Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption

We report the first genome-wide association study of habitual caffeine intake. We included 47,341 individuals of European descent based on five population-based studies within the United States. In a meta-analysis adjusted for age, sex, smoking, and eigenvectors of population variation, two loci achieved genome-wide significance: 7p21 (P = 2.4 × 10(-19)), near AHR, and 15q24 (P = 5.2 × 10(-14)), between CYP1A1 and CYP1A2. Both the AHR and CYP1A2 genes are biologically plausible candidates as CYP1A2 metabolizes caffeine and AHR regulates CYP1A2.     

Position dependence of ankle joint dynamics--II. Active mechanics

System identification techniques were used to examine the position dependence of active ankle joint mechanics. Subjects were required to maintain tonic contractions in either the tibialis anterior (TA) or triceps surae (TS) muscles while the ankle was stochastically displaced about different mean angular positions. The dynamic relation between ankle position and torque was determined for each mean position/tonic torque combination; a non-linear minimization technique was used to estimate the three parameters (inertial, viscous and elastic) of a second-order, underdamped system. Whereas the inertial parameter remained essentially invariant across all test conditions, the viscous and elastic (K) parameters became larger as the level of tonic activity increased and as the joint was rotated toward the extremes of the range of motion. The relation between K and torque was linear at all ankle angles. The slope of this relation remained constant at all mean positions during plantarflexor contractions; during dorsiflexor contractions the slope increased as the ankle was rotated from maximum plantarflexion to maximum dorsiflexion. These findings are discussed in terms of: the physiological correlates of ankle mean position, the relative significance of passive and active joint mechanics and contrasts in joint behaviour during active dorsiflexor and plantarflexor contractions.     

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins

Quantitative LC-MS/MS assays were designed for tryptic peptides representing 53 high and medium abundance proteins in human plasma using a multiplexed multiple reaction monitoring (MRM) approach. Of these, 47 produced acceptable quantitative data, demonstrating within-run coefficients of variation (CVs) (n = 10) of 2-22% (78% of assays had CV <10%). A number of peptides gave CVs in the range 2-7% in five experiments (10 replicate runs each) continuously measuring 137 MRMs, demonstrating the precision achievable in complex digests. Depletion of six high abundance proteins by immunosubtraction significantly improved CVs compared with whole plasma, but analytes could be detected in both sample types. Replicate digest and depletion/digest runs yielded correlation coefficients (R(2)) of 0.995 and 0.989, respectively. Absolute analyte specificity for each peptide was demonstrated using MRM-triggered MS/MS scans. Reliable detection of L-selectin (measured at 0.67 microg/ml) indicates that proteins down to the microg/ml level can be quantitated in plasma with minimal sample preparation, yielding a dynamic range of 4.5 orders of magnitude in a single experiment. Peptide MRM measurements in plasma digests thus provide a rapid and specific assay platform for biomarker validation, one that can be extended to lower abundance proteins by enrichment of specific target peptides (stable isotope standards and capture by anti-peptide antibodies (SISCAPA)).     

Natural variation in the sexually selected feather ornaments of crested auklets (Aethia cristatella) does not predict future survival

We evaluated whether sexually selected crest and auricular plumefeather ornaments of crested auklet (Aethia cristatella) adultscovaried with individual local survival over 11 years (1991–2001).Crested auklets (n = 364 total) were captured near breedingsites, marked with color rings, and local survival estimateswere based on color ring resightings at a breeding colony. Survivalestimates and relationships among local survival and crest length,auricular plume length, mass and tarsus were evaluated usingthe program MARK. The best models included four groups, definedby sex and ease of resighting, that differed in resighting rate(p) but not local survival rate (). This model structure effectivelyexplained sources of variation in local survival and resightabilityamong individuals. The best fitting model showed local survivalrate varying annually, while accounting for differences in resightabilityof marked individuals between the sexes and groups ([t], p[sex*easeof resighting]). Annual local survival varied from 0.940 ±0.029 (SE) in 1993–1994 to 0.767 ± 0.034 in 1997–1998and averaged 0.859 ± 0.019. We found no evidence thatcrested auklet local survival covaried with continuous variationin individuals' ornaments. Simulations indicated that our dataset was sufficient to detect a relationship between local survivaland a covariate that equaled or exceeded a range of 8%. Theimplications for competing sexual selection mechanisms of empiricallymeasured survival–ornament relationships are controversial,but our study emphasizes that survival estimates for such investigationsmust control for confounding factors such as resighting rateas well as have sufficient statistical power and time scaleto be biologically meaningful. Our results are most consistentwith the idea that the conspicuous variation in crested auklet'sshowy ornaments is arbitrary with respect to individual viabilityas quantified by their long-term survival.     

Copy Number Variation of CCL3-like Genes Affects Rate of Progression to Simian-AIDS in Rhesus Macaques (Macaca mulatta)

Variation in genes underlying host immunity can lead to marked differences in susceptibility to HIV infection among humans. Despite heavy reliance on non-human primates as models for HIV/AIDS, little is known about which host factors are shared and which are unique to a given primate lineage. Here, we investigate whether copy number variation (CNV) at CCL3-like genes (CCL3L), a key genetic host factor for HIV/AIDS susceptibility and cell-mediated immune response in humans, is also a determinant of time until onset of simian-AIDS in rhesus macaques. Using a retrospective study of 57 rhesus macaques experimentally infected with SIVmac, we find that CCL3L CNV explains approximately 18% of the variance in time to simian-AIDS (p<0.001) with lower CCL3L copy number associating with more rapid disease course. We also find that CCL3L copy number varies significantly (p<10⁻⁶) among rhesus subpopulations, with Indian-origin macaques having, on average, half as many CCL3L gene copies as Chinese-origin macaques. Lastly, we confirm that CCL3L shows variable copy number in humans and chimpanzees and report on CCL3L CNV within and among three additional primate species. On the basis of our findings we suggest that (1) the difference in population level copy number may explain previously reported observations of longer post-infection survivorship of Chinese-origin rhesus macaques, (2) stratification by CCL3L copy number in rhesus SIV vaccine trials will increase power and reduce noise due to non-vaccine-related differences in survival, and (3) CCL3L CNV is an ancestral component of the primate immune response and, therefore, copy number variation has not been driven by HIV or SIV per se.     

