Response to comment on "Human-specific gain of function in a developmental enhancer"

Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive selection. We reinforce our previous conclusion by analyzing hypothesized BGC events genomewide and assessing the effect of recombination rates on human-accelerated conserved noncoding sequence ascertainment. We also provide evidence that AT → GC substitution bias can coexist with positive selection

The Rise of the s-Process in the Galaxy

From newly-obtained high-resolution, high signal-to-noise ratio spectra the abundances of the elements La and Eu have been determined over the stellar metallicity range -3<[Fe/H]<+0.3 in 159 giant and dwarf stars. Lanthanum is predominantly made by the s-process in the solar system, while Eu owes most of its solar system abundance to the r-process. The changing ratio of these elements in stars over a wide metallicity range traces the changing contributions of these two processes to the Galactic abundance mix. Large s-process abundances can be the result of mass transfer from very evolved stars, so to identify these cases, we also report carbon abundances in our metal-poor stars. Results indicate that the s-process may be active as early as [Fe/H]=-2.6, alalthough we also find that some stars as metal-rich as [Fe/H]=-1 show no strong indication of s-process enrichment. There is a significant spread in the level of s-process enrichment even at solar metallicity.Comment: 64 pages, 15 figures; ApJ 2004 in pres

Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses

BACKGROUND: Novel methods to identify anthelmintic drug and vaccine targets are urgently needed, especially for those parasite species currently being controlled by singular, often limited strategies. A clearer understanding of the transcriptional components underpinning helminth development will enable identification of exploitable molecules essential for successful parasite/host interactions. Towards this end, we present a combinatorial, bioinformatics-led approach, employing both statistical and network analyses of transcriptomic data, for identifying new immunoprophylactic and therapeutic lead targets to combat schistosomiasis. METHODOLOGY/PRINCIPAL FINDINGS: Utilisation of a Schistosoma mansoni oligonucleotide DNA microarray consisting of 37,632 elements enabled gene expression profiling from 15 distinct parasite lifecycle stages, spanning three unique ecological niches. Statistical approaches of data analysis revealed differential expression of 973 gene products that minimally describe the three major characteristics of schistosome development: asexual processes within intermediate snail hosts, sexual maturation within definitive vertebrate hosts and sexual dimorphism amongst adult male and female worms. Furthermore, we identified a group of 338 constitutively expressed schistosome gene products (including 41 transcripts sharing no sequence similarity outside the Platyhelminthes), which are likely to be essential for schistosome lifecycle progression. While highly informative, statistics-led bioinformatics mining of the transcriptional dataset has limitations, including the inability to identify higher order relationships between differentially expressed transcripts and lifecycle stages. Network analysis, coupled to Gene Ontology enrichment investigations, facilitated a re-examination of the dataset and identified 387 clusters (containing 12,132 gene products) displaying novel examples of developmentally regulated classes (including 294 schistosomula and/or adult transcripts with no known sequence similarity outside the Platyhelminthes), which were undetectable by the statistical comparisons. CONCLUSIONS/SIGNIFICANCE: Collectively, statistical and network-based exploratory analyses of transcriptomic datasets have led to a thorough characterisation of schistosome development. Information obtained from these experiments highlighted key transcriptional programs associated with lifecycle progression and identified numerous anti-schistosomal candidate molecules including G-protein coupled receptors, tetraspanins, Dyp-type peroxidases, fucosyltransferases, leishmanolysins and the netrin/netrin receptor complex

Biomphalaria glabrata transcriptome: cDNA microarray profiling identifies resistant- and susceptible-specific gene expression in haemocytes from snail strains exposed to Schistosoma mansoni

