ShiftDetector: detection of shift mutations

MOTIVATION: Sequencing of a bi-allelic PCR product, which contains an allele with a deletion/insertion mutation results in a superimposed tracefile following the site of this shift mutation. A trace file of this type hampers the use of current computer programs for base calling. ShiftDetector analyses a sequencing trace file in order to discover if it is a superimposed sequence of two molecules that differ in a shift mutation of 1 to 25 bases. The program calculates a probability score for the existence of such a shift and reconstructs the sequence of the original molecule. AVAILABILITY: ShiftDetector is available from http://cowry.agri.huji.ac.il     

Discovering statistically significant biclusters in gene expression data

In gene expression data, a bicluster is a subset of the genes exhibiting consistent patterns over a subset of the conditions. We propose a new method to detect significant biclusters in large expression datasets. Our approach is graph theoretic coupled with statistical modelling of the data. Under plausible assumptions, our algorithm is polynomial and is guaranteed to find the most significant biclusters. We tested our method on a collection of yeast expression profiles and on a human cancer dataset. Cross validation results show high specificity in assigning function to genes based on their biclusters, and we are able to annotate in this way 196 uncharacterized yeast genes. We also demonstrate how the biclusters lead to detecting new concrete biological associations. In cancer data we are able to detect and relate finer tissue types than was previously possible. We also show that the method outperforms the biclustering algorithm of Cheng and Church (2000).     

Mental competence and elderly care

Competence or decision-making capacity are concepts, which are far from clear-cut. The normative consequences of an incapacity-judgment in elderly care require a balanced approach, which takes into consideration the risk of misuse in the context of the justification of interventions that are applied without consent of the patient. In this article a number of central issues in the debate on decision-making capacity are discussed. The different criteria, which are proposed to assess capacity, are discussed as well as the development of instruments in order to objectify capacity. It is concluded that the common approach towards decision-making capacity, which is strongly cognitive-oriented, is inadequate. A number of relevant aspects remain underexposed within this approach. A broader approach is explored, which takes into account the role of emotions, identity, and dialogue and deliberation. The different approaches are illustrated by way of a case example.     

DEFOG: a practical scheme for deciphering families of genes

We developed a novel efficient scheme, DEFOG (for "deciphering families of genes"), for determining sequences of numerous genes from a family of interest. The scheme provides a powerful means to obtain a gene family composition in species for which high-throughput genomic sequencing data are not available. DEFOG uses two key procedures. The first is a novel algorithm for designing highly degenerate primers based on a set of known genes from the family of interest. These primers are used in PCR reactions to amplify the members of the gene family. The second combines oligofingerprinting of the cloned PCR products with clustering of the clones based on their fingerprints. By selecting members from each cluster, a low-redundancy clone subset is chosen for sequencing. We applied the scheme to the human olfactory receptor (OR) genes. OR genes constitute the largest gene superfamily in the human genome, as well as in the genomes of other vertebrate species. DEFOG almost tripled the size of the initial repertoire of human ORs in a single experiment, and only 7% of the PCR clones had to be sequenced. Extremely high degeneracies, reaching over a billion combinations of distinct PCR primer pairs, proved to be very effective and yielded only 0.4% nonspecific products.     

Cysteine residues in the nucleotide binding domains regulate the conductance state of CFTR channels

Gating of cystic fibrosis transmembrane conductance regulator (CFTR) channels requires intermolecular or interdomain interactions, but the exact nature and physiological significance of those interactions remains uncertain. Subconductance states of the channel may result from alterations in interactions among domains, and studying mutant channels enriched for a single conductance type may elucidate those interactions. Analysis of CFTR channels in inside-out patches revealed that mutation of cysteine residues in NBD1 and NBD2 affects the frequency of channel opening to the full-size versus a 3-pS subconductance. Mutating cysteines in NBD1 resulted in channels that open almost exclusively to the 3-pS subconductance, while mutations of cysteines in NBD2 decreased the frequency of subconductance openings. Wild-type channels open to both size conductances and make fast transitions between them within a single open burst. Full-size and subconductance openings of both mutant and wild-type channels are similarly activated by ATP and phosphorylation. However, the different size conductances open very differently in the presence of a nonhydrolyzable ATP analog, with subconductance openings significantly shortened by ATPgammaS, while full-size channels are locked open. In wild-type channels, reducing conditions increase the frequency and decrease the open time of subconductance channels, while oxidizing conditions decrease the frequency of subconductance openings. In contrast, in the cysteine mutants studied, altering redox potential has little effect on gating of the subconductance.     

RNA interference of signal peptide-binding protein SRP54 elicits deleterious effects and protein sorting defects in trypanosomes

Trypanosomes are protozoan parasites that have a major impact on health. This family diverged very early from the eukaryotic lineage and possesses unique RNA processing mechanisms such as trans-splicing and RNA editing. The trypanosome signal recognition particle (SRP) has a unique composition compared with all known SRP complexes, because it contains two RNA molecules, the 7SL RNA and a tRNA-like molecule. RNA interference was utilized to elucidate the essentiality of the SRP pathway and its role in protein translocation in Trypanosoma brucei. The production of double stranded RNA specific for the signal peptide-binding protein SRP54 induced the degradation of the mRNA and a loss of the SRP54 protein. SRP54 depletion elicited inhibition in growth and cytokinesis, suggesting that the SRP pathway is essential. The translocation of four signal peptide-containing proteins was examined. Surprisingly, the proteins were translocated to the endoplasmic reticulum and properly processed. However, the surface EP procyclin, the lysosomal protein p67, and the flagellar pocket protein CRAM were mislocalized and accumulated in megavesicles, most likely because of a secondary effect on protein sorting. The translocation of these proteins to the endoplasmic reticulum under SRP54 depletion suggests that an alternative pathway for protein translocation exists in trypanosomes.     

Effects of environmental salinity and 17alpha-methyltestosterone on growth and oxygen consumption in the tilapia, Oreochromis mossambicus

Effects of environmental salinity and 17α-methyltestosterone (MT) on growth and oxygen consumption were examined in the tilapia, Oreochromis mossambicus. Yolk-sac fry were collected from brood stock in fresh water (FW). After yolk-sac absorption, they were assigned randomly to one of four groups: FW, MT treatment in FW, seawater (SW) and MT treatment in SW. All treatment groups were fed to satiation three times daily. The fish reared in SW (both control and MT-treated groups) grew significantly larger than either group in FW from day 43 throughout the experiment (195 days). The fish fed with MT added to their feed grew significantly larger than their respective controls from day 85 in FW and in SW until the end of the experiment. The routine metabolic rate (RMR) was determined monthly from month 2 (day 62) to month 5 (day 155). A significant negative correlation was seen between RMR and body mass in all treatment groups. Among fish of the same age, the SW-reared tilapia had significantly lower RMRs than the FW-reared fish. The MT-treated fish in SW showed significantly lower RMRs than the SW control group at months 3–5, whereas MT treatment in FW significantly increased the RMR at month 3. Comparison of regression lines between RMR and body mass indicates that MT treatment in FW caused a significant increase in oxygen consumption at a given mass of the fish, whereas MT treatment was without effect on RMR in SW-reared fish. These results clearly indicate that SW-rearing and MT treatment accelerate growth of tilapia, and that RMR decreases as fish size increased. It is also likely that the increased RMR and growth in MT-treated tilapia in FW may be due to the metabolic actions of MT, although the reason for the absence of MT treatment in SW is unclear.