Enzymatic [4+2] Cycloadditions in the Biosynthesis of Spirotetramates and Spirotetronates

The Diels-Alder reaction is a quintessential type of [4+2] cycloaddition that remains one of the most intriguing transformations in synthetic chemistry. This reaction has long been envisaged to participate in the biosynthesis of a number of cyclohexene-containing natural products, although the question of whether a bona fide Diels-Alderase exists remains unsolved. In nature, there are remarkably few enzymes known to have the activity of [4+2] cycloaddition. These enzymes are phylogenetically distinct and are often classified according to the specific chemical structures. The variation of protein ancestors and in many cases the instability/complexity of the substrates and products pose a significant challenge in identification of the [4+2] cycloaddition catalysts using general homology-based mining approaches. We here provide the detailed description of the multiple comparison-based strategy and methods for the characterization of two distinct types of dedicated [4+2] cyclases (eg, PyrE3 and PyrI4) in the biosynthesis of spirotetramates and spirotetronates, where they act in tandem for coordinated cross-bridging of a linear polyene intermediate into a enantiomerically pure pentacyclic core. The search of new protein scaffolds with the [4+2] cycloaddition activity could enrich the pool of the candidates for mechanistic examination of a true enzymatic Diels-Alder reaction. The protocols presented in this study would also be applicable to the study of other functionally similar but phylogenetically different proteins, eg, the spiroketal cyclases.

Adiponectin Promotes Human Jaw Bone Marrow Stem Cell Osteogenesis

Human jaw bone marrow mesenchymal stem cells (h-JBMMSCs) are multipotent progenitor cells with osteogenic differentiation potential. The relationship between adiponectin (APN) and the metabolism of h-JBMMSCs has not been fully elucidated, and the underlying mechanism remains unclear. The aim of the study was to investigate the effect and mechanism of APN on h-JBMMSC metabolism. h-JBMMSCs were obtained from the primary culture of human jaw bones and treated with or without APN (1 µg/mL). Osteogenesis-related gene expression was evaluated by real-time polymerase chain reaction (PCR), alkaline phosphatase (ALP) activity assay, and enzyme-linked immunosorbent assay (ELISA). To further investigate the signaling pathway, mechanistic studies were performed using Western blotting, immunofluorescence, lentiviral transduction, and SB202190 (a specific p38 inhibitor). Alizarin Red staining showed that APN promoted h-JBMMSC osteogenesis. Real-time PCR, ALP assay, and ELISA showed that ALP, osteocalcin (OCN), osteopontin, and integrin-binding sialoprotein were up-regulated in APN-treated cells compared to untreated controls. Immunofluorescence revealed that adaptor protein containing a pleckstrin homology domain, phosphotyrosine domain, and leucine zipper motif (APPL1) translocated from the nucleus to the cytoplasm with APN treatment. Additionally, the phosphorylation of p38 mitogen-activated protein kinase (MAPK) increased over time with APN treatment. Moreover, knockdown of APPL1 or p38 MAPK inhibition blocked the expression of APN-induced calcification-related genes including ALP, Runt-related transcription factor 2 (RUNX2), and OCN. Furthermore, Alizarin Red staining of calcium nodes was not increased by the knockdown of APPL1 or p38 inhibition. Our data suggest that this regulation is mediated through the APPL1–p38 MAPK signaling pathway. These findings collectively provide evidence that APN induces the osteogenesis of h-JBMMSCs through APPL1-mediated p38 MAPK activation.

Recessive dystrophic epidermolysis bullosa caused by a de novo interstitial deletion spanning COL7A1 and a hemizygous splicing mutation in trans

BACKGROUND

Recessive dystrophic epidermolysis bullosa (RDEB) is a rare heritable blistering skin condition caused by loss-of-function mutations in the COL7A1 gene. Incongruent gene transmission is occasionally reported in recessive diseases, and its underlying mechanism is often uniparental disomy (UPD).

AIM

To understand the genetic basis of incongruent gene transmission in a Chinese family with RDEB, in which a discrepancy of COL7A1 genotyping was encountered during our mutation analysis.

METHODS

We used a pCAS2 minigene-based in vitro splicing assay to confirm the pathogenicity of the splicing variant we identified in the proband. Next, a combination of genetic tools, including whole-genome SNP array analysis and multiplex ligation-dependent probe amplification copy number analysis, was used to unravel the cause of the discrepancy in the COL7A1 genotyping.

