Dictionary-driven prokaryotic gene finding

Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified in a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm’s implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method’s generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed in detail.     

Synthesis and anti-hepatitis C virus activity of nucleoside derivatives of N3, 5'-anhydro-4-(beta-D-ribofuranosyl)-8-aza-purin-2-ones

A series of N3, 5-Anhydro-4-(beta-D-ribofuranosyl)-8-azapurin-2-ones were prepared in multistep reactions from uridine as potential anti-hepatitis C virus (HCV) agents. The synthetic details as well as biological evaluations are discussed.     

Synthesis and biological evaluation of benzamides and benzamidines as selective inhibitors of VEGFR tyrosine kinases

A series of benzamidines and benzamides was synthesized as selective inhibitors of vascular endothelial growth factor receptor (VEGFR) tyrosine kinases, and tested for inhibitory activity toward autophosphorylation by the enzyme assay. Selective inhibition of VEGFR-2 tyrosine kinase was observed in the salicylic amide 4e and the anthranilic amidine 5a, and their percent inhibitions of VEGFR-2 tyrosine kinase were 44-60% at a 10 microM concentration of compounds. The salicylic amide 4a showed inhibition of both VEGFR-1 and VEGFR-2 tyrosine kinases at a 10 microM concentration.     

Health Insurance Coverage and Hypertension Control in China: Results from the China Health and Nutrition Survey

Background

China has rapidly expanded health insurance coverage over the past decade but its impact on hypertension control is not well known. We analyzed factors associated with hypertension and the impact of health insurance on the management of hypertension in China from 1991 to 2009.

Methods and Findings

We used individual-level data from the China Health and Nutrition Survey (CHNS) for blood pressure, BMI, and other socio-economic variables. We employed multi-level logistic regression models to estimate the factors associated with prevalence and management of hypertension. We also estimated the effects of health insurance on management of hypertension using propensity score matching. We found that prevalence of hypertension increased from 23.8% (95% CI: 22.5–25.1%) in 1991 to 31.5% (28.5–34.7%) in 2009. The proportion of hypertensive patients aware of their condition increased from 31.7% (28.7–34.9%) to 51.1% (45.1–57.0%). The proportion of diagnosed hypertensive patients in treatment increased by 35.5% in the 19 years, while the proportion of those in treatment with controlled blood pressure remained low. Among diagnosed hypertensives, health insurance increased the probability of receiving treatment by 28.7% (95% CI: 10.6–46.7%) compared to propensity-matched individuals not covered by health insurance.

Conclusions

Hypertension continues to be a major health threat in China and effective control has not improved over time despite large improvements in awareness and treatment access. This suggests problems in treatment quality, medication adherence and patient understanding of the condition. Improvements in hypertension management, quality of medical care for those at high risk, and better health insurance packages are needed.     

Effects of PFOS and PFOA on L-type Ca2+ currents in guinea-pig ventricular myocytes

Perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) are amphiphiles found ubiquitously in the environment, including wildlife and humans, and are known to have toxic effects on physiological functions of various tissues. We investigated the effects of PFOS and PFOA on action potentials and L-type Ca(2+) currents, I(CaL), in isolated guinea-pig ventricular myocytes using whole-cell patch-clamp recording. In current-clamp experiments, PFOS significantly decreased the rate of spike, action potential duration, and peak potential at doses over 10 microM. In voltage-clamp experiments, PFOS increased the voltage-activated peak amplitude of I(CaL), and shifted the half-activation and inactivation voltages of I(CaL) to hyperpolarization. PFOA had similar effects PFOS, but showed significantly lower potency. These findings are consistent with previous observations for anionic n-alkyl surfactants, suggesting that PFOS and PFOA may change membrane surface potential, thereby eliciting general effects on calcium channels. These findings provide further insights into the mechanisms of PFOA and PFOS toxicities.     

Mutation induction by N-propyl-N-nitrosourea in eight MutaMouse organs.

As a part of the 2nd Collaborative Study for the Transgenic Mouse Mutation Assay, we studied the organ specificity and the temporal changes in mutant frequency (MF) of the lacZ gene following intraperitoneal injection of 250 mg/kg N-propyl-N-nitrosourea into male MutaMouse. We used a positive selection system and examined eight organs, i.e., bone marrow, liver, kidney, lung, spleen, brain, heart, and testis. The chemical caused a significant increase in MF in all organs except for brain, and the bone marrow was the most sensitive organ, exhibiting a MF on day 7 that was 10 times that of the control. The MF increased from day 7 to day 28 in liver, kidney, and testis, while it decreased in bone marrow. The relationship between the results of this study and the target organs of carcinogenesis, and the cause of the temporal changes in MF, are discussed.     

