Functional architecture of the inner pore of a voltage-gated Ca2+ channel

The inner pore of voltage-gated Ca2+ channels (VGCCs) is functionally important, but little is known about the architecture of this region. In K+ channels, this part of the pore is formed by the S6/M2 transmembrane segments from four symmetrically arranged subunits. The Ca2+ channel pore, however, is formed by four asymmetric domains of the same (alpha1) subunit. Here we investigated the architecture of the inner pore of P/Q-type Ca2+ channels using the substituted-cysteine accessibility method. Many positions in the S6 segments of all four repeats of the alpha1 subunit (Ca(v)2.1) were modified by internal methanethiosulfonate ethyltrimethylammonium (MTSET). However, the pattern of modification does not fit any known sequence alignment with K+ channels. In IIS6, five consecutive positions showed clear modification, suggesting a likely aqueous crevice and a loose packing between S6 and S5 segments, a notion further supported by the observation that some S5 positions were also accessible to internal MTSET. These results indicate that the inner pore of VGCCs is indeed formed by the S6 segments but is different from that of K+ channels. Interestingly some residues in IIIS6 and IVS6 whose mutations in L-type Ca2+ channels affect the binding of dihydropyridines and phenylalkylamines and are thought to face the pore appeared not to react with internal MTSET. Probing with qBBr, a rigid thiol-reactive agent with a dimension of 12 angstroms x 10 angstroms x 6 angstroms suggests that the inner pore can open to >10 angstroms. This work provides an impetus for future studies on ion permeation, gating, and drug binding of VGCCs.     

Generalized linear mixture models for handling nonignorable dropouts in longitudinal studies

This paper presents a method for analysing longitudinal data when there are dropouts. In particular, we develop a simple method based on generalized linear mixture models for handling nonignorable dropouts for a variety of discrete and continuous outcomes. Statistical inference for the model parameters is based on a generalized estimating equations (GEE) approach (Liang and Zeger, 1986). The proposed method yields estimates of the model parameters that are valid when nonresponse is nonignorable under a variety of assumptions concerning the dropout process. Furthermore, the proposed method can be implemented using widely available statistical software. Finally, an example using data from a clinical trial of contracepting women is used to illustrate the methodology.     

Copper-induced structural changes in the ovine prion protein are influenced by a polymorphism at codon 112

Prion diseases are associated with conformational change in the copper-binding protein PrP. The copper-binding sites in PrP are located in the N-terminal region of the molecule and comprise a series of tandem repeats of the sequence PHGGGWGQ together with two histidines at residues 96 and 111 (human PrP numbering). The co-ordination of copper ions within the non-octapeptide repeat metal ion-binding site involves Met109 (human numbering, which corresponds with Met112 in ovine PrP) and the binding of copper to this site leads to an increase in beta-sheet formation in PrP. Here we have investigated the influence of the M112T polymorphism on copper-induced structural changes in ovine recombinant PrP. M112ARQ and T112ARQ ovine PrP show similar secondary structure although M112ARQ appears more thermostable than T112ARQ. Following treatment with copper, M112ARQ showed a greater increase in beta-sheet content than did T112ARQ when measured by CD spectroscopy and by ELISA using anti-PrP monoclonal antibodies. These biochemical and biophysical differences between M112ARQ and T112ARQ correlate with similar differences seen between allelic variants of ovine PrP associated with susceptibility and resistance to classical scrapie. These observations suggest that T112ARQ may provide a measure of resistance to classical scrapie pathogenesis compared to M112ARQ.     

Some aspects of the biology of gudgeon Gobio gobio (L.) in Irish waters

Data on some aspects of the biology of gudgeon were obtained during a programme of research on Irish coarse fishes. Eggs of gudgeon, were collected on 3 occasions—on June 8 and again on June 29, 1965 in a small rivulet entering a hydro-electric reservoir in Co. Cork; and on June 2, 1966 in a millstream on the Grand Canal in Co. Dublin. The eggs were greyish-white in colour, opaque, and 1·375–1·625 mm diam. Newly-hatched larvae from eggs from Co. Cork measured 5·45 mm and were distinguished by the presence of black pigment largely confined to the ventral aspect of the yolk sac and tail. They began to feed after 3 days; in 5–6 days the yolk was fully absorbed, the fish then measuring 6·2 mm. Following the creation of 2 hydro-electric reservoirs on the River Lee in Co. Cork, large populations of gudgeon developed in them for a time. It was found that, in the reservoirs, gudgeon less than 7·5 cm were feeding mainly on Cladocera, especially Chydoridae. The larger reservoir gudgeon and gudgeon in rivers and streams in Co. Cork fed mainly on molluscs, Gammarus, chironomid larvae, caddis larvae and ephemeropteran nymphs. Some gudgeon held a good deal of filamentous algae. Gudgeon were aged by means of scale reading, the results of which were confirmed by length-frequency distribution analysis in the case of the reservoirs. In the Lee system, gudgeon grew relatively rapidly at first, attaining a mean fork-length at 3 years old of 9·5–10·8 cm according to year-class. In the River Allow, a Cork Blackwater tributary, early growth was slower than in the Lee, but the length increments in the third and subsequent seasons were bigger than in the Lee reservoirs. In the Lee, most gudgeon of both sexes spawned for the first time when 2 years old, at a minimum fork-length of 6·9 cm in the case of males and 7·9 cm in the case of females. The trematode parasite Paracoenogonimus ovatus was of frequent occurrence in Irish gudgeon aged 2 years and upwards.     

