Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world.

The idea that life may have started with an "RNA world" is attractive. Wherein, a crucial event (perhaps at the very beginning of the scenario) should have been the emergence of a ribozyme that catalyzes its own replication, i.e., an RNA replicase. Although now there is experimental evidence supporting the chemical feasibility of such a ribozyme, the evolutionary dynamics of how the replicase could overcome the "parasite" problem (because other RNAs may also exploit this ribozyme) and thrive, as described in the scenario, remains unclear. It has been suggested that spatial limitation may have been important for the replicase to confront parasites. However, more studies showed that such a mechanism is not sufficient when this ribozyme's altruistic trait is taken into full consideration. "Tag mechanism", which means labeling the replicase with a short subsequence for recognition in replication, may be a further mechanism supporting the thriving of the replicase. However, because parasites may also "equip" themselves with the tag, it is far from clear whether the tag mechanism could take effect. Here, we conducted a computer simulation using a Monte-Carlo model to study the evolutionary dynamics surrounding the development of a tag-driven (polymerase-type) RNA replicase in the RNA world. We concluded that (1) with the tag mechanism the replicase could resist the parasites and become prosperous, (2) the main underlying reason should be that the parasitic molecules, especially those strong parasites, are more difficult to appear in the tag-driven system, and (3) the tag mechanism has a synergic effect with the spatial limitation mechanism-while the former provides "time" for the replicase to escape from parasites, the latter provides "space" for the replicase to escape. Notably, tags may readily serve as "control handles", and once the tag mechanism was exploited, the evolution towards complex life may have been much easier.

In vivo assessment of contractile strength distinguishes differential gene function in skeletal muscle of zebrafish larvae.

The accessible genetics and extensive skeletal musculature of the zebrafish make it a versatile and increasingly used model for studying muscle contraction. We here describe the development of an in vivo assay for measuring the contractile force of intact zebrafish at the larval stage. In addition, as proof of applicability, we have used this assay to quantify contractile strength of zebrafish larvae in a morphant model of deranged rbfox function. Average maximum tetanic (180 Hz) whole body forces produced by wild-type larvae at 2, 3, 4, and 5 days postfertilization amounted to 3.0, 7.2, 9.1, and 10.8 mN, respectively. To compare at potentially different stages of muscle development, we developed an immunohistological assay for empirically determining the cross-sectional area of larval trunk skeletal muscle to quantify muscle-specific force per cross-sectional area. At 4-5 days postfertilization, specific force amounts to ∼ 300 mN/mm(2), which is similar to fully developed adult mammalian skeletal muscle. We used these assays to measure contractile strength in zebrafish singly or doubly deficient for two rbfox paralogs, rbfox1l and rbfox2, which encode RNA-binding factors shown previously to modulate muscle function and muscle-specific splicing. We found rbfox2 morphants produce maximal tetanic forces similar to wild-type larvae, whereas rbfox1l morphants demonstrate significantly impaired function. rbfox1l/rbfox2 morphants are paralyzed, and their lack of contractile force production in our assay suggests that paralysis is a muscle-autonomous defect. These quantitative functional results allow measurement of muscle-specific phenotypes independent of neural input.

Quantitative assessment of ultrastructure and light scatter in mouse corneal debridement wounds.

PURPOSE: The mouse has become an important wound healing model with which to study corneal fibrosis, a frequent complication of refractive surgery. The aim of the current study was to quantify changes in stromal ultrastructure and light scatter that characterize fibrosis in mouse corneal debridement wounds. METHODS: Epithelial debridement wounds, with and without removal of basement membrane, were produced in C57BL/6 mice. Corneal opacity was measured using optical coherence tomography, and collagen diameter and matrix order were quantified by x-ray scattering. Electron microscopy was used to visualize proteoglycans. Quantitative PCR (Q-PCR) measured mRNA transcript levels for several quiescent and fibrotic markers. RESULTS: Epithelial debridement without basement membrane disruption produced a significant increase in matrix disorder at 8 weeks, but minimal corneal opacity. In contrast, basement membrane penetration led to increases in light scatter, matrix disorder, and collagen diameter, accompanied by the appearance of abnormally large proteoglycans in the subepithelial stroma. This group also demonstrated upregulation of several quiescent and fibrotic markers 2 to 4 weeks after wounding. CONCLUSIONS: Fibrotic corneal wound healing in mice involves extensive changes to collagen and proteoglycan ultrastructure, consistent with deposition of opaque scar tissue. Epithelial basement membrane penetration is a deciding factor determining the degree of ultrastructural changes and resulting opacity.

