Haplotype inference in crossbred populations without pedigree information

Background

Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations. In animal breeding this is called crossbreeding and hybridization in plant breeding. In these situations, association between marker and putative gene alleles might differ between the founding populations and origin of alleles should be accounted for in studies which estimate breeding values with marker data. The sequence of alleles from one parent constitutes one haplotype of an individual. Haplotypes thus reveal allele origin in data of crossbred individuals.

Results

We introduce a new method for haplotype inference without pedigree that allows nonrandom mating and that can use genotype data of the parental populations and of a crossbred population. The aim of the method is to estimate line origin of alleles. The method has a Bayesian set up with a Dirichlet Process as prior for the haplotypes in the two parental populations. The basic idea is that only a subset of the complete set of possible haplotypes is present in the population.

Conclusion

Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating.     

Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses

Cassava is infected by numerous geminiviruses in Africa and India that cause devastating losses to poor farmers. We here describe the molecular diversity of seven representative cassava mosaic geminiviruses (CMGs) infecting cassava from multiple locations in Tanzania. We report for the first time the presence of two isolates in East Africa: (EACMCV-[TZ1] and EACMCV-[TZ7]) of the species East African cassava mosaic Cameroon virus, originally described in West Africa. The complete nucleotide sequence of EACMCV-[TZ1] DNA-A and DNA-B components shared a high overall sequence identity to EACMCV-[CM] components (92% and 84%). The EACMCV-[TZ1] and -[TZ7] genomic components have recombinations in the same genome regions reported in EACMCV-[CM], but they also have additional recombinations in both components. Evidence from sequence analysis suggests that the two strains have the same ancient origin and are not recent introductions. EACMCV-[TZ1] occurred widely in the southern part of the country. Four other CMG isolates were identified: two were close to the EACMV-Kenya strain (named EACMV-[KE/TZT] and EACMV-[KE/TZM] with 96% sequence identity); one isolate, TZ10, had 98% homology to EACMV-UG2Svr and was named EACMV-UG2 [TZ10]; and finally one isolate was 95% identical to EACMV-[TZ] and named EACMV-[TZ/YV]. One isolate of African cassava mosaic virus with 97% sequence identity with other isolates of ACMV was named ACMV-[TZ]. It represents the first ACMV isolate from Tanzania to be sequenced. The molecular variability of CMGs was also evaluated using partial B component nucleotide sequences of 13 EACMV isolates from Tanzania. Using the sequences of all CMGs currently available, we have shown the presence of a number of putative recombination fragments that are more prominent in all components of EACMV than in ACMV. This new knowledge about the molecular CMG diversity in East Africa, and in Tanzania in particular, has led us to hypothesize about the probable importance of this part of Africa as a source of diversity and evolutionary change both during the early stages of the relationship between CMGs and cassava and in more recent times. The existence of multiple CMG isolates with high DNA genome diversity in Tanzania and the molecular forces behind this diversity pose a threat to cassava production throughout the African continent.     

GGtools: analysis of genetics of gene expression in bioconductor

This paper reviews the central concepts and implementation of data structures and methods for studying genetics of gene expression with the GGtools package of Bioconductor. Illustration with a HapMap+expression dataset is provided. Availability: Package GGtools is part of Bioconductor 1.9 (http://bioconductor.org). Open source with Artistic License.     

Mir-190b negatively contributes to the Trypanosoma cruzi- infected cell survival by repressing PTEN protein expression

Chagas disease, which is caused by the intracellular protozoanTrypanosoma cruzi, is a serious health problem in Latin America. The heart is one of the major organs affected by this parasitic infection. The pathogenesis of tissue remodelling, particularly regarding cardiomyocyte behaviour after parasite infection, and the molecular mechanisms that occur immediately following parasite entry into host cells are not yet completely understood. Previous studies have reported that the establishment of parasitism is connected to the activation of the phosphatidylinositol-3 kinase (PI3K), which controls important steps in cellular metabolism by regulating the production of the second messenger phosphatidylinositol-3,4,5-trisphosphate. Particularly, the tumour suppressor PTEN is a negative regulator of PI3K signalling. However, mechanistic details of the modulatory activity of PTEN on Chagas disease have not been elucidated. To address this question, H9c2 cells were infected with T. cruzi Berenice 62 strain and the expression of a specific set of microRNAs (miRNAs) were investigated. Our cellular model demonstrated that miRNA-190b is correlated to the decrease of cellular viability rates by negatively modulating PTEN protein expression in T. cruzi-infected cells.     

