1
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Neal AL, Barrat HA, Bacq-Lebreuil A, Qin Y, Zhang X, Takahashi T, Rubio V, Hughes D, Clark IM, Cárdenas LM, Gardiner LJ, Krishna R, Glendining ML, Ritz K, Mooney SJ, Crawford JW. Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype. Nat Food 2023; 4:51-60. [PMID: 37118575 DOI: 10.1038/s43016-022-00671-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/14/2022] [Indexed: 04/30/2023]
Abstract
Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Success relies on understanding coupled nitrogen and carbon metabolism in soils, their associated influences on soil structure and the processes controlling nitrogen transformations at scales relevant to microbial activity. Here we show that the influence of organic matter on arable soil nitrogen transformations can be decoded by integrating metagenomic data with soil structural parameters. Our approach provides a mechanistic explanation of why organic matter is effective in reducing nitrous oxide losses while supporting system resilience. The relationship between organic carbon, soil-connected porosity and flow rates at scales relevant to microbes suggests that important increases in nutrient-use efficiency could be achieved at lower organic carbon stocks than currently envisaged.
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Affiliation(s)
- Andrew L Neal
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK.
| | - Harry A Barrat
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
- The Carbon Trust, London, UK
| | - Aurélie Bacq-Lebreuil
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
- Genesis, Lisors, France
| | - Yuwei Qin
- Department of Environmental Sciences, Wageningen University, Wageningen, The Netherlands
| | - Xiaoxian Zhang
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Taro Takahashi
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
- Bristol Veterinary School, University of Bristol, Langford, UK
| | - Valentina Rubio
- Programa de Producción y Sustentabilidad Ambiental, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - David Hughes
- Intelligent Data Ecosystems, Rothamsted Research, Harpenden, UK
| | - Ian M Clark
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Laura M Cárdenas
- Net Zero and Resilient Farming, Rothamsted Research, North Wyke, UK
| | | | - Ritesh Krishna
- IBM Research Europe - Daresbury, The Hartree Centre, Warrington, UK
| | | | - Karl Ritz
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - Sacha J Mooney
- School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - John W Crawford
- Adam Smith Business School, University of Glasgow, Glasgow, UK
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2
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Whiteford S, van’t Hof AE, Krishna R, Marubbi T, Widdison S, Saccheri IJ, Guest M, Morrison NI, Darby AC. Recovering individual haplotypes and a contiguous genome assembly from pooled long-read sequencing of the diamondback moth (Lepidoptera: Plutellidae). G3 (Bethesda) 2022; 12:jkac210. [PMID: 35980174 PMCID: PMC9526047 DOI: 10.1093/g3journal/jkac210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The assembly of divergent haplotypes using noisy long-read data presents a challenge to the reconstruction of haploid genome assemblies, due to overlapping distributions of technical sequencing error, intralocus genetic variation, and interlocus similarity within these data. Here, we present a comparative analysis of assembly algorithms representing overlap-layout-consensus, repeat graph, and de Bruijn graph methods. We examine how postprocessing strategies attempting to reduce redundant heterozygosity interact with the choice of initial assembly algorithm and ultimately produce a series of chromosome-level assemblies for an agricultural pest, the diamondback moth, Plutella xylostella (L.). We compare evaluation methods and show that BUSCO analyses may overestimate haplotig removal processing in long-read draft genomes, in comparison to a k-mer method. We discuss the trade-offs inherent in assembly algorithm and curation choices and suggest that "best practice" is research question dependent. We demonstrate a link between allelic divergence and allele-derived contig redundancy in final genome assemblies and document the patterns of coding and noncoding diversity between redundant sequences. We also document a link between an excess of nonsynonymous polymorphism and haplotigs that are unresolved by assembly or postassembly algorithms. Finally, we discuss how this phenomenon may have relevance for the usage of noisy long-read genome assemblies in comparative genomics.
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Affiliation(s)
- Samuel Whiteford
- Corresponding author: Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Arjen E van’t Hof
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- IBM Research UK, STFC Daresbury Laboratory, Warrington WA4 4AD, UK
| | | | - Stephanie Widdison
- General Bioinformatics, Jealott's Hill International Research Centre, Bracknell RG42 6EY, UK
| | - Ilik J Saccheri
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Marcus Guest
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | | | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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3
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Elisseev V, Gardiner LJ, Krishna R. Scalable in-memory processing of omics workflows. Comput Struct Biotechnol J 2022; 20:1914-1924. [PMID: 35521547 PMCID: PMC9052061 DOI: 10.1016/j.csbj.2022.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Vadim Elisseev
- IBM Research Europe, Hartree Centre, Daresbury Laboratory, Keckwick Lane, WarringtonWA4 4AD, Cheshire, UK
- Wrexham Glyndwr University, Mold Rd, Wrexham LL11 2AW, Wales, UK
| | - Laura-Jayne Gardiner
- IBM Research Europe, Hartree Centre, Daresbury Laboratory, Keckwick Lane, WarringtonWA4 4AD, Cheshire, UK
| | - Ritesh Krishna
- IBM Research Europe, Hartree Centre, Daresbury Laboratory, Keckwick Lane, WarringtonWA4 4AD, Cheshire, UK
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4
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Gardiner LJ, Krishna R. Bluster or Lustre: Can AI Improve Crops and Plant Health? Plants (Basel) 2021; 10:plants10122707. [PMID: 34961177 PMCID: PMC8707749 DOI: 10.3390/plants10122707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
In a changing climate where future food security is a growing concern, researchers are exploring new methods and technologies in the effort to meet ambitious crop yield targets. The application of Artificial Intelligence (AI) including Machine Learning (ML) methods in this area has been proposed as a potential mechanism to support this. This review explores current research in the area to convey the state-of-the-art as to how AI/ML have been used to advance research, gain insights, and generally enable progress in this area. We address the question-Can AI improve crops and plant health? We further discriminate the bluster from the lustre by identifying the key challenges that AI has been shown to address, balanced with the potential issues with its usage, and the key requisites for its success. Overall, we hope to raise awareness and, as a result, promote usage, of AI related approaches where they can have appropriate impact to improve practices in agricultural and plant sciences.
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Pradhan T, Kumar V, Surya H E, Krishna R, John S, Jissa VT, Anjana S, Chandramohan K, Nair SA. STIL Endows Oncogenic and Stem-Like Attributes to Colorectal Cancer Plausibly by Shh and Wnt Signaling. Front Oncol 2021; 11:581671. [PMID: 34485108 PMCID: PMC8416176 DOI: 10.3389/fonc.2021.581671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/21/2021] [Indexed: 11/28/2022] Open
Abstract
The discovery of a potent gene regulating tumorigenesis and drug resistance is of high clinical importance. STIL is an oncogene; however, its molecular associations and role in colorectal oncogenesis are unknown. In this study, we have explored the role of STIL gene in tumorigenesis and studied its molecular targets in colorectal cancer (CRC). STIL silencing reduced proliferation and tumor growth in CRC. Further, STIL was found to regulate stemness markers CD133 and CD44 and drug resistant markers thymidylate synthase, ABCB1, and ABCG2 both in in-vitro and in-vivo CRC models. In addition, high expression of STIL mRNA was found to be associated with reduced disease-free survival in CRC cases. Interestingly, we observed that STIL-mediated regulation of stemness and drug resistant genes is not exclusively governed by Sonic hedgehog (Shh) signaling. Remarkably, we found STIL regulate β-catenin levels through p-AKT, independent of Shh pathway. This partially answers Shh independent regulatory mechanism of cancer stem cell (CSC) markers by STIL. Our study suggests an instrumental role of STIL in molecular manifestation of CRC and progression.
