Diets of young Colorado squawfish and other small fish in backwaters of the Green River, Colorado and Utah

We compared diet of young-of-year Colorado squawfish ( Ptychocheilus lucius ), an endangered cyprinid, with diets of other fish Rhinichthys osculus, Catostomus discobolus, and C. latipinnts , and nonnative Cyprinella lutrensis, Notropis stramineus, Pimephales promelas, Ictalurus punctatus, and Lepomis cyanellus. For each species, diet varied with size and between upper and lower river reaches but not between seasons for fish of similar size. Larval chironomids and ccratopogonids were principal foods of most fishes. Copepods and cladocerans were important in diets of P. lucius L. cyanellus Catostomus discobolus was the only species that ate moderate amounts of algae. Fish (all larvae) were in digestive tracts of only 10 P. lucius (21-73 mm TL), about 1% of P. lucius analyzed. High diet overlap occurred between some size-reach groups of P. lucius and C. lutrensis, R. osculus, C. latipinnis, I. punctatus, and L. cyanellus . Potential for food competition between young-of-year P. lucius and other fishes in backwaters appeared greatest with the very abundant C. lutrensis .     

Distribution of sculpins in the Clearwater River Basin, Idaho

The distributions of Cottus bairdi, C. rhotheus, and C. beldingi exhibited a highly significant positive degree of association. Conversely, the distribution of C. confusus exhibited a highly significant negative association with the distributional complex, C. bairdi, C. rhotheus, and C. beldingi. These species of sculpins can be grouped into two assemblages; one based on the distribution of C. confusus and the other based on the combined distributions of the other three species. The factor or factors limiting the downstream distribution of C. confusus or the upstream distribution of the other three species could not be positively identified. However, we hypothesize that competition between C. confusus and one or more members of the C. bairdi, C. rhotheus and C. beldingi complex is involved. In the area of overlapping distributions among C. bairdi, C. rhotheus, and C. bairdi we hypothesize that resource partitioning is occurring. However, the data did not allow evaluation of this hypothesis.        

Breeding behavior of the Plumbeous Vireo in New Mexico

The Plumbeous Vireo ( Vireo plumbeus ) is a poorly studied songbird species that breeds within the interior western United States and Mexico. We studied the breeding behavior of Plumbeous Vireos within pinyon-juniper habitats in northeastern New Mexico in 1996 and 1997. Over both years we located and monitored 40 nests and conducted behavioral observations throughout the nesting cycle. From these observations we described and compared basic behavioral traits of male and female vireos during their nest-building, egg-laying, incubation, and nestling stages, and their response to potential predators near the nest. Male vireos displayed potential nest sites to females, but the females selected the site to be used and built most of the nest. Vireos often did not initiate egg-laying until 2-3 d after nest completion. The female tended to incubate eggs and brood nestlings more than the male, but both parents contributed equally in provisioning the young. Brown-headed Cowbirds ( Molothrus ater ) parasitized 77% of nests in 1996, 63% in 1997, and parasitism was the primary cause of nest failure in this population. The conspicuousness of vireos around the nest, particularly during the nest-building stage, may contribute to high parasitism levels. Vireo aggression near the nest may also act as a cue to help cowbirds locate nests.     

Daily and yearly movement of the Devil's Hole pupfish Cyprinodon diabolis Wales in Devil's Hole, Nevada

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Chance and necessity in the evolution of a bacterial pathogen

The combination of genomic, epidemiological and evolutionary analyses provides a powerful toolbox for understanding how pathogens adapt to their human hosts. By sequencing 112 Burkholderia dolosa genomes from an outbreak among patients with cystic fibrosis, a new study documents evolution in action and identifies a set of genes that contributed to the pathogen's adaptation.     

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.     

Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia

The evolutionarily conserved SLX4 protein, a key regulator of nucleases, is critical for DNA damage response. SLX4 nuclease complexes mediate repair during replication and can also resolve Holliday junctions formed during homologous recombination. Here we describe the phenotype of the Btbd12 knockout mouse, the mouse ortholog of SLX4, which recapitulates many key features of the human genetic illness Fanconi anemia. Btbd12-deficient animals are born at sub-Mendelian ratios, have greatly reduced fertility, are developmentally compromised and are prone to blood cytopenias. Btbd12(-/-) cells prematurely senesce, spontaneously accumulate damaged chromosomes and are particularly sensitive to DNA crosslinking agents. Genetic complementation reveals a crucial requirement for Btbd12 (also known as Slx4) to interact with the structure-specific endonuclease Xpf-Ercc1 to promote crosslink repair. The Btbd12 knockout mouse therefore establishes a disease model for Fanconi anemia and genetically links a regulator of nuclease incision complexes to the Fanconi anemia DNA crosslink repair pathway.     

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease

The Alzheimer Disease Genetics Consortium (ADGC) performed a genome-wide association study of late-onset Alzheimer disease using a three-stage design consisting of a discovery stage (stage 1) and two replication stages (stages 2 and 3). Both joint analysis and meta-analysis approaches were used. We obtained genome-wide significant results at MS4A4A (rs4938933; stages 1 and 2, meta-analysis P (P(M)) = 1.7 × 10(-9), joint analysis P (P(J)) = 1.7 × 10(-9); stages 1, 2 and 3, P(M) = 8.2 × 10(-12)), CD2AP (rs9349407; stages 1, 2 and 3, P(M) = 8.6 × 10(-9)), EPHA1 (rs11767557; stages 1, 2 and 3, P(M) = 6.0 × 10(-10)) and CD33 (rs3865444; stages 1, 2 and 3, P(M) = 1.6 × 10(-9)). We also replicated previous associations at CR1 (rs6701713; P(M) = 4.6 × 10(-10), P(J) = 5.2 × 10(-11)), CLU (rs1532278; P(M) = 8.3 × 10(-8), P(J) = 1.9 × 10(-8)), BIN1 (rs7561528; P(M) = 4.0 × 10(-14), P(J) = 5.2 × 10(-14)) and PICALM (rs561655; P(M) = 7.0 × 10(-11), P(J) = 1.0 × 10(-10)), but not at EXOC3L2, to late-onset Alzheimer's disease susceptibility.     

Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1

We report a genome-wide association study for open-angle glaucoma (OAG) blindness using a discovery cohort of 590 individuals with severe visual field loss (cases) and 3,956 controls. We identified associated loci at TMCO1 (rs4656461[G] odds ratio (OR) = 1.68, P = 6.1 × 10(-10)) and CDKN2B-AS1 (rs4977756[A] OR = 1.50, P = 4.7 × 10(-9)). We replicated these associations in an independent cohort of cases with advanced OAG (rs4656461 P = 0.010; rs4977756 P = 0.042) and two additional cohorts of less severe OAG (rs4656461 combined discovery and replication P = 6.00 × 10(-14), OR = 1.51, 95% CI 1.35-1.68; rs4977756 combined P = 1.35 × 10(-14), OR = 1.39, 95% CI 1.28-1.51). We show retinal expression of genes at both loci in human ocular tissues. We also show that CDKN2A and CDKN2B are upregulated in the retina of a rat model of glaucoma.     

Translation initiation: variations in the mechanism can be anticipated

Translation initiation is a critical step in protein synthesis. Previously, two major mechanisms of initiation were considered as essential: prokaryotic, based on SD interaction; and eukaryotic, requiring cap structure and ribosomal scanning. Although discovered decades ago, cap-independent translation has recently been acknowledged as a widely spread mechanism in viruses, which may take place in some cellular mRNA translations. Moreover, it has become evident that translation can be initiated on the leaderless mRNA in all three domains of life. New findings demonstrate that other distinguishable types of initiation exist, including SD-independent in Bacteria and Archaea, and various modifications of 5′ end-dependent and internal initiation mechanisms in Eukarya. Since translation initiation has developed through the loss, acquisition, and modification of functional elements, all of which have been elevated by competition with viral translation in a large number of organisms of different complexity, more variation in initiation mechanisms can be anticipated.