Brain antioxidant systems in human methamphetamine users

Animal data suggest that the widely abused psychostimulant methamphetamine can damage brain dopamine neurones by causing dopamine-dependent oxidative stress; however, the relevance to human methamphetamine users is unclear. We measured levels of key antioxidant defences [reduced (GSH) and oxidized (GSSG) glutathione, six major GSH system enzymes, copper-zinc superoxide dismutase (CuZnSOD), uric acid] that are often altered after exposure to oxidative stress, in autopsied brain of human methamphetamine users and matched controls. Changes in the total (n = 20) methamphetamine group were limited to the dopamine-rich caudate (the striatal subdivision with the most severe dopamine loss) in which only activity of CuZnSOD (+ 14%) and GSSG levels (+ 58%) were changed. In the six methamphetamine users with severe (- 72 to - 97%) caudate dopamine loss, caudate CuZnSOD activity (+ 20%) and uric acid levels (+ 63%) were increased with a trend for decreased (- 35%) GSH concentration. Our data suggest that brain levels of many antioxidant systems are preserved in methamphetamine users and that GSH depletion, commonly observed during severe oxidative stress, might occur only with severe dopamine loss. Increased CuZnSOD and uric acid might reflect compensatory responses to oxidative stress. Future studies are necessary to establish whether these changes are associated with oxidative brain damage in human methamphetamine users.     

Relationship of Physical Fitness to Prevalence and Incidence of Overweight among Schoolchildren

Objectives: We examined the relationship between comprehensive fitness tests and overweight using a school surveillance system in a racially diverse city in the United States. Research Methods and Procedures: Trained physical education teachers measured weight, height, and fitness annually from 2001 to 2003. We compiled data for a cross‐sectional analysis (11, 845 measurements on 6297 students, 5 to14 years of age) and a 1‐year prospective analysis (4215 measurements on 2927 students not overweight at baseline, 5 to 13 years of age). Overweight was defined as a BMI ≥95th percentile (Centers for Disease Control and Prevention 2000 growth charts), and underfit was defined as failing at least one of five fitness tests: endurance run, abdominal strength, flexibility, upper body strength, and agility (Amateur Athletic Union and Fitnessgram). Associations between fitness and overweight were examined using multivariate logistic regression models, adjusting for sociodemographic status and repeated measurements over time. Results: The mean number of fitness tests passed was lower among students with a BMI above the 80th percentile. Overweight incidence over 1 year was 7% and 2% for underfit and fit girls, respectively (odds ratio, 3.3; 95% confidence interval, 2.0 to 5.6). Not passing either the endurance run or upper body strength test was associated with overweight incidence in both boys and girls. After adjusting for baseline BMI, the endurance run remained a significant predictor of incident overweight among girls (odds ratio, 2.0; 95% confidence interval, 1.1 to 3.5). Discussion: Findings support a cross‐sectional inverse relationship between physical fitness and overweight among school‐aged children. The direction of causation between fitness and overweight is not clearly established and merits further study.     

Nucleotide sequence and properties of the cohesive DNA termini from bacteriophage HP1c1 of Haemophilus influenzae Rd

The termini of the mature DNA of phage HP1c1 of Haemophilus influenzae Rd have been characterized by DNA ligation, nucleotide sequencing, and deoxynucleotide incorporation experiments. A hybrid plasmid containing the joined phage termini (the cos site) inserted into pBR322 has been constructed. The phage DNA has cohesive termini composed of complementary 5' single-stranded extensions which are seven residues long. The left cohesive terminal extension consists only of pyrimidines and the right only of purines. When the ends of the phage are joined, the terminal sequences constitute the central 7 bp of an 11 bp sequence containing only purines on one strand and pyrimidines on the other strand. This oligopyrimidine/oligopurine sequence does not possess rotational symmetry. A 10-bp sequence and its inverted repeat are located approx. 20 bp to the left and right of the fused ends.     

A bivariate pseudolikelihood for incomplete longitudinal binary data with nonignorable nonmonotone missingness

For analyzing longitudinal binary data with nonignorable and nonmonotone missing responses, a full likelihood method is complicated algebraically, and often requires intensive computation, especially when there are many follow-up times. As an alternative, a pseudolikelihood approach has been proposed in the literature under minimal parametric assumptions. This formulation only requires specification of the marginal distributions of the responses and missing data mechanism, and uses an independence working assumption. However, this estimator can be inefficient for estimating both time-varying and time-stationary effects under moderate to strong within-subject associations among repeated responses. In this article, we propose an alternative estimator, based on a bivariate pseudolikelihood, and demonstrate in simulations that the proposed method can be much more efficient than the previous pseudolikelihood obtained under the assumption of independence. We illustrate the method using longitudinal data on CD4 counts from two clinical trials of HIV-infected patients.