Theoretical and empirical power of regression and maximum-likelihood methods to map quantitative trait loci in general pedigrees

Both theoretical calculations and simulation studies have been used to compare and contrast the statistical power of methods for mapping quantitative trait loci (QTLs) in simple and complex pedigrees. A widely used approach in such studies is to derive or simulate the expected mean test statistic under the alternative hypothesis of a segregating QTL and to equate a larger mean test statistic with larger power. In the present study, we show that, even when the test statistic under the null hypothesis of no linkage follows a known asymptotic distribution (the standard being chi(2)), it cannot be assumed that the distribution under the alternative hypothesis is noncentral chi(2). Hence, mean test statistics cannot be used to indicate power differences, and a comparison between methods that are based on simulated average test statistics may lead to the wrong conclusion. We illustrate this important finding, through simulations and analytical derivations, for a recently proposed new regression method for the analysis of general pedigrees to map quantitative trait loci. We show that this regression method is not necessarily more powerful nor computationally more efficient than a maximum-likelihood variance-component approach. We advocate the use of empirical power to compare trait-mapping methods.     

Influence of primate lentiviral Vif and proteasome inhibitors on human immunodeficiency virus type 1 virion packaging of APOBEC3G

The Vif protein of human immunodeficiency virus type 1 (HIV-1) is essential for viral evasion of the host antiviral protein APOBEC3G, also known as CEM15. Vif mutant but not wild-type HIV-1 viruses produced in the presence of APOBEC3G have been shown to undergo hypermutations in newly synthesized viral DNA upon infection of target cells, presumably resulting from C-to-U modification during minus-strand viral DNA synthesis. We now report that HIV-1 Vif could induce rapid degradation of human APOBEC3G that was blocked by the proteasome inhibitor MG132. The efficiency of Vif-induced downregulation of APOBEC3G expression depended on the level of Vif expression. A single amino acid substitution in the conserved SLQXLA motif reduced Vif function. Vif proteins from distantly related primate lentiviruses such as SIVagm were unable to suppress the antiviral activity of human APOBEC3G or the packaging of APOBEC3G into HIV-1 Vif mutant virions, due to a lack of interaction with human APOBEC3G. In the presence of the proteasome inhibitor MG132, virion-associated Vif increased dramatically. However, increased virion packaging of Vif did not prevent virion packaging of APOBEC3G when proteasome function was impaired, and the infectivity of these virions was significantly reduced. These results suggest that Vif function is required during virus assembly to remove APOBEC3G from packaging into released virions. Once packaged, virion-associated Vif could not efficiently block the antiviral activity of APOBEC3G.     

The role of the p38 mitogen-activated protein kinase, extracellular signal-regulated kinase, and phosphoinositide-3-OH kinase signal transduction pathways in CD40 ligand-induced dendritic cell activation and expansion of virus-specific CD8+ T cell memory responses

Mature dendritic cells (DCs) are central to the development of optimal T cell immune responses. CD40 ligand (CD40L, CD154) is one of the most potent maturation stimuli for immature DCs. We studied the role of three signaling pathways, p38 mitogen-activated protein kinase (MAPK), extracellular signal-regulated kinase (ERK), and phosphoinositide-3-OH kinase (PI3K), in CD40L-induced monocyte-derived DC activation, survival, and expansion of virus-specific CD8(+) T cell responses. p38 MAPK pathway was critical for CD40L-mediated up-regulation of CD83, a marker of DC maturation. CD40L-induced monocyte-derived DC IL-12 production was mediated by both the p38 MAPK and PI3K pathways. CD40L-mediated DC survival was mostly mediated by the PI3K pathway, with smaller contributions by p38 MAPK and ERK pathways. Finally, the p38 MAPK pathway was most important in mediating CD40L-stimulated DCs to induce strong allogeneic responses as well as expanding virus-specific memory CD8(+) T cell responses. Thus, although the p38 MAPK, PI3K, and ERK pathways independently affect various parameters of DC maturation induced by CD40L, the p38 MAPK pathway within CD40L-conditioned DCs is the most important pathway to maximally elicit T cell immune responses. This pathway should be exploited in vivo to either completely suppress or enhance CD8(+) T cell immune responses.     

Acanthoparyphium tyosenense (Digenea: Echinostomatidae): experimental confirmation of the cercaria and its complete life history in Korea

Cercaria yamagutii Ito, 1957, was found in the marine mesogastropods Lunatia fortuni and Glossaulax didyma from the tidelands of Simpo located at the estuary of the Mankyoung River, which runs to the western coast of Korea. Metacercariae were found in a marine bivalve Mactra veneriformis after being infected with C. yamagutii experimentally. When a sea gull, Larus crassiostris, was fed with the metacercariae collected from the infected M. veneriformis, adult worms were recovered 10 days later. It was confirmed that the parasites collected from L. crassiostris were Acanthoparyphium tyosenense Yamaguti, 1939. From the results of this life cycle study, it was determined that the first intermediate hosts of A. tyosenense are L. fortuni and G. didyma. The second intermediate and final hosts are M. veneriformis and L. crassiostris, respectively. Mactra veneriformis was experimentally infected with C. yamagutii isolated from L. fortuni and G. didyma by maintaining them in a water tank for 30 min at about 20 C. The cercariae entered M. veneriformis through their incurrent siphons. Five hours after infection, the cercariae tails began to separate from the bodies, and the cercariae formed cysts. Mature cysts were formed 340 hr (14 days) after infection and identified as the metacercariae of A. tyosenense. The prevalence of A. tyosenense metacercariae was 99.5% in naturally infected M. veneriformis. This is the first report of C. yamagutii as the cercaria of A. tyosenense, and the complete life cycle of A. tyosenense was established in Korea.     

