A fractional programming approach to efficient DNA melting temperature calculation

MOTIVATION: In a wide range of experimental techniques in biology, there is a need for an efficient method to calculate the melting temperature of pairings of two single DNA strands. Avoiding cross-hybridization when choosing primers for the polymerase chain reaction or selecting probes for large-scale DNA assays are examples where the exact determination of melting temperatures is important. Beyond being exact, the method has to be efficient, as these techniques often require the simultaneous calculation of melting temperatures of up to millions of possible pairings. The problem is to simultaneously determine the most stable alignment of two sequences, including potential loops and bulges, and calculate the corresponding melting temperature. RESULTS: As the melting temperature can be expressed as a fraction in terms of enthalpy and entropy differences of the corresponding annealing reaction, we propose to use a fractional programming algorithm, the Dinkelbach algorithm, to solve the problem. To calculate the required differences of enthalpy and entropy, the Nearest Neighbor model is applied. Using this model, the substeps of the Dinkelbach algorithm in our problem setting turn out to be calculations of alignments which optimize an additive score function. Thus, the usual dynamic programming techniques can be applied. The result is an efficient algorithm to determine melting temperatures of two DNA strands, suitable for large-scale applications such as primer or probe design. AVAILABILITY: The software is available for academic purposes from the authors. A web interface is provided at http://www.zaik.uni-koeln.de/bioinformatik/fptm.html     

GeneRank: Using search engine technology for the analysis of microarray experiments

Background  

Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method – based on the PageRank algorithm employed by the popular search engine Google – that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information.     

Haemophilia A: from mutation analysis to new therapies

Haemophilia is caused by hundreds of different mutations and manifests itself in clinical conditions of varying severity. Despite being inherited in monogenic form, the clinical features of haemophilia can be influenced by other genetic factors, thereby confounding the boundary between monogenic and multifactorial disease. Unlike sufferers of other genetic diseases, haemophiliacs can be treated successfully by intravenous substitution of coagulation factors. Haemophilia is also the most attractive model for developing gene-therapy protocols, as the normal life expectancy of haemophiliacs allows the side effects of gene therapy, as well as its efficiency, to be monitored over long periods.     

Modelling energetic costs of fish swimming

The oxygen consumption rates of two cyprinid fishes, carp (Cyprinus carpio L.) and roach (Rutilus rutilus (L.)), were analysed for a wide range of body mass and swimming speed by computerized intermittent-flow respirometry. Bioenergetic models were derived, based on fish mass (M) and swimming speed (U), to predict the minimal speed and mass-specific active metabolic rate (AMR) in these fishes (AMR=aMbUc). Mass and speed together explained more than 90% of the variance in total swimming costs in both cases. The derived models show that carp consume far more oxygen at a specific speed and body mass, thus being less efficient in energy use during swimming than roach. It was further found that in carp (AMR=0.02M0.8U0.95) the metabolic increment during swimming is more strongly effected by speed, whereas in roach (AMR=0.02M0.93U0.6) it is more strongly effected by body mass. The different swimming traits of carp and roach are suitable for their respective lifestyles and ecological demands.     

Determination of telithromycin in human plasma and microdialysates by high-performance liquid chromatography

A high-performance liquid chromatography method for the quantitative determination of telithromycin in biological fluids is described. The method is suitable for plasma and microdialysates from the interstitial space fluid of skeletal muscle and subcutaneous adipose tissue. Plasma samples were deproteinised with trichloroacetic acid and neutralised with sodium hydroxide. Microdialysates were analysed without further preparation step. Telithromycin was separated isocratically on a reverse-phase column using acetonitrile-0.03 M ammonium acetate, pH 5.2 (43:57, v/v) at a flow rate of 0.8 mlmin(-1), and fluorescence detection (excitation 263 nm, emission 460 nm). The calibration curve was linear from 0.01 to 5 microgml(-1). Within- and between-day imprecision and inaccuracy was < or =10%. The limits of quantification were 0.02 and 0.015 microgml(-1) for plasma and microdialysates, respectively. Since telithromycin is decomposed in aqueous solution at ambient temperature, it is strongly recommended to store samples frozen at -80 degrees C, to maintain the temperature at 4 degrees C during all preparation steps, and to analyse samples within 120 min after thawing.     

Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases

Selection experiments and protein engineering were used to identify an amino acid position in integral membrane alkane hydroxylases (AHs) that determines whether long-chain-length alkanes can be hydroxylated by these enzymes. First, substrate range mutants of the Pseudomonas putida GPo1 and Alcanivorax borkumensis AP1 medium-chain-length AHs were obtained by selection experiments with a specially constructed host. In all mutants able to oxidize alkanes longer than C13, W55 (in the case of P. putida AlkB) or W58 (in the case of A. borkumensis AlkB1) had changed to a much less bulky amino acid, usually serine or cysteine. The corresponding position in AHs from other bacteria that oxidize alkanes longer than C13 is occupied by a less bulky hydrophobic residue (A, V, L, or I). Site-directed mutagenesis of this position in the Mycobacterium tuberculosis H37Rv AH, which oxidizes C10 to C16 alkanes, to introduce more bulky amino acids changed the substrate range in the opposite direction; L69F and L69W mutants oxidized only C10 and C11 alkanes. Subsequent selection for growth on longer alkanes restored the leucine codon. A structure model of AHs based on these results is discussed.     

The cockroach Leucophaea maderae needs more than juvenile hormone, vitellogenin and reserves to make a yolky egg

For the cockroach Leucophaea maderae the developmental profile of lipophorin (Lp) concentrations in the hemolymph was determined through the entire vitellogenic period. At mid-vitellogenesis the concentrations of Lp had risen to 6 times the level at emergence and then declined to 2/3 of such high values at ovulation. The racemic 10R,10S-JH-III bound to Lp with an affinity of K(d) = 5.76 nM and the natural enantiomer 10R-JH-III with a K(d) = 1.60 nM. Injections of anti-Lp into mated females caused a significantly reduced rate of oocyte growth and a substantial degree of oosorption. Injections of gamma-globulin did not significantly reduce oocyte growth and caused only a small number of oocytes to resorb. Starvation after mating had similar effects as treatment with anti-Lp. Because of the high affinity of JH to Lp and since Lp occurs in micromolar concentrations during vitellogenesis one can assume that practically all JH is bound and not available for hydrolysis by the JH esterases. Lp appears to function as an inhibitor of JH metabolism by the JHEs through substrate depletion. One may conclude that a normal rate of egg growth is only achieved when titers of Lp exceed those of JH and remove major portions of this substrate from degradation by the JHEs.