Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.)

Background

Despite great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in tea (Camellia sinensis L.). The development of microsatellite markers will have a major impact on genetic analysis, gene mapping and marker assisted breeding. Unigene derived microsatellite (UGMS) markers identified from publicly available sequence database have the advantage of assaying variation in the expressed component of the genome with unique identity and position. Therefore, they can serve as efficient and cost effective alternative markers in such species.

Results

Considering the multiple advantages of UGMS markers, 1,223 unigenes were predicted from 2,181 expressed sequence tags (ESTs) of tea (Camellia sinensis L.). A total of 109 (8.9%) unigenes containing 120 SSRs were identified. SSR abundance was one in every 3.55 kb of EST sequences. The microsatellites mainly comprised of di (50.8%), tri (30.8%), tetra (6.6%), penta (7.5%) and few hexa (4.1%) nucleotide repeats. Among the dinucleotide repeats, (GA)n.(TC)n were most abundant (83.6%). Ninety six primer pairs could be designed form 83.5% of SSR containing unigenes. Of these, 61 (63.5%) primer pairs were experimentally validated and used to investigate the genetic diversity among the 34 accessions of different Camellia spp. Fifty one primer pairs (83.6%) were successfully cross transferred to the related species at various levels. Functional annotation of the unigenes containing SSRs was done through gene ontology (GO) characterization. Thirty six (60%) of them revealed significant sequence similarity with the known/putative proteins of Arabidopsis thaliana. Polymorphism information content (PIC) ranged from 0.018 to 0.972 with a mean value of 0.497. The average heterozygosity expected (H _E ) and observed (H _o ) obtained was 0.654 and 0.413 respectively, thereby suggesting highly heterogeneous nature of tea. Further, test for IAM and SMM models for the UGMS loci showed excess heterozygosity and did not show any bottleneck operating in the tea population.

Conclusion

UGMS markers identified and characterized in this study provided insight about the abundance and distribution of SSR in the expressed genome of C. sinensis. The identification and validation of 61 new UGMS markers will not only help in intra and inter specific genetic diversity assessment but also be enriching limited microsatellite markers resource in tea. Further, the use of these markers would reduce the cost and facilitate the gene mapping and marker-aided selection in tea. Since, 36 of these UGMS markers correspond to the Arabidopsis protein sequence data with known functions will offer the opportunity to investigate the consequences of SSR polymorphism on gene functions.     

Motor grading of elbow flexion – is Medical Research Council grading good enough?

We present a new surgical technique for a pedicled teres major muscle transfer to improve shoulder abduction and flexion in children with sequelae of obstetric brachial plexus palsy. In addition, we provide the clinical outcome in the first 17 operated children.     

Development of nanostructured biomedical micro-drug testing device based on in situ cellular activity monitoring

Integration of micro and nanofabrication techniques with biotechnology has resulted in the development of in vitro analytical and diagnostic tools for biomedical applications. The focus of such technology has primarily been on therapeutic and sensing applications. The long-term integration of cells with inorganic materials provides the basis for novel sensing platforms. This paper describes the creation of, nanoporous, biocompatible, alumina membranes as a platform for incorporation into a cell based device targeted for in situ recording of cellular electrical activity variations due to the changes associated with the surrounding microenvironments more specifically due to the effect of therapeutic drugs. Studies described herein focus on the interaction of nanoporous alumina substrates embedded in silicon, patterned with cells of interest. The cells that have been used to develop the in vitro test platform are primary hippocampal neurons. Demonstrated here, is the fidelity of such a system in terms of determination of cell viability, proliferation, and functionality. The response of the cells to the "drug" molecules is electro-optically characterized in an in situ manner. The capability of such, micro fabricated nanoporous membranes as in vitro drug testing platforms, is first theoretically estimated using two dimensional finite element modeling of the diffusion of the molecules of interest through the nanoporous substrate using CFDRC. It is then experimentally established, using glucose and immunoglobulin G (IgG).     

A Direct Interaction with NEDD1 Regulates γ-Tubulin Recruitment to the Centrosome

The centrosome is the primary microtubule organizing centre of the cell. γ-tubulin is a core component of the centrosome and is required for microtubule nucleation and centrosome function. The recruitment of γ-tubulin to centrosomes is mediated by its interaction with NEDD1, a WD40-repeat containing protein. Here we demonstrate that NEDD1 is likely to be oligomeric in vivo and binds directly to γ-tubulin through a small region of just 62 residues at the carboxyl-terminus of the protein. This carboxyl-terminal domain that binds γ-tubulin has a helical structure and is a stable tetramer in solution. Mutation of residues in NEDD1 that disrupt binding to γ-tubulin result in a mis-localization of γ-tubulin away from the centrosome. Hence, this study defines the binding site on NEDD1 that is required for its interaction with γ-tubulin, and shows that this interaction is required for the correct localization of γ-tubulin.     

Ameliorating imidacloprid induced oxidative stress by 24-epibrassinolide in <Emphasis Type="Italic">Brassica juncea</Emphasis> L.

