Multiple ancient horizontal gene transfers and duplications in lepidopteran species

Eukaryotic horizontal gene transfer (HGT) events are increasingly being discovered yet few reports have summarized multiple occurrences in a wide range of species. We systematically investigated HGT events in the order Lepidoptera by employing a series of filters. Bombyx mori, Danaus plexippus and Heliconius melpomene had 13, 12 and 12 HGTs, respectively, from bacteria and fungi. These HGTs contributed a total of 64 predicted genes: 22 to B. mori, 22 to D. plexippus and 20 to H. melpomene. Several new genes were generated by post-transfer duplications. Post-transfer duplication of a suite of functional HGTs has rarely been reported in higher organisms. The distributional patterns of paralogues for certain genes differed in the three species, indicating potential independent duplication or loss events. All of these HGTs had homologues expressed in some other lepidopterans, indicating ancient transfer events. Most HGTs were involved in the metabolism of sugar and amino acids. These HGTs appeared to have experienced amelioration, purifying selection and accelerated evolution to adapt to the background genome of the recipient. The discovery of ancient, massive HGTs and duplications in lepidopterans and their adaptive evolution provides further insights into the evolutionary significance of the events from donors to multicellular host recipients.

The PP2A-Aβ gene is regulated by multiple transcriptional factors including Ets-1, SP1/SP3, and RXRα/β

Protein phosphatase-2A (PP-2A) is a major serine/threonine phosphatase abundantly expressed in eukaryotes. PP-2A is a heterotrimer that contains a 65 kD scaffold A subunit, a 36 kD catalytic C subunit, and a regulatory B subunit of variable isoforms ranging from 54-130 kDs. The scaffold subunits, PP2A-Aα/β, act as platforms for both the C and B subunits to bind, and thus are key structural components for PP-2A activity. Mutations in both genes encoding PP2A-Aα and PP2A-Aβ lead to carcinogenesis and likely other human diseases. Our previous work showed that the gene coding for PP2A-Aα is positively regulated by multiple transcription factors including Ets-1, CREB, and AP-2α but negatively regulated by SP-1/SP-3. In the present study, we have functionally dissected the promoter of the mouse PP2A-Aβ gene. Our results demonstrate that three major cis-elements, including the binding sites for Ets-1, SP1/SP3, and RXRα/β, are present in the proximal promoter of the mouse PP2A-Aβ gene. Gel mobility shifting assays reveal that Ets-1, SP1/SP3, and RXRα/β all bind to PP2A-Aβ gene promoter. In vitro mutagenesis and reporter gene activity assays demonstrate that while Ets-1 displays negative regulation, SP1/SP3 and RXRα/β positively regulate the promoter of the PP2A-Aβ gene. Co-expression of the cDNAs encoding Ets-1, SP1/SP3, or RXRα/β and the luciferase reporter gene driven by PP2A-Aβ promoter further confirm their control over the PP2A-Aβ promoter. Finally, ChIP assays demonstrate that Ets-1, SP1/SP3, and RXRα/β can all bind to the PP2A-Aβ gene promoter. Together, our results reveal that multiple transcription factors regulate the PP2A-Aβ gene. Moreover, our results provide important information explaining why PP2A-Aα and PP2A-Aβ display distinct expression levels.

Measurement of Z boson production in Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV with the ATLAS detector

The ATLAS experiment has observed 1995 Z boson candidates in data corresponding to 0.15  nb(-1) of integrated luminosity obtained in the 2011 LHC Pb+Pb run at sqrt[s(NN)]=2.76  TeV. The Z bosons are reconstructed via dielectron and dimuon decay channels, with a background contamination of less than 3%. Results from the two channels are consistent and are combined. Within the statistical and systematic uncertainties, the per-event Z boson yield is proportional to the number of binary collisions estimated by the Glauber model. The elliptic anisotropy of the azimuthal distribution of the Z boson with respect to the event plane is found to be consistent with zero.

