Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation.

Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months posttransplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses, and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities.

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis.

BACKGROUND: The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been gained of the symbionts, the host has remained largely unstudied. Here, we generated transcriptomes and proteomes of O. algarvensis to better understand how this annelid worm gains nutrition from its symbionts, how it adapted physiologically to a symbiotic lifestyle, and how its innate immune system recognizes and responds to its symbiotic microbiota. RESULTS: Key adaptations to the symbiosis include (i) the expression of gut-specific digestive enzymes despite the absence of a gut, most likely for the digestion of symbionts in the host's epidermal cells; (ii) a modified hemoglobin that may bind hydrogen sulfide produced by two of the worm's symbionts; and (iii) the expression of a very abundant protein for oxygen storage, hemerythrin, that could provide oxygen to the symbionts and the host under anoxic conditions. Additionally, we identified a large repertoire of proteins involved in interactions between the worm's innate immune system and its symbiotic microbiota, such as peptidoglycan recognition proteins, lectins, fibrinogen-related proteins, Toll and scavenger receptors, and antimicrobial proteins. CONCLUSIONS: We show how this worm, over the course of evolutionary time, has modified widely-used proteins and changed their expression patterns in adaptation to its symbiotic lifestyle and describe expressed components of the innate immune system in a marine oligochaete. Our results provide further support for the recent realization that animals have evolved within the context of their associations with microbes and that their adaptive responses to symbiotic microbiota have led to biological innovations.

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.

While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case.

Microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. To this end, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data. More specifically, the function of the microbial community initially involved biomass growth, protein production, and lipid metabolism, and then switched to more complex metabolic functions, such as carbohydrate metabolism, once the community stabilized and matured. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Likewise, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. This study provides the first snapshot of coordinated human and microbial protein expression in a preterm infant's gut during early development.

Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts.

Transposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that the expression of transposase genes is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine worm Olavius algarvensis with metaproteomics. At least 26 different transposases from 12 different families were detected, and genomic and proteomic analyses suggest that many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or no longer exist.

Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus.

The CRISPR/Cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (Cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. While the mechanism of action for this acquired immunity is currently under investigation, the response of Cas protein expression to phage infection has yet to be elucidated. In this study, we employed shotgun proteomics to measure the global proteome expression in a model system for studying the CRISPR/Cas response in S. thermophilus DGCC7710 infected with phage 2972. Host and viral proteins were simultaneously measured following inoculation at two different multiplicities of infection and across various time points using two-dimensional liquid chromatography tandem mass spectrometry. Thirty-seven out of forty predicted viral proteins were detected, including all proteins of the structural virome and viral effector proteins. In total, 1,013 of 2,079 predicted S. thermophilus proteins were detected, facilitating the monitoring of host protein synthesis changes in response to virus infection. Importantly, Cas proteins from all four CRISPR loci in the S. thermophilus DGCC7710 genome were detected, including loci previously thought to be inactive. Many Cas proteins were found to be constitutively expressed, but several demonstrated increased abundance following infection, including the signature Cas9 proteins from the CRISPR1 and CRISPR3 loci, which are key players in the interference phase of the CRISPR/Cas response. Altogether, these results provide novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.

neonatally primed lymph node, but not splenic T cells, display a Gly-Gly motif within the TCR beta-chain complementarity-determining region 3 that controls affinity and may affect lymphoid organ retention.

Ig-proteolipid protein 1 (Ig-PLP1) is an Ig chimera expressing the encephalitogenic PLP1 peptide corresponding to amino acid residues 139-151 of PLP. Newborn mice given Ig-PLP1 in saline on the day of birth and challenged 7 wk later with PLP1 peptide in CFA develop an organ-specific neonatal immunity that confers resistance against experimental allergic encephalomyelitis. The T cell responses in these animals are comprised of Th2 cells in the lymph node and anergic Th1 lymphocytes in the spleen. Intriguingly, the anergic splenic T cells, although nonproliferative and unable to produce IFN-gamma or IL-4, secrete significant amounts of IL-2. Studies were performed to determine whether the two populations display any structural differences in the TCR H chain variable region that could contribute to the differential affinity and retention in different organs. Responsive Th2 lymph node T cells and anergic splenic lymphocytes were immortalized, and the structures of their TCR Vbeta were determined. The results show that Vbeta and Jbeta usage was random, but the CDR3 regions of the lymph node cells had a conserved Gly-Gly motif. Analysis of TCR affinity/avidity correlated the Gly-Gly motif with lower affinity and retention of the Th2 cells in the lymph node. Also, it is suggested that a higher TCR affinity may be a contributing factor for the development of the neonatal Th1 response in the spleen.

