Theoretical analysis of noncanonical base pairing interactions in RNA molecules

Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their 'away from equilibrium' geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H...O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H...O/N and/or one C-H...O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.     

Partial characterization of 5′(3′)-ribonucleotide and 3′-ribonucleotide phosphohydrolases from Tradescantia albiflora leaves

Two acid phosphomonoesterases, 5′(3′)-ribonucleotide phosphohydrolase and 3′-ribonucleotide phosphohydrolase, were isolated from Tradescantia albiflora leaf tissue and purified by ammonium sulphate precipitation, gel filtration on Sephadex G-200 and repeated chromatography on DEAE-cellulose. The enzymes differed in their sensitivity to dialysis against 1 mM EDTA; the activity of 5′(3′)-ribonucleotide phosphohydrolase was unaffected, while 3′-ribonucleotide phosphohydrolase showed an increase of 60–90%. Both enzymes were rapidly inactivated above 50°. Their ion sensitivity was identical: 1 m M Zn²⁺ and Fe²⁺ were inhibitors for both by 20–80%; while Mg²⁺, Ca²⁺, Co²⁺, K⁺, Na⁺ at 1–10 mM had no significant effect on the activity of either enzyme. Inorganic phosphate inhibited both enzymes almost completely. EDTA (1 mM) did not inhibit either enzyme; none of the divalent cations tested were enzyme activators. 3′-Ribonucleotide phosphohydrolase hydrolysed both 3′- and 5′-nucleoside monophosphates (3′-AMP, 3′-CMP, 3′-GMP, 3′-UMP, 5′-AMP, 5′-CMP, 5′-GMP, 5′-UMP). 5′(3′)-Ribonucleotide phosphohydrolase showed a preference for the 3′-nucleoside monophosphates. Adenosine 3′,5′-cyclic monophosphate, purine and pyrimidine 2′,3′-cyclic mononucleotides at 0.1–1.OmM did not inhibit the enzymes.     

Association of metabolic and genetic factors with cholesterol esterification rate in HDL plasma and atherogenic index of plasma in a 40 years old Slovak population

We assessed association between novel biomarkers of cardiovascular disease and conventional factors in 40 years old subjects (208 men and 266 women) from the general population of Slovakia. FER(HDL) (cholesterol esterification rate in HDL plasma), AIP--Atherogenic Index of Plasma [Log(TG/HDL-C)] as markers of lipoprotein particle size, and CILP2, FTO and MLXIPL polymorphisms, were examined in relation to biomarkers and conventional risk factors. Univariate analyses confirmed correlation between AIP, FER(HDL) and the most of measured parameters. Relations between AIP and CILP2, FTO and MLXIPL were not significant. However, CILP2 was significantly related to FER(HDL) in both genders. In multivariate analysis BMI was the strongest correlate of AIP levels. In multivariate model variability of FER(HDL) was best explained by AIP (R(2) = 0.55) in both genders with still significant effect of CILP2 SNP in men. In a model where AIP was omitted, TG levels explained 43 % of the FER(HDL) variability in men, while in women HDL-C was the major determinant (42 %). In conclusions, FER(HDL) and AIP related to the known markers of cardiovascular risk provide means to express their subtle interactions by one number. Our novel finding of association between CILP2 polymorphism and FER(HDL) supports its role in lipid metabolism.     

Field Trial Evaluation of the Performances of Point-of-Care Tests for Screening G6PD Deficiency in Cambodia

Background

User-friendly, accurate, point-of-care rapid tests to detect glucose-6-phosphate dehydrogenase deficiency (G6PDd) are urgently needed at peripheral level to safely recommend primaquine for malaria elimination.

Methods

The CareStart G6PD RDT (AccessBio, New Jersey, USA), a novel rapid diagnostic test and the most commonly used test, the fluorescent spot test (FST) were assessed against the quantitatively measured G6PD enzyme activity for detecting G6PDd. Subjects were healthy males and non-pregnant females aged 18 years or older residing in six villages in Pailin Province, western Cambodia.

Findings

Of the 938 subjects recruited, 74 (7.9%) were severe and moderately severe G6PD deficient (enzyme activity <30%), mostly in male population; population median G6PD activity was 12.0 UI/g Hb. The performances of the CareStart G6PD RDT and the FST, according to different cut-off values used to define G6PDd were very similar. For the detection of severe and moderately severe G6PDd (enzyme activity <30%, <3.6 UI/g Hb) in males and females, sensitivity and negative (normal status) predictive value were 100% for both point-of-care tools. When the G6PDd cut-off value increased (from <40% to <60%), the sensitivity for both PoCs decreased: 93.3% to 71.7% (CareStart G6PD RDT, p = 10⁻⁶) and 95.5% to 73.2% (FST, p = 10⁻⁶) while the specificity for both PoCs remained similar: 97.4% to 98.3% (CareStart G6PD RDT, p = 0.23) and 98.7% to 99.6% (FST, p = 0.06). The cut-off values for classifying individuals as normal were 4.0 UI/g Hb and 4.3 UI/g Hb for the CareStart G6PD RDT and the FST, respectively.

