Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.

BACKGROUND: In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. RESULTS: Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system. CONCLUSIONS: This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.

Autoimmunity against dopamine receptors in neuropsychiatric and movement disorders: a review of Sydenham chorea and beyond.

Antineuronal autoantibodies are associated with the involuntary movement disorder Sydenham chorea (SC) and paediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS) which are characterized by the acute onset of tics and/or obsessive compulsive disorder (OCD). In SC and PANDAS, autoantibodies signal human neuronal cells and activate calcium calmodulin-dependent protein kinase II (CaMKII). Animal models immunized with group A streptococcal antigens demonstrate autoantibodies against dopamine receptors and concomitantly altered behaviours. Human monoclonal antibodies (mAbs) derived from SC target and signal the dopamine D2L (long) receptor (D2R). Antibodies against D2R were elevated over normal levels in SC and acute-onset PANDAS with small choreiform movements, but were not elevated over normal levels in PANDAS-like chronic tics and OCD. The expression of human SC-derived anti-D2R autoantibody V gene in B cells and serum of transgenic mice demonstrated that the human autoantibody targets dopaminergic neurones in the basal ganglia and other types of neurones in the cortex. Here, we review current evidence supporting the hypothesis that antineuronal antibodies, specifically against dopamine receptors, follow streptococcal exposures and may target dopamine receptors and alter central dopamine pathways leading to movement and neuropsychiatric disorders.

Comprehensive genome-wide evaluation of lapatinib-induced liver injury yields a single genetic signal centered on known risk allele HLA-DRB1*07:01.

Lapatinib is associated with a low incidence of serious liver injury. Previous investigations have identified and confirmed the Class II allele HLA-DRB1*07:01 to be strongly associated with lapatinib-induced liver injury; however, the moderate positive predictive value limits its clinical utility. To assess whether additional genetic variants located within the major histocompatibility complex locus or elsewhere in the genome may influence lapatinib-induced liver injury risk, and potentially lead to a genetic association with improved predictive qualities, we have taken two approaches: a genome-wide association study and a whole-genome sequencing study. This evaluation did not reveal additional associations other than the previously identified association for HLA-DRB1*07:01. The present study represents the most comprehensive genetic evaluation of drug-induced liver injury (DILI) or hypersensitivity, and suggests that investigation of possible human leukocyte antigen associations with DILI and other hypersensitivities represents an important first step in understanding the mechanism of these events.

A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures.

The copepod Calanus glacialis plays a key role in the Arctic pelagic ecosystem. Despite its ecological importance and ongoing climate changes, limited knowledge at the genomic level has hindered the understanding of the molecular processes underlying environmental stress responses and ecological adaptation. Transcriptome data was generated from an experiment with C. glacialis copepodite (CV) subjected to five different temperatures. We obtained a total of 512,352 high-quality 454 pyrosequencing reads, which were assembled into 55,562 contigs distributed in 128 KEGG pathways. Functional analysis revealed numerous genes related to diverse biological functions and processes, including members of all major conserved signaling pathways. Comparative analysis of acclimated individuals to experimental temperatures has provided information about gene variations observed in several pathways (e.g. genes involved in energy, lipid and amino acid metabolism were shown to be down-regulated with increasing temperatures). These mRNA sequence resources will facilitate further studies on genomics and physiology-driven molecular processes in C. glacialis and related species.

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts.

Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and ∼30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.

Evolutionary conservation of TFIIH subunits: implications for the use of zebrafish as a model to study TFIIH function and regulation.

Transcriptional factor IIH (TFIIH) is involved in cell cycle regulation, nucleotide excision repair, and gene transcription. Mutations in three of its subunits, XPB, XPD, and TTDA, lead to human recessive genetic disorders such as trichothiodystrophy and xeroderma pigmentosum, the latter of which is sometimes associated with Cockayne's syndrome. In the present study, we investigate the sequence conservation of TFIIH subunits among several teleost fish species and compare their characteristics and putative regulation by transcription factors to those of human and zebrafish. We report the following findings: (i) comparisons among protein sequences revealed a high sequence identity for each TFIIH subunit analysed; (ii) among transcription factors identified as putative regulators, OCT1 and AP1 have the highest binding-site frequencies in the promoters of TFIIH genes, and (iii) TFIIH genes have alternatively spliced isoforms. Finally, we compared the protein primary structure in human and zebrafish of XPD and XPB - two important ATP-dependent helicases that catalyse the unwinding of the DNA duplex at promoters during transcription - highlighting the conservation of domain regions such as the helicase domains. Our study suggests that zebrafish, a widely used model for many human diseases, could also act as an important model to study the function of TFIIH complex in repair and transcription regulation in humans.

Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva.

Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently "intra-specific" poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges.

July 2012 Greenland melt extent enhanced by low-level liquid clouds.

Melting of the world's major ice sheets can affect human and environmental conditions by contributing to sea-level rise. In July 2012, an historically rare period of extended surface melting was observed across almost the entire Greenland ice sheet, raising questions about the frequency and spatial extent of such events. Here we show that low-level clouds consisting of liquid water droplets ('liquid clouds'), via their radiative effects, played a key part in this melt event by increasing near-surface temperatures. We used a suite of surface-based observations, remote sensing data, and a surface energy-balance model. At the critical surface melt time, the clouds were optically thick enough and low enough to enhance the downwelling infrared flux at the surface. At the same time they were optically thin enough to allow sufficient solar radiation to penetrate through them and raise surface temperatures above the melting point. Outside this narrow range in cloud optical thickness, the radiative contribution to the surface energy budget would have been diminished, and the spatial extent of this melting event would have been smaller. We further show that these thin, low-level liquid clouds occur frequently, both over Greenland and across the Arctic, being present around 30-50 per cent of the time. Our results may help to explain the difficulties that global climate models have in simulating the Arctic surface energy budget, particularly as models tend to under-predict the formation of optically thin liquid clouds at supercooled temperatures--a process potentially necessary to account fully for temperature feedbacks in a warming Arctic climate.

Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva

Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently "intraspecific" poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges

Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta).

Pleurocarpous mosses, characterized by lateral female gametangia and highly branched, interwoven stems, comprise three orders and some 5000 species, or almost half of all moss diversity. Recent phylogenetic analyses resolve the Ptychomniales as sister to the Hypnales plus Hookeriales. Species richness is highly asymmetric with approximately 100 Ptychomniales, 750 Hookeriales, and 4400 Hypnales. Chloroplast DNA (cpDNA) sequences were obtained to compare partitioning of molecular diversity among the orders with estimates of species richness, and to test the hypothesis that either the Hookeriales or Hypnales underwent a period (or periods) of exceptionally rapid diversification. Levels of biodiversity were quantified using explicitly historical "phylogenetic diversity" and non-historical estimates of standing sequence diversity. Diversification rates were visualized using lineage-through-time (LTT) plots, and statistical tests of alternative diversification models were performed using the methods of Paradis (1997). The effects of incomplete sampling on the shape of LTT plots and performance of statistical tests were investigated using simulated phylogenies with incomplete sampling. Despite a much larger number of accepted species, the Hypnales contain lower levels of (cpDNA) biodiversity than their sister group, the Hookeriales, based on all molecular measures. Simulations confirm previous results that incomplete sampling yields diversification patterns that appear to reflect a decreasing rate through time, even when the true phylogenies were simulated with constant rates. Comparisons between simulated results and empirical data indicate that a constant rate of diversification cannot be rejected for the Hookeriales. The Hypnales, however, appear to have undergone a period of exceptionally rapid diversification for the earliest 20% of their history.

Acute care testing. Blood gases and electrolytes at the point of care.

