smyRNA: A Novel Ab Initio ncRNA Gene Finder

Background

Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs.

Methodology/Principal Findings

We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences.

Conclusions/Significance

Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. Availability: http://compbio.cs.sfu.ca/taverna/smyrna     

Catalytic pyrolysis of Miscanthus x giganteus over activated alumina

The catalytic effects of activated alumina (Al(2)O(3)) on the pyrolysis of Miscanthusxgiganteus, a new energy crop, were investigated. Catalytic pyrolysis experiments carried out under static and nitrogen atmospheres were performed in a fixed-bed reactor. The final pyrolysis temperature was kept constant at 550 degrees C in all of the experiments. The effect of catalyst loading (by weight of feedstock as 10%, 20%, 40%, 60%, 80% and 100%), heating rate (10 degrees C and 50 degrees Cmin(-1)), nitrogen flow rate (50, 100, 150 and 200cm(3)min(-1)) on the pyrolysis conversion and product yields were investigated. The results were compared with those obtained in non-catalytic pyrolysis. Activated alumina catalyst has a strong influence on the Miscanthusxgiganteus pyrolysis product and conversion yield. Furthermore, the catalytic bio-oils obtained from catalytic pyrolysis under static and nitrogen atmospheres were examined using elemental analysis, column chromatography, Fourier transform infrared (FTIR) and nuclear magnetic resonance ((1)H NMR) spectroscopy methods.     

A simpler way of comparing the labelling densities of cellular compartments illustrated using data from VPARP and LAMP-1 immunogold labelling experiments

Quantitative immunoelectron microscopy of gold label in intracellular compartments often involves calculating labelling densities (LDs). These are related to antigen concentrations and usually refer gold particle counts to the sizes of compartments on sections (for example, golds per microm(2) of organelle profile area or per microm of membrane trace length). Here, we show how LD values can be estimated more simply (without estimating areas or lengths) and also how observed and expected LD values can be used to calculate a relative labelling index (RLI) for each compartment and then test statistically for preferential (non-random) labelling. For random labelling, RLI=1. Compartment size is estimated stereologically by superimposing random test points (which hit organelle profiles in proportion to their area) or test lines (which intersect membrane traces in proportion to their length). By this means, the observed LD of a compartment (LD(obs)) can be expressed simply as golds per test point (organelles) or per intersection (membranes). Furthermore, the LD obtained by dividing total golds (on all compartments) by total points or intersections (on all compartments) is the value to be expected (LD(exp)) when compartments label randomly. For each compartment, RLI=LD(obs)/LD(exp). Statistical analysis is undertaken by comparing observed distributions of golds with predicted random distributions (calculated from point or intersection counts). A compartment is preferentially labelled if two criteria are met: (1) its RLI>1 (i.e. LD(obs) is greater than LD(exp)) and (2) its partial chi-squared value makes a substantial contribution to total chi-squared value. This approach provides a simple and efficient way of comparing LDs in different compartments. Its utility is illustrated using data from VPARP and LAMP-1 labelling experiments.     

Neutrophil superoxide anion production,and CAT and GSSGR activity in patients with tuberculosis

Tuberculosis (TB) is a chronic infection disease caused by Mycobacterium tuberculosis (MTB), as an intracellular pathogen. Various cytokines (TNF-alpha, IL's, GSF etc.) and other factors play important preventing roles and are secreted during the infection. It may cause changes in the metabolism of neutrophils. Production of superoxide anion and antioxidative enzymes activities, such as glutathione reductase (GSSGR) and catalase (CAT) may be changed during MTB infection in the host. In this study, the control group consisted of ten healthy subjects and ten patients with TB were studied before anti-TB treatment. Level of superoxide anion production, activity of CAT and activity of GSSGR were studied from peripheral neutrophils of healthy subjects and patients with TB. Catalase activities of the neutrophils were significantly lower in patients with TB than normal subjects (p < 0.01). Glutathione reductase activities of the neutrophils were also significantly lower in patients with TB than normal subjects (p < 0.05). Superoxide anion production in the neutrophils did not show any significant difference between TB and normal subjects (p > 0.05). As a result, the activities of CAT and GSSGR were lower in the peripheral neutrophils of patients with TB than normal subjects, whereas superoxide anion production in the neutrophils did not differ between in TB patients than normal subjects.     

