Molecular and functional analyses of COPT/Ctr-type copper transporter-like gene family in rice

<p>Abstract</p> <p>Background</p> <p>The copper (Cu) transporter (COPT/Ctr) gene family has an important role in the maintenance of Cu homeostasis in different species. The rice COPT-type gene family consists of seven members (<it>COPT1 </it>to <it>COPT7</it>). However, only two, <it>COPT1 </it>and <it>COPT5</it>, have been characterized for their functions in Cu transport.</p> <p>Results</p> <p>Here we report the molecular and functional characterization of the other five members of the rice <it>COPT </it>gene family (<it>COPT2</it>, <it>COPT3</it>, <it>COPT4</it>, <it>COPT6</it>, and <it>COPT7</it>). All members of the rice <it>COPT </it>family have the conserved features of known <it>COPT/Ctr</it>-type Cu transporter genes. Among the proteins encoded by rice <it>COPTs</it>, COPT2, COPT3, and COPT4 physically interacted with COPT6, respectively, except for the known interaction between COPT1 and COPT5. COPT2, COPT3, or COPT4 cooperating with COPT6 mediated a high-affinity Cu uptake in the yeast <it>Saccharomyces cerevisiae </it>mutant that lacked the functions of ScCtr1 and ScCtr3 for Cu uptake. COPT7 alone could mediate a high-affinity Cu uptake in the yeast mutant. None of the seven COPTs alone or in cooperation could complement the phenotypes of <it>S. cerevisiae </it>mutants that lacked the transporter genes either for iron uptake or for zinc uptake. However, these <it>COPT </it>genes, which showed different tissue-specific expression patterns and Cu level-regulated expression patterns, were also transcriptionally influenced by deficiency of iron, manganese, or zinc.</p> <p>Conclusion</p> <p>These results suggest that COPT2, COPT3, and COPT4 may cooperate with COPT6, respectively, and COPT7 acts alone for Cu transport in different rice tissues. The endogenous concentrations of iron, manganese, or zinc may influence Cu homeostasis by influencing the expression of <it>COPTs </it>in rice.</p

C2H N=1-0 and N2H+ J=1-0 observations of Planck Galactic cold clumps

A survey of C2H N=1-0 and N2H+ J=1-0 toward Planck Galactic cold clumps (PGCCs) was performed using the Purple Mountain Observatory's 13.7 m telescope. C2H and N2H+ were chosen to study the chemical evolutionary states of PGCCs. Among 121 observed molecular cores associated with PGCCs, 71 and 58 are detected with C2H N=1-0 and N2H+ J=1-0, respectively. The detected lines of most sources can be fitted with a single component with compatible Vlsr and line widths, which confirms that these PGCC cores are very cold (with gas temperatures 9-21 K) and quiescent while still dominanted by turbulence. The ratio between the column densities of C2H and N2H+ (N(C2H)/N(N2H+)) is found to be a good tracer for the evolutionary states of PGCC cores. Gas-grain chemical model can reproduce the decreasing trend of N(C2H)/N(N2H+) as a function of time. The cores with the lowest abundances of N2H+ (X[N2H+] < 10^{-10}) are the youngest, and have nearly constant abundances of C2H. In evolved cores with X[N2H+] ~ 1E-9, abundances of C2H drop quickly as the exhaustion of carbon atoms. Although these PGCC cores are in different evolutionary states, they are all quite young ( N(N2H+). Mapping observations are carried out toward 20 PGCC cores. The PGCC cores in Cepheus have lower N(C2H)/N(N2H+) and larger line widths compared with those in Taurus. This implies that PGCC cores in Taurus are less chemically evolved than those in Cepheus.Comment: 23 pages, 6 figures, 5 table

Sequential Star Formation in the filamentary structures of Planck Galactic cold clump G181.84+0.31