Pesticide toxicity causes oxidative stress to plants by generating reactive oxygen species (ROS). The aim of the present study was to observe the role of 24-epibrassinolide (24-EBL) in protection of Brassica juncea L. plants from oxidative stress caused by imidacloprid (IMI) pesticide. Generation of ROS, activities of antioxidative enzymes and chlorophyll contents were estimated using spectrophotometer, whereas organic acid contents were determined using gas chromatography-mass spectrometry (GC-MS). Statistical analysis of data revealed that 24-EBL significantly decreased ROS contents, accompanied by enhanced levels of shoot biomass, chlorophyll contents, organic acid contents and the activities of antioxidative enzymes in B. juncea plants under IMI toxicity.     

Enhancing effects of 24-epibrassinolide and Putrescine on the antioxidant capacity and free radical scavenging activity of <Emphasis Type="Italic">Raphanus sativus</Emphasis> seedlings under Cu ion stress

The present investigation recorded significant restoration of seedling growth (root length, shoot length and fresh weight) upon application of 24-epibrassinolide (EBL) and putrescine (Put) to 7-day-old seedlings of Raphanus sativus L. cv. Pusa chetki grown under copper (Cu) ion stress. EBL and Put with/or without Cu ion treated seedlings showed increased titers of ascorbic acid, total phenols and proline when compared with Cu-stressed seedlings. Differential responses in the activities of guaiacol peroxidase (GPOX) and catalase (CAT) were noted for EBL and Put alone or with/or without Cu ion treatment. Decreased activities of glutathione reductase (GR) and superoxide dismutase (SOD) noted for EBL and Put alone were observed to enhance significantly when applied in combination with Cu ion solution. A remarkable decrease in malondialdehyde contents was observed in seedlings treated with EBL and Put alone and with/or without Cu ion stress. Enhanced free radical scavenging activities were also recorded for seedlings given EBL and Put alone or in combination over Cu ion stressed seedlings. Maximum DPPH activity was observed in seedlings treated with Put and EBL 10⁻⁹ M + Put. Significant enhancements in deoxyribose and reducing power activities were too recorded for Put, EBL and Put + 10⁻⁹ M EBL treatments. Improved seedling growth, antioxidant levels (ascorbic acid, total phenols and proline) and enzymic (GPOX, CAT, SOD and GR) activities and free radical scavenging capacities along with reduced membrane damage in seedlings given EBL and Put with/or without Cu stress suggests significant and positive interactions of EBL and Put in alleviating the Cu ion induced oxidative damage in radish seedlings.     

Ambient ozone and two black gram cultivars: an assessment of amelioration by the use of ethylenediurea

Ethylenediurea (EDU) was applied as soil drench in two Indian cultivars of black gram (Vigna mungo L. cv. Azad-1 and BHU-1) and its ameliorating effect against ozone (O₃) stress was studied on selected growth, physiological, biochemical, and yield characteristics. The study site experienced a high O₃ concentration of 41.3–59.9 ppb during the experimental period. It was found that growth parameters showed positive impact on plants treated with EDU and yield attributes were also higher than that of non-EDU-treated ones. Significant increments in ascorbic acid and protein contents were observed in EDU-treated plants as compared to control plants. Lipid peroxidation, however, showed a reverse trend in both the cultivars. Photosynthetic efficiency increased by EDU treatment as depicted by higher values for photosynthetic rate (Ps) and Fv/Fm ratio. EDU-treated plants had more efficient antioxidant enzyme defense system with higher SOD and POX activities. Both the cultivars showed differential response against O₃ and cultivar BHU-1 proved to be resistant as compared to Azad-1. This investigation proves the usefulness of EDU as a biomonitoring tool against O₃ for the remote areas having higher concentrations of O₃ and problem of frequent electricity failure.     

Regulation of the mutually exclusive exons 8a and 8 in the CaV1.2 calcium channel transcript by polypyrimidine tract-binding protein

CaV1.2 calcium channels play roles in diverse cellular processes such as gene regulation, muscle contraction, and membrane excitation and are diversified in their activity through extensive alternative splicing of the CaV1.2 mRNA. The mutually exclusive exons 8a and 8 encode alternate forms of transmembrane segment 6 (IS6) in channel domain 1. The human genetic disorder Timothy syndrome is caused by mutations in either of these two CaV1.2 exons, resulting in disrupted Ca(2+) homeostasis and severe pleiotropic disease phenotypes. The tissue-specific pattern of exon 8/8a splicing leads to differences in symptoms between patients with exon 8 or 8a mutations. Elucidating the mechanisms controlling the exon 8/8a splicing choice will be important in understanding the spectrum of defects associated with the disease. We found that the polypyrimidine tract-binding protein (PTB) mediates a switch from exon 8 to 8a splicing. PTB and its neuronal homolog, nPTB, are widely studied splicing regulators controlling large sets of alternative exons. During neuronal development, PTB expression is down-regulated with a concurrent increase in nPTB expression. Exon 8a is largely repressed in embryonic mouse brain but is progressively induced during neuronal differentiation as PTB is depleted. This splicing repression is mediated by the direct binding of PTB to sequence elements upstream of exon 8a. The nPTB protein is a weaker repressor of exon 8a, resulting in a shift in exon choice when nPTB replaces PTB in cells. These results provide mechanistic understanding of how these two exons, important for human disease, are controlled.     

Atomic structure of bacteriophage Sf6 tail needle knob

Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the “tail needle” likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.