Conditional QTL mapping of protein content in wheat with respect to grain yield and its components

Grain protein content in wheat (Triticum aestivum L.) is generally considered a highly heritable character that is negatively correlated with grain yield and yield-related traits. Quantitative trait loci (QTL) for protein content was mapped using data on protein content and protein content conditioned on the putatively interrelated traits to evaluate possible genetic interrelationships between protein content and yield, as well as yield-related traits. Phenotypic data were evaluated in a recombinant inbred line population with 302 lines derived from a cross between the Chinese cultivar Weimai 8 and Luohan 2. Inclusive composite interval mapping using IciMapping 3.0 was employed for mapping unconditional and conditional QTL with additives. A strong genetic relationship was found between protein content and grain yield, and yield-related traits. Unconditional QTL mapping analysis detected seven additive QTL for protein content, with additive effects ranging in absolute size from 0.1898% to 0.3407% protein content, jointly accounting for 43.45% of the trait variance. Conditional QTL mapping analysis indicated two QTL independent from yield, which can be used in marker-assisted selection for increasing yield without affecting grain protein content. Three additional QTL with minor effects were identified in the conditional mapping. Of the three QTLs, two were identified when protein content was conditioned on yield, which had pleiotropic effects on those two traits. Conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the individual QTL level for closely correlated traits. Further, conditional QTL mapping can reveal additional QTL with minor effects that are undetectable in unconditional mapping.     

Impacts of hunting on mammals in African tropical moist forests: a review and synthesis

• 1 Available information on the consumption of wild meat in West and Central Africa is reviewed. We show that mammals are the prime source of bushmeat, and that ungulates and rodents make up the highest proportion of biomass extracted.
• 2 We present data on current knowledge of extraction patterns of wild mammals in West and Central Africa, and evidence that at current off‐take levels, within the range states, mammals as bushmeat are being depleted on an unprecedented scale. Extraction rates are orders of magnitude higher there than in comparable ecosystems like the Amazon, and much less likely to be sustainable.
• 3 However, basic knowledge of the biology of harvestable tropical moist forest mammals, and the consequences of hunting on mammalian communities, which permits accurate estimation of maximal production rate (the excess of growth over replacement rate), is largely unavailable, and this hinders estimation of hunting quotas and sustainability. Comparisons are made with the existing information available on Amazon basin mammals and hunting patterns reported there.

     

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Background  

Gene selection is an important step when building predictors of disease state based on gene expression data. Gene selection generally improves performance and identifies a relevant subset of genes. Many univariate and multivariate gene selection approaches have been proposed. Frequently the claim is made that genes are co-regulated (due to pathway dependencies) and that multivariate approaches are therefore per definition more desirable than univariate selection approaches. Based on the published performances of all these approaches a fair comparison of the available results can not be made. This mainly stems from two factors. First, the results are often biased, since the validation set is in one way or another involved in training the predictor, resulting in optimistically biased performance estimates. Second, the published results are often based on a small number of relatively simple datasets. Consequently no generally applicable conclusions can be drawn.     

Osmotic stress,glucose transport capacity and consequences for glutamate overproduction in Corynebacterium glutamicum

Glucose uptake by Corynebacterium glutamicum is predominantly assured by a mannose phosphotransferase system (PTS) with a high affinity for glucose (Km=0.35 mM). Mutants selected for their resistance to 2-deoxyglucose (2DG) and lacking detectable PEP-dependent glucose-transporting activity, retained the capacity to grow on media in which glucose was the only carbon and energy source, albeit at significantly diminished rates, due to the presence of a low affinity (Ks=11 mM) non-PTS uptake system. During growth in media of different osmolarity, specific rates of glucose consumption and of growth of wild type cells were diminished. Cell samples from these cultures were shown to possess similar PTS activities when measured under standard conditions. However, when cells were resuspended in buffer solutions of different osmolarity measurable PTS activity was shown to be dependent upon osmolarity. This inhibition effect was sufficient to account for the decreased rates of both sugar uptake and growth observed in fermentation media of high osmolarity. The secondary glucose transporter was, however, not influenced by medium osmolarity. During industrial fermentation conditions with accumulation of glutamic acid and the corresponding increase in medium osmolarity, similar inhibition of the sugar transport capacity was observed. This phenomenon provokes a major process constraint since the decrease in specific rates leads to an increasing proportion of sugar catabolised for maintenance requirements with an associated decrease in product yields.     

