Comparison of statistics for candidate-gene association studies using cases and parents.

Studies of association between candidate genes and disease can be designed to use cases with disease, and in place of nonrelated controls, their parents. The advantage of this design is the elimination of spurious differences due to ethnic differences between cases and nonrelated controls. However, several statistical methods of analysis have been proposed in the literature, and the choice of analysis is not always clear. We review some of the statistical methods currently developed and present two new statistical methods aimed at specific genetic hypotheses of dominance and recessivity of the candidate gene. These new methods can be more powerful than other current methods, as demonstrated by simulations. The basis of these new statistical methods is a likelihood approach. The advantage of the likelihood framework is that regression models can be developed to assess genotype-environment interactions, as well as the relative contribution that alleles at the candidate-gene locus make to the relative risk (RR) of disease. This latter development allows testing of (1) whether interactions between alleles exist, on the scale of log RR, and (2) whether alleles originating from the mother or father of a case impart different risks, i.e., genomic imprinting.     

Polypyrimidine Tract Binding Protein Prevents Activity of an Intronic Regulatory Element That Promotes Usage of a Composite 3��-Terminal Exon

Alternative splicing of 3′-terminal exons plays a critical role in gene expression by producing mRNA with distinct 3′-untranslated regions that regulate their fate and their expression. The Xenopus α-tropomyosin pre-mRNA possesses a composite internal/3′-terminal exon (exon 9A9′) that is differentially processed depending on the embryonic tissue. Exon 9A9′ is repressed in non-muscle tissue by the polypyrimidine tract binding protein, whereas it is selected as a 3′-terminal or internal exon in myotomal cells and adult striated muscles, respectively. We report here the identification of an intronic regulatory element, designated the upstream terminal exon enhancer (UTE), that is required for the specific usage of exon 9A9′ as a 3′-terminal exon in the myotome. We demonstrate that polypyrimidine tract binding protein prevents the activity of UTE in non-muscle cells, whereas a subclass of serine/arginine rich (SR) proteins promotes the selection of exon 9A9′ in a UTE-dependent way. Morpholino-targeted blocking of UTE in the embryo strongly reduced the inclusion of exon 9A9′ as a 3′-terminal exon in the endogenous mRNA, demonstrating the function of UTE under physiological circumstances. This strategy allowed us to reveal a splicing pathway that generates a mRNA with no in frame stop codon and whose steady-state level is translation-dependent. This result suggests that a non-stop decay mechanism participates in the strict control of the 3′-end processing of the α-tropomyosin pre-mRNA.     

Normal thymic cortical epithelial cells developmentally regulate the expression of a B-lineage transformation-associated antigen

Nonlymphoid, stromal cells in the mouse thymus are believed to be important in T cell maturation and have been proposed to play a central role in the acquisition of major histocompatibility complex (MHC) restriction and self-tolerance by maturing thymocytes. Both cortical and medullary epithelial cells in the thymus express high levels of class II (A) major histocompatibility antigens (MHC Ags). We show here that a specific subset of these A^– epithelial cells express a transformation-associated antigen (6C3Ag) found previously on the surfaces of Abelson murine leukemia virus-transformed pre-B cells and on those bone marrow-derived stromal cell clones which support normal and preneoplastic pre-B cell proliferation. Among solid lymphoid organs, only the thymus contains 6C3Ag¹ cells and within the thymus, this antigen is found exclusively on A^– epithelial cells in cortical regions. It is striking that the expression of the 6C3Ag on thymic epithelium is developmentally regulated, suggesting a role for this lymphostromal antigen in the maturation of the thymic microenvironment.     

Suppressive effects of soluble histocompatibility antigens on the in vitro generation of cytotoxic T cells to D-end alloantigens

Murine histocompatibility antigens were solubilized from the spleens and lungs of C57BL/6 (H-2b) animals with hypertonic salt (3 M KC1). Aggregate-free soluble antigens were incubated with nonadherent lymph node cells from BALB/c (H-2d) mice for 18 hr prior to their use as responder cells in the mixed-lymphocyte reaction (MLR). It was found that the generation of cytotoxic cells was suppressed while the proliferative response was not affected. The observed suppression was not due to a shift in the kinetics of the generation of cytotoxicity as determined throughout a 10-day culture period. The suppression was specific in that the response in MLR to unrelated H-2f stimulator cells and the subsequent generation of cytotoxic cells were unchanged. Using various H-2 recombinant strains as target cells in the assay of cell-mediated lympholysis, suppression of cytotoxicity was observed when the D end, but not the K end, was shared with the C57BL/6 strain from which the antigens were derived.     

In vitro regeneration of apomictic bluestem grasses

Explants from immature inflorescences of four genotypes of Old World bluestem grasses, (Bothriochloa spp.), produced callus tissue on Linsmaier and Skoog (RM) and 1/2 Murashige and Skoog (1/2 MS) media containing high levels of growth regulators. Callus masses were composed of two distinct tissue types, one a compact, white, embryogenic portion (E calli), the other soft, translucent, gelatinous and nonembryogenic (NE calli). When transferred to medium with a reduced level of 2,4-D, and/or supplemented with zeatin, E callus underwent further organization culminating in shoot production. Light and scanning electron microscopy confirmed the embryogenic pathway of differentiation. Genotype significantly affected callus induction frequency and the number of plants regenerated. The RM medium induced more explants to initiate callus compared to the 1/2 MS medium. Age of the inflorescence explant, as indicated by size, was critical for callus induction. Inflorescences with racemes 8 mm in length were superior to older ones. Five-hundred-twenty-two plantlets were regenerated and grown to maturity.     

Competition between Dunaliella species at high salinity

Information on the distribution of more than 225 species of planktonic, periphytic, and benthic rotifers from diverse waters in south and central Sweden was analyzed for pH preference. No particularly strong correlation was found between pH and any other environmental factor, with regards to rotifer distribution. However, species indicating oligotrophy generally have their pH optima at or below 7.0, while those indicating eutrophy occur at or above this level. Rotifers found in acidic waters are often non-planktonic or semiplanktonic.     

Male reproductive success in harem troops of hanuman langurs (Presbytis entellus)

Based on cross-sectional and longitudinal data collected in 1967–1988 by various observers, male reproductive success was studied in the Hanuman langurs of Jodhpur, India. The harem-structured social organization ensures a high degree of paternity certainty. Births occur throughout the year, with significant peaks and minima in March and November, respectively (n =398).The interbirth interval averages 16.7 months (n = 114).The duration of harem residencies varies between 3 days and ≥ 74.0 months, with a mean of 26.5 (n = 64). Harem holder replacements occur during all months of the year. No male achieves residency in more than one troop, suggesting that residency is associated with a distinct peak in the resource holding potential of a given male. Reproductive success among males varies considerably. Male mortality is high due to migration and intrasexual competition, leading to an adult sex ratio of 1:4.9. It is estimated that one-quarter of all adult males will never gain harem residency. Conceptions achieved outside harem residencies are so rare (4.7%) that a viable low-risk strategy, opting for longevity instead of harem residency, is unlikely. Tenure length has a stronger influence on male reproductive success than harem size because interbirth intervals are significantly shorter in small harems than in larger ones. It is assumed that females in one-male breeding structures compete for sperm and that such competition is more intense in larger harems.