All-male production by marker-assisted selection for sex determining loci of admixed Oreochromis niloticus and Oreochromis aureus stocks.

Crossing Oreochromis niloticus (On) females with Oreochromis aureus (Oa) males results in all-male progeny that are essential for effective tilapia farming. However, a reproductive barrier between these species limits mating and mass-fry production. One approach to overcoming this barrier is to select parental stocks of mixed genetic backgrounds, which allow interspecific reproductive recognition, while closely maintaining the genetic profiles for sex-determination (SD) of the respective purebred species. Here, we test this approach in a data set of 160 On × Oa spawns of 109 male and 100 female parents randomly collected from admixed stocks, and genotyped for microsatellite markers representing the known SD loci on linkage groups (LGs) 1, 3, and 23. Following crossbreeding, the most significant paternal effects on male proportions in progeny were found for LG1-BYL018 (P < 2 × 10-32 ) and for LG3-UNH168 × LG23-UNH898 interaction (P < 1 × 10-17 ; R2  = 0.98). Furthermore, a maternal effect for LG3-UNH168 (P < 9 × 10-7 ) was associated with low female proportions in progeny (<7%), indicating a non-Mendelian effect on SD. Eighty-four males (77%) and 30 females (30%) were selected as parents, based on their genetic profiles for the SD loci that were associated with male production. Of these, 51 of 53 crosses produced all-male progeny, while two crosses had low female proportions in their progeny (<4%). This suggests that selection could be improved using the causative sequence variation underlying SD on LG3, since the large non-recombining block of the SD region in purebred Oa readily breaks down in hybrids. Nevertheless, marker-assisted selection for sex determining loci of admixed parental stocks may be used for all-male production.

A duplication of the Anti-Müllerian hormone gene is associated with genetic sex determination of different Oreochromis niloticus strains.

Sex determination (SD) mechanisms are ancient and conserved, yet much diversity is exhibited in primary sex-determining signals that trigger male or female development. In O. niloticus, SD is associated with a male-specific locus on linkage group (LG) 23 which harbors the Y-linked Anti-Müllerian hormone (amh) gene, and a truncated duplication, denoted amhΔy. We have evaluated the possible role of identified indels and SNPs in the amh gene on SD, based on conservation in different O. niloticus strains. A fluorescent assay for the detection of a 5 bp insertion in amhΔy exon VI, efficiently discriminated between XX, XY, and YY genotypes. Concordance rate between amhΔy and sex varied in six Oreochromis strains, from 100% (Ghana) through 90% (Swansea) to 85% (Thai-Chitralada). The association of amhΔy with sex was found to be conserved in all tested O. niloticus strains, and thus supports its key role in SD. However, the previously identified missense SNP (C/T) in amh exon II was found only in the Swansea strain, thus excluding its candidacy for the causal variation of SD across all strains. Effects of markers on LGs 1, 3, and 23 (amhΔy) fully explained sex distribution in one Thai-Chitralada family (R2 = 1.0), whereas in another family only the major effect of LG23 (amhΔy) was significant (R2 = 0.37). Thus, amhΔy on LG23 is associated with genetic SD, either as a single causal gene in different O. niloticus strains, or in combination with segregating genes on LGs 1 and 3 in the Thai-Chitralada hybrid strain.

Identification of the sex-determining region in flathead grey mullet (Mugil cephalus).

Elucidation of the sex-determination mechanism in flathead grey mullet (Mugil cephalus) is required to exploit its economic potential by production of genetically determined monosex populations and application of hormonal treatment to parents rather than to the marketed progeny. Our objective was to construct a first-generation linkage map of the M. cephalus in order to identify the sex-determining region and sex-determination system. Deep-sequencing data of a single male was assembled and aligned to the genome of Nile tilapia (Oreochromis niloticus). A total 245 M. cephalus microsatellite markers were designed, spanning the syntenic tilapia genome assembly at intervals of 10 Mb. In the mapping family of full-sib progeny, 156 segregating markers were used to construct a first-generation linkage map of 24 linkage groups (LGs), corresponding to the number of chromosomes. The linkage map spanned approximately 1200 cM with an average inter-marker distance of 10.6 cM. Markers segregating on LG9 in two independent mapping families showed nearly complete concordance with gender (R2  = 0.95). The sex determining locus was fine mapped within an interval of 8.6 cM on LG9. The sex of offspring was determined only by the alleles transmitted from the father, thus indicating an XY sex-determination system.

Gene expression profiles of AML derived stem cells; similarity to hematopoietic stem cells.

Tumors contain a fraction of cancer stem cells that maintain the propagation of the disease. The CD34(+)CD38(-) cells, isolated from acute myeloid leukemia (AML), were shown to be enriched leukemic stem cells (LSC). We isolated the CD34(+)CD38(-) cell fraction from AML and compared their gene expression profiles to the CD34(+)CD38(+) cell fraction, using microarrays. We found 409 genes that were at least twofold over- or underexpressed between the two cell populations. These include underexpression of DNA repair, signal transduction and cell cycle genes, consistent with the relative quiescence of stem cells, and chromosomal aberrations and mutations of leukemic cells. Comparison of the LSC expression data to that of normal hematopoietic stem cells (HSC) revealed that 34% of the modulated genes are shared by both LSC and HSC, supporting the suggestion that the LSC originated within the HSC progenitors. We focused on the Notch pathway since Jagged-2, a Notch ligand was found to be overexpressed in the LSC samples. We show that DAPT, an inhibitor of gamma-secretase, a protease that is involved in Jagged and Notch signaling, inhibits LSC growth in colony formation assays. Identification of additional genes that regulate LSC self-renewal may provide new targets for therapy.