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Affiliation(s)
- Tapas Pradhan
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Vikas Kumar
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Evangeline Surya H
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - R Krishna
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Samu John
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - V T Jissa
- Achutha Menon Centre for Health Science Studies (AMCHSS), Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - S Anjana
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - K Chandramohan
- Department of Surgical Oncology, Regional Cancer Centre, Trivandrum, India
| | - S Asha Nair
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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6
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Gardiner LJ, Haiminen N, Utro F, Parida L, Seabolt E, Krishna R, Kaufman JH. Re-purposing software for functional characterization of the microbiome. Microbiome 2021; 9:4. [PMID: 33422152 PMCID: PMC7797099 DOI: 10.1186/s40168-020-00971-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classification of the microorganisms that are present in a given environment. Additional investigation is then required to uncover the functionality of the microbial community, in order to characterize its currently or potentially active biological processes. Such functional analysis of metagenomic data can be computationally demanding for high-throughput sequencing experiments. Instead, we can directly compare sequencing reads to a functionally annotated database. However, since reads frequently match multiple sequences equally well, analyses benefit from a hierarchical annotation tree, e.g. for taxonomic classification where reads are assigned to the lowest taxonomic unit. RESULTS To facilitate functional microbiome analysis, we re-purpose well-known taxonomic classification tools to allow us to perform direct functional sequencing read classification with the added benefit of a functional hierarchy. To enable this, we develop and present a tree-shaped functional hierarchy representing the molecular function subset of the Gene Ontology annotation structure. We use this functional hierarchy to replace the standard phylogenetic taxonomy used by the classification tools and assign query sequences accurately to the lowest possible molecular function in the tree. We demonstrate this with simulated and experimental datasets, where we reveal new biological insights. CONCLUSIONS We demonstrate that improved functional classification of metagenomic sequencing reads is possible by re-purposing a range of taxonomic classification tools that are already well-established, in conjunction with either protein or nucleotide reference databases. We leverage the advances in speed, accuracy and efficiency that have been made for taxonomic classification and translate these benefits for the rapid functional classification of microbiomes. While we focus on a specific set of commonly used methods, the functional annotation approach has broad applicability across other sequence classification tools. We hope that re-purposing becomes a routine consideration during bioinformatic resource development. Video abstract.
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Affiliation(s)
| | - Niina Haiminen
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 USA
| | - Filippo Utro
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 USA
| | - Laxmi Parida
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 USA
| | - Ed Seabolt
- IBM Almaden Research Center, San Jose, CA 95120 USA
| | - Ritesh Krishna
- IBM Research, The Hartree Centre, Warrington, WA4 4AD UK
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7
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Abstract
Genomics is both a data- and compute-intensive discipline. The success of genomics depends on an adequate informatics infrastructure that can address growing data demands and enable a diverse range of resource-intensive computational activities. Designing a suitable infrastructure is a challenging task, and its success largely depends on its adoption by users. In this article, we take a user-centric view of the genomics, where users are bioinformaticians, computational biologists, and data scientists. We try to take their point of view on how traditional computational activities for genomics are expanding due to data growth, as well as the introduction of big data and cloud technologies. The changing landscape of computational activities and new user requirements will influence the design of future genomics infrastructures.
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Affiliation(s)
- Ritesh Krishna
- IBM Research Europe, The Hartree Centre STFC Laboratory, Warrington WA4 4AD, UK.,IBM Research Europe, The Hartree Centre STFC Laboratory, Warrington WA4 4AD, UK
| | - Vadim Elisseev
- IBM Research Europe, The Hartree Centre STFC Laboratory, Warrington WA4 4AD, UK.,IBM Research Europe, The Hartree Centre STFC Laboratory, Warrington WA4 4AD, UK
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8
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Utro F, Haiminen N, Siragusa E, Gardiner LJ, Seabolt E, Krishna R, Kaufman JH, Parida L. Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes. iScience 2020; 23:100988. [PMID: 32248063 PMCID: PMC7125348 DOI: 10.1016/j.isci.2020.100988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022] Open
Abstract
Increasingly available microbial reference data allow interpreting the composition and function of previously uncharacterized microbial communities in detail, via high-throughput sequencing analysis. However, efficient methods for read classification are required when the best database matches for short sequence reads are often shared among multiple reference sequences. Here, we take advantage of the fact that microbial sequences can be annotated relative to established tree structures, and we develop a highly scalable read classifier, PRROMenade, by enhancing the generalized Burrows-Wheeler transform with a labeling step to directly assign reads to the corresponding lowest taxonomic unit in an annotation tree. PRROMenade solves the multi-matching problem while allowing fast variable-size sequence classification for phylogenetic or functional annotation. Our simulations with 5% added differences from reference indicated only 1.5% error rate for PRROMenade functional classification. On metatranscriptomic data PRROMenade highlighted biologically relevant functional pathways related to diet-induced changes in the human gut microbiome.
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Affiliation(s)
- Filippo Utro
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Niina Haiminen
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Enrico Siragusa
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | | | - Ed Seabolt
- IBM Research, Almaden Research Center, San Jose, CA 95120, USA
| | - Ritesh Krishna
- IBM Research, The Hartree Centre, Warrington, WA4 4AD, UK
| | - James H Kaufman
- IBM Research, Almaden Research Center, San Jose, CA 95120, USA.
| | - Laxmi Parida
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA.
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9
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Goodhead I, Blow F, Brownridge P, Hughes M, Kenny J, Krishna R, McLean L, Pongchaikul P, Beynon R, Darby AC. Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microb Genom 2020; 6:e000285. [PMID: 31922467 PMCID: PMC7067036 DOI: 10.1099/mgen.0.000285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/10/2019] [Indexed: 01/30/2023] Open
Abstract
The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple 'omic' strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.
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Affiliation(s)
- Ian Goodhead
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- School of Science, Engineering and Environment, Peel Building, University of Salford, M5 4WT, UK
| | - Frances Blow
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA
| | - Philip Brownridge
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Margaret Hughes
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- IBM Research UK, STFC Daresbury Laboratory, Warrington, WA4 4AD, UK
| | - Lynn McLean
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Pisut Pongchaikul
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Rob Beynon
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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10
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Gopi T, Swetha G, Shekar SC, Krishna R, Ramakrishna C, Saini B, Rao P. Ozone catalytic oxidation of toluene over 13X zeolite supported metal oxides and the effect of moisture on the catalytic process. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2016.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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11
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Turner J, Krishna R, Van't Hof AE, Sutton ER, Matzen K, Darby AC. The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti. Parasit Vectors 2018; 11:549. [PMID: 30342535 PMCID: PMC6195999 DOI: 10.1186/s13071-018-3090-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/31/2018] [Indexed: 11/26/2022] Open
Abstract
Background Aedes aegypti is the principal vector of several important arboviruses. Among the methods of vector control to limit transmission of disease are genetic strategies that involve the release of sterile or genetically modified non-biting males, which has generated interest in manipulating mosquito sex ratios. Sex determination in Ae. aegypti is controlled by a non-recombining Y chromosome-like region called the M locus, yet characterisation of this locus has been thwarted by the repetitive nature of the genome. In 2015, an M locus gene named Nix was identified that displays the qualities of a sex determination switch. Results With the use of a whole-genome bacterial artificial chromosome (BAC) library, we amplified and sequenced a ~200 kb region containing the male-determining gene Nix. In this study, we show that Nix is comprised of two exons separated by a 99 kb intron primarily composed of repetitive DNA, especially transposable elements. Conclusions Nix, an unusually large and highly repetitive gene, exhibits features in common with Y chromosome genes in other organisms. We speculate that the lack of recombination at the M locus has allowed the expansion of repeats in a manner characteristic of a sex-limited chromosome, in accordance with proposed models of sex chromosome evolution in insects. Electronic supplementary material The online version of this article (10.1186/s13071-018-3090-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joe Turner
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Oxitec Ltd., 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Ritesh Krishna
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,IBM Research UK, STFC Daresbury Laboratory, Warrington, WA4 4AD, UK
| | - Arjen E Van't Hof
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Elizabeth R Sutton
- Oxitec Ltd., 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK.,Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.,Sistemic, West of Scotland Science Park, Glasgow, G20 0SP, UK
| | - Kelly Matzen
- Oxitec Ltd., 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Alistair C Darby
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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12
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Cipcigan F, Carrieri AP, Pyzer-Knapp EO, Krishna R, Hsiao YW, Winn M, Ryadnov MG, Edge C, Martyna G, Crain J. Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions. J Chem Phys 2018; 148:241744. [DOI: 10.1063/1.5027261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Flaviu Cipcigan
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | | | | | - Ritesh Krishna
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | - Ya-Wen Hsiao
- STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom
| | - Martyn Winn
- STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom
| | - Maxim G. Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, United Kingdom
| | - Colin Edge
- GSK Medicines Research Centre, Stevenage SG1 2NY, United Kingdom
| | - Glenn Martyna
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Jason Crain
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, United Kingdom
- Maxwell Centre, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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13
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Lindley RI, Anderson CS, Billot L, Forster A, Hackett ML, Harvey LA, Jan S, Li Q, Liu H, Langhorne P, Maulik PK, Murthy GVS, Walker MF, Pandian JD, Alim M, Felix C, Syrigapu A, Tugnawat DK, Verma SJ, Shamanna BR, Hankey G, Thrift A, Bernhardt J, Mehndiratta MM, Jeyaseelan L, Donnelly P, Byrne D, Steley S, Santhosh V, Chilappagari S, Mysore J, Roy J, Padma MV, John L, Aaron S, Borah NC, Vijaya P, Kaul S, Khurana D, Sylaja PN, Halprashanth DS, Madhusudhan BK, Nambiar V, Sureshbabu S, Khanna MC, Narang GS, Chakraborty D, Chakraborty SS, Biswas B, Kaura S, Koundal H, Singh P, Andrias A, Thambu DS, Ramya I, George J, Prabhakar AT, Kirubakaran P, Anbalagan P, Ghose M, Bordoloi K, Gohain P, Reddy NM, Reddy KV, Rao TNM, Alladi S, Jalapu VRR, Manchireddy K, Rajan A, Mehta S, Katoch C, Das B, Jangir A, Kaur T, Sreedharan S, Sivasambath S, Dinesh S, Shibi BS, Thangaraj A, Karunanithi A, Sulaiman SMS, Dehingia K, Das K, Nandini C, Thomas NJ, Dhanya TS, Thomas N, Krishna R, Aneesh V, Krishna R, Khullar S, Thouman S, Sebastian I. Family-led rehabilitation after stroke in India (ATTEND): a randomised controlled trial. Lancet 2017; 390:588-599. [PMID: 28666682 DOI: 10.1016/s0140-6736(17)31447-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/17/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Most people with stroke in India have no access to organised rehabilitation services. The effectiveness of training family members to provide stroke rehabilitation is uncertain. Our primary objective was to determine whether family-led stroke rehabilitation, initiated in hospital and continued at home, would be superior to usual care in a low-resource setting. METHODS The Family-led Rehabilitation after Stroke in India (ATTEND) trial was a prospectively randomised open trial with blinded endpoint done across 14 hospitals in India. Patients aged 18 years or older who had had a stroke within the past month, had residual disability and reasonable expectation of survival, and who had an informal family-nominated caregiver were randomly assigned to intervention or usual care by site coordinators using a secure web-based system with minimisation by site and stroke severity. The family members of participants in the intervention group received additional structured rehabilitation training-including information provision, joint goal setting, carer training, and task-specific training-that was started in hospital and continued at home for up to 2 months. The primary outcome was death or dependency at 6 months, defined by scores 3-6 on the modified Rankin scale (range, 0 [no symptoms] to 6 [death]) as assessed by masked observers. Analyses were by intention to treat. This trial is registered with Clinical Trials Registry-India (CTRI/2013/04/003557), Australian New Zealand Clinical Trials Registry (ACTRN12613000078752), and Universal Trial Number (U1111-1138-6707). FINDINGS Between Jan 13, 2014, and Feb 12, 2016, 1250 patients were randomly assigned to intervention (n=623) or control (n=627) groups. 33 patients were lost to follow-up (14 intervention, 19 control) and five patients withdrew (two intervention, three control). At 6 months, 285 (47%) of 607 patients in the intervention group and 287 (47%) of 605 controls were dead or dependent (odds ratio 0·98, 95% CI 0·78-1·23, p=0·87). 72 (12%) patients in the intervention group and 86 (14%) in the control group died (p=0·27), and we observed no difference in rehospitalisation (89 [14%]patients in the intervention group vs 82 [13%] in the control group; p=0·56). We also found no difference in total non-fatal events (112 events in 82 [13%] intervention patients vs 110 events in 79 [13%] control patients; p=0·80). INTERPRETATION Although task shifting is an attractive solution for health-care sustainability, our results do not support investment in new stroke rehabilitation services that shift tasks to family caregivers, unless new evidence emerges. A future avenue of research should be to investigate the effects of task shifting to health-care assistants or team-based community care. FUNDING The National Health and Medical Research Council of Australia.
