Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency.

To reveal how cells exit human pluripotency, we designed a CRISPR-Cas9 screen exploiting the metabolic and epigenetic differences between naïve and primed pluripotent cells. We identify the tumor suppressor, Folliculin(FLCN) as a critical gene required for the exit from human pluripotency. Here we show that FLCN Knock-out (KO) hESCs maintain the naïve pluripotent state but cannot exit the state since the critical transcription factor TFE3 remains active in the nucleus. TFE3 targets up-regulated in FLCN KO exit assay are members of Wnt pathway and ESRRB. Treatment of FLCN KO hESC with a Wnt inhibitor, but not ESRRB/FLCN double mutant, rescues the cells, allowing the exit from the naïve state. Using co-immunoprecipitation and mass spectrometry analysis we identify unique FLCN binding partners. The interactions of FLCN with components of the mTOR pathway (mTORC1 and mTORC2) reveal a mechanism of FLCN function during exit from naïve pluripotency.

Transmission strategies in a chemosynthetic symbiosis: detection and quantification of symbionts in host tissues and their environment.

Transmission of bacteria vertically through host tissues ensures offspring acquire symbionts; however, horizontal transmission is an effective strategy for many associations and plays a role in some vertically transmitted symbioses. The bivalve Solemya velum and its gammaproteobacterial chemosynthetic symbionts exhibit evolutionary evidence of both transmission modes, but the dominant strategy on an ecological time scale is unknown. To address this, a specific primer set was developed and validated for the S. velum symbiont using a novel workflow called specific marker design (SMD). Symbionts were quantified in spawned eggs and sediment and seawater samples from S. velum habitats with qPCR. Each egg was estimated to contain 50-100 symbiont genomes. By contrast, symbiont DNA was found at low abundance/occurrence in sediment and seawater, often co-occurring with host mitochondrial DNA, obscuring its origin. To ascertain when eggs become infected, histological sections of S. velum tissues were labelled for symbiont 16S rRNA via in situ hybridization. This revealed symbionts in the ovary walls and mature oocytes, suggesting association in late oogenesis. These data support the hypothesis that S. velum symbionts are vertically transmitted every host generation, thus genetic signatures of horizontal transmission are driven by ecologically infrequent events. This knowledge furthers our understanding of vertical and horizontal mode integration and provides insights across animal-bacterial chemosynthetic symbioses.

Microbiota-derived tryptophan indoles increase after gastric bypass surgery and reduce intestinal permeability in vitro and in vivo.

BACKGROUND: The diet and microbiome contribute to metabolic disease in part due to increased intestinal inflammation and permeability. Dietary tryptophan is metabolized by both mammalian and bacterial enzymes. Using in vitro, in vivo models, and clinical data, we tested whether bacterial tryptophan indole derivatives underlie the positive benefits of microbiota on inflammation that is associated with metabolic disease. METHODS: In high-fat diet (HFD)-fed mice intestinal permeability and plasma endotoxin levels were measured after indole-3-propionic acid (IPA; 20 mg kg-1 p.o. for 4 days). Tryptophan derivatives effect on permeability and gene expression were assessed in T84 intestinal cell monolayers, in the presence or absence of pro-inflammatory cytokines. Plasma tryptophan metabolites were analyzed from lean, or obese T2D subjects undergoing Roux-en-Y gastric bypass surgery (RYGB). KEY RESULTS: IPA reduced the increased intestinal permeability observed in HFD-fed mice. Of 16 metabolites tested in vitro, only IPA, and tryptamine reduced T84 cell monolayer permeability compromised by pro-inflammatory cytokines. In T84 cells, IPA reversed the IFN-γ induced increase of fructose transporter SLC2A5 (GLUT5) mRNA, but not induction of inflammatory or metabolic genes. In obese subjects, IPA levels were reduced relative to lean counterparts, and these levels were increased by 3 months after RYGB. CONCLUSIONS AND INFERENCES: The novel findings are that obese subjects have lower levels of IPA, a solely bacterially derived tryptophan derivative, and IPA improved intestinal barrier function in vitro and DIO mice. Reduced plasma IPA levels and reversal by surgery may be a consequence of intestinal indole-producing microbiota but underlying mechanisms warrant further investigation.

Isotopic discrimination and kinetic parameters of RubisCO from the marine bloom-forming diatom, Skeletonema costatum.

