High quality RNA extraction protocol for polyphenolics-rich Cotton tissue.

The extraction of high-quality RNA from cotton (Gossypium spp.) is challenging because of the presence of high polyphenolics, polysaccharides, quinones, and other secondary metabolites. A high-throughput RNA extraction protocol is a prerequisite. This Triton-X-100-based RNA extraction method utilizes Polyvinyl pyrrolidone polymer (PVPP) treatment which efficiently removes phenolics, and the application of Lithium chloride (LiCl) has been found that successfully precipitated the high-quality RNA from cotton tissue. Cytoplasmic male sterility (CMS) is a maternally inherited trait associated with specific mitochondrial genome rearrangements or mutations. The suitability of RNA extracted from Cotton CMS lines was assessed. cDNA was synthesized from RNA and assayed for mitochondrial genes (cox3, nad3, nad9) associated with male sterility. This paper discuss the advantages and limitation of this protocol over existing protocol for RNA extraction for polyphenolics-rich plant tissue.

Phylogenetic implications and secondary structure analyses of Vigna mungo (L.) Hepper genotypes based on nrDNA ITS2 sequences.

The internal transcribed spacers are highly preferred nuclear markers for the phylogenetic assessment of most eukaryotes, including plants. More recently, ITS2 has shown to possess equivalent phylogenetic significance as the entire ITS region. Vigna mungo L. Hepper is comparatively less explored from the molecular aspects as compared to the other species of the Vigna genus. The study presents the intra-individual characterization of 24 distinct genotypes Vigna mungo L. Hepper, using morphological as well as nrDNA ITS2 sequences and secondary structural data. The morphological characterization has been carried out using nine important agro-morphological traits. The molecular phylogeny of the sequence data, using the maximum parsimony and neighbor joining methods, shows the significant distinction based on the haplotypic variations amongst blackgram genotypes. The ITS2 secondary structures predicted using the homology modeling approach were compatible with the eukaryote-universal ITS2 secondary structure. The sequence-structure phylogeny reconstructed using the profile neighbour joining approach, also showed the presence of haplotypic variations in form of clusters on the phylogenetic tree. Further, the high GC content in the sequence data and highly negative ΔG values of the folded secondary structures ruled out the possibilities of the presence of any pseudogenes in the data set. Our analysis recommends the use of ITS2 sequence and secondary structure data at the intraspecific levels of plant taxonomical classification. Moreover, this study for the very first time reports the combined use morphological, and molecular data (using ITS2 sequence and secondary structural information) for the characterization of plants at the varietal level of taxonomical classification.

The complete chloroplast genome of Cenchrus ciliaris (Poaceae).

Cenchrus ciliaris is an important pasture resource for arid region and owing to apomixis, it has been very important for development and distribution of cultivars and agro-types. In present study complete chloroplast genome of C. ciliaris was sequenced. The size of chloroplast genome is 138737 bp length with overall GC content 38.6%. It exhibited regular quadripartite structure with 81053 bp of LSC region, 16108 bp of SSC region and 20788 bp of each IR region. A total of 130 genes were identified, including 87 coding genes, 32 tRNAs, 7 ribosomal RNAs and 4 pseudogenes. Phylogenetic analysis was performed using 13 other members representing major subfamilies of Poaceae.

DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation.

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

Genome sequence of Ochrobactrum anthropi strain SUBG007, a plant pathogen and potential xenobiotic compounds degradation bacterium.

Ochrobactrum anthropi SUBG007 was isolated from the fruit of Prunus dulcis in Rajkot (22.30°N, 70.78°E), Gujarat, India. Here we present the 4.37 Mb genome sequence strain SUBG007, which may provide the genetic information for the application in environment pollution degradation and agriculture field. The strain also posses many genes cluster which involved in production of important secondary metabolites. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession LUAY00000000.

Changes in radical scavenging activity of normal, endoreduplicated and depolyploid root tip cells of Allium cepa.

The plant cell responds to abiotic stress conditions by adjusting its cellular metabolism and various defensive mechanisms. Cellular metabolism involves changes in the cell cycle, in which the cell undergoes repeated rounds of endocycles leading to polyploidization. Defense mechanisms such as role of antioxidants are a key to understand plant adaptation. The present work describes endoreduplication and radical scavenging activity as two different defense mechanisms adapted by plants for their survival under stress condition. The work describes linkage of these two processes with each other under abiotic stress. Endoreduplicated root tip cells of Allium cepa were depolyploidized by exogenous phytohormones. Further, free radical scavenging activity from normal, endoreduplicated and depolyploidized root tips cells was observed to understand the role of phytohormones. Elevated free radical scavenging potential was observed in endoreduplicated cells compared to normal and depolyploidized cells. Based on these results, it was concluded that endoreduplication and antioxidant pathways are linked with each other through phytohormonal activities. The concentration of auxin and cytokinin regulates the activity of ascorbate oxidase enzyme, which in turn maintains the concentration of AsA within the cell. AsA level directs the prolyl-hydroxylation process of cell division proteins in quiescent center cells either toward endoreduplication process or cell division process.

Whole genome sequences and annotation of Micrococcus luteus SUBG006, a novel phytopathogen of mango.

Actinobaceria, Micrococcus luteus SUBG006 was isolated from infected leaves of Mangifera indica L. vr. Nylon in Rajkot, (22.30°N, 70.78°E), Gujarat, India. The genome size is 3.86 Mb with G + C content of 69.80% and contains 112 rRNA sequences (5S, 16S and 23S). The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JOKP00000000.

Whole genome sequencing of Halomonas sp. SUBG004 isolated from Little Rann of Kutch, a desert of India.

