Efficient extraction of RNA from mammalian tissue

RNA extraction from mammalian tissue has been compared using the different deproteinizing agents: a) guanidine-HCl, b) guanidinium-thiocyanate, c) buffer-saturated phenol, or d) buffer-saturated phenol followed by a proteinase K digestion of the aqueous phase. Both solid tissues (first, second, and third trimester fetal bovine pancreas), and human white blood cell populations were studied. Degradation, as seen in citric acid-urea agarose gels, and the ability to serve as templates for cell-free protein synthesis were used as criteria to assess the efficiency of the different methods. We conclude that employing buffer-saturated phenol with proteinase K digestion is a superior method for consistent extraction of relatively undegraded RNA in quantitative amounts from mammalian tissue.     

Sesquiterpene lactone and friedelane derivative from drypetes molunduana

A new sesquiterpene lactone, drypemolundein A and a new friedelane derivative, drypemolundein B, along with seven known compounds have been isolated from the whole stems of Drypetes molunduana Pax and Hoffm. Their structures were established on the basis of one- and two-dimensional NMR, homo- and hetero-nuclear spectroscopic evidence.     

Comparative analysis of genetic relationship and diagnostic markers of several taxa of Guizotia Cass. (Asteraceae) as revealed by AFLPs and RAPDs

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) were employed to examine the genetic relationship between Guizotia taxa, to suggest the taxonomic status of some of these taxa, and to identify their diagnostic markers. Results from AFLPs and RAPDs share some features in common, both revealing G. scabra ssp. schimperi as the most closely related taxon to G. abyssinica, and indicating that G. arborescens and G. zavattarii are the most divergent taxa. Most of the diagnostic markers revealed in this study were specific to G. arborescens and G. zavattarii. Our analysis suggests that G. scabra ssp. scabra, G. scabra ssp. schimperi, Chelelu and Ketcha are separate species. In this study, AFLP was found to be superior to RAPD in detecting genetic variation, in internal consistency of the data and in the fitness of its clusters to genetic similarity data. AFLPs revealed genetic relationship between Guizotia taxa that is more inline with the cytogenetic and hybridization studies than that revealed by RAPDs.     

8-Oxoerythrinine: An alkaloid from Erythrina brucei

The flowers of Erythrina brucei afforded, in addition to known compounds, a new erythrina alkaloid, 8-oxoerythrinine. Its structure was elucidated by spectroscopic investigations as well as by chemical transformations.     

DNA photocleavage and biological activity of a pyrene dihydrodioxin

A pyrene dihydrodioxin has been synthesized, shown to bind to duplex DNA by intercalation, and cleave the phiX 174 supercoiled plasmid upon irradiation with UV light. This compound also exhibits cytotoxic activity at the micromolar range in a number of human cancer cell lines.     

Genetic Diversity and Population Structure of Ethiopian Chickpea (Cicer arietinum L.) Germplasm Accessions from Different Geographical Origins as Revealed by Microsatellite Markers

Genetic diversity and population structure were studied in 155 chickpea (Cicer arietinum L.) entries using 33 polymorphic microsatellite (SSR) markers. Molecular analysis of variance showed variations of 73% within and 27% among populations. Introduced genotypes exhibited highest polymorphism (70.27%) than the landraces (36?C57%). Collections from Shewa, Harerge, W. Gojam and S. Gonder regions also showed higher polymorphism (50?C57%) than the rest of the local accessions (36?C45%). Analyses of pairwise population Nei genetic distance and PhiPT coefficients, expected heterozygosity (He) and unbiased expected heterozygosity (UHe), Shannon??s information index (I) and percent polymorphism (% P) showed existence of high genetic variation between geographical regions. Accessions from adjoining geographical regions mostly showed more genetic similarities than those from origins far isolated apart. This could be associated with the ease and likelihood of inter-regional gene flow and seed movement particularly during times of drought. The 155 entries were grouped into five clusters following analysis of population structure. The first cluster (C₁) constituted accessions from Arsi; the second (C₂) from Gojam and Gonder; the third (C₃) from Harerge and E. and N. Shewa; and the fourth (C₄) from W. Shewa, Tigray, and Wello regions. The fifth cluster (C₅) was entirely consisted of improved genotypes. Improved genotypes of both Kabuli and Desi types distinctly fell into cluster five (C₅) regardless of their difference in seed types. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. Further implications of the findings as regards to chickpea germplasm management and its utilization in breeding program are also discussed.     

