Rare-variant association analysis reveals known and new age-related hearing loss genes

Age-related (AR) hearing loss (HL) is a prevalent sensory deficit in the elderly population. Several studies showed that common variants increase ARHL susceptibility. Here, we demonstrate that rare-variants play a crucial role in ARHL etiology. We analyzed exome and imputed data from white-European UK Biobank volunteers, performing both single-variant and rare-variant aggregate association analyses using self-reported ARHL phenotypes. We identified and replicated associations between ARHL and rare-variants in KLHDC7B, PDCD6, MYO6, SYNJ2, and TECTA. PUS7L and EYA4 also revealed rare-variant associations with ARHL. EYA4, MYO6, and TECTA are all known to underline Mendelian nonsyndromic HL. PDCD6, a new HL gene, plays an important role in apoptosis and has widespread inner ear expression, particularly in the inner hair cells. An unreplicated common variant association was previously observed for KHLDC7B, here we demonstrate that rare-variants in this gene also play a role in ARHL etiology. Additionally, the first replicated association between SYNJ2 and ARHL was detected. Analysis of common variants revealed several previously reported, i.e., ARHGEF28, and new, i.e., PIK3R3, ARHL associations, as well as ones we replicate here for the first time, i.e., BAIAP2L2, CRIP3, KLHDC7B, MAST2, and SLC22A7. It was also observed that the odds ratios for rare-variant ARHL associations, were higher than those for common variants. In conclusion, we demonstrate the vital role rare-variants, including those in Mendelian nonsyndromic HL genes, play in the etiology of ARHL.

The genetic contribution of the X chromosome in age-related hearing loss

Age-related (AR) hearing loss (HL) is the most common sensory impairment with heritability of 55%. The aim of this study was to identify genetic variants on chromosome X associated with ARHL through the analysis of data obtained from the UK Biobank. We performed association analysis between self-reported measures of HL and genotyped and imputed variants on chromosome X from ∼460,000 white Europeans. We identified three loci associated with ARHL with a genome-wide significance level (p < 5 × 10^-8), ZNF185 (rs186256023, p = 4.9 × 10^-10) and MAP7D2 (rs4370706, p = 2.3 × 10^-8) in combined analysis of males and females, and LOC101928437 (rs138497700, p = 8.9 × 10^-9) in the sex-stratified analysis of males. In-silico mRNA expression analysis showed MAP7D2 and ZNF185 are expressed in mice and adult human inner ear tissues, particularly in the inner hair cells. We estimated that only a small amount of variation of ARHL, 0.4%, is explained by variants on the X chromosome. This study suggests that although there are likely a few genes contributing to ARHL on the X chromosome, the role that the X chromosome plays in the etiology of ARHL may be limited.

Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology

Background

Essential tremor (ET), one of the most common neurological disorders, has a phenotypically heterogeneous presentation characterized by bilateral kinetic tremor of the arms and, in some patients, tremor involving other body regions (e.g., head, voice). Genetic studies suggest that ET is genetically heterogeneous.

Methods

We analyzed whole genome sequence data (WGS) generated on 104 multi-generational white families with European ancestry affected by ET. Genome-wide parametric linkage and association scans were analyzed using adjusted logistic regression models through the application of the Pseudomarker software. To investigate the additional contribution of rare variants in familial ET, we also performed an aggregate variant non-parametric linkage (NPL) analysis using the collapsed haplotype method implemented in CHP-NPL software.

Findings

Parametric linkage analysis of common variants identified several loci with significant evidence of linkage (HLOD ≥3.6). Among the gene regions within the strongest ET linkage peaks were BTC (4q13.3, HLOD=4.53), N6AMT1 (21q21.3, HLOD=4.31), PCDH9 (13q21.32, HLOD=4.21), EYA1 (8q13.3, HLOD=4.04), RBFOX1 (16p13.3, HLOD=4.02), MAPT (17q21.31, HLOD=3.99) and SCARB2 (4q21.1, HLOD=3.65). CHP-NPL analysis identified fifteen additional genes with evidence of significant linkage (LOD ≥3.8). These genes include TUBB2A, VPS33B, STEAP1B, SPINK5, ZRANB1, TBC1D3C, PDPR, NPY4R, ETS2, ZNF736, SPATA21, ARL17A, PZP, BLK and CCDC94. In one ET family contributing to the linkage peak on chromosome 16p13.3, we identified a likely pathogenic heterozygous canonical splice acceptor variant in exon 2 of RBFOX1 (ENST00000547372; c.4-2A>G), that co-segregated with the ET phenotype in the family.

Interpretation

Linkage and association analyses of WGS identified several novel ET candidate genes, which are implicated in four major pathways that include 1) the epidermal growth factor receptor-phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha-AKT serine/threonine kinase 1 (EGFR-PI3K-AKT) and Mitogen-activated protein Kinase 1 (ERK) pathways, 2) Reactive oxygen species (ROS) and DNA repair, 3) gamma-aminobutyric acid-ergic (GABAergic) system and 4) RNA binding and regulation of RNA processes. Our study provides evidence for a possible overlap in the genetic architecture of ET, neurological disease, cancer and aging. The genes and pathways identified can be prioritized in future genetic and functional studies.

Funding

National Institutes of Health, NINDS, NS073872 (USA) and NIA AG058131(USA).

The stability of Cl-, Br-, and I-passivated Si(100)-(2 × 1) in ambient environments for atomically-precise pattern preservation

Atomic precision advanced manufacturing (APAM) leverages the highly reactive nature of Si dangling bonds relative to H- or Cl-passivated Si to selectively adsorb precursor molecules into lithographically defined areas with sub-nanometer resolution. Due to the high reactivity of dangling bonds, this process is confined to ultra-high vacuum (UHV) environments, which currently limits its commercialization and broad-based appeal. In this work, we explore the use of halogen adatoms to preserve APAM-derived lithographic patterns outside of UHV to enable facile transfer into real-world commercial processes. Specifically, we examine the stability of H-, Cl-, Br-, and I-passivated Si(100) in inert N₂and ambient environments. Characterization with scanning tunneling microscopy and x-ray photoelectron spectroscopy (XPS) confirmed that each of the fully passivated surfaces were resistant to oxidation in 1 atm of N₂for up to 44 h. Varying levels of surface degradation and contamination were observed upon exposure to the laboratory ambient environment. Characterization byex situXPS after ambient exposures ranging from 15 min to 8 h indicated the Br- and I-passivated Si surfaces were highly resistant to degradation, while Cl-passivated Si showed signs of oxidation within minutes of ambient exposure. As a proof-of-principle demonstration of pattern preservation, a H-passivated Si sample patterned and passivated with independent Cl, Br, I, and bare Si regions was shown to maintain its integrity in all but the bare Si region post-exposure to an N₂environment. The successful demonstration of the preservation of APAM patterns outside of UHV environments opens new possibilities for transporting atomically-precise devices outside of UHV for integrating with non-UHV processes, such as other chemistries and commercial semiconductor device processes.

A quantitative trait rare variant nonparametric linkage method with application to age-at-onset of Alzheimer's disease

To analyze pedigrees with quantitative trait (QT) and sequence data, we developed a rare variant (RV) quantitative nonparametric linkage (QNPL) method, which evaluates sharing of minor alleles. RV-QNPL has greater power than the traditional QNPL that tests for excess sharing of minor and major alleles. RV-QNPL is robust to population substructure and admixture, locus heterogeneity, and inclusion of nonpathogenic variants and can be readily applied outside of coding regions. When QNPL was used to analyze common variants, it often led to loci mapping to large intervals, e.g., >40 Mb. In contrast, when RVs are analyzed, regions are well defined, e.g., a gene. Using simulation studies, we demonstrate that RV-QNPL is substantially more powerful than applying traditional QNPL methods to analyze RVs. RV-QNPL was also applied to analyze age-at-onset (AAO) data for 107 late-onset Alzheimer's disease (LOAD) pedigrees of Caribbean Hispanic and European ancestry with whole-genome sequence data. When AAO of AD was analyzed regardless of APOE ε4 status, suggestive linkage (LOD = 2.4) was observed with RVs in KNDC1 and nominally significant linkage (p < 0.05) was observed with RVs in LOAD genes ABCA7 and IQCK. When AAO of AD was analyzed for APOE ε4 positive family members, nominally significant linkage was observed with RVs in APOE, while when AAO of AD was analyzed for APOE ε4 negative family members, nominal significance was observed for IQCK and ADAMTS1. RV-QNPL provides a powerful resource to analyze QTs in families to elucidate their genetic etiology.

A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data

To analyze family-based whole-genome sequence (WGS) data for complex traits, we developed a rare variant (RV) non-parametric linkage (NPL) analysis method, which has advantages over association methods. The RV-NPL differs from the NPL in that RVs are analyzed, and allele sharing among affected relative-pairs is estimated only for minor alleles. Analyzing families can increase power because causal variants with familial aggregation usually have larger effect sizes than those underlying sporadic diseases. Differing from association analysis, for NPL only affected individuals are analyzed, which can increase power, since unaffected family members can be susceptibility variant carriers. RV-NPL is robust to population substructure and admixture, inclusion of nonpathogenic variants, as well as allelic and locus heterogeneity and can readily be applied outside of coding regions. In contrast to analyzing common variants using NPL, where loci localize to large genomic regions (e.g., >50 Mb), mapped regions are well defined for RV-NPL. Using simulation studies, we demonstrate that RV-NPL is substantially more powerful than applying traditional NPL methods to analyze RVs. The RV-NPL was applied to analyze 107 late-onset Alzheimer disease (LOAD) pedigrees of Caribbean Hispanic and European ancestry with WGS data, and statistically significant linkage (LOD ≥ 3.8) was found with RVs in PSMF1 and PTPN21 which have been shown to be involved in LOAD etiology. Additionally, nominally significant linkage was observed with RVs in ABCA7, ACE, EPHA1, and SORL1, genes that were previously reported to be associated with LOAD. RV-NPL is an ideal method to elucidate the genetic etiology of complex familial diseases.

SEQSpark: A Complete Analysis Tool for Large-Scale Rare Variant Association Studies Using Whole-Genome and Exome Sequence Data

Massively parallel sequencing technologies provide great opportunities for discovering rare susceptibility variants involved in complex disease etiology via large-scale imputation and exome and whole-genome sequence-based association studies. Due to modest effect sizes, large sample sizes of tens to hundreds of thousands of individuals are required for adequately powered studies. Current analytical tools are obsolete when it comes to handling these large datasets. To facilitate the analysis of large-scale sequence-based studies, we developed SEQSpark which implements parallel processing based on Spark to increase the speed and efficiency of performing data quality control, annotation, and association analysis. To demonstrate the versatility and speed of SEQSpark, we analyzed whole-genome sequence data from the UK10K, testing for associations with waist-to-hip ratios. The analysis, which was completed in 1.5 hr, included loading data, annotation, principal component analysis, and single variant and rare variant aggregate association analysis of >9 million variants. For rare variant aggregate analysis, an exome-wide significant association (p < 2.5 × 10^-6) was observed with CCDC62 (SKAT-O [p = 6.89 × 10^-7], combined multivariate collapsing [p = 1.48 × 10^-6], and burden of rare variants [p = 1.48 × 10^-6]). SEQSpark was also used to analyze 50,000 simulated exomes and it required 1.75 hr for the analysis of a quantitative trait using several rare variant aggregate association methods. Additionally, the performance of SEQSpark was compared to Variant Association Tools and PLINK/SEQ. SEQSpark was always faster and in some situations computation was reduced to a hundredth of the time. SEQSpark will empower large sequence-based epidemiological studies to quickly elucidate genetic variation involved in the etiology of complex traits.

The Rare-Variant Generalized Disequilibrium Test for Association Analysis of Nuclear and Extended Pedigrees with Application to Alzheimer Disease WGS Data

Whole-genome and exome sequence data can be cost-effectively generated for the detection of rare-variant (RV) associations in families. Causal variants that aggregate in families usually have larger effect sizes than those found in sporadic cases, so family-based designs can be a more powerful approach than population-based designs. Moreover, some family-based designs are robust to confounding due to population admixture or substructure. We developed a RV extension of the generalized disequilibrium test (GDT) to analyze sequence data obtained from nuclear and extended families. The GDT utilizes genotype differences of all discordant relative pairs to assess associations within a family, and the RV extension combines the single-variant GDT statistic over a genomic region of interest. The RV-GDT has increased power by efficiently incorporating information beyond first-degree relatives and allows for the inclusion of covariates. Using simulated genetic data, we demonstrated that the RV-GDT method has well-controlled type I error rates, even when applied to admixed populations and populations with substructure. It is more powerful than existing family-based RV association methods, particularly for the analysis of extended pedigrees and pedigrees with missing data. We analyzed whole-genome sequence data from families affected by Alzheimer disease to illustrate the application of the RV-GDT. Given the capability of the RV-GDT to adequately control for population admixture or substructure and analyze pedigrees with missing genotype data and its superior power over other family-based methods, it is an effective tool for elucidating the involvement of RVs in the etiology of complex traits.

[Clinical effect analysis of endovascular repair for aortic pseudoaneurysms in 13 cases]

Objective: To discuss the clinical safety and efficacyof endovascular aneurysm repair (EVAR) for aortic pseudoaneurysms. Methods: From October 2008 to October 2015, 13 patients (11 male, 2 female, with a mean age of 55.6) with aortic pseudoaneurysms treated by EVAR wereenrolled. All the 13 casesunderwentcomputed tomographic arteriography (CTA). The etiology diagnosis withdescendingaortic pseudoaneurysms, infected abdominal aortic pseudoaneurysms, abdominal aortic pseudoaneurysmsin Behcet's syndrome, and uncertain reasons were 4, 4, 4, and 1 case, respectively. Results: In this group, 14 stentswere planted.All the patients hadno accidents and complications in perioperative period.Twelve patients were successfully followed up, 1 patient died of recurrent abdominal aortic pseudoaneurysmsin Behcet's syndrome, and 1 patient with recurrent infected abdominal aortic pseudoaneurysm wascured by pseudoaneurysm resection and extra-anatomic bypass grafting. Concluson: EVAR is a safe and effective option for aortic pseudoaneurysms.

Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic Aneurysms

Background

Intracranial aneurysms (IAs), abdominal aortic aneurysms (AAAs), and thoracic aortic aneurysms (TAAs) all have a familial predisposition. Given that aneurysm types are known to co‐occur, we hypothesized that there may be shared genetic risk factors for IAs, AAAs, and TAAs.

Methods and Results

We performed a mega‐analysis of 1000 Genomes Project‐imputed genome‐wide association study (GWAS) data of 4 previously published aneurysm cohorts: 2 IA cohorts (in total 1516 cases, 4305 controls), 1 AAA cohort (818 cases, 3004 controls), and 1 TAA cohort (760 cases, 2212 controls), and observed associations of 4 known IA, AAA, and/or TAA risk loci (9p21, 18q11, 15q21, and 2q33) with consistent effect directions in all 4 cohorts. We calculated polygenic scores based on IA‐, AAA‐, and TAA‐associated SNPs and tested these scores for association to case‐control status in the other aneurysm cohorts; this revealed no shared polygenic effects. Similarly, linkage disequilibrium–score regression analyses did not show significant correlations between any pair of aneurysm subtypes. Last, we evaluated the evidence for 14 previously published aneurysm risk single‐nucleotide polymorphisms through collaboration in extended aneurysm cohorts, with a total of 6548 cases and 16 843 controls (IA) and 4391 cases and 37 904 controls (AAA), and found nominally significant associations for IA risk locus 18q11 near RBBP8 to AAA (odds ratio [OR]=1.11; P=4.1×10⁻⁵) and for TAA risk locus 15q21 near FBN1 to AAA (OR=1.07; P=1.1×10⁻³).