A perfusion-independent role of blood vessels in determining branching stereotypy of lung airways

Blood vessels have been shown to play perfusion-independent roles in organogenesis. Here, we examined whether blood vessels determine branching stereotypy of the mouse lung airways in which coordinated branching of epithelial and vascular tubes culminates in their co-alignment. Using different ablative strategies to eliminate the lung vasculature, both in vivo and in lung explants, we show that proximity to the vasculature is indeed essential for patterning airway branching. Remarkably, although epithelial branching per se proceeded at a nearly normal rate, branching stereotypy was dramatically perturbed following vascular ablation. Specifically, branching events requiring a rotation to change the branching plane were selectively affected. This was evidenced by either the complete absence or the shallow angle of their projections, with both events contributing to an overall flat lung morphology. Vascular ablation also led to a high frequency of ectopic branching. Regain of vascularization fully rescued arrested airway branching and restored normal lung size and its three-dimensional architecture. This role of the vasculature is independent of perfusion, flow or blood-borne substances. Inhibition of normal branching resulting from vascular loss could be explained in part by perturbing the unique spatial expression pattern of the key branching mediator FGF10 and by misregulated expression of the branching regulators Shh and sprouty2. Together, these findings uncovered a novel role of the vasculature in organogenesis, namely, determining stereotypy of epithelial branching morphogenesis.     

Studies on the mechanism of specificity of human natural killer cells for tumor cells: correlation between target cell transferrin receptor expression and competitive activity

Previous studies to determine the nature of the specificity of natural killer (NK) cells for leukemic cells indicated that functional transferrin (Tf) receptors may be one of the determinants recognized by NK cells. To further investigate these observations, the relationship between cellular Tf receptor expression and ability to compete with a control K562 cell preparation in a standard chromium release assay was studied. K562 cells were selected at different phases of growth by removing cells from tissue culture at 1, 3, and 5 days postfeeding. Under these conditions, K562 cells, respectively, displayed relatively high, medium, and low numbers of Tf receptors and corresponding competitive activity against a control K562 cell preparation. K562 cells were modified by either trypsin, heat, or sodium butyrate (differentiation inducer) pretreatment. An NK-resistant clone was also studied. There was a good correlation between Tf receptor expression and cold competitive activity of the above K562 cell preparations (r = 0.82, P less than 0.01). The different tumor target cell lines, K562, Molt-4, Raji, HL-60, and MeWo, which would be expected to express different ranges of specificity, did not show a significant correlation between Tf receptor expression and their cold competitive activities against Cr-51-labeled K562 cells. Rabbit reticulocytes which express high numbers of Tf receptors were tested for their ability to compete with K562 cells for NK cells. These cells were able to compete with K562 cells while mature rabbit red blood cells which do not express Tf receptors did not compete well. These findings support the contention that the Tf receptor may be involved in NK cell recognition of some tumor cells.     

THE POLLINATION DYNAMICS OF SYMPATRIC SPECIES OF PEDICULARIS (SCROPHULARIACEAE)

Sympatric populations of Pedicularis oederi, P. cystopteridifolia, and P. groenlandica on the Beartooth Plateau (Montana) were obligately dependent on Bombus pollinators. Their corolla colors were mutually distinct to insect vision, but their nectars had identical sugar components. Analysis of corbicular pollen loads of pollinating insects indicated a high degree of polylecty. Queen/worker ratios of pollinators on plant species corresponded to the parallel phenological sequences of plant blooming and insect caste development. The total number of individual pollinators of each Bombus species on all plants was directly related to the number of plant species it pollinated, but a comparable relationship between the number of pollinators on a plant species to the number of Bombus species pollinating it was not found. Morphological and behavioral correspondence of floral mechanisms and pollinators form an integral part of the general pattern of coadaptive evolution of the floral ecology of Pedicularis in North America known from previous studies. Reproductive isolation between Pedicularis species in this study is attributed to internal barriers. Wide overlaps of blooming seasons, proboscis lengths of bumblebee species and castes, and pollinator species on Pedicularis species suggest resource sharing, rather than resource partitioning or competition for resources among plant and insect species and individuals.     