Maternal prenatal anxiety and downregulation of placental 11ß-HSD2.

BACKGROUND: Raised maternal anxiety during pregnancy is associated with increased risk of adverse neurodevelopmental outcomes for her child. The mechanisms underlying this are not known but animal studies suggest prenatal stress may alter the function of the placenta. Here we determined whether maternal prenatal anxiety was associated with a downregulation of placental 11ß-hydroxysteroid dehydrogenase type 2 (11ß-HSD2), the enzyme which metabolises cortisol. METHODS: We recruited mothers the day before delivery by elective caesarean, and gave them the Spielberger Trait and State anxiety and Edinburgh Depression self-rating scales. Placentae were collected and aliquots stored for later analysis. RESULTS: Prenatal Trait anxiety was negatively correlated with placental 11ß-HSD2 mRNA expression (r=-0.40, p<0.01, n=56). Results were similar with male and female fetuses (r=-0.39, p=0.04, n=28; r=-0.40, p=0.03, n=28) respectively. Results were also significant with State anxiety (r=-0.27, p=0.05, n=56) but somewhat weaker for depression (r=-0.20, p=0.13, n=56). Preliminary analyses on a subset of cases (n=25) suggested parallel results for enzyme activity. CONCLUSIONS: These findings provide evidence for an association between prenatal maternal mood and downregulation of placental 11ß-HSD2. Results are consistent with raised maternal anxiety being associated with increased fetal exposure to maternal cortisol, and support the hypothesis that this may be one mechanism underlying fetal programming by prenatal stress.

Energy expenditure regulation via macrophage migration inhibitory factor in obesity and in vitro anti-macrophage migration inhibitory factor effect of Alpinia officinarum Hance extraction.

OBJECTIVE: To compare the resting energy expenditure in different macrophage migration inhibitory factor (MIF) genotypes and to identify the in vitro effects of Alpinia officinarum Hance extract (AOHE) on MIF expression in obese and nonobese persons. METHODS: In the fasting state, obese and nonobese persons were assessed for the measurement of resting energy expenditure rate (REE) by indirect calorimetry. We compared it with the expected amount ([REE measured by indirect calorimetry / predicted REE according to Harris Benedict equations] x 100). Participants were classified into those with normal REE (≥100) vs those with impaired REE (<100). Body composition was analyzed. Real-time polymerase chain reaction was performed using specific primer pairs for MIF messenger RNA, and ß-actin was used as the internal control. RESULTS: The study included 69 obese and 103 non-obese participants. The proportions of MIF genotypes were slightly different in obese and nonobese participants. However, the proportions of MIF genotypes were significantly different in participants with normal REE and those with low REE. The MIF gene was highly expressed in the obese group compared with MIF expression in the nonobese group. Body fat mass and MIF expression were higher in participants with the GG genotype than in the other genotype groups. MIF expression was inversely associated with REE in both groups (r = -0.36, P = .04). After treatment of peripheral blood mononuclear cells with AOHE, MIF expression differed according to MIF genotype. CONCLUSIONS: Our results indicate that AOHE is a major modulator of MIF-dependent pathologic conditions in obesity and are consistent with mounting evidence that defines a regulating role for MIF in cytokine production in an inflammatory state in in vitro studies.

A composite SWNT-collagen matrix: characterization and preliminary assessment as a conductive peripheral nerve regeneration matrix.

