Marker-assisted introgression using non-unique marker alleles I: selection on the presence of linked marker alleles

This paper investigates marker-assisted introgression of a major gene into an outbred line, where identification of the introgressed gene is incomplete because marker alleles are not unique to the base populations (the same marker allele can occur in both donor and recipient population). Those markers are used to identify the introgressed allele as well as the background genotype. The effect of using those markers, as if they were completely informative on the retention of the introgressed allele, was examined over five generations of backcrossing by using a single marker or a marker bracket for different starting frequencies of the marker alleles. Results were calculated by using both a deterministic approach, where selection is only for the desired allele, and by a stochastic approach, where selection is also on background genotype. When marker allele frequencies in donor and recipient population diverged from 1 and 0 (using a diallelic marker), the ability to retain the desired allele rapidly declined. Marker brackets performed notably better than single markers. If selection on background marker genotype was applied, the desired allele could be lost even more quickly than expected at random because the chance that the allele, which is common in the donor line, is present on the locus identifying the introgressed allele and is surrounded by alleles common in the recipient line on the background marker loci, will descend from the donor line (double recombination has taken place), is a lot smaller than the chance that this allele will stem from the recipient line (in which the allele occurs in low frequency). Marker brackets again performed better. Preselection against marker homozygotes (producing uninformative gametes) gave a slightly better retention of the introgressed allele.     

GTPase from rod outer segments: characterization by photoaffinity labeling and tryptic peptide mapping

The photoaffinity label [γ-³²P]8-N₃GTP has been used to identify GTP-binding components in highly purified preparations of GTPase from bovine rod outer segments. These preparations contain two major polypeptides of 37,000 and 39,000 daltons. In the presence of photolyzing radiation, [γ-³²P]8-N₃GTP is covalently attached to the 37,000 dalton polypeptide. Tryptic peptide mapping of this polypeptide indicates that it is highly related to the 39,000 dalton species that has been previously identified as a GTP-binding component.     

Decreased 8N3-[gamma-32P]GTP photolabeling of Gs alpha in tumorigenic lung epithelial cell lines: association with decreased hormone responsiveness and loss of contact-inhibited growth

The 45-kDa alpha subunit of the signal transducing Gs protein complex, which stimulates receptor-coupled adenylate cyclase, incorporated less of the photoaffinity probe, 8N3-[gamma-32P]GTP, in extracts from tumorigenic cell lines in comparison with nontumorigenic cell lines derived from mouse lung epithelium. Immunoblotting experiments using anti-Gs alpha antibodies demonstrated that tumor cells do not have a decreased amount of Gs alpha and photolabeling of tumor cell Gs alpha increased when the rate of nucleotide exchange was promoted. Therefore, tumor cell Gs alpha function may be altered. Consistent with this hypothesis is the observation that the tumor cells exhibited decreased responsiveness to the beta-adrenergic agonist, isoproterenol. Gs alpha photolabeling in growing nontumorigenic cells was reduced to a level resembling that observed in tumor cells, but photolabeling increased when cells became contact-inhibited. This increase in 8N3-[gamma-32P]GTP incorporation into Gs alpha by normal cells at confluence was not seen in the tumorigenic cells. Since Gs alpha photolabeling was inversely proportional to the percentage of [3H]thymidine-labeled nuclei at confluence, we suggest that the altered Gs alpha in tumor cells is involved in the loss of cell growth regulation.     

RFLP and linkage analysis of the porcine casein loci—CASAS1, CASAS2, CASB and CASK

Restriction fragment length polymorphisms (RFLPs) were revealed at the porcine casein loci with the following combinations of restriction endonucleases and porcine cDNA clones: α_s1,-casein (TaqI); α_s2-casein (BamHI); and ß-casein (Sacl). These RFLPs were shown to be under simple monogenic control by segregation analysis of two- and three-generation families. The CASAS1, CASAS2 and CASB casein loci were also shown to be linked with no recombinant haplotypes observed amongst 77 meioses in Large White and Meishan F₁ and F₂ crosses. No recombinants were observed in a further 106 meioses that were informative for linkage between CASAS1 and CASAS2.     

Male Horn Dimorphism and its Function in the Neotropical Dung Beetle <Emphasis Type="Italic">Sulcophanaeus velutinus</Emphasis>

Horned beetles are emerging models in the study of coevolution between novel morphologies and behavior. In Onthophagus beetles, large males use horns to fight other males in brood tunnels while small males with higher mobility sneak around the large males to gain access to females. Mating tactics have rarely been described in other dung beetle genera. We studied the horned dung beetle Sulcophanaeus velutinus that exhibits two parallel horns on the prothorax and one on the head. We put two males of different horn lengths, but similar mass, in observation chambers and found that the large male with longer horns won access to the female in physical competition. Speed tests in artificial tunnels show that locomotion is impeded in large males, suggesting an advantage in mobility for males with small horns. This work contributes to the limited existing evidence on the function of alternative morphologies in horned dung beetles taxa.     

integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth

Background

The integration of high-quality, genome-wide analyses offers a robust approach to elucidating genetic factors involved in complex human diseases. Even though several methods exist to integrate heterogeneous omics data, most biologists still manually select candidate genes by examining the intersection of lists of candidates stemming from analyses of different types of omics data that have been generated by imposing hard (strict) thresholds on quantitative variables, such as P-values and fold changes, increasing the chance of missing potentially important candidates.

Methods

To better facilitate the unbiased integration of heterogeneous omics data collected from diverse platforms and samples, we propose a desirability function framework for identifying candidate genes with strong evidence across data types as targets for follow-up functional analysis. Our approach is targeted towards disease systems with sparse, heterogeneous omics data, so we tested it on one such pathology: spontaneous preterm birth (sPTB).

Results

We developed the software integRATE, which uses desirability functions to rank genes both within and across studies, identifying well-supported candidate genes according to the cumulative weight of biological evidence rather than based on imposition of hard thresholds of key variables. Integrating 10 sPTB omics studies identified both genes in pathways previously suspected to be involved in sPTB as well as novel genes never before linked to this syndrome. integRATE is available as an R package on GitHub (https://github.com/haleyeidem/integRATE).

Conclusions

Desirability-based data integration is a solution most applicable in biological research areas where omics data is especially heterogeneous and sparse, allowing for the prioritization of candidate genes that can be used to inform more targeted downstream functional analyses.

     

The Identity of “Chromium Malate”

Recently, several studies on the effects of a compound named “chromium malate,” with the proposed formula “Cr₂malate₃·xH₂O” where x = 3.5 or 5, on the health of healthy and diabetic rats have appeared. However, the compound is poorly characterized, and knowing the identity of this material could be important in the interpretation of the previous and of future studies on the effects of this compound in animals. Consequently, the synthesis, characterization, and identity of this material were explored. A combination of spectroscopic, magnetic, and elemental analyses and mass spectral studies reveal that the compound is probably a polymer, not a discrete molecule, and does not have the composition previously reported. The repeating unit of the polymer possesses an antiferromagnetically coupled trinuclear Cr(III) core. The current study suggests that previous reports on chromium malate and its effects in animals must be viewed with caution.

     

Bear's Hiding Place: Ishi's Last Refuge

Bear's Hiding Place: Ishi's Last Refuge. 1998. 18 minutes, color. video by Jed Riffe. For more information, contact University of California Extension, Center for Media and Independent Learning, 2000 Center Street. Fourth Floor, Berkeley. CA 94704.