Discrete stochastic models for compliance analysis based on an AIDS Clinical Trial Group (ACTG) study

Compliance is the extent to which a patient follows the prescribed regimen. Here we investigate the statistical properties of two popular measures of compliance - percentage of compliant days and percentage of doses taken. We use a stationary Markov chain to model the dependence structure of successive data points for each subject. We illustrate our model using discrete compliance data collected from an AIDS Clinical Trial Group study (ACTG 398). We check the model assumptions and evaluate the small sample as well as large sample properties of our estimators. We show that ignoring the within-subject dependence will usually underestimate the standard errors of the estimates of these compliance measures. Our model allows the application of meta-analytic approaches to assess the variation across subjects in these compliance indices and changes in them due to intervention.     

A simple preparation method of crystals of soybean hull peroxidase

Soybean hull peroxidase (SHP) was crystallised from an enzyme solution with low purity by a simple method. The enzyme solution was purified by cooperation salting out of acetone and ammonium sulphate, and lumpy crystals were obtained with the size of about 40 × 30 μm when ammonium sulphate was quickly added to the enzyme solution. The crystal was examined and confirmed to be an SHP crystal by the method of activity test. The result shows that, though the purity of the enzyme solution was not high, crystals could be formed when the enzyme solution rapidly reached to a degree of supersaturation, which was different from the traditional methods of protein crystallisation. Additionally, a purification method of acetone and ammonium sulphate fractional salting out was also studied, in which the procedure was simplified, and a satisfactory purification effect was obtained.     

淫羊藿花粉萌发及花粉管生长研究

运用方差分析、多重比较和正交实验方法对淫羊藿花粉的萌发和花粉管生长进行了研究.结果表明:培养基内硼酸、硝酸钙、蔗糖在一定浓度范围内,对花粉萌发及花粉管生长起促进作用,但超过一定浓度时则起抑制作用;镁和钾对花粉萌发及花粉管生长影响不显著.在正交实验中蔗糖和H3BO3对淫羊藿花粉萌发有显著影响,而培养基组分间没有明显的交互作用.淫羊藿最适花粉液体培养基为15%蔗糖 40 mg/L H3BO3 40 mg/LCa(NO3)2·4H2O;在pH值为5.0、25℃和600 lx光照时淫羊藿花粉萌发和花粉管生长最好.     

Myosin V movement: lessons from molecular dynamics studies of IQ peptides in the lever arm

Myosin V moves along actin filaments by an arm-over-arm motion, known as the lever mechanism. Each of its arms is composed of six consecutive IQ peptides that bind light chain proteins, such as calmodulin or calmodulin-like proteins. We have employed a multistage approach in order to investigate the mechanochemical structural basis of the movement of myosin V from the budding yeast Saccharomyces cerevisiae. For that purpose, we previously carried out molecular dynamics simulations of the Mlc1p-IQ2 and the Mlc1p-IQ4 protein-peptide complexes, and the present study deals with the structures of the IQ peptides when stripped from the Mlc1p protein. We have found that the crystalline structure of the IQ2 peptide retains a stable rodlike configuration in solution, whereas that of the IQ4 peptide grossly deviates from its X-ray conformation exhibiting an intrinsic tendency to curve and bend. The refolding process of the IQ4 peptide is initially driven by electrostatic interactions followed by nonpolar stabilization. Its bending appears to be affected by the ionic strength, when ionic strength higher than approximately 300 mM suppresses it from flexing. Considering that a poly-IQ sequence is the lever arm of myosin V, we suggest that the arm may harbor a joint, localized within the IQ4 sequence, enabling the elasticity of the neck of myosin V. Given that a poly-IQ sequence is present at the entire class of myosin V and the possibility that the yeast's myosin V molecule can exist either as a nonprocessive monomer or as a processive dimer depending on conditions (Krementsova, E. B., Hodges, A. R., Lu, H., and Trybus, K. M. (2006) J. Biol. Chem. 281, 6079-6086), our observations may account for a general structural feature for the myosins' arm embedded flexibility.     

