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The bacteriophage mu lysis system–A new mechanism of host lysis?

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BIOCELL 2021年第5期45卷 1175-1186页

作者： SAIKAT SAMANTA ASHISH RANJAN SHARMA ABINIT SAHA MANOJ KUMAR SINGH arpita das MANOJIT BHATTACHARYA RUDRA PRASAD SAHA SANG-SOO LEE CHIRANJIB CHAKRABORTY Department of Biotechnology School of Life Science&BiotechnologyAdamas UniversityKolkata700126India Institute for Skeletal Aging&Orthopedic Surgery Hallym University-Chuncheon Sacred Heart HospitalChuncheon-si24252Korea Department of Zoology Fakir Mohan UniversityBalasore56020India

Bacteriophages are viruses that infect bacteria and can choose any one of the two alternative pathways for infection,i.e.,lysis or lysogeny.Phage lysis is one of the conventional biological processes required to spread infection from one bacterium to another.Our analysis suggests that in the paradigm bacteriophage Mu,six proteins might be involved in host cell lysis.Mu has a broad host range,and Mu-like phages were found in both Gram-negative and Gram-positive bacteria.An analysis of the genomes of Mu and Mu-like phages could be useful in elucidating the lysis mechanism in this group of phages.A detailed review of the various mechanisms of phage lysis and different proteins associated with the process will help researchers understand the phage biology and their life cycle in different bacteria.The recent increase in the number of multidrug-resistant(MDR)strains of bacteria and the usual long-term nature of new drug development has encouraged scientists to look for alternative strategies like phage therapy and the discovery of new lysis mechanisms.Understanding the lysis mechanism in the Mu-like phages could be exploited to develop alternative therapeutics to kill drug-resistant pathogenic bacteria.In this review article,we have analyzed the phage Mu-mediated host lysis system,which is unknown till now,and our analysis indicates a possibility of the existence of a new lysis mechanism operating in Mu.

关键词： Bacteriophage Mu Host cell lysis Endolysin Holin Spanin

OCSO-CA:opposition based competitive swarm optimizer in energy efficient IoT clustering

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Frontiers of Computer Science 2022年第1期16卷 77-87页

作者： arpita BISWAS Abhishek MAJUMDAR Soumyabrata das Krishna Lal BAISHNAB Department of Electronics and Communication Engineering National Institute of Technology SilcharSilchar788010India Department of Computer Science&Engineering Karunya Institute of Technology&SciencesCoimbatore641114India Department of Electrical Engineering National Institute of Technology SilcharSilchar788010India

With the advent of modern technologies,IoT has become an alluring field of research.Since IoT connects everything to the network and transmits big data frequently,it can face issues regarding a large amount of energy loss.In this respect,this paper mainly focuses on reducing the energy loss problem and designing an energy-efficient data transfer scenario between IoT devices and clouds.Consequently,a layered architectural framework for IoT-cloud transmission has been proposed that endorses the improvement in energy efficiency,network lifetime and latency.Furthermore,an Opposition based Competitive Swarm Optimizer oriented clustering approach named OCSO-CA has been proposed to get the optimal set of clusters in the IoT device network.The proposed strategy will help in managing intra-cluster and inter-cluster data communications in an energy-efficient way.Also,a comparative analysis of the proposed approach with the state-of-the-art optimization algorithms for clustering has been performed.

关键词： competitive swarm optimization cloud computing clustering IoT

Analysis of phytochemical profile of Terminalia arjuna bark extract with antioxidative and antimicrobial properties

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Asian Pacific Journal of Tropical Biomedicine 2013年第12期3卷 960-966页

作者： Shreya Mandal arpita Patra Animesh Samanta Suchismita Roy arpita Mandal Tapasi das Mahapatra Shrabani Pradhan Koushik das Dilip Kumar Nandi Department of Nutrition Microbiology and Human PhysiologyRaja N L Khan Women's College

