Detecting Identity by Descent and Estimating Genotype Error Rates in Sequence Data

Existing methods for identity by descent (IBD) segment detection were designed for SNP array data, not sequence data. Sequence data have a much higher density of genetic variants and a different allele frequency distribution, and can have higher genotype error rates. Consequently, best practices for IBD detection in SNP array data do not necessarily carry over to sequence data. We present a method, IBDseq, for detecting IBD segments in sequence data and a method, SEQERR, for estimating genotype error rates at low-frequency variants by using detected IBD. The IBDseq method estimates probabilities of genotypes observed with error for each pair of individuals under IBD and non-IBD models. The ratio of estimated probabilities under the two models gives a LOD score for IBD. We evaluate several IBD detection methods that are fast enough for application to sequence data (IBDseq, Beagle Refined IBD, PLINK, and GERMLINE) under multiple parameter settings, and we show that IBDseq achieves high power and accuracy for IBD detection in sequence data. The SEQERR method estimates genotype error rates by comparing observed and expected rates of pairs of homozygote and heterozygote genotypes at low-frequency variants in IBD segments. We demonstrate the accuracy of SEQERR in simulated data, and we apply the method to estimate genotype error rates in sequence data from the UK10K and 1000 Genomes projects.     

Stream microhabitat selectivity,resource partitioning,and niche shifts in grazing caddisfly larvae

Microhabitat selectivity, resource partitioning, and niche shifts in five species of grazing caddisfly larvae (Glossosoma califica, G. penitum, Dicosmoecus gilvipes, Neophylax rickeri, and N. splendens) were quantified by underwater measurement of microhabitat availability and utilization in three northern California streams. The microhabitat parameters water depth and velocity and rock size, roughness, and slope were measured. Comparisons of habitat available to habitat used revealed significant selection for at least two microhabitat parameters by each population, with depth and velocity being the most important. Comparisons of habitat used by different species showed significant partitioning of at least two microhabitat parameters at each site, with depth being partitioned at all sites. Non-parametric discriminant analysis revealed significant microhabitat partitioning on a multivariate level at two sites. Comparisons of habitat used at different sites quantified a major niche shift by D. gilvipes in its preference for riffles versus pools. Size-selective predation by dippers (Cinclus mexicanus) and steelhead (Salmo gairdneri gairdneri) is proposed as a hypothesis to explain the observed resource partitioning and niche shift.     

Centromeric Regions Control Autonomous Segregation Tendencies in Single-Division Meiosis of Saccharomyces Cerevisiae

We have previously shown that yeast cdc5 or cdc14 homozygotes can be led through a single-division meiosis in which some of the chromosomes segregate reductionally whereas others, within the same cell, segregate equationally. Chromosomes XI tend to segregate reductionally, whereas chromosomes IV tend to segregate equationally. In this report we present experiments with cdc5 homozygous strains, in which the centromeres of one or both chromosomes XI was replaced by the centromeric region from chromosome IV. Analysis of the products of single-division meioses in these strains demonstrates that the choice between reductional or equational segregation is directed by sequences in the vicinity of the centromeres. Although the choice is made separately for each individual chromosome, the analysis also reveals the existence of a system responsible for coordinated segregation of the two chromosomes of a given pair.     

The role of plant genotype,environment and gender in resistance to a specialist chrysomelid herbivore

Summary Patchiness in herbivore attack is a well-documented phenomenon. When neighboring plants suffer vastly different levels of attack, then one suspects genotypic differences among plants to be the underlying mechanism. In this study, I use common garden experiments in two natural, but divergent, habitats at the Cedar Creek Natural History Area in central Minnesota to determine the role of plant genotype, environment and gender in plant resistance to a specialist herbivore. Resistance was measured by larval survivorship and weight. Eight clones ofRhus glabra were selected and 12 equal-aged ramets were dug up and planted in two gardens (each garden received 6 ramets per clone). First instarBlepharida rhois (Coleoptera: Chrysomelidae) larvae of known parentage were transferred to ramets and censused every other day. At the end of the experiment, larvae were collected and weighed. Analysis of variance was used to determine the importance of plant genotype, environment and gender on larval mortality and weight. The experiment was repeated in its entirety one month later. Both plant genotype and environment significantly affected larval survivorship in the first run of the experiment. No interactions were significant. Results from the second run indicated marginally significant genotype and environment main effects, and a genotype by environment interaction in larval survivorship. There was a significant genotype by environment interaction in larval weight on the same run. In neither run did clone gender have significant affects on resistance.     