The standard turnaround time for acute care laboratory testing in tertiary care institutions is typically less than 15 minutes for blood gas or electrolyte values. From a clinical perspective, however, the desirable turnaround time is more on the order of 5 minutes, and this is technically achievable. The 15-minute standard can be met with strategically located STAT laboratories. To achieve a turnaround time of 5 minutes, it is necessary to move the "laboratory" closer to the patient and to have more than one instrument available. This latter configuration is called near or bedside patient testing. Why the 5-minute standard is not used universally throughout the nation is probably related to differing perspectives on "cost" and "quality." As manufacturers, hospitals and laboratories address the issue of rapid turnaround time in acute care settings, the 5-minute standard may become more widespread. Direct costs have been decreasing as more manufacturers enter the market for acute care testing. The overall quality is also improving, not only in the engineering features built into the instruments, but also as nonlaboratory staff gain skill in performing the testing. As more sites implement POCT, standards and guidelines for managing testing outside of the laboratory are being established. Solutions to preanalytic problems are being developed and implemented. POCT testing for blood gases and electrolytes was once considered to lie in the future but is now commonplace and may one day become the standard of care.

Detection of Mycobacterium tuberculosis group organisms in human and mouse joint tissue by reverse transcriptase PCR: prevalence in diseased synovial tissue suggests lack of specific association with rheumatoid arthritis.

Infection with mycobacterial species, including Mycobacterium tuberculosis, has long been implicated in the etiopathology of rheumatoid arthritis (RA) on the basis of clinical and pathological similarities between tuberculosis and RA. Despite evidence of immune responses to mycobacterial antigens in RA patient synovial fluid, cross-reactivity between these and host joint antigens, and the presence of M. tuberculosis protein antigen in RA synovial fluid, a definite causal association with RA has not been shown. Previous studies from our laboratory using reverse transcriptase PCR (RT-PCR) of bacterial rRNAs have shown RA synovium to be colonized by a diverse range of bacteria, most of commensal origin. However, M. tuberculosis group organism (MTG) RNA sequences were found in one RA patient tissue. Since this was considered of sufficient interest to warrant further investigation, we devised a M. tuberculosis-specific nested RT-PCR test which could be used for detection of MTG in a mixed pool of bacterial crDNAs. This test was used to investigate the distribution of MTG in RA synovial tissue and also non-RA arthritis and healthy control tissues and was also used to examine the tissue distribution of MTG in an acute and chronic model of M. tuberculosis infection in the BALB/c mouse. MTG sequences were found in a high proportion of RA patient synovial tissues but also in non-RA arthritis control tissues at lower frequency. This likely reflects trafficking of persistent M. bovis BCG to inflamed joint tissue, irrespective of cause. MTG were not found in healthy synovial tissue or the tissue of patients with undifferentiated arthritis. In both the acute and chronic models of infection in BALB/c mice, M. tuberculosis was also found to have trafficked to joint tissues, however, no signs of inflammation, arthritis, or pathology associated with M. tuberculosis infection was seen. These combined results would argue against a specific causal role of MTG in RA-like arthritis; however, their role as adjuvant in immune dysfunction in an innately susceptible host cannot be excluded.

Reverse transcriptase-PCR analysis of bacterial rRNA for detection and characterization of bacterial species in arthritis synovial tissue.

Onset of rheumatoid arthritis (RA) is widely believed to be preceded by exposure to some environmental trigger such as bacterial infectious agents. The influence of bacteria on RA disease onset or pathology has to date been controversial, due to inconsistencies between groups in the report of bacterial species isolated from RA disease tissue. Using a modified technique of reverse transcriptase-PCR amplification, we have detected bacterial rRNA in the synovial tissue of late-stage RA and non-RA arthritis controls. This may be suggestive of the presence of live bacteria. Sequencing of cloned complementary rDNA (crDNA) products revealed a number of bacterial sequences in joint tissue from each patient, and from these analyses a comprehensive profile of the organisms present was compiled. This revealed a number of different organisms in each patient, some of which are common to both RA and non-RA controls and are probably opportunistic colonizers of previously diseased tissue and others which are unique species. These latter organisms may be candidates for a specific role in disease pathology and require further investigation to exclude them as causative agents in the complex bacterial millieu. In addition, many of the detected bacterial species have not been identified previously from synovial tissue or fluid from arthritis patients. These may not be easily cultivable, since they were not revealed in previous studies using conventional in vitro bacterial culture methods. In situ hybridization analyses have revealed the joint-associated bacterial rRNA to be both intra- and extracellular. The role of viable bacteria or their nucleic acids as triggers in disease onset or pathology in either RA or non-RA arthritis controls is unclear and requires further investigation.

