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PubMed1987

In vitro synthesis of double stranded RNA and measurement of thermal stability: effect of base composition, formamide and ionic strength.

Double stranded RNA was prepared by transcription of complementary strands followed by annealing. RNA duplexes prepared in this way showed cooperative thermal transition. Thermal denaturation of RNA duplexes of 33%-70% G+C content shows that Tm increases more sharply [0.93 degrees C/(%G+C)] with increase in G+C than that of DNA. Formamide (up to 80%) reduces Tm of RNA duplex linearly, and the rate of reduction is much less than that of DNA. The relation between salt concentration and Tm of double stranded RNA was also determined. The following relationship has been derived based on the above observations: Tm (ds RNA) = 14.88 logM + 0.93 (%G+C) + 67.62 - 0.4 (%Formamide).

Base Sequence↗
PubMed2005

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.

BACKGROUND: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes. RESULTS: We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV), using a rigorous cross-validation procedure. A major advantage of this approach is that because it does not rely on beta-strand detection, it does not require resolved structures and thus larger, more representative, training sets could be used. It is therefore believed that this approach will be invaluable in complementing other, physicochemical and homology based methods. This was demonstrated by the correct reassignment of a number of proteins which other predictors failed to classify. We have used the algorithm to screen several genomes and have discussed our findings. CONCLUSION: TMB-Hunt achieves a prediction accuracy level better than other approaches published to date. Results were significantly enhanced by use of evolutionary information and a system for calibrating k-NN scoring. Because the program uses a distinct approach to that of other discriminators and thus suffers different liabilities, we believe it will make a significant contribution to the development of a consensus approach for bbtm protein detection.

Algorithms↗
PubMed1981

Characterization of rat liver oligonucleosomes enriched in transcriptionally active genes: evidence for altered base composition and a shortened nucleosome repeat.

A transcriptionally active chromatin fraction of oligonucleosome size has been separated and isolated by a modified micrococcal nuclease fractionation procedure. After mild enzymatic digestion, rat liver nuclei were lysed, and the chromatin was separated by centrifugation on linear sucrose gradients. Fractions from four regions of the gradient were pooled and labeled, from the top to the bottom, A, B, C, and D, respectively. Fraction A, which contained 20% or less of the total DNA, was determined to have a mean size of a hexanucleosome. By hybridization with [3H]cDNA transcribed from total cytoplasmic poly(A) mRNA, DNA from fraction A was shown to be 10-15-fold enriched in transcribing genes when compared with total DNA. This fraction also has a somewhat higher concentration of AT base sequences. Significant differences were observed in nucleosome phasing. Fraction A has the shortest repeat length, fractions B and C are intermediate, and fraction D, which is depleted in transcribing DNA sequences, has the longest. Thus, we have isolated a chromatin fraction of oligonucleosome size enriched in transcribing genes and organized with reduced nucleosome spacing.

Animals↗
PubMed2005

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes.

Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine-homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA-DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.

DNA↗
PubMed2000

PMMA-based composite materials with reactive ceramic fillers: IV. Radiopacifying particles embedded in PMMA beads for acrylic bone cements.

New acrylic bone cements were prepared from alumina particles previously treated by 3-(trimethoxysilyl)propylmethacrylate (gamma-MPS) and embedded in poly(methylmethacrylate-co-ethylacrylate) beads with about 7 mol% of ethyl acrylate repeating units. The encapsulation was performed through a conventional suspension polymerization process. The influence of (i) the concentration of the dispersion stabilizer and (ii) the alumina content upon the shape, size, and size distribution of the acrylic beads was studied. Cements were prepared from each batch by hand-mixing alumina-filled acrylic beads with a liquid monomer mixture containing methyl methacrylate, n-butyl methacrylate, and N,N-dimethyl-p-toluidine. Benzoyl peroxide was previously added to the solid part. The powder-to-liquid ratio was equal to 2 for each formulation. Compressive strength of cured cement decreases with alumina content, whereas compressive modulus remains roughly constant. These results are in contradiction to those obtained for cements based on a mixture of gamma-MPS-treated alumina and unfilled acrylic beads. Nevertheless, they are interpreted in terms of alumina arrangement in the cement. In the first case, alumina particles contribute to the reinforcement of the dispersed acrylic phase, with poor benefits for the whole materials. In the second case, they allow the reinforcement of the continuous acrylic phase and, therefore, the cement's one.

Acrylates↗
PubMed1989

In vitro color change of composite-based resins.

The adsorption of staining materials to resin restoratives was considered to be influenced by the physico-chemical properties of the resin-based monomers. To study the effects of the surface characteristics of resins on staining, we prepared five visible-light-cured experimental resins without fillers. Staining of these resins was colorimetrically measured. The staining solutions used were the Oil Orange and the Food Red 3 solutions. With the Oil Orange solution, the materials with higher hydrophobicity showed higher staining. With the Food Red 3 solution, the materials with higher water sorption showed higher staining.

Color↗
PubMed1985

A three-dimensional representation for base composition of protein-coding DNA sequences.

Multi-dimensional scaling is applied to our codon space data on the protein coding sequences of DNA from a wide variety of organisms in an attempt to find the smallest number of parameters which will accurately represent these sequences. I find that a three-dimensional representation is satisfactory. One of the three resulting co-ordinates separates eukaryotes and their associated viruses from prokaryotes and their associated phages, while an orthogonal co-ordinate separates those organisms capable of synthesizing proteins (eukaryotes and prokaryotes) from those not so capable (viruses and phages). Mitochondria show no relation in our plots to any of these groups.

