A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis

One of the challenges to the effective utilization of cDNA microarray analysis in mouse models of oncogenesis is the choice of a critical set of probes that are informative for human disease. Given the thousands of genes with a potential role in human oncogenesis and the hundreds of thousands of mouse sequences available for use as probes, selection of an informative set of mouse probes can be an overwhelming task. We have developed a web based sequence mining tool using DataBase Independent (DBI) Perl to annotate publicly available sequences. The Mouse Oncochip Design Tool uses the Mouse Genome Database (MGD) developed and maintained by the Jackson Laboratories for mouse DNA sequences. There are over 380 000 sequences in their database. The output list has been ordered to present the genes more likely to be informative in a mouse model of human cancer using a candidate set of oncogenes to order the list. Mouse sequences that represent genes that are homologous with a member of a human oncogene set are listed first. In addition it provides a set of links for information on clone source gene function. Contact: http://nciarray.nci.nih.gov/cgi-bin/me/mouse_design.cgi     

SARS transmission pattern in Singapore reassessed by viral sequence variation analysis

Background

Epidemiological investigations of infectious disease are mainly dependent on indirect contact information and only occasionally assisted by characterization of pathogen sequence variation from clinical isolates. Direct sequence analysis of the pathogen, particularly at a population level, is generally thought to be too cumbersome, technically difficult, and expensive. We present here a novel application of mass spectrometry (MS)–based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore.

Methods and Findings

The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. Analysis of 13 SARS-CoV isolates from the different stages of the Singapore outbreak identified nine sequence variations that could define the molecular relationship between them and pointed to a new, previously unidentified, primary route of introduction of SARS-CoV into the Singapore population. Our direct determination of viral sequence variation from a clinical sample also clarified an unresolved epidemiological link regarding the acquisition of SARS in a German patient. We were also able to detect heterogeneous viral sequences in primary lung tissues, suggesting a possible coevolution of quasispecies of virus within a single host.

Conclusion

This study has further demonstrated the importance of improving clinical and epidemiological studies of pathogen transmission through the use of genetic analysis and has revealed the MS-based analysis to be a sensitive and accurate method for characterizing SARS-CoV genetic variations in clinical samples. We suggest that this approach should be used routinely during outbreaks of a wide variety of agents, in order to allow the most effective control.     

T cell-induced expression of membrane IgG by 70Z/3 B cells

To study T cell regulation of B cell isotype differentiation, we determined the capacity of clonal T cell populations (hybridomas derived by fusing BW5147 with Con A-activated Peyer's patch (PP) and spleen T cells) to induce "downstream" isotype expression by the pre-B cell lymphoma 70Z/3. In initial studies, we found that 70Z/3 B cells cultured in the presence of LPS (1 microgram/ml) expressed membrane IgM (mIgM) but not membrane IgG (mIgG). In contrast, 70Z/3 B cells cultured with HAJ-3 T cells, a PP-derived T cell hybridoma (as well as other similarly derived PP and spleen hybridomas), or with HAJ-3 T cells plus LPS do express mIgG. Such expression occurred in spite of mitomycin C-induced blockage of cell proliferation, and is observed in 70Z/3 B cell subclones cultured with HAJ-3 T cells. For these reasons, it is not due to selective expansion of a small pre-switched mIgG-bearing 70Z/3 B cell subpopulation. In other studies it was shown that 70Z/3 B cells expressing mIgG after induction by HAJ-3 T cells continue to express mIgM and do not secrete IgG. Finally, exposure of 70Z/3 B cells to the macrophage factor IL 1 and the T cell factors IL 2, BSF-pl, and BCGF-II present in EL-4 cell supernatants did not result in mIgG expression. On the basis of these studies, we conclude that a clonal B cell population expressing mIgM can be induced by T cells to co-express mIgG. Because the B cells do not express mIgG unless exposed to T cells, this represents a T cell-induced isotype switch.     

