The probability density of the total IBD length over a single autosome in unilineal relationships

Several authors have studied identity by descent (IBD) by way of a continuous recombination process along a chromosome. Despite its potential uses in, for example, gene mapping or delineation of biological relationships there has been no exact algebraic result given for the probability density function of the IBD proportion in any familial relationship. Other authors have derived algebraic approximations in the case of half-sibs by way of the Poisson clumping heuristic and used computational methods to compute the distribution function of the IBD sharing for unilineal relationships. Here we provide a general numerical method for finding the density of IBD sharing that could be applied to any unilineal relationship and more importantly we derive algebraically an expression for the density for a grandparent-grandchild relationship. Initially we assume that recombination events occur at random along a chromosome, then go on to show how the method could be extended to incorporate a form of genetic interference.     

免疫活性细胞中的非神经元型胆碱能系统

本文对淋巴细胞、巨噬细胞、粒细胞、肥大细胞及胶质细胞等免疫活性细胞中非神经元型胆碱能系统的特点、药理学和病理生理学意义进行了综述。免疫活性细胞,尤其是淋巴细胞中存在完整、独立的胆碱能系统。与神经元型胆碱能系统相比,该系统具有不同特点,如乙酰胆碱(ACh)的合成存在于整个细胞内;ACh可能储存于细胞中某种储存结构,也可能不需储存,而是按需合成并直接释放。免疫活性细胞中的非神经元型胆碱能系统对机体免疫功能及炎症过程可能发挥重要的调控作用。对该系统的深入研究将有助于进一步阐明免疫性疾病、炎症/感染性疾病和神经退行性疾病等的病理生理和发现药物治疗的新靶标。     

Signaling function of PSGL-1 in neutrophil: tyrosine-phosphorylation-dependent and c-Abl-involved alteration in the F-actin-based cytoskeleton

P-selectin glycoprotein ligand-1 (PSGL-1) is the best-characterized selectin ligand that has been demonstrated to mediate leukocytes rolling on endothelium and leukocytes recruitment into inflamed tissue in vivo. In addition to its direct role in leukocyte capturing, PSGL-1 also functions as a signal-transducing receptor. The present work showed that after cross-linking of PSGL-1 with KPL1, an anti-PSGL-1 monoclonal antibody, PSGL-1 linked to the cytoskeleton and became a detergent-insoluble component in activated neutrophils. The antibody cross-linking led to the polymerization and redistribution of F-actin-based cytoskeleton, and this alteration of cytoskeleton was spatiotemporally related to the polarization of PSGL-1. PSGL-1's polarization was cytoskeleton-dependent because it was eliminated by cytochalasin B. Furthermore, the polymerization and redistribution of F-actin filaments were tyrosine-phosphorylation-dependent since the alteration of F-actin-based cytoskeleton was severely blocked by genistein, a universal tyrosine kinase inhibitor. STI571, a small molecule inhibitor for cytoplasmic tyrosine kinase c-Abl, also inhibited the alteration of F-actin-based cytoskeleton, and c-Abl was redistributed to where F-actin concentrated in the activated neutrophils. The results suggested that cross-linking of PSGL-1 induces the phosphorylation-dependent and c-Abl-involved alteration of F-actin-based cytoskeleton in neutrophils.     

Modeling the simple epidemic with deterministic differential equations and random initial conditions

In a simple epidemic the only transition in the population is from susceptible to infected and the total population size is fixed for all time. This paper investigates the effect of random initial conditions on the deterministic model for the simple epidemic. By assuming a Beta distribution on the initial proportion of susceptibles, we define a distribution that describes the proportion of susceptibles in a population at any time during an epidemic. The mean and variance for this distribution are derived as hypergeometric functions, and the behavior of these functions is investigated. Lastly, we define a distribution to describe the time until a given proportion of the population remains susceptible. A method for finding the quantiles of this distribution is developed and used to make confidence statements regarding the time until a given proportion of the population is susceptible.     

Prediction of functional class of novel plant proteins by a statistical learning method

In plant genomes, the function of a substantial percentage of the putative protein-coding open reading frames (ORFs) is unknown. These ORFs have no significant sequence similarity to known proteins, which complicates the task of functional study of these proteins. Efforts are being made to explore methods that are complementary to, or may be used in combination with, sequence alignment and clustering methods. A web-based protein functional class prediction software, SVMProt, has shown some capability for predicting functional class of distantly related proteins. Here the usefulness of SVMProt for functional study of novel plant proteins is evaluated. To test SVMProt, 49 plant proteins (without a sequence homolog in the Swiss-Prot protein database, not in the SVMProt training set, and with functional indications provided in the literature) were selected from a comprehensive search of MEDLINE abstracts and Swiss-Prot databases in 1999-2004. These represent unique proteins the function of which, at present, cannot be confidently predicted by sequence alignment and clustering methods. The predicted functional class of 31 proteins was consistent, and that of four other proteins was weakly consistent, with published functions. Overall, the functional class of 71.4% of these proteins was consistent, or weakly consistent, with functional indications described in the literature. SVMProt shows a certain level of ability to provide useful hints about the functions of novel plant proteins with no similarity to known proteins.     

