Robo-Therm, a pipeline to RNA Thermometer discovery and validation

RNA thermometers are highly structured noncoding RNAs located in the 5' untranslated regions (UTR) of genes that regulate expression by undergoing conformational changes in response to temperature. The discovery of RNA thermometers through bioinformatics is difficult because there is little sequence conservation among their structural elements. Thus, the abundance of these thermo-sensitive regulatory structures remains unclear. Herein, to advance the discovery and validation of RNA thermometers, we developed Robo-Therm, a pipeline that combines an adaptive and user-friendly in silico motif search with a well-established reporter system. Through our application of Robo-Therm, we discovered two novel RNA thermometers in bacterial and bacteriophage genomes found in the human gut. One of these thermometers is present in 5'-UTR of a gene that codes for σ70 RNA polymerase subunit in the bacteria Mediterraneibacter gnavus and Bacteroides pectinophilus, and in the bacteriophage Caudoviricetes, which infects Bacteroides pectinophilus. The other thermometer is in the 5'-UTR of a tetracycline resistance gene (tetR) in the intestinal bacteria Escherichia coli and Shigella flexneri. Our Robo-Therm pipeline can be applied to discover multiple RNA thermometers across various genomes.

Arsenic speciation in biological samples using XAS and mixed oxidation state calibration standards of inorganic arsenic

The speciation of elements without pre-edge features preformed with X-ray absorption near edge structure (XANES) can lead to problems when the energy difference between two species is small. The speciation of arsenic (As) in plant samples was investigated using the mixtures As2S3/As2O5, As2S3/As2O3, or As2O3/As2O5. The data showed that the energy separation (eV) between As2O5 and As2S3 was 5.8, between As2O3 and As2O5 was 3.6, and between As2S3 and As2O3 was 2.1. From the intensity of the white-line feature and the concentration of As species, calibration curves showing a limit of detection of approximately 10% were generated. In addition, an error of +/-10% was determined for the linear combination-XANES (LC-XANES) fitting technique. The difference between the LC-XANES fittings and calculations from the calibration curves was <10%. The data also showed that the speciation of As in a sample can be determined using EXAFS (extended X-ray absorption fine structure). Finally, it was also shown that both EXAFS and XANES of the sample should be examined to determine the true speciation of an element. Even though there is a difference of 2 eV between As(III) bound to O and As(III) bound to S, in the EXAFS region the As(III)-S and As(III)-O ligands are clearly visible. However, distinction between the As(III)-O and As(V)-O ligands in the EXAFS spectra was not clearly visible in this study.

Hyperhomocysteinemia is a risk factor of recurrent coronary event in young patients irrespective to the MTHFR C677T polymorphism

Despite the well-known pro-coagulant effect of hyperhomocysteinemia, data is limited regarding the result on recurrent coronary event (RCE) in young people. One hundred and forty patients <55 years old with a first acute coronary syndrome (ACS) were prospectively followed for a mean (+/-S.D.) follow-up of 49+/-14 months in order to investigate the relationship between homocysteine levels (tHcy) at admission and the incidence of RCE. The tHcy values were divided into quartiles to examine their relationship with end points. Furthermore, we determined the effect of C677T methylene tetrahydrofolate reductase (MTHFR) polymorphism, as well as other risk factors for developing a RCE. The median plasma homocysteine concentration was 9.6 mumol/L (interquartile range, 3.7). In the screening of MTHFR C677T polymorphism in patients with ACS, the T allele frequency was 0.4 and the genotype frequency distributions were in Hardy-Weinberg equilibrium. At time of final evaluation, 49 (35%) of the 140 valuable patients had developed a RCE. Increasing numbers of RCE were observed for increasing quartiles of tHcy according to Kaplan-Meier survival (Log-rank test=0.0092). The MTHFR C677T polymorphism was not associated with an increased incidence of RCE. In multivariate analysis, the variables independently associated with a higher risk of RCE were age older than 45 years [HR=2.7; (95% CI, 1.3-6.1); p=0.030], body mass index more than 25 [HR=2.6; (95% CI, 1.1-5.9); p=0.034] and tHcy levels into quartile 4 (tHcy>12.37 mumol/L) [HR=2.5; (95% CI, 1.1-4.7); p=0.04]. Elevated plasma homocysteine level at admission is an independent risk factor for RCE after the first episode of ACS in young patients irrespective of the status of MTHFR C677T.

Massive lymphocyte apoptosis in the thymus of functionally deficient TrkB mice

The occurrence of TrkB in the murine thymus (15-day and 3-month old) was investigated by Northern blot, Western blot and immunohistochemistry. Furthermore, the thymus of 15-day-old mice carrying a non-functional mutation on trkB was analyzed. Both trkB mRNA and 145 kDa TrkB protein were detected. In addition, isolated lymphocytes and stromal cells also expressed this protein. The thymus of homozygous functionally TrkB-deficient animals showed structural and ultrastructural changes consistent with massive death of cortical lymphocytes, confirmed with TUNEL. Present results suggest a role for TrkB in maintaining the survival or preventing massive death of lymphocytes in the mammalian thymus.

