Identification of a neuropeptide precursor protein that gives rise to a "cocktail" of peptides that bind Cu(II) and generate metal-linked dimers

The Transparency document associated with this article can be found,in online version.This work was supported by a Leverhulme Trust grant (RPG-2013-351) awarded to MRE and National Science Foundation (USA) grant awards DEB 1036416, 1036358, 1036366, and 1036368

MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families

Background: Phylogenetic study of protein sequences provides unique and valuable insights into the molecular and genetic basis of important medical and epidemiological problems as well as insights about the origins and development of physiological features in present day organisms. Consensus phylogenies based on the bootstrap and other resampling methods play a crucial part in analyzing the robustness of the trees produced for these analyses. Methodology: Our focus was to increase the number of bootstrap replications that can be performed on large protein datasets using the maximum parsimony, distance matrix, and maximum likelihood methods. We have modified the PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time. This paper discusses the methodology used to parallelize the PHYLIP programs and reports the performance of the parallel PHYLIP programs that are relevant to the study of protein evolution on several protein datasets. Conclusions: Calculations that currently take a few days on a state of the art desktop workstation are reduced to calculations that can be performed over lunchtime on a modern parallel computer. Of the three protein methods tested, the maximum likelihood method scales the best, followed by the distance method, and then the maximum parsimony method. However, the maximum likelihood method requires significant memory resources, which limits its application to mor

Influenza A H5N1 Immigration Is Filtered Out at Some International Borders

Geographic spread of highly pathogenic influenza A H5N1, the bird flu strain, appears a necessary condition for accelerating the evolution of a related human-to-human infection. As H5N1 spreads the virus diversifies in response to the variety of socioecological environments encountered, increasing the chance a human infection emerges. Genetic phylogenies have for the most part provided only qualitative evidence that localities differ in H5N1 diversity. For the first time H5N1 variation is quantified across geographic space.We constructed a statistical phylogeography of 481 H5N1 hemagglutinin genetic sequences from samples collected across 28 Eurasian and African localities through 2006. The MigraPhyla protocol showed southern China was a source of multiple H5N1 strains. Nested clade analysis indicated H5N1 was widely dispersed across southern China by both limited dispersal and long distance colonization. The UniFrac metric, a measure of shared phylogenetic history, grouped H5N1 from Indonesia, Japan, Thailand and Vietnam with those from southeastern Chinese provinces engaged in intensive international trade. Finally, H5N1's accumulative phylogenetic diversity was greatest in southern China and declined beyond. The gradient was interrupted by areas of greater and lesser phylogenetic dispersion, indicating H5N1 migration was restricted at some geopolitical borders. Thailand and Vietnam, just south of China, showed significant phylogenetic clustering, suggesting newly invasive H5N1 strains have been repeatedly filtered out at their northern borders even as both countries suffered recurring outbreaks of endemic strains. In contrast, Japan, while successful in controlling outbreaks, has been subjected to multiple introductions of the virus.The analysis demonstrates phylogenies can provide local health officials with more than hypotheses about relatedness. Pathogen dispersal, the functional relationships among disease ecologies across localities, and the efficacy of control efforts can also be inferred, all from viral genetic sequences alone

De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus

Starfish have been instrumental in many fields of biological and ecological research. Oocytes of Astropecten aranciacus, a common species native to the Mediterranean Sea and the East Atlantic, have long been used as an experimental model to study meiotic maturation, fertilization, intracellular Ca2+ signaling, and cell cycle controls. However, investigation of the underlying molecular mechanisms has often been hampered by the overall lack of DNA or protein sequences for the species. In this study, we have assembled a transcriptome for this species from the oocytes, eggs, zygotes, and early embryos, which are known to have the highest RNA sequence complexity. Annotation of the transcriptome identified over 32,000 transcripts including the ones that encode 13 distinct cyclins and as many cyclin-dependent kinases (CDK), as well as the expected components of intracellular Ca2+ signaling toolkit. Although the mRNAs of cyclin and CDK families did not undergo significant abundance changes through the stages from oocyte to early embryo, as judged by real-time PCR, the transcript encoding Mos, a negative regulator of mitotic cell cycle, was drastically reduced during the period of rapid cleavages. Molecular phylogenetic analysis using the homologous amino acid sequences of cytochrome oxidase subunit I from A. aranciacus and 30 other starfish species indicated that Paxillosida, to which A. aranciacus belongs, is not likely to be the most basal order in Asteroidea. Taken together, the first transcriptome we assembled in this species is expected to enable us to perform comparative studies and to design gene-specific molecular tools with which to tackle long-standing biological questions

Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum

Single nucleotide polymorphisms (SNPs) have been shown to be useful in revealing population structure with continental-and regional-scale samples. In epidemiological study, a careful selection of SNPs to track disease spread in local communities would provide an important addition to traditional disease surveillance. This study used SNPs and microsatellites to examine population structure of Plasmodium falciparum at fine- scale in malaria-endemic areas of Western Kenya. A set of high performance (HP) SNPs were selected from a large SNP panel based on BELS ranking, FST values and minor allele frequency criteria. The discriminative power and assignment accuracy of different SNP panels including nonsynonymous SNPs, silent SNPs, previously published barcode SNPs, and the HP SNPs were evaluated together with microsatellites. Among all SNP panels, HP SNPs showed the highest level of differentiation and self-assignment accuracy on average among sites. Clear distinction was observed between the northern and southern P. falciparum samples, whereas samples from the south were least diverged from one another. These results were comparable to those by microsatellites. Nonsynonymous, silent, and barcode SNPs all showed similar levels of genetic variability to one another and weaker structure than the HP SNPs. We described here the procedure of selecting a set of HP SNPs from a large panel of SNPs that resolve population structure of P. falciparum between the northern and southern regions of Western Kenya. Future work is needed to determine if this procedure can result in SNPs panels capable of tracing Plasmodium spread at finer geographical scales

Frequent expansion of plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance

Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the extent of PvDBP copy number variation, the type of PvDBP multiplications, as well as its significance across broad samples are still unclear. We determined the prevalence and type of PvDBP duplications, as well as PvDBP copy number variation among 178 Ethiopian P. vivax isolates using a PCR-based diagnostic method, a novel quantitative real-time PCR assay and whole genome sequencing. For the 145 symptomatic samples, PvDBP duplications were detected in 95 isolates, of which 81 had the Cambodian and 14 Malagasy-type PvDBP duplications. PvDBP varied from 1 to >4 copies. Isolates with multiple PvDBP copies were found to be higher in symptomatic than asymptomatic infections. For the 33 asymptomatic samples, PvDBP was detected with two copies in two of the isolates, and both were the Cambodian-type PvDBP duplication. PvDBP copy number in Duffy-negative heterozygotes was not significantly different from that in Duffy-positives, providing no support for the hypothesis that increased copy number is a specific association with Duffy-negativity, although the number of Duffy-negatives was small and further sampling is required to test this association thoroughly

An ancient Antarctic endemic genus restored: morphological and molecular support for Gomphiocephalus hodgsoni (Collembola: Hypogastruridae)

Gomphiocephalus hodgsoni Carpenter was only the second collembolon‡ to be described from the Antarctic continent. It was collected first in 1902 from Granite Harbour, southern Victoria Land, Eastern Antarctica, by the British National Antarctic Expedition (1901–1904). Since then several studies have investigated the distribution, ecology, ecophysiology and molecular composition of the species. Despite two morphological redescriptions and an absence of detailed evolutionary phylogenetic studies, the genus Gomphiocephalus was recently reduced to a subgenus of Schoettella Schäffer. Here, we redescribe the species in detail and use morphological and molecular (cytochrome c oxidase subunit I and 28S) data to indicate its generic relationships within Hypogastruridae. Characters of Gomphiocephalus do not conform with those of any extant genus in the family, including Schoettella. In addition, the only Schoettella species described from the southern hemisphere, Schoettella subcorta Salmon, is shown here to belong in the genus Xenylla. Furthermore, molecular data indicates the genus has no close relationship to any other in Poduromorpha, and in particular Hypogastruridae. Therefore, we restore Gomphiocephalus to generic status. Our results reinforce the already recognized high level of endemism in the Antarctic fauna at both species and generic levels, and emphasise the necessity of using both morphological and molecular data in determining the systematics and evolutionary relationships of the fauna.Penelope Greenslade, Mark I. Stevens, Giulia Torricelli and Cyrille A. D'Haes