Conclusions

Although there was no evidence for polygenic overlap between IAs, AAAs, and TAAs, we found nominally significant effects of two established risk loci for IAs and TAAs in AAAs. These two loci will require further replication.

Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits

MOTIVATION

There is great interest in analyzing next generation sequence data that has been generated for pedigrees. However, unlike for population-based data there are only a limited number of rare variant methods to analyze pedigree data. One limitation is the ability to evaluate type I and II errors for family-based methods, due to lack of software that can simulate realistic sequence data for pedigrees.

SUMMARY

We developed RarePedSim (Rare-variant Pedigree-based Simulator), a program to simulate region/gene-level genotype and phenotype data for complex and Mendelian traits for any given pedigree structure. Using a genetic model, sequence variant data can be generated either conditionally or unconditionally on pedigree members' qualitative or quantitative phenotypes. Additionally, qualitative or quantitative traits can be generated conditional on variant data. Sequence data can either be simulated using realistic population demographic models or obtained from sequence-based studies. Variant sites can be annotated with positions, allele frequencies and functionality. For rare variants, RarePedSim is the only program that can efficiently generate both genotypes and phenotypes, regardless of pedigree structure. Data generated by RarePedSim are in standard Linkage file (.ped) and Variant Call (.vcf) formats, ready to be used for a variety of purposes, including evaluation of type I error and power, for association methods including mixed models and linkage analysis methods.

AVAILABILITY AND IMPLEMENTATION

bioinformatics.org/simped/rare

CONTACT

sleal@bcm.edu.

Pre-hospital emergency values of hypertonic-hyperonconic limited resuscitation for traumatic shock

Traumatic shock is a serious threat to life and health. The aim of this study is to investigate the effect of different resuscitation fluid compositions on the emergency resuscitation for patients with traumatic shock. Sixty patients were enrolled and divided into two groups, Group A and Group B. The patients in Group A were treated with resuscitation fluid, with 2:1 ratio of crystal (0.9% sodium chloride injection) and colloid (hydroxyethyl starch 40 injection). The patients in Group B were treated with hypertonic sodium chloride hydroxyethyl starch 40 injection (HSH40). Both vital signs and fluid dosage were monitored and recorded. At the beginning of resuscitation (T₀) and 30 min (T₁), 60 min (T₂) and 120 min (T₃) after resuscitation, indicator parameters including hemoglobin (HB), hematocrit (HCT), prothrombin time (PT), arterial blood lacic acid (LA) and C-reactive protein (CRP) were monitored and recorded. Tissue oxygenation and hemodynamic profile were also analyzed. At T₁, T₂and T₃after fluid resuscitation, the heart rates of the patients in Group B were lower than those in Group A, whereas the average arterial pressure in Group B was significantly higher than that in Group A. Notably, significant decreases of HB and HCT were detected at T₁, T₂and T₃compared with T0 in Group A. In contrast, no significant difference was shown in detected HCT at T₂and T₃compared with T₀ in Group B, while the detected HB value was smaller. a statistically significant decrease of LA was detected at T₁, T₂and T₃in Group A and Group B compared with that at T₀. At T₂and T₃in Group A and Group B, a statistically significant increase of PT was detected compared with the beginning of resuscitation. At T₂and T₃after resuscitation, CRP in both Group A and Group B was significantly increased compared with that upon admission to hospital, and was lower in Group B than in Group A.

Rare A2ML1 variants confer susceptibility to otitis media

A duplication variant within the middle ear-specific gene A2ML1 cosegregates with otitis media in an indigenous Filipino pedigree (LOD score = 7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by 3 otitis-prone European-American and Hispanic-American children but is absent in non-otitis-prone children and >62,000 next-generation sequences. We identified seven additional A2ML1 variants in six otitis-prone children. Collectively, our studies support a role for A2ML1 in the pathophysiology of otitis media.

Collapsed haplotype pattern method for linkage analysis of next-generation sequence data

Recent advances in next-generation sequencing (NGS) make it possible to directly sequence genomes and exomes of individuals with Mendelian diseases and screen sequence data for causal variants. With the reduction in cost of NGS, DNA samples from entire families can be sequenced and linkage analysis can be performed directly using NGS data. Inspired by 'burden' tests, which are used for complex trait rare variant association studies, we developed the collapsed haplotype pattern (CHP) method for linkage analysis. Using data from several deafness genes we demonstrate that the CHP method is substantially more powerful than analyzing individual variants. Unlike applying NGS data filtering approaches, the CHP method provides statistical evidence of a gene's involvement in disease etiology and is also less likely to exclude causal variants in the presence of phenocopies and/or reduced penetrance. The CHP method was implemented in the SEQLinkage software package, which can perform linkage analysis on NGS data or can generate data compatible with many linkage analysis programs, reviving them for use in NGS era.

RNF213 rare variants in an ethnically diverse population with Moyamoya disease

BACKGROUND AND PURPOSE

Moyamoya disease (MMD) is a rare, genetically heterogeneous cerebrovascular disease resulting from occlusion of the distal internal carotid arteries. A variant in the Ring Finger 213 gene (RNF213), altering arginine at position 4810 (p.R4810K), is associated with MMD in Asian populations. However, there are a lack of data on the role of RNF213 in patients with MMD of additional ethnicities and diasporic Asian populations. We investigate the contribution of RNF213 alterations to MMD in an ethnically diverse population based in the United States.

METHODS

We initially sequenced RNF213 exons 43, 44, and 45 (encoding the eponymous RING finger domain) and exon 60 (encoding p.R4810K) in 86 ethnically diverse patients with MMD. Comprehensive exome sequencing data from 24 additional patients with MMD was then analyzed to identify RNF213 variants globally. Segregation of variants with MMD and other vascular diseases was assessed in families.

RESULTS

RNF213 p.R4810K was identified in 56% (9/16) of patients with MMD of Asian descent and not in 94 patients of non-Asian descent. 3.6% (4/110) of patients had variants in the exons encoding the RING finger domain. Seven additional variants were identified in 29% (7/24) of patients with MMD who underwent exome sequencing. Segregation analysis supported an association with MMD for 2 variants and a lack of association with disease for 1 variant.

CONCLUSIONS

These results confirm that alterations in RNF213 predispose patients of diverse ethnicities to MMD, and that the p.R4810K variant predisposes individuals of Asian descent in the United States to MMD.

Variant association tools for quality control and analysis of large-scale sequence and genotyping array data

Currently there is great interest in detecting associations between complex traits and rare variants. In this report, we describe Variant Association Tools (VAT) and the VAT pipeline, which implements best practices for rare-variant association studies. Highlights of VAT include variant-site and call-level quality control (QC), summary statistics, phenotype- and genotype-based sample selection, variant annotation, selection of variants for association analysis, and a collection of rare-variant association methods for analyzing qualitative and quantitative traits. The association testing framework for VAT is regression based, which readily allows for flexible construction of association models with multiple covariates and weighting themes based on allele frequencies or predicted functionality. Additionally, pathway analyses, conditional analyses, and analyses of gene-gene and gene-environment interactions can be performed. VAT is capable of rapidly scanning through data by using multi-process computation, adaptive permutation, and simultaneously conducting association analysis via multiple methods. Results are available in text or graphic file formats and additionally can be output to relational databases for further annotation and filtering. An interface to R language also facilitates user implementation of novel association methods. The VAT's data QC and association-analysis pipeline can be applied to sequence, imputed, and genotyping array, e.g., "exome chip," data, providing a reliable and reproducible computational environment in which to analyze small- to large-scale studies with data from the latest genotyping and sequencing technologies. Application of the VAT pipeline is demonstrated through analysis of data from the 1000 Genomes project.

