Horizontal gene transfer in herpesviruses identified by using support vector machine

Horizontal gene transfer (HGT) is the probable origin of new genes. Identification of HGT-introduced genes would be helpful to the understanding of the genome evolution and the function prediction of new genes. In this study, a method using support vector machine (SVM) was used to distinguish horizontally transferred genes and non-horizontally transferred genes of mammalian herpesviruses based on the atypical composition identification, with accuracy higher than 95% within a reasonable length of time by using just a common PC. This identified 302 putative horizontally transferred genes, 171 genes being identified for the first time. Although most putative transferred genes are of unknown function, many genes have been discovered or predicted to encode glycoproteins or membrane proteins.

Azilsartan treatment improves insulin sensitivity in obese spontaneously hypertensive Koletsky rats

AIM

Hypertension often coexists with insulin resistance. However, most metabolic effects of the antihypertensive agents have been investigated in nomotensive animals, in which different conclusions may arise. We investigated the metabolic effects of the new angiotensin II type 1 receptor blocker azilsartan using the obese Koletsky rats superimposed on the background of the spontaneously hypertensive rats.

METHODS

Male Koletsky rats were treated with azilsartan (2 mg/kg/day) over 3 weeks. Blood pressure was measured by tail-cuff. Blood biochemical and hormonal parameters were determined by enzymatic or ELISA methods. Gene expression was assessed by RT-PCR.

RESULTS

In Koletsky rats, azilsartan treatment lowered blood pressure, basal plasma insulin concentration and the homeostasis model assessment of insulin resistance index, and inhibited over-increase of plasma glucose and insulin concentrations during oral glucose tolerance test. These effects were accompanied by decreases in both food intake and body weight (BW) increase. Although two treatments showed the same effect on BW gain, insulin sensitivity was higher after azilsartan treatment than pair-feeding. Azilsartan neither affected plasma concentrations of triglyceride and free fatty acids, nor increased adipose mRNA levels of peroxisome proliferator-activated receptor (PPAR)γ and its target genes such as adiponectin, aP2. In addition, azilsartan downregulated 11β-hydroxysteroid dehydrogenase type 1 expression.

CONCLUSIONS

These results show the insulin-sensitizing effect of azilsartan in obese Koletsky rats. This effect is independent of decreases in food intake and BW increase or of the activation of adipose PPARγ. Our findings indicate the possible usefulness of azilsartan in the treatment of metabolic syndrome.

Determination of InN/Diamond Heterojunction Band Offset by X-ray Photoelectron Spectroscopy

Diamond is not only a free standing highly transparent window but also a promising carrier confinement layer for InN based devices, yet little is known of the band offsets in InN/diamond system. X-ray photoelectron spectroscopy was used to measure the energy discontinuity in the valence band offset (VBO) of InN/diamond heterostructure. The value of VBO was determined to be 0.39 ± 0.08 eV and a type-I heterojunction with a conduction band offset (CBO) of 4.42 ± 0.08 eV was obtained. The accurate determination of VBO and CBO is important for the application of III-N alloys based electronic devices.

The diagnostic accuracy of cervical biopsies in determining cervical lesions: an audit

OBJECTIVE

The present audit was carried out to assess the diagnostic accuracy of cervical punch biopsy during colposcopy in comparison with diagnosis from subsequent cone excision.

DESIGN AND SETTING

Retrospective analysis was performed by examining the histopathology reports for paired cervical punch biopsies and cervical cone excisions for cases reported from April 2004 to March 2005 (when cervical biopsies and cones were reported by general pathologists) and from January to December 2008 (when reporting by specialist gynaecological pathologists was instituted).

SAMPLE

150 women had both cervical punch and cone biopsies performed in the 2004-2005 period, while 149 women had both biopsies performed in 2008.

