The Bose–Hubbard model with squeezed dissipation

The stationary properties of the Bose–Hubbard model under squeezed dissipation are investigated. The dissipative model does not possess aU (1) symmetry but conserves parity. We find that 〈a j 〉 = 0 always holds, so no symmetry breaking occurs. Without the onsite repulsion, the linear case is known to be critical. At the critical point the system freezes to an EPR state with infinite two mode entanglement. We show here that the correlations are rapidly destroyed whenever the repulsion is switched on. As we increase the latter, the system approaches a thermal state with an effective temperature defined in terms of the squeezing parameter in the dissipators. We characterize this transition by means of a Gutzwiller ansatz and the Gaussian Hartree–Fock–Bogoliubov approximation

Architecting new diffraction-resistant light structures and their possible applications in atom guidance

CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOIn this work we extend the so called frozen wave method in order to obtain new diffraction resistant light structures that can be shaped on demand, with possible applications in atom guidance. The resulting beams and the corresponding optical dipole potentials exhibit a strong resistance to diffraction effects and their longitudinal and transverse intensity patterns can be chosen a priori. Besides the theoretical development, we also present the experimental confirmation of our approach; specifically, by generating three different beam profiles using a spatial light modulator that is addressed by a computer-generated hologram. In addition to its many potential applications in atom guiding, the method developed here can also lead to many new developments in optics and photonics in general. (C) 2016 Optical Society of AmericaIn this work we extend the so called frozen wave method in order to obtain new diffraction resistant light structures that can be shaped on demand, with possible applications in atom guidance. The resulting beams and the corresponding optical dipole potentials exhibit a strong resistance to diffraction effects and their longitudinal and transverse intensity patterns can be chosen a priori. Besides the theoretical development, we also present the experimental confirmation of our approach, specifically, by generating three different beam profiles using a spatial light modulator that is addressed by a computer-generated hologram. In addition to its many potential applications in atom guiding, the method developed here can also lead to many new developments in optics and photonics in general.24222540325408CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO141977/2013-2, 312376/2013-82015/26444-

ATTED-II provides coexpressed gene networks for Arabidopsis

ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein–protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis

PlantTFDB: a comprehensive plant transcription factor database

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26 402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis

Red wine consumption increases antioxidant status and decreases oxidative stress in the circulation of both young and old humans

Background: Red wine contains a naturally rich source of antioxidants, which may protect the body from oxidative stress, a determinant of age-related disease. The current study set out to determine the in vivo effects of moderate red wine consumption on antioxidant status and oxidative stress in the circulation.Methods: 20 young (18&ndash;30 yrs) and 20 older (&ge; 50 yrs) volunteers were recruited. Each age group was randomly divided into treatment subjects who consumed 400 mL/day of red wine for two weeks, or control subjects who abstained from alcohol for two weeks, after which they crossed over into the other group. Blood samples were collected before and after red wine consumption and were used for analysis of whole blood glutathione (GSH), plasma malondialdehyde (MDA) and serum total antioxidant status.Results: Results from this study show consumption of red wine induced significant increases in plasma total antioxidant status (P &lt; 0.03), and significant decreases in plasma MDA (P &lt; 0.001) and GSH (P &lt; 0.004) in young and old subjects. The results show that the consumption of 400 mL/day of red wine for two weeks, significantly increases antioxidant status and decreases oxidative stress in the circulation.Conclusion: It may be implied from this data that red wine provides general oxidative protection and to lipid systems in circulation via the increase in antioxidant status.<br /

Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria

Draft genome sequence of Wickerhamomyces anomalus LBCM1105, isolated from cachaça fermentation

Wickerhamomyces anomalus LBCM1105 is a yeast isolated from cachaça distillery fermentation vats, notable for exceptional glycerol consumption ability. We report its draft genome with 20.5x in-depth coverage and around 90% extension and completeness. It harbors the sequences of proteins involved in glycerol transport and metabolism.The authors gratefully acknowledge Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE) and the Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) for support with the sequencing of LBCM1105. This work was supported by CAPES/Brazil (PNPD 2755/2011; PCF-PVE 021/2012), by CNPq (Brazil), processes 304815/2012 (research grant) and 305135/2015-5, and by AUXPE-PVES 1801/2012 (Process 23038.015294/2016-18) from Brazilian Government and by UFOP. C.L. is supported by the strategic program UID/BIA/04050/2013 [POCI-01-0145-FEDER-007569] funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 - Programa Operacional de Competitividade e Internacionalizacao (POCI). DMRP is a fellow from the CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico) - Brazil (310080/2018-5)

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

<div><h3>Background</h3><p>The development of rice (<em>Oryza sativa</em>) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement.</p> <h3>Principal Findings</h3><p>Our analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of <em>Arabidopsis</em> seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant <em>cultivar</em> Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development.</p> <h3>Conclusions</h3><p>These results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.</p> </div

Soybean Trihelix Transcription Factors GmGT-2A and GmGT-2B Improve Plant Tolerance to Abiotic Stresses in Transgenic Arabidopsis

BACKGROUND:Trihelix transcription factors play important roles in light-regulated responses and other developmental processes. However, their functions in abiotic stress response are largely unclear. In this study, we identified two trihelix transcription factor genes GmGT-2A and GmGT-2B from soybean and further characterized their roles in abiotic stress tolerance. FINDINGS:Both genes can be induced by various abiotic stresses, and the encoded proteins were localized in nuclear region. In yeast assay, GmGT-2B but not GmGT-2A exhibits ability of transcriptional activation and dimerization. The N-terminal peptide of 153 residues in GmGT-2B was the minimal activation domain and the middle region between the two trihelices mediated the dimerization of the GmGT-2B. Transactivation activity of the GmGT-2B was also confirmed in plant cells. DNA binding analysis using yeast one-hybrid assay revealed that GmGT-2A could bind to GT-1bx, GT-2bx, mGT-2bx-2 and D1 whereas GmGT-2B could bind to the latter three elements. Overexpression of the GmGT-2A and GmGT-2B improved plant tolerance to salt, freezing and drought stress in transgenic Arabidopsis plants. Moreover, GmGT-2B-transgenic plants had more green seedlings compared to Col-0 under ABA treatment. Many stress-responsive genes were altered in GmGT-2A- and GmGT-2B-transgenic plants. CONCLUSION:These results indicate that GmGT-2A and GmGT-2B confer stress tolerance through regulation of a common set of genes and specific sets of genes. GmGT-2B also affects ABA sensitivity