Differentiation of naive CD4<Superscript>+</Superscript> T cells towards T helper 2 cells is not impaired in rheumatoid arthritis patients

An impaired differentiation of naive CD4+ T cells towards Th2 cells may contribute to the chronic tissue-destructive T-cell activity in rheumatoid arthritis (RA). The differentiation of naive CD4+ T cells into memory Th2 cells by IL-7 in comparison with that by IL-4 was studied in RA patients and in healthy controls. Naive CD4+ T cells from peripheral blood were differentiated by CD3/CD28 costimulation in the absence of or in the presence of IL-7 and/or IL-4. The production of IFN-gamma and IL-4 was measured by ELISA and by single-cell FACS analysis to indicate Th1 and Th2 cell activity. CD3/CD28 costimulation and IL-7 were early inducers of IL-4 production, but primarily stimulated IFN-gamma production. In contrast, in short-term cultures exogenously added IL-4 did not prime for IL-4 production but suppressed IL-7-induced IFN-gamma production. Upon long-term stimulation of naive CD4+ T cells, IFN-gamma production was differentially regulated by IL-7 and IL-4, but IL-4 production was increased by both IL-7 and IL-4. IL-7 and IL-4 additively induced polarization towards a Th2 phenotype. This susceptibility of naive CD4+ T cells to become Th2 cells upon culture with IL-7 and IL-4 was increased in RA patients compared with that in healthy controls. These findings demonstrate that, in RA patients, differentiation of naive CD4+ T cells towards a Th2 phenotype by CD3/CD28 costimulation, IL-7 and IL-4 is not impaired. The perpetuation of arthritogenic T-cell activity in RA therefore seems not to be the result of intrinsic defects of naive CD4+ T cells to develop towards suppressive memory Th2 cells.     

Modified antibiotics-methylated ampicillin and ethylated ampicillin-inhibit growth of ampicillin-resistant strain of bacteria

Bacterial resistance to antibiotics is a significant problem in health facilities and results in higher costs for health care and increased fatalities due to infection. The work presented here suggests that antibiotic molecular structure can be altered in a selected manner, which will revive the bacterial growth inhibiting capability. A bacterial strain PKK3535(DH1), which is resistant to the antibiotic ampicillin, was found to be highly growth inhibited by these altered forms of ampicillin when tested in tissue culture. The level of growth inhibition of bacterial strain PKK3535(DHI) was greater than 50%, for both molecular variants of ampicillin that were investigated. The bacteria strain used for testing was a clinical isolate obtained from the University Hospital of the University of Nebraska, Omaha. These two antibiotic variants were methylated ampicillin and ethylated ampicillin. The synthetic procedure for generating these variants is presented as well as the molecular structure. The methylated and ethylated ampicillin were found to be stable at 0 degrees C for many weeks, were somewhat less soluble than normal ampicillin, but dissolved in LB plate media. The resistant bacteria strain was plated onto LB media with altered ampicillin and profound inhibition of bacteria growth was seen within the first 24 hours of incubation. These molecular variants of ampicillin provide evidence of a means to combat the proliferation of resistant bacterial strains. The molecular alteration of antibiotics may provide a suitable means to study and combat the appearance of antibiotic-resistant bacteria.     

DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea,Philippines

Diet studies provide base understanding of trophic structure and are a valuable initial step for many fields of marine ecology, including conservation and fisheries biology. Considerable complexity in marine trophic structure can exist due to the presence of highly mobile species with long life spans. Mobula rays are highly mobile, large, planktivorous elasmobranchs that are frequently caught either directly or as bycatch in fisheries, which, combined with their conservative life history strategy, makes their populations susceptible to decline in intensely fished regions. Effective management of these iconic and vulnerable species requires an understanding of the diets that sustain them, which can be difficult to determine using conventional sampling methods. We use three DNA metabarcode assays to identify 44 distinct taxa from the stomachs (n = 101) of four sympatric Mobula ray species (Mobula birostris, Mobula tarapacana, Mobula japanica, and Mobula thurstoni) caught over 3 years (2013–2015) in a direct fishery off Bohol in the Philippines. The diversity and incidence of bony fishes observed in ray diets were unprecedented. Nevertheless, rays showed dietary overlap, with krill (Euphausia) dominating their diet. Our results provide a more detailed assessment of sympatric ray diets than was previously described and reveal the complexity that can exist in food webs at critical foraging habitats.     

Estimation of Physical Distance in the Genome through Probabilistic Analysis of Marker Density and Yeast Artificial Chromosome (YAC) Size

Knowledge of the physical distance separating polymorphic markers which flank a region of interest can be usefully exploited in positional cloning methodology. We present a mathematical model for estimating this distance based on simple conditions generally met in practice. We illustrate estimation and construction of confidence intervals based on the model with data from a recent positional cloning experiment.     

