Bayesian Analysis of Composite Quantile Regression

This paper introduces a Bayesian approach for composite quantile regression employing the skewed Laplace distribution for the error distribution. We use a two-level hierarchical Bayesian model for coefficient estimation and future selection which assumes a prior distribution that favors sparseness. An efficient Gibbs sampling algorithm is developed to update the unknown quantities from the posteriors. The proposed approach is illustrated via simulation studies and two real datasets. Results indicate that the proposed approach performs quite good in comparison to the other approaches.     

Analysis of simple sequence repeat markers linked with blast disease resistance genes in a segregating population of rice (Oryza sativa)

Among 120 simple sequence repeat (SSR) markers, 23 polymorphic markers were used to identify the segregation ratio in 320 individuals of an F(2) rice population derived from Pongsu Seribu 2, a resistant variety, and Mahsuri, a susceptible rice cultivar. For phenotypic study, the most virulent blast (Magnaporthe oryzae) pathotype, P7.2, was used in screening of F(2) population in order to understand the inheritance of blast resistance as well as linkage with SSR markers. Only 11 markers showed a good fit to the expected segregation ratio (1:2:1) for the single gene model (d.f. = 1.0, P < 0.05) in chi-square (χ(2)) analyses. In the phenotypic data analysis, the F(2) population segregated in a 3:1 (R:S) ratio for resistant and susceptible plants, respectively. Therefore, resistance to blast pathotype P7.2 in Pongsu Seribu 2 is most likely controlled by a single nuclear gene. The plants from F(2) lines that showed resistance to blast pathotype P7.2 were linked to six alleles of SSR markers, RM168 (116 bp), RM8225 (221 bp), RM1233 (175 bp), RM6836 (240 bp), RM5961 (129 bp), and RM413 (79 bp). These diagnostic markers could be used in marker assisted selection programs to develop a durable blast resistant variety.     

Comparison of Real-time PCR to ELISA for the detection of human cytomegalovirus infection in renal transplant patients in the Sudan

Background

This study was carried out to detect human cytomegalovirus (HCMV) IgG and IgM antibodies using an Enzyme-linked immunosorbent assay (ELISA) in renal transplant patients in Khartoum state, Sudan and to improve the diagnosis of HCMV through the introduction of Real-time Polymerase Chain Reaction (PCR) testing. A total of 98 plasma samples were collected randomly from renal transplant patients at Ibin Sina Hospital and Salma Centre for Transplantation and Haemodialysis during the period from August to September 2006.

Results

Among the 98 renal transplant patients, 65 were males and 33 females. The results revealed that HCMV IgG was present in all patients' plasma 98/98 (100%), while only 6/98 (6.1%) had IgM antibodies in their plasma. HCMV DNA viral loads were detected in 32 patients 32/98 (32.7%) using Real-time PCR.

Conclusions

The HCMV IgG results indicate a high prevalence of past HCMV infection in all tested groups, while the finding of IgM may reflect a recent infection or reactivation. HCMV detection by real-time PCR in the present study indicated a high prevalence among renal transplant patients in Khartoum. In conclusion, the prevalence of HCMV in Khartoum State was documented through detection of HCMV-specific antibodies. Further study using various diagnostic methods should be considered to determine the prevalence of HCMV disease at the national level.

     

N-terminal peptide of Rhizopus oryzae lipase is important for its catalytic properties

In a culture medium, the Rhizopus oryzae strain produces only one form of lipase, ROL32. When the concentrated culture medium was stored at 0 degrees C during several months or kept at 6 degrees C during a few days, we noticed the appearance of a second shorter form of ROL32 lacking its N-terminal 28 amino acid (ROL29). ROL29 was purified to homogeneity and its 21 N-terminal amino acid residues were found to be identical to the 29-49 sequence of ROL32. The cleavage of the N-terminal peptide reduced the specific activity of ROL29 by 50% using either triolein or tributyrin as substrates. In order to explain this decrease of the specific activity of ROL29, we measured its critical surface pressure of penetration into phosphatidyl choline from egg yolk films which was found to be 10 mN/m, in contrast to a value of 23 mN/m found in ROL32. A kinetic study on the surface pressure dependency, stereoselectivity and regioselectivity of ROL29 was performed using the three dicaprin isomers spread as monomolecular films at the air-water interface. Our results showed that in contrast to ROL32, ROL29 presented a preference for the distal ester groups of one diglyceride isomer (1,3-sn-dicaprin). Furthermore, ROL32 was markedly more stereoselective than ROL29 for the sn-3 position of the 2,3-sn-enantiomer of dicaprin. A structural explanation of the enhanced penetration capacity as well as the catalytic activity of ROL32 was proposed by molecular modeling. We concluded that the N-terminal peptide of ROL32 can play an important role in the specific activity, the regioselectivity, the stereoselectivity and the binding of the enzyme to its substrate.     

Heavy metal biosorption by biomass of Ochrobactrum anthropi producing exopolysaccharide in activated sludge

The removal of chromium, cadmium and copper, toxic metals of high environmental priority due to their toxicity, from dilute aqueous solutions has been studied in the present work, applying a dead exopolysaccharide producing bacterium, Ochrobactrum anthropi, isolated from activated sludge. Particularly, the effect of pH, metal concentration and the effects of contact time were considered. Optimum adsorption pH values of chromium(VI), cadmium(II) and copper(II) were 2.0, 8.0 and 3.0 respectively. Experimental results also showed the influence of initial metal concentration on the metal uptake for dried biomass. Both the Freundlich and Langmuir adsorption models were suitable for describing the short-term biosorption of chromium(VI), cadmium(II) and copper(II) by O. anthropi.     

Isolation of enterotoxigenic, hemolytic, and antibiotic-resistant Aeromonas hydrophila strains from infected fish in Bangladesh

Strains of Aeromonas hydrophila isolated from skin infections of common freshwater fish in Bangladesh were tested for enterotoxin production, hemolysin production, and any correlation between these two activities. We also tested the resistance patterns of A. hydrophila to different drugs, especially in relation to ampicillin. The A. hydrophila strains produced an enterotoxin that was related to their beta-hemolytic activities. Production of beta-hemolysin may thus be an indicator of enterotoxicity. As 50% of the strains of A. hydrophila were found to be susceptible to 12.5 micrograms of ampicillin per ml, media containing this antibiotic may not be suitable for their isolation.     

PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia

Haruan (Channa striatus) is in great demand in the Malaysian domestic fish market. In the present study, mtDNA cyt b was used to investigate genetic variation of C. striatus among populations in Peninsular Malaysia. The overall population of C. striatus demonstrated a high level of haplotype diversity (h) and a low-to-moderate level of nucleotide diversity (π). Analysis of molecular variance (AMOVA) results showed a significantly different genetic differentiation among 6 populations (F_ST = 0.37566, P = 0.01). Gene flow (Nm) was high and ranged from 0.32469 to infinity (∞). No significant relationship between genetic distance and geographic distance was detected. A UPGMA tree based on the distance matrix of net interpopulation nucleotide divergence (d_A) and haplotype network of mtDNA cyt b revealed that C. striatus is divided into 2 major clades. The neutrality and mismatch distribution tests for all populations suggested that C. striatus in the study areas had undergone population expansion. The estimated time of population expansion in the mtDNA cyt b of C. striatus populations occurred 0.72-6.19 million years ago. Genetic diversity of mtDNA cyt b and population structure among Haruan populations in Peninsular Malaysia will be useful in fisheries management for standardization for Good Agriculture Practices (GAP) in fish-farming technology, as well as providing the basis for Good Manufacturing Practices (GMP).