The cosmopolitan, bloom-forming diatom, Skeletonema costatum, is a prominent primary producer in coastal oceans, fixing CO2 with ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) that is phylogenetically distinct from terrestrial plant RubisCO. RubisCOs are subdivided into groups based on sequence similarity of their large subunits (IA-ID, II, and III). ID is present in several major oceanic primary producers, including diatoms such as S. costatum, coccolithophores, and some dinoflagellates, and differs substantially in amino acid sequence from the well-studied IB enzymes present in most cyanobacteria and in green algae and plants. Despite this sequence divergence, and differences in isotopic discrimination apparent in other RubisCO enzymes, stable carbon isotope compositions of diatoms and other marine phytoplankton are generally interpreted assuming enzymatic isotopic discrimination similar to spinach RubisCO (IB). To interpret phytoplankton δ(13) C values, S. costatum RubisCO was characterized via sequence analysis, and measurement of its KCO2 and Vmax , and degree of isotopic discrimination. The sequence of this enzyme placed it among other diatom ID RubisCOs. Michaelis-Menten parameters were similar to other ID enzymes (KCO2 = 48.9 ± 2.8 µm; Vmax = 165.1 ± 6.3 nmol min(-1 ) mg(-1) ). However, isotopic discrimination (ε = [(12) k/(13) k - 1] × 1000) was low (18.5‰; 17.0-19.9, 95% CI) when compared to IA and IB RubisCOs (22-29‰), though not as low as ID from coccolithophore, Emiliania huxleyi (11.1‰). Variability in ε-values among RubisCOs from primary producers is likely reflected in δ(13) C values of oceanic biomass. Currently, δ(13) C variability is ascribed to physical or chemical factors (e.g. illumination, nutrient availability) and physiological responses to these factors (e.g. carbon-concentrating mechanisms). Estimating the importance of these factors from δ(13) C measurements requires an accurate ε-value, and a mass-balance model using the ε-value for S. costatum RubisCO is presented. Clearly, appropriate ε-values must be included in interpreting δ(13) C values of environmental samples.

Sexually transmitted infections among pregnant heroin- or cocaine-addicted women in treatment: the significance of psychiatric co-morbidity and sex trade.

Psychiatric co-morbidity and sex trade were tested as correlates of sexually transmitted infections (STIs) among 76 pregnant heroin- or cocaine-dependent women. Participants were recruited from a drug treatment programme and attended a clinician-administered assessment including the Structured Clinical Interview for DSM-IV (SCID-IV-TR) and self-report questionnaires about lifetime histories of sex trade and STIs (i.e. gonorrhoea, syphilis, chlamydia, herpes, genital warts or trichomonas). Lifetime and six month rates of STIs were 53.9% and 18.4%, respectively. The majority of women also had lifetime histories of psychiatric co-morbidity (61.8%) and/or sex trade (60.5%). Participants with psychiatric co-morbidity (adjusted odds ratio [AOR] 3.9; 95% confidence interval [CI] 1.3-11.6) and/or sex trade (AOR 3.2; 95% CI 1.1-9.5) were more likely to report STIs during their lifetime compared with those without such histories while controlling for age, education and race/ethnicity. Results suggest that as many as one-in-five pregnant heroin- or cocaine-dependent women in treatment have one or more STIs that are concurrent with their pregnancy and may contribute to risk for contracting HIV and pregnancy complications; psychiatric co-morbidity and/or sex trade were associated with greater STI risk. Findings underscore the importance of identifying and addressing co-morbid psychiatric disorders and sex trade behaviour in this population.

Patterns of illegal drug use among an adult alcohol dependent population: results from the National Survey on Drug Use and Health.

The use of illegal drugs is common in alcohol dependence and significant psychological and social consequences are associated with the concurrent use of alcohol and illegal drugs. However, little literature has examined the patterns of concurrent-drug use in alcohol dependent individuals. A latent class analysis (LCA) was used to determine whether patterns of past year illegal drug use existed in a national sample of 6059 alcohol dependent respondents of the combined 2005, 2006 and 2007 National Survey on Drug Use and Health. Multinomial logistic regression was then used to determine whether demographic variables, mental health disturbance and social consequences were predictive of drug use classes. Results of the LCA demonstrated a 5-class solution with optimal fit deduced by Bayesian Information Criterion minima. The five classes included: a close to zero probability of illegal drug use (class 1: 65%), medium marijuana, medium sedatives/tranquilizers and high analgesics (class 2: 7%), high marijuana, medium cocaine use (class 3: 21%), high probabilities of marijuana, cocaine, sedatives and analgesic use (class 4: 6%) and a high concurrent-drug use except other hallucinogens (class 5: 1%). Regression results suggest that younger age, comorbidity, engaging in deviant behaviors, sexually transmitted infection and incarceration are associated with concurrent illegal drug use in alcohol dependent individuals. Findings advocate that more intense psychiatric and drug dependence treatment resources may be needed for concurrent-drug using alcohol dependent populations and provide evidence for targeted prevention and treatment interventions.