RESULTS

Sanger sequencing identified a novel, single-peak mutation, c.4980+5G>C, in COL7A1 in the proband, which was heterozygous in his father and wild type in his mother. In vitro splicing assay showed that c.4980+5G>C was pathogenic and led to skipping of COL7A1 exon 53. SNP array analysis and multiplex ligation-dependent probe amplification of the proband's DNA revealed a maternally derived, de novo, interstitial deletion on chromosome 3p21.31, which removed COL7A1 and 15 flanking genes, excluding the possibility of UPD.

CONCLUSION

Our findings favour an exceptionally rare event, namely a de novo COL7A1 microdeletion in concurrence with an inherited mutation in trans. This study should aid molecular diagnosis and genetic counselling of RDEB and possibly other recessive diseases in which genotyping discrepancy is encountered.

Correcting for accidental correlations in saturated avalanche photodiodes

In this paper we present a general method for estimating rates of accidental coincidence between a pair of single photon detectors operated within their saturation regimes. By folding the effects of recovery time of both detectors and the detection circuit into an "effective duty cycle" we are able to accomodate complex recovery behaviour at high event rates. As an example, we provide a detailed high-level model for the behaviour of passively quenched avalanche photodiodes, and demonstrate effective background subtraction at rates commonly associated with detector saturation. We show that by post-processing using the updated model, we observe an improvement in polarization correlation visibility from 88.7% to 96.9% in our experimental dataset. This technique will be useful in improving the signal-to-noise ratio in applications which depend on coincidence measurements, especially in situations where rapid changes in flux may cause detector saturation.

Centrality and Transverse Momentum Dependence of Elliptic Flow of Multistrange Hadrons and ϕ Meson in Au+Au Collisions at √[sNN]=200 GeV

We present high precision measurements of elliptic flow near midrapidity (|y|<1.0) for multistrange hadrons and ϕ meson as a function of centrality and transverse momentum in Au+Au collisions at center of mass energy √[sNN]=200  GeV. We observe that the transverse momentum dependence of ϕ and Ω v2 is similar to that of π and p, respectively, which may indicate that the heavier strange quark flows as strongly as the lighter up and down quarks. This observation constitutes a clear piece of evidence for the development of partonic collectivity in heavy-ion collisions at the top RHIC energy. Number of constituent quark scaling is found to hold within statistical uncertainty for both 0%-30% and 30%-80% collision centrality. There is an indication of the breakdown of previously observed mass ordering between ϕ and proton v2 at low transverse momentum in the 0%-30% centrality range, possibly indicating late hadronic interactions affecting the proton v2.

Observation of Transverse Spin-Dependent Azimuthal Correlations of Charged Pion Pairs in p^{↑}+p at sqrt[s]=200 GeV

We report the observation of transverse polarization-dependent azimuthal correlations in charged pion pair production with the STAR experiment in p^{↑}+p collisions at RHIC. These correlations directly probe quark transversity distributions. We measure signals in excess of 5 standard deviations at high transverse momenta, at high pseudorapidities η>0.5, and for pair masses around the mass of the ρ meson. This is the first direct transversity measurement in p+p collisions.

Azimuthal Anisotropy in U+U and Au+Au Collisions at RHIC

Collisions between prolate uranium nuclei are used to study how particle production and azimuthal anisotropies depend on initial geometry in heavy-ion collisions. We report the two- and four-particle cumulants, v_{2}{2} and v_{2}{4}, for charged hadrons from U+U collisions at sqrt[s_{NN}]=193  GeV and Au+Au collisions at sqrt[s_{NN}]=200  GeV. Nearly fully overlapping collisions are selected based on the energy deposited by spectators in zero degree calorimeters (ZDCs). Within this sample, the observed dependence of v_{2}{2} on multiplicity demonstrates that ZDC information combined with multiplicity can preferentially select different overlap configurations in U+U collisions. We also show that v_{2} vs multiplicity can be better described by models, such as gluon saturation or quark participant models, that eliminate the dependence of the multiplicity on the number of binary nucleon-nucleon collisions.

Methylation-sensitive amplified polymorphism-based genome-wide analysis of cytosine methylation profiles in Nicotiana tabacum cultivars

This study aimed to investigate cytosine methylation profiles in different tobacco (Nicotiana tabacum) cultivars grown in China. Methylation-sensitive amplified polymorphism was used to analyze genome-wide global methylation profiles in four tobacco cultivars (Yunyan 85, NC89, K326, and Yunyan 87). Amplicons with methylated C motifs were cloned by reamplified polymerase chain reaction, sequenced, and analyzed. The results show that geographical location had a greater effect on methylation patterns in the tobacco genome than did sampling time. Analysis of the CG dinucleotide distribution in methylation-sensitive polymorphic restriction fragments suggested that a CpG dinucleotide cluster-enriched area is a possible site of cytosine methylation in the tobacco genome. The sequence alignments of the Nia1 gene (that encodes nitrate reductase) in Yunyan 87 in different regions indicate that a C-T transition might be responsible for the tobacco phenotype. T-C nucleotide replacement might also be responsible for the tobacco phenotype and may be influenced by geographical location.