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Krishna R, Gheyas F, Liu Y, Hagen DR, Walker B, Chawla A, Cote J, Blaustein RO, Gutstein DE. Chronic Administration of Anacetrapib Is Associated With Accumulation in Adipose and Slow Elimination. Clin Pharmacol Ther 2017; 102:832-840. [DOI: 10.1002/cpt.700] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/14/2017] [Accepted: 03/28/2017] [Indexed: 11/07/2022]
Affiliation(s)
- R Krishna
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | - F Gheyas
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | - Y Liu
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | - DR Hagen
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | - B Walker
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | - A Chawla
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | - J Cote
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
| | | | - DE Gutstein
- MRL, Merck & Co., Inc.; Kenilworth New Jersey
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15
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Gopi T, Swetha G, Chandra Shekar S, Ramakrishna C, Saini B, Krishna R, Rao P. Catalytic decomposition of ozone on nanostructured potassium and proton containing δ-MnO2 catalysts. CATAL COMMUN 2017. [DOI: 10.1016/j.catcom.2017.01.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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16
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John J, Saranathan R, Adigopula LN, Thamodharan V, Singh SP, Lakshmi TP, CharanTej MA, Rao RS, Krishna R, Rao HSP, Prashanth K. The quorum sensing molecule N-acyl homoserine lactone produced by Acinetobacter baumannii displays antibacterial and anticancer properties. Biofouling 2016; 32:1029-1047. [PMID: 27643959 DOI: 10.1080/08927014.2016.1221946] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Secretory N-acyl homoserine lactones (AHLs) mediate quorum sensing (QS) in bacteria. AHLs are shown to be inhibitory for an unrelated group of bacteria and might mimic host signalling elements, thereby subverting the regulatory events in host cells. This study investigated the AHL produced by Acinetobacter baumannii and analysed its effect on other bacterial species and mammalian cells. Chemically characterized AHL had an m/z value of 325 with a molecular formula C18H31NO4 and showed its inhibitory potential against Staphylococcus aureus. Molecular docking studies identified D-alanine-D-alanine synthetase A, a cell wall synthesizing enzyme of S. aureus having a strong binding affinity towards AHL. Electron microscopy showed the disruption and sloughing off of the S. aureus cell wall when treated with AHL. In vitro experiments revealed that this bacteriostatic AHL showed time-dependent activity and induced apoptosis in cancer cell lines. This compound could be a potential structural backbone for constructing new AHL analogues against S. aureus. The findings emphasize the need to re-evaluate all previously characterized AHLs for any additional new biological functions other than QS.
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Affiliation(s)
- James John
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
- d Department of Biotechnology , SRF, Interdisciplinary Program in Life Sciences, Pondicherry University , Puducherry , India
| | - Rajagopalan Saranathan
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | | | - Vasanth Thamodharan
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - Satya Prakash Singh
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - T Pragna Lakshmi
- c Centre for Bioinformatics , School of Life Sciences, Pondicherry University , Puducherry , India
| | - Mallu Abhiram CharanTej
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - R Srinivasa Rao
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - R Krishna
- c Centre for Bioinformatics , School of Life Sciences, Pondicherry University , Puducherry , India
| | | | - K Prashanth
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
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Affiliation(s)
- Jenny A. Hodgson
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
| | - David W. Wallis
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
| | - Ritesh Krishna
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
| | - Stephen J. Cornell
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
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18
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Armstrong SD, Xia D, Bah GS, Krishna R, Ngangyung HF, LaCourse EJ, McSorley HJ, Kengne-Ouafo JA, Chounna-Ndongmo PW, Wanji S, Enyong PA, Taylor DW, Blaxter ML, Wastling JM, Tanya VN, Makepeace BL. Stage-specific Proteomes from Onchocerca ochengi, Sister Species of the Human River Blindness Parasite, Uncover Adaptations to a Nodular Lifestyle. Mol Cell Proteomics 2016; 15:2554-75. [PMID: 27226403 PMCID: PMC4974336 DOI: 10.1074/mcp.m115.055640] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 04/30/2016] [Indexed: 12/13/2022] Open
Abstract
Despite 40 years of control efforts, onchocerciasis (river blindness) remains one of the most important neglected tropical diseases, with 17 million people affected. The etiological agent, Onchocerca volvulus, is a filarial nematode with a complex lifecycle involving several distinct stages in the definitive host and blackfly vector. The challenges of obtaining sufficient material have prevented high-throughput studies and the development of novel strategies for disease control and diagnosis. Here, we utilize the closest relative of O. volvulus, the bovine parasite Onchocerca ochengi, to compare stage-specific proteomes and host-parasite interactions within the secretome. We identified a total of 4260 unique O. ochengi proteins from adult males and females, infective larvae, intrauterine microfilariae, and fluid from intradermal nodules. In addition, 135 proteins were detected from the obligate Wolbachia symbiont. Observed protein families that were enriched in all whole body extracts relative to the complete search database included immunoglobulin-domain proteins, whereas redox and detoxification enzymes and proteins involved in intracellular transport displayed stage-specific overrepresentation. Unexpectedly, the larval stages exhibited enrichment for several mitochondrial-related protein families, including members of peptidase family M16 and proteins which mediate mitochondrial fission and fusion. Quantification of proteins across the lifecycle using the Hi-3 approach supported these qualitative analyses. In nodule fluid, we identified 94 O. ochengi secreted proteins, including homologs of transforming growth factor-β and a second member of a novel 6-ShK toxin domain family, which was originally described from a model filarial nematode (Litomosoides sigmodontis). Strikingly, the 498 bovine proteins identified in nodule fluid were strongly dominated by antimicrobial proteins, especially cathelicidins. This first high-throughput analysis of an Onchocerca spp. proteome across the lifecycle highlights its profound complexity and emphasizes the extremely close relationship between O. ochengi and O. volvulus The insights presented here provide new candidates for vaccine development, drug targeting and diagnostic biomarkers.
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Affiliation(s)
- Stuart D Armstrong
- From the ‡Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Dong Xia
- From the ‡Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Germanus S Bah
- §Institut de Recherche Agricole pour le Développement, Regional Centre of Wakwa, BP65 Ngaoundéré, Cameroon
| | - Ritesh Krishna
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Henrietta F Ngangyung
- §Institut de Recherche Agricole pour le Développement, Regional Centre of Wakwa, BP65 Ngaoundéré, Cameroon
| | - E James LaCourse
- ‖Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Henry J McSorley
- **The Queens Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4JT
| | - Jonas A Kengne-Ouafo
- ‡‡Research Foundation for Tropical Diseases and Environment, PO Box 474 Buea, Cameroon
| | | | - Samuel Wanji
- ‡‡Research Foundation for Tropical Diseases and Environment, PO Box 474 Buea, Cameroon
| | - Peter A Enyong
- ‡‡Research Foundation for Tropical Diseases and Environment, PO Box 474 Buea, Cameroon; §§Tropical Medicine Research Station, Kumba, Cameroon
| | - David W Taylor
- From the ‡Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, UK; ¶¶Division of Pathway Medicine, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Mark L Blaxter
- ‖‖Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Jonathan M Wastling
- From the ‡Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, UK; ‡‡‡The National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L3 5RF, UK
| | - Vincent N Tanya
- §Institut de Recherche Agricole pour le Développement, Regional Centre of Wakwa, BP65 Ngaoundéré, Cameroon
| | - Benjamin L Makepeace
- From the ‡Institute of Infection & Global Health, University of Liverpool, Liverpool L3 5RF, UK;
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Ramakrishna C, Krishna R, Saini B, Gopi T, Swetha G, Chandra Shekar S. A simple and controlled oxidative decontamination of sulfur mustard and its simulants using ozone gas. PHOSPHORUS SULFUR 2016. [DOI: 10.1080/10426507.2015.1130047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- C. Ramakrishna