Unique in their structure and function, single-walled carbon nanotubes (SWNTs) have received significant attention due to their potential to create unique conductive materials. For neural applications, these conductive materials hold promise as they may enhance regenerative processes. However, like other nano-scaled biomaterials it is important to have a comprehensive understanding how these materials interact with cell systems and how the biological system responds to their presence. These investigations aim to further our understanding of SWNT-cell interactions by assessing the effect SWNT/collagen hydrogels have on PC12 neuronal-like cells seeded within and (independently) on top of the composite material. Two types of collagen hydrogels were prepared: (1) SWNTs dispersed directly within the collagen (SWNT/COL) and (2) albumin-coated SWNTs prepared using the surfactant 'sodium cholate' to improve dispersion (AL-SWNT/COL) and collagen alone serving as a control (COL). SWNT dispersion was significantly improved when using surfactant-assisted dispersion. The enhanced dispersion resulted in a stiffer, more conductive material with an increased collagen fiber diameter. Short-term cell interactions with PC12 cells and SWNT composites have shown a stimulatory effect on cell proliferation relative to plain collagen controls. In parallel to these results, p53 gene displayed normal expression levels, which indicates the absence of nanoparticle-induced DNA damage. In summary, these mechanically tunable SWNT-collagen scaffolds show the potential for enhanced electrical activity and have shown positive in vitro biocompatibility results offering further evidence that SWNT-based materials have an important role in promoting neuronal regeneration.

Hypercapnia induced shifts in gill energy budgets of Antarctic notothenioids.

Mechanisms responsive to hypercapnia (elevated CO(2) concentrations) and shaping branchial energy turnover were investigated in isolated perfused gills of two Antarctic Notothenioids (Gobionotothen gibberifrons, Notothenia coriiceps). Branchial oxygen consumption was measured under normo- versus hypercapnic conditions (10,000 ppm CO(2)) at high extracellular pH values. The fractional costs of ion regulation, protein and RNA synthesis in the energy budgets were determined using specific inhibitors. Overall gill energy turnover was maintained under pH compensated hypercapnia in both Antarctic species as well as in a temperate zoarcid (Zoarces viviparus). However, fractional energy consumption by the examined processes rose drastically in G. gibberifrons (100-180%), and to a lesser extent in N. coriiceps gills (7-56%). In conclusion, high CO(2) concentrations under conditions of compensated acidosis induce cost increments in epithelial processes, however, at maintained overall rates of branchial energy turnover.

alpha-Lipoic acid increases energy expenditure by enhancing adenosine monophosphate-activated protein kinase-peroxisome proliferator-activated receptor-gamma coactivator-1alpha signaling in the skeletal muscle of aged mice.

Skeletal muscle mitochondrial dysfunction is associated with aging and diabetes, which decreases respiratory capacity and increases reactive oxygen species. Lipoic acid (LA) possesses antioxidative and antidiabetic properties. Metabolic action of LA is mediated by activation of adenosine monophosphate-activated protein kinase (AMPK), a cellular energy sensor that can regulate peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha), a master regulator of mitochondrial biogenesis. We hypothesized that LA improves energy metabolism and mitochondrial biogenesis by enhancing AMPK-PGC-1alpha signaling in the skeletal muscle of aged mice. C57BL/6 mice (24 months old, male) were supplemented with or without alpha-LA (0.75% in drinking water) for 1 month. In addition, metabolic action and cellular signaling of LA were studied in cultured mouse myoblastoma C2C12 cells. Lipoic acid supplementation improved body composition, glucose tolerance, and energy expenditure in the aged mice. Lipoic acid increased skeletal muscle mitochondrial biogenesis with increased phosphorylation of AMPK and messenger RNA expression of PGC-1alpha and glucose transporter-4. Besides body fat mass, LA decreased lean mass and attenuated phosphorylation of mammalian target of rapamycin (mTOR) signaling in the skeletal muscle. In cultured C2C12 cells, LA increased glucose uptake and palmitate beta-oxidation, but decreased protein synthesis, which was associated with increased phosphorylation of AMPK and expression of PGC-1alpha and glucose transporter-4, and attenuated phosphorylation of mTOR and p70S6 kinase. We conclude that LA improves skeletal muscle energy metabolism in the aged mouse possibly through enhancing AMPK-PGC-1alpha-mediated mitochondrial biogenesis and function. Moreover, LA increases lean mass loss possibly by suppressing protein synthesis in the skeletal muscle by down-regulating the mTOR signaling pathway. Thus, LA may be a promising supplement for treatment of obesity and/or insulin resistance in older patients.