Comparison of partial excision with simple section of the transverse carpal ligament in the treatment of carpal tunnel syndrome

In the surgical treatment of carpal tunnel syndrome, debate has commonly focused on whether decompression should be performed by open or blind techniques. Contrarily, the goal of the present study was to determine whether instead of simple section, partial excision of the transverse carpal ligament has contributed to better results. Because complete healing of the transverse carpal ligament observed during reoperations has been reported elsewhere, the charts of 75 carpal tunnel syndrome patients who had been treated with open technique at Dokuz Eylül University were reviewed. Statistical analysis was performed using the Fisher's exact test and Student's t test when appropriate. Thirty-five patients had been treated with simple section of the transverse carpal ligament, whereas 40 had been treated with partial excision. Internal neurolysis was also performed in 19 of the patients, 11 of whom were treated with partial excision. The average follow-up time was 3.8 years. The comparisons regarding the overall operative outcomes did not show any significant difference between the two different techniques of releasing the transverse carpal ligament. In patients treated without neurolysis, results of partial excision of the transverse carpal ligament improved when compared with those of simple section, but this superiority was not statistically significant. There seemed to be statistically higher reoperation rates and worse outcomes after neurolysis (p < 0.05). Reoperation was required in eight patients (11 percent). Five of the patients who underwent reoperation had initially been treated with partial excision and neurolysis, whereas two had been treated with simple section and neurolysis. Another patient who had undergone reoperation had initially undergone only simple section. The mean time to return to work or daily activities did not differ between the types of applied technique for releasing the transverse carpal ligament. However, neurolysis lengthened these periods significantly when performed (p < 0.05). In the present study, partial excision of the transverse carpal ligament without adding neurolysis offered relatively better results than simple section. Verification of this finding endoscopically, if applicable, may improve the success rate of surgical therapy in patients with carpal tunnel syndrome.     

The effects of quercetin on bone minerals, biomechanical behavior, and structure in streptozotocin-induced diabetic rats

This study was designed to investigate the effect of quercetin (QE) on bone minerals and biomechanics in insulin-dependent diabetic rats. Diabetes was induced by 50 mg kg(-1) intraperitoneal streptozotocin (STZ) in a single dose. The rats were randomly allotted into four experimental groups: A (control), B (non-diabetic + QE), C (diabetic), and D (diabetic + QE) each containing 10 animals. The diabetic rats received QE (15 mg kg(-1) day(-1)) for 4 weeks following 8 weeks of STZ injection. Blood samples were taken to determine glucose, insulin, calcium, and magnesium levels. The rats' femora were assessed biomechanically at femoral mid-diaphysis and neck. It was found that QE treatment increased insulin, calcium, and magnesium levels. Three-point bending of the femoral mid-diaphysis and necks showed significantly lower maximum load values (F max) in animals in the STZ group than the QE + STZ or control groups (p < 0.05). The results support the conclusion that QE treatment may decrease blood glucose and increase plasma insulin, calcium, and magnesium. QE treatment may also be effective in bone mineral metabolism, biomechanical strength, and bone structure in STZ-induced diabetic rats.     

The effect of vaginal candidiasis on the levels of the oxidative biomarkers in plasma and tissue samples of diabetic rats

The aim of this study is to determine the relation between diabetes and vaginal candidiasis in terms of oxidative biomarker levels in a vaginal candidiasis model of the diabetic rats by evaluating malondialdehyde (MDA), sulphydrile groups or glutathione (RSH), and ascorbic acid (C vit) levels. All rats were randomly divided into five groups. All of the groups were observed for 21 days. In the treated diabetes groups, MDA (0.90, 0.68 nmol/ml and 3.78, 3.79 nmol/g tissue, plasma and vaginal tissue, respectively) and RSH (227, 171 nmol/100 ml 0.38, 0.37 μmol/g tissue, plasma and vaginal tissue, respectively) levels were found to be decreased while the levels of C vit were found to be increased (0.49, 0.37 μmol/l 2.39, 2.01 nmol/g tissue plasma, and vaginal tissue, respectively) (P < 0.05). In the groups of untreated diabetes, vaginal candidiasis were found to be more serious and oxidative biomarkers were found to be increased (MDA 1.30, 1.26 nmol/ml and 7.82, 2.37 nmol/g tissue and RSH 258, 145 nmol/100 ml and 0.31, 0.46 μmol/g tissue) while the antioxidant C vit levels were found to be decreased (0.24, 0.17 μmol/l 1.33, 2.66 nmol/g tissue) (P < 0.05). RSH, plasma MDA, blood glucose, and tissue MDA levels of vaginal candidiasis embedeled diabetic rats, were found to be higher than those in untreated diabetic and untreated vaginitis enbedeled rats ‹P < 0.05’. Vaginal candidiasis caused oxidative stress in diabetic rats working together. Systemic oxidative stress biomarkers were found to be affected from vaginal candidiasis although it was a local mucosal infection. This study was presented as a poster in the conference of ‹2nd Trends in Medical Mycology, 23–26 October 2005, Berlin, Germany’.     

Predictors of the paroxysmal atrial fibrillation recurrence following cryoballoon-based pulmonary vein isolation: Assessment of left atrial volume,left atrial volume index,galectin-3 level and neutrophil-to-lymphocyte ratio

Background

Cryoballoon-based pulmonary vein isolation (PVI) is a treatment option for atrial fibrillation (AF). Left atrial volume (LAV) and left atrial volume index (LAVi) are important parameters for long term success of PVI. Galectin-3 (Gal-3) and neutrophil to lymphocyte ratio (N/L ratio) are biomarkers to demonstrate the cardiac fibrosis and remodelling.