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  • 11
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    CDD: NCBI's conserved domain database (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: NCBI's CDD, the Conserved Domain Database, enters its 15 th year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 12
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    Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-15
    Description: The newly developed transcription activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression. In this article, we systematically investigated the potential of these new tools in activating the stringently silenced pluripotency gene Oct4 ( Pou5f1 ) in mouse and human somatic cells. First, with a number of TALEs and sgRNAs targeting various regions in the mouse and human Oct4 promoters, we found that the most efficient TALE-VP64s bound around –120 to –80 bp, while highly effective sgRNAs targeted from –147 to –89-bp upstream of the transcription start sites to induce high activity of luciferase reporters. In addition, we observed significant transcriptional synergy when multiple TFs were applied simultaneously. Although individual TFs exhibited marginal activity to up-regulate endogenous gene expression, optimized combinations of TALE-VP64s could enhance endogenous Oct4 transcription up to 30-fold in mouse NIH3T3 cells and 20-fold in human HEK293T cells. More importantly, the enhancement of OCT4 transcription ultimately generated OCT4 proteins. Furthermore, examination of different epigenetic modifiers showed that histone acetyltransferase p300 could enhance both TALE-VP64 and sgRNA/dCas9-VP64 induced transcription of endogenous OCT4 . Taken together, our study suggested that engineered TALE-TF and dCas9-TF are useful tools for modulating gene expression in mammalian cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 13
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    New high-spin structure and possible chirality in $^{109}\mathrm{In}$ (2018)
    American Physical Society (APS)
    Details
    Publication Date: 2018-07-06
    Description: Author(s): M. Wang, Y. Y. Wang, L. H. Zhu, B. H. Sun, G. L. Zhang, L. C. He, W. W. Qu, F. Wang, T. F. Wang, Y. Y. Chen, C. Xiong, J. Zhang, J. M. Zhang, Y. Zheng, C. Y. He, G. S. Li, J. L. Wang, X. G. Wu, S. H. Yao, C. B. Li, H. W. Li, S. P. Hu, and J. J. Liu The high-spin structure of In 109 has been investigated with the Mo 100 ( N 14 , 5 n ) In 109 reaction at a beam energy of 78 MeV using the in-beam γ spectroscopic method. The level scheme of In 109 has been modified considerably and extended by 46 new γ rays to the highest excited state at 8.980 MeV and J π = ( 4... [Phys. Rev. C 98, 014304] Published Thu Jul 05, 2018
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 14
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    Metal-insulator transitions in epitaxial LaVO_{3} and LaTiO_{3} films (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-08-02
    Description: Author(s): C. He, T. D. Sanders, M. T. Gray, F. J. Wong, V. V. Mehta, and Y. Suzuki We have demonstrated that epitaxial films of LaVO 3 and LaTiO 3 can exhibit metallicity though their bulk counterparts are Mott insulators. When LaTiO 3 films are compressively strained on SrTiO 3 substrates, we observe metallicity that is attributed largely to epitaxial strain-induced electronic struct... [Phys. Rev. B 86, 081401] Published Wed Aug 01, 2012
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 15
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    Retraction of: Evolutionary thinking in restoration under global environmental changes (2015)
    Oxford University Press
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    Publication Date: 2015-07-24
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 16
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    The Genotype–Phenotype Relationships in the Light of Natural Selection (2018)
    Oxford University Press
    Details
    Publication Date: 2018-03-06
    Description: Although any genotype–phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analyzing ∼500 yeast quantitative traits, we reveal a basic “supervisor–worker” gene architecture underlying a trait. Supervisors are often identified by “perturbational” approaches (such as gene deletion), whereas workers, which usually show small and statistically insignificant deletion effects, are tracked primarily by “observational” approaches that examine the correlation between gene activity and trait value across a number of conditions. Accordingly, supervisors provide most of the genetic understandings of the trait whereas workers provide rich mechanistic understandings. Further analyses suggest that most observed supervisor–worker interactions may evolve largely neutrally, resulting in pervasive between-worker epistasis that suppresses the tractability of workers. In contrast, a fraction of supervisors are recruited/maintained by natural selection to build worker co-expression, boosting the tractability of workers. Thus, by revealing a supervisor–worker gene architecture underlying complex traits, the opposite roles of natural selection versus neutral drift in shaping the gene architecture, and the complementary strengths of the perturbational and observational research strategies in characterizing the gene architecture, this study may lay a new conceptual foundation for understanding the molecular basis of complex traits.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 17
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    MICC: an R package for identifying chromatin interactions from ChIA-PET data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-21
    Description: : ChIA-PET is rapidly emerging as an important experimental approach to detect chromatin long-range interactions at high resolution. Here, we present M odel based I nteraction C alling from C hIA-PET data (MICC), an easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data. By applying a Bayesian mixture model to systematically remove random ligation and random collision noise, MICC could identify chromatin interactions with a significantly higher sensitivity than existing methods at the same false discovery rate. Availability and implementation: http://bioinfo.au.tsinghua.edu.cn/member/xwwang/MICCusage Contact: michael.zhang@utdallas.edu or xwwang@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 18
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    Bioreactors and in situ product recovery techniques for acetone-butanol-ethanol fermentation (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-02
    Description: The microbial fermentation process is one of the sustainable and environment-friendly ways to produce 1-butanol and other bio-based chemicals. The success of the fermentation process greatly relies on the choice of bioreactors and the separation methods. In this review, the history and the performance of bioreactors for the acetone–butanol–ethanol (ABE) fermentation is discussed. The subject is then focused on in situ product recovery (ISPR) techniques, particularly for the integrated extraction-gas stripping. The usefulness of this promising hybrid ISPR device is acknowledged by its incorporation with batch, fed-batch and continuous processes to improve the performance of ABE fermentation.
    Keywords: Biotechnology & Synthetic Biology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 19
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    Fertilization regulates the response of wheat yield to interannual temperature variation in North China (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-17
    Description: Aims Understanding the effect of long-term fertilization on the sensitivity of grain yield to temperature changes is critical for accurately assessing the impact of global warming on crop production. In this study, we aim to assess the impacts of temperature changes on grain yields of winter wheat ( Triticum aestivum L.) under different fertilization treatments in a long-term manipulative experiment in North China. Methods We measured grain yields of winter wheat under four fertilization treatments at the Yucheng Comprehensive Experimental Station each year from 1993 to 2012. We also measured air temperature at 0200, 0800, 1400 and 2000h each day since 1 January 1980. We then used the first-difference method and simple linear regression models to examine the relationship of crop yield changes to mean air temperature, mean daytime and nighttime air temperature in crop growing seasons. Important Findings We found that increases in mean daily temperature, mean daytime temperature and mean nighttime temperature each had a positive impact on the grain yield of winter wheat. Grain yield increased by 16.7–85.6% for winter wheat in response to a 1°C increase in growing season mean daily temperature. Winter wheat yield was more sensitive to variations of nighttime temperature than to that of daytime temperature. The observed temperature impacts also varied across different fertilization treatments. Balanced fertilization significantly enhanced grain yields for winter wheat under a warming climate. Wheat plots treated with nitrogen and phosphorous balanced fertilization (NPK- and NP-treated plots) were more responsive to temperature changes than those without. This report provides direct evidence of how temperature change impacts grain yields under different fertilization treatments, which is useful for crop management in a changing global climate.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 20
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    Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-02
    Description: Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N 6 -methyladenine (6mA), 5-methylcytosine (5mC) and N 4 -methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor , in which 4mC-related restriction is a major barrier to DNA transformation from other species. In combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.
    Keywords: Nucleic acid modification, Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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