Mutation screening and assessment of the effect of genetic variations on expression and RNA editing of serotonin receptor 2C in the human brain.

AIM: Serotonin receptor 2C (HTR2C) has been postulated as being involved in the etiology or pathophysiology of mental disorders such as bipolar disorder, major depression and schizophrenia. We previously revealed the altered mRNA expression and RNA editing of HTR2C in the postmortem brains of patients with mental disorders. Here we examined the relationship between genetic variations and expression level or RNA editing level of HTR2C in the human brain. METHODS: We performed mutation screening of the HTR2C gene by sequencing all exons, exon-intron boundaries, and promoter region in the same cohort used for expression and RNA editing studies (n = 58). Using the detected genetic variations, we examined the relationship between genetic variations and expression or RNA editing level. RESULTS AND CONCLUSION: We did not find novel mutations or single nucleotide polymorphisms that were specific to patients. Genotype and haplotype-based analyses revealed that genetic variations of HTR2C did not account for observed altered expression or RNA editing level of HTR2C in the brain.

Hazard assessment of methylmercury toxicity to neuronal induction in embryogenesis using human embryonic stem cells.

Pluripotent human embryonic stem cell (hESC) lines can to some extent mimic in vitro the development of the embryo, providing the scientific rationale for the use of these cells to establish tests for toxicity to embryogenesis. Such humanised in vitro tests have potential to improve human hazard prediction by avoiding interspecies differences. We explored the potential of a hESC-based assay for detection of toxicity to neuronal induction in embryonic development. Neuronal precursor differentiation was performed according to a previous publication, while we established a new protocol for maturation of the precursors into neuron-like cells. Appearance of neuronal derivatives was demonstrated by real-time PCR, showing up-regulation of several neuronal marker genes, and immunohistochemistry, demonstrating the appearance of neurofilament medium polypeptide, beta-tubulin III and microtubule-associated protein 2 positive cells. In order to assess whether the hESC model could detect chemically induced developmental toxicity, we exposed the differentiating cells to methylmercury (MeHg) causing structural developmental abnormalities in the brain. Two separate exposure intervals were used to determine the effects of MeHg on neuronal precursor formation and their further maturation, respectively. The formation of precursors was sensitive to MeHg in non-cytotoxic concentrations, as the expression of several neuronal mRNA markers changed. In contrast, non-cytotoxic MeHg concentrations did not effect the mRNA marker expression in matured cells, indicating that neuronal precursor formation is more sensitive to MeHg than later stages of neuronal differentiation. Overall, our experiments demonstrate that the hESC assay can provide alerts for the adverse effects of MeHg on neuronal induction.

Tail suspension increases energy expenditure independently of the melanocortin system in mice.

Space travelers experience anorexia and body weight loss in a microgravity environment, and microgravity-like situations cause changes in hypothalamic activity. Hypothalamic melanocortins play a critical role in the regulation of metabolism. Therefore, we hypothesized that microgravity affects metabolism through alterations in specific hypothalamic signaling pathways, including melanocortin signaling. To address this hypothesis, the microgravity-like situation was produced by an antiorthostatic tail suspension in wild-type and agouti mice, and the effect of tail suspension on energy expenditure and hypothalamic gene expression was examined. Energy expenditure was measured using indirect calorimetry before and during the tail suspension protocol. Hypothalamic tissues were collected for gene expression analysis at the end of the 3 h tail suspension period. Tail suspension significantly increased oxygen consumption, carbon dioxide production, and heat production in wild-type mice. Tail suspension-induced increases in energy expenditure were not attenuated in agouti mice. Although tail suspension did not alter hypothalamic proopiomelanocortin (POMC) and agouti-related protein (AGRP) mRNA levels, it significantly increased hypothalamic interleukin 6 (Il-6) mRNA levels. These data are consistent with the hypothesis that microgravity increases energy expenditure and suggest that these effects are mediated through hypothalamic signaling pathways that are independent of melanocortins, but possibly used by Il-6.

Gene expression profiling and differentiation assessment in primary human hepatocyte cultures, established hepatoma cell lines, and human liver tissues.