We present a multi-wavelength study of the Planck cold clump G181.84+0.31, which is located at the northern end of the extended filamentary structure S242. We have extracted 9 compact dense cores from the SCUBA-2 850 um map, and we have identified 18 young stellar objects (YSOs, 4 Class I and 14 Class II) based on their Spitzer, Wide-field Infrared Survey Explorer (WISE) and Two-Micron All-Sky Survey (2MASS) near- and mid-infrared colours. The dense cores and YSOs are mainly distributed along the filamentary structures of G181.84 and are well traced by HCO$^{+}$(1-0) and N$_{2}$H$^{+}$(1-0) spectral-line emission. We find signatures of sequential star formation activities in G181.84: dense cores and YSOs located in the northern and southern sub-structures are younger than those in the central region. We also detect global velocity gradients of about 0.8$\pm$0.05 km s$^{-1}$pc$^{-1}$ and 1.0$\pm$0.05 km s$^{-1}$pc$^{-1}$ along the northern and southern sub-structures, respectively, and local velocity gradients of 1.2$\pm$0.1 km s$^{-1}$pc$^{-1}$ in the central substructure. These results may be due to the fact that the global collapse of the extended filamentary structure S242 is driven by an edge effect, for which the filament edges collapse first and then further trigger star formation activities inward. We identify three substructures in G181.84 and estimate their critical masses per unit length, which are $\sim$ 101$\pm$15 M$_{\odot}$ pc$^{-1}$, 56$\pm$8 M$_{\odot}$ pc$^{-1}$ and 28$\pm$4 M$_{\odot}$ pc$^{-1}$, respectively. These values are all lower than the observed values ($\sim$ 200 M$_{\odot}$ pc$^{-1}$), suggesting that these sub-structures are gravitationally unstable.Comment: 20 pages, 17 figures, article, accepte

Comparing Partial Least Square Approaches in Gene-or Region-based Association Study for Multiple Quantitative Phenotypes

On thinking quantitatively of complex diseases, there are at least three statistical strategies for association study: single SNP on single trait, gene-or region (with multiple SNPs) on single trait and on multiple traits. The third of which is the most general in dissecting the genetic mechanism underlying complex diseases underpinning multiple quantitative traits. Gene-or region association methods based on partial least square (PLS) approaches have been shown to have apparent power advantage. However, few attempts are developed for multiple quantitative phenotypes or traits underlying a condition or disease, and the performance of various PLS approaches used in association study for multiple quantitative traits had not been assessed. We, from regression perspective, exploit association between multiple SNPs and multiple phenotypes or traits through exhaustive scan statistics (sliding window) using PLS and sparse PLS (SPLS) regression. Simulations are conducted to assess the performance of the proposed scan statistics and compare them with the existed method. The proposed methods are applied to 12 regions of GWAS data from the European Prospective Investigation of Cancer (EPIC)-Norfolk study

Gene- or region-based association study via kernel principal component analysis.

BACKGROUND: In genetic association study, especially in GWAS, gene- or region-based methods have been more popular to detect the association between multiple SNPs and diseases (or traits). Kernel principal component analysis combined with logistic regression test (KPCA-LRT) has been successfully used in classifying gene expression data. Nevertheless, the purpose of association study is to detect the correlation between genetic variations and disease rather than to classify the sample, and the genomic data is categorical rather than numerical. Recently, although the kernel-based logistic regression model in association study has been proposed by projecting the nonlinear original SNPs data into a linear feature space, it is still impacted by multicolinearity between the projections, which may lead to loss of power. We, therefore, proposed a KPCA-LRT model to avoid the multicolinearity. RESULTS: Simulation results showed that KPCA-LRT was always more powerful than principal component analysis combined with logistic regression test (PCA-LRT) at different sample sizes, different significant levels and different relative risks, especially at the genewide level (1E-5) and lower relative risks (RR = 1.2, 1.3). Application to the four gene regions of rheumatoid arthritis (RA) data from Genetic Analysis Workshop16 (GAW16) indicated that KPCA-LRT had better performance than single-locus test and PCA-LRT. CONCLUSIONS: KPCA-LRT is a valid and powerful gene- or region-based method for the analysis of GWAS data set, especially under lower relative risks and lower significant levels.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Strong coupling of surface plasmon polaritons in monolayer graphene sheet arrays