Precision Measurement of the Longitudinal Double-Spin Asymmetry for Inclusive Jet Production in Polarized Proton Collisions at sqrt[s]=200 GeV

We report a new measurement of the midrapidity inclusive jet longitudinal double-spin asymmetry, A_{LL}, in polarized pp collisions at center-of-mass energy sqrt[s]=200  GeV. The STAR data place stringent constraints on polarized parton distribution functions extracted at next-to-leading order from global analyses of inclusive deep-inelastic scattering (DIS), semi-inclusive DIS, and RHIC pp data. The measured asymmetries provide evidence at the 3σ level for positive gluon polarization in the Bjorken-x region x>0.05.

The inhibition of high-voltage-activated calcium current by activation of MrgC11 involves phospholipase C-dependent mechanisms

High-voltage-activated (HVA) calcium channels play an important role in synaptic transmission. Activation of Mas-related G-protein-coupled receptor subtype C (MrgC; mouse MrgC11, rat homolog rMrgC) inhibits HVA calcium current (ICa) in small-diameter dorsal root ganglion (DRG) neurons, but the intracellular signaling cascade underlying MrgC agonist-induced inhibition of HVA ICa in native DRG neurons remains unclear. To address this question, we conducted patch-clamp recordings in MrgA3-eGFP-wild-type mice, in which most MrgA3-eGFP(+) DRG neurons co-express MrgC11 and can be identified for recording. We found that the inhibition of HVA ICa by JHU58 (0.001-100nM, a dipeptide, MrgC-selective agonist) was significantly reduced by pretreatment with a phospholipase C (PLC) inhibitor (U73122, 1μM), but not by its inactive analog (U73343) or vehicle. Further, in rats that had undergone spinal nerve injury, pretreatment with intrathecal U73122 nearly abolished the inhibition of mechanical hypersensitivity by intrathecal JHU58. The inhibition of HVA ICa in MrgA3-eGFP(+) neurons by JHU58 (100nM) was partially reduced by pretreatment with a Gβγ blocker (gallein, 100μM). However, applying a depolarizing prepulse and blocking the Gαi and Gαs pathways with pertussis toxin (PTX) (0.5μg/mL) and cholera toxin (CTX) (0.5μg/mL), respectively, had no effect. These findings suggest that activation of MrgC11 may inhibit HVA ICa in mouse DRG neurons through a voltage-independent mechanism that involves activation of the PLC, but not Gαi or Gαs, pathway.

The mitochondrial thioredoxin is required for liver development in zebrafish

Thioredoxins (Trxs) are a class of small molecular redox proteins that play an important role in scavenging abnormally accumulated reactive oxygen species (ROS). Thioredoxin 2 (Trx2) is one member of this family located in mitochondria. Trx2 protects cells from increased oxidative stress and has anti-apoptosis function. Knockout of Trx2 in mice led to early embryonic lethality. However, the essential role of Trx2 during embryogenesis remains unclear. To further investigate the role of Trx2 during embryonic development, we performed Trx2 knockdown in zebrafish and investigated the regulation role of Trx2 during embryonic development. Our results indicate that Trx2 had a high expression in early zebrafish embryos and its knockdown in zebrafish led to defective liver development mainly due to increased hepatic cell death. The increased ROS and the imbalance of members of the Bcl-2 family were involved in cell death induced by Trx2 suppression in zebrafish. The dysregulation of Bax, puma and Bcl-xl promoted the reduction of mitochondrial trans-membrane potential and the mitochondria membrane permeabilization (MMP), which initiated the mitochondrial apoptosis pathway. Additionally, we found that the increase of relocated GAPDH in mitochondria may be another factor responsible for the mitochondrial catastrophe.

Enhanced magnetic anisotropies of single transition-metal adatoms on a defective MoS2 monolayer

Single magnetic atoms absorbed on an atomically thin layer represent the ultimate limit of bit miniaturization for data storage. To approach the limit, a critical step is to find an appropriate material system with high chemical stability and large magnetic anisotropic energy. Here, on the basis of first-principles calculations and the spin-orbit coupling theory, it is elucidated that the transition-metal Mn and Fe atoms absorbed on disulfur vacancies of MoS₂ monolayers are very promising candidates. It is analysed that these absorption systems are of not only high chemical stabilities but also much enhanced magnetic anisotropies and particularly the easy magnetization axis is changed from the in-plane one for Mn to the out-of-plane one for Fe by a symmetry-lowering Jahn-Teller distortion. The results point out a promising direction to achieve the ultimate goal of single adatomic magnets with utilizing the defective atomically thin layers.

