Are coiled-coil proteins evolutionarily related?

A modification to the standard Needleman-Wunsch sequence comparison scheme is presented. In cases where high levels of sequence similarity may arise from a common structural motif, this method discriminates between common ancestry and similarity due to structural constraints alone. Use of this algorithm is illustrated with the coiled-coil motif in the cases of idealized coiled-coil sequences, intermediate filaments and reovirus hemagluttinin.     

A method for multiple sequence alignment with gaps

A method that performs multiple sequence alignment by cyclical use of the standard pairwise Needleman-Wunsch algorithm is presented. The required central processor unit time is of the same order of magnitude as the standard Needleman-Wunsch pairwise implementation. Comparison with the one known case where the optimal multiple sequence alignment has been rigorously determined shows that in practice the proposed method finds the mathematically optimal solution. The more interesting question of the biological usefulness of such multiple sequence alignment over pairwise approaches is assessed using protein families whose X-ray structures are known. The two such cases studied, the subdomains of the ricin B-chain and the S-domains of virus coat proteins, have low pairwise similarity and thus fail to align correctly under standard pairwise sequence comparison. In both cases the multiple sequence alignment produced by the proposed technique, apart from minor deviations at loop regions, correctly predicts the true structural alignment. Thus, given many sequences of low pairwise similarity, the proposed multiple sequence method, can extract any familial similarity and so produce a sequence alignment consistent with the underlying structural homology.     

Amperometric micro-immunosensor for the detection of tumor biomarker

In this paper, a highly sensitive, reagentless, electrochemical strategy is reported for the detection of a cancer biomarker-Vascular Endothelial Growth Factor (VEGF). Disc shaped carbon fiber microelectrodes were used as the immunosensor platform. Ferrocene monocarboxylic acid labeled anti-VEGF was covalently immobilized on the microelectrode surface using a Jeffamine cross-linker. The formation of immunocomplexes leads to a decrease in the electrochemical signal of ferrocene monocarboxylic acid owing to increased spatial blocking of microelectrode surface. These signal changes enable quantitative detection of VEGF in solution. Voltammetric measurements were conducted to evaluate the interfacial immunoreactions and to quantitatively detect VEGF biomarker. The proposed immunosensing strategy allows a rapid and sensitive means of VEGF analysis with a limit of detection of about 38 pg/mL. This opens up the possibility of employing these electrodes for various single cell analysis and clinical applications. Further, experimental conditions such as concentration of the immobilized antibodies and incubation period were optimized. Following this, the stability and specificity of the immunosensors were also evaluated.     

APBioNet: the Asia-Pacific regional consortium for bioinformatics

Bioinformatics and computational biology, along with the related fields of genomics, proteomics, functional genomics and systems biology are new wave scientific disciplines that harness composite computational power across networks to advance biological knowledge at the most basic level and to direct traditional laboratory-based research efforts in the biomedical sciences. 'Fostering the growth of bioinformatics and allied disciplines in the Asia-Pacific region' is the motto of the first regional bioinformatics society, the Asia-Pacific Bioinformatics Network (APBioNet). APBioNet addresses the issues of hardware, software, databases and networks pertaining to bioinformatics, with the additional layer of pertinent education, training and research. Recent milestones achieved include hosting an international bioinformatics symposium in Asia and setting up large-scale regional grid-computing projects.     

Effect of ethinylestradiol on arachidonic acid incorporation, release, and conversion to prostaglandins in rabbit platelets

Intramuscular administration to female rabbits of 2 mg/kg ethinylestradiol every other day for 10 days increased the uptake and incorporation of [14C]arachidonic acid into platelet lipids, and increased the proportion of [14C]arachidonic acid released from platelets after stimulation by thrombin. The conversion of [14C]arachidonic acid to thromboxane B2 did not differ between the control and ethinylestradiol-treated groups. Thus, the results of this study indicate that the major site in the prostaglandin metabolic pathway influenced by estrogen is the incorporation and release of arachidonic acid in platelet phospholipids.     

The characteristics and metabolism of a genetically hypercholesterolemic strain of rats (RICO).

A genetically hypercholesterolemic strain of rats was selectively bred, starting from an ordinary albino mutant of Rattus norvegicus. The new strain was given the designation RICO, standing for rats with increased cholesterol. In these animals, hypercholesterolemia is established, in both sexes, one day after weaning, and it increases progressively thereafter. It is due to elevated concentrations of LDL- and HDL-cholesterol. As in the ordinary rat, the HDL fraction makes up the main part of the serum cholesterol in the RICO rat. Metabolic studies revealed that in the RICO strain the overall rate of hepatic cholesterol synthesis is accelerated, as a result of higher than normal activity of 3-hydroxy-3-methylglutaryl-CoA reductase. The activity of cholesterol-7 alpha-hydroxylase is decreased in RICO rats, indicating a lower than normal rate of cholesterol catabolism. No difference was found between RICO and ordinary rats with respect to fecal excretion of bile acids and cholesterol.     

Sterol and bile acid metabolism during development. 1. Studies on the gallbladder and intestinal bile acids of newborn and fetal rabbit

Bile acid composition and content in the intestine and gallbladder of newborn and fetal rabbits were investigated. Unlike the circumstances in adult rabbits, the bile acids were conjugated with both taurine and glycine. The major bile acids of the fetus and newborn rabbit were cholic acid, chenodeoxycholic acid, and deoxycholic acid. This is different from the known bile acid composition of adult rabbits, in which deoxycholic acid is the major bile acid (> 80%). The proportion of chenodeoxycholic acid was higher in the fetal than in the newborn tissues. The total bile acid pool in the newborn was higher than in the fetus. In the fetus, large proportions of bile acids (60.9%) were associated with the gallbladder fraction, whereas in the newborn the bulk of the bile acids were found with the intestinal fraction (64.4%),