persists to remain fuzzy. The survivors of severe COVID-19infection having defeated the virus are just the starting of an uncharted recovery path. Currently, there is no drug available that is safe to consume to combat this pandemic. However, researchers still struggling to find specific therapeutic solutions. The present study employed an
MeSH term(s)	Citrus/chemistry ; Humans ; COVID-19/complications ; Phytochemicals/chemistry ; Phytochemicals/therapeutic use ; Post-Acute COVID-19 Syndrome/drug therapy ; Molecular Docking Simulation ; Plant Extracts/chemistry ; Drug Development ; Cyclooxygenase 2/chemistry ; Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors ; Receptors, N-Methyl-D-Aspartate/chemistry ; Protein Binding ; Vascular Cell Adhesion Molecule-1/antagonists & inhibitors ; Cyclooxygenase 2 Inhibitors/chemistry ; Limonene/chemistry ; Limonene/pharmacology
Chemical Substances	Phytochemicals ; Plant Extracts ; Cyclooxygenase 2 (EC 1.14.99.1) ; Receptors, N-Methyl-D-Aspartate ; Vascular Cell Adhesion Molecule-1 ; Cyclooxygenase 2 Inhibitors ; Limonene (9MC3I34447)
Language	English
Publishing date	2022-03-17
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2051744
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2093: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Detection of the peptidyl epitope for vaccine development against MPV

Indrani Sarkar / Gargi Sen / Mohammd Ajmal Ali / Saeedah Musaed Almutairi / Joongku Lee / Arnab Sen

Journal of King Saud University: Science, Vol 35, Iss 1, Pp 102458- (2023)

1480

Abstract: Background: Monkeypox Virus (MPV) is the cause of zoonotic disease characterized by skin-eruption with pus cell formation and lymphadenopathy. This virus belongs to the Orthopoxvirus genus with DNA as its genetic material. Previously, this infection was ... ...

Abstract	Background: Monkeypox Virus (MPV) is the cause of zoonotic disease characterized by skin-eruption with pus cell formation and lymphadenopathy. This virus belongs to the Orthopoxvirus genus with DNA as its genetic material. Previously, this infection was reported from Africa and occasionally from USA and UK. However, recently there is a sudden surge of infection in non-epidemic countries and a new strain of MPVhas been discovered. Therefore it is important to revisit the phylogeny of MPV with the addition of new strains. Recently WHO also stressed the need of developing vaccines for new strains. In this scenario we have two objectives for this study -first, to reveal the exact phylogenetic position of the 2022 strain and second, to identify specific peptides which may be used for vaccine development in the future. Methods: The phylogenetic analysis was done with the help of Bayesian phylogeny. The dN/dS calculation was performed based on DNA polymerase genes of selected MPV strains. The peptidyl-epitope was searched in MPV2022/2 SLO strain with the help of several algorithms implemented in Allergen FP v.1.0, NetMHCII 2.3, MHCpred and Toxin Pred. The structure prediction of the proteins and peptides was performed through Hpepdock. The quality of the structures was validated through the Ramachandran plot. The molecular dynamics and simulation were performed through Gromacs software. The interaction between peptide and protein was assessed through Ligplot software. Results: The phylogenetic analysis revealed that the considered 2022 MPVstrains were close to the USA strains. The evolutionary analysis showed the volatile nature of the genome. Moreover, 9-mer peptide sequence was identified as an epitope for vaccine development. Conclusions: The emergence of more virulent strains in near future may not be ruled out. Immunocompromised patients are more susceptible to this virus hence sub-unit vaccine is a better choice than a recombinant or attenuated vaccine against monkeypox. We have identified a small stretch of ...
Keywords	Monkeypox virus ; Phylogenomics ; Evolution ; Epitopes ; Molecular docking and dynamics ; Science (General) ; Q1-390
Subject code	570
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED