Three novel components of the human exosome

The yeast exosome is a complex of 3' --> 5' exoribonucleases. Sequence analysis identified putative human homologues for exosome components, although several were found only as expressed sequence tags. Here we report the cloning of full-length cDNAs, which encode putative human homologues of the Rrp40p, Rrp41p, and Rrp46p components of the exosome. Recombinant proteins were expressed and used to raise rabbit antisera. In Western blotting experiments, these decorated HeLa cell proteins of the predicted sizes. All three human proteins were enriched in the HeLa cells nucleus and nucleolus, but were also clearly detected in the cytoplasm. Size exclusion chromatography revealed that hRrp40p, hRrp41p, and hRrp46p were present in a large complex. This cofractionated with the human homologues of other exosome components, hRrp4p and PM/Scl-100. Anti-PM/Scl-positive patient sera coimmunoprecipitated hRrp40p, hRrp41p, and hRrp46p demonstrating their physical association. The immunoprecipitated complex exhibited 3' --> 5' exoribonuclease activity in vitro. hRrp41p was expressed in yeast and shown to suppress the lethality of genetic depletion of yeast Rrp41p. We conclude that hRrp40p, hRrp41p, and hRrp46p represent novel components of the human exosome complex.     

Genetic diversity of a population of Schistosoma haematobium derived from schoolchildren in east central Zimbabwe

To characterize the extent of genetic diversity of Schistosoma haematobium within and among its definitive host (intra- and interhost parasite diversity), 133 individual isolates from 25 infected schoolchildren were compared using randomly amplified polymorphic DNA markers. With 4 primers, 53 unambiguous loci were identified, and of these, 22 were polymorphic. Mean heterozygosity in the population was 0.116 +/- 0.043. Analysis of molecular variance showed the majority of variance occurred within, rather than between, hosts. Frequencies of certain alleles segregated the parasite population into 13 distinct clusters of associated genotypes, with 4 of these first appearing 10 mo after the initial survey. Considering the level of diversity within this limited geographical area and the possibility of rapid turnover of genotypes, parasite variance may impact acquired immunity and clinical outcome of the infection.     

Growing of a Fuzzy Recurrent Artificial Neural Network (FRANN) for pattern classification

This paper describes a method for growing a recurrent neural network of fuzzy threshold units for the classification of feature vectors. Fuzzy networks seem natural for performing classification, since classification is concerned with set membership and objects generally belonging to sets of various degrees. A fuzzy unit in the architecture proposed here determines the degree to which the input vector lies in the fuzzy set associated with the fuzzy unit. This is in contrast to perceptrons that determine the correlation between input vector and a weighting vector. The resulting membership value, in the case of the fuzzy unit, is compared with a threshold, which is interpreted as a membership value. Training of a fuzzy unit is based on an algorithm for linear inequalities similar to Ho-Kashyap recording. These fuzzy threshold units are fully connected in a recurrent network. The network grows as it is trained. The advantages of the network and its training method are: (1) Allowing the network to grow to the required size which is generally much smaller than the size of the network which would be obtained otherwise, implying better generalization, smaller storage requirements and fewer calculations during classification; (2) The training time is extremely short; (3) Recurrent networks such as this one are generally readily implemented in hardware; (4) Classification accuracy obtained on several standard data sets is better than that obtained by the majority of other standard methods; and (5) The use of fuzzy logic is very intuitive since class membership is generally fuzzy.     

Vertebrate aristaless-related genes

Aristaless-related genes, a subset of the Paired-related homeobox genes, have in the past few years emerged as a group of regulators of essential events during vertebrate embryogenesis. One group of aristaless-related genes has been linked to the morphogenesis of the craniofacial and appendicular skeleton by their expression patterns and by the phenotypes of natural and artificial mouse mutants. Expression and function in the nervous system characterise a second group, and a third group, the Pitx genes, have been shown to have many different roles, including functions in the pituitary, left-right determination and limb development.     

Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs

An earlier study identified quantitative trait loci (QTLs) lb4, lb5b, and lb11b for quantitative resistance to Phytophthora infestans (late blight) in a backcross population derived from crossing susceptible cultivated tomato (Lycopersicon esculentum) with resistant L. hirsutum. The QTLs were located in intervals spanning 28–47 cM. Subsequently, near-isogenic lines (NILs) were developed for lb4, lb5b, and lb11b by marker-assisted backcrossing to L. esculentum. Sub-NILs containing overlapping L. hirsutum segments across each QTL region were selected and used to validate the QTL effects, fine-map QTLs, and evaluate potential linkage drag between resistance QTLs and QTLs for horticultural traits. The NILs and sub-NILs were evaluated for disease resistance and eight horticultural traits at three field locations. Resistance QTLs were detected in all three sets of NIL lines, confirming the BC₁ mapping results. Lb4 mapped near TG609, and between TG182 and CT194, on chromosome 4, a 6.9-cM interval; lb5b mapped to an 8.8-cM interval between TG69a and TG413 on chromosome 5, with the most likely position near TG23; and lb11b mapped to a 15.1-cM interval on chromosome 11 between TG194 and TG400, with the peak centered between CT182 and TG147. Most QTLs for horticultural traits were identified in intervals adjacent to those containing the late blight resistance QTLs. Fine mapping of these QTLs permits the use of marker-assisted selection for the precise introgression of L. hirsutum segments containing late blight resistance alleles separately from those containing deleterious alleles at horticulturally important QTLs.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by D.B. Neale     

