Characterization of superantigen-induced clonal deletion with a novel clan III-restricted avian monoclonal antibody: exploiting evolutionary distance to create antibodies specific for a conserved VH region surface

Evolution of the Ab system has yielded three clans of VH region genes that are represented in almost every known higher species with an adaptive immune system. These clans are defined by sequence homologies primarily in highly conserved framework (FR) subdomains, which serve a scaffolding function maintaining the conformation of loops responsible for Ag binding. Structural analyses indicate that the VH FR1 and FR3 form a conserved composite exposed surface, which has been implicated in interactions with B cell superantigens. To directly investigate the expression of clan-defined supraclonal sets, we exploited the evolutionary distance of the chicken immune system and the selection power of phage display, to derive Abs diagnostic for clan III Ig. Using a specially tailored immunization and selection strategy, we created recombinant avian single chain Fv Abs specific for the clan III products, including those from the human VH3 family, and the analogous murine 7183, S107, J606, X24, and DNA4 families, and binding was competitive with natural B cell superantigens. The archetype, LJ-26, was demonstrated to recognize a clan-specific surface expressed in diverse mammalian, and also the Xenopus and chicken, immune systems. In flow-cytometric studies with LJ-26, we found that treatment of heterozygous T15i transgenic mice with a model B cell superantigen induced a clan III-restricted clonal deletion. These studies demonstrate the utility of a novel recombinant serologic reagent to study the composition of the B cell compartment and also the consequences of B cell superantigen exposure.     

Lipid composition of deep-sea hydrothermal vent tubeworm Riftia pachyptila, crabs Munidopsis subsquamosa and Bythograea thermydron, mussels Bathymodiolus sp. and limpets Lepetodrilus spp

Lipid composition was determined for hydrothermal vent species collected by the Deep Submergence Vehicle ALVIN from chimneys at 2,500 m depth on the East Pacific Rise. These are the first lipid biomarker studies for most of these species. Lipid content was low and dominated by polar lipid in the vestimentiferan tubeworm Riftia pachyptila, mussels Bathymodiolus sp. and limpets Lepetodrilus spp. The galatheid (Munidopsis subsquamosa) and most brachyuran adult (Bythograea thermydron) crabs were characterized by higher storage lipid (triacylglycerol). Total polyunsaturated fatty acids were similar in R. pachyptila plume and body, but higher in the posterior part of the soft body, which had more docosahexaenoic acid (2-5% of total FA) compared to the anterior and plume (< or =0.3%). Two sulphur-oxidizing bacterial markers, 16:1(n-7)c and 18:1(n-7)c, were high in R. pachyptila and mussel (up to 23%), but lower in both crab species (4-17%). R. pachyptila had greater nonmethylene interrupted diunsaturated fatty acids (8-13%) than all other species (2-8%). R. pachyptila may desaturate and elongate 18:1(n-7)c to obtain essential polyunsaturated fatty acids 20:5(n-3) and 20:4(n-6). The sterol composition of R. pachyptila included similar amounts of cholesterol and desmosterol, whereas the other species had a more diverse sterol composition. These differences in lipids, fatty acids and sterols reflect diverse nutritional strategies and possibly temperature regimes in these species.     

Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat

Retrotransposon-based molecular markers have been developed to study bread wheat ( Triticum aestivum) and its wild relatives. SSAP (Sequence-Specific Amplification Polymorphism) markers based on the BARE-1/ Wis-2-1A retrotransposons were assigned to T. aestivum chromosomes by scoring nullisomic-tetrasomic chromosome substitution lines. The markers are distributed among all wheat chromosomes, with the lowest proportion being assigned the D wheat genome. SSAP markers for BARE-1/ Wis-2-1A and three other wheat retrotransposons, Thv19 , Tagermina and Tar1, are broadly distributed on a wheat linkage map. Polymorphism levels associated with these four retrotransposons vary, with BARE-1/ Wis-2-1A and Thv19 both showing approximately 13% of bands polymorphic in a mapping population, Tagermina showing approximately 17% SSAP band polymorphism and Tar1 roughly 18%. This suggests that Tagermina and Tar1 have been more transpositionally active in the recent evolutionary past, and are potentially the more useful source of molecular markers in wheat. Lastly, BARE-1 / Wis-2-1A markers have also been used to characterise the genetic diversity among a set of 35 diploid and tetraploid wheat species including 26 Aegilops and 9 Triticum accessions. The SSAP-based diversity tree for Aegilops species agrees well with current classifications, though the Triticum tree shows several significant differences, which may be associated with polyploidy in this genus.Communicated by M.-A. Grandbastien     