Bacteria↗
PubMed1998

[Estimation of body composition based on total body water determination using phenazone for assessment of body fat gain in cattle. 2. Relationship between body fat content and back fat thickness].

Back fat thickness was measured at six points in 251 beef heifers aged 3 to 17 months, in 27 beef bulls aged 15 months and in 200 Holstein dairy cows of different age. This was paralleled by estimation of body fat content based on total body water analysis. All groups of animals showed the same pattern of back fat thickness for the measuring points investigated, which lead to the result of one optimum measuring point for determination of back fat thickness. The correlation coefficients between back fat thickness and body fat content were estimated to be between 0.80 and 0.87 for all groups investigated. Change in back fat thickness by 1 mm corresponded to gain or loss of around 5 kg body fat in all animal groups. Therefore it is possible to make concrete assessments of body fat content on the basis of back fat thickness.

Adipose Tissue↗
PubMed2026

C-Reactive Protein-Based Composite Indices for Predicting Tumor Overgrowth Restenosis After Partially Covered Duodenal Stenting in Gastric Cancer: A Cohort Study.

BACKGROUND/OBJECTIVES: Partially covered duodenal stents rapidly relieve malignant gastric outlet obstruction, but tumor overgrowth restenosis limits durability. We compared six preprocedural inflammatory, nutritional, and immune indices for predicting this outcome in patients with gastric cancer. METHODS: We retrospectively analyzed 68 consecutive patients from a prospectively maintained cohort. The primary endpoint was endoscopically or radiologically confirmed tumor overgrowth restenosis. Discrimination was assessed using receiver operating characteristic curves (pairwise DeLong tests with Bonferroni correction) and time-dependent areas under the curve (AUCs) accounting for death as a competing risk. Multivariable cause-specific Cox models were restricted to preprocedural covariates; post-stenting chemotherapy or radiotherapy was examined in time-dependent sensitivity analyses. RESULTS: Technical and clinical success rates were 100% and 94.1%. Seventeen patients (25.0%) developed restenosis at a median of 66 days. The C-reactive protein-albumin-lymphocyte (CALLY) index showed the highest AUC (0.859), followed by the C-reactive protein-to-albumin ratio (CAR; 0.822) and neutrophil-to-lymphocyte ratio (0.774); these three indices did not differ significantly. At an exploratory, internally derived cutoff of ≤0.110, CALLY had 76.5% sensitivity and 84.3% specificity and remained associated with restenosis after adjustment for stenosis site and stent length (adjusted hazard ratio, 12.30; 95% confidence interval, 3.89-38.83; C-index, 0.836), with consistent results in continuous, time-dependent, and tumor-covariate-adjusted analyses. The 180-day cumulative incidence was 52.4% with low CALLY versus 4.3% with high CALLY. CONCLUSIONS: C-reactive protein-based indices showed the highest numerical discrimination, although pairwise differences among CALLY, CAR, and NLR were not statistically significant. CALLY is a promising exploratory biomarker for restenosis risk stratification, but its cutoff should not guide clinical decisions until externally validated.

C-reactive protein↗
PubMed1980

Compartmental body composition based on total-body nitrogen, potassium, and calcium.

The techniques of prompt gamma neutron-activation analysis for the measurement of total-body nitrogen and whole-body counting for the measurement of total-body potassium were used to determine the mass of muscle and nonmuscle lean tissue and their protein content in 135 normal male and female subjects, 20-80 yr of age. Age-related changes in the size of the muscle and nonmuscle compartments and their protein content provide basic data for the investigation of protein metabolism in aging subjects and in individuals with various metabolic disorders, particularly wasting diseases such as cancer. Significant age-related changes in the size of various body compartments were noted. The loss of muscle mass and its protein content contrasts with the relative constancy of the nonmuscle lean tissue and suggests that skeletal muscle is particularly vulnerable to the aging process.

Adult↗
PubMed1995

Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure.

Fourteen oligonucleotides 8-21 nucleotides in length and their complements were synthesized as DNA and RNA. For each sequence, four kinds of duplexes, DNA:DNA, RNA:RNA, DNA:RNA, and RNA:DNA, were prepared. Twelve sequences had A.T/U content varying from 25 to 80% and dPy content in the DNA strands varying from 0 to 100%. Thermodynamic stabilities of four duplexes for each sequence were determined in solution containing 100 mM Na+, 10 mM phosphate, and 0.1 mM EDTA, pH 7.1. CD spectra and electrophoretic mobility on native polyacrylamide gel were measured for most duplexes. Quantitative correlations of hybrid stability both with deoxypyrimidine content and, at fixed dPy content, with the fraction of A.T/U in duplexes were found. We also demonstrated that hybrids with 70-80% deoxypyrimidine DNA strand and a high or moderate A.T/U fraction displayed the highest relative stability compared to their RNA counterparts. Relationships of relative intensities of CD bands at 210 nm and relative electrophoretic mobilities of hybrids with relative hybrid stability suggested that hybrid conformation varies continuously between A- and B-form and is the decisive factor in relative hybrid stability.

Base Sequence↗