Statistical analysis of a linkage experiment in barley involving quantitative trait loci for height and ear-emergence time and two genetic markers on chromosome 4

Summary The quantitative traits height and ear-emergence date were analyzed in the F₂ progeny of a cross between a tall winter barley cultivar (Gerbel) and a short spring barley cultivar (Heriot). The trait distributions were found to be related to the genotypes at two biochemical loci, -amylase (Bmy1) and water-soluble protein (Wsp3), which are known to lie on the long arm of chromosome 4. Linkages between each trait and the markers were investigated using normal mixture models. The two parental phenotypes and the heterozygote phenotype of Bmy1 were distinguishable so the model could be used directly to estimate linkage between Bmy1 and a quantitative trait locus (QTL) for height (Height). The Gerbel homozygote and heterozygote phenotype of Wsp3 could not be distinguished and the model was adapted accordingly. The proportion of plants requiring vernalization was consistent with control by two independent genes acting epistatically, and a normal mixture model based on a two-gene hypothesis was fitted to the distribution of ear-emergence date to estimate linkage between the marker loci and a QTL for ear-emergence date (Vrn1). The parameters of each model were the recombination fraction between the marker locus and the QTL and the means and standard deviations associated with each QTL genotype; these were estimated by maximum likelihood. The fitted distributions correspond well to those observed and the order of the loci along the chromosome is inferred to be Height — Vrn1 — Bmy1 — Wsp3, with Wsp3 being the most distal.     

Using consecutive prescribed fires to reduce shrub encroachment in grassland by increasing shrub mortality

Woody plant encroachment into open grasslands occurs worldwide and causes multiple ecological and management impacts. Prescribed fire could be used to conserve grassland habitat but often has limited efficacy because many woody plants resprout after fire and rapidly reestablish abundance. If fire‐induced mortality could be increased, prescribed fire would be a more effective management tool. In California's central coast, shrub encroachment, especially of Baccharis pilularis (coyote brush), is converting coastal prairie into shrub‐dominated communities, with a consequent loss of native herbaceous species and open grassland habitat. B. pilularis has not been successfully controlled with single prescribed fire events because the shrub resprouts and reestablishes cover within a few years. We investigated whether two consecutive annual burns would control B. pilularis by killing resprouting shrubs, without reducing native herbaceous species or encouraging invasive plants. As expected, resprouting did occur; however, 2 years after the second burn, B. pilularis cover on burned plots was only 41% of the cover on unburned plots. Mortality of B. pilularis more than doubled following the second burn, likely maintaining a reduction in B. pilularis cover for longer than a single burn would have. Three native coastal prairie perennial grasses did not appear to be adversely affected by the two burns, nor did the burns result in increased cover of invasive species. Managers wanting to restore coastal prairie following B. pilularis encroachment should consider two consecutive annual burns, especially if moderate fire intensity is achievable.     

Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species

Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.     

Increased insulin-stimulated Akt pSer473 and cytosolic SHP2 protein abundance in human skeletal muscle following acute exercise and short-term training.

The purpose of the present study was to determine in human skeletal muscle whether a single exercise bout and 7 days of consecutive endurance (cycling) training 1) increased insulin-stimulated Akt pSer(473) and 2) altered the abundance of the protein tyrosine phosphatases (PTPases), PTP1B and SHP2. In healthy, untrained men (n = 8; 24 +/- 1 yr), glucose infusion rate during a hyperinsulinemic euglycemic clamp, when compared with untrained values, was not improved 24 h following a single 60-min bout of endurance cycling but was significantly increased ( approximately 30%; P < 0.05) 24 h following completion of 7 days of exercise training. Insulin-stimulated Akt pSer(473) was approximately 50% higher (P < 0.05) 24 h following the acute bout of exercise, with this effect remaining after 7 days of training (P < 0.05). Insulin-stimulated insulin receptor and insulin receptor substrate-1 tyrosine phosphorylation were not altered 24 h after acute exercise and short-term training. Insulin did not acutely regulate the localization of the PTPases, PTP1B or SHP2, although cytosolic protein abundance of SHP2 was increased (P < 0.05; main effect) 24 h following acute exercise and short-term training. In conclusion, insulin-sensitive Akt pSer(473) and cytosolic SHP2 protein abundance are higher after acute exercise and short-term training, and this effect appears largely due to the residual effects of the last bout of prior exercise. The significance of exercise-induced alterations in cytosolic SHP2 and insulin-stimulated Akt pSer(473) on the improvement in insulin sensitivity requires further elucidation.     