Promoter elements in the aflatoxin pathway polyketide synthase gene

PksA catalyzes the formation of the polyketide backbone necessary for aflatoxin biosynthesis. Based on reporter assays and sequence comparisons of the nor1-pksA intergenic region in different aflatoxin-producing Aspergillus species, cis-acting elements for the aflatoxin pathway-specific regulatory protein, AflR, and the global-acting regulatory proteins BrlA and PacC are involved in pksA promoter activity.     

Src and Pyk2 mediate G-protein-coupled receptor activation of epidermal growth factor receptor (EGFR) but are not required for coupling to the mitogen-activated protein (MAP) kinase signaling cascade

The epidermal growth factor receptor (EGFR) and the non-receptor protein tyrosine kinases Src and Pyk2 have been implicated in linking a variety of G-protein-coupled receptors (GPCR) to the mitogen-activated protein (MAP) kinase signaling cascade. In this report we apply a genetic strategy using cells isolated from Src-, Pyk2-, or EGFR-deficient mice to explore the roles played by these protein tyrosine kinases in GPCR-induced activation of EGFR, Pyk2, and MAP kinase. We show that Src kinases are critical for activation of Pyk2 in response to GPCR-stimulation and that Pyk2 and Src are essential for GPCR-induced tyrosine phosphorylation of EGFR. By contrast, Pyk2, Src, and EGFR are dispensable for GPCR-induced activation of MAP kinase. Moreover, GPCR-induced MAP kinase activation is normal in fibroblasts deficient in both Src and Pyk2 (Src-/-Pyk2-/- cells) as well as in fibroblasts deficient in all three Src kinases expressed in these cells (Src-/-Yes-/-Fyn-/- cells). Finally, experiments are presented demonstrating that, upon stimulation of GPCR, activated Pyk2 forms a complex with Src, which in turn phosphorylates EGFR directly. These experiments reveal a role for Src kinases in Pyk2 activation and a role for Pyk2 and Src in tyrosine phosphorylation of EGFR following GPCR stimulation. In addition, EGFR, Src family kinases, and Pyk2 are not required for linking GPCRs with the MAP kinase signaling cascade.     

Spatial Patterns in Antibiotic Resistance among Stream Bacteria: Effects of Industrial Pollution

The spatial distribution of antibiotic resistance to streptomycin and kanamycin was examined in natural bacterial communities of two streams. The proportion of resistant bacteria was substantially higher (P < 0.05) in the midreaches of an industrially perturbed stream, but no such pattern was apparent in an undisturbed reference stream. The highest relative frequency of resistance was found at the confluence of a tributary draining a nuclear reactor and industrial complex. Antibiotic resistance increased with distance upstream from the confluence and was positively correlated (r² = 0.54, P = 0.023) with mercury concentrations in the sediments. When the data for two years were compared, this pattern was stable for streptomycin resistance (paired t test, P < 0.05) but not for kanamycin resistance (P > 0.05). Our results imply that heavy metal pollution may contribute to increased antibiotic resistance through indirect selection.     

Evaluating Chlorinated Hydrocarbon Plume Behavior Using Historical Case Population Analyses

A nationwide survey of chlorinated volatile organic compound (CVOC) plumes was conducted across a spectrum of sites from diverse hydrogeologic environments and contaminant release scenarios. The goal was to evaluate significant trends in the data that relate plume behavior to site variables (e.g., source strength, mean groundwater velocity, reductive dehalogenation regime) through correlation and population analyses. Data from 65 sites (government facilities, dry cleaners, landfills) were analyzed, yielding 247 individual CVOC plumes by compound. Data analyses revealed several trends, notably correlations between plume length and maximum observed concentration (presumably reflecting the source term) and mean groundwater velocities. Reductive dehalogenation, indicated by daughter products and groundwater geochemistry, appears to exert a relatively subtle effect on plume length, apparent only after the contributions of source strength and groundwater velocity are factored out. CVOC properties (K_oc, Henry's Law constant) exert significant effects on variability in maximum observed concentrations between sites but hold little influence on plume length. Probabilistic plume modeling, entailing Monte Carlo simulation of an analytical solution for average plume behavior with parameter distributions derived from site data, was used to produce a synthetic plume set for comparison with field data. Modeling results exhibited good agreement with field data in terms of parameter sensitivity.     

Ciprofloxacin Modulates Cytokine/Chemokine Profile in Serum,Improves Bone Marrow Repopulation,and Limits Apoptosis and Autophagy in Ileum after Whole Body Ionizing Irradiation Combined with Skin-Wound Trauma

Radiation combined injury (CI) is a radiation injury (RI) combined with other types of injury, which generally leads to greater mortality than RI alone. A spectrum of specific, time-dependent pathophysiological changes is associated with CI. Of these changes, the massive release of pro-inflammatory cytokines, severe hematopoietic and gastrointestinal losses and bacterial sepsis are important treatment targets to improve survival. Ciprofloxacin (CIP) is known to have immunomodulatory effect besides the antimicrobial activity. The present study reports that CIP ameliorated pathophysiological changes unique to CI that later led to major mortality. B6D2F1/J mice received CI on day 0, by RI followed by wound trauma, and were treated with CIP (90 mg/kg p.o., q.d. within 2 h after CI through day 10). At day 10, CIP treatment not only significantly reduced pro-inflammatory cytokine and chemokine concentrations, including interleukin-6 (IL-6) and KC (i.e., IL-8 in human), but it also enhanced IL-3 production compared to vehicle-treated controls. Mice treated with CIP displayed a greater repopulation of bone marrow cells. CIP also limited CI-induced apoptosis and autophagy in ileal villi, systemic bacterial infection, and IgA production. CIP treatment led to LD_0/10 compared to LD_20/10 for vehicle-treated group after CI. Given the multiple beneficial activities of CIP shown in our experiments, CIP may prove to be a useful therapeutic drug for CI.     

Prevention of preharvest aflatoxin contamination through genetic engineering of crops

Current practices on prevention of aflatoxin contamination of crop species include time consuming, expensive agronomic practices. Of all the methods available to-date, conventional breeding and/or genetic engineering to develop host plant-based resistance to aflatoxin-producing fungi appear to be valuable for several reasons. However, breeding for disease-resistant crops is very time consuming, especially in tree crops, and does not lend itself ready to combat the evolution of new virulent fungal races. Moreover, availability of known genotypes with natural resistance to mycotoxin-producing fungi is a prerequisite for the successful breeding program. While it is possible to identify a few genotypes of corn or peanuts that are naturally resistant toAspergillus we do not know whether these antifungal factors are specific toA. flavus. In crops like cotton, there are no known naturally resistant varieties toAspergillus. Availability of transgenic varieties with antifungal traits is extremely valuable as a breeding tool. Several antifungal proteins and peptides are available for genetic engineering of susceptible crop species, thanks to the availability of efficient modern tools to understand and evaluate protein interactions by proteomics of host, and genomics and field ecology of the fungus. Transgenic approaches are being undertaken in several industry and academic laboratories to prevent invasion byAspergillus fungi or to prevent biosynthesis of aflatoxin. Recent trends in reducing aflatoxin contamination through genetic engineering of cultivated crop species with antifungal proteins are summarized in this report. Presented at the EU-USA Bilateral Workshop on Toxigenic Fungi & Mycotoxins, New Orleans, USA, July 5–7, 2005     

Analysis of Crossover Designs with a Categorical Response

In the analysis of two-period crossover designs, one frequently must consider the case of a categorical response with binary as a special case. These circumstances are considered in this paper and the proposed method—an extension of GART'S tests for the binary case—is similar to that of PIKE, CASAGRANDE and SMITH for the analysis of pair-matched case-control studies. The results are illustrated with a numerical example.