Frequently, primary hepatocytes are used as an in vitro model for the liver in vivo. However, the culture conditions reported vary considerably, with associated variability in performance. In this study, we characterized the differentiation character of primary human hepatocytes cultured using a highly defined, serum-free two-dimensional sandwich system, one that configures hepatocytes with collagen I as the substratum together with a dilute extracellular matrix (Matrigeltrade mark) overlay combined with a defined serum-free medium containing nanomolar levels of dexamethasone. Gap junctional communication, indicated by immunochemical detection of connexin 32 protein, was markedly enhanced in hepatocytes cultured in the Matrigel sandwich configuration. Whole genome expression profiling enabled direct comparison of liver tissues to hepatocytes and to the hepatoma-derived cell lines, HepG2 and Huh7. PANTHER database analyses were used to identify biological processes that were comparatively over-represented among probe sets expressed in the in vitro systems. The robustness of the primary hepatocyte cultures was reflected by the extent of unchanged expression character when compared directly to liver, with more than 77% of the probe sets unchanged in each of the over-represented categories, representing such genes as C/EBPalpha, HNF4alpha, CYP2D6, and ABCB1. In contrast, HepG2 and Huh7 cells were unchanged from the liver tissues for fewer than 48% and 55% of these probe sets, respectively. Further, hierarchical clustering of the hepatocytes, but not the cell lines, shifted from donor-specific to treatment-specific when the probe sets were filtered to focus on phenobarbital-inducible genes, indicative of the highly differentiated nature of the hepatocytes when cultured in a highly defined two-dimensional sandwich system.

Assessment of the U937 cell line for the detection of contact allergens.

The human myeloid cell line U937 was evaluated as an in vitro test system to identify contact sensitizers in order to develop alternatives to animal tests for the cosmetic industry. Specific culture conditions (i.e., presence of interleukin-4, IL-4) were applied to obtain a dendritic cell-like phenotype. In the described test protocol, these cells were exposed to test chemicals and then analyzed by flow cytometry for CD86 expression and by quantitative real-time reverse transcriptase-polymerase chain reaction for IL-1beta and IL-8 gene expressions. Eight sensitizers, three non-sensitizers and five oxidative hair dye precursors were examined after 24-, 48- and 72-h exposure times. Test item-specific modulations of the chosen activation markers (CD86, IL-1beta and IL-8) suggest that this U937 activation test could discriminate test items classified as contact sensitizers or non-sensitizers in the local lymph node assay in mice (LLNA). More specifically, a test item can be considered as a potential sensitizer when it significantly induced the upregulation of the expression of at least two markers. Using this approach, we could correctly evaluate the dendritic cell (DC) activation potential for 15 out of 16 tested chemicals. We conclude that the U937 activation test may represent an useful tool in a future in vitro test battery for predicting sensitizing properties of chemicals.

Effluent impact assessment using microarray-based analysis in common carp: a systems toxicology approach.

Effluents are a main source of direct and continuous input of pollutants to the aquatic environment, and can cause ecotoxicological effects at different levels of biological organization. Since gene expression responses represent the primary interaction site between environmental contaminants and biota, they provide essential clues to understand how chemical exposure can affect organismal health. The aim of the present study was to investigate the applicability of a microarray approach for unraveling modes of action of whole effluent toxicity and impact assessment. A chronic toxicity test with common carp (Cyprinus carpio) was conducted where fish were exposed to a control and 100% effluent for 21 days under flow-through conditions. Microarray analysis revealed that effluent treatment mainly affected molecular pathways associated with the energy balance of the fish, including changes in carbohydrate and lipid metabolism, as well as digestive enzyme activity. These gene expression responses were in clear agreement with, and provided additional mechanistic information on various cellular and higher level effects observed for the same effluent. Our results demonstrate the benefit of toxicogenomic tools in a "systems toxicology" approach, involving the integration of adverse effects of chemicals and stressors across multiple levels of biological complexity.

Assessment of the effects of chemicals on the expression of ten steroidogenic genes in the H295R cell line using real-time PCR.