Porphyromonas gingivalis lipopolysaccharides regulate functions of bone marrow mesenchymal stem cells

OBJECTIVES

Periodontitis is one of the most widespread inflammatory diseases; it causes tooth loss and is also associated with a variety of systemic diseases. Mesenchymal stem cells (MSCs) have been used to treat periodontitis. However, it is unknown whether bacterial toxins in the periodontal environment affect MSC-mediated periodontal regeneration. Porphyromonas gingivalis lipopolysaccharides (Pg-LPS) are key toxins for development of periodontitis. The purpose of the present study was to investigate effects of P. gingivalis LPS on biological properties of MSCs.

MATERIALS AND METHODS

Mesenchymal stem cells from bone marrow (BMMSCs) were treated with different concentrations of P. gingivalis LPS (0.1-10 μg/ml), then its effects were evaluated on biological properties of BMMSCs including proliferation, apoptosis, osteogenic differentiation and capacities to inhibit activated T cells.

RESULTS

Low concentration of P. gingivalis LPS (0.1 μg/ml) accelerated MSC proliferation, osteogenic differentiation and capacities to inhibit activated T cells via up-regulation of nitric oxide. However, high concentration of P. gingivalis LPS (10 μg/ml) reduced MSC proliferation, osteogenic differentiation and capacities to inhibit activated T cells.

CONCLUSIONS

Mesenchymal stem cells were functionally different following exposure to P. gingivalis LPS at the investigated concentrations. These findings suggest that MSC-mediated periodontal regeneration may be regulated by P. gingivalis LPS.

Folic acid supplementation and dietary folate intake, and risk of preeclampsia

BACKGROUND/OBJECTIVES

Folic acid supplementation has been suggested to reduce the risk of preeclampsia. However, results from few epidemiologic studies have been inconclusive. We investigated the hypothesis that folic acid supplementation and dietary folate intake before conception and during pregnancy reduce the risk of preeclampsia.

SUBJECTS/METHODS

A birth cohort study was conducted in 2010-2012 at the Gansu Provincial Maternity & Child Care Hospital in Lanzhou, China. A total of 10,041 pregnant women without chronic hypertension or gestational hypertension were enrolled.

RESULTS

Compared with nonusers, folic acid supplement users had a reduced risk of preeclampsia (OR=0.61, 95% CI: 0.43-0.87). A significant dose-response of duration of use was observed among women who used folic acid supplemention during pregnancy only (P-trend=0.007). The reduced risk associated with folic acid supplement was similar for mild or severe preeclampsia and for early- or late-onset preeclampsia, although the statistical significant associations were only observed for mild (OR=0.50, 95% CI: 0.30-0.81) and late-onset (OR=0.60, 95% CI: 0.42-0.86) preeclampsia. The reduced risk associated with dietary folate intake during pregnancy was only seen for severe preeclampsia (OR=0.52, 95% CI: 0.31-0.87, for the highest quartile of dietary folate intake compared with the lowest).

CONCLUSIONS

Our study results suggest that folic acid supplementation and higher dietary folate intake during pregnancy reduce the risk of preeclampsia. Future studies are needed to confirm the associations.

ΛΛ Correlation function in Au+Au collisions at √[S(NN)]=200 GeV

We present ΛΛ correlation measurements in heavy-ion collisions for Au+Au collisions at sqrt[s_{NN}]=200  GeV using the STAR experiment at the Relativistic Heavy-Ion Collider. The Lednický-Lyuboshitz analytical model has been used to fit the data to obtain a source size, a scattering length and an effective range. Implications of the measurement of the ΛΛ correlation function and interaction parameters for dihyperon searches are discussed.

Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population

AIM

To use microarrays to detect 11 selected bacteria in infected root canals, revealing bacterial combinations that are associated with clinical symptoms and signs of primary endodontic infections in a Chinese population.

METHODOLOGY

DNA was extracted from 90 samples collected from the root canals of teeth with primary endodontic infections in a Chinese population, and the 16S rRNA gene was amplified by polymerase chain reaction (PCR). The PCR products were hybridized to microarrays containing specific oligonucleotide probes targeting 11 species, and the arrays were screened with a confocal laser scanner. Pearson's chi-squared test and cluster analysis were performed to investigate the associations between the bacterial combinations and clinical symptoms and signs using SAS 8.02.

RESULTS

Seventy-seven samples (86%) yielded at least one of the 11 target species. Parvimonas micra (56%), Porphyromonas endodontalis (51%), Tannerella forsythia (48%), Prevotella intermedia (44%) and Porphyromonas gingivalis (37%) were the most prevalent taxa and were often concomitant. The following positive associations were found between the bacterial combinations and clinical features: P. endodontalis and T. forsythia with abscess; P. gingivalis and P. micra with sinus tract; P. gingivalis and P. endodontalis or P. micra and P. endodontalis with abscess and sinus tract; and the combination of P. endodontalis, P. micra, T. forsythia and P. gingivalis with sinus tract (P < 0.05).

CONCLUSIONS

Various combinations of P. micra, P. endodontalis, T. forsythia and P. gingivalis may contribute to abscesses or sinus tracts of endodontic origin with bacterial synergism in a Chinese population.

Rhodium catalysed conversion of carbenes into ketenes and ketene imines using PNN pincer complexes

PNN pincer-type rhodium complexes catalyze ketene and ketene imine synthesis, using CO or an isocyanide and a carbene precursor.

Theoretical study of population inversion in active doped MIR chalcogenide glass fibre lasers (invited)

We study the mechanism of the population inversion in mid-infrared fibre lasers based on a chalcogenide glass host doped with active lanthanide ions. Three lanthanide dopant ions are considered: terbium, dysprosium and praseodymium. We predict the relevant trivalent ion level populations and gain. The simulation parameters were obtained by fabricating and optically characterising a series of trivalent ion doped chalcogenide glass samples. We also provide simple analytical expressions that aid the design of the cascade lasing process.

Observation of D0 meson nuclear modifications in Au+Au collisions at sqrt[s(NN)] = 200 GeV

We report the first measurement of charmed-hadron (D(0)) production via the hadronic decay channel (D(0) → K(-) + π(+)) in Au+Au collisions at sqrt[s(NN)] = 200 GeV with the STAR experiment. The charm production cross section per nucleon-nucleon collision at midrapidity scales with the number of binary collisions, N(bin), from p+p to central Au+Au collisions. The D(0) meson yields in central Au + Au collisions are strongly suppressed compared to those in p+p scaled by N(bin), for transverse momenta p(T) > 3 GeV/c, demonstrating significant energy loss of charm quarks in the hot and dense medium. An enhancement at intermediate p(T) is also observed. Model calculations including strong charm-medium interactions and coalescence hadronization describe our measurements.

Superior photoluminescence (PL) of Pr³⁺-In, compared to Pr³⁺-Ga, selenide-chalcogenide bulk glasses and PL of optically-clad fiber

The photoluminescent-(PL)-properties of Pr³⁺-ions in indium-containing selenide-chalcogenide bulk-glasses are found to be superior when compared with gallium-containing analogues. We observe circa doubling of mid-infrared (MIR) PL intensity from 3.5 to 6 μm for bulk glasses, pumped at 1.55 μm wavelength, and an increased excited state lifetime at 4.7 μm. PL is reported in optically-clad fiber. Ga addition is well known to enhance RE³⁺ solubility and PL behavior, and is believed to form ([RE³⁺]-Se-[Ga(III)]) in the glasses. Indium has the same outer electronic-structure as gallium for solvating the RE-ions. Moreover, indium is heavier and promotes lower phonon energy locally around the RE-ion, thereby enhancing the RE-ion PL behavior, as observed here.

Beam energy dependence of moments of the net-charge multiplicity distributions in Au+Au collisions at RHIC

We report the first measurements of the moments--mean (M), variance (σ(2)), skewness (S), and kurtosis (κ)--of the net-charge multiplicity distributions at midrapidity in Au+Au collisions at seven energies, ranging from sqrt[sNN]=7.7 to 200 GeV, as a part of the Beam Energy Scan program at RHIC. The moments are related to the thermodynamic susceptibilities of net charge, and are sensitive to the location of the QCD critical point. We compare the products of the moments, σ(2)/M, Sσ, and κσ(2), with the expectations from Poisson and negative binomial distributions (NBDs). The Sσ values deviate from the Poisson baseline and are close to the NBD baseline, while the κσ(2) values tend to lie between the two. Within the present uncertainties, our data do not show nonmonotonic behavior as a function of collision energy. These measurements provide a valuable tool to extract the freeze-out parameters in heavy-ion collisions by comparing with theoretical models.

