Indrani Sarkar - Academia.edu (original) (raw)

Papers by Indrani Sarkar

Journal of King Saud University - Science

South African Journal of Botany

NBU Journal of Plant Sciences

The 19th International conference on Frankia and Actinorhizal plants which I attended along with ... more The 19th International conference on Frankia and Actinorhizal plants which I attended along with one of my colleague Miss Reha Labar was held from 17th-10th March, 2018 at Hammamet, Tunisia Since my research is about Frankia and other actinobacteria, this conference provided a full opportunity to meet with people from different parts of the world who are working on the same topic and also learned some new techniques they are using for better understanding of Frankia and Actinorhizal symbiosis.

World Journal of Microbiology and Biotechnology

Malaria, caused by a parasite known as Plasmodium, is one of the leading causes of death, worldwi... more Malaria, caused by a parasite known as Plasmodium, is one of the leading causes of death, worldwide, especially in the third world countries of Africa and Asia. Plasmodium does not only infect humans but also reptiles, birds and other mammals. However, they are the secondary hosts for this parasite. The primary host of Plasmodium is female Anopheles mosquitoes. Long term researchers have formulated drugs against this deadly pathogen but the current emergence of multi-drug resistance strains of Plasmodium has created a recurring concern. Identification of new drug molecules and understanding their mechanism of action is an urgent need to combat this battle. However, for that, we need to first understand the genomic strategies taken up by Plasmodium to survive the host immune system. With the advancement of high-throughput sequencing techniques, the whole genomes of Plasmodium have been sequenced which can help us in advancing our strategies against Plasmodium. In this study, we perfo...

Computational Advancement in Communication Circuits and Systems, 2019

Malaria remains one of the most devastating diseases, causing as many as 2.7 million deaths annua... more Malaria remains one of the most devastating diseases, causing as many as 2.7 million deaths annually with an estimated 400 to 900 million new cases each year 1. Malaria endemic areas include Africa, South east asia, India and South America. However, the disease is spreading to new areas, such as Central Asia and Eastern Europe. Local transmission of malaria in the United States, unheard of in the era between World War II and 1980, now accounts for an increasing number of cases 2. Clinical cases in the US now average 1,300 per year 3. Worldwide, the majority of deaths occur in children; other high risk groups include pregnant women, refugees, migrant workers and non immune travelers-over 20 million Western tourists at risk annually (fact sheets from Malaria Foundation International). Although four species of the genus Plasmodium cause human malaria, Plasmodium falciparum is the deadliest and will be the subject of this review. During the past two decades an increasing number of quantitative structure-activity/property relationship (QSAR/ QSPR) models have been studied using theoretical molecular descriptors for predicting biomedical, activity, toxicological and technological properties of chemicals. QSAR/QSPR are mathematical models that seek to predict complicated physico

SSRN Electronic Journal, 2022

Journal of Biomolecular Structure and Dynamics, 2022

One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however... more 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 in silico approach to assessing the inhibitory potential of the phytochemicals obtained from GC-MS analysis of Citrus macroptera against inflammatory proteins like COX-2, NMDAR and VCAM-1 which remains in a hyperactive state even after a patient is fully cured of this deadly mRNA virus. An extensive molecular docking investigation of the phyto-compounds at the active binding pockets of the inflammatory proteins revealed the promising inhibitory potential of the phytochemicals. Reasonable physicochemical attributes of the compounds following Lipinski's rule of five, VEBER and PAINS analysis further established them as potential therapeutic candidates against aforesaid inflammatory proteins. MM-GBSA binding free energy estimation revealed that Limonene was the most promising candidate displaying the highest binding efficacy with the concerned VCAM-1 protein included in the present analysis. An interesting finding is the phytochemicals exhibited better binding energy scores with the concerned COX-2, VCAM-1 and NMDA receptor proteins than the conventional drugs that are specifically targeted against them. Our in silico results suggest that all the natural phyto-compounds derived from C. macroptera could be employed in Post covid inflammation complexities after appropriate pre-clinical and clinical trials for further scientific validation.Communicated by Ramaswamy H. Sarma.