Charge separation relative to the reaction plane in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

Measurements of charge-dependent azimuthal correlations with the ALICE detector at the LHC are reported for Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV. Two- and three-particle charge-dependent azimuthal correlations in the pseudorapidity range |η| < 0.8 are presented as a function of the collision centrality, particle separation in pseudorapidity, and transverse momentum. A clear signal compatible with a charge-dependent separation relative to the reaction plane is observed, which shows little or no collision energy dependence when compared to measurements at RHIC energies. This provides a new insight for understanding the nature of the charge-dependent azimuthal correlations observed at RHIC and LHC energies.

Search for dark matter candidates and large extra dimensions in events with a photon and missing transverse momentum in pp collision data at sqrt[s]=7 TeV with the ATLAS detector

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV are reported. Data collected by the ATLAS experiment at the LHC corresponding to an integrated luminosity of 4.6 fb(-1) are used. Good agreement is observed between the data and the standard model predictions. The results are translated into exclusion limits on models with large extra spatial dimensions and on pair production of weakly interacting dark matter candidates.

BOLDMirror: a global mirror system of DNA barcode data

DNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well-organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open-sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding.

A simple QSPR model for the prediction of the adsorbability of organic compounds onto activated carbon cloth

A quantitative structure-property relationship (QSPR) model was proposed between the molecular descriptors representing the molecular structure and the Freundlich adsorbability parameter (K) for a set of 55 organic compounds onto activated carbon cloth. The best linear model was composed of three descriptors, which were selected by stepwise multiple linear regression (MLR) analysis. The statistical parameters provided by the linear model were r² = 0.7744, r²(adj) = 0.7551, s = 0.169 for the training set; and r² = 0.6725, r²(adj) = 0.6316, s = 0.196 for the external test set, respectively. The stability and predictive power of the proposed model were further verified using Y-randomization tests, five-fold cross-validation and leave-many-out cross-validation. The model may give some insight into the main structural features that affect the adsorption of the investigated compounds onto activated carbon cloth.

Protective effect of the nitric oxide pathway in L-citrulline renal ischaemia-reperfusion injury in rats

To observe the protective effects of L-citrulline on the renal I/R injury and elucidate the mechanisms involved, 48 rats were randomized into eight groups: Group 1: sham operated; Group 2: I/R (45 min renal ischaemia and 24 h reperfusion); Group 3: I/R + L-citrulline (300 mg/kg, i.g.); Group 4: I/R + L-citrulline (600 mg/kg, i.g.); Group 5: I/R + L-citrulline (900 mg/kg, i.g.); Group 6: I/R + normal saline (NS, i.g.); Group 7: I/R + N sup ω nitro-L-arginine ester (L-NAME, 20 mg/kg, i.p.); Group 8: I/R + L-citrulline (900 mg/kg, i.g.) + L-NAME (20 mg/ kg, i.p.). At the end of the reperfusion period, serum was collected and the kidneys underwent histological and biochemical examinations. Our results showed that pre-treatment with L-citrulline (300, 600, and 900 mg/kg) significantly ameliorated the renal injury caused by I/R. Moreover, L-citrulline prevented induction of lipid peroxidation and increased the activity of superoxide dismutase and the levels of glutathione and nitric oxide. The I/R-induced decreases in total nitric oxide synthase activity, inducible nitric oxide activity, constitutive nitric oxide activity and endothelial nitric oxide protein expression in the renal cortex were significantly prevented. However, the L-citrulline-mediated protection was significantly antagonized by co-administration of L-NAME. These results suggested that L-citrulline administration exhibited significant protection against renal I/R injury. This protective effect, at least in part, via up-regulation of the endothelial nitric oxide protein expression and constitutive nitric oxide synthase activity, maintained production of nitric oxide at the basal level.