Objective:To investigate phytochemical screening,antimicrobial activity and qualitative thin layer chromatographic separation of flavonoid components,antioxidant activity and total flavonoid compound of Terminalia arjuna.Methods:For phytochemical screening,some common and available standard tests were done.Antimicrobial bioassay was done through agar well diffusion method.Detection of antioxidant activity and flavonoid compounds were done through thin layer chromatography.Total antioxidant activity was measured by 2,2-diphenyl-1-picrylhydrazyl(DPPH)in colorimetric method.Aluminum chloride colorimetric method was used for total flavonoid determination.Results:Phytochemical screening showed the active compounds presence in high concentration,such as phytosterol,lactones,flavonoids,phenolic compounds and tannins and glycosides.The anlimicrobial activity of extract showed that greater inhibition zone against Gram negative bacteria than Gram positive bacteria.This methanolic extract showed a promising antioxidant activity,as absorption of DPPH redicles decreased in DPPH free radical scavenging assay.Flavonoids components having antioxidant property present in the methanol extract at a level of199.00 mg quercetin equivalent/g of dried methanol extract in colorimetric method.Conclusions:The Terminalia arjuna bark extract revealed the presence of bio-active constituents which are known to exhibit medicinal as well as physiological activities.

关键词： Terminalia arjuna Phytocompound TLC Antioxidant Total flavonoid Antimicrobial activity DPPH

Finding neoepitopes in mouse models of personalized cancer immunotherapy

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Frontiers in Biology 2016年第5期11卷 366-375页

作者： Sahar Al Seesi Alok das Mohapatra arpita Pawashe Ion I. Mandoiu Fei Duan Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center University of Connecticut Cancer Center Farmington CT 06030 USA Department of Computer Science & Engineering University of Connecticut Storrs CT 06269 USA

BACKGROUND： Cancer immunotherapy uses one＇s own immune system to fight cancerous cells. As immune system is hard- wired to distinguish self and non-self, cancer immunotherapy is predicted to target cancerous cells specifically, therefore is less toxic than chemotherapy and radiation therapy, two major treatments for cancer. Cancer immunologists have spent decades to search for the specific targets in cancerous cells. METHODS： Due to the recent advances in high throughput sequencing and bioinformatics, evidence has merged that the neoantigens in cancerous cells are probably the cancer-specific targets that lead to the destruction of cancer. We will review the transplantable murine tumor models for cancer immunotherapy and the bioinformatics tools used to navigate mouse genome to identify tumor-rejecting neoantigens. RESULTS： Several groups have independently identified point mutations that can be recognized by T cells of host immune system. It is consistent with the note that the formation ofpeptide-MHC I-TCR complex is critical to activate T cells. Both anchor residue and TCR-facing residue mutations have been reported. While TCR-facing residue mutations may directly activate specific T cells, anchor residue mutations improve the binding of peptides to MHC I molecules, which increases the presentation of peptides and the T cell activation indirectly. CONCLUSIONS： Our work indicates that the affinity of neoepitopes for MHC I is not a predictor for anti-tumor immune responses in mice. Instead differential agretopic index （DAI）, the numerical difference of epitope-MHC I affinities between the mutated and un-mutated sequences is a significant predictor. A similar bioinformatics pipeline has been developed to generate personalized vaccines to treat human ovarian cancer in a Phase I clinical trial.

关键词： cancer immunotherapy tumor antigens neoantigens neoepitopes differential agretopic index （DAI） RNA-Seq single nucleotide variant （SNV）

Microbial Removal of Phenol and P-Chlorophenol from Industrial Waste Water Using Rhodococcus sp.RSP8 and Its Growth Kinetic Modeling

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Journal of Water Resource and Protection 2011年第8期3卷 634-642页

作者： Pronoy Kumar Sinha arpita Sinha Manas das 不详

A phenol-degrading microorganism, Rhodococcus sp.RSP8, was used to study the substrate interactions during cell growth on phenol and p-chlorophenol dual substrates. Both phenol and p-chlorophenol could be utilized by the bacteria as the sole carbon and energy sources. When cells grew on the mixture of phenol and p-chlorophenol, strong substrate interactions were observed. The p-chlorophenol inhibited the degradation of phenol, on the other hand, phenol also inhibited the utilization of p-chlorophenol. The overall cell growth rate depends on the co-actions of phenol and p-chlorophenol. In addition, the cell growth and substrate degradation kinetics of phenol, p-chlorophenol as single and mixed substrates for Rhodococcus sp.RSP8 in batch cultures were also investigated over a wide range of initial phenol concentrations (5-1600 mg.L–1) and initial p-chlorophenol concentrations (5 – 250 mg.L–1). The single-substrate kinetics was described well using the Haldane-type kinetic models, with model constants of μm1 = 0.15 h–1, KS1 = 2.22 mg.L–1 and Ki1 = 245.37 mg.L–1 for cell growth on phenol and of μm2 = 0.0782 h–1, KS2 = 1.30 mg.L–1 and Ki2 = 71.77 mg.L–1, K′i2 = 5480 (mg.L–1)2 for cell growth on p-chlorophenol. Proposed cell growth kinetic model was used to characterize the substrates interactions in the dual substrates system.

