Highly variable SSR markers suitable for rice genotyping using agarose gels

Simple sequence repeats (SSR) are the DNA markers of choice for genetic analysis in rice (Oryza sativa L.) due to their abundance, high polymorphism and simple assays using agarose gel electrophoresis. In an attempt to find most variable SSR loci for the agarose gel system, the relationship between SSR length and level of polymorphism was evaluated in a set of eight diverse rice genotypes using 201 random SSR loci of different repeat motifs and lengths, representing both genic and intergenic sequences from the 12 rice chromosomes. There was a positive correlation between SSR length and average number of alleles per locus but linearity of this relationship was limited to the SSR length range of 10–70 bp. The highest level of polymorphism was in the SSR length range of 51–70 bp, beyond which there was stabilization and then decline of polymorphism in SSRs longer than 70 bp. Proportion of polymorphic loci in the different SSR length groups also followed similar pattern with even sharper decline of polymorphism in the highest size range. Here we describe a genome wide set of 436 validated highly variable SSR (HvSSR) markers with repeat lengths of 51–70 bp for their consistent amplification and high polymorphism. In the parental lines of three different mapping populations, the HvSSR loci showed more than twice the level of polymorphism than random SSR markers with average repeat length of 34 bp, and therefore are suitable for QTL mapping and fingerprinting studies in rice employing agarose gels.     

Biosynthetic approach for functional protein microarrays

Protein microarrays have emerged as an indispensable research tool for providing information about protein functions and interactions through high-throughput screening. Traditional methods for immobilizing biomolecules onto solid surfaces have been based on covalent and noncovalent binding, entrapment in semipermeable membranes, microencapsulation, sol gel, and hydrogel methods. Each of these techniques has its own strengths but fails to combine the most important tenets of a functional protein microarray such as covalent attachment, native protein conformation, homogeneity of the protein monolayer, control over active site orientation, and retention of protein activity. Here we present a selective and site-directed covalent immobilization technique for proteins via a benzoxazine ring formation through a Diels-Alder reaction in water and a genetically encoded 3-amino-L-tyrosine (3-NH(2)Tyr) amino acid. Fully functional protein microarrays, with monolayer arrangements and complete control over their orientations, were generated using this strategy.     

Regulator of G protein signaling 6 (RGS6) protein ensures coordination of motor movement by modulating GABAB receptor signaling

γ-Aminobutyric acid (GABA) release from inhibitory interneurons located within the cerebellar cortex limits the extent of neuronal excitation in part through activation of metabotropic GABA(B) receptors. Stimulation of these receptors triggers a number of downstream signaling events, including activation of GIRK channels by the Gβγ dimer resulting in membrane hyperpolarization and inhibition of neurotransmitter release from presynaptic sites. Here, we identify RGS6, a member of the R7 subfamily of RGS proteins, as a key regulator of GABA(B)R signaling in cerebellum. RGS6 is enriched in the granule cell layer of the cerebellum along with neuronal GIRK channel subunits 1 and 2 where RGS6 forms a complex with known binding partners Gβ(5) and R7BP. Mice lacking RGS6 exhibit abnormal gait and ataxia characterized by impaired rotarod performance improved by treatment with a GABA(B)R antagonist. RGS6(-/-) mice administered baclofen also showed exaggerated motor coordination deficits compared with their wild-type counterparts. Isolated cerebellar neurons natively expressed RGS6, GABA(B)R, and GIRK channel subunits, and cerebellar granule neurons from RGS6(-/-) mice showed a significant delay in the deactivation kinetics of baclofen-induced GIRK channel currents. These results establish RGS6 as a key component of GABA(B)R signaling and represent the first demonstration of an essential role for modulatory actions of RGS proteins in adult cerebellum. Dysregulation of RGS6 expression in human patients could potentially contribute to loss of motor coordination and, thus, pharmacological manipulation of RGS6 levels might represent a viable means to treat patients with ataxias of cerebellar origin.     

Assessing Population Level Genetic Instability via Moving Average

Tumoral tissues tend to generally exhibit aberrations in DNA copy number that are associated with the development and progression of cancer. Genotyping methods such as array-based comparative genomic hybridization (aCGH) provide means to identify copy number variation across the entire genome. To address some of the shortfalls of existing methods of DNA copy number data analysis, including strong model assumptions, lack of accounting for sampling variability of estimators, and the assumption that clones are independent, we propose a simple graphical approach to assess population-level genetic alterations over the entire genome based on moving average. Furthermore, existing methods primarily focus on segmentation and do not examine the association of covariates with genetic instability. In our methods, covariates are incorporated through a possibly mis-specified working model and sampling variabilities of estimators are approximated using a resampling method that is based on perturbing observed processes. Our proposal, which is applicable to partial, entire or multiple chromosomes, is illustrated through application to aCGH studies of two brain tumor types, meningioma and glioma.     

