Kodiveri Muthukaliannan Gothandam

Bio: Kodiveri Muthukaliannan Gothandam is an academic researcher from VIT University. The author has contributed to research in topic(s): Gene & Publication bias. The author has an hindex of 19, co-authored 78 publication(s) receiving 1108 citation(s). Previous affiliations of Kodiveri Muthukaliannan Gothandam include Chungbuk National University & C. Abdul Hakeem College.

OsPPR1, a pentatricopeptide repeat protein of rice is essential for the chloroplast biogenesis.

Abstract: In this paper, we report a novel pentatricopeptide repeat (PPR) protein gene in rice. PPR, a characteristic repeat motif consisted of tandem 35 amino acids, has been found in various biological systems including plant. Sequence analysis revealed that the gene designated OsPPR1 consisted of an open reading frame of 2433 nucleotides encoding 810 amino acids that include 11 PPR motifs. Blast search result indicated that the gene did not align with any of the characterized PPR genes in plant. The OsPPR1 gene was found to contain a putative chloroplast transit peptide in the N-terminal region, suggesting that the gene product targets to the chloroplast. Southern blot hybridization indicated that the OsPPR1 is the member of a gene family within the rice genome. Expression analysis and immunoblot analysis suggested that the OsPPR1 was accumulated mainly in rice leaf. Antisense transgenic strategy was used to suppress the expression of OsPPR1 and the resulted transgenic rice showed the typical phenotypes of chlorophyll-deficient mutants; albinism and lethality. Cytological observation using microscopy revealed that the antisense transgenic plant contained a significant defect in the chloroplast development. Taken together, the results suggest that the OsPPR1 is a nuclear gene of rice, encoding the PPR protein that might play a role in the chloroplast biogenesis. This is the first report on the PPR protein required for the chloroplast biogenesis in rice.

The effect of salinity on growth, hormones and mineral elements in leaf and fruit of tomato cultivar PKM1.

Abstract: Tomato cultivar PKM 1 were subjected to 25, 50, 100, 150 and 200 mM NaCl stress and response of tomato plant to saltstress were determined by assessing the variability of different biochemical parameters In this present study endogenouscontent of growth hormones IAA and ABA in leaves, proline and mineral (Na+ and K+) content in leaves and maturefruits were estimated Leaf area and dry matter content of tomato fruits under salt stress were determined to study theeffect of salinity on photosynthetic yield Results showed that leaf area and dry matter content of tomato fruits decreasedwith application of elevated salt stress, however endogenous content of IAA, ABA and proline was found to beincreasing with increase in salt treatment Application of NaCl caused increase in Na+ content, while K+ content andK+/Na+ ratio decreased with increase in salt stress Another striking point is that increase in proline and Na+ contentwas more in leaves than fruits, which suggests that leaves are more sensitive than fruitsKeyword: Salt stress, IAA, ABA, Proline, Na+, dry matter

Screening and optimization of protease production from a halotolerant Bacillus licheniformis isolated from saltern sediments

Abstract: Protease producing halotolerant bacterium was isolated from saltern pond sediment (Tuticorin) and identified as Bacillus licheniformis (TD4) by 16S rRNA gene sequencing. Protease production was enhanced by optimizing the culture conditions. The nutritional factors such as carbon and nitrogen sources, NaCl and also physical parameters like incubation time, pH, agitation, inoculum size were optimized for the maximum yield of protease. Studies on the effect of different carbon and nitrogen sources revealed that xylose and urea enhances the enzyme production. Thus, with selected C–N sources along with 1 M NaCl the maximum protease production (141.46 U/mg) was obtained in the period of 24 h incubation at pH 8 under 250 rpm compared to the initial enzyme production (89.87 U/mg).

BcXTH1, a Brassica campestris homologue of Arabidopsis XTH9, is associated with cell expansion.