The electrophysiological effects of neurotensin on spontaneously active neurons in the nucleus accumbens: an in vivo study.

Considerable evidence obtained from neuroanatomical and neurochemical studies suggests an interaction between the endogenous tridecapeptide neurotensin (NT) and central nervous system dopamine (DA) neurons. Centrally administered NT blocks many of the actions of synaptic DA in limbic brain areas; the specific mechanism and receptors involved remain under investigation. The electrophysiological effects of NT were studied using extracellular recording techniques and iontophoretic application in 243 spontaneously active neurons in the nucleus accumbens (NAc), with a positive/negative waveform. NT was directly applied to 208 neurons in a pulsatile fashion by iontophoresis (21+/-1 nA). NT had no effect on the firing rate of 120 neurons ((0.31+/-0.72)%), decreased the firing rate in 51 neurons ((-27.87+/-1.52)%), and increased the firing rates of 37 neurons ((33.38+/-2.6)%). One hundred ninety nine (81.9%) of the neurons studied were sensitive to iontophoretically applied DA (>15% decrease in firing rate). The effects of continuous NT application on DA-induced inhibitions were studied in 169 neurons. NT attenuated neuronal responses to directly applied DA by (49.95+/-4.52)%, with antagonism in the "core" subregion (n=96) of (33.41+/-7.75)% when compared with antagonism in the "shell" subregion (n=71) of (61.39+/-5.2)%. The effects of NT on DA were consistent and independent of the effects of NT alone. These data provide further evidence that NT functions as a true neuromodulator in the NAc, exerting minimal direct effects, but blocking the actions of DA.

On the role of dendritic cells in peripheral T cell tolerance and modulation of autoimmunity.

Recently, it has become clear that dendritic cells (DCs) are essential for the priming of T cell responses. However, their role in the maintenance of peripheral T cell tolerance remains largely undefined. Herein, an antigen-presenting cell (APC) transfer system was devised and applied to experimental allergic encephalomyelitis (EAE), to evaluate the contribution that DCs play in peripheral T cell tolerance. The CD8alpha(-)CD4(+) subset, a minor population among splenic DCs, was found to mediate both tolerance and bystander suppression against diverse T cell specificities. Aggregated (agg) Ig-myelin oligodendrocyte glycoprotein (MOG), an Ig chimera carrying the MOG 35-55 peptide, binds and cross-links FcgammaR on APC leading to efficient peptide presentation and interleukin (IL)-10 production. Furthermore, administration of agg Ig-MOG into diseased mice induces relief from clinical EAE involving multiple epitopes. Such recovery could not occur in FcgammaR-deficient mice where both uptake of Ig-MOG and IL-10 production are compromised. However, reconstitution of these mice with DC populations incorporating the CD8alpha(-)CD4(+) subset restored Ig-MOG-mediated reversal of EAE. Transfer of CD8alpha(+) or even CD8alpha(-)CD4(-) DCs had no effect on the disease. These findings strongly implicate DCs in peripheral tolerance and emphasize their functional potency, as a small population of DCs was able to support effective suppression of autoimmunity.

Specific features of chronic astrocyte gliosis after experimental central nervous system (CNS) xenografting and in Wobbler neurological mutant CNS.