Power analysis and sample size estimation for sequence-based association studies

MOTIVATION

Statistical methods have been developed to test for complex trait rare variant (RV) associations, in which variants are aggregated across a region, which is typically a gene. Power analysis and sample size estimation for sequence-based RV association studies are challenging because of the necessity to realistically model the underlying allelic architecture of complex diseases within a suitable analytical framework to assess the performance of a variety of RV association methods in an unbiased manner.

SUMMARY

We developed SEQPower, a software package to perform statistical power analysis for sequence-based association data under a variety of genetic variant and disease phenotype models. It aids epidemiologists in determining the best study design, sample size and statistical tests for sequence-based association studies. It also provides biostatisticians with a platform to fairly compare RV association methods and to validate and assess novel association tests.

AVAILABILITY AND IMPLEMENTATION

The SEQPower program, source code, multi-platform executables, documentation, list of association tests, examples and tutorials are available at http://bioinformatics.org/spower.

Updated morphology, histopathology and molecular phylogeny of Myxobolus hearti, cardiac myxosporea in gibel carp, Carassius gibelio (Bloch)

The original description of Myxobolus hearti is supplemented with new data on spore morphology, histopathology and molecular phylogeny. Myxobolus hearti are found in the heart ventricle of the gibel carp, Carassius gibelio (Bloch), where they form whitish oval or irregularly shaped plasmodia. Mature spores are oval or shortly ellipsoidal in frontal view, lemon-shaped in sutural view and eye-shaped in apical view. The spores are 14.12 ± 0.35 (13.6-15) μm long (mean ± SD), 11.85 ± 0.34 ± 0.36 (11-12) μm wide and 7.32 ± 0.36 (7-8) μm thick. The two polar capsules are equal in size, 6.11 ± 0.29 (6-7) μm long and 3.89 ± 0.31(3-4) μm wide, and are long pyriform in shape. Polar filaments have six or seven coils situated perpendicular to the longitudinal axis of the polar capsules. Histopathology indicates that the plasmodia are encased by the host connective tissue, and no inflammatory responses are found in the heart ventricles. Phylogenetic analysis based on the 18S small-subunit ribosomal DNA sequences indicates that M. hearti is, genetically, most similar to Henneguya doneci, a gill-infecting species.

Tuning the surface charge properties of epitaxial InN nanowires

We have investigated the correlated surface electronic and optical properties of [0001]-oriented epitaxial InN nanowires grown directly on silicon. By dramatically improving the epitaxial growth process, we have achieved, for the first time, intrinsic InN both within the bulk and at nonpolar InN surfaces. The near-surface Fermi-level was measured to be ∼0.55 eV above the valence band maximum for undoped InN nanowires, suggesting the absence of surface electron accumulation and Fermi-level pinning. This result is in direct contrast to the problematic degenerate two-dimensional electron gas universally observed on grown surfaces of n-type degenerate InN. We have further demonstrated that the surface charge properties of InN nanowires, including the formation of two-dimensional electron gas and the optical emission characteristics can be precisely tuned through controlled n-type doping. At relatively high doping levels in this study, the near-surface Fermi-level was found to be pinned at ∼0.95-1.3 eV above the valence band maximum. Through these trends, well captured by the effective mass and ab initio materials modeling, we have unambiguously identified the definitive role of surface doping in tuning the surface charge properties of InN.

Effects of disulfide bridges glycoprotein E1 on fusogenic activity of Rubella virus

Rubella virus (RUBV) infects cells via an acid-triggered membrane fusion process. RUBV virions contain two cysteine-rich glycoproteins, E2 and E1. The latter is believed to be involved in the membrane fusion. Using a recombinant plasmid containing RUBV E1 and E2, 11 of total 20 cysteines present in the ectodomain of wild type E1 were mutated to test their role in the fusion via the formation of disulfide bridges. The recombinant plasmids containing mutated E1 (Cys2-Cys20) or wild type (wt) E1 were expressed in BHK-21 cells. Their fusogenic and hemadsorption activities in addition to a potential of cell surface expression of E1 and E2 were assayed. The results showed that the fusogenic activity was lost in all tested mutants, while the hemadsorption activity and cell surface expression potential were affected differently in individual mutants. Since only the Cys5 and Cys8 mutations led to a reduction of both hemadsorption and cell surface expression, we assume that these mutations prevented the formation of the disulfide bridge, what led to a misfolding of E1 and consequently to a failure of recognition of E1 by E2. In conclusion, the disulfide bridges disrupted in all the tested mutants appear essential for the cell fusion, while only the disulfide bridge C(5)-C(8) seems to be crucial for the transport of E1 and E2 in the cell.

Elastic moduli of faceted aluminum nitride nanotubes measured by contact resonance atomic force microscopy

A new methodology for determining the radial elastic modulus of a one-dimensional nanostructure laid on a substrate has been developed. The methodology consists of the combination of contact resonance atomic force microscopy (AFM) with finite element analysis, and we illustrate it for the case of faceted AlN nanotubes with triangular cross-sections. By making precision measurements of the resonance frequencies of the AFM cantilever-probe first in air and then in contact with the AlN nanotubes, we determine the contact stiffness at different locations on the nanotubes, i.e. on edges, inner surfaces, and outer facets. From the contact stiffness we have extracted the indentation modulus and found that this modulus depends strongly on the apex angle of the nanotube, varying from 250 to 400 GPa for indentation on the edges of the nanotubes investigated.

A surface-tailored, purely electronic, mott metal-to-insulator transition

Mott transitions, which are metal-insulator transitions (MITs) driven by electron-electron interactions, are usually accompanied in bulk by structural phase transitions. In the layered perovskite Ca(1.9)Sr(0.1)RuO4, such a first-order Mott MIT occurs in the bulk at a temperature of 154 kelvin on cooling. In contrast, at the surface, an unusual inherent Mott MIT is observed at 130 kelvin, also on cooling but without a simultaneous lattice distortion. The broken translational symmetry at the surface causes a compressional stress that results in a 150% increase in the buckling of the Ca/Sr-O surface plane as compared to the bulk. The Ca/Sr ions are pulled toward the bulk, which stabilizes a phase more amenable to a Mott insulator ground state than does the bulk structure and also energetically prohibits the structural transition that accompanies the bulk MIT.

Phylogeny of freshwater parasitic copepods in the Ergasilidae (Copepoda: Poecilostomatoida) based on 18S and 28S rDNA sequences

The phylogenetic relationships among the Ergasilidae genera are poorly understood. In this study, 14 species from four genera in the Ergasilidae including Sinergasilus, Ergasilus, Pseudergasilus, and Paraergasilus were collected in China, and their phylogenetic relationships were examined using neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods based on partial sequences of 18S and 28S ribosomal deoxyribonucleic acid, respectively. All the analyses suggest that the Sinergasilus and Paraergasilus are both monophyletic, but the Ergasilus is polyphyletic rather than monophyletic. Considering the relationships among the four genera, the phylogenetic analyses and subsequent hypothesis tests all suggest that Pseudergasilus clustered with some Ergasilus species may have a closer relationship with Sinergasilus rather than with Paraergasilus. It is proposed that the Sinergasilus and the Pseudergasilus species might have evolved from Ergasilus species.

