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aria-live="polite">Scholarly Works (46 results)</h2></header><div class="c-sortpagination"><div class="c-sort"><div class="o-input__droplist1"><label for="c-sort1">Sort By:</label><select name="sort" id="c-sort1" form="facetForm"><option selected="" value="rel">Relevance</option><option value="a-title">A-Z By Title</option><option value="z-title">Z-A By Title</option><option value="a-author">A-Z By Author</option><option value="z-author">Z-A By Author</option><option value="asc">Date Ascending</option><option value="desc">Date Descending</option></select></div><div class="o-input__droplist1 c-sort__page-input"><label for="c-sort2">Show:</label><select name="rows" id="c-sort2" form="facetForm"><option selected="" value="10">10</option><option value="20">20</option><option value="30">30</option><option value="40">40</option><option value="50">50</option></select></div></div><input type="hidden" name="start" form="facetForm" value="0"/><nav class="c-pagination"><ul><li><a href="" aria-label="you are on result set 1" class="c-pagination__item--current">1</a></li><li><a href="" aria-label="go to result set 2" class="c-pagination__item">2</a></li><li><a href="" aria-label="go to result set 3" class="c-pagination__item">3</a></li><li><a href="" aria-label="go to result set 4" class="c-pagination__item">4</a></li><li><a href="" aria-label="go to result set 5" class="c-pagination__item">5</a></li></ul></nav></div><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/5mx5597j"><div class="c-clientmarkup">Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/lbnl">Lawrence Berkeley National Laboratory</a> (2011)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Some ionic liquids (ILs) have been shown to be very effective solvents for biomass pretreatment. It is known that some ILs can have a strong inhibitory effect on fungal cellulases, making the digestion of cellulose inefficient in the presence of ILs. The identification of IL-tolerant enzymes that could be produced as a cellulase cocktail would reduce the costs and water use requirements of the IL pretreatment process. Due to their adaptation to high salinity environments, halophilic enzymes are hypothesized to be good candidates for screening and identifying IL-resistant cellulases. Using a genome-based approach, we have identified and characterized a halophilic cellulase (Hu-CBH1) from the halophilic archaeon, Halorhabdus utahensis. Hu-CBH1 is present in a gene cluster containing multiple putative cellulolytic enzymes. Sequence and theoretical structure analysis indicate that Hu-CBH1 is highly enriched with negatively charged acidic amino acids on the surface, which may form a solvation shell that may stabilize the enzyme, through interaction with salt ions and/or water molecules. Hu-CBH1 is a heat tolerant haloalkaliphilic cellulase and is active in salt concentrations up to 5 M NaCl. In high salt buffer, Hu-CBH1 can tolerate alkali (pH 11.5) conditions and, more importantly, is tolerant to high levels (20percent w/w) of ILs, including 1-allyl-3-methylimidazolium chloride ([Amim]Cl). Interestingly, the tolerances to heat, alkali and ILs are found to be salt-dependent, suggesting that the enzyme is stabilized by the presence of salt. Our results indicate that halophilic enzymes are good candidates for the screening of IL-tolerant cellulolytic enzymes.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/5mx5597j"><img src="/cms-assets/4b8796f73b9dd99aeb7c5192ce98235bb6d550335a9cb9b4110e04d17e2dda62" alt="Cover page: Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/3cn0b88b"><div class="c-clientmarkup">Identification of ioncic liquids tolerant cellulases for biomass processing</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/lbnl_rw">LBL Publications</a> (2012)</div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/3cn0b88b"><img src="/cms-assets/45a9f3503cd0e5cdac64e493a1421d2065d5d1a410418a193fa51829a2923c1f" alt="Cover page: Identification of ioncic liquids tolerant cellulases for biomass processing"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/6032p5g4"><div class="c-clientmarkup">Barcode labeling of short reads for detection of large scale genomic variations</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/lbnl_rw">LBL Publications</a> (2012)</div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/6032p5g4"><img