Here we investigate theoretically and numerically the coupling between surface plasmon polaritons (SPPs) in monolayer graphene sheet arrays that have a period much smaller than the wavelength. We show that when the collective SPP is excited with an out-of-phase illumination, the beam tends to propagate toward the opposite direction of the Bloch momentum, reflecting a negative coupling between the constituent SPPs. In contrast, for in-phase illumination, the incident beam is split into two collective SPPs that are highly collimated and display low propagation loss. Moreover, the coupling between the individual SPPs results in a reduction of the modal wavelength of the SPP in comparison with that of a single graphene sheetThe work is partially supported by the Agency for Science, Technology, and Research (A*STAR) under Grant Nos. 0921450030, 0921540099, 0921540098 and the Ministry of Science and Technology of China under Grant No. 2009DFA52300 for China-Singapore collaborations. F. J. G.-V. acknowledges financial support from the European Research Council under Grant No. 290981 (PLASMONANOQUANTA

A Survey of Serious Games for Cybersecurity Education and Training

Serious games can challenge users in competitive and entertaining ways. Educators have used serious games to increase student engagement in cybersecurity education. Serious games have been developed to teach students various cybersecurity topics such as safe online behavior, threats and attacks, malware, and more. They have been used in cybersecurity training and education at different levels. Serious games have targeted different audiences such as K-12 students, undergraduate and graduate students in academic institutions, and professionals in the cybersecurity workforce. In this paper, we provide a survey of serious games used in cybersecurity education and training. We categorize these games into four types based on the topics they cover and the purposes of the games: security awareness, network and web security, cryptography, and secure software development. We provide a catalog of games available online. This survey informs educators of available resources for cybersecurity education and training using interactive games. Keywords: Serious games; Game-based Learning; Cybersecurity

High-mass Starless Clumps in the inner Galactic Plane: the Sample and Dust Properties

We report a sample of 463 high-mass starless clump (HMSC) candidates within $-60\deg<l<60\deg$ and $-1\deg<b<1\deg$. This sample has been singled out from 10861 ATLASGAL clumps. All of these sources are not associated with any known star-forming activities collected in SIMBAD and young stellar objects identified using color-based criteria. We also make sure that the HMSC candidates have neither point sources at 24 and 70 \micron~nor strong extended emission at 24 $\mu$m. Most of the identified HMSCs are infrared ($\le24$ $\mu$m) dark and some are even dark at 70 $\mu$m. Their distribution shows crowding in Galactic spiral arms and toward the Galactic center and some well-known star-forming complexes. Many HMSCs are associated with large-scale filaments. Some basic parameters were attained from column density and dust temperature maps constructed via fitting far-infrared and submillimeter continuum data to modified blackbodies. The HMSC candidates have sizes, masses, and densities similar to clumps associated with Class II methanol masers and HII regions, suggesting they will evolve into star-forming clumps. More than 90% of the HMSC candidates have densities above some proposed thresholds for forming high-mass stars. With dust temperatures and luminosity-to-mass ratios significantly lower than that for star-forming sources, the HMSC candidates are externally heated and genuinely at very early stages of high-mass star formation. Twenty sources with equivalent radius $r_\mathrm{eq}<0.15$ pc and mass surface density $\Sigma>0.08$ g cm$^{-2}$ could be possible high-mass starless cores. Further investigations toward these HMSCs would undoubtedly shed light on comprehensively understanding the birth of high-mass stars.Comment: 16 pages, 15 figures, and 5 tables. Accepted for publication in ApJS. FITS images for the far-IR to sub-mm data, H2 column density and dust temperature maps of all the HMSC candidates are available at https: //yuanjinghua.github.io/hmscs.html. Codes used for this work are publicly available from https://github.com/yuanjinghua/HMSCs_ca