Population dynamics and maturation cycle of Camallanus cotti (Nematoda: Camallanidae) in the Chinese hooksnout carp Opsariichthys bidens (Osteichthyes: Cyprinidae) from a reservoir in China

The seasonal population dynamics and maturation cycle of the nematode Camallanus cotti in the posterior intestine of Chinese hooksnout carp Opsariichthys bidens have been studied in the Danjiangkou Reservoir of the Hubei Province in central China from September 2004 to November 2005. The overall prevalence, mean abundance and intensity of C. cotti among fish sampled (n=700 fish) were 47%, 2.29+/-12.38 (+/-S.D.) and 1-307 (average 4.89+/-17.74), respectively. The overall sexual ratio of female to male nematodes (excluding L3 and L4 juveniles) was 1.17:1. Statistical results showed weakly positive correlations between fish length and the number of nematodes per host. The dynamics of infection of the nematode exhibited significant seasonal pattern in changes in mean abundance. A similar pattern was found for changes in nematode prevalence, although this was not statistically significant. Higher levels of infection were observed among fish sampled in summer months and the lower in the winter. Neither the prevalence nor the abundance of the parasite was significantly different between male and female hosts. The pattern of frequency distribution of the parasite in the host was found to be over-dispersed throughout the sampling period. In addition, studies on the development and maturation of the parasite in O. bidens revealed that development (maturation), recruitment of the next generation, and reproduction may be continuous year-round, although reproduction may peak during the winter.

Phylogeny of diplozoids in five genera of the subfamily Diplozoinae Palombi, 1949 as inferred from ITS-2 rDNA sequences

The phylogenetic relationship of 5 genera, i.e. Diplozoon Nordmann, 1832, Paradiplozoon Achmerov, 1974, Inustiatus Khotenovsky, 1978, Sindiplozoon Khotenovsky, 1981, and Eudiplozoon Khotenovsky, 1985 in the subfamily Diplozoinae Palombi, 1949 (Monogenea, Polyopisthocotylea) was inferred from rDNA ITS-2 region using neighbour-joining (NJ), maximum likelihood (ML) and Bayesian methods. The phylogenetic trees produced by using NJ, ML and Bayesian methods exhibit essentially the same topology. Surprisingly, freshwater species of Paradiplozoon from Europe clustered together with species of Diplozoon, but separated from Chinese Paradiplozoon species. The results of molecular phylogeny and lower level of divergence (4.1-15.7%) in ITS-2 rDNA among Paradiplozoon from Europe and Diplozoon and, on the other hand, high level of divergence (45.3-53.7%) among Paradiplozoon species from Europe and China might indicate the non-monophyletic origin of the genus Paradiplozoon. Also, the generic status of European Paradiplozoon needs to be revised. The species of Paradiplozoon in China is a basal group in Diplozoinae as revealed by NJ and Bayesian methods, and Sindiplozoon appears to be closely related to European Paradiplozoon and Diplozoon with their relationship to Eudiplozoon and Inustiatus being unresolved.

Photoassisted Charge Behavior of Hydrogen Storage Alloy-TiO2/Pt Electrodes

The photoassisted charge behavior of hydrogen storage alloy modified with TiO2/Pt nanocomposites (HSA-TiO2/Pt electrode) was investigated. The HSA-TiO2/Pt electrode can be photocharged under current. The mechanism of photoassisted behavior of the HSA-TiO2/Pt electrode was explained through the results of cyclic voltammogram and impedance measurements of the HSA-TiO2/Pt electrode. Upon illumination, the photogenerated electrons can charge the electrode, but the photogenerated holes may oxidize the hydrogen storage alloy to form a layer of metal oxide. Because the current could keep the electrode active, the H atoms produced by photogenerated electrons diffused to the hydrogen storage alloy and a metal hydride formed. The electrode delivered a higher discharge capacity due to the assistance of photocharge.

Genetic differentiation in populations of the cestode Bothriocephalus acheilognathi (Cestoda, Pseudophyllidea) as revealed by eight microsatellite markers

The genetic structure of populations of the fish cestode, Bothriocephalus acheilognathi collected from Bailianhe Reservoir (BLH), Changshou (CSH) and Liangzi (LZH) Lakes was investigated by using 8 microsatellite loci. A total of 108 adult worms were genotyped at each of the 8 loci. For the 3 populations, the mean number of alleles per locus ranged from 2.38 to 5.5, and the mean expected heterozygosity ranged from 0.432 to 0.559. The average polymorphic information content (PIC) was from 0.384 to 0.492. The significant Fis values indicated non-random mating within LZH and BLH populations. On the other hand, when samples were further classified into subpopulations at the level of host fish species, no or little heterozygote deficiency was detected at most loci, showing that cross-fertilization, predominantly, but not exclusively, must have occurred within the subpopulations. Microsatellite markers also revealed an unexpected high level of genetic differentiation, as measured by R(st) and N(m) values or by delta(u)2 genetic distance among subpopulations from different hosts. Factors influencing the population genetic structure and the parasite host specificity are discussed.

Is the genus Digramma synonymous to the genus Ligula (Cestoda: Pseudophyllidea)? Evidence from ITS and 5' end 28S rDNA sequences

The genus Digramma (Cestoda: Pseudophyllidea) described by Cholodkovsky in 1915 differs from the genus Ligula only by the number of the reproductive organs per proglottis. However, the occurrence of transitional forms in Digramma raises much confusion concerning its generic validity. In the present study, cestodes previously designated as Digramma and Ligula were collected from lakes in the lower and middle reaches of the Yangtze River, and also from Qinghai Lake on Qingzang plateau, China. The entire internal transcribed spacer of the ribosomal DNA (ITS rDNA) and 5' end of 28S rDNA were compared between the Digramma and Ligula specimens. The low level of nucleotide variation between the two genera may imply that cestodes in the genus Digramma are paraphyletic to the Ligula genus, and Digramma is a synonym of Ligula. However, whether previously identified Digramma cestodes represent different species in the genus Ligula requires further investigation.

Molecular variation of Bothriocephalus acheilognathi Yamaguti, 1934 (Cestoda: Pseudophyllidea) in different fish host species based on ITS rDNA sequences

The molecular variation in Bothriocephalus acheilognathi Yamaguti, 1934 from 11 species of freshwater fish collected in Australia, China, the Czech Republic, England and Hawaii was investigated by determining the nucleotide sequences of the internal transcribed spacer region. The length of the first and second internal transcribed spacer sequences of multiple individuals ranged from 553 to 571 bp and 553 to 615 bp, and the G + C content from 53.1 to 53.5%. The percentage sequence divergence varied between 0 and 0.9% in the ITS1 and 0 and 6.6% in the ITS2, respectively, indicating the occurrence of intraspecific variation. It is demonstrated that the fragment length variation resulted primarily from microsatellite polymorphisms present in the ITS region, especially in the ITS2 region. Phylogenetic analyses revealed that B. acheilognathi examined in this study consisted of three closely related genotypes with certain degrees of host-specificity, and the genotype representing isolates from Cyprinus carpio L. was the most common and diverse form within the species B. acheilognathi.

Selection for resistance to macrocyclic lactones by Haemonchus contortus in sheep

An anthelmintic-sensitive Haemonchus contortus strain was selected for moxidectin and ivermectin resistance concurrently for 22 generations. Treatment with 0.002 mg moxidectin/kg BW or 0.02 mg ivermectin/kg BW produced >99% efficacy against the susceptible parent strain passaged for 22 generations without any anthelmintic exposure. However, to obtain similar efficacy the moxidectin-selected and the ivermectin-selected strains of H. contortus required 0.05 mg moxidectin/kg BW or 0.4 mg ivermectin/kg BW. These results indicate that development of resistance to one macrocyclic lactone, simultaneously results in resistance to another macrocyclic lactone. However, rates of resistance development differ between compounds and occurs more slowly with moxidectin than with ivermectin.

Activity of an injectable, sustained-release formulation of moxidectin administered prophylactically to mixed-breed dogs to prevent infection with Dirofilaria immitis

OBJECTIVE

To test the ability of a single injection of a sustained-release formulation of moxidectin (moxidectin SR) to protect dogs against heartworm infection for 180 days after inoculation with infective third-stage larvae (L3) of Dirofilaria immitis.

ANIMALS

32 adult mixed-breed dogs.

PROCEDURE

Dogs were allocated to 4 groups on the basis of weight and sex. Dogs were injected SC with saline (0.9% NaCl) solution or moxidectin SR at the rate of 0.06, 0.17, or 0.5 mg/kg of body weight (day 0). Each dog was inoculated SC with 50 D immitis L3 180 days later. On days 330 and 331, dogs were euthanatized. The heart, lungs, and thoracic cavity were examined, and number and sex of heartworms were determined.

