Genome Sequence of Pseudomonas putida S12, a Potential Platform Strain for Industrial Production of Valuable Chemicals

Pseudomonas putida strain S12, a well-studied solvent-tolerant bacterium, is considered a platform strain for the production of many chemicals. Here, we present a 6.28-Mb assembly of its genome sequence. We have annotated 32 coding sequences (CDSs) encoding efflux systems of organic compounds and 195 CDSs responsible for the metabolism of aromatic compounds.     

Relative Accuracy Evaluation

The quality of data plays an important role in business analysis and decision making, and data accuracy is an important aspect in data quality. Thus one necessary task for data quality management is to evaluate the accuracy of the data. And in order to solve the problem that the accuracy of the whole data set is low while a useful part may be high, it is also necessary to evaluate the accuracy of the query results, called relative accuracy. However, as far as we know, neither measure nor effective methods for the accuracy evaluation methods are proposed. Motivated by this, for relative accuracy evaluation, we propose a systematic method. We design a relative accuracy evaluation framework for relational databases based on a new metric to measure the accuracy using statistics. We apply the methods to evaluate the precision and recall of basic queries, which show the result''s relative accuracy. We also propose the method to handle data update and to improve accuracy evaluation using functional dependencies. Extensive experimental results show the effectiveness and efficiency of our proposed framework and algorithms.     

ATP Impedes the Inhibitory Effect of Hsp90 on Aβ40 Fibrillation

Heat shock protein 90 (Hsp90) is a molecular chaperone that assists protein folding in an Adenosine triphosphate (ATP)-dependent way. Hsp90 has been reported to interact with Alzheime?s disease associated amyloid-β (Aβ) peptides and to suppress toxic oligomer- and fibril formation. However, the mechanism remains largely unclear. Here we use a combination of atomic force microscopy (AFM) imaging, circular dichroism (CD) spectroscopy and biochemical analysis to quantify this interaction and put forward a microscopic picture including rate constants for the different transitions towards fibrillation. We show that Hsp90 binds to Aβ₄₀ monomers weakly but inhibits Aβ₄₀ from growing into fibrils at substoichiometric concentrations. ATP impedes this interaction, presumably by modulating Hsp90’s conformational dynamics and reducing its hydrophobic surface. Altogether, these results might indicate alternative ways to prevent Aβ₄₀ fibrillation by manipulating chaperones that are already abundant in the brain.     

Silencing long non-coding RNA DLX6-AS1 or restoring microRNA-193b-3p enhances thyroid carcinoma cell autophagy and apoptosis via depressing HOXA1

Long non-coding RNA DLX6 antisense RNA 1 (DLX6-AS1) lists a critical position in thyroid carcinoma (TC) development. However, the overall comprehension about DLX6-AS1, microRNA (miR)-193b-3p and homeobox A1 (HOXA1) in TC is not thoroughly enough. Concerning to this, this work is pivoted on DLX6-AS1/miR-193b-3p/HOXA1 axis in TC cell growth and autophagy. TC tissues and adjacent normal thyroid tissues were collected, in which expression of DLX6-AS1, miR-193b-3p and HOXA1 was tested, together with their interactions. TC cells were transfected with DLX6-AS1/miR-193b-3p-related oligonucleotides or plasmids to test cell growth and autophagy. Tumorigenesis in nude mice was observed. DLX6-AS1 and HOXA1 were up-regulated, and miR-193b-3p was down-regulated in TC. Depleted DLX6-AS1 or restored miR-193b-3p disturbed cell growth and promoted autophagy. DLX6-AS1 targeted miR-193b-3p and positively regulated HOXA1. miR-193b-3p inhibition mitigated the impaired tumorigenesis induced by down-regulated DLX6-AS1. Tumorigenesis in nude mice was consistent with that in cells. It is clear that DLX6-AS1 depletion hinders TC cell growth and promotes autophagy via up-regulating miR-193b-3p and down-regulating HOXA1.     

The evaluation of the oxidative stress parameters in patients with primary angle-closure glaucoma

Objective

To clarify the presence of oxidative stress in patients with primary angle-closure glaucoma (PACG) and to investigate the relationship between oxidative stress and PACG.

Methods

Fifty patients with primary angle-closure glaucoma and fifty healthy controls of matched age and gender were included in the study prospectively. Serum samples were obtained to detect the oxidation degradation products malondialdehyde (MDA), conjugated diene (CD), 4-hydroxynonenal (4-HNE), advanced oxidation protein products (AOPP), protein carbonyl (PC), ischemia-modified albumin (IMA) and 8-hydroxydeoxyguanosin (8-OHdG).

Results

The concentration of MDA and CD in PACG patients was significantly higher than those of the control subjects (P<0.05, P<0.01). The serum 4-HNE concentrations were increased in PACG patients, but the differences with those of the healthy controls were not statistically significant. Compared to normal subjects, there was significant higher in serum AOPP and PC in PACG patients (P<0.01). PACG patients had higher levels of 8-OHdG in serum with respect to the comparative group of normal subjects (P<0.01). When plasma IMA levels in the PACG group were compared with those in the control group, significant increases in IMA were observed in the former (P<0.05).

Conclusions

Our study demonstrated that IMA is a new biomarker available for assessing oxidative stress in PCAG. Oxidative stress is an important risk factor in the development of primary angle-closure glaucoma. Increased levels of oxidative stress products may be associated with primary angle-closure glaucoma.     

Tamoxifen inhibits migration of estrogen receptor‐negative hepatocellular carcinoma cells by blocking the swelling‐activated chloride current

Tamoxifen is a triphenylethylene non‐steroidal antiestrogen anticancer agent. It also shows inhibitory effects on metastasis of estrogen receptor (EsR)‐independent tumors, but the underlying mechanism is unclear. It was demonstrated in this study that, in EsR‐negative and highly metastatic human hepatocellular carcinoma MHCC97H cells, tamoxifen‐inhibited cell migration, volume‐activated Cl^? currents (I_Cl,vol) and regulatory volume decrease (RVD) in a concentration‐dependent manner with a similar IC₅₀. Analysis of the relationships between migration, I_Cl,vol and RVD showed that cell migration was positively correlated with I_Cl,vol and RVD. Knockdown of the expression of ClC‐3 Cl^? channel proteins by ClC‐3 shRNA or siRNA inhibited I_Cl,vol, and cell migration, and these inhibitory effects could not be increased further by addition of tamoxifen in the medium. The results suggest that knockdown of ClC‐3 expression may deplete the effects of tamoxifen; tamoxifen may inhibit cell migration by modulating I_Cl,vol and cell volume. Moreover, tamoxifen decreased the activity of protein kinase C (PKC) and the effects were reversed by the PKC activator PMA. Activation of PKC by PMA could competitively downregulate the inhibitory effects of tamoxifen on I_Cl,vol. PMA promoted cell migration, and knockdown of ClC‐3 expression by ClC‐3 siRNA abolished the PMA effect on cell migration. The results suggest that tamoxifen may inhibit I_Cl,vol by suppressing PKC activation; I_Cl,vol may be an EsR‐independent target for tamoxifen in the anti‐metastatic action on cancers, especially on EsR‐negative cancers. The finding may have an implication in the clinical use of tamoxifen in the treatments of both EsR‐positive and EsR‐negative cancers. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.