Protein conformational changes of Agrobacterium phytochrome Agp1 during chromophore assembly and photoconversion

Phytochromes are widely distributed photochromic biliprotein photoreceptors. Typical bacterial phytochromes such as Agrobacterium Agp1 have a C-terminal histidine kinase module; the N-terminal chromophore module induces conformational changes in the protein that lead to modulation of kinase activity. We show by protein cross-linking that the C-terminal histidine kinase module of Agp1 mediates stable dimerization. The fragment Agp1-M15, which comprises the chromophore module but lacks the histidine kinase module, can also form dimers. In this fragment, dimer formation was stronger for the far-red-absorbing form Pfr than for the red-absorbing form Pr. The same or similar behavior was found for Agp1-M15Delta9N and Agp1-M15Delta18N, which lack 9 and 18 amino acids of the N-terminus, respectively. The fragment Agp1-M20, which is derived from Agp1-M15 by truncation of the C-terminal "PHY domain" (191 amino acids), can also form dimers, but dimerization is independent of irradiation conditions. The cross-linking data also showed that the PHY domain is in tight contact with Lys 16 of the protein and that the nine N-terminal amino acids mediate oligomer formation. Limited proteolysis shows that the hinge region between the chromophore module and the histidine kinase and a part of the PHY domain become exposed upon Pr to Pfr photoconversion.     

Cdk5 is involved in NFT-like tauopathy induced by transient cerebral ischemia in female rats

Although neurofibrillary tangle (NFT) formation is a central event in both familial and sporadic Alzheimer's disease (AD), neither cellular origin nor functional consequence of the NFTs are fully understood. This largely is due to the lack of available in vivo models for neurofibrillary degeneration (NFD). NFTs have only been identified in transgenic mice, bearing a transgene for a rare hereditary neurodegenerative disease, frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP17). Epidemiological evidence suggests a much higher occurrence of dementia in stroke patients. This may represent the underlying cause of the pathogenesis of sporadic AD, which accounts for the majority of AD cases. We examined pathological markers of AD in a rodent stroke model. Here we show that after transient cerebral ischemia, hyperphosphorylated tau accumulates in neurons of the cerebral cortex in the ischemic area, forms filaments similar to those present in human neurodegenerative tauopathies and colocalizes with markers of apoptosis. As a potential underlying mechanism, we were able to determine that transient ischemia induced tau hyperphosphorylation and NFT-like conformations are associated with aberrant activation of cyclin dependent kinase 5 (Cdk5) and can be rescued by delivery of a potent, but non-specific cyclin dependent kinase inhibitor, roscovitine to the brain. Our study further indicates that accumulation of p35 and its calpain-mediated cleavage product, p25 may account for the deregulation of Cdk5 induced by transient ischemia. We conclude that Cdk5 may be the principal protein kinase responsible for tau hyperphosphorylation and may be a hallmark of the tauopathies in this stroke model.     

Comparison of two preparation methods for endocervical evaluation

OBJECTIVE: To assess the validity of SurePath liquid-based preparation method for examination of endocervical brush specimens as a substitute for conventionally prepared cytology methods for evaluating the endocervical canal during colposcopic examination and biopsy. STUDY DESIGN: Paired SurePath liquid-based test slides and conventional smears were obtained using an endocervical brush in a split sample protocol before biopsy at the time of colposcopy. The level of agreement between cytologic results obtained was assessed. Accuracy and operating characteristics were evaluated compared to histologic follow-up. RESULTS: Agreement between cytology results for the methods was excellent. The overall kappa was 0.924 (p = 0.0000). There was exact agreement on interpretation between the methods in 283 of 299 cases (94.6%). Cytohistologic follow-up results correlation were: SurePath liquid-based Pap test results and conventional smear results agreed with histology results in 47.8% and 49.2% of cases, respectively. Allowing for a discrepancy within 1 level of severity of cytologic grade, agreements were 76.6% and 77.2%, respectively. CONCLUSION: This study demonstrates that the SurePath method is equivalent to conventional endocervical brush cytology preparation and performs well for detection of cervical intraepithelial lesions and cancer. SurePath is acceptable for endocervical evaluation as a substitute for endocervical curettage at colposcopic biopsy.     

Production of gamma-aminobutyric acid (GABA) by Lactobacillus buchneri isolated from kimchi and its neuroprotective effect on neuronal cells

Lactic acid bacteria that accumulated gamma-aminobutyric acid (GABA) in culture medium were screened to identify strains with high GABA-producing ability. One strain, MS, which was isolated from kimchi, showed the highest GABA-producing ability among the screened strains. MS was identified as Lactobacillus buchneri based on Gram-staining, metabolic characteristics, and 16S rDNA sequence determination. Optimum culture conditions for GABA production were determined: MRS broth containing 5% MSG, 1% NaCl, and 1% glucose, at an initial pH of 5.0, the incubation temperature at 30 degrees C for 36 h. Under these conditions, MS produced GABA at a concentration of 251 mM with a 94% GABA conversion rate. Moreover, culture extracts of Lb. buchneri MS partially or completely protected neuronal cells against neurotoxicant-induced cell death.