Early exposure to genistein exerts long-lasting effects on the endocrine and immune systems in rats

BACKGROUND: Although the immunologic effects of endogenous and synthetic estrogens are well studied, few studies have examined the hormonal effects of phytoestrogens (i.e., plant-derived estrogens) on the immune system. The primary goal of this study was to compare the effects of perinatal exposure with life-long exposure to genistein, an estrogenic compound in soy, on the endocrine and immune system in adulthood. MATERIALS AND METHODS: Pregnant female rats were exposed to no, low (5 mg/kg diet), or high (300 mg/kg diet) genistein diets throughout gestation and lactation. At weaning, male offspring exposed to genistein perinatally were either switched to the genistein-free diet or remained on the genistein-dosed diets. At 70 days of age, immune organ masses, lymphocyte subpopulations, cytokine concentrations, and testosterone concentrations were assessed in male offspring. RESULTS: Data were analyzed based on the diets that males were exposed to during gestation and lactation because life-long exposure to genistein had no additional effect on any of the dependent measures. Relative thymus masses were greater among males exposed to the high genistein diet than among males exposed to no genistein. Although the proportions of splenic and thymic CD4+ T cells were not altered by genistein, the percentages of CD4+CD8+ thymocytes, CD8+ splenocytes, and total T cells in the spleen were higher and the percentages of CD4-CD8- thymocytes were lower among males exposed to genistein than among males not exposed to genistein. Synthesis of interferon-gamma (IFN-gamma) was marginally higher and testosterone concentrations were lower among genistein-exposed than genistein-free males. DISCUSSION: These data illustrate that exposure to genistein during pregnancy and lactation exerts long-lasting effects on the endocrine and immune systems in adulthood. Whether exposure to phytoestrogens during early development affects responses to infectious or autoimmune diseases, as well as cancers, later in life requires investigation.     

Light meromyosin paracrystal formation

Studies of paracrystal formation by column purified light meromyosin (LMM) prepared in a variety of ways led to the following conclusions: (a) different portions of the myosin rod may be coded for different stagger relationships. This was concluded from observations that paracrystals with different axial repeat periodicities could be obtained either with LMM framents of different lengths prepared with the same enzyme, or with LMM fragments of identical lengths but prepared with different enzymes. (b) Paracrystals with a 14-nm axial repeat periodicity are most likely formed by the aggregation of sheets with a 44-nm axial repeat within the sheets which are staggered by 14 nm. All of the axial repeat patterns expected from one sheet or aggregates of more than one sheet, on this basis, were observed in the same electron micrograph. (c) C-protein binding probably occurs preferentially to LMM molecules related in some specific way. This was concluded from the observation that the same axial repeat pattern was obtained in paracrystals formed from different LMM preparations in the presence of C-protein, regardless of differences in the axial repeat obtained in the absence of C-protein. (d) Nucleic acid is responsible for the 43-nm axial repeat patterns observed in paracrystals formed by the ethanol-resistant fraction of LMM. In the absence of nuclei acid, paracrystals with a 14nm axial repeat are obtained. (e) The 43-nm axial repeat pattern observed with the ethanol-resistant fraction of LMM is different for LMM preparations obtained by trypsin and papain digestions.     

Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression

Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the antitumor immune response. T cell surface receptors and surface proteins that influence interactions and function in the TME are proven targets for cancer immunotherapy. However, how the entire surface proteome remodels in primary human T cells in response to specific suppressive factors in the TME remains to be broadly and systematically characterized. Here, using a reductionist cell culture approach with primary human T cells and stable isotopic labeling with amino acids in cell culture–based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8⁺ surface proteome (surfaceome). Surprisingly, coculturing primary CD8⁺ T cells with Tregs only modestly affected the CD8⁺ surfaceome but did partially reverse activation-induced surfaceomic changes. In contrast, hypoxia drastically altered the CD8⁺ surfaceome in a manner consistent with both metabolic reprogramming and induction of an immunosuppressed state. The CD4⁺ T cell surfaceome similarly responded to hypoxia, revealing a common hypoxia-induced surface receptor program. Our surfaceomics findings suggest that hypoxic environments create a challenge for T cell activation. These studies provide global insight into how Tregs and hypoxia remodel the T cell surfaceome and we believe represent a valuable resource to inform future therapeutic efforts to enhance T cell function.