A salt tolerant strain, designated as SUBG004, was isolated from the desert of India, Little Rann of Kutch. The organism is a Gram-negative, facultatively anaerobic and rod shaped bacterium. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Halomonas. Here we report the whole genome sequence of Halomonas sp. SUBG004 deposited in DDBJ/EMBL/GenBank under accession number JPEU0100000 which provides insights for salt stress adaptation through betaine synthesis.

High-quality complete genome sequence of Microbacterium sp. SUBG005, a plant pathogen.

Microbacterium sp. SUBG005 is a Gram positive bacterium, isolated from infected leaf of Mangifera indica L. in Rajkot (22.30°N, 70.78°E), Gujarat, India. The genome sequencing of Microbacterium sp. SUBG005 is having type I secretion system genes of pathogenicity as well as heavy metal resistance unique genes. The genome size is 7.01 Mb with G + C content of 64.80% and contains rRNA sequences. Genome sequencing analysis provides information about the microbe role in host-pathogen interaction. The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JNNT00000000.

Genomic analysis of novel phytopathogenic Georgenia sp. strain SUB25.

A Gram positive bacterium, Georgenia sp. SUB25 was isolated from infected leaves of Solanum lycopersicum L. in Rajkot (22.30°N, 70.78°E), Gujarat, India. We sequenced and analyzed Georgenia sp. SUB25 that is novel plant pathogen using next generation sequencing platform and assembly yielded contigs representing a size of 4.84 Mb with 81 tRNAs and 88 rRNAs. The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JNFL00000000. This genome sequence contains Type II secretion system genes, which involved in pathogenicity mechanism that may help to understand plant microbial interaction.

X-ray computed tomography to study rice (Oryza sativa L.) panicle development.

Computational tomography is an important technique for developing digital agricultural models that may help farmers and breeders for increasing crop quality and yield. In the present study an attempt has been made to understand rice seed development within the panicle at different developmental stages using this technique. During the first phase of cell division the Hounsfield Unit (HU) value remained low, increased in the dry matter accumulation phase, and finally reached a maximum at the maturation stage. HU value and seed dry weight showed a linear relationship in the varieties studied. This relationship was confirmed subsequently using seven other varieties. This is therefore an easy, simple, and non-invasive technique which may help breeders to select the best varieties. In addition, it may also help farmers to optimize post-anthesis agronomic practices as well as deciding the crop harvest time for higher grain yield.

Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

BACKGROUND: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. OBJECTIVE: To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. MATERIALS AND METHODS: The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. RESULTS: The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. CONCLUSION: A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel rapid and economic procedure, especially in cases when protein coding loci are considered. SUMMARY: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. A herbal powder was obtained from a herbalist in the local vicinity of Rajkot, Gujarat. An integrated approach using DNA barcoding and structural analyses was carried out to identify the herbal powder. The herbal powder was identified as Cassia javanica L.

Systemic control of cell division and endoreduplication by NAA and BAP by modulating CDKs in root tip cells of Allium cepa.

Molecular mechanism regulated by auxin and cytokinin during endoreduplication, cell division, and elongation process is studied by using Allium cepa roots as a model system. The activity of CDK genes modulated by auxin and cytokinin during cell division, elongation, and endoreduplication process is explained in this research work. To study the significance of auxin and cytokinin in the management of cell division and endoreduplication process in plant meristematic cells at molecular level endoreduplication was developed in root tips of Allium cepa by giving colchicine treatment. There were inhibition of vegetative growth, formation of c-tumor at root tip, and development of endoreduplicated cells after colchicine treatment. This c-tumor was further treated with NAA and BAP to reinitiate vegetative growth in roots. BAP gave positive response in reinitiation of vegetative growth of roots from center of c-tumor. However, NAA gave negative response in reinitiation of vegetative growth of roots from c-tumor. Further, CDKs gene expression analysis from normal, endoreduplicated, and phytohormone (NAA or BAP) treated root tip was done and remarkable changes in transcription level of CDK genes in normal, endoreduplicated, and phytohormones treated cells were observed.

Scientific retraction: a synonym for pseudoscience? / Retractación científica: un sinónimo de seudociencia? / Retratação científica: um sinônimo de pseudociência?

The phenomenon of scientific retraction is a shameful act for the scientific community, but a necessity to maintain the purity of science. The two main causes for retractions include plagiarism and research misconduct. The post retraction citation of articles is again a repetition of inappropriateness. Hence the editorial, peer review policies should be revised and the retractions should be publicized more to avoid the citation of the invalid literature. Also, the scientific readership has a responsibility to evaluate the scientific validity of published studies.

El fenómeno de la retractación científica constituye una vergüenza para la comunidad científica, pero es necesario para mantener la pureza de la ciencia. Las dos causas principales de retractación son el plagio y faltas en la conducta de investigación. La citación de artículos posterior a su retractación es, de nuevo, una repetición inapropiada. Por lo tanto, la editorial y las normas de evaluación por pares debieran revisarse y las retractaciones publicarse más para evitar las citaciones de literatura inválida. También los lectores científicos tienen la responsabilidad de evaluar la validez científica de los estudios publicados.

O fenômeno de retratação científica é uma vergonhosa atitude para a comunidade científica, mas uma necessidade para manter a pureza da ciência. As duas principais causas para a retratação incluem o plágio e a má conduta na pesquisa. A citação após retratação de artigos é novamente uma repetida inadequação. Daí porque o editorial e a política de revisão por pares devem ser revistas e as retratações deveriam ser mais divulgadas para evitar uma citação inválida da literatura. Ademais, o revisor científico tem uma responsabilidade de avaliar a validade científica dos estudos publicados.

Plant systems biology: insights, advances and challenges.

Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.