Studies on the structure-activity relationship of 2',6'-dimethyl-l-tyrosine (Dmt) derivatives: bioactivity profile of H-Dmt-NH-CH(3)

The 2',6'-dimethyl-l-tyrosine (Dmt) enhances receptor affinity, functional bioactivity and in vivo analgesia of opioid peptides. To further investigate its direct influence on these opioid parameters, we developed a series of compounds (H-Dmt-NH-X). Among them, H-Dmt-NH-CH(3) showed the highest affinity (K(i)mu=7.45 nM) equal to that of morphine, partial mu-opioid agonism (E(max)=66.6%) in vitro and a moderate antinociception in mice.     

Role of 2′,6′-dimethyl-l-tyrosine (Dmt) in some opioid lead compounds

Here we evaluated how the interchange of the amino acids 2′,6′-dimethyl-l-tyrosine (Dmt), 2′,6′-difluoro-l-tyrosine (Dft), and tyrosine in position 1 can affect the pharmacological characterization of some reference opioid peptides and pseudopeptides. Generally, Dft and Tyr provide analogues with a similar pharmacological profile, despite different pK_a values. Dmt/Tyr(Dft) replacement gives activity changes depending on the reference opioid in which the modification was made. Whereas, H-Dmt-Tic-Asp1-Bid is a potent and selective δ agonist (MVD, IC₅₀ = 0.12 nM); H-Dft-Tic-Asp1-Bid and H-Tyr-Tic-Asp1-Bid are potent and selective δ antagonists (pA₂ = 8.95 and 8.85, respectively). When these amino acids are employed in the synthesis of deltorphin B and its Dmt¹ and Dft¹ analogues, the three compounds maintain a very similar δ agonism (MVD, IC₅₀ 0.32–0.53 nM) with a decrease in selectivity relative to the Dmt¹ analogue. In the less selective H-Dmt-Tic-Gly1-Bid the replacement of Dmt with Dft and Tyr retains the δ agonism but with a decrease in potency. Antagonists containing the Dmt-Tic pharmacophore do not support the exchange of Dmt with Dft or Tyr.     

Comparison of radiolarian and sedimentologic paleoproductivity proxies in the latest Miocene–Recent Benguela Upwelling System

Estimating past ocean productivity from ocean sediments often gives different results depending on the measurement used. We have examined a suite of paleoproductivity proxies in latest Miocene–Recent sediments from DSDP Site 532 and ODP Site 1084, two deep-sea sections underlying the Benguela Upwelling System off the Atlantic coast of southern Africa. The productivity history of this system has been previously established via organic carbon concentration, diatom floras and alkenone based estimates of surface water temperature, and shows a change from low productivity in the early Pliocene to sustain high productivity in the late Pliocene–Recent. Each of our samples was split and simultaneously analysed for several proxies of ocean productivity, including organic carbon (TOC%), carbonate, abundance of opaline radiolarians, accumulation rate of benthic foraminifera (BFAR); the radiolarian faunal composition indices Upwelling Radiolarian Index (URI) and the Water Depth Ecology index (WADE); other proxies for opal and carbonate dissolution, plus stable isotopes of benthic foraminifera. Comparisons between proxies in the same measured samples, between sites in downcore plots and to the published productivity record for this region suggest that TOC and radiolarian faunal composition, particularly the WADE index, are good indicators of past productivity, albeit with different sensitivities (log–linear correlation WADE–TOC% r = 0.78, n = 65, p < 0.01). In contrast, carbonate, and carbonate-based proxies such as BFAR primarily reflect changes in dissolution. Radiolarian faunal composition indices do not appear to be affected by bulk opal accumulation or changes in opal preservation. WADE analysis of radiolarian faunas and TOC% measurements appear to be useful proxies for productivity in late Neogene sediments, particularly for sections where opal or carbonate dissolution is significant.