Genome-wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa

Parameswari Paul,Vignesh Dhandapani,Jana Jeevan Rameneni,Xiaonan Li,Ganesan Sivanandhan,Su Ryun Choi,Wenxing Pang,Subin Im,Yong Pyo Lim 한국원예학회 2016 한국원예학회 학술발표요지 Vol.2016 No.5

Genome wide identification and functional prediction of long non-coding RNAs in Brassica rapa

임용표,Parameswari Paul,Vignesh Dhandapani,최수련 한국유전학회 2016 Genes & Genomics Vol.38 No.6

Long non-coding RNAs (LncRNAs) are a large, diverse class of RNA molecules that has garnered attention for their potential to regulate gene expression and been identified in various organisms. Here we report the first prediction of lncRNAs in Brassica rapa (B. rapa) genome using computational method. We subjected the publicly available full length cDNA sequences and identified 2237 candidate lncRNAs, characterized their functions based on insilico methods. Housekeeping and small regulatory non-coding RNAs (ncRNAs) were removed from the pool. Although 14–15 % of the total sequences were predicted to be non-coding initially, on filtering only 4.6 % of the total sequences were predicted as lncRNAs carrying a large number of simple repeats. The lncRNAs had an average length of 497 bp and were mapped on each chromosome of B. rapa. They were classified to 4 groups based on their origin. Thirty six motifs involving transcription related activities, signaling mechanism and stress response were identified in the lncRNAs. Repeat elements and neighboring genes of the lncRNAs were analyzed since they were associated in function and regulating the expression of these long non-coding RNAs. We believe that this study would be an initial and reference for any further studies regarding long non-coding RNAs in B. rapa and other Brassica crops.

MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics

Vignesh, Dhandapani,Parameswari, Paul,Im, Su-Bin,Kim, Hae-Jin,Lim, Yong-Pyo Korea Genome Organization 2011 Genomics & informatics Vol.9 No.1

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

Dry and wet lab analysis on benzofused heterocyclic compounds as effective corrosion inhibitors for mild steel in acidic medium

Hemapriya, V.,Prabakaran, M.,Parameswari, K.,Chitra, S.,Kim, S.H.,Chung, I.M. Korean Society of Industrial and Engineering Chemi 2016 Journal of industrial and engineering chemistry Vol.40 No.-

<P>The influence of two benzofused heterocyclic compounds, namely 2-phenylquinazolin-4(3H)-one(PQO) and 2-phenyl-4H-benzo[d]oxazin-4-one(POO) in controlling mild steel corrosion in 1 M H2SO4 solution was investigated using gravimetric and electrochemical methods. The experimental results revealed that both the inhibitors inhibit corrosion and their inhibition efficiency follows the order PQO > POO. A mixed mode of inhibition from polarization and a charge transfer mechanism from impedance study in the absence and presence of inhibitors were found. The passive film formed on the mild steel surface was characterized using SEM-EDX. Quantum chemical parameters derived using DFT performed at B3LYP/6-31G(d, p) level were used to correlate the molecular structure. (C) 2016 The Korean Society of Industrial and Engineering Chemistry. Published by Elsevier B.V. All rights reserved.</P>

Mixed Infection of Sugarcane Yellow Leaf Virus and Grassy Shoot Phytoplasma in Yellow Leaf Affected Indian Sugarcane Cultivars

Kadirvel Nithya,Balasubramaniam Parameswari,Rasappa Viswanathan 한국식물병리학회 2020 Plant Pathology Journal Vol.36 No.4

Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases af- fecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome charac- terization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restric- tion fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phyto- plasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.