ABCB1/MDR1 gene polymorphism and colorectal cancer risk: a meta-analysis of case-control studies

AIM

ABCB1/MDR1 protein is found in high concentrations on the apical surfaces of colonic epithelial cells. It acts as an efflux pump by transporting toxic endogenous substances, drugs and xenobiotics out of cells. Polymorphisms in the ABCB1/MDR1 gene may either change expression of the ABCB1/MDR1 protein or alter its function, suggesting its possible association with colorectal cancer. Several studies have reported a relationship between ABCB1 gene polymorphisms and colorectal cancer risk, but no consistent conclusion has been reached. We therefore conducted a meta-analysis to identify any association between the ABCB1 gene and CRC risk.

METHOD

PubMed, Embase, Google Scholar, Cbmdisc and CNKI were searched for studies on the relationship of ABCB1/MDR1 gene SNPs and the incidence of colorectal cancer. Eligible articles were included for data extraction. The main outcome was the frequency of ABCB1/MDR1 gene SNPs among cases and controls. Comparison of the distribution of SNPs was performed mainly using Review Manager 5.0.

RESULTS

Ten, four and two trials were identified that focussed on the ABCB1 gene SNPs rs1045642, rs2032582 and rs3789243, respectively. A total of 3175 cases and 3715 controls were included. The meta-analysis, stratified by ethnicity or population source, indicated no association between the ABCB1 gene rs1045642 polymorphism and colorectal cancer risk. However, when the study by Bae et al. was removed from the analysis, there was some evidence to indicate a higher T-allele frequency in Asian colorectal cancer patients (OR = 1.30, 95% CI: 1.02-1.67, P = 0.03). Neither ABCB1 rs2032582 nor ABCB1 rs3789243 indicated an association with colorectal cancer risk. An increased frequency only of the wild-type combined allele (rs2032582G/rs1045642C) was found in Caucasian patients (OR = 1.22, 95% CI: 1.03-1.44, P = 0.02).

CONCLUSION

There is some evidence to indicate an association between ABCB1 rs1045642T and colorectal cancer risk in Asians. Compared with the ABCB1 gene SNPs rs1045642, rs2032582 or rs3789243 alone, combined haplotypes of several SNPs might be a better marker to determine the genetic influence on the susceptibility to colorectal cancer among Caucasians.

ABCB1/MDR1 gene polymorphism and colorectal cancer risk: a meta-analysis of case-control studies

AIM

ABCB1/MDR1 protein is found in high concentrations on the apical surfaces of colonic epithelial cells. It acts as an efflux pump by transporting toxic endogenous substances, drugs and xenobiotics out of cells. Polymorphisms in the ABCB1/MDR1 gene may either change expression of the ABCB1/MDR1 protein or alter its function, suggesting its possible association with colorectal cancer. Several studies have reported a relationship between ABCB1 gene polymorphisms and colorectal cancer risk, but no consistent conclusion has been reached. We therefore conducted a meta-analysis to identify any association between the ABCB1 gene and CRC risk.

METHOD

PubMed, Embase, Google Scholar, Cbmdisc and CNKI were searched for studies on the relationship of ABCB1/MDR1 gene SNPs and the incidence of colorectal cancer. Eligible articles were included for data extraction. The main outcome was the frequency of ABCB1/MDR1 gene SNPs among cases and controls. Comparison of the distribution of SNPs was performed mainly using Review Manager 5.0.

RESULTS

Ten, four and two trials were identified that focussed on the ABCB1 gene SNPs rs1045642, rs2032582 and rs3789243, respectively. A total of 3175 cases and 3715 controls were included. The meta-analysis, stratified by ethnicity or population source, indicated no association between the ABCB1 gene rs1045642 polymorphism and colorectal cancer risk. However, when the study by Bae et al. was removed from the analysis, there was some evidence to indicate a higher T-allele frequency in Asian colorectal cancer patients (OR = 1.30, 95% CI: 1.02-1.67, P = 0.03). Neither ABCB1 rs2032582 nor ABCB1 rs3789243 indicated an association with colorectal cancer risk. An increased frequency only of the wild-type combined allele (rs2032582G/rs1045642C) was found in Caucasian patients (OR = 1.22, 95% CI: 1.03-1.44, P = 0.02).