Abstract: Xyloglucan endotransglucosylase/hydrolases (XTHs) are a group of the enzymes that are responsible for reorganization of the cellulose–xyloglucan framework by catalyzing cleavage and religation of the xyloglucan chains in the plant cell wall. In this study, we report the isolation and characterization of a XTH gene from a pistil cDNA library of Brassica campestris. Sequence analysis of the gene, designated BcXTH1, revealed that it is homologous to the XTH9 gene of Arabidopsis. The highly conserved domain (DEIDFEFLG) found among all XTHs was also present in BcXTH1 but with the two amino acid substitutions (NEFDFEFLG) also found in Arabidopsis XTH9. These results suggest that BcXTH1 is the B. campestris homologue of XTH9. Expression analysis of BcXTH1 revealed that it was expressed in most of the plant organs. In situ hybridization showed that the gene is highly expressed in the floral primodia, especially in the epidermal cell layer. Southern blot analysis indicated that the BcXTH1 gene exists as a multi-copy gene in the B. campestris genome. The function of the BcXTH1 gene was deduced from using an overexpression strategy in Arabidopsis. Interestingly, the transgenic plants showed a pronounced cell expansion phenotype. Immunoelectron microscopy shows that BcXTH1 is localized almost exclusively to the cell wall, supporting our conclusion that it participates in the regulation of cell expansion in B. campestris.

Prognostic significance of blood inflammatory biomarkers NLR, PLR, and LMR in cancer-A protocol for systematic review and meta-analysis.

Abstract: Background The neutrophil-lymphocyte-ratio, platelet-lymphocyte-ratio, and monocyte-lymphocyte-ratio have been explored as a simple, inexpensive, and effective method for cancer prognosis. However, there are no studies that have investigated the comparative utility of these markers, in multiple cancers. Methods The preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) guidelines were used to design this meta-analysis protocol. The final study will also be conducted under the PRISMA guidelines for systematic reviews and meta-analyses. The core bibliographic database search will be carried out by 2 reviewers working individually, with each conducting an initial screening based on titles and abstracts. The shortlisted articles will be selected for review and quantitative analysis, based on predefined inclusion and exclusion criteria. Study characteristics, relevant clinicopathological characteristics, and statistical data required for meta-analysis (hazard ratios [HRs] and 95% confidence intervals [CIs]) will be extracted and compiled into a MS Excel datasheet. Meta-analysis will be performed, using a random-effects model, and the results (pooled HR and 95% CI) will be presented in the form of a forest plot. Publication bias will also be assessed by use of Egger bias indicator test and funnel plot symmetry. If statistical data from included studies is insufficient, a qualitative literature review will be pursued.PROSPERO registration: PROSPERO CRD42019121008.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Pentatricopeptide repeat proteins: a socket set for organelle gene expression.

Abstract: Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that are particularly prevalent in terrestrial plants. Although the PPR protein family was only recognized eight years ago, it is already clear that these proteins have a range of essential functions in post-transcriptional processes (including RNA editing, RNA splicing, RNA cleavage and translation) within mitochondria and chloroplasts. Several PPR proteins have been shown to act as fertility restorer genes in commercially important cytoplasmic male sterility systems. Here, we discuss several recent papers that cover their evolutionary history and molecular mode of action. We use these new data to propose hypotheses for their physiological roles that could explain why PPR proteins are so numerous in terrestrial plants.

Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing

Abstract: Cytoplasmic male sterility (CMS) and nucleus-controlled fertility restoration are widespread plant reproductive features that provide useful tools to exploit heterosis in crops. However, the molecular mechanism underlying this kind of cytoplasmic-nuclear interaction remains unclear. Here, we show in rice (Oryza sativa) with Boro II cytoplasm that an abnormal mitochondrial open reading frame, orf79, is cotranscribed with a duplicated atp6 (B-atp6) gene and encodes a cytotoxic peptide. Expression of orf79 in CMS lines and transgenic rice plants caused gametophytic male sterility. Immunoblot analysis showed that the ORF79 protein accumulates specifically in microspores. Two fertility restorer genes, Rf1a and Rf1b, were identified at the classical locus Rf-1 as members of a multigene cluster that encode pentatricopeptide repeat proteins. RF1A and RF1B are both targeted to mitochondria and can restore male fertility by blocking ORF79 production via endonucleolytic cleavage (RF1A) or degradation (RF1B) of dicistronic B-atp6/orf79 mRNA. In the presence of both restorers, RF1A was epistatic over RF1B in the mRNA processing. We have also shown that RF1A plays an additional role in promoting the editing of atp6 mRNAs, independent of its cleavage function.

Stress‐responsive microRNAs in Populus

Abstract: MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become the subject of intense study. They are a class of post-transcriptional negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in the responses of trees to the stressful environments incurred over their long-term growth. Here, we report the cloning of small RNAs from abiotic stressed tissues of Populus trichocarpa (Ptc) and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, nine families are novel, increasing the number of the known Ptc-miRNA families from 33 to 42. A total of 346 targets was predicted for the cloned Ptc-miRNAs using penalty scores of