Measurement of longitudinal spin asymmetries for weak boson production in polarized proton-proton collisions at RHIC

We report measurements of single- and double-spin asymmetries for W^{±} and Z/γ^{*} boson production in longitudinally polarized p+p collisions at sqrt[s]=510  GeV by the STAR experiment at RHIC. The asymmetries for W^{±} were measured as a function of the decay lepton pseudorapidity, which provides a theoretically clean probe of the proton's polarized quark distributions at the scale of the W mass. The results are compared to theoretical predictions, constrained by polarized deep inelastic scattering measurements, and show a preference for a sizable, positive up antiquark polarization in the range 0.05<x<0.2.

Beam-energy dependence of charge separation along the magnetic field in Au+Au collisions at RHIC

Local parity-odd domains are theorized to form inside a quark-gluon plasma which has been produced in high-energy heavy-ion collisions. The local parity-odd domains manifest themselves as charge separation along the magnetic field axis via the chiral magnetic effect. The experimental observation of charge separation has previously been reported for heavy-ion collisions at the top RHIC energies. In this Letter, we present the results of the beam-energy dependence of the charge correlations in Au+Au collisions at midrapidity for center-of-mass energies of 7.7, 11.5, 19.6, 27, 39, and 62.4 GeV from the STAR experiment. After background subtraction, the signal gradually reduces with decreased beam energy and tends to vanish by 7.7 GeV. This implies the dominance of hadronic interactions over partonic ones at lower collision energies.

Dielectron mass spectra from Au+Au collisions at √[s(NN)]=200 GeV

We report the STAR measurements of dielectron (e(+)e(-)) production at midrapidity (|y(ee)|<1) in Au+Au collisions at √[s(NN)]=200  GeV. The measurements are evaluated in different invariant mass regions with a focus on 0.30-0.76 (ρ-like), 0.76-0.80 (ω-like), and 0.98-1.05 (ϕ-like)   GeV/c(2). The spectrum in the ω-like and ϕ-like regions can be well described by the hadronic cocktail simulation. In the ρ-like region, however, the vacuum ρ spectral function cannot describe the shape of the dielectron excess. In this range, an enhancement of 1.77±0.11(stat)±0.24(syst)±0.33(cocktail) is determined with respect to the hadronic cocktail simulation that excludes the ρ meson. The excess yield in the ρ-like region increases with the number of collision participants faster than the ω and ϕ yields. Theoretical models with broadened ρ contributions through interactions with constituents in the hot QCD medium provide a consistent description of the dilepton mass spectra for the measurement presented here and the earlier data at the Super Proton Synchrotron energies.

Transposon variation by order during allopolyploidisation between Brassica oleracea and Brassica rapa

Although many studies have shown that transposable element (TE) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE-associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE, and determined the impact of TE-associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the Inter-Retrotransposon Amplified Polymorphism (IRAP) method to detect variation in TE-associated sequences during the process of allopolyploidisation between Brassica rapa (AA) and Brassica oleracea (CC), and in successive generations of self-pollinated progeny. In addition, fragments with TE insertions were used to perform Blast2GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety-two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TEs could be classed in ascending frequency into LTR-REs, TIRs, LINEs, SINEs and unknown TEs. The frequency of novel variation (putative activation) detected for the four orders of TEs was highest from the F1 to F2 generations, and lowest from the F2 to F3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation.

Systematic review with meta-analysis: meat consumption and the risk of hepatocellular carcinoma

BACKGROUND

The association between meat consumption and the risk of hepatocellular carcinoma (HCC) is still inconclusive.

AIM

To conduct a systematic review and meta-analysis to quantitatively assess the relationship between meat intake and the risk of HCC.

METHODS

We searched the PubMed, Web of Science and EMBASE databases for relevant studies published before July 2013. The summary relative risks were pooled using the fixed-effects model when no substantial heterogeneity was detected, otherwise, the random-effects model was used. Heterogeneity and publication bias were also analysed.

RESULTS

Finally, seven cohort studies and 10 case-control studies were included. The pooled relative risks (RRs) of HCC for the highest vs. lowest consumption levels were 1.10 (95% confidence interval, CI: 0.85-1.42) for red meat, 1.01 (95% CI: 0.79-1.28) for processed meat and 0.97 (95% CI: 0.85-1.11) for total meat. Moreover, white meat and fish consumption were found to be inversely associated with HCC risk, the summary RRs were 0.69 (95% CI: 0.58-0.81) and 0.78 (95% CI: 0.67-0.90) respectively, and the results remained quite stable after stratification by the confounding factors.

CONCLUSIONS

The present meta-analysis indicates that a high level of white meat or fish consumption can reduce the risk of HCC significantly, while intake of red meat, processed meat or total meat is not associated with HCC risk. Our findings suggest that dietary intervention may be a promising approach for prevention of HCC, which still need to be confirmed by further well-designed prospective studies and experimental research.

Beam-energy dependence of the directed flow of protons, antiprotons, and pions in Au+Au collisions

Rapidity-odd directed flow (v1) measurements for charged pions, protons, and antiprotons near midrapidity (y=0) are reported in sNN=7.7, 11.5, 19.6, 27, 39, 62.4, and 200 GeV Au+Au collisions as recorded by the STAR detector at the Relativistic Heavy Ion Collider. At intermediate impact parameters, the proton and net-proton slope parameter dv1/dy|y=0 shows a minimum between 11.5 and 19.6 GeV. In addition, the net-proton dv1/dy|y=0 changes sign twice between 7.7 and 39 GeV. The proton and net-proton results qualitatively resemble predictions of a hydrodynamic model with a first-order phase transition from hadronic matter to deconfined matter, and differ from hadronic transport calculations.

Clinical significance of polypeptide N-acetylgalactosaminyl transferase-5 (GalNAc-T5) expression in patients with gastric cancer

BACKGROUND

The family of polypeptide N-acetylgalactosaminyl transferases is responsible for the altered O-linked glycosylation occurring during the development of various cancers and their progression via altering O-glycan biosynthesis. Our studies were designed to investigate the expression and prognostic values of GalNAc-T5 and improve the risk stratification in patients with gastric cancer.

METHODS

Tissue samples from a training set and a validation set of patients with gastric adenocarcinoma from China were used for analyses. GalNAc-T5 expression was retrospectively analysed by immunohistochemistry. Results were assessed for association with clinicopathological parameters and overall survival by using Kaplan-Meier analysis. Prognostic values of GalNAc-T5 expression and clinical outcomes were evaluated by Cox regression analysis. A molecular prognostic stratification scheme incorporating GalNAc-T5 expression was determined by using receiver operating characteristic analysis.

RESULTS

GalNAc-T5 expression was markedly reduced in gastric cancer tissues compared with non-malignant gastric mucosa. Low intratumoral GalNAc-T5 density, which was associated with tumour cell differentiation, T classification, N classification, and TNM stage in the two independent sets, was an independent prognosticator for poor prognosis of gastric cancer patients. Applying the prognostic value of intratumoral GalNAc-T5 density to the conventional clinicopathologic TNM stage system showed a better prognostic value in patients with gastric cancer.

CONCLUSIONS

Intratumoral GalNAc-T5 expression was recognised as an independent prognostic marker for the overall survival of gastric cancer patients. Detection of GalNAc-T5 expression in gastric cancer tissues might add some prognostic information for patients with this disease and lead to a more accurate classification under the TNM stage system.

Jet-hadron correlations in √[s(NN)]=200 GeV p+p and central Au+Au collisions

Azimuthal angular correlations of charged hadrons with respect to the axis of a reconstructed (trigger) jet in Au+Au and p+p collisions at √[s(NN)]=200  GeV in STAR are presented. The trigger jet population in Au+Au collisions is biased toward jets that have not interacted with the medium, allowing easier matching of jet energies between Au+Au and p+p collisions while enhancing medium effects on the recoil jet. The associated hadron yield of the recoil jet is significantly suppressed at high transverse momentum (pTassoc) and enhanced at low pTassoc in 0%-20% central Au+Au collisions compared to p+p collisions, which is indicative of medium-induced parton energy loss in ultrarelativistic heavy-ion collisions.

Increased levels of IL-21 responses are associated with the severity of liver injury in patients with chronic active hepatitis B

Interleukin-21 (IL-21) participates in tissue damage in various immune-mediated diseases. Its role in the pathogenesis of chronic active hepatitis B (CAHB) has not been clarified. The frequency of circulating IL-21(+) T cells and the levels of serum and intrahepatic IL-21 have been characterized in 70 CAHB patients, 32 inactive carrier (IC), 18 chronic hepatitis C (CHC) and 20 healthy controls (HC). Their potential association with liver injury was analysed. The percentages of IL-21(+) CD3(+) CD8(-) and IL-21(+) CD3(+) CD8(+) T cells and the levels of serum IL-21 in CAHB patients were significantly higher than that in the IC, CHC patients and HC (P < 0.001) and were correlated positively with the levels of serum alanine aminotransferase (ALT, r = 0.424, P < 0.001; r = 0.392, P = 0.001) and aspartate aminotransferase (AST, r = 0.388, P = 0.001; r = 0.329, P = 0.005) in CAHB patients, respectively. The levels of IL-21 expression in the liver tissues were associated significantly with increased degrees of inflammation and fibrosis in CAHB patients (P < 0.01 or P < 0.05). Our findings suggest that aberrant IL-21 responses may be associated with the progression of CHB.