Endoplasmic reticulum stress-induced death of mouse embryonic fibroblasts requires the intrinsic pathway of apoptosis

Members of the caspase family are essential for many apoptotic programs. We studied mouse embryonic fibroblasts (MEFs) deficient in caspases 3 and 7 and in caspase 9 to determine the role of these proteases in endoplasmic reticulum (ER) stress-induced apoptosis. Both caspase 3(-/-)/caspase 7(-/-) and caspase 9(-/-) MEFs were resistant to cytotoxicity induced via ER stress and failed to exhibit apoptotic morphology. Specifically, apoptosis induced by increased intracellular calcium was shown to depend only on caspases 3 and 9, whereas apoptosis induced by disruption of ER function depended additionally on caspase 7. Caspase 3(-/-)/caspase 7(-/-) and caspase 9(-/-) MEFs also exhibited decreased loss of mitochondrial membrane potential, which correlated with altered caspase 9 processing, increased induction of procaspase 11, and decreased processing of caspase 12 in caspase 3(-/-)/caspase 7(-/-) cells. Furthermore, disruption of ER function was sufficient to induce accumulation of cleaved caspase 3 and 7 in a heavy membrane compartment, suggesting a potential mechanism for caspase 12 processing and its role as an amplifier in the death pathway. Caspase 8(-/-) MEFs were not resistant to ER stress-induced cytotoxicity, and processing of caspase 8 was not observed upon induction of ER stress. This study thus demonstrates a requirement for caspases 3 and 9 and a key role for the intrinsic pathway in ER stress-induced apoptosis.     

A Simple and Non-destructive Method of Direct-PCR for Plant Systems

To date, PCR is a fundamental tool for most of the research concerning plant diversity analysis, marker-assisted selection, genetic purity testing, disease diagnostics, and transgene analysis. In all of these analyses, good-quality DNA serves as a template for amplification of target sequences. Extraction of good-quality DNA requires many steps, making the whole process time consuming, tedious, labor intensive, and expensive due to costlier and toxic chemicals. To overcome these preparatory steps from PCR-based DNA amplification, we have developed a direct-PCR amplification method for plants without isolating DNA. The method is unique and beneficial over some previously described methods of direct-PCR which fail due to inefficient amplification of target DNA in the presence of PCR inhibitors and crop specificity. Moreover, such methods are non-specific and, being destructive, cannot be replicated; one cannot completely rely on them due to lack of reproducibility. This method was streamlined from our earlier observation that alcohol-desiccated tissues maintain intact DNA for a long time. This method is specific, rapid, and, being non-destructive, allows replication, giving advantages over existing methods. The method was tested over a wide range of plant species and found very effective and quick in generating data. The method was successfully used to test the genetic purity of pearl millet hybrid (RHB-127) and its restorer (RIB 3135-18) and CMS line (ICMA 93333A). Our method is especially important for developing inexpensive and high-throughput non-invasive genetic analyses.     

Nutritional constituents of mulberry and their potential applications in food and pharmaceuticals: A review

Mulberry is a fast growing deciduous plant found in wide variety of climatic, topographical and soil conditions, and is widely distributed from temperate to subtropical regions. Due to presence of valuable phytochemical constituents, mulberry as a whole plant has been utilized as a functional food since long time. Mulberry fruits are difficult to preserve as they have relatively high water content. Therefore for proper utilization, different value-added products like syrups, squashes, teas, pestil sand köme, pekmez (turkuish by-products), yogurts, jams, jellies, wines, vinegar, breads, biscuits, parathas, and many more are made. In overseas, these value-added products are commercially sold and easily available, though in India, this versatile medicinal plant is still missing its identity at commercial and industrial scale. Leaves of mulberry are economically viable due to their important role in the sericulture industry since ancient times. Mulberries or its extracts exhibit excellent anti-microbial, anti-hyperglycaemic, anti-hyperlipidemic, anti-inflammatory, anti-cancer effects and is used to combat different acute and chronic diseases. Different parts of Morus species like fruits, leaves, twigs, and bark exhibit strong anti-tyrosinase inhibition activity that makes it a suitable candidate in cosmetic industries as a whitening agent. The current review provides a comprehensive discussion concerning the phytochemical constituents, functionality and nutraceutical potential of mulberry and as a common ingredient in various cosmetic products.