The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes.     

Parasites from two species of suckers (Catostomidae) from southern Utah

Twenty Catostomus latipinnis and 50 Catostomus discobolis from La Verkin Creek and the Fremont River in southern Utah were collected and surveyed for parasites. Data from the survey indicated that 83 percent of the fish were infected with at least one parasite, with the fish from La Verkin Creek harboring more parasites. Twelve genera and 12 species of parasites were identified from these fish. A monogenetic trematode, Gyrodactylus elegans, which was found in 90 percent of the fish, was the most common parasite. Comments are included on habitat and host variations for the parasitofauna from suckers taken from the two locations.     

Pressure activates colon cancer cell adhesion via paxillin phosphorylation, Crk, Cas, and Rac1

Physical forces can activate colon cancer cell adhesion, critical for metastasis. Paxillin is phosphorylated by FAK and required for pressure-stimulated adhesion. However, whether paxillin acts as an inert scaffolding protein or whether paxillin phosphorylation is required is unknown. Transfection with paxillin point-phosphorylation mutants demonstrated that phosphorylation at tyrosines 31 and 118 together is necessary for pressure-stimulated adhesion. We further evaluated potential paxillin partners. Reducing the adaptor protein Crk or the focal adhesion protein p130^Cas blocked pressure-stimulated adhesion. Furthermore, Crk and p130^Cas both displayed increased co-immunoprecipitation with paxillin in response to increased pressure, except in cells transfected with a Y31Y118 paxillin mutant. Inhibiting the small GTPase Rac1 also abolished pressure-stimulated adhesion, and reducing paxillin by siRNA blocked Rac1 phosphorylation by pressure. Thus, paxillin phosphorylation at tyrosines 31 and 118 together is necessary for pressure-induced adhesion. Paxillin, Crk and Cas form a trimeric complex that activates Rac1 and mediates this effect. Received 21 January 2008; received after revision 4 March 2008; accepted 19 March 2008     

Colour and size reveal hidden diversity of Necturus (Caudata: Proteidae) from the Gulf Coastal Plain of the United States

ABSTRACT

Recent data from the mitochondrial genome reveal six lineages of Gulf Coast Waterdogs traditionally classified as Necturus beyeri. Here, we use patterns of colour and body size, along with previously published data, to reveal a large, heavily spotted phenotype with an unstriped larva possessing numerous white spots; we re-describe N. beyeri to correspond to this phenotype. We also reveal a small, weakly spotted phenotype possessing an unstriped larva lacking numerous white spots. This phenotype characterises the Apalachicola and Escambia lineages, which current evidence suggests are paraphyletic. We reject taxonomies that place these two lineages in N. lodingi because the type specimen of this species appears to be a melanistic member of N. beyeri. Therefore, we describe the Apalachicola and Escambia lineages as independent new species.

http://ww.zoobank.org/urn:lsid:zoobank.org:act:C8508CCB-F54F-4DC8-B61D-56966A3F1CC8

http://www.zoobank.org/urn:lsid:zoobank.org:act:F044B2CC-55F0-4FFA-A312-9CAD9E73CD69     

Increased soil emissions of potent greenhouse gases under increased atmospheric CO2

Increasing concentrations of atmospheric carbon dioxide (CO(2)) can affect biotic and abiotic conditions in soil, such as microbial activity and water content. In turn, these changes might be expected to alter the production and consumption of the important greenhouse gases nitrous oxide (N(2)O) and methane (CH(4)) (refs 2, 3). However, studies on fluxes of N(2)O and CH(4) from soil under increased atmospheric CO(2) have not been quantitatively synthesized. Here we show, using meta-analysis, that increased CO(2) (ranging from 463 to 780 parts per million by volume) stimulates both N(2)O emissions from upland soils and CH(4) emissions from rice paddies and natural wetlands. Because enhanced greenhouse-gas emissions add to the radiative forcing of terrestrial ecosystems, these emissions are expected to negate at least 16.6 per cent of the climate change mitigation potential previously predicted from an increase in the terrestrial carbon sink under increased atmospheric CO(2) concentrations. Our results therefore suggest that the capacity of land ecosystems to slow climate warming has been overestimated.     

Modulation of Rab GTPase function by a protein phosphocholine transferase

The intracellular pathogen Legionella pneumophila modulates the activity of host GTPases to direct the transport and assembly of the membrane-bound compartment in which it resides. In vitro studies have indicated that the Legionella protein DrrA post-translationally modifies the GTPase Rab1 by a process called AMPylation. Here we used mass spectrometry to investigate post-translational modifications to Rab1 that occur during infection of host cells by Legionella. Consistent with in vitro studies, DrrA-mediated AMPylation of a conserved tyrosine residue in the switch II region of Rab1 was detected during infection. In addition, a modification to an adjacent serine residue in Rab1 was discovered, which was independent of DrrA. The Legionella effector protein AnkX was required for this modification. Biochemical studies determined that AnkX directly mediates the covalent attachment of a phosphocholine moiety to Rab1. This phosphocholine transferase activity used CDP-choline as a substrate and required a conserved histidine residue located in the FIC domain of the AnkX protein. During infection, AnkX modified both Rab1 and Rab35, which explains how this protein modulates membrane transport through both the endocytic and exocytic pathways of the host cell. Thus, phosphocholination of Rab GTPases represents a mechanism by which bacterial FIC-domain-containing proteins can alter host-cell functions.     

A high-resolution map of human evolutionary constraint using 29 mammals

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ～4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ～60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.