Energy dependence of moments of net-proton multiplicity distributions at RHIC

We report the beam energy (sqrt[sNN]=7.7-200  GeV) and collision centrality dependence of the mean (M), standard deviation (σ), skewness (S), and kurtosis (κ) of the net-proton multiplicity distributions in Au+Au collisions. The measurements are carried out by the STAR experiment at midrapidity (|y|<0.5) and within the transverse momentum range 0.4<pT<0.8  GeV/c in the first phase of the Beam Energy Scan program at the Relativistic Heavy Ion Collider. These measurements are important for understanding the quantum chromodynamic phase diagram. The products of the moments, Sσ and κσ2, are sensitive to the correlation length of the hot and dense medium created in the collisions and are related to the ratios of baryon number susceptibilities of corresponding orders. The products of moments are found to have values significantly below the Skellam expectation and close to expectations based on independent proton and antiproton production. The measurements are compared to a transport model calculation to understand the effect of acceptance and baryon number conservation and also to a hadron resonance gas model.

Poled-fiber source of broadband polarization-entangled photon pairs

We demonstrate broadband polarization-entangled photon pair generation in a poled fiber phase matched for Type II downconversion in the 1.5 μm telecom band. Even with signal-idler separation greater than 100 nm, we observe fringe visibilities greater than 97% and tangle greater than 0.8. A Hong-Ou-Mandel interference experiment is also used to experimentally confirm the broadband nature of the entanglement.

Genetic deficiency of β2-containing nicotinic receptors attenuates brain injury in ischemic stroke

One of the major consequences of stroke is brain injury caused by glutamate-mediated excitotoxicity. Glutamate-mediated excitatory activities are partially driven by β2-containing nicotinic acetylcholine receptors (β2-nAChRs). In examining the role of β2-nAChRs in cerebral ischemic injury, excitotoxicity and stroke outcome, we found that deficiency of β2-nAChRs attenuated brain infarction and neurological deficit at 24 and 72 h after transient middle cerebral artery occlusion (MCAO). Genetic deletion of β2-nAChRs associated with reduced terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL(+)) and cleaved caspase-3(+) cells after MCAO, together with a reduction of extracellular glutamate and oxygen-glucose deprivation-induced increase of excitatory inputs in cortical neurons. Pharmacologic pretreatment with a selective β2-nAChRs antagonist reduced brain infarction, neurological deficit, and MCAO-induced glutamate release. These findings suggest that deficiency of β2-nAChRs, also achievable by pharmacological blockade, can decrease brain infarction and improve the neurological status in ischemic stroke. The improved outcome is associated with reduced extracellular glutamate level and lower excitatory inputs into ischemic neurons, suggesting a reduction of glutamate-mediated excitotoxicity in the mechanisms of neuroprotection.

Tuning interlayer exchange coupling of co-doped TiO2/VO2 multilayers via metal-insulator transition

Reversibly switching interlayer exchange coupling (IEC) of magnetic semiconductor multilayers between ferromagnetic (FM) and antiferromagnetic (AFM) modes is a difficult but key issue for fabricating semiconductor giant magnetoresistance devices. Here, we show that such tunable IEC is achievable around room temperature in Co-doped TiO2/VO2 diluted magnetic semiconductor multilayers. On the basis of first-principles calculations of electronic structure and fermiology, it is clarified that, associated with the metal-insulator transition (MIT) of nanosized VO2 spacers, exotic short-range magnetic orders are developed in the multilayers so that the IEC can be tuned reversibly from FM mode to AFM mode by varying temperature crossing the MIT (∼340  K).

Measurement of J/ψ azimuthal anisotropy in Au+Au collisions at sqrt[s(NN)]=200 GeV

The measurement of J/ψ azimuthal anisotropy is presented as a function of transverse momentum for different centralities in Au+Au collisions at sqrt[s(NN)]=200 GeV. The measured J/ψ elliptic flow is consistent with zero within errors for transverse momentum between 2 and 10 GeV/c. Our measurement suggests that J/ψ particles with relatively large transverse momenta are not dominantly produced by coalescence from thermalized charm quarks, when comparing to model calculations.