The Calyptogena magnifica chemoautotrophic symbiont genome.

Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur.

A coastal marine sulfide-oxidizing autotrophic bacterium produces hydrophilic filamentous sulfur as a novel metabolic end product. Phylogenetic analysis placed the organism in the genus Arcobacter in the epsilon subdivision of the Proteobacteria. This motile vibrioid organism can be considered difficult to grow, preferring to grow under microaerophilic conditions in flowing systems in which a sulfide-oxygen gradient has been established. Purified cell cultures were maintained by using this approach. Essentially all 4',6-diamidino-2-phenylindole dihydrochloride-stained cells in a flowing reactor system hybridized with Arcobacter-specific probes as well as with a probe specific for the sequence obtained from reactor-grown cells. The proposed provisional name for the coastal isolate is "Candidatus Arcobacter sulfidicus." For cells cultured in a flowing reactor system, the sulfide optimum was higher than and the CO(2) fixation activity was as high as or higher than those reported for other sulfur oxidizers, such as Thiomicrospira spp. Cells associated with filamentous sulfur material demonstrated nitrogen fixation capability. No ribulose 1,5-bisphosphate carboxylase/oxygenase could be detected on the basis of radioisotopic activity or by Western blotting techniques, suggesting an alternative pathway of CO(2) fixation. The process of microbial filamentous sulfur formation has been documented in a number of marine environments where both sulfide and oxygen are available. Filamentous sulfur formation by "Candidatus Arcobacter sulfidicus" or similar strains may be an ecologically important process, contributing significantly to primary production in such environments.

Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria.

Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57 degrees C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.

Biogeography and ecological setting of Indian Ocean hydrothermal vents.

Within the endemic invertebrate faunas of hydrothermal vents, five biogeographic provinces are recognized. Invertebrates at two Indian Ocean vent fields (Kairei and Edmond) belong to a sixth province, despite ecological settings and invertebrate-bacterial symbioses similar to those of both western Pacific and Atlantic vents. Most organisms found at these Indian Ocean vent fields have evolutionary affinities with western Pacific vent faunas, but a shrimp that ecologically dominates Indian Ocean vents closely resembles its Mid-Atlantic counterpart. These findings contribute to a global assessment of the biogeography of chemosynthetic faunas and indicate that the Indian Ocean vent community follows asymmetric assembly rules biased toward Pacific evolutionary alliances.

Population Dynamics of Two Toluene Degrading Bacterial Species in a Contaminated Stream.

Toluene uptake by a benthic biofilm community was previously shown to vary seasonally from 0.03 m hr?1 in winter to 0.2 m hr?1 in summer in a solvent-contaminated stream of the Aberjona watershed. We used quantitative PCR to estimate the population dynamics of previously isolated species of toluene-degrading Xanthobacter autotrophicus and Mycobacterium sp. in both toluene-contaminated and uncontaminated reaches of the stream, and to estimate their relative roles in overall biodegradation rate. Quantification using specific 16S rDNA primers forX. autotrophicus and Mycobacterium sp. showed that populations of both species were much larger in the toluene-contaminated than the toluene-free reach, in agreement with earlier culture-based investigations. A relatively brief bloom of X. autotrophicus occurred in the contaminated reach in the summer, while Mycobacterium sp. populations occurred at elevated densities for more than 5 months. Calculations showed that Mycobacterium, previously thought to be less important than Xanthobacter in annual toluene degradation based on single time-point CFU estimates, appears actually more important because of this longer persistence.

Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae.

The diversity of a microbial community covering the surface of a marine nematode was analyzed by performing a 16S ribosomal DNA (rDNA) restriction cutting and sequencing analysis. In two clone libraries constructed by using individual nematodes, 54 and 85 restriction patterns were identified, and only 13 of these patterns were common to both libraries. Sequence analysis indicated that the common patterns belonged to four groups related to sequences of cytophagas, sulfate-reducing bacteria, members of the gamma subclass of the class Proteobacteria, and caulobacters. At least two groups appeared to be permanent members of the community as they were also detected in a 16S rDNA library constructed 3 years previously by using 100 pooled nematode specimens. A surprising outcome was that very dominant filamentous bacteria were apparently not represented in the clone libraries, as quantitative probing showed that none of the common operational taxonomic unit groups displayed the expected overwhelming dominance. Nevertheless, our analysis revealed both an unexpectedly high level of bacterial diversity and heterogeneity in samples representing presumably very similar microenvironments.

Importance of Xanthobacter autotrophicus in toluene biodegradation within a contaminated stream.