Terpenoid, Benzenoid, and Phenylpropanoid Compounds in the Floral Scent of Vanda Mimi Palmer

Ab. Rahim Mohd-Hairul,Parameswari Namasivayam,Gwendoline Ee Cheng Lian,Janna Ong Abdullah 한국식물학회 2010 Journal of Plant Biology Vol.54 No.5

Vanda Mimi Palmer is the product of a cross between Vanda Tan Chay Yan and Vanda tessellata. The flower of this hybrid produces a sweet-smelling fragrance during day time at the open-flower stage. This study aimed to investigate the floral scent constituents in Vanda Mimi Palmer. Scent emission analysis of this orchid was carried out at different time points in a 24-h cycle and also at different floral developmental stages. A comparison was also made on the volatiles emitted by Vanda Mimi Palmer and both of its parents. Gas chromatography-mass spectrometry (GC-MS) analysis showed that the scent of Vanda Mimi Palmer was dominated by terpenoid, benzenoid, and phenylpropanoid compounds. The identified terpenoids were ocimene, linalool oxide, linalool, and nerolidol;while the benzenoid and phenylpropanoid compounds were methylbenzoate, benzyl acetate, phenylethanol, and phenylethyl acetate. The emission of terpenoid, benzenoid,and phenylpropanoid compounds was developmentally and temporally regulated. Comparison of the volatiles emitted by both of its parents showed that the scent of Vanda Mimi Palmer is dissimilar to that of its fragrant parent, V. tessellata.

MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics

Dhandapani Vignesh,Paul Parameswari,임수빈,김해진,임용표 한국유전체학회 2011 Genomics & informatics Vol.9 No.1

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA’s is a method in practice, computational identification of miRNA’s has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user’s interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk(Tool kit widgets) scripting languages. It is user friendly,portable offline software that works in all windows OS, sized to 3 MB.

Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production

Somnath Kadappa Holkar,Parameswari Balasubramaniam,Atul Kumar,Nithya Kadirvel,Prashant Raghunath Shingote,Manohar Lal Chhabra,Shubham Kumar,Praveen Kumar,Rasappa Viswanathan,Rakesh Kumar Jain,Ashwini 한국식물병리학회 2020 Plant Pathology Journal Vol.36 No.6

Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.

Development of EST database and transcriptome analysis in the leaves of Brassica rapa using a newly developed pipeline

Vignesh Dhandapani,최수련,Parameswari Paul,김용권,Nirala Ramchiary,허윤강,임용표 한국유전학회 2012 Genes & Genomics Vol.34 No.6

Brassica rapa L. (AA, 2n = 20), an A genome diploid species of Brassica genus is of researchers interest recent days since enormous amount of data is available about the genome. Since EST analysis is a powerful tool in gene discovery we compared different existing methods and developed a new pipeline for EST computational analysis to analyze the available data. A total of 1,438 expressed sequence tags sizing from 83 to 2,023 base pairs were generated and subjected to various types of analysis. Cluster analysis of these ESTs identified 969unique sequences called unigenes, with 162 contigs and 807singlets. Similarity search produced 704 significant hits with E-value ≥ 10-5. The functions of the best hits were annotated by gene ontology (GO) analysis. Additionally, we classified 293 and 541 unigenes based on their functions, using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and protein structural domain databases, respectively. We also identified and categorized 171 microsatellites into di-, tri-, tetra-,and penta nucleotide repeats, and designed primers. Possible open reading frames (ORFs) were predicted for 960unigenes, by the comparison with a primary protein sequence database. In silico mapping of partial unigenes were done in bacterial artificial chromosome (BAC) sequences, downloaded from the Brassica genome project website. We determined 149single nucleotide polymorphisms (SNPs) and 3 indels from the coding region of 27 unigenes of B. rapa and similar Brassica napus ESTs clusters. All the generated EST sequences were submitted to the GenBank EST database (dbEST) as accessions from CO749247 to CO750425.

Research Articles : Designing and Synthesis of Antifungal Active Macrocyclic Ligand and Its Complexes Derived from Diethylphthalate and Benzidine

( N. Raman ),( S. Parameswari ) 한국균학회 2007 Mycobiology Vol.35 No.2