Journal of Forest Research, 2022

Neisseria, a genus from beta-proteobacteria class, is of potent clinical importance. This genus c... more Neisseria, a genus from beta-proteobacteria class, is of potent clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance (AMR) capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole genome sequences and computational biology it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our anal...

International Journal of English Learning & Teaching Skills, 2021

The revolution of mobile phones is not merely limited to calling or texting; it has reached almos... more The revolution of mobile phones is not merely limited to calling or texting; it has reached almost every sphere of humankind. In this 21st century, studies have claimed that mobile phones' accessibility is comparatively higher than the toilet. Nearly 6 billion people worldwide now are accessing a working mobile handset (UNESCO, 2014). The ubiquitous use of mobile phones brings mobility to its users and helps them accept this ICT based technology worldwide. This new technology of communication also has a remarkable contribution to the educational sector. Its real-time communication makes learning effortless and congenial to the potential learners. This study will explore mobile-based learning technology among the higher education aspirants of suburban colleges in North 24parganas of West Bengal. Suburban students are not getting the same facilitates as metro city students. Besides that, suburban culture and social taboos sometimes make problems to use or access mobile phones by s...

Journal of Biomolecular Structure and Dynamics, 2021

Coronavirus (SARS-CoV-2), the causative agent of the Covid-19 pandemic has proved itself as the d... more Coronavirus (SARS-CoV-2), the causative agent of the Covid-19 pandemic has proved itself as the deadliest pathogen. A major portion of the population has become susceptible to this strain. Scientists are pushing their limits to formulate a vaccine against Covid-19 with the least side effects. Although the recent discoveries of vaccines have shown some relief from the covid infection rate, however, physical fatigue, mental abnormalities, inflammation and other multiple organ damages are arising as post-Covid symptoms. The long-term effects of these symptoms are massive. Patients with such symptoms are known as long-haulers and treatment strategy against this condition is still unknown. In this study, we tried to explore a strategy to deal with the post-Covid symptoms. We targeted three human proteins namely ACE2, Interleukin-6, Transmembrane serine protease and NRP1 which are already reported to be damaged via Covid-19 proteins and upregulated in the post-Covid stage. Our target plant in this study is Cannabis (popularly known as 'Ganja' in India). The molecular docking and simulation studies revealed that Cannabidiol (CBD) and Cannabivarin (CVN) obtained from Cannabis can bind to post-Covid symptoms related central nervous system (CNS) proteins and downregulate them which can be beneficial in post-covid symptoms treatment strategy. Thus we propose Cannabis as an important therapeutic plant against post-Covid symptoms.Communicated by Ramaswamy H. Sarma.

Macrobrachium dayanum is a fresh water commercially important fish and highly preferred by the co... more Macrobrachium dayanum is a fresh water commercially important fish and highly preferred by the consumers. This study revealed that it was not a continuous breeder and showed two breeding peak periods in a year related to monsoon. Males were larger than the female. The largest male (largest carapace length and longest chelate legs) showed its dominance over recessive and non breeding males. Both male and female attained maturity at the age of about 5 months (male 5 cm in length, weight 1.3 gr in average; female 4.2 cm in length and weight 1.36 gr in average). GSI of prawn indicated the maximum size groups did not show maximum GSI. The male showed peculiar behavior or tactics during mating such as protection or guarding the female with the largest chelate leg, aggression, climbing over the female etc. Spawning took place after 20 ± 2 hours of mating. The fertilized eggs were deep green color, about 2.5-3.0 mm in length and 1.52-2.0 mm in breadth. The incubation period was 22-24 days. ...