Conclusions

The CareStart G6PD RDT reliably detected moderate and severe G6PD deficient individuals (enzyme activity <30%), suggesting that this novel point-of-care is a promising tool for tailoring appropriate primaquine treatment for malaria elimination by excluding individuals with severe G6PDd for primaquine treatment.     

Early lipoic acid intake protects retina of diabetic mice

The aim of this study was to test the effect of lipoic acid treatment on the retina after a short diabetic insult. Diabetes was induced by alloxan and mice were divided into sub-groups; control, diabetic, diabetic+insulin and all groups received±lipoic acid (100 mg/kg body weight) for 3 weeks. GSH content, MDA concentration, GPx activity were measured and electroretinograms (ERG) were recorded. Early administration of lipoic acid to diabetic mice prevented the statistically significant decreases of GSH content and GPx activity and normalized MDA concentration. Moreover, lipoic acid restored electroretinogram b-wave amplitude of diabetic animals to control values. Lipoic acid has a protective effect on the diabetic retina.     

A longitudinal study of urinary dipstick parameters in wild chimpanzees (Pan troglodytes verus) in Côte d'Ivoire

We performed 796 dip‐stick tests on urine from 100 wild West African chimpanzees (Pan troglodytes verus) from 4 habituated groups in the tropical rain forest of Taï National Park, Cote d'Ivoire, to establish reference values for health monitoring. Specific gravity was also measured on 359 urine samples from 62 chimpanzees. The effect of age, sex, group, month, estrus, pregnancy, meat consumption, and acute respiratory disease on pH, leucocytes, protein, blood, hemoglobin, and glucose was examined using ordinal logistic regression. The presence of nitrite, ketones, bilirubin, and urobilinogen in urine was also recorded. Outbreak of acute respiratory disease did not influence any of the urinary parameters. Thirty‐seven percent of the samples had a pH <7 and the whole range of pH was found through the year, in all age groups, and in both sexes. Meat consumption lowered the urinary pH. Our results show that all pH levels must be considered normal for the West African chimpanzee subspecies P. troglodytes verus living in the rainforest. We also found a cluster of glucose‐positive samples at a specific point in time which was not attributed to diabetes mellitus. These findings highlight that there are differences in normal physiological parameters among wild chimpanzees living in different habitats. Am. J. Primatol. 72:689–698, 2010. © 2010 Wiley‐Liss, Inc.     

Unscheduled DNA synthesis correlated to alkylation of hemoglobin in individuals occupationally exposed to propylene oxide

Exposure to propylene oxide was determined previously by the degree of alkylation of hemoglobin measured on the histidine residue as N-3-(2-hydroxypropyl) histidine, using blood samples from 8 propylene oxide-exposed employees and 13 unexposed referents. Mononuclear leukocytes isolated from the same blood samples were used to quantify DNA repair proficiency following an in vitro challenge with the carcinogen, N-acetoxy-2-acetylamino-fluorene. Decreases in the DNA repair proficiency index correlated significantly to in vivo exposure levels to propylene oxide (r = –0.64, p <0.03). These data suggest a possible short-term biological assay for monitoring the in vivo genotoxic effects of propylene oxide exposure in the human population.Abbreviations EO ethylene oxide - NA-AAF N-acetoxy-2-acetylaminofluorene - HOPrHIS N-3-(2-hydroxypropyl) histidine - PO propylene oxide - UDS unscheduled DNA synthesis     

Variant in the FTO gene and biomarkers related to health in mature Slovak women

The purpose of this study was to investigate whether variant (rs178 17449, G/T) in the first intron of the fat mass and obesity-associated gene (FTO) was related to different obesity parameters and blood pressure in mature women from Slovakia. A total of 419 Slovak women (241 premenopausal and 178 postmenopausal) ranging in age from 39 to 65 years were recruited from different parts of Slovakia. The subgroups were categorized based on the WHO (1996) criteria. All participants gave written informed consent for participation in this study. Anthropometric parameters were measured using standard methods. Fat mass was examined by bioimpedance and blood pressure was measured in the morning during the medical examination. Genomic DNA was extracted from blood or saliva samples by the JET-QUICK Tissue DNA spine kit. The FTO variant was determined by PCR and restriction analysis according to the methodology of Hubacek et al. (2008). The obtained data were statistically analyzed by SPSS 17.0 for Windows. The FTO genotype and allele frequencies in the entire sample and in subgroups according to their menopausal and blood pressure status fell within the Hardy-Weinberg equilibrium. In postmenopausal women the FTO (rs178 17449) genotype was significantly associated with systolic blood pressure (SBP) (p = 0.024) in the dominant GG/GT vs.TT model and with diastolic blood pressure (DBP) (p = 0.030) in the recessive GG vs. GT/TT and the additive model (p = 0.043), respectively. In these postmenopausal women regression analysis showed a statistically significant effect of age, BMI and FTO dominant model on SBP, and of BMI on DBP among the other variables capable of inducing blood pressure differences. This study demonstrates that the SNP rs178 17449 in the FTO gene is associated with systolic and diastolic blood pressure but not with BMI and obesity variables, as already replicated in several populations throughout the world.