- Evaluation Facility, Chemical Defence Equipments Evaluation Facility (CDEF), Defence R&D Establishment, Gwalior, India
| | - R. Krishna
- Evaluation Facility, Chemical Defence Equipments Evaluation Facility (CDEF), Defence R&D Establishment, Gwalior, India
| | - Bijendra Saini
- Evaluation Facility, Chemical Defence Equipments Evaluation Facility (CDEF), Defence R&D Establishment, Gwalior, India
| | - T. Gopi
- Evaluation Facility, Chemical Defence Equipments Evaluation Facility (CDEF), Defence R&D Establishment, Gwalior, India
| | - G. Swetha
- Evaluation Facility, Chemical Defence Equipments Evaluation Facility (CDEF), Defence R&D Establishment, Gwalior, India
| | - S. Chandra Shekar
- Evaluation Facility, Chemical Defence Equipments Evaluation Facility (CDEF), Defence R&D Establishment, Gwalior, India
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20
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Cui X, Chen K, Xing H, Yang Q, Krishna R, Bao Z, Wu H, Zhou W, Dong X, Han Y, Li B, Ren Q, Zaworotko MJ, Chen B. Pore chemistry and size control in hybrid porous materials for acetylene capture from ethylene. Science 2016; 353:141-4. [DOI: 10.1126/science.aaf2458] [Citation(s) in RCA: 839] [Impact Index Per Article: 104.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/05/2016] [Indexed: 01/18/2023]
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21
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Parthiban A, Kumaravel M, Muthukumaran J, Rukkumani R, Krishna R, Rao HSP. Synthesis, in vitro and in silico anti-proliferative activity of 4-aryl-4H-chromene derivatives. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1569-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Ramakrishna C, Krishna R, Gopi T, Swetha G, Saini B, Chandra Shekar S, Srivastava A. Complete oxidation of 1,4-dioxane over zeolite-13X-supported Fe catalysts in the presence of air. Chinese Journal of Catalysis 2016. [DOI: 10.1016/s1872-2067(15)61030-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Park S, Gupta R, Krishna R, Kim ST, Lee DY, Hwang DJ, Bae SC, Ahn IP. Proteome Analysis of Disease Resistance against Ralstonia solanacearum in Potato Cultivar CT206-10. Plant Pathol J 2016; 32:25-32. [PMID: 26889112 PMCID: PMC4755672 DOI: 10.5423/ppj.oa.05.2015.0076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 10/15/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Potato is one of the most important crops worldwide. Its commercial cultivars are highly susceptible to many fungal and bacterial diseases. Among these, bacterial wilt caused by Ralstonia solanacearum causes significant yield loss. In the present study, integrated proteomics and genomics approaches were used in order to identify bacterial wilt resistant genes from Rs resistance potato cultivar CT-206-10. 2-DE and MALDI-TOF/TOF-MS analysis identified eight differentially abundant proteins including glycine-rich RNA binding protein (GRP), tomato stress induced-1 (TSI-1) protein, pathogenesis-related (STH-2) protein and pentatricopeptide repeat containing (PPR) protein in response to Rs infection. Further, semi-quantitative RT-PCR identified up-regulation in transcript levels of all these genes upon Rs infection. Taken together, our results showed the involvement of the identified proteins in the Rs stress tolerance in potato. In the future, it would be interesting to raise the transgenic plants to further validate their involvement in resistance against Rs in potato.
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Affiliation(s)
- Sangryeol Park
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707,
Korea
| | - R. Krishna
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707,
Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707,
Korea
| | - Dong Yeol Lee
- Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 660-701,
Korea
| | - Duk-ju Hwang
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
| | - Shin-Chul Bae
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
| | - Il-Pyung Ahn
- Molecular Breeding Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 560-500,
Korea
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Krishna R, Iqbal J, Gorai AK, Pathak G, Tuluri F, Tchounwou PB. Groundwater vulnerability to pollution mapping of Ranchi district using GIS. Appl Water Sci 2015; 5:345-358. [PMID: 26557470 PMCID: PMC4636214 DOI: 10.1007/s13201-014-0198-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Groundwater pollution due to anthropogenic activities is one of the major environmental problems in urban and industrial areas. The present study demonstrates the integrated approach with GIS and DRASTIC model to derive a groundwater vulnerability to pollution map. The model considers the seven hydrogeological factors [Depth to water table (D), net recharge (R), aquifer media (A), soil media (S), topography or slope (T), impact of vadose zone (I) and hydraulic Conductivity(C)] for generating the groundwater vulnerability to pollution map. The model was applied for assessing the groundwater vulnerability to pollution in Ranchi district, Jharkhand, India. The model was validated by comparing the model output (vulnerability indices) with the observed nitrate concentrations in groundwater in the study area. The reason behind the selection of nitrate is that the major sources of nitrate in groundwater are anthropogenic in nature. Groundwater samples were collected from 30 wells/tube wells distributed in the study area. The samples were analyzed in the laboratory for measuring the nitrate concentrations in groundwater. A sensitivity analysis of the integrated model was performed to evaluate the influence of single parameters on groundwater vulnerability index. New weights were computed for each input parameters to understand the influence of individual hydrogeological factors in vulnerability indices in the study area. Aquifer vulnerability maps generated in this study can be used for environmental planning and groundwater management.
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Affiliation(s)
- R. Krishna
- Environmental Science and Engineering Group, Birla Institute of Technology Mesra, Ranchi 835215, India
| | - J. Iqbal
- Environmental Science and Engineering Group, Birla Institute of Technology Mesra, Ranchi 835215, India
| | - A. K. Gorai
- Environmental Science and Engineering Group, Birla Institute of Technology Mesra, Ranchi 835215, India
| | - G. Pathak
- Environmental Science and Engineering Group, Birla Institute of Technology Mesra, Ranchi 835215, India
| | - F. Tuluri
- Department of Technology, Jackson State University, Jackson, MS 39217, USA
| | - P. B. Tchounwou
- Department of Biology, Jackson State University, Jackson, MS 39217, USA
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25
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Parthiban A, Muthukumaran J, Manhas A, Srivastava K, Krishna R, Rao HSP. Synthesis, in vitro and in silico antimalarial activity of 7-chloroquinoline and 4H-chromene conjugates. Bioorg Med Chem Lett 2015; 25:4657-63. [PMID: 26338359 DOI: 10.1016/j.bmcl.2015.08.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/23/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
A new series of chloroquinoline-4H-chromene conjugates incorporating piperizine or azipane tethers were synthesized and their anti-malarial activity were evaluated against two Plasmodium falciparum strains namely 3D7 chloroquine sensitive (CQS) and K1 chloroquine resistant (CQR). Chloroquine was used as the standard and also reference for comparison. The conjugates exhibit intense UV absorption with λmax located at 342 nm (log ε=4.0), 254 nm (log ε=4.2), 223 nm (log ε=4.4) which can be used to spectrometrically track the molecules even in trace amounts. Among all the synthetic compounds, two molecules namely 6-nitro and N-piperazine groups incorporated 7d and 6-chloro and N-azapane incorporated 15b chloroquinoline-4H-chromene conjugates showed significant anti-malarial activity against two strains (3D7 and K1) of P. falciparum. These values are lesser than the values of standard antimalarial compound. Molecular docking results suggested that these two compounds showing strong binding affinity with P. falciparum lactate dehydrogenase (PfLDH) and also they occupy the co-factor position which indicated that they could be the potent inhibitors for dreadful disease malaria and specifically attack the glycolytic pathway in parasite for energy production.
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Affiliation(s)
- A Parthiban
- Department of Chemistry, School of Physical, Chemical and Applied Sciences, Pondicherry University, Puducherry 605 014, India
| | - J Muthukumaran
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ashan Manhas
- Parasitology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kumkum Srivastava
- Parasitology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
| | - R Krishna
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India.
| | - H Surya Prakash Rao
- Department of Chemistry, School of Physical, Chemical and Applied Sciences, Pondicherry University, Puducherry 605 014, India.
