Siddhartha Sankar Satapathy

Tezpur University

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Suvendra Kumar Ray

Tezpur University

Piyali Sen

Tezpur University

Madhusmita Dash

National Institute of Technology Arunachal Pradesh

Malay Kishore Dutta

Amity University

Alak Kumar Buragohain

Tezpur University

Ramesh Chandra Deka

Tezpur University

Suvendra Kumar Ray

Tezpur University

Nima D. Namsa

Tezpur University

Annushree Kurmi

Tezpur University

Edward J. Feil

University of Bath

Cooperative Institutions

Tezpur University

Indian Institute of Technology Guwahati

Indian Institute of Technology Mandi

Dibrugarh University

Post Graduate Institute of Medical Education and Research

The University of Tokyo

University of Delhi

University of Oxford

Indian Institute of Science Bangalore

University of Calcutta

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Selection on GGU and CGU Codons in the High Expression Genes in Bacteria

Journal of Molecular Evolution (2013)

Siddhartha Sankar Satapathy Bhesh Raj Powdel Malay Kishore Dutta Alak Kumar Buragohain Suvendra Kumar Ray

Negative selection

Coding region

Bacterial genome size

10.1007/s00239-013-9596-6

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Citations (14)

Codon usage in conserved sites is more biased compared to variable sites in the SARS-CoV-2 genome

International Journal of Bioinformatics Research and Applications (2024)

Madhusmita Dash Annushree Kurmi Preetisudha Meher Siddhartha Sankar Satapathy Nima D. Namsa

High error rate in SARS-CoV-2 genome replication allows the virus to adapt to different environments and selective pressures. In this study, 35% of codons of the protein-coding sequences of the genome were observed to have undergone base substitution mutations. Machine learning based comparative analysis of usage between conserved codons and the remaining variable codons of the protein-coding genes revealed that the codon usage patterns between the two groups are significantly different. Codon usage values in the variable region resemble genome composition, whereas the values in the conserved regions were highly variable. This differential codon usage suggests that the conserved regions are under influence of selection pressure in this virus genome. Further, the selection pressure on codon usage and the nucleotide substitution biases act towards increasing A and T base composition in SARS-CoV-2 genome. Our observations on the base substitution will help us in understanding evolution of this SARS-CoV-2 virus genome.

2019-20 coronavirus outbreak

Sars virus

10.1504/ijbra.2024.137368

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TREEPSI: tree based energy efficient protocol for sensor information

Siddhartha Sankar Satapathy Nityananda Sarma

Limited battery powers of sensor nodes demand routing protocol for sensor network that consume minimum possible amount of energy and hence give longer life to the system. In a sensor network, sensor nodes are the potential source of information and they need to send their sensed/collected information to a remote base station (BS)/Sink. Generally, it needs a fixed amount of energy to receive one bit of information and an additional amount of energy to transmit the same. This additional amount depends on the transmission range. So, if all nodes transmit directly to the BS, then they will quickly deplete their energy. Therefore, a multi-hop routing protocol is needed to give longer life of the network. LEACH (aW. Heinzelman et al., 2000) (aW. Heinzelman et al., 2000) is an elegant energy efficient protocol where clusters are formed to fuse data before transmission to base station. By randomizing the cluster heads chosen to transmit to the base station, LEACH achieves a factor of 8 improvements over direct transmission, as measured in terms of nodes longevity. PEGASIS (aS. Lindsey and C. Raghavendra, 2001, 2002) is a chain based protocol that is an improvement over LEACH. In PEGASIS, each node communicates only with a close neighbor and takes turns in transmitting to the base station, thus reducing the amount of energy spent per round. It performs better than LEACH by about 100 - 300% for different network sizes and topologies. In this paper, we propose TREEPSI (tree based energy efficient protocol for sensor information) which gives up to 30% better performance (in terms of energy efficiency) than PEGASIS

Sink (geography)

Zone Routing Protocol

10.1109/wocn.2006.1666530

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Citations (90)

A symmetric key based secured data gathering protocol for WSN

Prabhudutta Mohanty Sangram Panigrahi Nityananda Sarma Siddhartha Sankar Satapathy

Wireless sensor network (WSN) is usually used in civil and military applications for gathering data from the surrounding environment. As WSN is a self configured network and mostly works in an unattended wireless environment, there is a lot of scope for the adversaries to tamper the sensed data as well as may try to alter the underlying working principle of the network. Several factors like, physical exposure of the sensor nodes to the adversaries, the ad-hoc network infrastructure etc. makes WSN more prone to security threats. Providing security solution to the WSN is again a difficult task due to inherent constraints associated with the sensor nodes like, limited processing power, smaller memory and fixed battery power. Security solutions based on public key cryptography are not usually recommended for WSN because of comparatively more computational cost. In this paper we have analyzed different security threats associated with the energy efficient data gathering protocol HCEPSN and proposed a symmetric key based security solution to it.