CONCLUSION

There is some evidence to indicate an association between ABCB1 rs1045642T and colorectal cancer risk in Asians. Compared with the ABCB1 gene SNPs rs1045642, rs2032582 or rs3789243 alone, combined haplotypes of several SNPs might be a better marker to determine the genetic influence on the susceptibility to colorectal cancer among Caucasians.

Low-Dose Azithromycin Attenuates OVA-Induced Airway Remodeling and Inflammation via Down-Regulating TGF-βl Expression in RAT

Asthma is characteristic with chronic airway inflammation and remodeling. Azithromycin (AZM), the 15-member macrolide, is known to present an anti-inflammatory effect and is increasingly being used in the treatment of chronic inflammatory pulmonary diseases. We hypothesize that low-dose azithromycin can inhibit allergen-induced airway remodeling except allergic airway inflammation in rat model. Male SD rats underwent intraperitoneal ovalbumin sensitization on days 1 and 6 followed by an intranasal challenge on day 7–13. On day 14, airway inflammation and remodeling were assessed by quantifying leukocytes in the airway, expression of multiple inflammatory mediators in BALF, histological examination in lung and TGF-β1 mRNA and protein levels by qRT-PCR, immunohistochemistry and Western blotting. Treatment with low-dose azithromycin at the dose of 25 mg/kg significantly reduced ovalbumin-dependent airway inflammation, including accumulation of neutrophils, lymphocytes and eosinophils, secretion of IL-2, IL-4, IL-13 and TNF-α. Moreover, airway remodeling was significantly abrogated by azithromycin in this model. The mucus cell hyperplasia, thickening of the peribronchial smooth muscle layer, secretion of ET-1, IL-2, IL-4, IL-13 and TNF-α, and increasing mRNA and protein expressions of TGF-β1 in lung tissue were all significantly decreased in azithromycin-treated rats. These findings demonstrate the protective effect of low-dose azithromycin on allergic airway remodeling in rat and suggest low-dose azithromycin may have beneficial effects in treating allergic airway inflammation.

C-Jun terminal kinases play an important role in regulating embryonic survival and eye development in vertebrates

The c-Jun N-terminal kinases (JNKs) constitute one of the three major types of mitogen-activated protein kinases. Previous studies showed that JNK mediates multiple signaling transduction pathways implicated in cell proliferation, differentiation, inflammation, stress response and apoptosis in mammals. In the present study, we use goldfish as a model system and demonstrate that JNK kinases are necessary to promote embryonic survival and regulate eye development in vertebrates. During goldfish development, JNK1 and JNK2 are expressed at every stage from cleavage to hatching larvae. JNK3 is turned on at the gastrulation stage and then expressed at similar level to that of JNK2. JNK1 activity remains slightly fluctuated during different developmental stages. Inhibition of JNK activity caused massive apoptosis of blastula cells and significant death of goldfish embryos, which are associated with altered expression of the anti-apoptotic regulator, Mcl-1 and the proapoptotic regulator, Bak. These results provide novel information regarding the mechanisms by which JNKs promote embryonic survival. In addition, the embryos that survived inhibition of JNK activity displayed severe phenotype in the eye with clear microphthalmia and lens coloboma. To confirm that the observed phenotype is derived from JNK activity deficiency, we expressed JNK dominant negative mutant (DNM-JNK) in goldfish. Expression of DNM-JNK also caused similar phenotypes with altered expression of pax-6, Sox-2 and β-crystallin. Together, our results demonstrate that JNKs play important roles in promoting survival of vertebrate embryos and regulating development of vertebrate eye.

Resveratrol attenuates hydrogen peroxide-induced apoptosis in human umbilical vein endothelial cells

BACKGROUND AND OBJECTIVES

  Vascular endothelium injury caused by reactive oxygen species (ROS) plays an initial role in the pathogenesis of atherosclerosis. Resveratrol, a natural polyphenolic compound, is well known to possess a variety of cardioprotective activities. In this study we first investigated the effects of resveratrol against apoptosis of human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2) in vitro and the possible mechanisms.