RESULTS

A mean of 35.9 heartworms was recovered from untreated control dogs. Fourteen worms were recovered from 1 of 8 dogs given moxidectin SR at the lowest dosage, and none of the dogs in the 2 highest moxidectin treatment groups were infected. Small barely palpable granulomas were detected at injection sites of moxidectin-treated dogs. Frequency and size of granulomas were positively correlated with dose of moxidectin administered.

CONCLUSIONS AND CLINICAL RELEVANCE

A single dose of moxidectin SR at a dosage as low as 0.17 mg/kg can safely and reliably confer complete protection against infection after challenge-exposure with D. immitis L3, and protection lasts for at least 180 days. This mode of prophylactic treatment against infection with heartworms effectively eliminates failure of prophylaxis that results from erratic administration of medications designed for monthly administration.

Design, synthesis, and structural analysis of influenza neuraminidase inhibitors containing pyrrolidine cores

The discovery of (+/-)-(2S,3R,4R)-2-(trifluoroacetamido)methyl-3-amino-1-(N'-ethyl-N'-isopropylcarbamyl)pyrrolidine-4-carboxylic acid (A-192558, 20e) as a potent inhibitor of influenza neuraminidase (NA) is described. Efficient syntheses of two core structures, cis-3-(allyloxycarbonyl)amino-1-(9'-fluorenylmethoxycarbonyl)pyrrolidine-4-carboxylic acid (7) and tert-butyl (+/-)-(2S,3R,4R)-2-aminomethyl-3-bis(tert-butyloxycarbonyl)amino-1-(N'-ethyl-N'-isopropylcarbamyl)pyrrolidine-4-carboxylate (18b), were developed. Starting with these core structures and using available structural information of the NA active site as the guide, analogues were synthesized in both the tri- and tetrasubstituted pyrrolidine series by means of high-throughput parallel synthesis in solid or solution phase for expeditious SAR. These studies accelerated the identification of (+/-)-(2S,3R,4R)-2-(trifluoroacetamido)methyl-3-amino-1-(N-ethyl-N-isopropylcarbamyl)pyrrolidine-4-carboxylate (20e, A-192558) as the most potent NA inhibitor in this series (IC50 = 0.2 microM against NA A and 8 microM against NA B). The X-ray crystallographic structure of A-192558 bound to NA revealed the predicted interaction of the carboxylic group with the positively charged pocket (Arg118, Arg292, Arg371) and interaction of the trifluoroacetamino residue with the hydrophobic pocket (Ile222, Trp178) of the enzyme active site. Surprisingly, the ethyl and isopropyl groups of the urea functionality induced a conformational change of Glu276, turning the Glu276/Glu277 hydrophilic pocket, which normally accommodates the triglycerol side chain of substrate sialic acid, into an induced hydrophobic pocket.

Synthesis of 2-substituted (+/-)-(2r,3r,5r)-tetrahydrofuran-3,5-dicarboxylic acid derivatives

An efficient synthesis of 2-substituted (+/-)-(2R,3R,5R)-tetrahydrofuran-3,5-dicarboxylic acid derivatives has been developed. Starting from 5-norborne-2-ol, the key intermediate (+/-)-methyl 5,6-exo,exo-(isopropylidenedioxy)-2-oxabicyclo[2.2.1]heptane-3-exo-carboxylate (15) was synthesized in an efficient six-step sequence. The key transformation is the base-catalyzed methanolysis-rearrangement of (+/-)-6,7-exo,exo-(isopropylidenedioxy)-4-exo-iodo-2-oxabicyclo[3.2.1]octan-3-one (14). Further manipulation of the 3-substituent of (+/-)-methyl 5,6-exo,exo-(isopropylidenedioxy)-2-oxabicyclo[2.2.1]heptane-3-exo-carboxylate (15) followed by deprotection of the diol moiety and ring opening catalyzed by RuCl(3)/NaIO(4) gave the title compounds in good yield.

Seasonal occurrence of Dollfustrema vaneyi (Digenea: Bucephalidae) metacercariae in the bullhead catfish Pseudobagrus fulvidraco in a reservoir in China

The seasonal population dynamics of metacercariae of the bucephalid Dollfustrema vaneyi (Tseng, 1930) Echmann, 1934 in the bullhead catfish Pseudobagrus fulvidraco (Richardson) were investigated in Jiangkou reservoir, Jiangxi Province, east China, during the period from April 1990 to August 1991. In total, 523 fish were obtained, and the overall prevalence of the metacercariae was 89.87% and mean abundance 136.25 +/- 308.09 (mean +/- SD). A pattern of seasonal changes in prevalence and mean abundance was observed, with higher levels of metacercariae infection in late spring and summer. An analysis of the distribution of D. vaneyi in different organs of P. fulvidraco suggested that the eyes might be a suitable location for the parasite. Furthermore, the possible role of metacercariae in bullhead catfish was discussed in relation to the life cycle of this parasite.

Occurrence of Bothriocephalus acheilognathi in cyprinid fish from three lakes in the flood plain of the Yangtze River, China

Cyprinid fish, Hemiculter leucisculus, Cultrichthys erythropterus and Culter dabryi, were sampled from Liangzi, Honghu and Tangxun lakes in the flood plain of the Yangtze River. The cestode Bothriocephalus acheilognathi Yamaguti, 1934 was found in the 3 lakes, but C. erythropterus sampled from Liangzi lake was found uninfected due probably to the small sample size. Findings of the cestode in the 3 lakes represent the first record of the parasite in the flood plain of the Yangtze River, indicating that B. acheilognathi may be distributed much wider in China than previously recognized.

Th1 and Th2 deviation of myelin-autoreactive T cells by altered peptide ligands is associated with reciprocal regulation of Lck, Fyn, and ZAP-70

Th0 clones recognizing an immunodominant peptide of myelin basic protein (residues 83-99) were derived from patients with multiple sclerosis. We demonstrate that analogue peptides with alanine substitution at Val86 and His88 had a unique partial agonistic property in inducing Th0 -->Th1 and Th0 -->Th2 deviation of the myelin basic protein-reactive T cell clones, respectively. Th0 to Th1 deviation induced by peptide 86V-->A correlated with up-regulation of Fyn and ZAP-70 kinase activities. Conversely, Th0 to Th2 deviation induced by peptide 88H-->A was associated with complete failure to activate Fyn and ZAP-70 kinases. The observed Th1 and Th2 shift also correlated, to a lesser extent, with Lck kinase activity that was down-regulated with Th1 deviation and increased with Th2 deviation in some T cell clones. We demonstrated that the Th1 and Th2 shift induced by the analogue peptides was a reversible process, as the T cell clones previously exposed to either 86V-->A or 88H-->A peptide could revert to an opposite phenotype when rechallenged reciprocally with a different analogue peptide. The study has important implications in our understanding of regulation of TCR-associated tyrosine kinases by altered peptide ligands and its role in cytokine regulation of autoreactive T cells.

Decreased ivermectin and moxidectin sensitivity in Haemonchus contortus selected with moxidectin over 14 generations

Ivermectin resistance in the nematode Haemonchus contortus has been reported in many parts of the world and many ivermectin resistant isolates have been found to have reduced sensitivity to moxidectin. However, it is unclear whether parasites that are selected with moxidectin would demonstrate reduced sensitivity to ivermectin. In this study, the effects of moxidectin and ivermectin on an unselected strain and a strain of H. contortus derived from the unselected strain but selected over 14 generations with moxidectin, were compared in jirds. The recovery of adult worms and fourth stage (L4) larvae following treatment were compared between strains and anthelmintics. Moxidectin-selected H. contortus showed reduced sensitivity to ivermectin as well as to moxidectin. Doses of 0.1 mg/kg of moxidectin and 0.4 mg/kg of ivermectin were necessary to obtain an efficacy of 95% or above against the moxidectin-selected strain of H. contortus compared with 0.025 mg/kg for moxidectin and 0.1 mg/kg for ivermectin required for a similar efficacy in the unselected strain.

