Expression of a class I MHC transgene: effects of in vivo α/β-interferon treatment

Transgenic mice containing a swine class I major histocompatibility complex (MHC) gene,PD1, express swine MHC (SLA) antigen. The tissue distribution of PD1 RNA parallels that observed in the swine, indicating that the expression ofPD1 is regulated and thattrans-acting factors involved in this regulation have been conserved between the species. Although PD1 RNA levels were much greater in transgenic spleen than in thymus, no difference in the chromatin organization of thePD1 gene was detected. In both tissues, a single DNase I hypersensitive site mapped within the 5′ flanking region. In vivo treatment of the transgenics with mouse α, β-interferon increases PD1 expression in a number of tissues. In the spleen, this increase parallels that observed for the endogenous transplantation antigen, K^b, but differs markedly from the differentiation antigen, Qa-2. Increases in cell surface expression of both PD1 and K^b occurred equally in splenic T- and B-cell populations following α,β-interferon treatment. In contrast, Qa-2 expression in B cells was enhanced by α,β-interferon, whereas it was unaffected in T cells and thymocytes.     

Differential effect of antigen-nonspecific T-cell factors and lipopolysaccharide on the Ia antigens and surface immunoglobulins of BALB/c lymphoma cell lines

In order to study the mechanism of B-cell differentiation using B lymphoid tumor cells as models, we investigated the effects of antigen-nonspecific T-cell factors in combination with lipopolysaccharide (LPS) on the expression of surface markers on B lymphoid cell lines. This study demonstrated that culture supernatant from concanavalin A-activated spleen cells (CAS) gave 2- to 3.5-fold enhancement of the expression of Ia antigens. The effect of CAS was dose dependent and as little as 2% CAS gave maximum enhancement of Ia antigen expression. The CAS effect was due to concanavalin A-activated cell products and was not due to the concanavalin A. The effects of allogeneic effect factor (AEF) on Ia antigens were similar to those of CAS. In contrast to CAS and AEF, LPS did not affect the expression of Ia antigens on ×16C 8.5. LPS enhanced 1.5- to 3-fold the expression of sIgM on this cell line. The expression of sIgM was minimally affected by T-cell factors; CAS induced 20 to 70% enhancement of sIgM expression while AEF induced no significant effects. This study showed that antigen-nonspecific factors (CAS and AEF) influenced mainly Ia expression on the B-cell lymphoma, ×16C 8.5, while LPS selectively affected sIgM expression. Therefore, it was concluded that the mechanisms by which B cells are activated by T-cell factors and mitogens are different.     

<i>Streptomyces</i> PRIO41 as plant growth promoter of jalapeño pepper plants and as biocontrol agent of <i>Fusarium</i>

Chili pepper is one of the main crops of economic importance in Mexico, and Fusarium wilting is a disease that limits its production. In addition, the inappropriate use of agrochemicals in farming activities generate environmental and health problems. Therefore, in this study the effectiveness of Streptomyces sp PRIO41 was evaluated as a (1) biocontrol agent of Fusarium spp and (2) plant growth promoter bacteria. Assays of pathogenicity and virulence of Fusarium spp. in jalapeño pepper seeds, and interactions of these pathogens with Streptomyces PRIO41 were evaluated under two nutritional conditions. In the greenhouse, the effectiveness of Streptomyces sp. PRIO41 was determined as a (1) biocontrol of Fusarium, and (2) plant growth promoter of wilt of pepper plants. The results showed that all fungal isolates caused symptoms in pepper seeds and seedlings with different degrees of virulence. Interactions in vitro showed that Streptomyces showed the most effective range of virulence against Fusarium isolates in the poor medium (37.6%-100%), with fungicidal effects in some cases. In the greenhouse, Streptomyces PRIO41 reduced Fusarium wilting up to a 40%, and positively affected all vegetative growth parameters, particularly plant height, leaf area, root length, and leaf and root dry biomasses. This study showed the potential of Streptomyces PRIO41 as a biocontrol agent of Fusarium spp., and as a biofertilizer of pepper plants.     

In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae

Background

The PCR technique and its variations have been increasingly used in the clinical laboratory and recent advances in this field generated new higher resolution techniques based on nucleic acid denaturation dynamics. The principle of these new molecular tools is based on the comparison of melting profiles, after denaturation of a DNA double strand. Until now, the secondary structure of single-stranded nucleic acids has not been exploited to develop identification systems based on PCR. To test the potential of single-strand RNA denaturation as a new alternative to detect specific nucleic acid variations, sequences from viruses of the Totiviridae family were compared using a new in silico melting curve approach. This family comprises double-stranded RNA virus, with a genome constituted by two ORFs, ORF1 and ORF2, which encodes the capsid/RNA binding proteins and an RNA-dependent RNA polymerase (RdRp), respectively.

Results

A phylogenetic tree based on RdRp amino acid sequences was constructed, and eight monophyletic groups were defined. Alignments of RdRp RNA sequences from each group were screened to identify RNA regions with conserved secondary structure. One region in the second half of ORF2 was identified and individually modeled using the RNAfold tool. Afterwards, each DNA or RNA sequence was denatured in silico using the softwares MELTSIM and RNAheat that generate melting curves considering the denaturation of a double stranded DNA and single stranded RNA, respectively. The same groups identified in the RdRp phylogenetic tree were retrieved by a clustering analysis of the melting curves data obtained from RNAheat. Moreover, the same approach was used to successfully discriminate different variants of Trichomonas vaginalis virus, which was not possible by the visual comparison of the double stranded melting curves generated by MELTSIM.

Conclusion

In silico analysis indicate that ssRNA melting curves are more informative than dsDNA melting curves. Furthermore, conserved RNA structures may be determined from analysis of individuals that are phylogenetically related, and these regions may be used to support the reconstitution of their phylogenetic groups. These findings are a robust basis for the development of in vitro systems to ssRNA melting curves detection.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-243) contains supplementary material, which is available to authorized users.     

Subpopulations of fetal thymocytes defined by expression of T cell receptor/CD3 and IL-2 receptor. CD3 and IL-2 receptor alpha-chain are expressed on reciprocal cell populations

The expression of the TCR/CD3 complex and the IL-2R alpha chain (p55) on fetal thymocytes has been analyzed by flow cytometry (FCM). Two-parameter immunofluorescence identified three subpopulations which were respectively IL-2R alpha-/CD3+, IL-2R alpha+/CD3-, or IL-2R alpha-/CD3-; no detectable population of IL-2R alpha+/CD3+ cells was found in unstimulated fetal thymocytes. Fractionation by "panning" and by sterile flow cytometric separation was used to characterize the functional responsiveness of these three subpopulations to a variety of stimuli. All three populations proliferated in response to PMA + ionomycin + rIL-2. In contrast, stimulation with anti-CD3 + IL-2 induced proliferation in IL-2R alpha-/CD3+ and IL-2R alpha-/CD3- but not in IL-2R alpha+/CD3- thymocytes. IL-2R alpha- cells, including sorted IL-2R alpha-/CD3- thymocytes, underwent a phenotypic change in response to in vitro stimulation with anti-CD3 + IL-2, resulting in the appearance of an IL-2R alpha+/CD3+ population that was not detected in freshly isolated thymocytes. The ability of fractionated fetal thymocytes to produce lymphokine in response to PMA + ionomycin was also evaluated. Only the IL-2R alpha-/CD3- fraction generated detectable IL-2. These findings demonstrate for the first time that CD3 and IL-2R alpha are expressed in a mutually exclusive fashion in fetal thymocytes and define three subpopulations of thymocytes that differ significantly in their proliferative and differentiative responses to TCR-mediated, IL-2R-mediated, and pharmacologic stimulation.     

Amino acid catabolism in cheese-related bacteria: selection and study of the effects of pH, temperature and NaCl by quadratic response surface methodology

AIMS: To screen the cystathionine lyase and L-methionine aminotransferase activities of cheese-related bacteria (lactococci, non-starter lactobacilli and smear bacteria) and to determine the individual and interactive effects of temperature, pH and NaCl concentration on selected enzyme activities. METHODS AND RESULTS: A subcellular fractionation protocol and specific enzyme assays were used, and a quadratic response surface methodology was applied. The majority of the strains, 21 of 33, had detectable cystathionine lyase activity which differed in the specificity. Aminotransferase activity on L-methionine was observed in only three strains. The cystathionine lyase activities of Lactobacillus reuteri DSM20016, Lactococcus lactis subsp. cremoris MG1363, Brevibacterium linens 10 and Corynebacterium ammoniagenes 8 and the L-methionine aminotransferase activity of Lact. reuteri DSM20016 had temperature and pH optima of 30-45 degrees C, and 7.5-8.0, respectively. As shown by the quadratic response surface methodology these enzymes retained activities in the range of temperature, pH and NaCl concentration which characterized the cheeses from which the bacteria originated. CONCLUSION: The enzyme activities may have a role in flavour development during cheese ripening. SIGNIFICANCE AND IMPACT OF THE STUDY: The findings of this work contribute to the knowledge about the amino acid catabolic enzymes in order to improve cheese ripening.     

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

Role of L3T4+ and Lyt-2+ donor cells in graft-versus-host immune deficiency induced across a class I, class II, or whole H-2 difference

The i.v. injection of parental T cells into F1 hybrid mice can result in a graft-vs-host (GVH)-induced immune deficiency that is Ag nonspecific and of long duration. The effect of the GVH reaction (GVHR) on the host's immune system depends on the class of F1 MHC Ag recognized by the donor cells. To determine the role of different subsets of donor-derived T cells in the induction of GVHR, donor spleen cells were negatively selected by anti-T cell mAb and C, and the cells were injected into F1 mice that differed from the donor by both class I and II MHC Ag or by class I or class II MHC only. The induction of GVHR across class I + II differences was found to require both L3T4+ and Lyt-2+ parental cells. Induction of GVHR across a class II difference required only L3T4+ parental T cells in the combination tested [B6-into-(B6 x bm12)F1]. In contrast, B6 Lyt-2+ cells were sufficient to induce GVHR across a class I difference in (B6 x bm1)F1 recipients. In addition, a direct correlation was observed between the cell types required for GVH induction and the parental T cell phenotypes detected in the spleens of the GVH mice. The number of parental cells detected in the unirradiated F1 hosts was dependent upon the H-2 differences involved in the GVHR. Induction of a class I + class II GVHR resulted in abrogation of both TNP-self and allogeneic CTL responses. In contrast, induction of a class II GVHR resulted in only a selective loss of TNP-self but not of allogeneic CTL function. Unexpectedly, the induction of a class I GVHR also resulted in the selective loss of the TNP-self CTL response. Thus, these class I and class II examples of GVH both result in the selective abrogation of L3T4+ Th cell function. The data are discussed in terms of respective roles of killer cells and/or suppressor cells in the induction of host immune deficiency by a GVHR, and of the selective deficiency in host Th cell function induced by different classes of GVHR.