Cnidarians and ancestral genetic complexity in the animal kingdom

Eleven of the twelve recognized wingless (Wnt) subfamilies are represented in the sea anemone Nematostella vectensis, indicating that this developmentally important gene family was already fully diversified in the common ancestor of 'higher' animals. In deuterostomes, although duplications have occurred, no novel subfamilies of Wnts have evolved. By contrast, the protostomes Drosophila and Caenorhabditis have lost half of the ancestral Wnts. This pattern -- loss of genes from an ancestrally complex state -- might be more important in animal evolution than previously recognized.     

Design of a data model for developing laboratory information management and analysis systems for protein production

Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.     

Addressing the intrinsic disorder bottleneck in structural proteomics

The Center for Eukaryotic Structural Genomics (CESG), as part of the Protein Structure Initiative (PSI), has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm (the Predictor of Naturally Disordered Regions, PONDR to avoid proteins that were likely to be disordered. We report a retrospective analysis of the effect of this filtering on the yield of viable structure determination candidates. In addition, we have used our current database of results on 70 protein targets from Arabidopsis thaliana and 1 from Caenorhabditis elegans, which were labeled uniformly with nitrogen-15 and screened for disorder by NMR spectroscopy, to compare the original algorithm with 13 other approaches for predicting disorder from sequence. Our study indicates that the efficiency of structural proteomics of eukaryotes can be improved significantly by removing targets predicted to be disordered by an algorithm chosen to provide optimal performance.     

Theoretical study of hydrogenation of the doubly aromatic B 7 − cluster

We have studied the influence of hydrogenation on the relative stability of the low-lying isomers of the anionic B₇⁻ cluster, computationally. It is known that the pure-boron B₇⁻ cluster has a doubly (σ- and π-) aromatic C_6v (³A₁) quasi-planar wheel-type triplet global minimum (structure 1), a low-lying σ-aromatic and π-antiaromatic quasi-planar singlet C_2v (¹A₁) isomer 2 (0.7 kcal mol⁻¹ above the global minimum), and a planar doubly (σ- and π-) antiaromatic C_2v (¹A₁) isomer 3 (7.8 kcal mol⁻¹ above the global minimum). However, upon hydrogenation, an inversion in the stability of the species occurs. The planar B₇H₂⁻ (C_2v, ¹A₁) isomer 4, originated from the addition of two hydrogen atoms to the doubly antiaromatic B₇⁻ isomer 3, becomes the global minimum structure. The second most stable B₇H₂⁻ isomer 5, originated from the quasi-planar triplet wheel isomer 1 of B₇⁻, was found to be 27 kcal mol⁻¹ higher in energy. The inversion in stability occurs due to the loss of the doubly aromatic character in the wheel-type global minimum isomer (C_6v, ³A₁) of B₇⁻ upon H₂−addition. In contrast, the planar isomer of B₇⁻ (C_2v, ¹A₁) gains aromatic character upon addition of two hydrogen atoms, which makes it more stable. Figure The B₇H₂-global minimum structure and its σ-aromatic and π-antiaromatic MOs Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday.     

Identification and characterization of 17 microsatellite primers for the tick,Ixodes ricinus,using enriched genomic libraries

Ixodes ricinus is the main vector for important infectious diseases in both humans and in animals. Microsatellite loci were isolated from a dinucleotide‐enriched library made from I. ricinus sampled in Norway. Seventeen polymorphic microsatellites were further characterized among 24 individuals sampled from an island in the Oslofjord region. The number of observed alleles ranged from two to 17 and the observed heterozygosities between 0.10 and 0.83. Analysis of family materials gives evidence of non‐Mendelian inheritance of several of the characterized loci, among which most could be explained by presence of null alleles.     

Coalescent processes when the distribution of offspring number among individuals is highly skewed

We report a complex set of scaling relationships between mutation and reproduction in a simple model of a population. These follow from a consideration of patterns of genetic diversity in a sample of DNA sequences. Five different possible limit processes, each with a different scaled mutation parameter, can be used to describe genetic diversity in a large population. Only one of these corresponds to the usual population genetic model, and the others make drastically different predictions about genetic diversity. The complexity arises because individuals can potentially have very many offspring. To the extent that this occurs in a given species, our results imply that inferences from genetic data made under the usual assumptions are likely to be wrong. Our results also uncover a fundamental difference between populations in which generations are overlapping and those in which generations are discrete. We choose one of the five limit processes that appears to be appropriate for some marine organisms and use a sample of genetic data from a population of Pacific oysters to infer the parameters of the model. The data suggest the presence of rare reproduction events in which approximately 8% of the population is replaced by the offspring of a single individual.     

First Record of Teratopactus nodicollis (Coleoptera: Curculionidae) in Dry Bean (Phaseolus vulgaris)

Observations on the bioecology and damage of Teratopactus nodicollis Boheman on Phaseolus vulgaris were carried out on field samples by assessing the number of larvae and root damage in 40?ha of a dry bean field from the Federal District, Brazil (16°4??28.41???W; 47°30??21.13???S). Larvae caused the greatest damage at the stage of germination, emergence, and primary leaves, producing 50?% stand reduction. Most larvae pupated in August and September, and adult emergence occurred in middle October. Some larvae were infected with the fungus Metarhizium spp., a biological agent that would be naturally controlling this insect.     

Opening the pericardium during pulmonary artery constriction improves cardiac function.

During acute pulmonary hypertension, both the pericardium and the right ventricle (RV) constrain left ventricular (LV) filling; therefore, pericardiotomy should improve LV function. LV, RV, and pericardial pressures and RV and LV dimensions and LV stroke volume (SV) were measured in six anesthetized dogs. The pericardium was closed, the chest was left open, and the lungs were held away from the heart. Data were collected at baseline, during pulmonary artery constriction (PAC), and after pericardiotomy with PAC maintained. PAC decreased SV by one-half. RV diameter increased, and septum-to-LV free wall diameter and LV area (our index of LV end-diastolic volume) decreased. Compared with during PAC, pericardiotomy increased LV area and SV increased 35%. LV and RV compliance (pressure-dimension relations) and LV contractility (stroke work-LV area relations) were unchanged. Although series interaction accounts for much of the decreased cardiac output during acute pulmonary hypertension, pericardial constraint and leftward septal shift are also important. Pericardiotomy can improve LV function in the absence of other sources of external constraint to LV filling.