Journal of Ethnic Foods, 2021

Eu," is a traditional millet-based mild alcoholic beverage consumed by the Toto tribe of West Ben... more Eu," is a traditional millet-based mild alcoholic beverage consumed by the Toto tribe of West Bengal. Eu is prepared through the fermentation of millet with locally groomed starter culture "Moaa." The study highlighted the overview of the traditional process of Eu preparation along with its molecular and biochemical characterization. Semi-structured interviews were conducted for collecting the ethnobotanical data and the samples. We have also included qualitative assays like acute toxicity, antioxidant, gas chromatography-mass spectrometry (GC-MS), molecular docking, and physiochemical characteristics such as pH and alcohol content. Moreover, metagenomics of the starter culture has been reported. This type of study on Eu has not been done previously. Therefore, it seems to be a pioneer report especially on the metagenomic analysis of Eu. Results revealed that Eu has a very low alcohol content (approximately 1-3%) and a high antioxidant capacity. GC-MS analysis identified thirteen different bioactive compounds. Metagenomics analysis revealed that the Eu has a high source of various beneficial gut microflora. Overall Lactobacillus, Lactococcus, Enterococcus, Leuconostoc, and Pediococcus are dominant genera identified in the starter culture. The present study revealed that the consumption of Eu is safe and has the potential to scavenge reactive oxygen species (ROS). Hence, the commercialization of Eu can be an alternative source of income for the poor endangered Toto tribe.

Mitochondrial genome provides useful information about species with respect to its evolution and ... more Mitochondrial genome provides useful information about species with respect to its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,671 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with 2 rRNAs and 22 tRNAs were detected along with duplicated control regions. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over all the thirteen protein-coding genes in yellow-billed babbler mito...

International Journal of Data Mining and Bioinformatics, 2019

Mycobacterium tuberculosis RGTB423 is the causative agent of Tuberculosis. Our aim here is to che... more Mycobacterium tuberculosis RGTB423 is the causative agent of Tuberculosis. Our aim here is to check the efficacy of a few herbal medicines to counter the rage of this highly infectious disease. The workflow here is purely data mining and bioinformatics based, here a comparative pathway analysis of the host and causative organism is done. The proteins present in these pathways are screened to obtain targets protein for in-silico drug designing. The ligands are selected from Withania somnifera, Oplopanax horridus and Aloe vera plants. Molecular docking of the phytochemicals is performed with the selected targets. Few ADMET parameters and in silico toxicology data was also checked for the ligands to confirm their druglikeness characteristics. Among the phytochemicals aloeemodin, a compound present in Aloe vera showed the best result. Aloeemodin even had better results than a few prescribed drugs and thus can be further considered for potent drug trail runs against tuberculosis.

Gynecologic Oncology, 2019

Atezolizumab monotherapy was well tolerated in pre-treated patients with epithelial ovarian or ut... more Atezolizumab monotherapy was well tolerated in pre-treated patients with epithelial ovarian or uterine cancer. • No new safety signals were seen; safety profile in both cohorts was consistent with that known for atezolizumab monotherapy. • Preliminary evidence of anti-tumor activity with long durability of response was observed in patients from both cohorts.

Antonie van Leeuwenhoek, 2018

Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simple... more Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role. Keywords Carbohydrate active enzymes Á Frankia Á Nodulation Á Codon usage Á Amino acid usage Á Comparative genomics Á Evolution Á Phylogeny Electronic supplementary material The online version of this article (

JAMA oncology, Jan 13, 2018

Atezolizumab (anti-programmed cell death ligand 1 [PD-L1]) is well tolerated and clinically activ... more Atezolizumab (anti-programmed cell death ligand 1 [PD-L1]) is well tolerated and clinically active in multiple cancer types. Its safety and clinical activity in metastatic triple-negative breast cancer (mTNBC) has not been reported. To evaluate the safety, clinical activity, and biomarkers associated with the use of single-agent atezolizumab in patients with mTNBC. Women with mTNBC (defined by investigator assessment) were enrolled between January 2013 and February 2016 in a multicohort open-label, phase 1 study at US and European academic medical centers. Median follow-up was 25.3 months (range, 0.4-45.6 months). Eligible patients regardless of line of therapy had measurable disease by Response Evaluation Criteria in Solid Tumors, version 1.1; Eastern Cooperative Oncology Group performance status of 0 to 1; and a representative tumor sample for assessment of immune cell (IC) PD-L1 expression. Atezolizumab was given intravenously every 3 weeks until unacceptable toxic effects or los...

Genomics, Jan 28, 2018

Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pa... more Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationsh...