A graphical method for detecting recombination in phylogenetic data sets

Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.      

The gall of subordination: changes in gall bladder function associated with social stress

Diverse physiological and behavioural mechanisms allow animals to effectively deal with stressors, but chronic activation of the stress axis can have severe consequences. We explored the effects of chronic social stress on agonistic behaviour and gall bladder function, a critical but widely neglected component of stress-induced gastrointestinal dysfunction. Prolonged cohabitation with dominant individuals elicited behavioural modifications and dramatically increased bile retention in subordinate convict cichlid fish (Archocentrus nigrofasciatum). The key predictor of gall bladder hypertrophy was social subordination rather than status-related differences in food intake or body size. Stress-induced inhibition of gall bladder emptying could affect energy assimilation such that subordinate animals would not be able to effectively convert energy-rich food into mass gain. These results parallel changes in gall bladder function preceding cholesterol gallstone formation in humans and other mammals. Thus, social stress may be an important diagnostic criterion in understanding pathologies associated with gall bladder dysfunction.     

Multicopy suppression of a gacA mutation by the infC operon in Pseudomonas fluorescens CHA0: competition with the global translational regulator RsmA

The gacA gene of the biocontrol strain Pseudomonas fluorescens CHA0 codes for a response regulator which, together with the sensor kinase GacS (=LemA), is required for the production of exoenzymes and secondary metabolites involved in biocontrol, including hydrogen cyanide (HCN). A gacA multicopy suppressor was isolated from a cosmid library of strain CHA0 and identified as the infC-rpmI-rplT operon, which encodes the translation initiation factor IF3 and the ribosomal proteins L35 and L20. The efficiency of suppression was about 30%, as determined by the use of a GacA-controlled reporter construct, i.e. a translational hcnA'-'lacZ fusion. Overexpression of the rsmA gene (coding for a global translational repressor) reversed the suppressive effect of the amplified infC operon. This finding suggests that some product(s) of the infC operon can compete with RsmA at the level of translation in P. fluorescens CHA0 and that important biocontrol traits can be regulated at this level.     

Development and Use of a Polyvalent Conjugate to Differentiate Histoplasma capsulatum and Histoplasma duboisii from Other Pathogens

Previous investigations have demonstrated the existence of five Histoplasma capsulatum serotypes. Available specific fluorescent-antibody reagents stain only four of the five serotypes. Antibodies produced against the most complete H. capsulatum serotype were labeled with fluorescein isothiocyanate to develop a reagent specific for H. capsulatum that was reactive with all the known serotypes. The unadsorbed reagent not only stained all the H. capsulatum serotypes, but it also stained cultures of Blastomyces dermatitidis, H. duboisii, several Candida species, and a variety of other fungi. Adsorption of the conjugate with antigens of C. albicans produced a reagent that intensely stained only H. capsulatum, H. duboisii, and B. dermatitidis. Differentiation of B. dermatitidis from the Histoplasma species was accomplished by application of a B. dermatitidis specific fluorescent antibody to antigens positive with the H. capsulatum reagent. At present, differentiation of H. capsulatum from H. duboisii may be accomplished only by animal inoculation. Our data substantiate the antigenic relationships hypothesized earlier, and they indicate that H. capsulatum shares at least two antigens with the other fungi that were studied.     

Evaluation of Probiotic Potential of Bacteriocinogenic Lactic Acid Bacteria Strains Isolated from Meat Products

In this study, the probiotic potential of five bacteriocin-producing lactic acid bacteria (LAB) strains, isolated from meat products, was investigated. They were presumptively identified as Lactococcus lactis subsp. cremoris CTC 204 and CTC 483, L. lactis subsp. hordinae CTC 484, and Lactobacillus plantarum CTC 368 and CTC 469 according to morphological, biochemical, and physiological characteristics. Analysis of genetic variability (random amplified polymorphic (RAPD)-PCR) and whole-cell proteins (SDS-PAGE) revealed similarity between Lactobacillus strains and variability among Lactococcus strains. The evaluation of the probiotic potential showed that the five LAB strains were tolerant to pH 2.0, and only strain CTC 469 was tolerant to the lowest concentration of the bile salts evaluated (0.1%). All strains showed survival or growth ability at 4, 25, and 37 °C, and tolerance at ??20 °C. Although strain CTC 204 in TSB Broth supplemented with MgSO₄ showed the highest intensity of biofilm production, this compound was produced by all of them. The safety assessment showed that no thermonuclease, hemolytic, or gelatinase activities were detected. All strains were resistant to erythromycin and sensitive to amoxicillin and phenoxymethylpenicillin; furthermore, CTC 204 was resistant to chloramphenicol, CTC 368 and CTC 469 to chloramphenicol and vancomycin, CTC 483 to tetracycline and vancomycin, and CTC 484 to clindamycin and chloramphenicol. The evaluated strains showed biogenic amine production; the lowest levels were produced by CTC 204 and CTC 368 strains. It was concluded that CTC 204 and CTC 368 strains have the greatest potential for becoming probiotics.     