10.1109/icasid.2009.5276918

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Citations (6)

Higher frequency of transition mutation over transversion mutation in genomes: evidence from the binding energy calculation of base pairs using DFT

bioRxiv (Cold Spring Harbor Laboratory) (2024)

N. Deka Nand Kishor Gour Pradeep Pant Siddhartha Sankar Satapathy Nasimul Hoda

Base substitution mutations such as transition (ti) and transversion (tv) in organisms are major driving force in molecular evolution. In this study, different possible types of base pairing that can cause ti and tv were investigated using the density functional theory (DFT) method. The chemical structures of bases as well as base pairs were optimized using B3LYP hybrid functional along with 6-31G(d,p) basis set. We performed single point energy calculation of all optimized species using the same functional but combined with higher diffuse and polarized basis set i.e. 6-311++G(d,p) to get more refined energy of all species. The binding energy of various base pairs was calculated considering basis set superposition error (BSSE) as well as without BSSE. The binding energy of the base pairs leading to ti were found to be more stable than that of the base pairs leading to tv. This was interesting considering the observations in organisms that tis are more frequent than tvs. Among the base pairs leading to the same ti, G(keto): T (enol) was found to be more stable than A(imino):C(amino) base pairs. This theoretical study of binding energy of different base pairs using the DFT method has provided additional evidences in support to the biological observations of a higher transition rate than transversion in genomes.

Transversion

Base (topology)

Mutation frequency

10.1101/2024.11.28.625875

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Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria

Journal of Molecular Evolution (2022)

Piyali Sen Ruksana Aziz Ramesh Chandra Deka Edward J. Feil Suvendra Kumar Ray

Transversion

Intergenic region

10.1007/s00239-021-10045-x

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Citations (8)

SINR based Vertical Handoff Algorithm between GPRS and Wi-Fi Networks

International Journal of Computer and Communication Technology (2011)

Sudipta Patowary Nityananda Sarma Siddhartha Sankar Satapathy

Next generation wireless network is foreseen as the combination of heterogeneous wireless networks capable of providing enhanced services to mobile users. Vertical handoff is a crucial issue in providing service to mobile users, in a heterogeneous network. To maintain continuous service during vertical handoff period, the handoff procedure should consider the noise and interference in the networks. In this article, we have proposed an algorithm based on the received signal to inference plus noise ratio (SINR) for handoff between GPRS and Wi-Fi networks. Here SINR from Wi-Fi network is converted to the equivalent SINR of the GPRS network and vice-versa, so that the handoff algorithm can have the knowledge of achievable bandwidths in both the networks. This helps in taking a handoff decision. Simulation study on handoff between GPRS and Wi-Fi networks using QualNet showed that consideration of received SINR during the vertical handoff period maintains better system throughput than considering received signal strength (RSS) as handoff criteria.

RSS

Signal-to-interference-plus-noise ratio

Vertical Handover

10.47893/ijcct.2011.1072

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Citations (5)

Entner–Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP inRalstonia solanacearum

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Poonam Jyoti Manu Shree Chandrakant Joshi Tulika Prakash Suvendra Kumar Ray

Abstract In Ralstonia solanacearum , a devastating phytopathogen whose metabolism is poorly understood, we observed that Entner-Doudoroff (ED) pathway and NonOxidative pentose phosphate pathway (OxPPP) bypasses glycolysis and OxPPP under glucose oxidation. Evidences derived from 13 C stable isotopes feeding and genome annotation based comparative metabolic network analysis supported the observations. Comparative metabolic network analysis derived from the currently available 53 annotated R. solanacearum strains also including the recently reported strain (F1C1), representing the four phylotypes confirmed the lack of key genes coding for phosphofructokinase ( pfk-1 ) and phosphogluconate dehydrogenase ( gnd ) enzymes that are relevant for glycolysis and OxPPP respectively. R. solanacearum F1C1 cells fed with 13 C Glucose (99%[1- 13 C]- or 99%[1,2- 13 C]- or 40%[ 13 C 6 ]-glucose) followed by GC-MS based labelling analysis of fragments from amino acids, glycerol and ribose provided clear evidence that rather than Glycolysis and OxPPP, ED pathway and NonOxPPP are the main routes sustaining metabolism in R. solanacearum . The 13 C incorporation in the mass ions of alanine (m/z 260, m/z 232); valine (m/z 288, m/z 260), glycine (m/z 218), serine (m/z 390, m/z 362), histidine (m/z 440, m/z 412), tyrosine (m/z 466, m/z 438), phenylalanine (m/z 336, m/z 308), glycerol (m/z 377) and ribose (m/z 160) mapped the pathways supporting the observations. The outcomes help better defining the central carbon metabolic network of R. solanacearum that can be integrated with 13 C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. Importance Understanding the metabolic versatility of Ralstonia solanacearum is important as it regulates the tradeoff between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on potential roles of Glycolysis and Oxidative pentose phosphate pathways (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13 C stable isotopes feeding and genome annotation based comparative metabolic network analysis that Entner-Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP during the oxidation of Glucose, one of the host xylem pool that serves as a potential carbon source (5). The outcomes help better defining the central carbon metabolic network of R. solanacearum that can be integrated with 13 C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood.

Ralstonia solanacearum

Biovar

Metabolic pathway

10.1101/2020.01.31.929778

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Citations (0)

Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins

Journal of Genetics (2016)

Vishwa Jyoti Baruah Siddhartha Sankar Satapathy Bhesh Raj Powdel Rocktotpal Konwarh Alak Kumar Buragohain

Genetic Code

10.1007/s12041-016-0667-5

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