A randomized test for the conditional odds ratio of matched pairs in an inverse binomial sampling design

Matched case‐control paired data are commonly used to study the association between a disease and an exposure of interest. This work provides a consistent test for this association with respect to the conditional odds ratio (), which is a measure of association that is also valid in prospective studies. We formulate the test from the maximum likelihood (ML) estimate of by using data under inverse binomial sampling, in which individuals are selected sequentially to form matched pairs until for the first time one obtains either a prefixed number of index pairs with the case unexposed but the control exposed or with the case exposed but the control unexposed. We discuss the situation of possible early stopping. We compare numerically the performance of our procedure with a competitor proposed by Lui ( 1996 ) in terms of type I error rate, power, average sample number (ASN) and the corresponding standard error. Our numerical study shows a gain in sample size without loss in power as compared to the competitor. Finally, we use the data taken from a case‐control study on the use of X‐rays and the risk of childhood acute myeloid leukemia for illustration.     

QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.)

High temperature (>30 °C) at the time of grain filling is one of the major causes of yield reduction in wheat in many parts of the world, especially in tropical countries. To identify quantitative trait loci (QTL) for heat tolerance under terminal heat stress, a set of 148 recombinant inbred lines was developed by crossing a heat-tolerant hexaploid wheat (Triticum aestivum L.) cultivar (NW1014) and a heat-susceptible (HUW468) cultivar. The F(5), F(6), and F(7) generations were evaluated in two different sowing dates under field conditions for 2 years. Using the trait values from controlled and stressed trials, four different traits (1) heat susceptibility index (HSI) of thousand grain weight (HSITGW); (2) HSI of grain fill duration (HSIGFD); (3) HSI of grain yield (HSIYLD); and (4) canopy temperature depression (CTD) were used to determine heat tolerance. Days to maturity was also investigated. A linkage map comprising 160 simple sequence repeat markers was prepared covering the whole genome of wheat. Using composite interval mapping, significant genomic regions on 2B, 7B and 7D were found to be associated with heat tolerance. Of these, two (2B and 7B) were co-localized QTL and explained more than 15 % phenotypic variation for HSITGW, HSIGFD and CTD. In pooled analysis over three trials, QTL explained phenotypic variation ranging from 9.78 to 20.34 %. No QTL × trial interaction was detected for the identified QTL. The three major QTL obtained can be used in marker-assisted selection for heat stress in wheat.     

Nucleotide triplet based molecular phylogeny of class I and class II aminoacyl t-RNA synthetase in three domain of life process: bacteria, archaea, and eukarya

The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. These important enzymes have been the subject of intense scientific inquiry for nearly half a century, but their complete evolutionary history has yet to emerge. Amino acids sequence based phylogeny has some limitation due to very low sequence similarity amongst the different tRNA synthetases and structure based phylogeny has also its limitation. In our study, tRNA nucleotide sequences of E. coli K12 (Bacteria), Saccharomyces cerevisiae (Eukarya), Thermococcus kodakaraensis KOD1, and Archaeoglobus fulgidus DSM 4304 (Archaea) were used for phylogenetic analysis. Our results complement the observation with the earlier studies based on multiple sequence alignment and structural alignment. We observed that relationship between archaeal tRNA synthetases are different that of bacteria and eucarya. Violation of Class rule of LysRS is observed here also. The uniqueness of this method is that it does not employ sequence alignment of complete nucleotide sequence of the corresponding gene.     

Synthesis of metallic nanoparticles using plant extracts

Biomolecules present in plant extracts can be used to reduce metal ions to nanoparticles in a single-step green synthesis process. This biogenic reduction of metal ion to base metal is quite rapid, readily conducted at room temperature and pressure, and easily scaled up. Synthesis mediated by plant extracts is environmentally benign. The reducing agents involved include the various water soluble plant metabolites (e.g. alkaloids, phenolic compounds, terpenoids) and co-enzymes. Silver (Ag) and gold (Au) nanoparticles have been the particular focus of plant-based syntheses. Extracts of a diverse range of plant species have been successfully used in making nanoparticles. In addition to plant extracts, live plants can be used for the synthesis. Here we review the methods of making nanoparticles using plant extracts. Methods of particle characterization are reviewed and potential applications of the particles in medicine are discussed.     