Spatial variations in xylem sap flux density in evergreen oak trees with radial-porous wood: comparisons with anatomical observations

To estimate whole-tree water use when employing sap flow measurements, integration of the sap flux density (F _d) over the sapwood area is needed. Accordingly, it is necessary to obtain information on the characteristics of stem water transportation such as spatial variations in F _d and the active xylem area in the stem cross-section. Although evergreen oak trees with radial-porous wood represent a major component of secondary forests in western Japan, detailed information on their stem water transportation characteristics remains unclear. In the present study, we used the heat dissipation method (Granier method) to conduct measurements of azimuthal and radial variations in the F _d of Quercus glauca Thunb. ex Murray, a representative evergreen broad-leaved tree in western Japan. Further, by analyzing the anatomy of the xylem structure, we examined why F _d varies spatially in the stem cross-section. By using a dye solution injected into a radial hole bored into the tree trunk, we confirmed that the entire stem is hydroactive. We also compared the spatial variations in F _d and water conductivity per xylem area (K _s) which were estimated by using the observed vessel diameters and their density over the stem cross-section and Hagen–Poiseuille’s law. Azimuthal and radial variations in F _d reached about 60 and 50% of the maximum values, respectively, and could be explained by spatial variation in K _s. As a result, we obtained statistical parameters describing the spatial variation in F _d in Q. glauca and determined that whole-tree water use estimated from measurements in one direction had at most ±20% potential errors for studied trees.     

The docking protein FRS2alpha is an essential component of multiple fibroblast growth factor responses during early mouse development

The docking protein FRS2alpha is a major mediator of fibroblast growth factor (FGF) signaling. However, the physiological role of FRS2alpha in vivo remains unknown. In this report, we show that Frs2alpha-null mouse embryos have a defect in anterior-posterior (A-P) axis formation and are developmentally retarded, resulting in embryonic lethality by embryonic day 8. We demonstrate that FRS2alpha is essential for the maintenance of self-renewing trophoblast stem (TS) cells in response to FGF4 in the extraembryonic ectoderm (ExE) that gives rise to tissues of the placenta. By analyzing chimeric embryos, we found that FRS2alpha also plays a role in cell movement through the primitive streak during gastrulation. In addition, experiments are presented demonstrating that Bmp4 expression in TS cells is controlled by mitogen-activated protein kinase-dependent FGF4 stimulation. Moreover, both the expression of Bmp4 in ExE and activation of Smad1/5 in epiblasts are reduced in Frs2alpha-null embryos. These experiments underscore the critical role of FRS2alpha in mediating multiple processes during embryonic development and reveal a potential new link between FGF and Bmp4 signaling pathways in early embryogenesis.     

Mutant yields and mutational spectra of the heterocyclic amines MeIQ and PhIP at the S1 locus of human-hamster AL cells with activation by chick embryo liver (CELC) co-cultures

Cooking meat and fish at high temperature creates heterocyclic amines (HA) including 2-amino-3,4-dimethylimidazo[4,5-f]quinoline (MeIQ) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Several HA are mutagens in the Ames' S9/Salmonella assay. While PhIP is a substantial Ames' test mutagen, it is 1000-fold less active than the extraordinarily potent MeIQ. In contrast, MeIQ is significantly less mutagenic than PhIP in several mammalian cell assays, especially in repair-deficient Chinese hamster ovary (CHO) cells. HA are suspect human carcinogens on the basis of (i) epidemiological evidence, (ii) induction of tumors in rodents and monkeys, (iii) DNA adduct formation and (iv) mutagenic capacity. In this study, MeIQ and PhIP were significant mutagens at the S1 locus of co-cultivated human/hamster hybrid AL cells following metabolic activation by beta-napthoflavone (betaNF)-induced chick embryonic liver cultures (CELC). MeIQ was more mutagenic than PhIP in the CELC+AL cell assay. The mutant response curves increase with dose and then plateau (PhIP), or decrease (MeIQ). The inflections in these response curves coincide with dose-dependent decreases in cytochrome CYP1A1 activity. Molecular analysis of S1- mutants indicates that a substantial fraction, >65%, of the mutations induced by PhIP are deletions of 4.2 to 133 (Mbp); half are larger than 21 Mbp. Mutations induced by MeIQ were smaller, most (56%) being less than 5.7 Mbp. When appropriate metabolic activation is combined with a target locus, which can detect both small and large chromosomal mutations, both MeIQ and PhIP are significant mutagens and clastogens in repair proficient mammalian cells.