Microstructures in high-Tc Bi(Pb)-family 2212 superconductors as revealed by scanning and transmission electron microscopy.

Microstructures of Bi(Pb)-family 2212 superconductors, which were prepared by a sol-gel method with three different compositions, were examined mainly by scanning and transmission electron microscopy. The magnetization of the specimens strongly depends on the ratio between Bi and Pb content, while Tc is almost constant. In specimen 1, prepared with the nominal composition of Bi/Pb = 9/1, small grains of 2212 phase are formed with a minor fraction of some impurity phases. In specimen 2, with Bi/Pb = 17/3, which is optimum from the viewpoint of magnetization, large grains of the 2212 phase are formed during heating at 800 degrees C, also with the impurity phases. In specimen 3, with Bi/Pb = 8/2, the 2212 grains are divided by layers of (Bi0.86, Pb0.14) (Ca0.7, Sr0.3)Ox. Moreover, plate-like 2212 crystals are severely bent so that small cracks appear often with an inclusion of amorphous substance being rich in Ca and Pb. These layers and cracks must degrade the magnetization. A modulated structure of Bi-type is formed in the 2212 grains of specimens 1 and 2, while not only Bi-type but also Pb-type are formed in specimen 3. The wavelength of Bi-type is different for each specimen.

Generation of unpredictable time series by a neural network.

A perceptron that "learns" the opposite of its own output is used to generate a time series. We analyze properties of the weight vector and the generated sequence, such as the cycle length and the probability distribution of generated sequences. A remarkable suppression of the autocorrelation function is explained, and connections to the Bernasconi model are discussed. If a continuous transfer function is used, the system displays chaotic and intermittent behavior, with the product of the learning rate and amplification as a control parameter.

Multichoice minority game.

The generalization of the problem of adaptive competition, known as the minority game, to the case of K possible choices for each player, is addressed, and applied to a system of interacting perceptrons with input and output units of a type of K-state Potts spins. An optimal solution of this minority game, as well as the dynamic evolution of the adaptive strategies of the players, are solved analytically for a general K and compared with numerical simulations.

Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices.

SUMMARY: We introduce a novel unsupervised approach for the organization and visualization of multidimensional data. At the heart of the method is a presentation of the full pairwise distance matrix of the data points, viewed in pseudocolor. The ordering of points is iteratively permuted in search of a linear ordering, which can be used to study embedded shapes. Several examples indicate how the shapes of certain structures in the data (elongated, circular and compact) manifest themselves visually in our permuted distance matrix. It is important to identify the elongated objects since they are often associated with a set of hidden variables, underlying continuous variation in the data. The problem of determining an optimal linear ordering is shown to be NP-Complete, and therefore an iterative search algorithm with O(n3) step-complexity is suggested. By using sorting points into neighborhoods, i.e. SPIN to analyze colon cancer expression data we were able to address the serious problem of sample heterogeneity, which hinders identification of metastasis related genes in our data. Our methodology brings to light the continuous variation of heterogeneity--starting with homogeneous tumor samples and gradually increasing the amount of another tissue. Ordering the samples according to their degree of contamination by unrelated tissue allows the separation of genes associated with irrelevant contamination from those related to cancer progression. AVAILABILITY: Software package will be available for academic users upon request.

Confidence in prediction by neural networks.

The idea that a trained network can assign a confidence number to its prediction, indicating the level of its reliability, is addressed and exemplified by an analytical examination of a perceptron with discrete and continuous output units. Results are derived for both Gibbs and Bayes scenarios. The information gain by the confidence number is estimated by various entropy measurements.

Morphometric studies of pancreatic acinar granule formation in NCTR-Balb/c mice.

NCTR-Balb/c mice are afflicted with a cholesterol lysosomal storage disorder stemming from a defect in intracellular cholesterol processing. The clinical and biochemical abnormalities expressed in the mice resemble Niemann-Pick type C and D disorders in humans. One of the proposed mechanisms to explain the pathophysiology of the disorder implies a defect in the process of membrane transport that normally takes place in the vesicular movement of cholesterol to specific target sites in the cell. Secretory granule formation in pancreatic acinar cells is one of the biological processes known to involve massive membrane flow. Thus, we have undertaken a morphometric study of the regranulation mechanism in the pancreatic acinar cells of the mutant mice, as a way of studying cellular membrane movement. Electron micrographs of pancreatic acinar cells from mutant and normal mice were taken at several time points after extensive degranulation induced by pilocarpine injection. Two hours after stimulation the pancreatic cells demonstrated a complete loss of granules, and at later time points newly formed granules appeared. Identical unit granule volumes were observed in both groups, indicating that the progranules were of normal size. However, the rate of granule formation and maturation was reduced in the mutant mice, which might be the result of a defect in membrane function.