A blocking Gibbs sampling method to detect major genes with phenotypic data from a diallel mating

Diallel mating is a frequently used design for estimating the additive and dominance genetic (polygenic) effects involved in quantitative traits observed in the half- and full-sib progenies generated in plant breeding programmes. Gibbs sampling has been used for making statistical inferences for a mixed-inheritance model (MIM) that includes both major genes and polygenes. However, using this approach it has not been possible to incorporate the genetic properties of major genes with the additive and dominance polygenic effects in a diallel mating population. A parent block Gibbs sampling method was developed in this study to make statistical inferences about the major gene and polygenic effects on quantitative traits for progenies derived from a half-diallel mating design. Using simulated data sets with different major and polygenic effects, the proposed method accurately estimated the major and polygenic effects of quantitative traits, and possible genotypes of parents and progenies. The impact of specifying different prior distributions was examined and was found to have little effect on inference on the posterior distribution. This approach was applied to an experimental data set of Loblolly pine (Pinus taeda L.) derived from a 6-parent half-diallel mating. The result indicated that there might be a recessive major gene affecting height growth in this diallel population.     

A Gibbs sampling approach to linkage analysis.

We present a Monte Carlo approach to estimation of the recombination fraction theta and the profile likelihood for a dichotomous trait and a single marker gene with 2 alleles. The method is an application of a technique known as 'Gibbs sampling', in which random samples of each of the unknowns (here genotypes, theta and nuisance parameters, including the allele frequencies and the penetrances) are drawn from their posterior distributions, given the data and the current values of all the other unknowns. Upon convergence, the resulting samples derive from the marginal distribution of all the unknowns, given only the data, so that the uncertainty in the specification of the nuisance parameters is reflected in the variance of the posterior distribution of theta. Prior knowledge about the distribution of theta and the nuisance parameters can be incorporated using a Bayesian approach, but adoption of a flat prior for theta and point priors for the nuisance parameters would correspond to the standard likelihood approach. The method is easy to program, runs quickly on a microcomputer, and could be generalized to multiple alleles, multipoint linkage, continuous phenotypes and more complex models of disease etiology. The basic approach is illustrated by application to data on cholesterol levels and an a low-density lipoprotein receptor gene in a single large pedigree.     

More robust detection of motifs in coexpressed genes by using phylogenetic information

Background  

Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number lacking the motif might not be sufficiently high to allow detection by classical motif detection tools. To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates.     

A polymerase chain reaction-based method to detect cisplatin adducts in specific genes.

Every bulky lesion in DNA can potentially inhibit the Taq DNA polymerase and thereby decrease the amplification produced in the polymerase chain reaction. We investigated the feasibility of using this inhibition to quantify DNA lesions produced by the anticancer drug cisplatin. Products were detected by electrophoresis followed by ethidium bromide staining. Quantitation was obtained by including [32P]dCTP in the amplification reaction and subsequently assessing the incorporated radioactivity. Hamster genomic DNA was platinated in vitro to defined levels and amplified with primers that produce either a 150, 750 or 2,000 base pair fragment. The degree of inhibition of PCR agreed with the predicted level of DNA platination in each size of fragment, suggesting that the polymerase was inhibited by every cisplatin-induced lesion. This method was used to detect cisplatin-induced lesions in the adenine phosphoribosyltransferase gene of CHO cells. Cells were incubated with 0-125 microM cisplatin for 2 h, the DNA was purified and subjected to PCR. A significant decrease in amplification of the 2 kbp fragment was observed in DNA from cells incubated with cisplatin at 75 microM. The degree of inhibition agreed closely with the amount of DNA damage in the overall genome as measured by atomic absorption. No change was detected in amplification of the 150 base fragment which can therefore be used to normalize data for any variations between DNA samples. This assay has the same sensitivity as other methods currently used for the analysis of gene-specific damage. The advantage of this assay is that it obviates the need for specific endonuclease complexes to recognize and cleave DNA adducts as previously required when analyzing damage in specific genomic sequences.     

Conserved sequence motifs upstream from the co-ordinately expressed vitellogenin and apoVLDLII genes of chicken.

The vitellogenin and apoVLDLII yolk protein genes of chicken are transcribed in the liver upon estrogenization. To get information on putative regulatory elements, we compared more than 2 kb of their 5' flanking DNA sequences. Common sequence motifs were found in regions exhibiting estrogen-induced changes in chromatin structure. Stretches of alternating pyrimidines and purines of about 30-nucleotides long are present at roughly similar positions. A distinct box of sequence homology in the chicken genes also appears to be present at a similar position in front of the vitellogenin genes of Xenopus laevis, but is absent from the estrogen-responsive egg-white protein genes expressed in the oviduct. In front of the vitellogenin (position -595) and the VLDLII gene (position -548), a DNA element of about 300 base-pairs was found, which possesses structural characteristics of a mobile genetic element and bears homology to the transposon-like Vi element of Xenopus laevis.     