Antagonistic experimental coevolution with a parasite increases host recombination frequency

Background  

One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei.     

A Note on Plots of P-Values to Evaluate Many Tests Simultaneously

Schweder and Spjøtvoll (1982) proposed an informal graphical procedure for simultaneous evaluation of possibly related tests, based on a plot of cumulative p-values using the observed significance probabilities. We formalize this notion by application of Holm's (1979) sequentially rejective Bonferroni procedure: this maintains an overall experimentwise significance level, and yields an immediate estimate of the number of true hypotheses.     

A note on efficient estimation of mutation rates using Luria-Delbrück fluctuation analysis

The maximum likelihood and Luria-Delbrück P0 methods for the estimation of spontaneous mutation rates are compared. The maximum likelihood method is fully efficient, utilizing all available information in a fluctuation experiment, but can be numerically cumbersome. Under certain conditions, there is little loss of efficiency using the P0 method, which is readily implemented numerically. Design considerations should aid investigators in minimizing statistical errors associated with the statistical analysis of fluctuation experiments.     

Gene technology in agriculture,environment and biopharming: beyond Bt-rice and building better breeding budgets for crops

Applications of gene technology in agriculture, the environment and human health fields are reviewed. This case study of the intricate historical details of the development of Bt crops like cotton and rice unveils essential elements of productive funding schemes and effective multinational collaborations. Gene technology applied to pest resistance traits in global cotton is analyzed using nation-specific data from India to demonstrate ‘ricochet’ results: Regulatory approval for one crop catalyzes an ‘Enhancer Effect’ for promoting more research funding and more competitive results for other crops-in-waiting, namely rice. Just as cotton commerce promoted philanthropy in unpredictable situations like the Kreenholm dynasty of Ludwig Knoop, research budgets for pesticide and biocide technology have yielded intended effects, but several surprising unintended effects as well. Finally, the case is made for greater control of gene flow and identity preserve issues in plant biotechnology research by invoking Appellation d’Origine Contrôlée for Bt genes.     

Plant as a plenteous reserve of lectin

Lectins are clusters of glycoproteins of nonimmune foundation that combine specifically and reversibly to carbohydrates, mainly the sugar moiety of glycoconjugates, resulting in cell agglutination and precipitation of glycoconjugates. They are universally distributed in nature, being established in plants, fungi, viruses, bacteria, crustacea, insects, and animals, but leguminacae plants are rich source of lectins. The present review reveals the structure, biological properties, and application of plant lectins.     

Transcriptome analyses suggest a disturbance of iron homeostasis in soybean leaves during white mould disease establishment

Sclerotinia sclerotiorum is a serious pathogen of numerous crops around the world. The major virulence factor of this pathogen is oxalic acid (OA). Mutants that cannot produce OA do not cause disease, and plants that express enzymes that degrade OA, such as oxalate oxidase (OxO), are very resistant to S. sclerotiorum. To examine the effect of OA on plants, we infiltrated soybean leaves with 5 mm OA and examined the gene expression changes at 2 h post‐infiltration. By comparing the gene expression levels between leaves of a transgenic soybean carrying an OxO gene (OxO) and its parent AC Colibri (AC) infiltrated with OA (pH 2.4) or water (pH 2.4 or 5.5), we were able to compare the effects of OA dependent or independent of its pH. Gene expression by microarray analysis identified 2390 genes that showed changes in expression, as determined using an overall F‐test P‐value cut‐off of 0.001. The additional requirement that at least one pairwise t‐test false discovery rate (FDR)‐corrected P value should be less than 0.001 reduced the list of the most highly significant differentially expressed genes to 1054. Independent of pH, OA altered the expression levels of 78 genes, with ferritin showing the strongest induction by OA. The combination of OA plus its low pH caused 1045 genes (99% of all significant genes) to be differentially expressed, with many of the up‐regulated genes being related to basal defence, such as genes of the phenylpropanoid pathway and various cytochrome P450s. RNA‐seq was also conducted on four samples: OxO and AC genotypes infiltrated with either OA pH 2.4 or water pH 2.4. The RNA‐seq analysis also identified ferritin paralogues as being strongly induced by OA. As the expression of ferritin, a gene that encodes for an iron storage protein, is induced by free iron, these results suggest that S. sclerotiorum benefits from the ability of OA to free iron from plant proteins, as this induces host cell death, and also allows the uptake and assimilation of the iron for its own metabolic needs.