Mutations in the calcium-binding motifs of CDH23 and the 35delG mutation in GJB2 cause hearing loss in one family

We have ascertained a multi-generation family with apparent autosomal recessive non-syndromic childhood hearing loss (DFNB). Failure to demonstrate linkage in a genome-wide scan with 300 polymorphic markers has suggested genetic heterogeneity for the hearing loss in this family. This heterogeneity could be demonstrated by analysis of candidate loci and genes for DFNB. Patients in one branch of the family (branch C) are homozygous for the 35delG mutation in the GJB2 gene (DFNB1). Patients in two other branches (A and B) carry two new mutations in the cadherin 23 ( CDH23) gene (DFNB12). A homozygous CDH23 c.6442G-->A (D2148N) mutation is present in branch A. Patients in branch B are compound heterozygous for this mutation and the c.4021G-->A (D1341N) mutation. The substituted aspartic acid residues are highly conserved and are part of the calcium-binding sites of the extracellular cadherin (EC) domains. Molecular modeling of the mutated EC domains of CDH23 based on the structure of E-cadherin indicates that calcium-binding is impaired. In addition, other aspartic and glutamic acid residue substitutions in the highly conserved calcium-binding sites reported to cause DFNB12 are also likely to result in a decreased affinity for calcium. Since calcium provides rigidity to the elongated structure of cadherin molecules enabling homophilic lateral interaction, these mutations are likely to impair interactions of CDH23 molecules either with CDH23 or with other proteins. DFNB12 is the first human disorder that can be attributed to inherited missense mutations in the highly conserved residues of the extracellular calcium-binding domain of a cadherin.     

Clofibrate-induced relocation of phosphatidylcholine transfer protein to mitochondria in endothelial cells

The phosphatidylcholine transfer protein (PC-TP) is a specific transporter of phosphatidylcholine (PC) between membranes. To get more insight into its physiological function, we have studied the localization of PC-TP by microinjection of fluorescently labeled PC-TP in foetal bovine heart endothelial (FBHE) cells and by expression of an enhanced yellow fluorescent protein-PC-TP fusion protein in FBHE cells, human umbilical vein endothelial cells, and HepG2 cells. Analysis by confocal laser scanning microscopy showed that PC-TP was evenly distributed throughout the cytosol with an apparently elevated level in nuclei. By measuring the fluorescence recovery after bleaching it was established that PC-TP is highly mobile throughout the cell, with its transport into the nucleus being hindered by the nuclear envelope. Given the proposed function of PC-TP in lipid metabolism, we have tested a number of compounds (phorbol ester, bombesin, A23187, thrombin, dibutyryl cyclic AMP, oleate, clofibrate, platelet-derived growth factor, epidermal growth factor, and hydrogen peroxide) for their ability to affect intracellular PC-TP distribution. Only clofibrate (100 microM) was found to have an effect, with PC-TP moving to mitochondria within 5 min of stimulation. This relocation did not occur with PC-TP(S110A), lacking the putative protein kinase C (PKC)-dependent phosphorylation site, and was restricted to the primary endothelial cells. Relocation did not occur in HepG2 cells, possibly due to the fact that clofibrate does not induce PKC activation in these cells.     

A discrete fully recurrent network of max product units for associative memory and classification

This paper defines the truncated normalized max product operation for the transformation of states of a network and provides a method for solving a set of equations based on this operation. The operation serves as the transformation for the set of fully connected units in a recurrent network that otherwise might consist of linear threshold units. Component values of the state vector and outputs of the units take on the values in the set [0, 0.1,..., 0.9, 1]. The result is a much larger state space given a particular number of units and size of connection matrix than for a network based on threshold units. Since the operation defined here can form the basis of transformations in a recurrent network with a finite number of states, fixed points or cycles are possible and the network based on this operation for transformations can be used as an associative memory or pattern classifier with fixed points taking on the role of prototypes. Discrete fully recurrent networks have proven themselves to be very useful as associative memories and as classifiers. However they are often based on units that have binary states. The effect of this is that the data to be processed consisting of vectors in R(n) have to be converted to vectors in [0, 1]m with m much larger than n since binary encoding based on positional notation is not feasible. This implies a large increase in the number of components. The effect can be lessened by allowing more states for each unit in our network. The network proposed demonstrates those properties that are desirable in an associative memory very well as the simulations show.     

Esa1, an Arabidopsis mutant with enhanced susceptibility to a range of necrotrophic fungal pathogens, shows a distorted induction of defense responses by reactive oxygen generating compounds

An Arabidopsis thaliana mutant, esa1, that shows enhanced susceptibility to the necrotrophic pathogens Alternaria brassicicola, Botrytis cinerea and Plectosphaerella cucumerina, but has wild-type levels of resistance to the biotrophic pathogens Pseudomonas syringae pv. tomato and Peronospora parasitica. The enhanced susceptibility towards necrotrophic pathogens correlated with a delayed induction of phytoalexin accumulation and delayed induction of the plant defensin gene PDF1.2 upon inoculation with pathogens. Two reactive oxygen generating compounds, paraquat and acifluorfen, were found to cause induction of both phytoalexin accumulation and PDF1.2 expression in wild-type plants, but this induction was almost completely abolished in esa1. This finding suggests that esa1 may somehow be involved in transduction of signals generated by reactive oxygen species.