Comparison of upstream regions of X- and Y-chromosomal amelogenin genes

The amelogenin genes encode abundant enamel proteins that are required for the development of normal tooth enamel. These genes are active only in enamel-forming ameloblasts within the dental organ of the developing tooth, and are part of a small group of genes that are active on both sex chromosomes. The upstream regions of the bovine X- and Y-chromosomal and the sole murine X-chromosomal amelogenin genes have been cloned and sequenced, and conservation at nearly 60% is found in the 300 bp upstream of exon 1 for the 3 genes. A region of the bovine X-chromosomal gene that has inhibitory activity when assayed by gene transfer into heterologous cells includes motifs that have a silencing activity in other genes, and may be important to the mechanism that represses amelogenin expression in non-ameloblast cells in vivo. A comparison of sequences from three genes has led to the identification of several regions with conserved motifs that are strong candidates for having positive or negative regulatory functions, and these regions can now be tested further for interaction with nuclear proteins, and for their ability to regulate expression in vivo.     

A high-throughput analysis method to detect regions of interest and quantify zebrafish embryo images

Zebrafish is widely used to understand neural development and model various neurodegenerative diseases. Zebrafish embryos are optically transparent, have a short development period, and can be kept alive in microplates for days, making them amenable to high-throughput microscopic imaging. As a result of high-throughput experiments, a large number of images can be generated in a single experiment, posing a challenge to researchers to analyze them efficiently and quantitatively. In this work, we develop an image processing focused on detecting and quantifying pigments in zebrafish embryos. The algorithm automatically detects a region of interest (ROI) enclosing an area around the pigments and then segment the pigments for quantification. In this process, the algorithm identifies the head and torso at first, and then finds the boundaries corresponding to the back and abdomen by taking advantage of a priori information about the anatomy of zebrafish embryos. The method is robust in terms that it can detect and quantify pigments even when the embryos have different orientations and curvatures. We used real data to demonstrate the performance of the method to extract phenotypic information from zebrafish embryo images and compared its results with manual analysis for verification.     

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

MOTIVATION: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respectively. The binding sites for these factors share a common core CACGTG. We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus. RESULTS: We scanned upstream regions of methionine, phosphate and control genes with position-specific weight matrices for Pho4p, Met4p/Met28p/Cbf1p and Met31p/Met32p, and applied discriminant analysis to classify genes according to matrix matching scores. This analysis showed that matrix scores provided a good discrimination between phosphate, methionine and control genes. The optimal parameters have then been used to predict phosphate and methionine regulation at a genome scale. The genome-scale analysis predicts 37 genes as methionine-regulated and 40 as phosphate-regulated. We compare the predictive results with high throughput data and discuss the difference. AVAILABILITY: The programs for sequence retrieval and analysis, as well as the complete data and results, are available on the website on regulatory sequence analysis tools (http://rsat.scmbb.ulb.ac.be/rsat/). CONTACT: jvanheld@scmbb.ulb.ac.be SUPPLEMENTARY INFORMATION: The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/     

Developing an efficient multiplex PCR method to detect mcr-like genes

<正>Dear Editor,Since 2016, a growing number of mobile colistin resistance(mcr) genes have been identified and characterized (Liu et al., 2016). In addition to mcr-1 and its variants, mcr-2 to mcr-8 have now been reported, which reflects a significant threat to public health and agricultural production (Sun et al.,2018). These diverse new genes (mcr-2 to mcr-8) share     

Mouse NKR-P1. A family of genes selectively coexpressed in adherent lymphokine-activated killer cells

NK cells are a subpopulation of large granular lymphocytes. They are able to recognize and lyse a wide variety of virally infected or neoplastic target cells without previous sensitization or MHC restriction. The molecules involved in target recognition and subsequent triggering of the killing process are still undefined. Recently, a 30-kDa protein highly expressed on rat NK cells and capable of mediating transmembrane signaling was identified and the gene coding for it cloned and sequenced. To better understand the role of this protein in NK cell-mediated cytotoxicity, we cloned its mouse homologue by cross-hybridization of the rat gene to a cDNA library generated from highly purified mouse lymphokine-activated NK cells. Three messages, differing in size and sequence and encoded by different genes, are specifically cotranscribed in mouse NK cells. The protein products of this gene family express the lectin-like motif characteristic of type II transmembrane molecules. Both the rat and mouse proteins have conserved tyrosine and serine residues in their cytoplasmatic portion that are potential phosphorylation sites. They also share a sequence that could be the binding site of the P56lck tyrosine kinase. These observations are consistent with the signaling function hypothesized for these proteins.