MAIN OUTCOME MEASURES AND RESULTS

In 2004-5, the rate of consistent diagnosis was 68.7%, compared with 75.8% in 2008. This was due to a decrease in the rates of overdiagnosis (16.7% vs. 14.8%) and underdiagnosis (14.7% vs. 9.4%), which was statistically significant. The sensitivity rates for 2004-5 and 2008 were 87.5% and 89.7%, and the specificity rates for the same periods were 39.8% and 39.4% respectively.

CONCLUSIONS

This audit highlights the importance of planning patient management on the basis of co-ordinated information from smear results, history, colposcopy findings and cervical biopsies. The introduction of specialist gynaecological histopathology reporting has significantly improved the rates of consistent diagnosis.

Transformation of LRP gene into Brassica napus mediated by Agrobacterium tumefaciens to enhance lysine content in seeds

Lysine rich protein (LRP) gene derived from the seed of Psophocarpus tetragonolobus was transformed into Brassica napus, employing cotyledon petiole as explants and by using the Agrobacterium tumefaciens strain LBA4404. Transformation efficiency was found to be closely related with phytohormone concentration, infection incubation, and co-cultured time. A medium containing 4 mg/l 6-benzyladenine (6-BA) and 0.3 mg/l naphthalene acetic acid (NAA) was used for plant regeneration. With infection incubation of A. tumefaciens (OD600 = 0.4) for 20 min and co-culture of infected cotyledon petiole for 3 days, the highest transformation efficiency of 8.5% was obtained. To confirm LRP gene expression, PCR and Southern blot analysis were performed on leaf-isolated DNA from regenerated plants resistant to kanamycin. All transgenic plants of the generation T0 formed fertile seeds, which were sowed for the inheritance study of generational T1 and amino acid analysis. It was found that the lysine content of seeds from T1 generation increased by 16.7% compared with non-transgenic lines.

Search for supersymmetry at the LHC in events with jets and missing transverse energy

A search for events with jets and missing transverse energy is performed in a data sample of pp collisions collected at √s=7 TeV by the CMS experiment at the LHC. The analyzed data sample corresponds to an integrated luminosity of 1.14 fb(-1). In this search, a kinematic variable α(T) is used as the main discriminator between events with genuine and misreconstructed missing transverse energy. No excess of events over the standard model expectation is found. Exclusion limits in the parameter space of the constrained minimal supersymmetric extension of the standard model are set. In this model, squark masses below 1.1 TeV are excluded at 95% C.L. Gluino masses below 1.1 TeV are also ruled out at 95% C.L. for values of the universal scalar mass parameter below 500 GeV.

Treatment of angiostrongyliasis using a combination of albendazole and dexamethasone: the results of a retrospective and comparative study

As the information available on the treatment of angiostrongyliasis with a combination of albendazole and dexamethasone is limited, the efficacy of such therapy was assessed using data collected during the 2006 outbreak of angiostrongyliasis in Beijing. In a retrospective and controlled study, 35 patients treated with albendazole-dexamethasone (given 20 mg albendazole/kg and 3 mg dexamethasone daily for 7 days) were compared with 34 controls who were treated only symptomatically (with acetaminophen or other drugs). Compared with the controls, the patients given the combination were less likely to have headaches after 7 days (P = 0·038), tended to have headaches that cleared quicker (P = 0·010), and received fewer doses of acetaminophen (P = 0·036). Since no serious adverse effects were observed, a 1-week treatment with a combination of albendazole and dexamethasone appears both safe and beneficial in the treatment of angiostrongyliasis.

Determination of f(s)/f(d) for 7 TeV pp collisions and measurement of the B0→D-K+ branching fraction

The relative abundance of the three decay modes B(0)→D(-)K(+), B(0)→D(-)π(+), and B(s)(0)→D(s)(-)π(+) produced in 7 TeV pp collisions at the LHC is determined from data corresponding to an integrated luminosity of 35 pb(-1). The branching fraction of B(0)→D(-)K(+) is found to be B(B(0)→D(-)K(+)) = (2.01 ± 0.18(stat) ± 0.14(syst)) × 10(-4). The ratio of fragmentation fractions f(s)/f(d) is determined through the relative abundance of B(s)(0)→D(s)(-)π(+) to B(0)→D(-)K(+) and B(0)→D(-)π(+), leading to f(s)/f(d) = 0.253 ± 0.017 ± 0.017 ± 0.020, where the uncertainties are statistical, systematic, and theoretical, respectively.

Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting

Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species.

Search for new physics with a monojet and missing transverse energy in pp collisions at √s = 7 TeV

A study of events with missing transverse energy and an energetic jet is performed using pp collision data at a center-of-mass energy of 7 TeV. The data were collected by the CMS detector at the LHC, and correspond to an integrated luminosity of 36 pb(-1). An excess of these events over standard model contributions is a signature of new physics such as large extra dimensions and unparticles. The number of observed events is in good agreement with the prediction of the standard model, and significant extension of the current limits on parameters of new physics benchmark models is achieved.

Search for the rare decays K(L)→π0π0μ+μ- and K(L)→π0π0X0→π0π0μ+μ-

The KTeV E799 experiment has conducted a search for the rare decays, K(L)→π(0)π(0)μ(+)μ(-) and K(L)→π(0)π(0)X(0)→π(0)π(0)μ(+)μ(-), where the X(0) is a possible new neutral boson that was reported by the HyperCP experiment with a mass of (214.3 ± 0.5) MeV/c(2). We find no evidence for either decay. We obtain upper limits of Br(K(L)→π(0)π(0)X(0)→π(0)π(0)μ(+)μ(-)) < 1.0 × 10(-10) and Br(K(L)→π(0)π(0)μ(+)μ(-)) < 9.2 × 10(-11) at the 90% confidence level. This result rules out the pseudoscalar X(0) as an explanation of the HyperCP result under the scenario that the dsX(0) coupling is completely real.

Metabolic specialization of mouse embryonic stem cells

Mouse embryonic stem (ES) cells are endowed with four unusual properties. They are exceedingly small, exhibiting an intracellular volume two to three orders of magnitude smaller than that of normal mammalian cells. Their rate of cell division, wherein cell doubling takes place in only 4-5 h, is more rapid than even the fastest growing cancer cell lines. They do not senesce. Finally, mouse ES cells retain pluripotency adequate to give rise to all cell types present in either gender of adult mice. We have investigated whether some or all of these unusual features might relate to the possibility that mouse ES cells exist in a specialized metabolic state. By evaluating the abundance of common metabolites as a function of the conversion of mouse ES cells into differentiated embryoid bodies, it was observed that the most radical changes in metabolite abundance related to cellular building blocks associated with one carbon metabolism. These observations led to the discovery that mouse ES cells use the threonine dehydrogenase (TDH) enzyme to convert threonine into acetyl-coenzyme A and glycine, thereby facilitating consumption of threonine as a metabolic fuel. Here we describe the results of a combination of nutritional and pharmacological studies, providing evidence that mouse ES cells are critically dependent on both threonine and the TDH enzyme for growth and viability.

Search for B(s)(0) → μ+ μ- and B(0) → μ+ μ- decays in pp collisions at sqrt[s] = 7 TeV

A search for the rare decays B(s)(0) → μ+ μ- and B(0) → μ+ μ- is performed in pp collisions at sqrt[s] = 7 TeV, with a data sample corresponding to an integrated luminosity of 1.14 fb(-1), collected by the CMS experiment at the LHC. In both cases, the number of events observed after all selection requirements is consistent with expectations from background and standard-model signal predictions. The resulting upper limits on the branching fractions are B(B(s)(0) → μ+ μ-) < 1.9 × 10(-8) and B(B(0) → μ+ μ-)<4.6 × 10(-9), at 95% confidence level.

Homozygous carriers of the G allele of rs4664447 of the glucagon gene (GCG) are characterised by decreased fasting and stimulated levels of insulin, glucagon and glucagon-like peptide (GLP)-1

AIMS/HYPOTHESIS

The glucagon gene (GCG) encodes several hormones important for energy metabolism: glucagon, oxyntomodulin and glucagon-like peptide (GLP)-1 and -2. Variants in GCG may associate with type 2 diabetes, obesity and/or related metabolic traits.