Regulation of Kainate Receptor Subunit mRNA by Stress and Corticosteroids in the Rat Hippocampus

Kainate receptors are a class of ionotropic glutamate receptors that have a role in the modulation of glutamate release and synaptic plasticity in the hippocampal formation. Previous studies have implicated corticosteroids in the regulation of these receptors and recent clinical work has shown that polymorphisms in kainate receptor subunit genes are associated with susceptibility to major depression and response to anti-depressant treatment. In the present study we sought to examine the effects of chronic stress and corticosteroid treatments upon the expression of the mRNA of kainate receptor subunits GluR5-7 and KA1-2. Our results show that, after 7 days, adrenalectomy results in increased expression of hippocampal KA1, GluR6 and GluR7 mRNAs, an effect which is reversed by treatment with corticosterone in the case of KA1 and GluR7 and by aldosterone treatment in the case of GluR6. 21 days of chronic restraint stress (CRS) elevated the expression of the KA1 subunit, but had no effect on the expression of the other subunits. Similarly, 21 days of treatment with a moderate dose of corticosterone also increased KA1 mRNA in the dentate gyrus, whereas a high corticosterone dose has no effect. Our results suggest an interaction between hippocampal kainate receptor composition and the hypothalamic-pituitary-adrenal (HPA) axis and show a selective chronic stress induced modulation of the KA1 subunit in the dentate gyrus and CA3 that has implications for stress-induced adaptive structural plasticity.     

Never say never. The NIMA-related protein kinases in mitotic control

Mitosis sees a massive reorganization of cellular architecture. The microtubule cytoskeleton is reorganized to form a bipolar spindle between duplicated microtubule organizing centers, the chromosomes are condensed, attached to the spindle at their kinetochores, and, through the action of multiple molecular motors, the chromosomes are segregated into two daughter cells. Mitosis also sees a substantial wave of protein phosphorylation, controlling signaling events that coordinate mitotic processes and ensure accurate chromosome segregation. The key switch for the onset of mitosis is the archetypal cyclin-dependent kinase, Cdc2. Under the direction of Cdc2 is an executive of protein serine/threonine kinases that fall into three families: the Polo kinases, Aurora kinases and the NIMA-related kinases (Nrk). The latter family has proven the most enigmatic in function, although recent advances from several sources are beginning to reveal a common functional theme.     

Alterations in pp60c-src accompany differentiation of neurons from rat embryo striatum.

Cultured neurons from rat embryo striatum were found to contain two structurally distinct forms of pp60c-src. The 60-kilodalton (kDa) form appeared similar to pp60c-src from cultured rat fibroblasts or astrocytes. The 61-kDa form was specific to neurons and differed in the NH2-terminal 18 kDa of the molecule. In undifferentiated neurons the predominant phosphorylated species of pp60c-src was the fibroblast form. Upon differentiation, a second phosphorylated form of pp60c-src was detected. This form had two or more additional sites of serine phosphorylation within the NH2-terminal 18-kDa region of the molecule, one of which was Ser-12. The specific protein-tyrosine kinase activity of the total pp60c-src population increased 14-fold, as measured by autophosphorylation, or 7-fold, as measured by phosphorylation of an exogenous substrate, as striatal neurons differentiated. This elevation in protein kinase activity occurred without a detectable decrease in Tyr-527 phosphorylation or increase in Tyr-416 phosphorylation. Our results support the idea that the expression of the neuron-specific form of pp60c-src and the increase in specific protein kinase activity may be important for neuronal differentiation.     

Eosinophils in a tri-cell multicellular tumor spheroid (MTS)/endothelium complex.

Eosinophils have been found in infiltrates of many different cancers. It is still unclear as to whether they are passive bystanders in the cellular milieu or active cellular agents in host responses. Thus their harmful or helpful nature remains equivocal. We have developed an in vitro tri-cell model of eosinophils, MCF-7 breast tumor cell spheroids and HUVEC endothelial cells to examine the binding and association of eosinophils with both the tumor and the endothelia and the ensuing action of the tumor. Eosinophils bound very rapidly to the tumor spheroid and remained tightly bound throughout the 24 hr culture period. Histological staining of the tri-cell complex revealed highly granulated eosinophils as well as large amounts of degranulated protein diffused throughout the spheroid. IL-5 treatment of eosinophil: MTS complexes resulted in destruction of the tumor cells, particularly those which had grown out from the spheroid onto the endothelial cells. Eosinophils, pretreated with IL-5 before interaction with the tumor or endothelial cells, bound aggressively to the endothelial cells, thereby preventing tumor attachment. This eosinophil tri-cell tumor model system mimics clinical observations with regards to binding to epithelial and endothelial cells, dispersal of granular proteins throughout the tumor and also tumor destruction. Because it closely mirrors in vivo cellular interactions, it allows one to study more closely the mechanism(s) of eosinophil killing, the modulation of eosinophil activity and the testing of therapeutic interventions. The accommodation of the model to tumor invasion, using metastatic tumor cells and extracellular matrices such as matrigel, will help to elucidate a role for eosinophils (and their mediators) in cancer invasion and metastasis.