Transcriptional Regulation of Cannabinoid Receptor-1 Expression in the Liver by Retinoic Acid Acting via Retinoic Acid Receptor-γ

Alcoholism can result in fatty liver that can progress to steatohepatitis, cirrhosis, and liver cancer. Mice fed alcohol develop fatty liver through endocannabinoid activation of hepatic CB₁ cannabinoid receptors (CB₁R), which increases lipogenesis and decreases fatty acid oxidation. Chronic alcohol feeding also up-regulates CB₁R in hepatocytes in vivo, which could be replicated in vitro by co-culturing control hepatocytes with hepatic stellate cells (HSC) isolated from ethanol-fed mice, implicating HSC-derived mediator(s) in the regulation of hepatic CB₁R (Jeong, W. I., Osei-Hyiaman, D., Park, O., Liu, J., Bátkai, S., Mukhopadhyay, P., Horiguchi, N., Harvey-White, J., Marsicano, G., Lutz, B., Gao, B., and Kunos, G. (2008) Cell Metab. 7, 227–235). HSC being a rich source of retinoic acid (RA), we tested whether RA and its receptors may regulate CB₁R expression in cultured mouse hepatocytes. Incubation of hepatocytes with RA or RA receptor (RAR) agonists increased CB₁R mRNA and protein, the most efficacious being the RARγ agonist CD437 and the pan-RAR agonist TTNPB. The endocannabinoid 2-arachidonoylglycerol (2-AG) also increased hepatic CB₁R expression, which was mediated indirectly via RA, because it was absent in hepatocytes from mice lacking retinaldehyde dehydrogenase 1, the enzyme catalyzing the generation of RA from retinaldehyde. The binding of RARγ to the CB₁R gene 5′ upstream domain in hepatocytes treated with RAR agonists or 2-AG was confirmed by chromatin immunoprecipitation and electrophoretic mobility shift and antibody supershift assays. Finally, TTNPB-induced CB₁R expression was attenuated by small interfering RNA knockdown of RARγ in hepatocytes. We conclude that RARγ regulates CB₁R expression and is thus involved in the control of hepatic fat metabolism by endocannabinoids.     

A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants：Case Analyses of Arabidopsis and Oryza

To systematically estimate the gene duplication events In closely related species, we have to use comparative genomlc approaches, either through genomlc sequence comparison or comparative genomlc hybridization （CGH）. Given the scarcity of complete genomlc sequences of plant species, in the present study we adopted an array based CGH to Investigate gene duplications In the genus Arabldopsls. Fragment genomlc DNA from four species, namely Arabidopsls thallana, A. lyrata subsp, lyrata, A. lyrata subsp, petraea, and A. halleri, was hybridized to Affymetrlx （Santa Clara, CA, USA） tiling arrays that are designed from the genomlc sequences of A. thallana. Pairwlse comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were Identified. Among them, the majority （69 of 94） were A. thallana lineage specific. This result indicates that the array based CGH approach may be used to Identify candidates of duplication In other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. satlva and A. thallana and found a strikingly higher number of chimera retroposed genes In rice. The higher rate of gene duplication through retroposltlon and other mechanisms may Indicate that the grass species Is able to adapt to more diverse environments.     

What Are the Health Benefits of Active Travel? A Systematic Review of Trials and Cohort Studies

Background

Increasing active travel (primarily walking and cycling) has been widely advocated for reducing obesity levels and achieving other population health benefits. However, the strength of evidence underpinning this strategy is unclear. This study aimed to assess the evidence that active travel has significant health benefits.

Methods

The study design was a systematic review of (i) non-randomised and randomised controlled trials, and (ii) prospective observational studies examining either (a) the effects of interventions to promote active travel or (b) the association between active travel and health outcomes. Reports of studies were identified by searching 11 electronic databases, websites, reference lists and papers identified by experts in the field. Prospective observational and intervention studies measuring any health outcome of active travel in the general population were included. Studies of patient groups were excluded.

Results

Twenty-four studies from 12 countries were included, of which six were studies conducted with children. Five studies evaluated active travel interventions. Nineteen were prospective cohort studies which did not evaluate the impact of a specific intervention. No studies were identified with obesity as an outcome in adults; one of five prospective cohort studies in children found an association between obesity and active travel. Small positive effects on other health outcomes were found in five intervention studies, but these were all at risk of selection bias. Modest benefits for other health outcomes were identified in five prospective studies. There is suggestive evidence that active travel may have a positive effect on diabetes prevention, which may be an important area for future research.

Conclusions

Active travel may have positive effects on health outcomes, but there is little robust evidence to date of the effectiveness of active transport interventions for reducing obesity. Future evaluations of such interventions should include an assessment of their impacts on obesity and other health outcomes.     