MATERIALS AND METHODS

HUVECs were pre-incubated with resveratrol (0.5-10 microM) for 120 min, and then challenged with 100 microM H2O2 for 30 min. The cell viability was evaluated by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide (MTT) assay. The superoxide dismutase (SOD) activities and the reduced glutathione (GSH) contents were measured spectrophotometrically by using commercially available kits. The apoptosis of HUVECs was detected by Hoechst 33258 and Annexin-V/PI staining by flow cytometry staining using Fluorescence microscope. We also measured the mitochondrial membrane potential with the fluorescent probe JC-1 through Fluorescence microscope.

RESULTS

The study showed that incubation with resveratrol caused significant increase of the viability of HUVECs and the SOD activities and GSH contents, and decrease of cell apoptosis induced by H2O2, which was accompanied with the restoration of the mitochondrial membrane potential.

CONCLUSIONS

Our data suggested that resveratrol protected HUVECs against apoptosis induced by H2O2 through enhancing the antioxidant defenses, and inhibiting the degression of the mitochondrial membrane potential.  

Design and assessment of urban drainage and water reuse systems for the reconstruction of formerly industrial areas: a case in Beijing

The Shougang Group is an industrial steel enterprise occupying 800 ha in Beijing that will cease production by 2010. The area will be converted to a new financial and commercial zone. The rebuilding of the water infrastructure in this area should address water shortages in Beijing and retain the industrial landmark of a large cooling water tank. A design framework and an assessment system with 11 indicators were developed for this purpose. Four reconstruction schemes are presented here. Scheme 1 is a traditional system that completely depends on outside the municipal facility. Schemes 2, 3, and 4 are systems to separately discharge greywater and blackwater. Scheme 4 uses a vacuum system that allows the reclamation of nutrients. Schemes 2 and 4 use wetland-treated greywater to fill the water tank. Scheme 3 reuses greywater for toilets after on-site treatment. Scheme 2 is recommended due to its lower cost, greater environmental benefit, moderate resource reclamation, and higher technical feasibility.

Inter-layer traffic engineering with hierarchical-PCE in MPLS-TP over wavelength switched optical networks

We present the implementation and validation of an Inter-layer Traffic Engineering (TE) architecture based on a hierarchical path computation element (PCE), where the parent PCE is notified of established optical layer Label Switched Paths that induce packet traffic engineering (TE) links, thus not requiring full topology visibility. We summarize the architecture, the control plane extensions and its experimental evaluation in a control plane testbed.

Search for magnetic monopoles in sqrt[s]=7 TeV pp collisions with the ATLAS detector

This Letter presents a search for magnetic monopoles with the ATLAS detector at the CERN Large Hadron Collider using an integrated luminosity of 2.0  fb(-1) of pp collisions recorded at a center-of-mass energy of sqrt[s]=7  TeV. No event is found in the signal region, leading to an upper limit on the production cross section at 95% confidence level of 1.6/ϵ  fb for Dirac magnetic monopoles with the minimum unit magnetic charge and with mass between 200 GeV and 1500 GeV, where ϵ is the monopole reconstruction efficiency. The efficiency ϵ is high and uniform in the fiducial region given by pseudorapidity |η|<1.37 and transverse kinetic energy 600-700<E(kin)sinθ<1400  GeV. The minimum value of 700 GeV is for monopoles of mass 200 GeV, whereas the minimum value of 600 GeV is applicable for higher mass monopoles. Therefore, the upper limit on the production cross section at 95% confidence level is 2 fb in this fiducial region. Assuming the kinematic distributions from Drell-Yan pair production of spin-1/2 Dirac magnetic monopoles, the efficiency is in the range 1%-10%, leading to an upper limit on the cross section at 95% confidence level that varies from 145 fb to 16 fb for monopoles with mass between 200 GeV and 1200 GeV. This limit is weaker than the fiducial limit because most of these monopoles lie outside the fiducial region.