src="/cms-assets/a8929f70b9ca088d9caafd2e66314fcd4082fcedbaf3941a0c33bd2ef1dc2143" alt="Cover page: Barcode labeling of short reads for detection of large scale genomic variations"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/2cv2f3nz"><div class="c-clientmarkup">Positional effects on efficiency of CRISPR/Cas9-based transcriptional activation in rice plants</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AGong%2C%20Xiaoyu">Gong, Xiaoyu</a>; </li><li><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3AXing%2C%20Jialing">Xing, Jialing</a>; </li><li><a href="/search/?q=author%3AWang%2C%20Rongchen">Wang, Rongchen</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AZhao%2C%20Yunde">Zhao, Yunde</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucsd_postprints">UC San Diego Previously Published Works</a> (2020)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">The nuclease-dead Cas9 (dCas9) has been reprogrammed for transcriptional activation by fusing dCas9 to a transcriptional activation domain. In the presence of a guide RNA (gRNA), the dCas9 fusions specifically bind to regions of a promoter to activate transcription. Significant amount of effort has been directed toward the identification and optimization of the fusions of dCas9-activation domain, but very little is known about the impact of gRNA target positions within a promoter in plants on transcriptional activation efficiency. The dCas9-6TAL-VP128 system (dCas9-TV) has been optimized to activate transcription in plants. Here we use the dCas9-TV to activate transcription of <i>OsWOX11</i> and <i>OsYUC1</i>, two genes that cause dramatic developmental phenotypes when overexpressed. We designed a series of gRNAs targeting the promoters of the two genes. We show that gRNAs that target regions within 350 bp upstream of the transcription start site were most effective in transcriptional activation. Moreover, we show that using two gRNAs that simultaneously target two discrete sites in a promoter can further enhance transcription. This work provides guidelines for designed transcriptional activation through CRISPR/dCas9 systems.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/2cv2f3nz"><img src="/cms-assets/c5c74b6fd5b6d1761a4a0c0bf71c066b9506d0a7e82085014f7fcefe672ba48f" alt="Cover page: Positional effects on efficiency of CRISPR/Cas9-based transcriptional activation in rice plants"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/5hs1j1dk"><div class="c-clientmarkup">Discovery of substrate-targeted enzymes for the degradation of biomass by Metatranscriptomics</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AHess%2C%20Matthias">Hess, Matthias</a>; </li><li><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3ATringe%2C%20Susanna">Tringe, Susanna</a>; </li><li><a href="/search/?q=author%3AMackie%2C%20R.">Mackie, R.</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ARubin%2C%20Eddy">Rubin, Eddy</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/lbnl_rw">LBL Publications</a> (2009)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Current bioethanol production from lignocellulosic biomass is a relatively inefficient process requiring energy-intensive chemical and physical pretreatments (Fig.1). The identification of robust cellulolytic enzymes (e.g., cellulases and hemicellulases) from lignocellulolytic microbial communities is a necessity to achieve the ambitious goal to replace 30percent of the national petroleum based gasoline with bioethanol by 2030.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/5hs1j1dk"><img src="/cms-assets/09a056c6d4fae8c0e0eb239ed147c9ef7318a2d44c6f70000179c561f4d9533a" alt="Cover page: Discovery of substrate-targeted enzymes for the degradation of biomass by Metatranscriptomics"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/62r679g0"><div class="c-clientmarkup">Non-canonical and developmental roles of the TCA cycle in plants.</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3APeng%2C%20Jesus">Peng, Jesus</a>; </li><li><a href="/search/?q=author%3AKlair%2C%20Amman">Klair, Amman</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ADickinson%2C%20Alexandra">Dickinson, Alexandra</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucsd_postprints">UC San Diego Previously Published Works</a> (2023)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/62r679g0"><img src="/cms-assets/954237c07c6e330fa3f16ed1bd635492721ed6f5651f01265fe0f019e4e703b5" alt="Cover page: Non-canonical and developmental roles of the TCA cycle in plants."