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Krishna R, Xia D, Sanderson S, Shanmugasundram A, Vermont S, Bernal A, Daniel-Naguib G, Ghali F, Brunk BP, Roos DS, Wastling JM, Jones AR. A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum. Proteomics 2015; 15:2618-28. [PMID: 25867681 PMCID: PMC4692086 DOI: 10.1002/pmic.201400553] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/09/2015] [Accepted: 04/09/2015] [Indexed: 01/08/2023]
Abstract
Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta-analysis. We identified a total of 201 996 and 39 953 peptide-spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein-level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA-Seq-derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA-Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes. The findings of this study have been integrated into the EuPathDB. The data have been deposited to the ProteomeXchange with identifiers PXD000297and PXD000298.
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Affiliation(s)
- Ritesh Krishna
- Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Dong Xia
- Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Sanya Sanderson
- Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Achchuthan Shanmugasundram
- Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Sarah Vermont
- Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Axel Bernal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Fawaz Ghali
- Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK
| | - Brian P Brunk
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan M Wastling
- Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK
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Prerana S, Saravanan M, Krunal L, Krishna R, Ruchi V. Prevalence, risk factors and coping strategies to work related musculoskeletal disorders reported by physiotherapists in Surat district, India. Physiotherapy 2015. [DOI: 10.1016/j.physio.2015.03.1268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kennedy RK, Naik PR, Veena V, Lakshmi B, Lakshmi P, Krishna R, Sakthivel N. 5-Methyl phenazine-1-carboxylic acid: A novel bioactive metabolite by a rhizosphere soil bacterium that exhibits potent antimicrobial and anticancer activities. Chem Biol Interact 2015; 231:71-82. [DOI: 10.1016/j.cbi.2015.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/25/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
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Kennedy RK, Veena V, Naik PR, Lakshmi P, Krishna R, Sudharani S, Sakthivel N. Phenazine-1-carboxamide (PCN) from Pseudomonas sp. strain PUP6 selectively induced apoptosis in lung (A549) and breast (MDA MB-231) cancer cells by inhibition of antiapoptotic Bcl-2 family proteins. Apoptosis 2015; 20:858-68. [DOI: 10.1007/s10495-015-1118-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ghali F, Krishna R, Perkins S, Collins A, Xia D, Wastling J, Jones AR. ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards. Proteomics 2014; 14:2731-41. [DOI: 10.1002/pmic.201400265] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/10/2014] [Accepted: 10/02/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Fawaz Ghali
- Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Ritesh Krishna
- Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Simon Perkins
- Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Andrew Collins
- Institute of Integrative Biology; University of Liverpool; Liverpool UK
| | - Dong Xia
- Department of Infection Biology; Institute of Infection and Global Health; University of Liverpool; Liverpool UK
| | - Jonathan Wastling
- Department of Infection Biology; Institute of Infection and Global Health; University of Liverpool; Liverpool UK
- Health Protection Research Unit in Emerging and Zoonotic Infections; The National Institute for Health Research; University of Liverpool; Liverpool UK
| | - Andrew R. Jones
- Institute of Integrative Biology; University of Liverpool; Liverpool UK
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Krishna R, Shenoy TV, Goneppanavar U. Airway management in an infant with congenital trismus: the role of retrograde intubation. Southern African Journal of Anaesthesia and Analgesia 2014. [DOI: 10.1080/22201173.2012.10872865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- R Krishna
- Department of Anesthesiology and Critical Care, Kasturba Medical College, Manipal, India
| | - TV Shenoy
- Department of Anesthesiology and Critical Care, Kasturba Medical College, Manipal, India
| | - U Goneppanavar
- Department of Anesthesiology and Critical Care, Kasturba Medical College, Manipal, India
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32
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Krishna R, Nataraj MS. Efficacy of a single dose of a transdermal diclofenac patch as pre-emptive postoperative analgesia: a comparison with intramuscular diclofenac. Southern African Journal of Anaesthesia and Analgesia 2014. [DOI: 10.1080/22201173.2012.10872852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- R Krishna
- Department of Anaesthesiology and Critical Care, Manipal University, India
| | - MS Nataraj
- Department of Anaesthesiology, Employees' State Insurance Corporation Medical College, Bangalore, India
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33
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Qi D, Krishna R, Jones AR. The jmzQuantML programming interface and validator for the mzQuantML data standard. Proteomics 2014; 14:685-8. [PMID: 24453188 PMCID: PMC4016760 DOI: 10.1002/pmic.201300281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 11/20/2013] [Accepted: 12/20/2013] [Indexed: 11/17/2022]
Abstract
The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard.
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Affiliation(s)
- Da Qi
- Institute of Integrative Biology, University of Liverpool, UK
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34
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Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR. Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol Cell Proteomics 2013; 12:3026-35. [PMID: 23813117 PMCID: PMC3820921 DOI: 10.1074/mcp.o113.029777] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator. The ProteoIDViewer is a desktop application allowing users to visualize mzIdentML-formatted results originating from any appropriate identification software; it supports visualization of all the features of the mzIdentML format. The mzidLibrary is a software library containing routines for importing data from external search engines, post-processing identification data (such as false discovery rate calculations), combining results from multiple search engines, performing protein inference, setting identification thresholds, and exporting results from mzIdentML to plain text files. The mzidValidator is able to process files and report warnings or errors if files are not correctly formatted or contain some semantic error. We anticipate that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mzIdentML into other software tools. All three tools are freely available in the public domain.
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Affiliation(s)
- Fawaz Ghali
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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35
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Müller TD, Müller A, Habegger K, Yi CX, Meyer CW, Gaylinn BD, Finan B, Heppner K, Trivedi C, Bielohuby M, Abplanalp W, Meyer F, Piechowski CL, Pratzka J, Stemmer K, Holland J, Hembree J, Bhardwaj N, Raver C, Ottaway N, Krishna R, Sah R, Sallee FR, Woods SC, Perez-Tilve D, Bidlingmaier M, Thorner MO, Krude H, Smiley D, DiMarchi R, Hofmann S, Pfluger PT, Kleinau G, Biebermann H, Tschöp MH. The orphan receptor GPR83 regulates systemic energy metabolism via ghrelin-dependent and -independent mechanisms. Exp Clin Endocrinol Diabetes 2013. [DOI: 10.1055/s-0033-1336629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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36
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Topno NS, Tangeti V, Rao HSP, Krishna R. (Z)-3-(1-Hy-droxy-3-oxobut-1-en-yl)-6-nitro-2H-chromen-2-one. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o284. [PMID: 23424556 PMCID: PMC3569810 DOI: 10.1107/s1600536812051872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 12/26/2012] [Indexed: 06/01/2023]
Abstract
In the title compound, C(13)H(9)NO(6), the coumarin system has the benzene ring aligned at 0.61 (18)° with respect to the pyrone ring. An intra-molecular O-H⋯O hydrogen bond stabilizes the mol-ecular conformation and a C-H⋯O contact also occurs. In the crystal, weak C-H⋯O inter-actions link the mol-ecules, forming inversion dimers.
