Bayesian tests for random mating in polyploids

Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Network https://cran.r-project.org/package=hwep .     

First evidence of human meconium glycoasparagines

During a systematic study of carbohydrate material present inhuman meconium, in addition to the previously described mucins,glycolipids and free oligosaccharides, we have now characterizeda significant quantity of free glycoasparagines. These glycoasparagineshave been isolated from human meconium by a combination of ion-exchange,concanavalin A (ConA)-affinity and high-performance liquid (HPLC)chromatographies. Their structures have been established by400 MHz ¹H-NMR spectroscopy. These compounds are related toN-acetyllactosaminic type structures and are based on the commoncore These glycoasparagines are probably derived from both proteaseand partial exoglycosidase hydrolysis of fetal gastrointestinalN-glycosyl proteins. Their structures are discussed in the contextof the known catabolic pathways of N-glycans glycoasparagine N-glycosyl protein catabolism meconium NMR     

Endocytosis of androgen-binding protein (ABP) by spermatogenic cells

To test whether Sertoli cell-secreted ABP could serve as steroid carrier to the germ cell (GC) lineage, radiolabeled ABP and SHBG and gold SHBG were used for binding studies and for internalization studies based on transmission electron microscope analyses and autoradiography of the radiolabeled samples. The data clearly showed that: (1) rat and human germ cells possess a single class of binding sites for rat ABP and human SHBG respectively (K_d of 0.78 and 0.56 nM); (2) 1.7 × 10¹⁰ and 2.7 × 10¹⁰ sites/mg protein was found in the corresponding plasma membrane preparations; (3) the receptor peak was eluted in the same position as dextran blue: 2000 kDa (M_r = 2 × 106) for labeled rat ABP; (4) in the whole GC lineage, the labeled ligand was internalized through an endocytic pathway involving clathrin coated structures and the distribution was similar throughout the maturation step, however striking differences in the internalization rate were revealed with regard to the maturation step; and (5) this internalization occurred even in ligated seminiferous tubules, via the Sertoli cells cytoplasm. When isolated rat GC were incubated in the presence of ABP, a dose dependent increase in labeled secreted protein was observed for spermatocytes (50–250%) whereas ABP had no effect on spermatids. Addition of steroids and ABP caused a 200 and 50% increase in labeled secreted proteins for spermatocytes and spermatids respectively. 2-D SDS-PAGE analysis revealed that ABP alone increased the secretion of specific spermatocyte proteins whereas steroids in the presence of ABP resulted in the synthesis of new spermatocyte secreted proteins. Taken together these results strongly suggest that ABP may be required for spermatogenesis either as a steroid transmembrane carrier or on its own.     

Purification, characterization and ion binding properties of human brain S100b protein

Human brain S100b (beta beta) protein was purified using zinc-dependent affinity chromatography on phenyl-Sepharose. The calcium- and zinc-binding properties of the protein were studied by flow dialysis technique and the protein conformation both in the metal-free form and in the presence of Ca2+ or Zn2+ was investigated with ultraviolet spectroscopy, sulfhydryl reactivity and interaction with a hydrophobic fluorescence probe 6-(p-toluidino)naphthalene-2-sulfonic acid (TNS). Flow dialysis measurements of Ca2+ binding to human brain S100b (beta beta) protein revealed six Ca2+-binding sites which we assumed to represent three for each beta monomer, characterized by the macroscopic association constants K1 = 0.44 X 10(5) M-1; K2 = 0.1 X 10(5) M-1 and K3 = 0.08 X 10(5) M-1. In the presence of 120 mM KCl, the affinity of the protein for calcium is drastically reduced. Zinc-binding studies on human S100b protein showed that the protein bound two zinc ions per beta monomer, with macroscopic constants K1 = 4.47 X 10(7) M-1 and K2 = 0.1 X 10(7) M-1. Most of the Zn2+-induced conformational changes occurred after the binding of two zinc ions per mole of S100b protein. These results differ significantly from those for bovine protein and cast doubt on the conservation of the S100 structure during evolution. When calcium binding was studied in the presence of zinc, we noted an increase in the affinity of the protein for calcium, K1 = 4.4 X 10(5) M-1; K2 = 0.57 X 10(5) M-1; K3 = 0.023 X 10(5) M-1. These results indicated that the Ca2+- and Zn2+-binding sites on S100b protein are different and suggest that Zn2+ may regulate Ca2+ binding by increasing the affinity of the protein for calcium.     