关键词： Rhodococcus sp.RSP8 Biodegradation Phenol p-chlorophenol Inhibition Kinetics

Insight to the Mode of Action of <i>Allium sativum</i>Leaf Agglutinin (ASAL) Expressing in T<sub>3</sub>Rice Lines on Brown Planthopper

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American Journal of Plant Sciences 2013年第2期4卷 400-407页

作者： arpita Bala Amit Roy Niranjana Behura Daniel Hess Sampa das Division of Plant Biology Bose Institute Kolkata India The Protein Analysis Facility Friedrich Miescher Institute for Biomedical Research Basel The Switzerland

Brown planthopper, the sap sucking hemipteran pest, is one of the major contributors to the yield loss of rice through the world. To combat the situation researchers are interested identifying genes from plant origin having potentiality to develop hemipteran pest resistance. Interestingly, it was observed that rice plants expressing ASAL, a monocot mannose binding lectin, showed significant resistance to brown planthopper and green leafhopper. Additionally, antibiotic resistant marker gene free ASAL expressing rice lines were developed to overcome the biosafety issues. However, the basis behind the resistance against planthoppers is still not clearly understood. Ligand blot assay was performed with total BBMV protein from BPH and a ~56 kDa receptor protein was detected. LC MS/MS analysis revealed that the receptor protein is NADH quinone oxidoreductase (NQO), a key player in electron transport chain, insect defense response and male/female gametogenesis. Presumably interaction of ASAL with NQO may lead to toxicity and loss of fecundity among BPH feeding on ASAL expressing transgenic rice plants. These findings provide a stable scientific basis for considering these transgenic ASAL expressing rice plants as significant product for combating BPH attack associated yield loss of rice.

关键词： Allium sativum leaf agglutinin (ASAL) Hemipteran Pest Management Brown Planthopper NADH Qui-none Oxidoreductase (NQO) Fecundity Transgenic Rice Brush Boarder Membrane Vesicle (BBMV) Protein

Investigation of lnter and Intra-fractional Uncertainties in Lung IMRT Delivery

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Chinese Journal of Biomedical Engineering(English Edition) 2017年第1期26卷 1-4页

作者： Maria das KJ arpita Agarwal Yoganathan SA Gowtharu Raj D Shaleen Kumar Department of Radiotherapy Sanjay Gandhi Postgraduate Institute of Medical SciencesLucknowIndia

Changes in the tumour position due to inter and intra-fractional motion introduce uncertainty in IMRT delivery. In this work, we experimentally evaluated the effect of inter and intra-fractional motion uncertainties in the IMRT delivery. A lung patient was planned with rive field dynamic IMRT for a total dose of60 Gy in 30 fractions using 6 MV photon beam at a dose rate of 400 MU/min. The plan was delivered on varian CL2100 CD linear accelerator with millennium 120 MLC for a single fraction and measured using IMRT Matri XX placed on Quasar motion platform, aligned with respect to isocentre for planar as well as point dose measurements. This measurement was summated for 30 fractions and taken as a reference. 30 measurements were performed for each inter-fractional, intra-fractional and combined effect. The setup errors(Mean+SD) used to simulate the inter-fractional displacements were RL:-0.10+0.27 mm, SI: 0.17+0.45 mm, AP:-0.04+0.38 mm and Rot: 0.02+0.86 degree. The intra-fractional motion was simulated using the motion platform parallel to the MLC leaf motion, for an amplitude of 1 cm and a period of 4 s. The planner fluence of inter, intra-fractional motion and combination of both was analyzed against the reference using gamma criteria of 3%/3 mm. Similarly, the point dose measurements were also compared. The maximum deviation in point dose during a single fraction was-3.8%, 3.1% and-5.9% for inter-fractional, intra-fractional and combined respectively. The same resulted in deviation of-0.4%,-0.3% and 0.1% respectively when summated for 30 fractions.The percentage of pixels failing the gamma criteria during a single fraction was28.0%, 16.4% and 28.5% for inter-fractional, intra-fractional and combined respectively. The same revealed 11.4%, 12.4% and 19.2% respectively when summated. Though the point dose deviations were nullified over 30 fractions, the planner fluence variation was observed to be considerable.

关键词： MRT inter-fraction intra-fraction uncertainties