Are Reports of Psychological Stress Higher in Occupational Studies? A Systematic Review across Occupational and Population Based Studies

Objectives

The general health questionnaire (GHQ) is commonly used to assess symptoms of common mental disorder (CMD). Prevalence estimates for CMD caseness from UK population studies are thought to be in the range of 14–17%, and the UK occupational studies of which we are aware indicate a higher prevalence. This review will synthesise the existing research using the GHQ from both population and occupational studies and will compare the weighted prevalence estimates between them.

Methods

We conducted a systematic review and meta-analysis to examine the prevalence of CMD, as assessed by the GHQ, in all UK occupational and population studies conducted from 1990 onwards.

Results

The search revealed 65 occupational papers which met the search criteria and 15 relevant papers for UK population studies. The weighted prevalence estimate for CMD across all occupational studies which used the same version and cut-off for the GHQ was 29.6% (95% confidence intervals (CIs) 27.3–31.9%) and for comparable population studies was significantly lower at 19.1% (95% CIs 17.3–20.8%). This difference was reduced after restricting the studies by response rate and sampling method (23.9% (95% CIs 20.5%–27.4%) vs. 19.2% (95 CIs 17.1%–21.3%)).

Conclusions

Counter intuitively, the prevalence of CMD is higher in occupational studies, compared to population studies (which include individuals not in employment), although this difference narrowed after accounting for measures of study quality, including response rate and sampling method. This finding is inconsistent with the healthy worker effect, which would presume lower levels of psychological symptoms in individuals in employment. One explanation is that the GHQ is sensitive to contextual factors, and it seems possible that symptoms of CMD are over reported when participants know that they have been recruited to a study on the basis that they belong to a specific occupational group, as in nearly all “stress” surveys.     

Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data��A Model-Based Study

Many missing-value (MV) imputation methods have been developed for microarray data, but only a few studies have investigated the relationship between MV imputation and classification accuracy. Furthermore, these studies are problematic in fundamental steps such as MV generation and classifier error estimation. In this work, we carry out a model-based study that addresses some of the issues in previous studies. Six popular imputation algorithms, two feature selection methods, and three classification rules are considered. The results suggest that it is beneficial to apply MV imputation when the noise level is high, variance is small, or gene-cluster correlation is strong, under small to moderate MV rates. In these cases, if data quality metrics are available, then it may be helpful to consider the data point with poor quality as missing and apply one of the most robust imputation algorithms to estimate the true signal based on the available high-quality data points. However, at large MV rates, we conclude that imputation methods are not recommended. Regarding the MV rate, our results indicate the presence of a peaking phenomenon: performance of imputation methods actually improves initially as the MV rate increases, but after an optimum point, performance quickly deteriorates with increasing MV rates.     

Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies—A Validation Study

Background

Metastases in the bone marrow (BM) in form of disseminated tumor cells (DTCs) are frequent events at diagnosis and also at relapse in high-risk neuroblastoma patients. The frequently highly diluted occurrence of DTCs requires adequate enrichment strategies to enable their detailed characterization. However, to avoid methodical artifacts we tested whether pre-analytical processing steps—including transport duration, temperature and, importantly, tumor cell enrichment techniques—are confounding factors for gene expression analysis in DTCs.

Methods

LAN-1 neuroblastoma cells were spiked into tumor free BM and/or peripheral blood and: i) kept at room temperature or at 4°C for 24, 48 and 72 hours; ii) frozen down at -80°C and thawed; iii) enriched via magnetic beads. The effect on the gene expression signature of LAN-1 cells was analyzed by qPCR arrays and gene expression microarrays.

Results

Neither storage at –80°C in DMSO and subsequent thawing nor enrichment of spiked-in neuroblastoma cells changed the expression of the analyzed genes significantly. Whereas storage at 4°C altered the expression of analyzed genes (14.3%) only at the 72h-timepoint in comparison to the 0h-timepoint, storage at room temperature had a much more profound effect on gene expression by affecting 20% at 24h, 26% at 48h and 43% at 72h of the analyzed genes.

Conclusion

Using neuroblastoma as a model, we show that tumor cell enrichment by magnetic bead separation has virtually no effect on gene expression in DTCs. However, transport time and temperature can influence the expression profile remarkably. Thus, the expression profile of routinely collected BM samples can be analyzed without concern as long as the transport conditions are monitored.     

Potential Difference Across the Nuclear Membrane: A Regulator of Gene Expression?