/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/26d4f1w8"><div class="c-clientmarkup">A reporter for noninvasively monitoring gene expression and plant transformation</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AHe%2C%20Yubing">He, Yubing</a>; </li><li><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3ASun%2C%20Hui">Sun, Hui</a>; </li><li><a href="/search/?q=author%3AZhan%2C%20Huadong">Zhan, Huadong</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AZhao%2C%20Yunde">Zhao, Yunde</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucsd_postprints">UC San Diego Previously Published Works</a> (2020)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">Reporters have been widely used to visualize gene expression, protein localization, and other cellular activities, but the commonly used reporters require special equipment, expensive chemicals, or invasive treatments. Here, we construct a new reporter <i>RUBY</i> that converts tyrosine to vividly red betalain, which is clearly visible to naked eyes without the need of using special equipment or chemical treatments. We show that <i>RUBY</i> can be used to noninvasively monitor gene expression in plants. Furthermore, we show that <i>RUBY</i> is an effective selection marker for transformation events in both rice and Arabidopsis. The new reporter will be especially useful for monitoring cellular activities in large crop plants such as a fruit tree under field conditions and for observing transformation and gene expression in tissue culture under sterile conditions.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/26d4f1w8"><img src="/cms-assets/c848af5f2212f2fa6fd4f244187c35609eaf922ca99db26b87663a9d12ce19c4" alt="Cover page: A reporter for noninvasively monitoring gene expression and plant transformation"/></a><a href="https://creativecommons.org/licenses/by/4.0/" class="c-scholworks__license"><img class="c-lazyimage" data-src="/images/cc-by-small.svg" alt="Creative Commons 'BY' version 4.0 license"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/6rc467bd"><div class="c-clientmarkup">Trust antecedents, trust and online microsourcing adoption: An empirical study from the resource perspective</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ALu%2C%20Baozhou">Lu, Baozhou</a>; </li><li><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3AWang%2C%20Liangyan">Wang, Liangyan</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AKeller%2C%20L%20Robin">Keller, L Robin</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/uci_postprints">UC Irvine Previously Published Works</a> (2016)</div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/6rc467bd"><img src="/cms-assets/7a90da1046e75f9d88f7ea8a0cabd9d1a47d6980ace1f5f11c76c15415f60f1e" alt="Cover page: Trust antecedents, trust and online microsourcing adoption: An empirical study from the resource perspective"/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/30w539v2"><div class="c-clientmarkup">Production of Guide RNAs in vitro and in vivo for CRISPR Using Ribozymes and RNA Polymerase II Promoters.</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3AGao%2C%20Yangbin">Gao, Yangbin</a>; </li><li><a href="/search/?q=author%3AWang%2C%20Rongchen">Wang, Rongchen</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AZhao%2C%20Yunde">Zhao, Yunde</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucsd_postprints">UC San Diego Previously Published Works</a> (2017)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">CRISPR/Cas9-mediated genome editing relies on a guide RNA (gRNA) molecule to generate sequence-specific DNA cleavage, which is a prerequisite for gene editing. Here we establish a method that enables production of gRNAs from any promoters, in any organisms, and in vitro (Gao and Zhao, 2014). This method also makes it feasible to conduct tissue/cell specific gene editing.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/30w539v2"><img src="/cms-assets/ef6816444b99939b55b153465b9f5816df5c2b4662d94b6858df7ca2a9692d51" alt="Cover page: Production of Guide RNAs in vitro and in vivo for CRISPR Using Ribozymes and RNA Polymerase II Promoters."