Resistance to chenodeoxycholic acid (CDCA) treatment in obese patients with gall stones

In most patients with radiolucent gall stones who were given chenodeoxycholic acid (CDCA) in doses of 13-15 mg/kg body weight/day the bile became unsaturated in cholesterol, and their gall stones dissolved. The patients whose stones did not dissolve were significantly heavier and fatter than the responders, which suggested that obese patients might be “resistant” to the effects of CDCA. To test this hypothesis, 32 consecutive patients presenting for medical treatment of gall stones had their ideal body weight (IBW) and estimated body fat mass calculated. The eight most obese and the eight least obese patients were then selected, and their fasting bile lipid responses to CDCA 13-15 mg/kg/day were measured. The very obese patients were also given larger doses, and any changes in bile lipid composition were studied in relation to subsequent gall-stone dissolution.Before treatment the obese patients had a higher mean biliary cholesterol saturation index than the non-obese patients, and this difference was maintained during treatment with the normal dose of CDCA: the bile in the obese patients remained supersaturated while that in the non-obese became unsaturated with cholesterol. When the obese patients were given larger doses of CDCA their bile ultimately became unsaturated in cholesterol. Gall stones dissolved partially or completely in five of the eight non-obese patients after 6-18 months of 13-15 mg CDCA/kg/day, but none of the obese patients showed any response after comparable periods of treatment with this standard dose. With increased doses and unsaturated bile, however, three of the obese patients showed partial gall-stone dissolution after 3-12 months'' treatment and one showed complete gall-stone dissolution after three years'' treatment.These results suggest that when giving CDCA to patients with gall stones, larger than normal doses (some 18-20 mg/kg/day) should be prescribed. Alternatively the lipid composition of the patients'' bile should be monitored by duodenal intubation and the CDCA dose increased until the bile becomes unsaturated in cholesterol.     

Fluorescent study of tobacco mosaic virus protein

The synthesis of two new variants of gramicidin is described. It is shown that the changes in the aromatic side groups do not influence the single channel conductivity. Experiments in which solutions having different molarities on the two sides of the bilayer lipid membrane are described and their results compared with a rate theory analysis. It is concluded that the gramicidin pore contains approximately 10 equal potential maxima.     

The diffusion of gibberellins into agar and water during early germination of Pharbitis nil Choisy

Agar diffusion of imbibed seeds yielded significant amounts of diffusible Gibberellin-like substances. An analysis of the extractable and diffusible gibberellin-like substance, including an analysis of the remaining imbibition water of the seeds, indicated that a significant part of these gibberellin-like substances could be attributed to a net biosynthesis of these substances in the imbibing seeds. At the same time it was found that water diffusion yielded considerably more gibberellin-like activities than comparable agar diffusions i.e. 10 to 12 fold in general.Agar as well as water diffusion showed a temperature effect with regard to the yield of gibberellin-like substances particularly during the first 6 h of diffusion. The yield of these substances is lower at 10°C, and remains lower as shown with consecutive diffusions, in comparison with the yields at 20°C or 30°C.With both agar and water diffusion the sum of activities obtained with consecutive diffusions is always higher, often considerably higher, than equal periods of continuous diffusion which is probably due to inactivation and/or interference of inhibitory substances with the bioassay responses. Finally, water diffusates of both seeds and seedlings of the normal growing cv. Violet of Japanese morning glory contained considerably more gibberellin-like activities than those of the dwarf cv. Kidachi which indicated that normals synthesize more gibberellins than dwarfs.     

Goiter in Tibetan Medicine

The visit of two Tibetan physicians provided a unique opportunity to gain insight into a practice of medicine very different from that of Western civilization. Initial discussions indicated that the practice of medicine and mysticism were inextricably interwoven in the Tibetan culture. Accordingly, the focus of the study was directed to goiter, which is both common in the Himalayas and easy to define.In Tibetan medical practice, illness is considered to be derived from both proximate and distant causes. Three humors, “wind,” “bile,” and “phlegm” are thought to be responsible for normal mental and physical functions when in balance, but disease when out of balance. Goiter was thought to be due to an imbalance of these humors. The Western discovery that endemic goiter in the Himalayas was due to iodine deficiency explained the proximate cause but did not explain why some individuals have goiter and others do not in the same iodine deficient village.