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Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement

Plant Phenomics 2020年第1期2卷 118-121页

作者： Ian R.Braun Colleen F.Yanarella carolyn j.lawrence-Dill Interdepartmental Bioinformatics and Computational Biology Iowa State UniversityAmesIA 50011USA Department of Genetics Development and Cell BiologyIowa State UniversityAmesIA 50011USA Department of Agronomy Iowa State UniversityAmesIA 50011USA

Many newly observed phenotypes are first described,then experimentally *** language-based descriptions appear in both the literature and in community *** standardize phenotypic descriptions and enable simple data aggregation and analysis,controlled vocabularies and specific data architectures have been *** simplified descriptions have several advantages over natural language:they can be rigorously defined for a particular context or problem,they can be assigned and interpreted programmatically,and they can be organized in a way that allows for semantic reasoning(inference of implicit facts).Because researchers generally report phenotypes in the literature using natural language,curators have been translating phenotypic descriptions into controlled vocabularies for decades to make the information ***,this methodology is highly dependent on human curation,which does not scale to the scope of all publications available across all of plant ***,researchers in other domains have been working to enable computation on natural *** has resulted in new,automated methods for computing on language that are now available,with early analyses showing great *** language processing(NLP)coupled with machine learning(ML)allows for the use of unstructured language for direct analysis of phenotypic ***,we have found that these automated methods can be used to create data structures that perform as well or better than those generated by human curators on tasks such as predicting gene function and biochemical pathway ***,we describe current and ongoing efforts to provide tools for the plant phenomics community to explore novel predictions that can be generated using these *** also describe how these methods could be used along with mobile speech-to-text tools to collect and analyze in-field spoken phenotypic descriptions for association genetics and breedin

关键词： stores translating enable

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G-Quadruplex(G4) Motifs in the Maize(Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status,Hypoxia,Low Sugar,and Nutrient Deprivation

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journal of Genetics and Genomics 2014年第12期41卷 627-647页

作者： Carson M.Andorf Mykhailo Kopylov Drena Dobbs Karen E.Koch M.Elizabeth Stroupe carolyn j.lawrence Hank W.Bass USDA-ARS Corn Insects and Crop Genetics Research Unit Iowa State University Department of Computer Science Iowa State University Institute of Molecular Biophysics Florida State University Department of Genetics Development and Cell BiologyIowa State University Plant Molecular and Cellular Biology Program Horticultural Sciences DepartmentGenetics InstituteUniversity of Florida Department of Biological Science Florida State University Department of Agronomy Iowa State University

The G-quadruplex （G4） elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This （34 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationaily identified 149,988 non-telomeric G4 motifs in maize （Zea mays L., B73 AGPv2）, 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5~ UTR and the other at the 5~ end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia （group VII ERFs）, oxidative stress （D j-1/GATasel）, and energy status （AMPK/ SnRK） pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.

关键词： Maize G-quadruplex G4 Hypoxia Sucrose synthase

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Projective Hilbert modules and sequential approximations

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Science China Mathematics 2025年第1期 137-168页

作者： lawrence G.Brown Huaxin Lin Department of Mathematics Purdue University Department of Mathematics East China Normal University Department of Mathematics University of Oregon Shanghai Institute for Mathematics and Interdisciplinary Sciences

We show that when A is a separable C*-algebra,every countably generated Hilbert A-module is projective（with bounded module maps as morphisms）.We also study the approximate extensions of bounded module *** the case where A is a σ-unital simple C*-algebra with strict comparison,and every strictly positive lower semicontinuous affine function on quasitraces can be realized as the rank of an element in the Cuntz semigroup,we show that the Cuntz semigroup is equivalent to unitarily equivalent classes of countably generated Hilbert A-modules if and only if A has stable rank one.

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Influence of supraphysiological cortisol manipulation on predator avoidance behaviors and physiological responses to a predation threat in a wild marine teleost fish

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Integrative Zoology 2018年第2期13卷 206-218页

作者： Michael j.lawrence Erika j.ELIASON jacob W.BROWNSCOMBE Kathleen M.GILMOUR john W.MANDELMAN Lee F.G.GUTOWSKY Steven j.COOKE Fish Ecology and Conservation Physiology Laboratory Department of BiologyCarleton UniversityOttawaOntarioCanada Department of Ecology Evolution&Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA Department of Biology University of OttawaOttawaOntarioCanada School for the Environment University of New EnglandBiddefordMaineUSA john H.Prescott Marine Laboratory New England AquariumBostonMassachusettsUSA

The stress axis in teleost fish attempts to maintain internal homeostasis in the face of allostatic ***,stress axis induction has been associated with a higher predation rate in *** date,the physiological and behavioral factors associated with this outcome are poorly *** purpose of the present study was to investigate the impact of experimental cortisol elevation on anti-predator behavior and physiological responses to predator *** hypothesized that semi-chronic cortisol elevation would increase susceptibility to predation by increasing stress-induced risk-taking *** test this hypothesis,schoolmaster snapper were given cocoa butter implants without cortisol(sham)or with cortisol(50 mg/kg body weight)and tethered to *** were exposed to either a lemon shark or control conditions for *** use and activity were recorded throughout and fish were terminally sampled for *** implantation,relative to shams,resulted in higher blood glucose and plasma cortisol concentrations with a lower plasma lactate *** exposure,relative to controls,elicited higher blood glucose and lactate concentrations but had no effect on plasma cortisol *** interactions were detected between shark exposure and cortisol treatment for any physiological *** metrics,including shelter use and activity,were unaffected by either cortisol implantation or shark *** responses to cortisol implantation likely resulted from enhanced gluconeogenic activity,whereas alterations under predator exposure may have been the product of catecholamine *** work should address context-specific influences of stress in mediating behavioral responses to predation.