What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background  

The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species.     

T-helper 17 cell cytokines and interferon type I: partners in crime in systemic lupus erythematosus?

Introduction

A hallmark of systemic autoimmune diseases like systemic lupus erythematosus (SLE) is the increased expression of interferon (IFN) type I inducible genes, so-called IFN type I signature. Recently, T-helper 17 subset (Th17 cells), which produces IL-17A, IL-17F, IL-21, and IL-22, has been implicated in SLE. As CCR6 enriches for Th17 cells, we used this approach to investigate whether CCR6⁺ memory T-helper cells producing IL-17A, IL-17F, IL-21, and/or IL-22 are increased in SLE patients and whether this increase is related to the presence of IFN type I signature.

Methods

In total, 25 SLE patients and 15 healthy controls (HCs) were included. SLE patients were divided into IFN type I signature-positive (IFN⁺) (n = 16) and negative (IFN^-) (n = 9) patients, as assessed by mRNA expression of IFN-inducible genes (IFIGs) in monocytes. Expression of IL-17A, IL-17F, IL-21, and IL-22 by CD4⁺CD45RO⁺CCR6⁺ T cells (CCR6⁺ cells) was measured with flow cytometry and compared between IFN⁺, IFN^- patients and HCs.

Results

Increased percentages of IL-17A and IL-17A/IL-17F double-producing CCR6⁺ cells were observed in IFN⁺ patients compared with IFN^- patients and HCs. IL-17A and IL-17F expression within CCR6⁺ cells correlated significantly with IFIG expression. In addition, we found significant correlation between B-cell activating factor of the tumor necrosis family (BAFF)–a factor strongly correlating with IFN type I - and IL-21 producing CCR6⁺ cells.

Conclusions

We show for the first time higher percentages of IL-17A and IL-17A/IL-17F double-producing CCR6⁺ memory T-helper cells in IFN⁺ SLE patients, supporting the hypothesis that IFN type I co-acts with Th17 cytokines in SLE pathogenesis.     

Ribosomal RNA sequence phylogeny is not congruent with ascospore morphology among species in Ceratocystis sensu stricto

The genus Ceratocystis sensu stricto includes important fungal pathogens of woody and herbaceous plants. This genus is distinguished from species in Ceratocystis sensu lato by the presence of Chalara anamorphs. Ascospore shape has been used extensively in delineating Ceratocystis taxa, which show a large variety of ascospore shapes. Sequence analysis of one region of he 18S ribosomal RNA subunit and two regions of the 28S ribosomal RNA subunit showed that there was a majority of multiple substitutions at nucleotide sites and that there was a low transition/transversion ratio, T = 0.72. Both of these results suggest that these are well established, old species. Ascospore morphology, for the most part, was not congruent with the molecular phylogeny, and the use of morphological characters may be misleading in the taxonomy of these species.      

The significance of biparental care in the brown bullhead,Ictalurus nebulosus

Synopsis Parental care in the brown bullhead is characterized by variation in the participation of each sex. Most broods are attended by both sexes, but some are attended by a male alone, or rarely, a female alone. Two care-givers were more successful than one alone in fostering offspring survival. However, there was no significant difference between two care-givers and one alone in the proportion of time that broods were unattended. Potential brood predators were chased less frequently by one adult alone than by adults aided by their mate. This difference may be unimportant since two adults simultaneously attended their brood only 19% of the time. Males alone attended their broods a significantly greater proportion of time than did either males or females aided by their mates. This difference suggests that males alone sustain a greater cost of care-giving (starvation and therefore reduced future reproduction) than do males aided by their mates. Thus, males alone may more often leave broods (and not return) than males that are aided in care-giving. The differential success observed may be due to a difference in the likelihood that the male (the principal care-giver) leaves the brood permanently, rather than differences in the quality of care one or two adults provide. I suggest that two care-givers are more successful than one because the net benefits of care-giving exceed the net benefits of leaving for males when aided by their mates.