Cardiac-specific troponin I levels and risk of coronary artery disease and graft failure following heart transplantation.

CONTEXT: Previous studies have yielded conflicting data regarding whether a relationship exists between elevated cardiac troponin levels and acute allograft rejection in patients who have received heart transplants. OBJECTIVE: To determine whether cardiac troponin I levels after heart transplantation were associated with a procoagulant microvasculature and long-term allograft outcome. DESIGN: Prospective cohort study with a mean (SE) follow-up of 45.1 (2.5) months. Serum troponin I levels were measured 9.9 (0.2) times per patient during the first 12 months after heart transplantation. SETTING: Heart transplant center in the United States. PATIENTS: A total of 110 consecutive patients who received a heart transplant between 1989 and 1997 and survived at least 1 year after transplantation. MAIN OUTCOME MEASURES: Histological and immunohistochemical biopsy findings, development of coronary artery disease (CAD), and graft failure in patients with vs without elevated serum cardiac troponin I levels. RESULTS: All recipients had elevated troponin I levels during the first month after transplantation. Troponin I levels remained persistently elevated during the first 12 months in 56 patients (51%) and became undetectable in 54 patients (49%). Persistently elevated troponin I levels were associated with increasing fibrin deposits in microvasculature and cardiomyocytes (P<.001). Patients with persistently elevated levels of troponin I had significantly increased risk for subsequent development of CAD (odds ratio [OR], 4. 3; 95% confidence interval [CI], 1.8-10.1; P<.001) and graft failure (OR, 3.4; 95% CI, 1.2-9.7; P =.02), and also developed more severe CAD (OR, 4.2; 95% CI, 1.9-9.3; P<.001) and showed more disease progression (OR, 3.7; 95% CI, 1.3-10.4; P =.009). CONCLUSION: In this study, elevated cardiac troponin I levels, which are considered to be a noninvasive surrogate marker of a procoagulant microvasculature, identified a subgroup of patients with high risk for developing CAD and graft failure after cardiac transplantation. JAMA. 2000;284:457-464

Event-related potentials and the recollection of associative information.

Event-related potentials (ERPs) were recorded from 13 scalp sites during the performance of an associative recall task. At study, subjects were presented with a series of word pairs and were required to incorporate the two members of each pair into a sentence. At test, the first members of each pair were presented intermixed with an equal number of unstudied items. Subjects were required to discriminate between new and studied (old) words and, for each word judged old, to attempt to recall the word with which it had been associated at study. Compared to the ERPs elicited by new words, the ERPs elicited by words correctly judged to be old and for which the associate was correctly recalled showed a sustained, positive-going shift (the "parietal old/new effect"). This effect was strongly lateralised to the left hemisphere and was maximal at temporo-parietal electrodes. The effect was absent in ERPs elicited by words that were correctly judged to be old, but for which the studied associate could not be recalled. The findings are taken as support for the idea that the parietal old/new effect reflects neural activity associated with the recollection of specific past episodes, and hence that the effect may index retrieval operations supported by the medial temporal lobe memory system.

Event-related potentials and the recollection of low and high frequency words.

A recognition memory test was conducted in which low and high frequency words were initially presented in one of two different study tasks. A word was defined as recollected if, at test, it was both confidently judged 'old', and confidently assigned to its correct study context. Low frequency words were more accurately recognised than high frequency items, and were also more likely to be assigned to their correct study context. The results are consistent with the view that low frequency words are better recognised because they are more likely to be recollected, rather than because they engender higher levels of relative familiarity. Event-related potentials (ERPs) evoked at test by correctly classified new words were contrasted with those evoked by old, recollected words. The ERPs to low frequency words exhibited large and reliable 'old/new' effects, in that from approx. 300 msec post-stimulus, waveforms were more positive-going for old than for new items. These effects were markedly smaller, and indeed non-significant, in the ERPs evoked by high frequency items. The results show that the interaction between word frequency and old/new differences in ERPs does not arise because of a confound between frequency and the probability of recollection. Together with other findings, they suggest that recollection is better conceived of as a graded, rather than as an all-or-none phenomenon.