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Affiliation(s)
- Nishith Saurav Topno
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | | | | | - R. Krishna
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
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Medina-Aunon JA, Krishna R, Ghali F, Albar JP, Jones AJ. A guide for integration of proteomic data standards into laboratory workflows. Proteomics 2013; 13:480-92. [DOI: 10.1002/pmic.201200268] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/14/2012] [Accepted: 09/10/2012] [Indexed: 01/28/2023]
Affiliation(s)
| | - Ritesh Krishna
- Institute of Integrative Biology; University of Liverpool; Liverpool; UK
| | - Fawaz Ghali
- Institute of Integrative Biology; University of Liverpool; Liverpool; UK
| | - Juan P. Albar
- Centro Nacional de Biotecnología; CSIC; Madrid; Spain
| | - Andrew J. Jones
- Institute of Integrative Biology; University of Liverpool; Liverpool; UK
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38
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Kannan M, Manivel P, Geetha K, Muthukumaran J, Rao HSP, Krishna R. Synthesis and in silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to understand their interacting mechanism with acetylcholinesterase. J Chem Biol 2012; 5:151-66. [PMID: 24052808 DOI: 10.1007/s12154-012-0084-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022] Open
Abstract
Anomalous action of human acetylcholinesterase (hAChE) in Alzheimer's disease (AD) was restrained by various AChE inhibitors, of which the specific and potent lead candidate Donepezil is used for treating the disease AD. Besides the specificity, the observed undesirable side effects caused by Donepezil invoked the quest for new lead molecules with the increased potency and specificity for AChE. The present study elucidates the potency of six 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives to form a specific interaction with the peripheral anionic site and catalytic anionic subsite residues of hAChE. The NMSMs were prepared in good yield from 1,1-di(methylsulfanyl)-2-nitroethylene and primary amine (or) amino acid esters. In silico interaction analysis reveals specific and potent interactions between hAChE and selected ligand molecules. The site-specific interactions formed between these molecules also results in a conformational change in the orientation of active site residues of hAChE, which prevents them from being accessed by beta-amyloid protein (Aβ), which is a causative agent for amyloid plaque formation and acetylcholine (ACh). In silico interaction analysis between the ligand-bounded hAChE with Aß and ACh confirms this observation. The variation in the conformation of hAChE associated with the decreased ability of Aβ and ACh to access the respective functional residues of hAChE induced by the novel NMSMs favors their selection for in vivo analysis to present themselves as new members of hAChE inhibitors.
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Affiliation(s)
- M Kannan
- Centre for Bioinformatics, Pondicherry University, Pondicherry, 605 014 India
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Muralikrishna A, Kannan M, Padmavathi V, Padmaja A, Krishna R. N-(4-Chloro-phen-yl)-1-(5-{[(2-phenyl-ethen-yl)sulfon-yl]meth-yl}-1,3,4-oxadiazol-2-yl)methane-sulfonamide. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2954. [PMID: 23125738 PMCID: PMC3470325 DOI: 10.1107/s1600536812037300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 08/29/2012] [Indexed: 11/21/2022]
Abstract
In the title compound, C18H16ClN3O5S2, the dihedral angles between the oxadiazole ring and the phenyl and chlorobenzene rings are 23.4 (2) and 45.4 (2)°, respectively. The C—S—N—C and Cox—C—S—C (ox = oxadiazole) torsion angles are 89.3 (5) and −69.1 (3)°, respectively. A short intramolecular C—H⋯O contact closes an S(6) ring. In the crystal, molecules are linked by N—H⋯O hydrogen bonds, generating C(10) chains propagating in [001]. The packing is consolidated by C—H⋯O, C—H⋯π and very weak aromatic π–π stacking interactions [centroid–centroid separation = 4.085 (2) Å].
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Affiliation(s)
- A Muralikrishna
- Department of Chemistry, Sri Venkateswara University, Tirupati 517 502, India
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Singh MK, Titus E, Krishna R, Hawaldar RR, Goncalves G, Marques PAAP, Gracio J. Direct nucleation of silver nanoparticles on graphene sheet. J Nanosci Nanotechnol 2012; 12:6731-6736. [PMID: 22962814 DOI: 10.1166/jnn.2012.4572] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Silver (Ag) nanoparticles were synthesized on the surface of graphene sheet by the simultaneous reduction of Ag+ and graphene oxide (GO) in the presence of simple reducing agent, hydrazine hydrate (N2H4 x H2O). Both the Ag+ and GO were reduced and Ag+ was nucleated onto graphene. GO flakes were prepared by conventional chemical exfoliation method and in the presence of strong acidic medium of potassium chlorate. Silver nanoparticles were prepared using 0.01 M AgNO3 solution. The reduced GO sheet decorated with Ag is referred as G-Ag sample. G-Ag was characterized by FTIR (Fourier transform infrared) spectroscopy using GO as standard. An explicit alkene peak appeared around 1625 cm(-1) was observed in G-Ag sample. Besides, the characteristic carbonyl and hydroxyl peaks shows well reduction of GO. The FTIR therefore confirms the direct interaction of Ag into Graphene. SEM (scanning electron microscopy) and TEM (transmission electron microscopy) analysis were performed for morphological probing. The average size of Ag nanoparticles was confirmed by around 5-10 nm by the high-resolution TEM (HRTEM). The Ag quantum dots incorporated nanocomposite material could become prominent candidate for diverse applications including photovoltaic, catalysis, and biosensors etc.
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Affiliation(s)
- Manoj K Singh
- Centre for Mechanical Technology and Automation, University of Aveiro, Aveiro, 3810-193, Portugal
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41
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Patterson E, Webb R, Weisbrod A, Bian B, He M, Zhang L, Holloway AK, Krishna R, Nilubol N, Pacak K, Kebebew E. The microRNA expression changes associated with malignancy and SDHB mutation in pheochromocytoma. Endocr Relat Cancer 2012; 19:157-66. [PMID: 22241719 PMCID: PMC4716660 DOI: 10.1530/erc-11-0308] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Currently, the diagnosis of malignant pheochromocytoma can only be made when there is clinical evidence of metastasis or extensive local invasion. Thus, there is a need for new diagnostic marker(s) to identify tumors with malignant potential. The purpose of this study was to identify microRNAs (miRNAs) that are differentially expressed between benign and malignant pheochromocytomas and assess their diagnostic accuracy. Toward this aim, we analyzed miRNA expression in benign and malignant pheochromocytoma tumor samples using whole genome microarray profiling. Microarray analysis identified eight miRNAs that were significantly differentially expressed between benign and malignant pheochromocytomas. We measured a subset of these miRNAs directly by RT-PCR and found that miR-483-5p, miR-183, and miR-101 had significantly higher expression in malignant tumors as compared to their benign counterparts. Area under the receiver operating curve (AUC) analysis indicated that miR-483-5p, miR-101, and miR-183 could be useful diagnostic markers for distinguishing malignant from benign pheochromocytomas. In addition, these miRNAs could be detected in pheochromocytoma patient serum. Overall our data suggest that misexpression of miR-483-5p, miR-101, and miR-183 is associated with malignant pheochromocytoma.