This study sets out to compare and contrast the astrocyte reaction in two unrelated experimental designs both resulting in marked chronic astrogliosis and natural motoneuron death in the wobbler mutant mouse and brain damage in the context of transplantation of xenogeneic embryonic CNS tissue into the striatum of newborn mice. The combined use of GFAP-labeling and confocal imaging allows the morphological comparison between these two different types of astrogliosis. Our findings demonstrate that, in mice, after tissue transplantation in the striatum, gliosis is not restricted to the regions of damage: it occurs not only near the site of transplantation, the striatum, but also in more distant regions of the CNS and particularly in the spinal cord. In the wobbler mutant mouse, a strong gliosis is observed in the spinal cord, site of motoneuronal cell loss. However, moderate astrocytic reaction (increased GFAP-immunoreactivity) can also be found in other wobbler CNS regions, remote from the spinal cord. In the wobbler ventral horn, where neurons degenerate, the hypertrophied reactive astrocytes exhibit a dramatic increase of glial fibrils and surround the motoneuron cell bodies, occupying most of the motoneuron environment. The striking and specific presence of hypertrophic astrocytes in wobbler mice accompanied by a dramatic increase of glial fibrils located in the vicinity of motoneuron cell bodies suggests that short astrogliosis fills the space left by degenerating motoneurons and interferes with their survival. In the spinal cord of xenografted mice, chronic astrogliosis is also observed, but only glial processes without hypertrophied cell bodies are found in the neuronal micro-environment. It is tempting to speculate that gliosis in the wobbler spinal cord, the local accumulation of astrocyte cell bodies, and high density of astrocytic processes may interfere with the diffusion of neuroactive substances in gliotic tissue, some of which are neurotoxic, and cooperate or even trigger neuronal death.

Cytokine signals propagate through the brain.

Interleukin-1 (IL-1) and tumor necrosis factor alpha (TNFalpha) are proinflammatory cytokines that are constitutively expressed in healthy, adult brain where they mediate normal neural functions such as sleep. They are neuromodulators expressed by and acting on neurons and glia. IL-1 and TNFalpha expression is upregulated in several important diseases/disorders. Upregulation of IL-1 and/or TNFalpha expression, elicited centrally or systemically, propagates through brain parenchyma following specific spatio-temporal patterns. We propose that cytokine signals propagate along neuronal projections and extracellular diffusion pathways by molecular cascades that need to be further elucidated. This elucidation is a prerequisite for better understanding of reciprocal interactions between nervous, endocrine and immune systems.

"Inflammatory" cytokines: neuromodulators in normal brain?

If cytokines are constitutively expressed by and act on neurons in normal adult brain, then we may have to modify our current view that they are predominantly inflammatory mediators. We critically reviewed the literature to determine whether we could find experimental basis for such a modification. We focused on two "proinflammatory" cytokines, interleukin (IL)-1 and tumor necrosis factor-alpha (TNFalpha) because they have been most thoroughly investigated in shaping our current thinking. Evidence, although equivocal, indicates that the genes coding for these cytokines and their accessory proteins are expressed by neurons, in addition to glial cells, in normal brain. Their expression is region- and cell type-specific. Furthermore, bioactive cytokines have been extracted from various regions of normal brain. The cytokines' receptors selectively are present on all neural cell types, rendering them responsive to cytokine signaling. Blocking their action modifies multiple neural "housekeeping" functions. For example, blocking IL-1 or TNFalpha by several independent means alters regulation of sleep. This indicates that these cytokines likely modulate in the brain behavior of a normal organism. In addition, these cytokines are likely involved in synaptic plasticity, neural transmission, and Ca2+ signaling. Thus, the evidence strongly suggests that these cytokines perform neural functions in normal brain. We therefore propose that they should be thought of as neuromodulators in addition to inflammatory mediators.

Astrocyte proliferation induced by wobbler astrocyte conditioned medium is blocked by tumor necrosis factor-alpha (TNF-alpha) and interleukin-1beta (IL-1beta) neutralizing antibodies in vitro.