METHODS

GCG was re-sequenced as a candidate gene in 865 European individuals. Twenty-nine variants were identified. Four variants that were considered to have a likelihood for altered functionality: rs4664447, rs7581952, Ile158Val and Trp169Ter, were genotyped in 17,584 Danes.

RESULTS

When examined in 5,760 treatment-naive individuals, homozygous carriers of the low frequency (minor allele frequency 2.3%) G allele of rs4664447, predicted to disrupt an essential splice enhancer binding site, had lower levels of fasting plasma glucose (mean ± SD, 4.8 ± 1.2 vs 5.5 ± 0.8 mmol/l, p = 0.004); fasting serum insulin (22 ± 14 vs 42 ± 27 pmol/l, p = 0.04); glucose-stimulated serum insulin (159 ± 83 vs 290 ± 183 pmol/l, p = 0.01) and adult height (165 ± 10 vs 172 ± 9 cm, p = 0.0009) compared with A allele carriers. During oral glucose tolerance and hyperglycaemic arginine stimulation tests, the plasma AUC for GLP-1 (730 ± 69 vs 1,334 ± 288 pmol/l × min, p = 0.0002) and basal and stimulated levels of serum insulin and plasma glucagon were ∼50% decreased (p < 0.001) among three homozygous carriers compared with nine matched wild-type carriers. rs7581952, Ile158Val and Trp169Ter (where 'Ter' indicates 'termination') variants of GCG did not significantly associate or co-segregate with the metabolic traits examined.

CONCLUSIONS/INTERPRETATION

Re-sequencing of GCG revealed a low frequency intronic variant, rs4664447, and follow-up physiological studies suggest that this variant in homozygous form may cause decreased fasting and stimulated levels of insulin, glucagon and GLP-1. Overall, our findings suggest that variation in GCG has no major impact on carbohydrate metabolism in the study populations examined.

Visualization of the internal cerebral veins on MR phase-sensitive imaging: comparison with 3D gadolinium-enhanced MR venography and fast-spoiled gradient recalled imaging

The purpose of this article is to compare the visualization quality of ICV and their tributaries on PSI-MRV, 3D CE-MRV, and 3D CE-FSPGR. PSI-MRV has been shown to delineate the ICV, TSV, SV, anterior caudate nucleus veins, and medial atrial veins effectively. Due to its advantages of no contrast material injection, acceptable examination times, and no arterial contamination, PSI-MRV should be considered in the evaluation of deep cerebral veins.

Mobility of acid-treated carbon nanotubes in water-saturated porous media

The production, use, and disposal of nanomaterials may inevitably lead to their appearance in water. With the development of new industries around nanomaterials, it seems necessary to be concerned about the transport of nanomaterials in the environment. In this paper, the transport of acid-treated carbon nanotubes (CNTs) in porous media was investigated. Before the mobility investigation, the stability of acid-treated CNT dispersions was studied using ultraviolet-visible spectra and it was indicated that, under the chemical conditions employed in this work, there was no apparent aggregation. The mobility investigation showed that transport of acid-treated CNTs increased with treatment time due to increase in particle zeta potential. Carbon nanotubes treated with nitric acid for 2, 6, and 12 h possessed measured zeta potentials of -30.0, -43.0, and -48.5 mV, respectively. Utilizing clean-bed filtration theory, we showed that acid-treated CNTs have the potential to migrate 3.28, 5.67, and 7.69 m in saturated glass beads, respectively. We showed that solution ionic strength and pH have important effects on the mobility of acid-treated CNTs. Increasing the pH from 6.0 to 7.9 resulted in an increase in migration potential from 2.96 to 10.86 m. Increasing the ionic strength from 0.005 to 0.020 M resulted in a decrease in CNT migration potential from 5.67 to 1.42 m.