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Affiliation(s)
- E Patterson
- Endocrine Oncology Section, NIH/NCI/Surgery Branch, National Cancer Institute, NIH, Hatfield Clinical Research Center, Bethesda, Maryland 20892, USA
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Reisinger F, Krishna R, Ghali F, Ríos1 D, Hermjakob H, Vizcaíno JA, Jones AR. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics 2012; 12:790-4. [PMID: 22539429 PMCID: PMC3933944 DOI: 10.1002/pmic.201100577] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/15/2011] [Indexed: 12/03/2022]
Abstract
We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.
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Affiliation(s)
- Florian Reisinger
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Fawaz Ghali
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Daniel Ríos1
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Henning Hermjakob
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Juan Antonio Vizcaíno
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, HinxtonCambridge, CB10 1SD, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
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Chakrabartty J, Krishna R, Balderamos L, Hunt C, Januszewski A, Ali S, Gabriel I, Marin D, Apperley J, Kishore B, Goldman J, Szydlo R, Busbridge M, Rezvani K. Impact of Hemochromatosis Gene (HFE) Polymorphisms and Iron Overload on Outcome of Allogeneic Stem Cell Transplantation for Chronic Myeloid Leukemia. Biol Blood Marrow Transplant 2012. [DOI: 10.1016/j.bbmt.2011.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Muthukumaran J, Parthiban A, Surya Prakash Rao H, Krishna R. 6-Ethyl-N-methyl-3-nitro-4-nitro-methyl-4H-chromen-2-amine. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o180-1. [PMID: 22259465 PMCID: PMC3254519 DOI: 10.1107/s1600536811053554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/12/2011] [Indexed: 05/26/2023]
Abstract
In the title compound, C13H15N3O5, the O and N atoms of the nitromethyl group and the methyl C atom of the ethyl group are disordered over two sets of sites with refined occupancies of 0.629 (7):0.371 (7) and 0.533 (8):0.467 (8), respectively. The dihydropyran ring has an extremely flattened conformation. An intramolecular N—H⋯O hydrogen bond occurs. In the crystal, pairs of N—H⋯O hydrogen bonds link molecules, forming inversion dimers. In addition, weak intermolecular C—H⋯O hydrogen bonds are also present.
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Gutstein DE, Krishna R, Johns D, Surks HK, Dansky HM, Shah S, Mitchel YB, Arena J, Wagner JA. Anacetrapib, a Novel CETP Inhibitor: Pursuing a New Approach to Cardiovascular Risk Reduction. Clin Pharmacol Ther 2011; 91:109-22. [DOI: 10.1038/clpt.2011.271] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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46
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van Baten J, Krishna R. Corrigendum to “CFD simulations of mass transfer from Taylor bubbles rising in circular capillaries” [Chem. Eng. Sci. 59 (2004) 2535–2545]. Chem Eng Sci 2011. [DOI: 10.1016/j.ces.2011.06.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Aswathy J, Jahnavi S, Krishna R, Manzoor K, Nair S, Menon D. Targeted labeling of cancer cells using biotin tagged avidin functionalized biocompatible fluorescent nanocrystals. J Nanosci Nanotechnol 2011; 11:7611-7620. [PMID: 22097465 DOI: 10.1166/jnn.2011.4726] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The present study details the development of biotin tagged avidin functionalized Zinc Sulphide [ZnS] nanocrystals through a simple aqueous chemistry route at room temperature for targeted imaging applications. Surface functionalization of Manganese doped ZnS nanocrystals with L-cysteine provided functional groups that facilitated its conjugation to avidin. Further biotinylation of these particles through the strong non-covalent interaction between biotin and avidin enabled highly specific labeling of the biotin receptors on human hepatocellular carcinoma (HepG2) cells. The nanobioconjugates thus developed exhibited stable and brilliant fluorescence upon labeling the biotin receptors on cells as observed through fluorescence microscopy. Characterization studies using X-ray diffraction, dynamic light scattering as well as Fourier transform infrared spectroscopy revealed the bioconjugated particles to be appropriately functionalized and stable, with size ranging from 50 to 80 nm. Cytotoxicity of this material system evaluated using MTT, LDH leakage and apoptosis assay revealed its non-toxic nature even for high concentrations extending upto 250 microM and 48 hours of incubation. Our results confirmed that biotinylated ZnS nanocrystals offer great potential for highly specific labeling and targeted imaging of cancer cells.
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Affiliation(s)
- J Aswathy
- Amrita Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwavidyapeetham, Kochi 682041, Kerala, India
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Muthukumaran J, Nachiappan M, Chitra S, Manisankar P, Bhattacharya S, Muthusubramanian S, Krishna R, Jeyakanthan J. 1-(2-Naphth-yl)-3-phenyl-3-(4,5,6,7-tetra-hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one. Acta Crystallogr Sect E Struct Rep Online 2011; 67:o2010-1. [PMID: 22091044 PMCID: PMC3213465 DOI: 10.1107/s1600536811027103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/06/2011] [Indexed: 11/10/2022]
Abstract
In the title compound, C(25)H(22)N(2)OSe, the fused six-membered cyclo-hexene ring of the 4,5,6,7-tetra-hydro-1,2,3-benzoselenadiazole group adopts a near half-chair conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.004 Å). There are weak inter-molecular C-H⋯O and C-H⋯π inter-actions in the crystal structure. Inter-molecular π-π stacking is also observed between the naphthyl units, with a centroid-centroid distance of 3.529 (15) Å.
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Muthukumaran J, Karthikeyan S, Satheesh G, Manimaran B, Krishna R. Butane-1,4-diyl bis(pyridine-4-carboxylate). Acta Crystallogr Sect E Struct Rep Online 2011; 67:o1803. [PMID: 21837176 PMCID: PMC3152005 DOI: 10.1107/s1600536811023646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 12/02/2022]
Abstract
The molecule of the title compound, C16H16N2O4, lies about an inversion centre; the butane chain adopts an extended zigzag conformation. The dihedral angle between the pyridine ring and the adjacent COO group is 3.52 (s14)°.
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Muthukumaran J, Nishandhini M, Chitra S, Manisankar P, Bhattacharya S, Muthusubramanian S, Krishna R, Jeyakanthan J. 3-(4-Methyl-phen-yl)-1-phenyl-3-(4,5,6,7-tetra-hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one. Acta Crystallogr Sect E Struct Rep Online 2011; 67:o1660-1. [PMID: 21837060 PMCID: PMC3151998 DOI: 10.1107/s160053681102174x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 06/06/2011] [Indexed: 11/10/2022]
Abstract
In the title compound, C(22)H(22)N(2)OSe, the fused six-membered ring of the 4,5,6,7-tetra-hydro-benzo[d][1,2,3] selenadiazole group adopts a near to envelope (E form) conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.0059 Å). In the crystal, adjacent mol-ecules are inter-linked through weak inter-molecular C-H⋯π inter-actions.
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Affiliation(s)
- J. Muthukumaran
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - M. Nishandhini
- Department of Bioinformatics, Alagappa University, Karaikudi 630 003, India
| | - S. Chitra
- Department of Industrial Chemistry, Alagappa University, Karaikudi 630 003, India
| | - P. Manisankar
- Department of Industrial Chemistry, Alagappa University, Karaikudi 630 003, India
| | - Suman Bhattacharya
- Department of Chemistry, Pondicherry University, Puducherry 605 014, India
| | - S. Muthusubramanian
- Department of Organic Chemistry, Madurai Kamaraj University, Madurai 625 021, India
| | - R. Krishna
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - J. Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi 630 003, India
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