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.

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.

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.

Preliminary in vitro investigation of the effects of pulsed Nd:YAG laser radiation on enamel and dentine

Data available on the effects of pulsed near IR laser energy on dental hard tissue are limited. This study investigates the changes in dental hard tissue when exposed to short duration, pulsed IR wavelength laser light emitted from a Neodymium Yttrium Aluminium Garnet laser (Nd:YAG laser, wavelength 1.06 microns). The results showed that, after treatment with an initiator, there was superficial melting of the enamel. Dentine was altered substantially. The lesions produced in dentine were larger than the cross-section of the delivery fibre optic wand. Considerable inter-sample variation was observed. The temperature rises producing these effects were large and affected the tissue at a distance from the tip.

An experimental evaluation of precision laser cutting of dental hard tissues and materials

This paper examines the use of excimer laser radiation in the controlled removal of tooth tissue and three plastic restorative materials. Freshly extracted human third molar teeth were filled with three restorative materials and sectioned longitudinally through the restoratives. The cut surfaces of the materials and surrounding enamel and dentine were exposed to three laser energy densities and the dimensions and topographical details of the irradiated sites assessed using optical and scanning electron microscopy. The results showed that the radiation produced lesions of uniformly reproducible size and shape.

Hereditary non-polyposis colorectal cancer (Lynch syndrome I) in a 13 year old male

A case of adenocarcinoma of the colon is reported. It presented in a family with hereditary non-polyposis colorectal cancer (HNPCC). Colonoscopic screening at a young age is recommended in such families. It also suggests a genetic basis for colorectal carcinogenesis in this family. Three of the members of this family also have peptic ulceration and an association between this syndrome and HNPCC is postulated.

Spontaneous bacterial peritonitis in a healthy adult male

A 44-year-old man was admitted with acute abdominal pain, anorexia, nausea and dry retching, with tenderness and rigidity of the abdominal wall. Exploratory laparotomy revealed generalized peritonitis. He developed delerium tremens soon after operation and dehiscence of the abdominal wound 36 hours postoperatively. When the wound was closed and reinforced his recovery was uneventful. This case was unusual because he did not have ascites or cirrhosis, which are commonly associated with the disease.

EKTACHEM bilirubin fraction Bc as a predictor of liver transplant rejection

Bilirubin fractions Bc and DELTA, not routinely available prior to the EKTACHEM Chemistry Analyzer and its slide methodology, were studied in an outpatient population of liver transplant recipients. A preliminary evaluation by the authors has shown that direct bilirubin (DBILI) levels in the normal range consist almost exclusively of DELTA (protein-bound conjugated bilirubin), while at elevated DBILI levels, an increasing amount of Bc (non-protein-bound conjugated bilirubin) is measured as well. The present study evaluated the clinical significance of Bc in the serum of 80 liver transplant recipients as a means of identifying episodes of rejection. Each patient was classified into rejection or nonrejection categories based on clinical status, liver biopsy results, and/or response to therapy. Eighteen patients were classified as experiencing an episode of rejection during the period of this study. Fourteen of these (77.8%) had Bc levels that ranged from 0.1 to 6.8 mg/dl. Sixty two patients were classified in the nonrejection category. Fourteen (22.6%) of these patients had Bc levels that ranged from 0.1 to 0.6 mg/dl. In our outpatient liver transplant recipients with Bc greater than or equal to 0.1 mg/dl, the relative risk of rejection (% of rejection patients with Bc/% of nonrejection patients with Bc) was 3.44. This value indicates that Bc determination may be a helpful adjunct in the assessment of rejection.

Lacto-N-fucopentaose III activity in the serum of patients with ovarian carcinoma

The expression of the lacto-N-fucopentaose III (LNF III) epitope by tumor cells of the gastrointestinal tract and ovary has been observed in tissue sections with the use of the murine monoclonal antibody GA 29-1. The presence of the LNF III epitope in the circulation of patients with colorectal cancer has also been reported. In this preliminary study, we describe the presence of LNF III activity in the serum of patients with adenocarcinoma of the ovary. Twelve of 18 (66%) patients with stage I-IV disease demonstrated high reactivity to the GA 29-1 monoclonal antibody. This serum reactivity was independent of disease stage and histologic cell type. In contrast, only 1 of 6 control patients demonstrated a false-positive level of reactivity to GA 29-1. These preliminary results suggest that LNF III warrants further study of its potential application as a serum tumor marker test in patients with adenocarcinoma of the ovary.

Evaluation of the Coulter Counter model S-Plus IV

Evaluation of linearity, carry-over, precision, and accuracy of a Coulter Counter model S-Plus IV prototype showed that they meet the manufacturer's specifications. The instrument also was compared with an earlier model. Correlations of the lymphocyte and granulocyte values in the three-part differential count with manual eye-count and a Technicon Hemalog D90 results were very close to the correlation of eye-count to Hemalog D90 results. The percentage of mononuclear cells showed acceptable correlation to the manual eye-count when monocytes were combined with blasts, eosinophils, and basophils. The medical effectiveness of the three-part differential was determined by comparison with manual eye-counts in 1,084 samples. The false positive and false negative values were 7.38% and 7.84%, respectively. The instrument has acceptable limits of operation. When combined with analysis of histograms by trained personnel, the three-part differential count is capable of screening for abnormalities that require further analysis.

Blood alcohol and road trauma survey

Since April 8, 1974, Victorian legislation has required that blood samples be taken from all persons aged 15 years or over after a road traffic crash. A survey was carried out of 474 such persons from June 10 until September 12, 1974. Of these, blood was taken from 350, and estimates of blood alcohol concentration were obtained from 271 samples. Sixty-five samples of the 271 (24%) gave positive results for alcohol and in about two-thirds of these the levels were higher than the legal limit of 0-05 g/100 ml. Over half of the subjects with positive results for blood alcohol concentration were under 30 years of age, 80% were males, and half were car drivers. This contrasted with the "alcohol-negative" subjects, who were older, and about half of whom were males. About 60% of both groups received minor injuries, and about 20% were admitted to hsopital. Research is continuing to define drinking habits and other social characteristics of these groups.