We propose a model for eukaryotic gene regulaion in which a variable electric field at the nuclear periphery, caused by a potential difference across the inner nuclear membrane, controls macroraolecular interactions, including those between DNA and regulatory proteins. Evidence for the existence of a nuclear membrane potential and DNA contact with the nuclear periphery is presented. The suggestion is made that each cell type is characterized by a specific magnitude of nuclear membrane potential.     

Genome-Wide Identification and Expression Analysis of Heavy Metal Stress–Responsive Metallothionein Family Genes in Nicotiana tabacum

Plant Molecular Biology Reporter - Tobacco (Nicotiana tabacum L.) is the most important non-food cash crop worldwide and has recently been considered a Cd hyperaccumulator. Metallothionein, a...     

Are Noncoding Sequences of Rickettsia prowazekii Remnants of ``Neutralized' Genes?

It has been hypothesized that a large fraction of 24% noncoding DNA in R. prowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of noncoding DNA. However, a comparison with other genomes also having a low overall G+C content shows that this argument would also apply to other bacteria. To test this hypothesis, we study the coding potential in sets of genes, pseudogenes, and intergenic regions. We find that the correlation function and the χ²-measure are clearly indicative of the coding function of genes and pseudogenes. However, both coding potentials make almost no indication of a preexisting reading frame in the remaining 23% of noncoding DNA. We simulate the degradation of genes due to single-nucleotide substitutions and insertions/deletions and quantify the number of mutations required to remove indications of the reading frame. We discuss a reduced selection pressure as another possible origin of this comparatively large fraction of noncoding sequences. Received: 27 December 1999 / Accepted: 5 July 2000     

Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?

Lateral gene transfer (LGT) and gene rearrangement are essential for shaping bacterial genomes during evolution. Separate attention has been focused on understanding the process of lateral gene transfer and the process of gene translocation. However, little is known about how gene translocation affects laterally transferred genes. Here we have examined gene translocations and lateral gene transfers in closely related genome pairs. The results reveal that translocated genes undergo elevated rates of evolution and gene translocation tends to take place preferentially in recently acquired genes. Translocated genes have a high probability to be truncated, suggesting that translocation followed by truncation/deletion might play an important role in the fast turnover of laterally transferred genes. Furthermore, more recently acquired genes have a higher proportion of genes on the leading strand, suggesting a strong strand bias of lateral gene transfer.GENE insertions and deletions, together with gene translocations play important roles in bacterial genome evolution (Garcia-Vallvé et al. 2000; Ochman and Jones 2000; Tillier and Collins 2000a; Fraser-Liggett 2005). Gene insertions and deletions, as the essential driving forces in influencing gene content (Kunin and Ouzounis 2003), have received a great deal of attention. Various methods have been employed to study gene insertions and deletions previously; for instance, there are studies of population dynamics (Nielsen and Townsend 2004), such as a birth-and-death model of evolution (Berg and Kurland 2002; Novozhilov et al. 2005), phylogeny-dependent studies including parsimony methods (Daubin et al. 2003a,b; Mirkin et al. 2003; Hao and Golding 2004), and maximum-likelihood methods (Hao and Golding 2006b, 2008b). It has been shown that recently laterally transferred genes have high evolutionary rates and high rates of gene turnover (Daubin et al. 2003b; Hao and Golding 2004, 2006b).Gene rearrangement has also been commonly studied as another important driving force that shapes bacterial genomes (for a review, see Rocha 2004). Gene order changes in genomes are history dependent; for instance, fewer gene rearrangements are expected among more closely related species. Gene order within genomes has therefore been used to reconstruct phylogeny (Sankoff et al. 2000; Tamames 2001; Rogozin et al. 2004; Belda et al. 2005). Previous studies have focused mainly on lateral gene transfer (LGT) and gene rearrangement individually, but little is known about any association between laterally transferred genes and gene rearrangements. The study of gene order of laterally acquired genes might shed some light on the understanding of the LGT process.In this study, we have examined gene translocations and lateral gene transfers in closely related genome pairs. It is shown that the proportion of translocated genes among recently acquired genes is always high, while the proportion of translocated genes is always low in ancient genes, suggesting that gene translocation tends to take place in recently transferred genes. The results also reveal that translocated genes have elevated rates of evolution compared with positionally conserved genes and gene truncation is more prevalent in translocated genes. These findings suggest that gene translocation might accelerate the gene turnover of recently transferred genes and/or that genes likely to undergo translocation are those genes more likely to be laterally transferred and dispensable for the genome. Furthermore, the proportion of recently acquired genes is higher on the leading strand, suggesting that laterally transferred genes are biased toward being on the leading strand. After lateral transfer, some genes could be translocated to the lagging strand and some translocated genes are likely to be eliminated during evolution.