Assessment of genetic diversity in Ethiopian cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.] germplasm using simple sequence repeat markers

The genetic diversity of cowpea (Vigna unguiculata L. Walp.) in Ethiopia was analyzed using 19 uniform accessions, 62 variable accessions (yielding 185 sub-types), and two mungbean (Vigna radiata) accessions (four subtypes) as outgroup. A set of 23 polymorphic simple sequence repeat (SSR) markers was identified, and polymorphism in the various accessions was scored by determining amplicon variability. Allele frequency, genetic diversity, and polymorphism information content (PIC) were determined for each SSR marker, and a neighbor joining dendrogram was generated to show the genetic relationship among the individual accessions. A total of 75 allelic variants was defined, with the average number of alleles per locus calculated to be three. The average genetic diversity (D) was 0.47, and PIC was 0.4. Three main clusters were identified by phylogenetic analysis, and the clusters and sub-grouping were supported by STRUCTURE and principal component analysis. This grouping had a moderate fixation index value of 0.075 and gene flow (Nm) of 3.176, indicating that the accessions possess wide diversity within individuals and populations. The accessions showed no clustering by geographical origins. Three well-characterized molecular markers (SSR1, C42-2B, and 61RM2) for race specific resistance to Striga gesnerioides in the cowpea cultivar B301 were used to evaluate the accessions for their potential for use in genetic improvement against this pest. Based on this analysis, only two accessions, 222890–2 from Gambela and 286–2 from the Southern Nations, Nationalities, and Peoples (SNNP) region, were found to cluster with B301 and contain the SSR1 resistance allele. These findings will assist in germplasm conservation efforts by the Institute of Biodiversity and Conservation of Ethiopia, and contribute to future studies aimed at the genetic improvement of local germplasm for improved overall agronomic performance as well as Striga resistance in particular.     

A Bayesian Approach to Joint Mixed‐Effects Models with a Skew‐Normal Distribution and Measurement Errors in Covariates

Summary In recent years, nonlinear mixed‐effects (NLME) models have been proposed for modeling complex longitudinal data. Covariates are usually introduced in the models to partially explain intersubject variations. However, one often assumes that both model random error and random effects are normally distributed, which may not always give reliable results if the data exhibit skewness. Moreover, some covariates such as CD4 cell count may be often measured with substantial errors. In this article, we address these issues simultaneously by jointly modeling the response and covariate processes using a Bayesian approach to NLME models with covariate measurement errors and a skew‐normal distribution. A real data example is offered to illustrate the methodologies by comparing various potential models with different distribution specifications. It is showed that the models with skew‐normality assumption may provide more reasonable results if the data exhibit skewness and the results may be important for HIV/AIDS studies in providing quantitative guidance to better understand the virologic responses to antiretroviral treatment.     

Hierarchical Bayesian Analysis of Correlated Zero‐inflated Count Data

This article presents two‐component hierarchical Bayesian models which incorporate both overdispersion and excess zeros. The components may be resultants of some intervention (treatment) that changes the rare event generating process. The models are also expanded to take into account any heterogeneity that may exist in the data. Details of the model fitting, checking and selecting alternative models from a Bayesian perspective are also presented. The proposed methods are applied to count data on the assessment of an efficacy of pesticides in controlling the reproduction of whitefly. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

AFLP and RAPD analyses of genetic diversity of wild and/or weedy Guizotia (Asteraceae) from Ethiopia

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers were used to provide estimates of the comparative genetic variation within and among populations of various Guizotia taxa with the goal of conserving and utilizing their genetic diversity. The percentage of polymorphic loci (P(S)) ranged from 28.5%-90% (AFLP) and 85.6%-99.6% (RAPD). The overall gene diversity estimate () has shown slight variation among taxa ranging from 0.32-0.37 (AFLP) and from 0.22 to 0.28 (RAPD). The within population diversity of "Chelelu" and "Ketcha" was found to be unexpectedly high. Both parameters used to estimate population differentiation (G(ST) and F(ST)) revealed the highest population differentiation G. zavattarii in followed by G. arborescens. Genetic variation among populations within a taxon was highly significant for all the five taxa as revealed by AMOVA (P<0.0001). The need for immediate conservation activities for G. arborescens and G. zavattarii, and factors that contribute to the existing genetic variability and population genetic structures are discussed.