The wobbler mutant mouse (wr/wr) displays motoneuron degeneration and astrocyte reactivity in the spinal cord. We have previously reported that, in vitro, primary wobbler astrocytes display morphological and biochemical changes. In this report, we show that wobbler astrocyte conditioned medium enhances the in vitro proliferation of normal neonatal primary astrocytes. This stimulated proliferation is correlated with high levels of IL1-beta and TNF-alpha cytokines in the conditioned medium of wobbler astrocytes. Neutralizing antibodies directed against both IL1-beta and TNF-alpha block the wobbler astrocyte conditioned medium-enhanced astrocyte proliferation. Moreover, IL1-beta and TNF-alpha mRNAs are elevated in the wobbler spinal cord. All these data suggest that diffusible IL1-beta and TNF-alpha are involved in the processus of astrogliosis observed in the wobbler spinal cord.

Expression of interleukin-1 genes and interleukin-1 receptors in the mouse brain after hippocampal injury.

In order to evaluate the role of IL-1 production in post-traumatic brain, transcripts for IL-1 (alpha, beta, RA) have been quantified following RT-PCR, in hippocampus and cortex after injury of either hippocampus (Hip) or striatum (Stri). Moreover, 125I IL-1alpha binding sites have been directly quantified using binding experiments on brain sections and quantitative autoradiography. Under basal conditions, levels of PCR products were very low. On day 1, IL-1RA transcripts only were strongly increased in the hippocampus after Hip-lesions and in cortex after Stri lesion. Transcripts were back to control values on day 7 post-lesion. IL-1 receptor densities in the hippocampus (dentate gyrus) were decreased at day 1 around the site of the lesion (but not on the contralateral side) and were back to controls on day 7 indicating a transient and local IL-1 production in the surroundings of the lesion. No changes were found following Stri lesion. This study provides further evidence of the role of the IL-1 molecules family, notably IL-1RA, in the brain reaction to trauma.

Expression of extracellular matrix degrading enzymes during migration of xenografted brain cells.

Proteolytic enzymes, postulated to create an avenue for cell migration by digestion of host extracellular matrix molecules, have been implicated in neoplastic glial cell migration. A similar process is likely to occur in the developing brain. Fetal rabbit brain fragments transplanted into the striatum of the neonatal Shiverer mouse give rise to cells which migrate from the graft site and differentiate into astrocytes and oligodendrocytes. Proteinase expression by transplanted brain cells was studied using immunohistochemistry and in situ hybridization. Immature donor cells expressed the mRNAs for matrix metalloproteinases (MMP) 1 (collagenase) and 3 (stromelysin). Northern blot analysis of rabbit brain showed that MMP-1 in particular is expressed in the immature rabbit cerebrum and down-regulated during maturation. Immature donor cells exhibited immunoreactivity for urokinase plasminogen activator. However, immunoreactivity was also present in maturing neurons. Donor and host astroglia in the vicinity of grafts were immunoreactive for MMP-2 and tissue-type plasminogen activator. This expression may represent a reactive phenomenon, not specifically related to cell migration, by mature astrocytes. Based upon our findings, MMP-1 appears to be a candidate for involvement in migration of immature brain cells in the cerebrum.

Specific pattern of nitric oxide synthase expression in glial cells after hippocampal injury.

In the central nervous system (CNS), nitric oxide (NO) is thought to be involved in a variety of functions including synaptic plasticity, long term potentiation, and neurotoxicity. The aim of the present study was to investigate the expression of nitric oxide synthase (NOS) in the mouse CNS, following surgical injury to the hippocampus. NOS expression was assessed by histochemical detection of nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-diaphorase) activity and immunohistochemistry of the inducible NOS (iNOS). Two days after injury to the CA1 hippocampal field, NADPH-diaphorase activity was detected in pyramidal and granular neurons and also in glial cells in the hippocampus, in contrast to the non-injured one where NADPH-diaphorase staining was observed only in a few interneurons. NADPH-diaphorase histochemistry combined with immunolabelling for GFAP and F4/80 demonstrated that these glial cells were astrocytes and microglia. This pattern of NOS expression is induced specifically after a hippocampal injury since lesion to the prefrontal or cerebellar cortex leads to NOS activity only in monocytes/macrophages like cells. Despite the large expression of NOS detected by NADPH-diaphorase histochemistry after lesioning the hippocampus, immunostaining for iNOS was confined to microglia. The fact that induction of high levels of NOS activity are detected in glial cells after a lesion to the hippocampus could be accounted for by the sensitivity of this structure to a high release of glutamate.