Random regression analyses using B-splines to model growth of Australian Angus cattle

Regression on the basis function of B-splines has been advocated as an alternative to orthogonal polynomials in random regression analyses. Basic theory of splines in mixed model analyses is reviewed, and estimates from analyses of weights of Australian Angus cattle from birth to 820 days of age are presented. Data comprised 84 533 records on 20 731 animals in 43 herds, with a high proportion of animals with 4 or more weights recorded. Changes in weights with age were modelled through B-splines of age at recording. A total of thirteen analyses, considering different combinations of linear, quadratic and cubic B-splines and up to six knots, were carried out. Results showed good agreement for all ages with many records, but fluctuated where data were sparse. On the whole, analyses using B-splines appeared more robust against "end-of-range" problems and yielded more consistent and accurate estimates of the first eigenfunctions than previous, polynomial analyses. A model fitting quadratic B-splines, with knots at 0, 200, 400, 600 and 821 days and a total of 91 covariance components, appeared to be a good compromise between detailedness of the model, number of parameters to be estimated, plausibility of results, and fit, measured as residual mean square error.     

Non-linear cancer classification using a modified radial basis function classification algorithm

Summary This paper proposes a modified radial basis function classification algorithm for non-linear cancer classification. In the algorithm, a modified simulated annealing method is developed and combined with the linear least square and gradient paradigms to optimize the structure of the radial basis function (RBF) classifier. The proposed algorithm can be adopted to perform non-linear cancer classification based on gene expression profiles and applied to two microarray data sets involving various human tumor classes: (1) Normal versus colon tumor; (2) acute myeloid leukemia (AML) versus acute lymphoblastic leukemia (ALL). Finally, accuracy and stability for the proposed algorithm are further demonstrated by comparing with the other cancer classification algorithms.     

The role of anion channels and Ca2+ in addition to K+ channels in the physiological volume regulation of murine spermatozoa

Studies in the human, transgenic mice, and cattle indicate that sperm cell volume regulation plays an important role in male fertility as spermatozoa encounter a hypo-osmotic challenge upon ejaculation into the female tract. Physiological regulatory volume decrease (RVD) was examined using flow cytometry in murine sperm released into incubation medium mimicking uterine osmolality and including putative channel inhibitors. The involvement of K+ channels was indicated by the recovery of volume regulation by the K+ ionophore valinomycin in defective sperm from infertile transgenic mice, and from blockage of RVD by quinine in normal sperm. However, in neither case was the recovery complete. The involvement of volume-sensitive osmolyte and anion channels (VSOAC) were investigated using blockers effective in other cell types. NPPB (5-nitro-2(3-phenylpropylamino) benzoic acid) and tamoxifen inhibited RVD but SITS (4-acetamido-4'-isothiocyanato-stilbene-2,2'-disulphonic acid) at 0.4 and 1 mM had no effect whereas DIDS (di-isothiocyanato-stilbene-2,2'-disulphonic acid) at 1 mM enhanced RVD. Verapamil, but not another P-glycoprotein antagonist cyclosporin, caused sperm swelling which persisted in the presence of valinomycin, in Ca2+-free medium and in the presence of thapsigargin, but swelling was abolished by the Ca2+ ionophore A23187. Nifedipine was slightly effective in blocking RVD. Analysis by Western blotting failed to reveal ClC-2 and ClC-3 members of the chloride channel family in murine or rat sperm proteins despite signal bands in positive tissue controls. These findings implicate the involvement of some unidentified VSOAC in sperm volume regulation, which is probably Ca+-dependent.     

Spatial Structure of BAM-12P Dodecapeptide and Its Analogues

Theoretical conformational analysis was used to study the spatial structure and conformational properties of the bovine adrenal medulla dodecapeptide BAM-12P (Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Arg7-Val8-Gly9-Arg10-Pro11-Glu12). Twenty-three low-energy conformations of the BAM-12P backbone were shown to represent the spatial structure of the peptide. The inverse structural problem was solved, and synthetic analogues of BAM-12P were proposed, the spatial structures of which correspond to a set of low-energy potentially physiologically active conformations of the natural dodecapeptide.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 3, 2005, pp. 245–250.Original Russian Text Copyright © 2005 by Akhmedov, Tagiev, Hasanov, Makhmudova.