/></a></div></section><section class="c-scholworks"><div class="c-scholworks__main-column"><ul class="c-scholworks__tag-list"><li class="c-scholworks__tag-article">Article</li><li class="c-scholworks__tag-peer">Peer Reviewed</li></ul><div><h3 class="c-scholworks__heading"><a href="/uc/item/1222z3x9"><div class="c-clientmarkup">The YUCCA-Auxin-WOX11 Module Controls Crown Root Development in Rice</div></a></h3></div><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhang%2C%20Tao">Zhang, Tao</a>; </li><li><a href="/search/?q=author%3ALi%2C%20Ruonan">Li, Ruonan</a>; </li><li><a href="/search/?q=author%3AXing%2C%20Jialing">Xing, Jialing</a>; </li><li><a href="/search/?q=author%3AYan%2C%20Lang">Yan, Lang</a>; </li><li><a href="/search/?q=author%3AWang%2C%20Rongchen">Wang, Rongchen</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AZhao%2C%20Yunde">Zhao, Yunde</a> </li></ul></div><div class="c-scholworks__publication"><a href="/uc/ucsd_postprints">UC San Diego Previously Published Works</a> (2018)</div><div class="c-scholworks__abstract"><div class="c-clientmarkup">A well-developed root system in rice and other crops can ensure plants to efficiently absorb nutrients and water. Auxin is a key regulator for various aspect of root development, but the detailed molecular mechanisms by which auxin controls crown root development in rice are not understood. We show that overexpression of a YUC gene, which encodes the rate-limiting enzyme in auxin biosynthesis, causes massive proliferation of crown roots. On the other hand, we find that disruption of TAA1, which functions upstream of YUC genes, greatly reduces crown root development. We find that YUC overexpression-induced crown root proliferation requires the presence of the transcription factor WOX11. Moreover, the crown rootless phenotype of taa1 mutants was partially rescued by overexpression of WOX11. Furthermore, we show that WOX11 expression is induced in OsYUC1 overexpression lines, but is repressed in the taa1 mutants. Our results indicate that auxin synthesized by the TAA/YUC pathway is necessary and sufficient for crown root development in rice. Auxin activates WOX11 transcription, which subsequently drives crown root initiation and development, establishing the YUC-Auxin-WOX11 module for crown root development in rice.</div></div><div class="c-scholworks__media"><ul class="c-medialist"></ul></div></div><div class="c-scholworks__ancillary"><a class="c-scholworks__thumbnail" href="/uc/item/1222z3x9"><img src="/cms-assets/0c4b3348b6981fe9be0947fb35728e6979ca2cfebcd7a400c6e114a35c77aecb" alt="Cover page: The YUCCA-Auxin-WOX11 Module Controls Crown Root Development in Rice"/></a><a href="https://creativecommons.org/licenses/by/4.0/" class="c-scholworks__license"><img class="c-lazyimage" data-src="/images/cc-by-small.svg" alt="Creative Commons 'BY' version 4.0 license"/></a></div></section><nav class="c-pagination"><ul><li><a href="" aria-label="you are on result set 1" class="c-pagination__item--current">1</a></li><li><a href="" aria-label="go to result set 2" class="c-pagination__item">2</a></li><li><a href="" aria-label="go to result set 3" class="c-pagination__item">3</a></li><li><a href="" aria-label="go to result set 4" class="c-pagination__item">4</a></li><li><a href="" aria-label="go to result set 5" class="c-pagination__item">5</a></li></ul></nav></section></main></form></div><div><div class="c-toplink"><a href="javascript:window.scrollTo(0, 0)">Top</a></div><footer class="c-footer"><nav class="c-footer__nav"><ul><li><a href="/">Home</a></li><li><a href="/aboutEschol">About eScholarship</a></li><li><a href="/campuses">Campus Sites</a></li><li><a href="/ucoapolicies">UC Open Access Policy</a></li><li><a href="/publishing">eScholarship Publishing</a></li><li><a href="https://www.cdlib.org/about/accessibility.html">Accessibility</a></li><li><a href="/privacypolicy">Privacy Statement</a></li><li><a href="/policies">Site Policies</a></li><li><a href="/terms">Terms of Use</a></li><li><a href="/login"><strong>Admin Login</strong></a></li><li><a href="https://help.escholarship.org"><strong>Help</strong></a></li></ul></nav><div class="c-footer__logo"><a href="/"><img class="c-lazyimage" data-src="/images/logo_footer-eschol.svg" alt="eScholarship, University of California"/></a></div><div class="c-footer__copyright">Powered by the<br/><a href="http://www.cdlib.org">California Digital Library</a><br/>Copyright 漏 2017<br/>The Regents of the University of California</div></footer></div></div></div></div> <script src="/js/vendors~app-bundle-2aefc956e545366a5d4e.js"></script> <script src="/js/app-bundle-4477d7630fb8c6f70662.js"></script> </body> </html>