BACKGROUND: Biomphalaria glabrata is an intermediate snail host for Schistosoma mansoni, one of the important schistosomes infecting man. B. glabrata/S. mansoni provides a useful model system for investigating the intimate interactions between host and parasite. Examining differential gene expression between S. mansoni-exposed schistosome-resistant and susceptible snail lines will identify genes and pathways that may be involved in snail defences. RESULTS: We have developed a 2053 element cDNA microarray for B. glabrata containing clones from ORESTES (Open Reading frame ESTs) libraries, suppression subtractive hybridization (SSH) libraries and clones identified in previous expression studies. Snail haemocyte RNA, extracted from parasite-challenged resistant and susceptible snails, 2 to 24 h post-exposure to S. mansoni, was hybridized to the custom made cDNA microarray and 98 differentially expressed genes or gene clusters were identified, 94 resistant-associated and 4 susceptible-associated. Quantitative PCR analysis verified the cDNA microarray results for representative transcripts. Differentially expressed genes were annotated and clustered using gene ontology (GO) terminology and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. 61% of the identified differentially expressed genes have no known function including the 4 susceptible strain-specific transcripts. Resistant strain-specific expression of genes implicated in innate immunity of invertebrates was identified, including hydrolytic enzymes such as cathepsin L, a cysteine proteinase involved in lysis of phagocytosed particles; metabolic enzymes such as ornithine decarboxylase, the rate-limiting enzyme in the production of polyamines, important in inflammation and infection processes, as well as scavenging damaging free radicals produced during production of reactive oxygen species; stress response genes such as HSP70; proteins involved in signalling, such as importin 7 and copine 1, cytoplasmic intermediate filament (IF) protein and transcription enzymes such as elongation factor 1α and EF-2. CONCLUSION: Production of the first cDNA microarray for profiling gene expression in B. glabrata provides a foundation for expanding our understanding of pathways and genes involved in the snail internal defence system (IDS). We demonstrate resistant strain-specific expression of genes potentially associated with the snail IDS, ranging from signalling and inflammation responses through to lysis of proteinacous products (encapsulated sporocysts or phagocytosed parasite components) and processing/degradation of these targeted products by ubiquitination

Mice Engrafted with Human Fetal Thymic Tissue and Hematopoietic Stem Cells Develop Pathology Resembling Chronic Graft-versus-Host Disease

AbstractChronic graft-versus-host disease (cGVHD) is a significant roadblock to long-term hematopoietic stem cell (HSC) transplantation success. Effective treatments for cGVHD have been difficult to develop, in part because of a paucity of animal models that recapitulate the multiorgan pathologies observed in clinical cGVHD. Here we present an analysis of the pathology that occurs in immunodeficient mice engrafted with human fetal HSCs and implanted with fragments of human fetal thymus and liver. Starting at time points generally later than 100 days post-transplantation, the mice developed signs of illness, including multiorgan cellular infiltrates containing human T cells, B cells, and macrophages; fibrosis in sites such as lungs and liver; and thickened skin with alopecia. Experimental manipulations that delayed or reduced the efficiency of the HSC engraftment did not affect the timing or progression of disease manifestations, suggesting that pathology in this model is driven more by factors associated with the engrafted human thymic organoid. Disease progression was typically accompanied by extensive fibrosis and degradation of the thymic organoid, and there was an inverse correlation of disease severity with the frequency of FoxP3+ thymocytes. Hence, the human thymic tissue may contribute T cells with pathogenic potential, but the generation of regulatory T cells in the thymic organoid may help to control these cells before pathology resembling cGVHD eventually develops. This model thus provides a new system to investigate disease pathophysiology relating to human thymic events and to evaluate treatment strategies to combat multiorgan fibrotic pathology produced by human immune cells

Staphylococcus aureus infects osteoclasts and replicates intracellularly

Osteomyelitis (OM), or inflammation of bone tissue, occurs most frequently as a result of bacterial infection and severely perturbs bone structure. OM is predominantly caused b

Transmission of Mycobacterium tuberculosis in a Rural Community, Arkansas, 1945–2000

A cluster of tuberculosis cases in a rural community in Arkansas persisted from 1991 to 1999. The cluster had 13 members, 11 linked epidemiologically. Old records identified 24 additional patients for 40 linked case-patients during a 54-year period. Residents of this neighborhood represent a population at high risk who should be considered for tuberculin testing and treatment for latent tuberculosis infection

Improved Laboratory Transition Probabilities for Neutral Chromium and Re-determination of the Chromium Abundance for the Sun and Three Stars

Branching fraction measurements from Fourier transform spectra in conjunction with published radiative lifetimes are used to determine transition probabilities for 263 lines of neutral chromium. These laboratory values are employed to derive a new photospheric abundance for the Sun: log $\epsilon$(Cr I)$_{\odot}$ = 5.64$\pm$0.01 ($\sigma = 0.07$). These Cr I solar abundances do not exhibit any trends with line strength nor with excitation energy and there were no obvious indications of departures from LTE. In addition, oscillator strengths for singly-ionized chromium recently reported by the FERRUM Project are used to determine: log $\epsilon$(Cr II)$_{\odot}$ = 5.77$\pm$0.03 ($\sigma = 0.13$). Transition probability data are also applied to the spectra of three stars: HD 75732 (metal-rich dwarf), HD 140283 (metal-poor subgiant), and CS 22892-052 (metal-poor giant). In all of the selected stars, Cr I is found to be underabundant with respect to Cr II. The possible causes for this abundance discrepancy and apparent ionization imbalance are discussed.Comment: 44 pages, 6 figure