The potential for a variety of environmental contaminants to disturb endocrine function in wildlife and humans has been of recent concern. While much effort is being focused on the assessment of effects mediated through steroid hormone receptor-based mechanisms, there are potentially several other mechanisms that could lead to endocrine disruption. Recent studies have demonstrated that a variety of xenobiotics can alter the gene expression or activity of enzymes involved in steroidogenesis. By altering the production or catalytic activity of steroidogenic or steroid-catabolizing enzymes, these chemicals have the potential to alter the steroid balance in organisms. To assess the potential of chemicals to alter steroidogenesis, an assay system was developed using a human adrenocortical carcinoma cell line, the H295R cell line, which retains the ability to synthesize most of the important steroidogenic enzymes. Methods were developed, optimized, and validated to measure the expression of 10 genes involved in steroidogenesis by the use of real-time quantitative reverse transcriptase PCR. The effects of several model chemicals known to alter steroid metabolism, both inducers and inhibitors, were assessed. Similar expression patterns were observed for chemicals acting through common mechanisms of action. Time-course studies demonstrated distinct time-dependent expression profiles for chemicals able to modulate steroid metabolism. The assay, which allows simultaneous analysis of the expression of numerous steroidogenic enzymes, would be useful as a sensitive and integrative screen for the many effects of chemicals on steroidogenesis.

Response of human cord blood cells to styrene exposure: evaluation of its effects on apoptosis and gene expression by genomic technology.

Styrene is one of the most important monomers produced worldwide, and it finds major use in the production of polystyrene, acrylonitrile-butadiene-styrene resins and unsaturated polystyrene resins. Epidemiological studies on styrene showed that the malignancies observed most frequently in humans after exposure are related to the lymphatic and haemopoietic system. IARC classified styrene a possible carcinogenic to humans (Group 2B). In this study, we evaluated the effect of styrene on gene expression profiles of human cord blood cells, as well as its activity on the apoptosis and bcl-2 related protein expression. Data demonstrated that, after 24 and 48 h of exposure, styrene (800 microM) induced an increase in the necrosis of mononuclear cord blood cells, whereas it did not cause any increase in the apoptotic process. Western blot analysis revealed a modified expression of Bax, BCl-2, c-Jun, c-Fos and Raf-1 proteins in the human cord blood cells after direct exposure to styrene, whereas p53 expression did not change. Furthermore, Macroarray analysis showed that styrene changed cord blood gene expression, inducing up-regulation of monocyte chemotactic protein 1 (MCP-1), and down-regulation of CC chemokine receptor type 1 (CCR-1) and SLP-76 tyrosine-phosphoprotein.

Increased efficacy of immersion vaccination in fish with hyperosmotic pretreatment.

Immersion vaccination is common practice in aquaculture, because of its convenience for mass vaccination with sufficient protection. However, the mechanisms of antigen uptake and presentation, resulting in a protective immune response and the role of the innate immune system therein are largely unknown. The impact of immersion vaccination on fish physiology and on the ensuing innate and specific immune response was characterized with fluorescently labeled particulate and soluble model antigens. Vaccination of common carp by direct immersion (DI) or hyperosmotic immersion (HI; direct immersion, preceded by a brief immersion in a hypertonic solution) greatly enhanced the uptake of soluble, but not particulate antigen through temporary disruption of the integrity of the epithelia of gills and skin. Damage induced is mild and does not impose additional stress over the handling associated with immersion vaccination. Especially HI briefly but strongly activates the innate immune system. We conclude that HI more effectively increased the uptake of vaccine and enhanced the efficacy by which vaccine components are processed and presented by the innate immune system, dually enhancing the mucosal immune response. Understanding the mechanisms involved in uptake and processing of vaccine in the early phase of the immune response will greatly benefit the design of immersion vaccination.

High macromolecular synthesis with low metabolic cost in Antarctic sea urchin embryos.

Assessing the energy costs of development in extreme environments is important for understanding how organisms can exist at the margins of the biosphere. Macromolecular turnover rates of RNA and protein were measured at -1.5 degrees C during early development of an Antarctic sea urchin. Contrary to expectations of low synthesis with low metabolism at low temperatures, protein and RNA synthesis rates exhibited temperature compensation and were equivalent to rates in temperate sea urchin embryos. High protein metabolism with a low metabolic rate is energetically possible in this Antarctic sea urchin because the energy cost of protein turnover, 0.45 joules per milligram of protein, is 1/25th the values reported for other animals.