An improved tripod amphiphile for membrane protein solubilization

Intrinsic membrane proteins represent a large fraction of the proteins produced by living organisms and perform many crucial functions. Structural and functional characterization of membrane proteins generally requires that they be extracted from the native lipid bilayer and solubilized with a small synthetic amphiphile, for example, a detergent. We describe the development of a small molecule with a distinctive amphiphilic architecture, a "tripod amphiphile," that solubilizes both bacteriorhodopsin (BR) and bovine rhodopsin (Rho). The polar portion of this amphiphile contains an amide and an amine-oxide; small variations in this polar segment are found to have profound effects on protein solubilization properties. The optimal tripod amphiphile extracts both BR and Rho from the native membrane environments and maintains each protein in a monomeric native-like form for several weeks after delipidation. Tripod amphiphiles are designed to display greater conformational rigidity than conventional detergents, with the long-range goal of promoting membrane protein crystallization. The results reported here represent an important step toward that ultimate goal.     

Clomiphene, an ovulation-inducing agent, mobilizes intracellular Ca2+ and causes extracellular Ca2+ influx in bladder female transitional carcinoma cells

BACKGROUND/METHODS: The effect of clomiphene, an ovulation-inducing agent, on cytosolic free Ca2+ levels ([Ca2+]i) in populations of BFTC human bladder cancer cells was explored by using fura-2 as a Ca2+ indicator. RESULTS: Clomiphene at concentrations between 10 and 75 microM increased [Ca2+]i in a concentration-dependent manner and the signal saturated at 50 microM. The [Ca2+]i signal was biphasic with an initial rise and a slow decay. Ca2+ removal inhibited the Ca2+ signal by about 40-50% in maximum [Ca2+]i. Adding 3 mM Ca2+ increased [Ca2+]i in cells pretreated with 50 microM clomiphene in Ca2+-free medium, suggesting that clomiphene induced capacitative Ca2+ entry. In Ca2+-free medium, pretreatment with 50 microM brefeldin A (to disrupt the Golgi complex Ca2+ store), 1 microM thapsigargin (to inhibit the endoplasmic reticulum Ca2+ pump), and CCCP (to uncouple mitochondria) inhibited 85% of clomiphene-induced intracellular Ca2+ release. Conversely, pretreatment with 50 microM clomiphene in Ca2+-free medium abolished the [Ca2+]i increase induced by brefeldin, thapsigargin or CCCP. The intracellular Ca2+ release was unaltered by inhibiting formation of inositol-1,4,5-trisphosphate (IP3) with 2 mM 1-(6-((17beta-3-methoxyestra-1,3,5(10)-trien-17-yl)amino)hexyl)-1H-pyrrole-2,5-dione (U73122; a phospholipase C inhibitor). CONCLUSION: The [Ca2+]i increase induced by 50 microM clomiphene was not affected by 10 microM of nifedipine, verapamil or diltiazem. Collectively, the results suggest that clomiphene releases intracellular Ca2+ in an IP3-independent manner and also activates extracellular Ca2+ influx.     

Spatial variations in aboveground net primary productivity along a climate gradient in Eurasian temperate grassland: effects of mean annual precipitation and its seasonal distribution

Concomitant changes of annual precipitation and its seasonal distribution within the context of global climate change have dramatic impacts on aboveground net primary productivity (ANPP) of grassland ecosystems. In this study, combining remote sensing products with in situ measurements of ANPP, we quantified the effects of mean annual precipitation (MAP) and precipitation seasonal distribution (PSD) on the spatial variations in ANPP along a climate gradient in Eurasian temperate grassland. Our results indicated that ANPP increased exponentially with MAP for the entire temperate grassland, but linearly for a specific grassland type, i.e. the desert steppe, typical steppe, and meadow steppe from arid to humid regions. The slope of the linear relationship appeared to be steeper in the more humid meadow steppe than that in the drier typical and desert steppes. PSD also had significant effect on the spatial variations in ANPP. It explained 39.4% of the spatial ANPP for the entire grassland investigated, being comparable with the explanatory power of MAP (40.0%). On the other hand, the relative contribution of PSD and MAP is grassland type specific. MAP exhibited a much stronger explanatory power than PSD for the desert steppe and the meadow steppe at the dry and wet end, respectively. However, PSD was the dominant factor affecting the spatial variation in ANPP for the median typical steppe. Our results imply that altered pattern of PSD due to climate change may be as important as the total amount in terms of effects on ANPP in Eurasian temperate grassland.