Incongruent patterns of local and global genome size evolution in cotton

Genome sizes in plants vary over several orders of magnitude, reflecting a combination of differentially acting local and global forces such as biases in indel accumulation and transposable element proliferation or removal. To gain insight into the relative role of these and other forces, approximately 105 kb of contiguous sequence surrounding the cellulose synthase gene CesA1 was compared for the two coresident genomes (AT and DT) of the allopolyploid cotton species, Gossypium hirsutum. These two genomes differ approximately twofold in size, having diverged from a common ancestor approximately 5-10 million years ago (Mya) and been reunited in the same nucleus at the time of polyploid formation, approximately 1-2 Mya. Gene content, order, and spacing are largely conserved between the two genomes, although a few transposable elements and a single cpDNA fragment distinguish the two homoeologs. Sequence conservation is high in both intergenic and genic regions, with 14 conserved genes detected in both genomes yielding a density of 1 gene every 7.5 kb. In contrast to the twofold overall difference in DNA content, no disparity in size was observed for this 105-kb region, and 555 indels were detected that distinguish the two homoeologous BACs, approximately equally distributed between AT and DT in number and aggregate size. The data demonstrate that genome size evolution at this phylogenetic scale is not primarily caused by mechanisms that operate uniformly across different genomic regions and components; instead, the twofold overall difference in DNA content must reflect locally operating forces between gene islands or in largely gene-free regions.     

Genetic linkage mapping of zebrafish genes and ESTs

Genetic screens in zebrafish (Danio rerio) have isolated mutations in hundreds of genes essential for vertebrate development, physiology, and behavior. We have constructed a genetic linkage map that will facilitate the identification of candidate genes for these mutations and allow comparisons among the genomes of zebrafish and other vertebrates. On this map, we have localized 771 zebrafish genes and expressed sequence tags (ESTs) by scoring single-stranded conformational polymorphisms (SSCPs) in a meiotic mapping panel. Of these sequences, 642 represent previously unmapped genes and ESTs. The mapping panel was comprised of 42 homozygous diploid individuals produced by heat shock treatment of haploid embryos at the one-cell stage (HS diploids). This "doubled haploid" strategy combines the advantages of mapping in haploid and standard diploid systems, because heat shock diploid individuals have only one allele at each locus and can survive to adulthood, enabling a relatively large quantity of genomic DNA to be prepared from each individual in the mapping panel. To integrate this map with others, we also scored 593 previously mapped simple-sequence length polymorphisms (SSLPs) in the mapping panel. This map will accelerate the molecular analysis of zebrafish mutations and facilitate comparative analysis of vertebrate genomes.     

Selecting for functional alternative splices in ESTs

The expressed sequence tag (EST) collection in dbEST provides an extensive resource for detecting alternative splicing on a genomic scale. Using genomically aligned ESTs, a computational tool (TAP) was used to identify alternative splice patterns for 6400 known human genes from the RefSeq database. With sufficient EST coverage, one or more alternatively spliced forms could be detected for nearly all genes examined. To identify high (>95%) confidence observations of alternative splicing, splice variants were clustered on the basis of having mutually exclusive structures, and sample statistics were then applied. Through this selection, alternative splices expected at a frequency of >5% within their respective clusters were seen for only 17%-28% of genes. Although intron retention events (potentially unspliced messages) had been seen for 36% of the genes overall, the same statistical selection yielded reliable cases of intron retention for <5% of genes. For high-confidence alternative splices in the human ESTs, we also noted significantly higher rates both of cross-species conservation in mouse ESTs and of validation in the GenBank mRNA collection. We suggest quantitative analytical approaches such as these can aid in selecting useful targets for further experimental characterization and in so doing may help elucidate the mechanisms and biological implications of alternative splicing.     

Dissemination of Youth ESTs: Ready for Prime Time?

Herschell, McNeil, and McNeil (this issue) provide a thoughtful assessment of and potential remedies for obstacles to dissemination of empirically supported child and adolescent treatments. Despite the compelling case for disseminating such treatments to clinical service settings, substantial differences between service clinics and research clinics justify the need for systematic effectiveness trials as part of the dissemination process. It is proposed that evidence from effectiveness trials will reveal features of treatments, such as engagement strategies, that require development or modification in order to optimize outcomes. Clear evidence for the superiority of empirically supported treatments (ESTs) over treatment as usual in service clinics will promote acceptance and implementation of ESTs in clinic practice. Key words: dissemination, empirically supported treatments, clinical child psychology, therapeutic alliance, clinical service settings, treatment outcomes, effectiveness trials.     

A global effect of capture saccades

When two target elements are presented in close proximity, the endpoint of a saccade is generally positioned at an intermediate location (‘global effect’). Here, we investigated whether the global effect also occurs for eye movements executed to distracting elements. To this end, we adapted the oculomotor capture paradigm such that on a subset of trials, two distractors were presented. When the two distractors were closely aligned, erroneous eye movements were initiated to a location in between the two distractors. Even though to a lesser extent, this effect was also present when the two distractors were presented further apart. In a second experiment, we investigated the global effect for eye movements in the presence of two targets. A strong global effect was observed when two targets were presented closely aligned, while this effect was absent when the targets were further apart. This study shows that there is a global effect when saccades are captured by distractors. This ‘capture global’ effect is different from the traditional global effect that occurs when two targets are presented because the global effect of capture saccades also occurs for remote elements. The spatial dynamics of this global effect will be explained in terms of the population coding theory.     

A device for preparing cotton wool plugs

Penza Division, Central Bureau for Design and Technology “Medoborudovanie”, Penza. Translated from Meditsinskaya Tekhnika, No. 4, p. 39, July–August, 1992.     

A genetic analysis of bacteriophage λ head assembly

The sequence of steps involved in bacteriophage λ head assembly has been studied by characterizing second-site mutatons that can compensate for the reduced level of synthesis of a particular phage “head” protein. Such studies reveal these classes of protein interactions: (1) A reduced level of either pA synthesis or activity can compensate for the reduced amount of pD made when λDam mutants are grown in a supC host. This result implies that pA acts before pD during the packaging of phage DNA. (2) A reduced level of either pB synthesis or activity can compensate for the reduced amount of pE made when λEam mutants are grown in a supC host, and vice versa. This result suggests an interaction between these proteins that is stringently dependent on maintaining a proper ratio between them. An identical argument has been made to explain the properties of groE hosts (Sternberg, 1973). (3) A very specific class of mutations in phage gene E can compensate for the reduced amount of pC made when λCam mutants are grown in a supC host. This suggests that the products of these two genes directly interact.Using the techniques described in this report it is possible to easily isolate a variety of mutations (am, oc, ts, and missense) in specific phage “head” genes (genes A, B and E).     

A quantitative assay of peptide-dependent class I assembly

We have developed a quantitative assay for the measurement of class I assembly induced by peptide. We have applied this assay to H-2Db, Kb and HLA-A2.1 with a panel of 49 overlapping peptides derived from HIV-1 gag protein. We find that the effects of peptide on assembly form a continuous distribution. By defining positives as those that increase the concentration of folded heavy chains more than three standard deviations from the control we show that 7/48 bind A2.1, 11/49 bind Db and 7/47 bind Kb. The assembly assay contrasts with solid-phase assays in being more discriminating (fewer peptides binding any given class I molecule), and showing less overlap in the patterns of peptides bound by the three class I molecules.