Purification and characterization of the yeast glycosylphosphatidylinositol-anchored, monobasic-specific aspartyl protease yapsin 2 (Mkc7p)

The Saccharomyces cerevisiae YPS2 (formerly MKC7) gene product is a glycosylphosphatidylinositol-linked aspartyl protease that functions as a yeast secretase. Here, the glycosylphosphatidylinositol-linked form of yapsin 2 (Mkc7p) was purified to homogeneity from the membrane fraction of an overexpressing yeast strain. Purified yapsin 2 migrated diffusely in SDS-polyacrylamide gel electrophoresis (molecular mass approximately 200 kDa), suggesting extensive, heterogeneous glycosylation. Studies using internally quenched fluorogenic peptide substrates revealed cleavage by the enzyme carboxyl to Lys or Arg. No cleavage was seen when both Lys and Arg were absent. No significant enhancement was seen with multiple basic residues. However, cleavage always occurred carboxyl to the most COOH-terminal basic residue. V(max)/K(m) was insensitive to P(2) and P(3) residues except that Pro at P(2) blocked cleavage entirely. These results suggest that yapsin 2 is a monobasic amino acid-specific protease that requires a basic residue at P(1) and excludes basic residues from P(1)'. The pH dependence of V(max)/K(m) for a substrate containing a pro-alpha factor cleavage site was bell-shaped, with a maximum near pH 4.0. However, V(max)/K(m) for a substrate mimicking the alpha-secretase site in human beta amyloid precursor protein was optimal near pH 6.0, consistent with cleavage of beta amyloid precursor protein by yapsin 2 when expressed in yeast.

Gating of cystic fibrosis transmembrane conductance regulator chloride channels by adenosine triphosphate hydrolysis. Quantitative analysis of a cyclic gating scheme

Gating of the cystic fibrosis transmembrane conductance regulator (CFTR) involves a coordinated action of ATP on two nucleotide binding domains (NBD1 and NBD2). Previous studies using nonhydrolyzable ATP analogues and NBD mutant CFTR have suggested that nucleotide hydrolysis at NBD1 is required for opening of the channel, while hydrolysis of nucleotides at NBD2 controls channel closing. We studied ATP-dependent gating of CFTR in excised inside-out patches from stably transfected NIH3T3 cells. Single channel kinetics of CFTR gating at different [ATP] were analyzed. The closed time constant (tauc) decreased with increasing [ATP] to a minimum value of approximately 0.43 s at [ATP] >1.00 mM. The open time constant (tauo) increased with increasing [ATP] with a minimal tauo of approximately 260 ms. Kinetic analysis of K1250A-CFTR, a mutant that abolishes ATP hydrolysis at NBD2, reveals the presence of two open states. A short open state with a time constant of approximately 250 ms is dominant at low ATP concentrations (10 microM) and a much longer open state with a time constant of approximately 3 min is present at millimolar ATP. These data suggest that nucleotide binding and hydrolysis at NBD1 is coupled to channel opening and that the channel can close without nucleotide interaction with NBD2. A quantitative cyclic gating scheme with microscopic irreversibility was constructed based on the kinetic parameters derived from single-channel analysis. The estimated values of the kinetic parameters suggest that NBD1 and NBD2 are neither functionally nor biochemically equivalent.

Inhibition of 3C protease from human rhinovirus strain 1B by peptidyl bromomethylketonehydrazides

The gene coding for the 3C protease from human rhinovirus strain 1B was efficiently expressed in an Escherichia coli strain which also overexpressed the rare argU tRNA. The protease was isolated from inclusion bodies, refolded, and exhibited a kcat/Km = 3280 M-1 s-1 using an internally quenched peptidyl fluorogenic substrate. This continuous fluorogenic assay was used to measure the kinetics of 3C protease inhibition by several conventional peptidyl chloromethylketones as well as a novel series of compounds, the bromomethylketonehydrazides. Compounds containing the bromomethylketonehydrazide backbone and a glutamine-like side chain at the P1 position were potent, time-dependent inhibitors of rhinovirus 3C protease with kinact/Kinact values as high as 23,400 M-1 s-1. The inhibitory activity of compounds containing modified P1 side chains suggests that the interactions between the P1 carboxamide group and the 3C protease contributes at least 30-fold to the kinact/Kinact rate constants for bromomethylketonehydrazide inhibition of 3C protease. Electrospray ionization mass spectrometry measurements of the molecular weights of native and inhibited 3C protease have established an inhibitory mechanism involving formation of a covalent adduct between the enzyme and the inhibitor with the loss of a bromide ion from the bromomethylketonehydrazide. Tryptic digestion of bromomethylketonehydrazide-inhibited 3C protease established adduct formation to a peptide corresponding to residues 145-154, a region which contains the active site cysteine-148 residue. The bromomethylketonehydrazides were fairly weak inhibitors of chymotrypsin, human elastase, and cathepsin B and several of these compounds also showed evidence for inhibition of human rhinovirus 1B replication in cell culture.

[Synthesis of adenine derivatives and their activities against herpes virus in vitro]

A series of 9-(N4-substituted acetaldehyde thiosemicarbazone) adenines were synthesized and evaluated for antiherpes virus activity. Compounds 4a-l were prepared by condensation of 9-(acetaldehyde) adenine(6) and the corresponding N4-substituted thiosemicarbazides (10). The antiviral effects of all compounds 4a-l were tested in vitro in primary rabbit kidney cell cultures infected with herpes simplex virus type 1 (HSV-1) and varicella-herpes zoster virus (VZV), and in primary human embryo cell cultures infected with herpes simplex virus type 2 (HSV-2). The results showed that the minimum inhibitory concentrations (MIC) of 4e and 4f for HSV-1 and VZV were 20, 40, 20 and 20 micrograms.ml-1, respectively, and other compounds were 200 micrograms.ml-1. For HSV-2, the MIC of all tested compounds were 300 micrograms.ml-1. We also evaluated the antiherpetic effect of 4e (and 4f) by combination with acyclovir (ACV) in the ratio of 1:1 in vitro. The MIC of the combined compounds were 2 micrograms.ml-1 for 4e and 6 micrograms.ml-1 for 4f, while their minimum cytotoxicities (MCC) in the cell were markedly reduced compared with the individual compounds.

Involvement of cell surface glycosyl-phosphatidylinositol-linked aspartyl proteases in alpha-secretase-type cleavage and ectodomain solubilization of human Alzheimer beta-amyloid precursor protein in yeast

Human beta-amyloid precursor protein (APP) introduced into yeast undergoes alpha-secretase-type cleavage, suggesting that yeast have alpha-secretase-like protease(s). Here we report that two structurally and functionally related glycosyl-phosphatidylinositol-linked yeast aspartyl proteases, Mkc7p and Yap3p (collectively termed yapsin), are responsible for alpha-secretase-type cleavage of APP expressed in yeast, resulting in release of soluble APP into the extracellular space. Disruption of MKC7 and YAP3 in a vacuolar protease-deficient strain abolished this APP cleavage/release, and APP cleavage/release could be restored by introduction of MKC7 or YAP3 on a single copy plasmid. Purified Mkc7p cleaved an internally quenched fluorogenic APP peptide substrate at the alpha-secretase cleavage site. Measurement of proteolytic activity either in yeast homogenates or on the yeast cell surface revealed that most Mkc7p and Yap3p activities were localized at the cell surface. These results establish a molecular basis for alpha-secretase-type cleavage in yeast and support the generally held concept that alpha-secretase cleavage of APP occurs at the cell surface.