Response over two growing seasons of a Sitka spruce stand to 15N-urea fertilizer

Urea fertilizer labelled with ¹⁵N (2.5 atom %) was applied to a 20 year old Sitka spruce stand on a peaty gley at a rate equivalent to 160 kg N ha⁻¹. The application of urea resulted in increased biomass and N concentration of needles and enhanced development of the crown. Differences in N concentrations of the amended trees were also observed for new wood and bark. Analysis of ¹⁵N in tree biomass showed a continued influence of fertilizer N in the second growing season following urea application. The overall recovery of fertilizer N in the trees was estimated to be about 10%.     

Class II genes of miniature swine

Genomic clones corresponding to class II genes of theSLA ^c haplotype of miniature swine have been isolated and characterized. These genes have been grouped into seven non-overlapping clusters on the basis of restriction mapping. Ordering of exons within each cluster was accomplished by hybridization of Southern blots of restriction fragments with exon-specific probes. The two clusters (clusters 2 and 3) encoding theDRB andDQB genes were identified on the basis of hybridization with locus-specific 3 untranslated cDNA probes. Cluster 4 contained exons of bothDOB andDQB genes, the basis for which remains to be determined. The remaining four clusters (1, 5, 6, 7) were identified as containingDP, DR, andDO coding sequences, respectively, on the basis of sequence analysis. The porcine class II region appears very similar to that of man in number and nature of the class II genes identified and in the intron/exon organization of corresponding genes.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the association number M29944. Address correspondence and offprint requests to: C. LeGuern.     

The lipid composition and conversion of tryptamine toN b-acetyltryptamine in aCatharanthus roseus cell line without indole alkaloids

Summary A cell line, NA13-2, was selected as a rapidly growing colony of protoplasts from a UV(254 nm)-fluorescent cell line, NA13-1, which originated from a tryptamine-resistant strain ofCatharanthus roseus NA13. Cell line NA13-2 lost the capability to produce indole alkaloids. Tryptophan fed to these cells was converted toN _b-acetyltryptamine as the major product. The free acetyl coenzyme A content of NA13-2 cells was 50% higher than in the mother cells. The total lipid content of the NA13-2 cells was 2.5-fold that in the NA13 cells. In spite of the similarity in the fatty acid content to that of the mother cell line NA13, the total lipid extract of NA13-2 cells appeared as a wax instead of an oil, resulting from the presence of sterol esters.This paper was presented in part at the Annual Meeting of the Society for Industrial Microbiology, Boston, MA, 1985, and the International Congress of the Plant Tissue Culture Association, Minneapolis, MN, 1986.     

Possible association between IL-2 receptors and class I HLA molecules on T cells

In the process of evaluating murine hybridomas for an antibody to the beta-subunit of the IL-2R (p70) we identified an antibody that immunoprecipitated a 55- to 57-kDa complex from cross-linked lysates. We demonstrate that this complex is composed of IL-2 (15.5 kDa) cross-linked to the H chain of HLA class I (40 to 42 kDa), suggesting a molecular interaction between HLA class I molecules and IL-2R. Although the exact role of this association remains to be determined, the specific cross-linking of IL-2 to HLA class I Ag is intriguing in view of published claims for a role of HLA class I in OKT3-induced lymphocyte proliferation and in NK cell lytic activity.     

The invariant tryptophan in an H chain V region is not essential to antibody binding

The first amino acid residue of the second framework region in all antibody H and L chain V regions sequenced to date is invariably tryptophan. To test whether this invariance is essential to proper domain folding and generation of a functional antibody, the tryptophan residue in the heavy chain V region of a mouse anti-p-azophenylarsonate antibody was converted to an alanine residue by oligonucleotide-directed mutagenesis of the H chain gene. The mutant gene was transfected into mouse hybridoma cells that produce the homologous L chain, and the resulting mutant antibody was purified from the cell supernatant. It was shown to have essentially the same reactivity as wild type toward a series of anti-idiotypic antibodies and to bind Ag with a Ka similar to that of wild type.