Generation of Internal Tides: An Interaction of Tides with Variable Topography and Coastal Geometry

Himansu K. Pradhan,A. D. Rao,Sachiko Mohanty 한국해양과학기술원 2015 Ocean science journal Vol.50 No.2

The paper describes tide-topography interaction with changeable width and angle of continental shelf. Experiments are designed with MITgcm over a study area representative of the western Bay of Bengal with an idealized bathymetry. As the actual coastline consists of an irregular configuration, the experiments are set with different coastline geometry. The tidal forcing is incorporated in the model to generate internal tides by adding tidal components in the momentum equations. The density stratification represents the region during May and is kept invariant for all the experiments. Spectral analysis suggests that semi-diurnal internal tides possess the maximum spectral estimate. The peak semi-diurnal estimate is computed to understand its variation over the shelfslope region. The analysis demonstrates that the estimate is smaller for wider shelves against narrow continental shelves. The peak estimate is observed close to 100m local depth over the shelf regardless of the angle and width. Experiments are further continued to distinguish the effect of rotation and geometry of the coast as the shelf width and shelf angle are kept constant. Comparison of spectral estimate is performed without and with rotation for three different coastline configurations: concave, convex and straight. The estimate is noticed maximum in the concave and minimum in the convex shape of the coast. Significant contribution of the rotational effect is seen as an increase in the semi-diurnal peak estimate towards the north of the domain. In order to confirm the effect of the rotation, a similar experiment is performed for the southern hemisphere revealing an enhancement of the estimate towards the south of the domain.

Stage specific transcriptome analysis of liver tissue from a crossbred Korean Native Pig (KNP × Yorkshire)

Himansu Kumar,Krishnamoorthy Srikanth,박원철,이경태,최봉환,김준모,임다정,박종은 충북대학교 동물의학연구소 2018 Journal of Biomedical and Translational Research Vol.19 No.4

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP × Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (|log2FC| > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

A Survey on Virtual Sensor Networks Framework

Himansu Das,Bighnaraj Naik,Bibudendu Pati,Chhabi Rani Panigrahi 보안공학연구지원센터 2014 International Journal of Grid and Distributed Comp Vol.7 No.5

Due to recent advancement in wireless sensor technology and extensive requirement of scalable applications, researchers are designing models of sensor network that can support wide multiplicity of services in a single heterogeneous sensor network infrastructure. In this work, we survey the virtual sensor networks (VSNs) design architecture, principles, service provisioning, sensor cloud architecture, and various applications that are widely used in different areas of VSNs. We propose a new framework for VSNs that can support multiple services and can give a new direction to Wireless Sensor Network (WSN) community.

Parameters Involved in Autophosphorylation in Chronic Myeloid Leukemia: a Systems Biology Approach

Kumar, Himansu,Tichkule, Swapnil,Raj, Utkarsh,Gupta, Saurabh,Srivastava, Swati,Varadwaj, Pritish Kumar Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.13

Background: Chronic myeloid leukemia (CML) is a stem cell disorder characterized by the fusion of two oncogenes namely BCR and ABL with their aberrant expression. Autophosphorylation of BCR-ABL oncogenes results in proliferation of CML. The study deals with estimation of rate constant involved in each step of the cellular autophosphorylation process, which are consequently playing important roles in the proliferation of cancerous cells. Materials and Methods: A mathematical model was proposed for autophosphorylation of BCR-ABL oncogenes utilizing ordinary differential equations to enumerate the rate of change of each responsible system component. The major difficulty to model this process is the lack of experimental data, which are needed to estimate unknown model parameters. Initial concentration data of each substrate and product for BCR-ABL systems were collected from the reported literature. All parameters were optimized through time interval simulation using the fminsearch algorithm. Results: The rate of change versus time was estimated to indicate the role of each state variable that are crucial for the systems. The time wise change in concentration of substrate shows the convergence of each parameter in autophosphorylation process. Conclusions: The role of each constituent parameter and their relative time dependent variations in autophosphorylation process could be inferred.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

Kumar, Himansu,Park, Woncheoul,Lim, Dajeong,Srikanth, Krishnamoorthy,Kim, Jun-Mo,Jia, Xin-Zheng,Han, Jian-Lin,Hanotte, Olivier,Park, Jong-Eun,Oyola, Samuel O. Elsevier 2020 Genomics Vol.112 No.2

<P><B>Abstract</B></P> <P>We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by <I>Bacteroidetes</I> and <I>Firmicutes.</I> We identified 2210 common genes in the two groups. LEfSe showed that the distribution of <I>Coprobacter, Geobacter, Cronobacter, Alloprevotella,</I> and <I>Dysgonomonas</I> were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microbial comparison of scavenging chicken's cecum content between high land and low land region of Ethiopia. </LI> <LI> Differential functional annotations of identified microbiota from both regions. </LI> <LI> Antibiotic resistant genes identification and their differential abundance. </LI> </UL> </P>

Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig

Kumar, Himansu,Srikanth, Krishnamoorthy,Park, Woncheol,Lee, Seung-Hoon,Choi, Bong-Hwan,Kim, Hana,Kim, Yong-Min,Cho, Eun-Seok,Kim, Jin Hyoung,Lee, Jang Hee,Jung, Ji Yeon,Go, Gwang-woong,Lee, Kyung-Tai Elsevier 2019 Gene Vol.703 No.-

<P><B>Abstract</B></P> <P>Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Analysis of lncRNAs in back fat tissues at different developmental stages in the pigs </LI> <LI> A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed. </LI> <LI> KEGG pathway and GO analysis for functional annotation of lncRNAs </LI> <LI> Top DE transcripts were validated by qRTPCR. </LI> <LI> Relation between back fat metabolism and lncRNAs were established. </LI> </UL> </P>

Novel DOT1L ReceptorNatural Inhibitors Involved in Mixed Lineage Leukemia: a Virtual Screening, Molecular Docking and Dynamics Simulation Study

Raj, Utkarsh,Kumar, Himansu,Gupta, Saurabh,Varadwaj, Pritish Kumar Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.9

Background: The human protein methyl-transferase DOT1L catalyzes the methylation of histone H3 on lysine 79 (H3K79) at homeobox genes and is also involved in a number of significant processes ranging from gene expression to DNA-damage response and cell cycle progression. Inhibition of DOT1L activity by shRNA or small-molecule inhibitors has been established to prevent proliferation of various MLL-rearranged leukemia cells in vitro, establishing DOT1L an attractive therapeutic target for mixed lineage leukemia (MLL). Most of the drugs currently in use for the MLL treatment are reported to have low efficacy, hence this study focused on various natural compounds which exhibit minimal toxic effects and high efficacy for the target receptor. Materials and Methods: Structures of human protein methyl-transferase DOT1L and natural compound databases were downloaded from various sources. Virtual screening, molecular docking, dynamics simulation and drug likeness studies were performed for those natural compounds to evaluate and analyze their anti-cancer activity. Results: The top five screened compounds possessing good binding affinity were identified as potential high affinity inhibitors against DOT1L's active site. The top ranking molecule amongst the screened ligands had a Glide g-score of -10.940 kcal/mol and Glide e-model score of -86.011 with 5 hydrogen bonds and 12 hydrophobic contacts. This ligand's behaviour also showed consistency during the simulation of protein-ligand complex for 20000 ps, which is indicative of its stability in the receptor pocket. Conclusions: The ligand obtained out of this screening study can be considered as a potential inhibitor for DOT1L and further can be treated as a lead for the drug designing pipeline.