Widespread neuronal expression of c-Fos throughout the brain and local expression in glia following a hippocampal injury.

Fos oncoprotein is an immediate early gene product and a marker of cell activation following a variety of insults. We have previously shown that a mechanical lesion to the hippocampus of adult mice induces a neuronal expression of the cytokines interleukin-1alpha (IL-1alpha) and tumor necrosis factor-alpha (TNF alpha) whereas a lesion to the striatum does not. The role of these inflammatory cytokines in the pathophysiology of central neurons is still unclear. The present work was undertaken to study a possible correlation between the central expression patterns of c-Fos on the one hand and IL-1alpha and TNF alpha on the other hand. We show that Fos is expressed in a majority of brain neurons after a unilateral lesion to the hippocampus whereas it is confined to the site of injury when applied to the striatum, as previously described for the expression of the cytokines.

Gene transfer to the central nervous system by transplantation of cerebral endothelial cells.

A cerebral endothelial immortalized cell line was used in transplantation experiments to deliver gene products to the adult rat brain. Survival of grafted cells was observed for at least 1 year, without any sign of tumor formation. When genetically modified to express bacterial beta-galactosidase and transplanted into the striatum, these cells were shown, by light and electron microscope analysis, to integrate into the host brain parenchyma and microvasculature. Following implantation into the striatum and nucleus basalis of adult rats, endothelial cells engineered to secrete mouse beta-nerve growth factor (NGF) induced the formation of a dense network of low-affinity NGF receptor-expressing fibers near the implantation sites. This biological response was observed from 3 to 8 weeks after engraftment. The present study establishes the cerebral endothelial cell as an efficient vector for gene transfer to the central nervous system.

Identification and topography of neuronal cell populations expressing TNF alpha and IL-1 alpha in response to hippocampal lesion.

In previous studies, we have shown that a traumatic lesion to the hippocampus of adult mice induces the transitory expression of TNF alpha and IL-1 alpha by neurons of different brain areas and also by glial cells at the site of injury. The aim of the present study was to establish whether the expression of TNF alpha and IL-1 alpha is restricted to defined subpopulations, or else is common to most of the central neuronal populations. Using polyclonal anti-GAD 67, anti-TH and monoclonal anti-ChAT, and anti-5-HT antibodies in a double-labeling immunohistochemical procedure in combination with murine anti-TNF alpha and anti-IL-1 alpha polyclonal antibodies, we show that most GABAergic, catecholaminergic, and serotoninergic neurons, and a subgroup of the cholinergic neurons, express these cytokines. Although not immunohistochemically characterized, neurons in some glutamatergic structures such as the hippocampus and the prefrontal cortex also express these cytokines. Thus, we conclude that the capacity of central neurons to express cytokines like TNF alpha and IL-1 alpha in reaction to a brain injury is not restricted to peculiar neuronal subtypes, but could include most of the neuronal populations of the brain.

Differential oligodendroglial expression of the tumor necrosis factor receptors in vivo and in vitro.

The cytokine tumor necrosis factor-alpha (TNF alpha) has been proposed to play a key role in the degenerative processes observed in demyelinating diseases such as multiple sclerosis (MS). In the immune system the cellular responses to TNF are mediated by two different receptors: TNF-RI, which is involved in cell death, and TNF-RII, which has been shown to mediate cell proliferation. We investigated the oligodendroglial expression of TNF-RI and -RII. In vivo, in normal adult rodent brain, oligodendrocytes express TNF-RII but not TNF-RI. However, after 3 days in culture, both types of receptors were expressed by mature oligodendrocytes, purified from 4-week-old rats, suggesting that expression of TNF-RI was induced by either the isolation process or the culture conditions. This inducibility of TNF-RI may explain the differences in oligodendrocyte cell death reported in various experimental conditions and in the pathology of MS lesions.