Drug block of the hERG potassium channel: insight from modeling

Many commonly used, structurally diverse, drugs block the human ether-a-go-go-related gene (hERG) K(+) channel to cause acquired long QT syndrome, which can lead to sudden death via lethal cardiac arrhythmias. This undesirable side effect is a major hurdle in the development of safe drugs. To gain insight about the structure of hERG and the nature of drug block we have produced structural models of the channel pore domain, into each of which we have docked a set of 20 hERG blockers. In the absence of an experimentally determined three-dimensional structure of hERG, each of the models was validated against site-directed mutagenesis data. First, hERG models were produced of the open and closed channel states, based on homology with the prokaryotic K(+) channel crystal structures. The modeled complexes were in partial agreement with the mutagenesis data. To improve agreement with mutagenesis data, a KcsA-based model was refined by rotating the four copies of the S6 transmembrane helix half a residue position toward the C-terminus, so as to place all residues known to be involved in drug binding in positions lining the central cavity. This model produces complexes that are consistent with mutagenesis data for smaller, but not larger, ligands. Larger ligands could be accommodated following refinement of this model by enlarging the cavity using the inherent flexibility about the glycine hinge (Gly648) in S6, to produce results consistent with the experimental data for the majority of ligands tested.     

Variations in heart rate and rhythm of harbor seal pups during rehabilitation

Heart rate and rhythm is regulated by the autonomic nervous system, which matures during the first months of life. Little is known about heart rate and rhythm development and potential arrhythmias in seal pups during rehabilitation in seal centers. Using an iPhone ECG device, 1 min ECGs were obtained from harbor seal pups admitted to a seal rehabilitation facility. ECGs were taken from 55 seals after admission, 53 seals after 14 d, and 52 seals prior to release. From 24 seal pups additional ECGs were taken daily for the first week of rehabilitation. At admission sinus rhythm with a median heart rate of 148 complexes per minute was detected, prior to release sinus bradycardia or sinus arrhythmia with a median heart rate of 104 complexes minute was present. P wave morphology was highly variable and single supra‐ and ventricular premature complexes were recorded in individual animals. The first 14 d were characterized by highly variable heart rates and rhythms, including episodes of sinus tachycardia and 2nd degree atrioventricular blocks. The reduction in heart rates and development of a regular heart rhythm during rehabilitation suggest adaptation to the unfamiliar environment, resolution of disease, and/or maturation of the autonomic nervous system.     

基于GIS的广州市中心城区城市森林可达性分析

城市森林是城市中主要的生态功能景观,已经成为城市生态环境建设的主体。基于居民方便获取城市森林服务的要求,根据大型城市森林斑块、道路网和街区单元数据,利用ArcGIS9.2的Network Analyst工具,分析了广州市中心城区在2km步行距离内街区单元到达城市森林斑块的可达性以及城市森林斑块的承载力,并结合航片解译的树冠覆盖数据对具有不同可达性的街区单元进行了分析。分析结果表明：广州中心城区的外环高速以内的区域范围,分别有73%、46%和18%的的街区单元在步行2km、1km和0.5km距离内能够到达大型城市森林绿地斑块。从街区单元的行政归属看,以越秀区的街区可达性最好,而海珠区和原芳村区的街区可达性较差。研究范围内,0.5km内不能到达大型城市森林斑块且树冠覆盖超过30%的街区类型中,以公共管理单位类型为主,单位绿化对于树冠覆盖的贡献率大;而绝大多数以住宅类型为主的街区单元的树冠覆盖率低于10%,其中64%的街区树冠覆盖率低于5%。以街区单元为基本对象进行可达性度量,分析城市森林斑块现状分布和服务状况,并结合其树冠覆盖特征,可以明确需要重点关注区域的空间分布,可为广州市在较小尺度上的城市森林空间布局优化提供参考。     

The complete mitochondrial genome of the Sichuan taimen (Hucho bleekeri): repetitive sequences in the control region and phylogenetic implications for Salmonidae

The complete mitochondrial DNA genome of the Sichuan taimen (Hucho bleekeri) was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequence method. The entire mitochondrial genome of this species is 16,997 bp in length, making it the longest among the completely sequenced Salmonidae mitochondrial genomes. It consists of two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one control region (CR). The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar to those of other teleosts. A T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region, which were almost identical among the three H. bleekeri individuals examined. Both phylogenetic analyses based on 12 concatenated protein-coding genes of the heavy strand and on just the control region show that H. bleekeri is a basal species in Salmoninae. In addition, Salmo, Salvelinus and Oncorhynchus all represent monophyletic groups, respectively. All freshwater species occupied basal phylogenetic positions, and also possessed various tandem repeats in their mitochondrial control regions. These results support established phylogenetic relationships among genera in Salmonidae based on morphological and molecular analyses, and are consistent with the hypothesis that Salmonidae evolved from freshwater species.     

Assessing treatment effect heterogeneity in clinical trials with blocked binary outcomes

This paper addresses treatment effect heterogeneity (also referred to, more compactly, as 'treatment heterogeneity') in the context of a controlled clinical trial with binary endpoints. Treatment heterogeneity, variation in the true (causal) individual treatment effects, is explored using the concept of the potential outcome. This framework supposes the existance of latent responses for each subject corresponding to each possible treatment. In the context of a binary endpoint, treatment heterogeniety may be represented by the parameter, pi2, the probability that an individual would have a failure on the experimental treatment, if received, and would have a success on control, if received. Previous research derived bounds for pi2 based on matched pairs data. The present research extends this method to the blocked data context. Estimates (and their variances) and confidence intervals for the bounds are derived. We apply the new method to data from a renal disease clinical trial. In this example, bounds based on the blocked data are narrower than the corresponding bounds based only on the marginal success proportions. Some remaining challenges (including the possibility of further reducing bound widths) are discussed.     

Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes

We report the first phylogenetic analysis of DNA sequence data for the Central American component of the genus Eleutherodactylus (Anura: Leptodactylidae: Eleutherodactylinae), one of the most ubiquitous, diverse, and abundant components of the Neotropical amphibian fauna. We obtained DNA sequence data from 55 specimens representing 45 species. Sampling was focused on Central America, but also included Bolivia, Brazil, Jamaica, and the USA. We sequenced 1460 contiguous base pairs (bp) of the mitochondrial genome containing ND2 and five neighboring tRNA genes, plus 1300 bp of the c-myc nuclear gene. The resulting phylogenetic inferences were broadly concordant between data sets and among analytical methods. The subgenus Craugastor is monophyletic and its initial radiation was potentially rapid and adaptive. Within Craugastor, the earliest splits separate three northern Central American species groups, milesi, augusti, and alfredi, from a clade comprising the rest of Craugastor. Within the latter clade, the rhodopis group as formerly recognized comprises three deeply divergent clades that do not form a monophyletic group; we therefore restrict the content of the rhodopis group to one of two northern clades, and use new names for the other northern (mexicanus group) and one southern clade (bransfordii group). The new rhodopis and bransfordii groups together form the sister taxon to a clade comprising the biporcatus, fitzingeri, mexicanus, and rugulosus groups. We used a Bayesian MCMC approach together with geological and biogeographic assumptions to estimate divergence times from the combined DNA sequence data. Our results corroborated three independent dispersal events for the origins of Central American Eleutherodactylus: (1) an ancestor of Craugastor entered northern Central America from South American in the early Paleocene, (2) an ancestor of the subgenus Syrrhophus entered northern Central America from the Caribbean at the end of the Eocene, and (3) a wave of independent dispersal events from South America coincided with formation of the Isthmus of Panama during the Pliocene. We elevate the subgenus Craugastor to the genus rank.     

Association of the ABCA1 gene polymorphisms with type 2 DM in a Japanese population

To examine the association of the ATP-binding cassette transporter 1 (ABCA1) gene with type 2 diabetes (DM), we studied genetic polymorphisms of the ABCA1 gene including its linkage disequilibrium (LD) and haplotype analyses using a Japanese population. A sample set (DM:72, IGT:75, and NGT:227) was genotyped with 34 SNPs distributed from the promoter region to the last exon of the ABCA1 gene. LD between SNPs was assessed in pairwise manner. Among 13 LD blocks constructed, an LD block at the 5'-region showed a significant difference in the haplotype distribution between the study groups (NGT vs. IGT + DM: overall p = 0.0180; NGT vs. DM: 0.0001). Fisher's exact probability test (NGT vs. DM) showed a significant association of the haplotype 2 of the LD block (p = 0.0001), with an odds ratio (OR) of 2.53 (95%CI:1.62-4.12). Diplotype analysis also showed a significant association of the diplotypes with the haplotype 2 (OR:2.59, 95%CI:1.48-4.54, p = 0.0013).     

Protons block BK channels by competitive inhibition with K+ and contribute to the limits of unitary currents at high voltages

Proton block of unitary currents through BK channels was investigated with single-channel recording. Increasing intracellular proton concentration decreased unitary current amplitudes with an apparent pKa of 5.1 without discrete blocking events, indicating fast proton block. Unitary currents recorded at pH(i) 8.0 and 9.0 had the same amplitudes, indicating that 10(-8) M H(+) had little blocking effect. Increasing H(+) by recording at pH(i) 7.0, 6.0, and 5.0 then reduced the unitary currents by 13%, 25%, and 53%, respectively, at +200 mV. Increasing K(+)(i) relieved the proton block in a manner consistent with competitive inhibition of K(+)(i) action by H(+)(i). Proton block was voltage dependent, increasing with depolarization, indicating that block was coupled to the electric field of the membrane. Proton block was not described by the Woodhull equation for noncompetitive voltage-dependent block, but was described by an equation for cooperative competitive inhibition that included voltage-dependent block from the Woodhull equation. Proton block was still present after replacing the eight negative charges in the ring of charge at the entrance to the intracellular vestibule by uncharged amino acids. Thus, the ring of charge is not the site of proton block or of competitive inhibition of K(+)(i) action by H(+)(i). With 150 mM symmetrical KCl, unitary current amplitudes increased with depolarization, reaching 66 pA at +350 mV (pH(i) 7.0). The increase in amplitude with voltage became sublinear for voltages >100 mV. The sublinearity was unaffected by removing from the intracellular solutions Ca(2+) and Ba(2+) ions, the Ca(2+) buffers EGTA and HEDTA, the pH buffer TES, or by replacing Cl(-) with MeSO(3)(-). Proton block accounted for approximately 40% of the sublinearity at +200 mV and pH 7.0, indicating that factors in addition to proton block contribute to the sublinearity of the unitary currents through BK channels.