Impact of human activities on the reproduction of Hooded Vultures Necrosyrtes monachus in Burkina Faso

During the last decades, the critically endangered Hooded Vulture Necrosyrtes monachus has strongly declined across its African range. Although direct persecution has been suggested as a major cause of this decline, little is known about the impact of humans on reproductive output in West Africa. We studied the impact of human activities on the reproductive output of Hooded Vultures in the Garango area of Burkina Faso. Twenty and 56 nesting attempts were monitored, respectively, during the breeding season in 2013/14 and 2014/15, to determine reproductive success and identify causes of nest failure. Annual breeding success varied between 0.68 and 0.71 chicks fledged per breeding pair per year and productivity was assessed at 0.57 chicks fledged per territorial pair in 2014/15. The main threats imposed by humans were poaching of eggs, chicks and collection of nest materials, leading to 20% (13 out of 64 breeding attempts) of nest failures over the two years. An additional important reason for nest failure was the pruning and (partial) cutting of nest trees. Despite this high level of human interference, we found that Hooded Vulture nest success increased with proximity to human settlements, probably because breeding vultures benefit from protection by people against persecution and disturbance.     

Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations

We have analyzed and compared mitochondrial DNA variation of populations from the Near East and Africa and found a very high frequency of African lineages present in the Yemen Hadramawt: more than a third were of clear sub-Saharan origin. Other Arab populations carried approximately 10% lineages of sub-Saharan origin, whereas non-Arab Near Eastern populations, by contrast, carried few or no such lineages, suggesting that gene flow has been preferentially into Arab populations. Several lines of evidence suggest that most of this gene flow probably occurred within the past approximately 2,500 years. In contrast, there is little evidence for male-mediated gene flow from sub-Saharan Africa in Y-chromosome haplotypes in Arab populations, including the Hadramawt. Taken together, these results are consistent with substantial migration from eastern Africa into Arabia, at least in part as a result of the Arab slave trade, and mainly female assimilation into the Arabian population as a result of miscegenation and manumission.     

A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes

The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (PhiST=0.342), which appears to be partially related to the geography (PhiCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (PhiST=0.332) and geographic (PhiCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo-speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon.     

The fingerprint of phantom mutations in mitochondrial DNA data

Phantom mutations are systematic artifacts generated in the course of the sequencing process itself. In sequenced mitochondrial DNA (mtDNA), they generate a hotspot pattern quite different from that of natural mutations in the cell. To identify the telltale patterns of a particular phantom mutation process, one first filters out the well-established frequent mutations (inferred from various data sets with additional coding region information). The filtered data are represented by their full (quasi-)median network, to visualize the character conflicts, which can be expressed numerically by the cube spectrum. Permutation tests are used to evaluate the overall phylogenetic content of the filtered data. Comparison with benchmark data sets helps to sort out suspicious data and to infer features and potential causes for the phantom mutation process. This approach, performed either in the lab or at the desk of a reviewer, will help to avoid errors that otherwise would go into print and could lead to erroneous evolutionary interpretations. The filtering procedure is illustrated with two mtDNA data sets that were severely affected by phantom mutations.     

Production, recovery and immunogenicity of the protective antigen from a recombinant strain of Bacillus anthracis

The protective antigen (PA) is one of the three components of the anthrax toxin. It is a secreted nontoxic protein with a molecular weight of 83 kDa and is the major component of the currently licensed human vaccine for anthrax. Due to limitations found in the existing vaccine formulation, it has been proposed that genetically modified PA may be more effective as a vaccine. The expression and the stability of two recombinant PA (rPA) variants, PA-SNKE-ΔFF-E308D and PA-N657A, were studied. These proteins were expressed in the nonsporogenic avirulent strain BH445. Initial results indicated that PA-SNKE-ΔFF-E308D, which lacks two proteolysis-sensitive sites, is more stable than PA-N657A. Process development was conducted to establish an efficient production and purification process for PA-SNKE-ΔFF-E308D. pH, media composition, growth strategy and protease inhibitors composition were analyzed. The production process chosen was based on batch growth of B. anthracis using tryptone and yeast extract as the only source of carbon, pH control at 7.5, and antifoam 289. Optimal harvest time was 14–18 h after inoculation, and EDTA (5 mM) was added upon harvest for proteolysis control. Recovery of the rPA was performed by expanded-bed adsorption (EBA) on a hydrophobic interaction chromatography (HIC) resin, eliminating the need for centrifugation, microfiltration and diafiltration. The EBA step was followed by ion exchange and gel filtration. rPA yields before and after purification were 130 and 90 mg/l, respectively. The purified rPA, without further treatment, treated with small amounts of formalin or adsorbed on alum, induced, high levels of IgG anti-PA with neutralization activities. Journal of Industrial Microbiology & Biotechnology (2002) 28, 232–238 DOI: 10.1038/sj/jim/7000239 Received 28 August 2001/ Accepted in revised form 20 December 2001