Physiological responses of marine Dendryphiella species from different geographical locations

The saprobic, cosmopolitan, marine fungi Dendryphiella arenaria and Dendryphiella salina, isolated from various plant and algal substrates from different geographical locations and climatic zones, were studied for their adaptations to the abiotic and biotic parameters commonly found in their natural marine habitats. All the tested strains of D. arenaria and D. salina grew optimally on culture media with added marine salts, at pH values between 6.5 and 8.0 and at an incubation temperature of 25°C. The D. arenaria strains had faster mean colony extension rates under all conditions of culture. All strains exhibited an increased salt optimum with increasing incubation temperature. The TLC profiles of strains of the two species were similar. The culture extracts were antimicrobial, though production of the biologically active metabolites was strain-specific. There were no significant correlations between source of origin and responses to the investigated parameters. These results demonstrate phenotypic plasticity and the ability of each isolate to adapt to diverse biotopes.     

New Brazilian species of Endecous Saussure, 1878: Phallic sclerites, calling song and tegmen morphometry (Orthoptera: Grylloidea: Phalangopsinae)

In this paper we describe the phalangopsid cricket Endecous alejomesai n. sp. collected from the cave "Lapa do Fuzil", Vila Propício, State of Goiás, Brazil. Diagnosis has been acquired by the combination of the following characteristics: phallic sclerite features; calling song with dominant frequency of 4.8 kHz and 52.9 ± 5.8 (42–60, n  = 22) cycles of sound per pulse; pars stridens with 90 ± 6.84 (78–99, n  = 12) teeth; mirror with one or two cross-veins; harp with two, three or four cross-veins.     

Genetic variability in G2 and F2 region between biological clones of human respiratory syncytial virus with or without host immune selection pressure

Human respiratory syncytial virus (HRSV) is an important respiratory pathogens among children between zero-five years old. Host immunity and viral genetic variability are important factors that can make vaccine production difficult. In this work, differences between biological clones of HRSV were detected in clinical samples in the absence and presence of serum collected from children in the convalescent phase of the illness and from their biological mothers. Viral clones were selected by plaque assay in the absence and presence of serum and nucleotide sequences of the G2 and F2 genes of HRSV biological clones were compared. One non-synonymous mutation was found in the F gene (Ile5Asn) in one clone of an HRSV-B sample and one non-synonymous mutation was found in the G gene (Ser291Pro) in four clones of the same HRSV-B sample. Only one of these clones was obtained after treatment with the child''s serum. In addition, some synonymous mutations were determined in two clones of the HRSV-A samples. In conclusion, it is possible that minor sequences could be selected by host antibodies contributing to the HRSV evolutionary process, hampering the development of an effective vaccine, since we verify the same codon alteration in absence and presence of human sera in individual clones of BR-85 sample.     

Application of Multivariate Analysis for the Selection of Candidates for Biological Control Agents

A survey of natural enemies ofSenna obtusifolia(Leguminosae: Cesalpinaceae) was made in 46 localities in Brazil. Twenty-one preselected insect species were used in a multivariate analysis in a search for potential biocontrol agents, based on frequency of occurrence of each species, degree of insect/host association, and damage level. Insect communities were organized in a binary matrix (presence/absence of the species); measures of distance and similarities were based on the Jaccard coefficient, and cluster analysis was then conducted. Construction of a dendogram showed similarities among geographically close localities where phenological stages of sicklepod plants were similar. Analysis of correspondence based on the correlation matrix showed that Eigen values of the three first axes explain only 40.1% of the observed variation. Correlation among the scores produced by species Eigenvectors in each locality on axis 1 and the latitude, altitude, and phenological stage showed that only phenological stage was correlated (r = 0.45,P = 0.02). The results indicate that weather will not be a limiting factor for the establishment of these insect species in an environmental gradient similar to that of the surveyed area (12 to 22° latitude and 6 to 1200 m altitude). Distribution in the ordinal space of axes 1 and 2 showed thatAgrilus oceanicum(Buprestidae),Fundella argentina(Pyralidae),Thyphedanus undulatus(Hesperidae), andPhoebis sennae(Pieridae) are grouped and separated from the others in axis 2, suggesting that these species co-occur with each other. Based on their feeding guilds, multiple introduction of these species can be considered. Multivariate analysis showed potential to be used as an additional tool to help in the selection of candidates for biocontrol agents.