Broadly directed virus-specific CD4+ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence

Vigorous proliferative CD4+ T cell responses are the hallmark of spontaneous clearance of acute hepatitis C virus (HCV) infection, whereas comparable responses are absent in chronically evolving infection. Here, we comprehensively characterized the breadth, specificity, and quality of the HCV-specific CD4+ T cell response in 31 patients with acute HCV infection and varying clinical outcomes. We analyzed in vitro T cell expansion in the presence of interleukin-2, and ex vivo staining with HCV peptide-loaded MHC class II tetramers. Surprisingly, broadly directed HCV-specific CD4+ T cell responses were universally detectable at early stages of infection, regardless of the clinical outcome. However, persistent viremia was associated with early proliferative defects of the HCV-specific CD4+ T cells, followed by rapid deletion of the HCV-specific response. Only early initiation of antiviral therapy was able to preserve CD4+ T cell responses in acute, chronically evolving infection. Our results challenge the paradigm that HCV persistence is the result of a failure to prime HCV-specific CD4+ T cells. Instead, broadly directed HCV-specific CD4+ T cell responses are usually generated, but rapid exhaustion and deletion of these cells occurs in the majority of patients. The data further suggest a short window of opportunity to prevent the loss of CD4+ T cell responses through antiviral therapy

Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae

The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular “dialogue” between the partners that includes interactions between the host’s innate immune system and the symbiont

New Frontiers-class Uranus Orbiter: Exploring the feasibility of achieving multidisciplinary science with a mid-scale mission

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Comparative Gene Analysis and Prediction of Innate Immunity and Apoptosis Machinery in Hydrothermal Vent Tubeworms

Siboglinid tubeworms are an emerging model system for symbiosis in extreme conditions. At deep-sea hydrothermal vents in the Pacific Ocean, they harbor a chemoautotrophic symbiont in a specialized organ, the trophosome, where the bacteria carry out primary production via oxidation of reduced sulfur compounds. The trophosome of siboglinid worms is suggested to be tightly regulated, symbiont-responsive, and developmentally homeostatic. The purported mechanism involves a cellular proliferative or apoptotic response to bacterial signals, environmental cues, or nutrition. Though these processes are well understood in more amenable model systems, there has been little work uncovering the tubeworm’s genetic potential for sensing and responding to symbiotic stimuli by canonical means, including pattern recognition receptors, innate immune effectors, and apoptotic regulators. In the present work, bioinformatics methods are employed to identify homologs to known regulatory genes, within two siboglinid tubeworms, Ridgeia piscesae, and Riftia pachyptila. Homologs found in EST libraries from each worm are characterized and evaluated for functional relevance to symbiosis by protein prediction, domain matching, and phylogenetic reconstruction. The major protein families here observed are the peptidoglycan recognition proteins (PGRPs) and the Caspases, accompanied by an overview of the worm’s potential apoptotic suite of genes. The siboglinid set of potential PGRPs presents similar characteristics to non-hydrothermal vent-associated symbiotic organisms. As well, the siboglinid apoptosis network is neither enriched nor reduced for any core components. The caspase gene family includes two major groups, and overall resembles the structural assortment recently seen in most non-derived apoptosis networks, but may present properties unique among annelids. The results of these analyses provide a suite of potential symbiosis-related genes for future investigations

The RNA-binding protein DND1 acts sequentially as a negative regulator of pluripotency and a positive regulator of epigenetic modifiers required for germ cell reprogramming.

The adult spermatogonial stem cell population arises from pluripotent primordial germ cells (PGCs) that enter the fetal testis around embryonic day (E)10.5. PGCs undergo rapid mitotic proliferation, then enter prolonged cell cycle arrest (G1/G0), during which they transition to pro-spermatogonia. In mice homozygous for the Ter mutation in the RNA-binding protein Dnd1 (Dnd1Ter/Ter ), many male germ cells (MGCs) fail to enter G1/G0 and instead form teratomas: tumors containing many embryonic cell types. To investigate the origin of these tumors, we sequenced the MGC transcriptome in Dnd1Ter/Ter mutants at E12.5, E13.5 and E14.5, immediately prior to teratoma formation, and correlated this information with DO-RIP-Seq-identified DND1 direct targets. Consistent with previous results, we found DND1 controls downregulation of many genes associated with pluripotency and active cell cycle, including mTor, Hippo and Bmp/Nodal signaling pathway elements. However, DND1 targets also include genes associated with male differentiation, including a large group of chromatin regulators activated in wild-type but not mutant MGCs during the E13.5 and E14.5 transition. Results suggest multiple DND1 functions and link DND1 to initiation of epigenetic modifications in MGCs

Targeted gene expression for individual worms.

<p>Values are fold change calculated with the 2^–ΔΔCt method and normalized to actin in trophosome compared to plume. <i>Outliers are shown in italics (</i>see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038267#s2" target="_blank">Materials and Methods</a><i>).</i></p

Box plot showing expression of target genes in the trophosome compared to the plume as determined by qPCR.

<p>The fold expression level differences, of 18 target genes, in the trophosome were compared to those of the plume. The upper and lower ends of the boxes indicate the 25th and 75th percentiles, respectively. The length of the box depicts the interquartile range within which 50% of the values are located. The solid black lines denote the median. Capped error bars represent the minimum and maximum values, excluding outliers (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038267#pone-0038267-t004" target="_blank">Table 4</a>). The dotted black line represents expression levels in the plume (y = 1), thus genes with medians >1 exhibit higher expression levels in the trophosome compared to the plume, and inversely genes with medians <1 show higher expression levels in the plume. All expression levels are normalized to the expression of actin. The gene abbreviations are as follows: hbB1, hemoglobin B1; HSP70, heat shock protein 70; LITAF, lipopolysaccharide-induced tumor necrosis factor-alpha; PGRPrpi1–5, peptidoglycan recognition protein 1–5; TLR2p, toll-like receptor 2 precursor; A2MRAP, alpha-2 macroglobulin receptor associated protein; CAbr, carbonic anhydrase (branchial plume); CAtr, carbonic anhydrase (trophosome); EF1α, elongation factor 1-alpha; LBPIP, LPS induced bactericidal permeability increasing protein; MMIF, macrophage migration inhibitory factor; MR, macrophage mannose receptor 1-like protein; NF-κBic, NF-κB inhibitor (cactus); ROSm, reactive oxygen species modulator.</p

Model of host-symbiont interactions between pattern recognition receptors (PRRs) and microbe-associated molecular patterns (MAMPs) in <i>R. piscesae</i>.

<p>The branchial plume (p) of <i>Ridgeia</i> exchanges metabolites with the environment. The plume lacks symbionts but may still use PRRs to interact with microorganisms found in the surrounding vent fluid and seawater. The center of the worm is comprised mainly of one organ, the trophosome (t) made up of lobules that contain bacteriocytes housing the intracellular bacterial symbionts (endosymbionts) as well as blood vessels (bv) that transfer metabolites. Central bacteriocytes (c) harbor healthy and actively dividing endosymbionts. Towards the periphery of the lobules, bacteriocytes and symbionts appear to undergo terminal differentiation and apoptosis with many of the degenerative symbionts undergoing autophagy. We suggest a significantly greater response of the trophosome to MAMPs via PRRs that may trigger signal transduction cascades, ultimately helping to regulate symbiostasis. PRR expression in the trophosome may occur in the bacteriocytes and/or in the surrounding vasculature. Given the densities of endosymbionts, bacteriocytes encounter high concentrations of MAMPs. A constant turnover of bacteriocytes may also release extracellular MAMPs into the trophosome periphery.</p