Inhibition of apoptosis via CHIP-mediated proteasomal degradation of TAp73α

TAp73, a homologous of tumor suppressor p53, regulates apoptosis in a p53-independent manner and its suppressive as well as stimulatory role in promoting angiogenesis has been reported. It exists in multiple isoforms which varies structurally in their N-terminus and C-terminus region and crucial interplay among them guides the decision of cell survival and death. As molecular chaperones control both stability and degradation of TAp73, selective regulation of p73 isoforms has implication upon developing new therapeutic for hypoxic tumor. We have discovered that under DNA damage carboxy terminus Hsp70 interacting protein (CHIP's) antiapoptotic function is displayed via its E3 ligase activity that inhibits exclusively TAp73α-mediated apoptosis in cancer cell. The decrease in TAp73α level by CHIP as it is supported by increased ubiquitination pattern is reverted back by sh-CHIP. Further, the transactivation of p53-downstream apoptotic genes BAX, PUMA and PIG3 by TAp73α is also shown to be subsequently inhibited by CHIP. The tetratricopeptide TPR-domain of CHIP in its amino-terminus interacts with the carboxy-terminus of TAp73α and ΔNp73α and as a result, U-BOX domain of CHIP in the carboxy-terminus is able to ubiquitinate TAp73α for proteasomal degradation. Due to lack of C-terminus in TAp73β, CHIP fails to interact with and degrade it. In conclusion, we have thus uncovered for the first time a novel mechanism of chaperone-assisted regulation of p73 stability as well as its apoptotic functions by CHIP that might be utilized to develop new anticancer strategies.     

Evaluation of different bio-kinetic parameters of Curvularia lunata at different environmental conditions

Growth kinetic parameters for Curvularia lunata were determined in yeast extract, peptone and dextrose medium under different environmental conditions. The values of specific growth rate () were found to be different at different cultivation (pH and temperature) conditions. At the optimum growth conditions (pH 7.0 and temperature 28 °C) the values of specific growth rate and maintenance coefficient for C. lunata were maximum (0.19 h^-1) and minimum (0.04 h^-1) respectively, whereas the growth yield coefficient (Y_EG) decreased with the increase of cultivation temperature. The values of saturation constant (K_S) did not change appreciably with the change of cultivation conditions.     

Cdc42-dependent localization of polarisome component Spa2 to the incipient bud site is independent of the GDP/GTP exchange factor Cdc24

Cdc42, a member of the Rho subfamily of small GTPases, is highly conserved in both sequence and function across eukaryotic species. In budding yeast, Cdc42 triggers polarized growth necessary for bud emergence via rearrangement of the actin cytoskeleton. It has been shown that the role of Cdc42 in bud emergence requires both Cdc28-Cln (G1) kinase and the passage through START. In this report, we show that Cdc42 also serves an essential function in the establishment of bud site prior to START by catalyzing the translocation of bud-site components such as Spa2 to the cell cortex. Our analysis of various conditional alleles of CDC42 suggests that these two functions (bud site establishment and bud emergence) are genetically separable. Surprisingly, the role of Cdc42 in the cortical localization of Spa2 appears to be independent of its well known GTP/GDP exchange factor Cdc24. We also provide evidence that this role of Cdc42 requires the function of the COPI coatomer complex.     

WOOD OF GINKGO IN THE TERTIARY OF WESTERN NORTH AMERICA

Scott , R. A., E. S. Barghoorn , and U. Prakash . (U.S. Geol. Sur., Denver, Colo.) Wood of Ginkgo in the Tertiary of western North America . Amer. Jour. Bot. 49(10): 1095–1101. Illus. 1962. —Woods of Ginkgo and extinct related genera are very rare in the fossil record in contrast to the numerous ginkgoalean leaves. Ginkgo wood may be distinguished from other gymnosperms by a combination of anatomical features herein described. Ginkgo wood from beds of Miocene age at Vantage, Washington, first identified by Beck, is assigned to a new species, G. beckii. Ginkgo wood from the upper Eocene Clarno Formation, John Day Basin, Oregon, is described as G. bonesii sp. nov. Scarcity of fossil ginkgoalean woods may reflect unusual susceptibility to degradation of their cell walls in contrast to the greater chemical resistance to degradation which features many coniferous woods.