Toluene-degrading strains T101 and T102 were isolated from rock surface biomass in a toluene-contaminated freshwater stream. These organisms were present at a density of 5.5 x 10(6) cells/g of rock surface biomass. Both are aerobic, rod-shaped, Gram-negative, non-motile, catalase-positive, oxidase-positive, with yellow pigments, and can grow on benzene. Phylogenetic analyses show that strains T101 and T102 have 16S rDNA sequences identical to Xanthobacter autotrophicus. Fatty acid analyses indicate that they are different strains of the same species Xanthobacter autotrophicus, and that they have high levels of cis-11-octadecenoic acid and cis-9-hexadecenoic acid; 3-hydroxyhexadecanoic acid is the major hydroxy fatty acid present. Strains T101 and T102 had maximal velocities (Vmax) for toluene biodegradation of 3.8 +/- 0.5 and 28.3 +/- 2.2 mumoles toluene/mgprotein-hr, and half-saturation constants (Ks) of 0.8 +/- 0.5 and 11.5 +/- 2.4 microM, respectively. Strain T102 has a higher capacity than strain T101 to degrade toluene, and kinetic calculations suggest that strain T102 may be a major contributor to toluene biodegradation in the stream.

Assessing the patient with a wound.

Assessment of the home care patient with a wound is critical to the planning and evaluation of care. This article presents the components of a comprehensive assessment that can be used as a guide to assessment of a patient with a wound. Topics include collection of a baseline history and physical examination, wound assessment, treatment plan and documentation, wound care orders, and follow-up visits.

Improving communication among health professionals through education: a pilot study.

Communication can be thought of as a message that is sent, received, and understood. Each discipline of the health profession has its own jargon and means of expressing ideas in shorthand. These separate forms of communicating are effective among those of the same background but are often at the root of misunderstandings between professional groups. This article reviews communication theory and traces the difficulties created when inter-disciplinary teams of healthcare try to work together and communicate. As multi-disciplinary teams are increasingly dealing with the complex problems of today's healthcare system, clear communication and understanding has never been more important. If educators could assist in creating an understanding of vocabulary used for decision processes, communication could improve. The authors of this study performed a multi-stage Delphi survey that grouped terms used by administrators and clinicians and produced a lexicon of corresponding terms. An expert panel then reviewed and modified the list. The result is a lexicon that can be useful to assist clinicians and administrators to communicate with each other. By utilizing clinical terminology, or vice versa, instead of management or clinical jargon, some of the translation done by administration or clinicians could be reduced. Examples of how the lexicon can be utilized are provided in the article. This includes using it in health administration education to demonstrate the variances in clinical/managerial terms. It could also be provided as a primer to physicians, nurses, and other health professionals who assume administrative positions to enhance their communication with administrators.

Bias in template-to-product ratios in multitemplate PCR.

Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.

Pharmacokinetic interaction between ondansetron and cyclophosphamide during high-dose chemotherapy for breast cancer.

PURPOSE: Both ondansetron and cyclophosphamide are thought to be metabolized by hepatic microsomal processes. The purpose of this study was to evaluate the potential pharmacokinetic interactions between ondansetron and high-dose alkylating agent chemotherapy. METHODS: A total of 54 breast cancer patients receiving high-dose cyclophosphamide, cisplatin and carmustine were treated prospectively in four sequential cohorts. Cohorts I and II received continuous infusions of both ondansetron and prochlorperazine, and cohorts III and IV received a continuous infusion of ondansetron alone at the same doses. All patients received lorazepam every 4 h. A group of 75 matched historical controls had received a continuous infusion of prochlorperazine with lorazepam. Pharmacokinetic monitoring of each drug used in the high-dose chemotherapy regimen was conducted. RESULTS: Median AUCs of cyclophosphamide in patients receiving ondansetron (73.6 mg/ml x min) were lower than those of the control patients (88.3 mg/ml x min, n = 75, P = 0.0004), but the median cisplatin AUC was approximately 10% higher and no difference in the disposition of carmustine was demonstrated. Patients treated with ondansetron displayed a higher frequency of headaches than the controls. The frequency of achieving complete emetic control was greater in the ondansetron + prochlorperazine groups compared to the ondansetron alone groups and was greater in both these groups than in the prochlorperazine alone group on the first day of therapy only. CONCLUSION: Ondansetron altered the systemic exposure to cyclophosphamide when these agents were administered concomitantly. Ondansetron did not substantially improve overall emetic control when used alone but may improve control in combination with prochlorperazine. Future randomized studies are needed to delineate the effect of ondansetron on the disposition of the active cyclophosphamide metabolites so that clinical implications can be addressed.