Complementary approaches to diagnosing marine diseases: a union of the modern and the classic

Linking marine epizootics to a specific aetiology is notoriously difficult. Recent diagnostic successes show that marine disease diagnosis requires both modern, cutting-edge technology (e.g. metagenomics, quantitative real-time PCR) and more classic methods (e.g. transect surveys, histopathology and cell culture). Here, we discuss how this combination of traditional and modern approaches is necessary for rapid and accurate identification of marine diseases, and emphasize how sole reliance on any one technology or technique may lead disease investigations astray. We present diagnostic approaches at different scales, from the macro (environment, community, population and organismal scales) to the micro (tissue, organ, cell and genomic scales). We use disease case studies from a broad range of taxa to illustrate diagnostic successes from combining traditional and modern diagnostic methods. Finally, we recognize the need for increased capacity of centralized databases, networks, data repositories and contingency plans for diagnosis and management of marine disease.     

Modification of Sindbis Virus Glycoprotein by Host-Specified Glycosyl Transferases

The amino acid sequence of the membrane glycoprotein of Sindbis virus is specified by the viral genome, but it has not been determined whether the carbohydrate portion of this molecule is specified by the cell or by the virus. We have examined two of the enzyme activities which catalyze transfer of monosaccharides to glycoprotein (sialyl and fucosyl transferases). Comparison of particulate enzyme preparations from infected and uninfected cells showed no difference in either the specific activity or acceptor specificity of these enzymes. This is impressive in view of the fact that the Sindbis membrane glycoprotein is the only glycoprotein synthesized in the infected cell. It was also determined that sialyl transferase from uninfected cells is capable of transferring ((3)H) sialic acid to acceptor prepared from Sindbis membrane glycoprotein. These results imply that at least some of the carbohydrate of the virus glycoprotein can arise by host modification.     

Genomic organization and chromosomal localization of three members of the UDP-N-acetylgalactosamine: polypeptide N- acetylgalactosaminyltransferase family

A homologous family of UDP- N -acetylgalactosamine: polypeptide N - acetylgalactosaminyltransferases (GalNAc-transferases) initiate O- glycosylation. These transferases share overall amino acid sequence similarities of approximately 45-50%, but segments with higher similarities of approximately 80% are found in the putative catalytic domain. Here we have characterized the genomic organization of the coding regions of three GalNAc-transferase genes and determined their chromosomal localization. The coding regions of GALNT1 , -T2 , and -T3 were found to span 11, 16, and 10 exons, respectively. Several intron/exon boundaries were conserved within the three genes. One conserved boundary was shared in a homologous C. elegans GalNAc- transferase gene. Fluorescence in situ hybridization showed that GALNT1 , -T2 , and -T3 are localized at chromosomes 18q12-q21, 1q41-q42, and 2q24-q31, respectively. These results suggest that the members of the polypeptide GalNAc-transferase family diverged early in evolution from a common ancestral gene through gene duplication.      

Letter to editor: Subunit arrangements in bacterial flagella

The subunit arrangements have been considered in flagella isolated from a wide range of gram-positive and gram-negative bacteria on the basis of both new and published meridional X-ray diffraction data from oriented pulled fibres. In agreement with the work of others, the subunits are found to be arranged on helices with close to 11 subunits in two turns. The helices are irrational in general and the small but significant differences between the arrangements of subunits may be related to the organism-dependent, long-wavelength periods characteristic of motile bacteria.     

DomSVR: domain boundary prediction with support vector regression from sequence information alone

Protein domains are structural and fundamental functional units of proteins. The information of protein domain boundaries is helpful in understanding the evolution, structures and functions of proteins, and also plays an important role in protein classification. In this paper, we propose a support vector regression-based method to address the problem of protein domain boundary identification based on novel input profiles extracted from AAindex database. As a result, our method achieves an average sensitivity of ∼36.5% and an average specificity of ∼81% for multi-domain protein chains, which is overall better than the performance of published approaches to identify domain boundary. As our method used sequence information alone, our method is simpler and faster.     

Single nucleotide polymorphism-based validation of exonic splicing enhancers

Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. As an application of this approach, we analyzed a set of 238 hexanucleotides previously predicted to have exonic splicing enhancer (ESE) activity in human exons using the relative enhancer and silencer classification by unanimous enrichment (RESCUE)-ESE method. Aligning the single nucleotide polymorphisms (SNPs) from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. Analyzing the set of SNPs that overlap RESCUE-ESE hexamers, we conclude that nearly one-fifth of the mutations that disrupt predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 +/- 0.05). This selection is strongest for the predicted ESEs that are located near splice sites. Our results demonstrate a novel approach for quantifying the extent of natural selection acting on candidate functional motifs and also suggest certain features of mutations/SNPs, such as proximity to the splice site and disruption or alteration of predicted ESEs, that should be useful in identifying variants that might cause a biological phenotype.     

Cytokinins and fruit development in the kiwifruit (Actinidia deliciosa). II. Effects of reduced pollination and CPPU application

The significance of changes in cytokinin content during early fruit growth was examined in the kiwifruit ( Actinidia deliciosa var. deliciosa cv. Hayward). Fruit growth was modified by the reduction of seed number or by the application of the synthetic phenylurea cytokinin N -(2-chloro-4-pyridyl)- N -phenylurea (CPPU). The influence of these treatments on cell division was monitored by flow cytometry and changes in the endogenous cytokinins were measured at days 10 and 20 after anthesis, using high-performance liquid chromatography and radioimmunoassay. Total cytokinin levels appeared not to be limiting growth since the highest total cytokinin concentration was detected in unpollinated fruit, which abscised by day 25 after anthesis. However, compared with control fruit which had the highest concentration of zeatin (Z) 10 days post anthesis, Z levels were low in unpollinated fruit. It is hypothesised that an increase in Z is the critical change in cytokinin metabolism required for the initiation of cell division and fruit growth. The synthetic cytokinin CPPU promoted fruit development, but there was a decrease in the endogenous cytokinin concentration. Zeatin was not detected in CPPU-treated fruit. Cell division was reduced in unpollinated fruitlets but there was no significant difference ( P > 0.05) between the other treatments. Differences in final fruit size appeared to be due to cell expansion.