[Saline load test for diet instruction in patients with essential hypertension]

The saline loading test was performed in 53 hospitalized patients with essential hypertension. According to Sullivan's standard, 22 of the 53 patients were salt-sensitive (SS), 31 were salt-resistant (SR). The blood pressure in two groups of patients response to salt restriction diet were compared. The results showed that the decrease in level of blood pressure in SS group was higher than that in SR group after salt restriction diet (SS, 23.2 +/- 1.9/14.0 +/- 1.4 vs 21.4 +/- 1.7/13.1 +/- 1.3kPa, P < 0.01-0.05; SR, 23.4 +/- 2.0/14.1 +/- 1.4 vs 23.1 +/- 1.8/13.8 +/- 1.4kPa, P > 0.05). It was concluded that salt restriction diet was stressed on SS than SR patients.

Internally consistent libraries of fluorogenic substrates demonstrate that Kex2 protease specificity is generated by multiple mechanisms

Kex2 protease from the yeast Saccharomyces cerevisiae is the prototype for a family of eukaryotic proprotein processing proteases. To clarify understanding of the interactions responsible for substrate recognition in this family of enzymes, we have carried out a systematic examination of Kex2 substrate specificity using internally consistent sets of substrates having substitutions at only one or two positions. We examined Kex2 sequence recognition for residues at P3, P2, and P1 using two types of fluorogenic peptide substrates, peptidyl-methylcoumarinamides and internally quenched substrates in which cleavage occurs at an actual peptide bond. Kinetic analysis of the two sets of substrates gave comparable data on specificity at these three positions. For the best substrate sequences, high catalytic constants (kCM/KM) of (2-5) x 10(7) M-1 s-1 were seen for cleavage of both peptidyl-methylcoumarinamides and peptide bonds. While no evidence for positive interactions with the P3 residue emerged, Kex2 was found to discriminate against at least one residue Asp. at this position. Specificity at P2 was shown to rely primarily on recognition of a positive charge, although steric constraints on the P2 side chain were also apparent. Kex2 was demonstrated to be exquisitely selective for Arg at P1. Substitutions with similar charge (Lys, ornithine) or similar hydrogen-bonding capability (citrulline) do not confer efficient catalysis. Comparison of otherwise identical substrates having either Arg or citrulline at P1 showed that the positive charge of the Arg guanidinium group stabilizes the transition state by approximately 6.8 kcal/mol.

Efficacy of moxidectin pour-on against gastrointestinal nematodes and Dictyocaulus viviparus in cattle

Twenty crossbred beef heifer calves were used for an efficacy evaluation of 0.5% moxidectin pour-on against gastrointestinal nematodes and Dictyocaulus viviparus. The latter parasite and Bunostomum phlebotomum were the target species. The calves were exposed to natural infection on pasture from late September to December 22. Additionally, all calves were experimentally infected with B. phlebotomum at 71 and 29 days before treatment and with D. viviparus at 29 days before treatment. The 20 calves were randomly allocated into two groups of ten, based on presence of patent lungworm and hookworm infections on days -6 and -1. Treatments were as follows: Group A, moxidectin 0.5% pour-on (PO) at 500 micrograms kg-1 BW; Group B, moxidectin vehicle (controls) by PO application. General strongyle and hookworm egg counts and lungworm larval counts were reduced to zero at 13 days after moxidectin treatment; treatment effect was significant (P < 0.05) only for the strongyle and hookworm counts. Percentage reduction for adult hookworms and mature-immature adult lungworms was 100.0 and also for adults and L4 Haemonchus placei and Ostertagia ostertagi and Trichostrongylus axei adults, adult males of Cooperia pectinata and C. spatulata, and Oesophagostomum radiatum adults. Efficacy values for C. punctata adult males, Cooperia spp. adult females, and Cooperia spp. L4 were > 99.9%, > 99.9%, and 92.4%, respectively. All efficacy values were significant (alpha = 0.05, 1-sided) except for Cooperia spp. L4.

Synthetic chemical diversity: solid phase synthesis of libraries of C2 symmetric inhibitors of HIV protease containing diamino diol and diamino alcohol cores

Solid phase synthesis of non-oligomeric organic compounds has been pursued for high-efficiency generation of large numbers of structurally diverse compounds for drug screening. Known as chemical diversity libraries or combinatorial libraries (when the synthesis is carried out in a combinatorial fashion), these compounds can be used for de novo discovery of drug leads or for expedient structure--activity relationship (SAR) studies. To expand the scope of solid phase synthesis beyond the capability of the traditional method of solid phase synthesis for peptides, a strategy was developed for bi-directional solid phase synthesis starting with diamino alcohol or diamino diol core structures. The strategy relies on using bifunctional linkers to modify the core structures, simultaneously protecting the hydroxyl group or the diol moiety of the core and providing a carboxyl group for attachment of the modified cores to a solid support. The two NH2 groups of the modified cores attached to the solid support were then deprotected and reacted with a wide variety of amine-reactive reagents (carboxylic acids, sulfonyl chlorides, isocyanates, chloroformates, etc.) to extend the molecule in both directions. This strategy was successfully applied to automated parallel synthesis of a library of C2 symmetric inhibitors of HIV protease containing the known symmetry-based diamino diol and diamino alcohol core structures, thus enabling expedient access of large numbers of analogs in this series. A library of over 300 discrete compounds was synthesized using this methodology in order to identify potent (IC50 < 100 nM) HIV protease inhibitors with reduced size. This paper describes the technical aspects of this technology.

Cathepsin D from Alzheimer's-diseased and normal brains

An acid protease activity from human brain was found to cleave a fluorogenic peptide substrate encompassing the amino terminus of Alzheimer's amyloid-beta peptide (A beta). The protease was isolated and determined to be cathepsin D based on chromatographic, immunological, and enzymatic data. Analysis of the cleavage sites indicated that cathepsin D hydrolyzed the methionine--aspartate bond generating the in vivo amino terminus of A beta. These data suggested that cathepsin D could be involved in amyloidogenic processing of the amyloid precursor protein. Consequently, cathepsin D from both Alzheimer's-diseased and control brains was compared to determine whether there were any differences which could account for an increase in A beta production in Alzheimer's disease. No differences were detected in isoform composition or tissue content of cathepsin D as measured by 2-D IEF-SDS-PAGE. Enzymological characterization of brain cathepsin D demonstrated that it could undergo a previously undescribed pH-dependent reversible activation. However, that activation appeared identical for both AD and normal brain enzymes. These data demonstrate that concentration, isoform distribution, and several enzymological characteristics of cathepsin D are not distinguishable between AD and normal brain. The pH dependence of cathepsin D activity suggests, however, that its intracellular localization may be important in considering the potential role of cathepsin D in Alzheimer's disease.

Evidence against a role for the Kunitz domain in amyloidogenic and secretory processing of the amyloid precursor protein

The effect of the Kunitz proteinase inhibitor (KPI) on potential beta-amyloid precursor protein (beta PP)-processing activities from control and Alzheimer's disease (AD) brains was examined using fluorogenic substrates designed to mimic the secretory and amyloidogenic cleavages in beta PP. In addition, the level of secretion of KPI-containing beta PP751 and KPI-lacking beta PP695 from transfected cells was examined to assess the effect of the KPI on beta PP secretion. beta PP751 and beta PP695, obtained from conditioned media of transfected cells, had no effect on proteinase activities against the secretory and amyloidogenic substrates in extracts from control and AD brains. At similar concentrations beta PP751, but not beta PP695, completely inhibited the activity of trypsin against these substrates. Serine proteinase inhibitors had only modest effects on activities from brain, whereas cysteine modification completely inhibited them, indicating that these proteinase activities were not of the serine type. Thus, the results do not support a role for the KPI in the secretion of beta PP or in the amyloidogenic cleavage of beta PP. The amounts of beta PP695 and beta PP751 collected from the media of transfected cells after 48 h of growth were similar, indicating an equal rate of secretion. This result suggests that the KPI domain in beta PP751 did not inhibit the secretory cleavage in transfected cells.