Ren1d and Ren2 cooperate to preserve homeostasis: evidence from mice expressing GFP in place of Ren1d

To distinguish the contributions of Ren1(d) and Ren2 to kidney development and blood pressure homeostasis, we placed green fluorescent protein (GFP) under control of the Ren1(d) renin locus by homologous recombination in mice. Homozygous Ren1(d)-GFP animals make GFP mRNA in place of Ren1(d) mRNA in the kidney and maintain Ren2 synthesis in the juxtaglomerular (JG) cells. GFP expression provides an accurate marker of Ren1(d) expression during development. Kidneys from homozygous animals are histologically normal, although with fewer secretory granules in the JG cells. Blood pressure and circulating renin are reduced in Ren1(d)-GFP homozygotes. Acute administration of losartan decreases blood pressure further, suggesting a role for Ren2 protein in blood pressure homeostasis. These studies demonstrate that, in the absence of Ren1(d), Ren2 preserves normal kidney development and prevents severe hypotension. Chronic losartan treatment results in compensation via recruitment of both Ren1(d)- and Ren2-expressing cells along the preglomerular vessels. This response is achieved by metaplastic transformation of arteriolar smooth muscle cells, a major mechanism to control renin bioavailability and blood pressure homeostasis.

Improvement of albendazole efficacy against enteral, but not against parenteral stages of Trichinella spiralis by preparing solid dispersions in polyvinylpyrrolidone

A comparison was made, in the Trichinella/mouse model, of the anthelmintic effects of albendazole (ABZ) and ricobendazole (RBZ) formulated as solid dispersions in polyvinylpyrrolidone with regard to ABZ formulated as a suspension in carboxymethylcellulose. A solid dispersion significantly increased (p < 0.01) the efficacy of the drugs against intestinal preadult but not against migrating and muscle stages of the parasite. The anthelmintic efficacy of RBZ given as a solid dispersion was equivalent to (against preadult and encysted larvae) or significantly lower than (against migrating larvae) that of ABZ with the same formulation. The pharmacokinetic profiles of ABZSO as measured by HPLC showed no significant differences in the Cmax and AUC following administration of ABZ formulated as a suspension or solid dispersion although the Tmax was significantly lower for the dispersion.

Longitudinal study of posterior subcapsular opacities using the National Eye Institute computer planimetry system

BACKGROUND

The National Eye Institute (NEI) computer planimetry system has proved to be helpful in cross sectional studies by providing clinically useful area measurements of posterior subcapsular cataracts (PSC) and other opacities from retroillumination photographs. In this study, we evaluated the worth of this system in detecting PSC area changes over time.

METHODS

Using the Neitz-Kawara camera, retroillumination photographs of the PSCs of 51 eyes were obtained every 6 months for an average of 25 months. The PSCs were outlined in a masked fashion on plastic overlays. Their tracings were then digitised on to a computer using a scanner. PSC area was determined using a special software program. For each eye, the rate of PSC area change was estimated by the slope of the regression line fitted to the follow up measurements. Cataract progression was classified as significant if the slope exceeded a critical value.

RESULTS

These showed that 14 of the 51 eyes had PSC progression, while 37 did not change.

CONCLUSION

This study suggests the system is useful for longitudinally monitoring PSC area changes from retroillumination photographs. This system would serve in natural history studies of PSCs and in clinical trials of anticataract drugs. The slope based test can play a part in longitudinal studies with irregular time intervals and variable number of visits.

Hydroxycinnamic acid-derived polymers constitute the polyaromatic domain of suberin

Suberin is an abundant, complex, intractable, plant cell wall polymeric network that forms both protective and wound-healing layers. Its function is, therefore, critical to the survival of all vascular plants. Its chemical structure and biosynthesis are poorly defined, although it is known to consist of both aromatic and aliphatic domains. While the composition of the aliphatic component has been fairly well characterized, that of the phenolic component has not. Using a combination of specific carbon-13 labeling techniques, and in situ solid state 13C NMR spectroscopic analysis, we now provide the first direct evidence for the nature of the phenolic domain of suberin and report here that it is almost exclusively comprised of a covalently linked, hydroxycinnamic acid-derived polymeric matrix.

Quantitative analysis of retroillumination images

We have developed a semi-automated image processing system for analysis and evaluation of retroillumination images. This paper describes methods used to compensate for illumination variations in the images, separation of data into cataractous and non-cataractous portions, how quantitative measurements are made and how they assess the pathological condition. In addition to the traditional area measurement, this system computes the net integral of density and several measurements involving the location of the opacity in relation to the pupillary margin. The computer measures of area, integral of density, area centrality, weighted area, density centrality and weighted density provide more data than previously described systems. Data produced by this interactive and automated system can be used in studies of posterior subcapsular and cortical cataracts, and to study the effect of these opacities on vision.

Reproducibility study of posterior subcapsular opacities on the NEI retroillumination image analysis system

We developed a semi-automated retroillumination image analysis system which combines speed, ease of operation and interactive analysis. The system measures cataract area and integral of cataract density (ID). For system reproducibility evaluation, 20 eyes with posterior subcapsular opacities were captured twice by two photographers. Variability was estimated under a random effects analysis of variance model. Measurement errors for area and for ID were each small contributors to total variability (the sum of variability between study eyes plus measurement error), being 0.4% and 0.1% respectively. The largest contributor to area measurement error was image analysis variability (97%). For ID measurement error, the variability in images (44%) and in image analysis (46%) were major contributors. The reproducibility is comparable to previously described retroillumination analysis systems. This easy to use system may therefore be useful in clinical research studies including possible clinical trials of anti-cataract drugs.

Presumptive identification of Salmonella enterica using two rapid tests

Two rapid test for early detection of Salmonella enterica, the cytochrome oxidase test and a fluorescence test, were evaluated in 1,200 colonies which had been isolated from human feces and cultured on MacConkey and Salmonella-Shigella media. Using the fluorescence test there were no false negative results (sensitivity 100%) and of 205 positive cases 62 did not correspond biochemically to salmonella (specificity 94.1%); 44 of these 62 were positive in the cytochrome oxidase test, raising the specificity to 98.2%. In conclusion, the combination of the two tests could be very useful due to the ease of performance, low cost and excellent results obtained.