关键词： homeostatic overload lemon shark predation refuging stress axis teleost physiology

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Effect of histone deacetylase inhibitor sodium butyrate on behavioral sensitization to a single morphine exposure in C57BL/6 mice

Effect of histone deacetylase inhibitor sodium butyrate on b...

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中国药理学会第十次全国学术会议

作者： Andrew j.lawrence Howard Florey Institute and Centre for Neuroscience ParkvilleVictoria 3010Australia

Background and purpose More recently behavioral sensitization induced by a single morphine exposure has been considered as behavioral plasticity associated with drug *** histone acetylation mediating chromatin remodeling plays a critical role in the mechanisms underlying some types of behavioral ***-fore, the present study was designed to investigate whether the HDAC inhibitor SB would alter the establishing processes of behavioral sensitization to a single injection of *** approach Appling a single morphine-induced behavioral sensitization model in male C57BL/6 mice,we chose in this study to multiply treat mice with SB in the phases of induction,transfer,and expression of behavioral sensitization and to measure the distance of horizonal locomotor activity.

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Protein synthesis inhibitors disrupt the induction of behavioral sensitization to a single morphine exposure and regulate Hsp70 expression in the mouse nucleus accumbens

Protein synthesis inhibitors disrupt the induction of behavi...

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中国药理学会第十次全国学术会议

作者： Andrew j.lawrence Howard Florey Institute and Centre for Neuroscience ParkvilleVictoria 3010 Australia

De novo protein synthesis has been implicated as necessary for long-lasting changes in neuronal *** sensitization to a single exposure to addictive drugs is a form of neuroplasticity,but little is known about the impo...

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Rolipram,a selective phosphodiesterase-4 inhibitor,decreases ethanol seeking and consumption in alcohol-preferring Fawn Hooded rats

Rolipram,a selective phosphodiesterase-4 inhibitor,decreases...

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中国神经科学学会第九届全国学术会议暨第五次会员代表大会

作者： Andrew j.lawrence Howard Florey Institute and Centre for Neuroscience ParkvilleVictoria 3010Australia

＜正＞Alcohol dependence is a complex psychiatric disorder demanding development of novel pharmacotherapy. Since the cyclic AMP（cAMP） signaling cascade has been implicated in mediating the behavioral response to alcohol, it would be of interest to determine whether phosphodiesterase-4（PDE4）,an enzyme that selectively hydrolyzes intracellular cAMP,is involved in the regulation of alcohol ***,the selective PDE4 inhibitor rolipram was used to measure its anti-drinking properties in alcohol-preferring Fawn-Hooded（FH/Wjd） *** showed that acute administration of rolipram（0.05,0.1,and 0.2 mg/kg） selectively and dose-dependently reduced 5%ethanol, but not 10%sucrose,operant self-administration;it also decreased voluntary 5%ethanol intake,but not water consumption,for the initial 30 min in rats showing high stable preference for *** course assessment revealed the significant anti-drinking effect of rolipram（0.1,0.2 mg/kg） lasted for 5 h in both continuous- and intermittentaccess to 5%or 10%***,chronic rolipram treatment decreased 5%ethanol consumption and preference during the drug treatment *** effect lasted even after withdrawal of drug *** locomotor activity was inhibited by rolipram at 0.1 and 0.2 mg/kg,the effect was present only in the initial about 20 min,which did not seem to alter long-term ethanol *** data suggest that PDE4 may play a promising role in ethanol drinking and dependent *** may be a potential treatment target for further development of anti-drinking drugs.

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区域经济可持续发展的路径优化研究

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经济纵横 2011年第7期 75-77页

作者：孙卫东 William j.lawrence 江苏大学财经学院江苏镇江212013 纽约理工大学管理学院美国纽约10023

区域经济可持续发展是以"代内公平"和"代际公平"为前提、以区域总体经济效益最大化为目标的路径优化问题。通过对一个地区经济发展路径的优化可发现:在该地区经济发展的前期和后期,宜分别采用较低和较高的经济可持续性发展标准;而通过... 详细信息

区域经济可持续发展是以"代内公平"和"代际公平"为前提、以区域总体经济效益最大化为目标的路径优化问题。通过对一个地区经济发展路径的优化可发现:在该地区经济发展的前期和后期,宜分别采用较低和较高的经济可持续性发展标准;而通过对一个区域内经济发展路径的优化发现:在区域经济发展的初期和中期,应集中资金分别投向经济发展水平较高和较低的地区。

关键词：区域经济可持续发展路径优化

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缓解中美贸易摩擦的战略分析——基于中国产业集群的视角

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科技进步与对策 2010年第2期27卷 97-100页

作者：孙卫东 William j.lawrence 江苏大学财经学院江苏镇江212013 纽约理工大学管理学院美国纽约10023

近年来,中国凭借产业集群获得了巨大的国际竞争力。中国产业集群的特点是产量大、劳动密集和生产成本低,其明显缺点是生产效率低、污染严重、附加值低。这些缺点为国外愈演愈烈的对中国反倾销及其它指责提供了口实。中美有各自的优势,... 详细信息

近年来,中国凭借产业集群获得了巨大的国际竞争力。中国产业集群的特点是产量大、劳动密集和生产成本低,其明显缺点是生产效率低、污染严重、附加值低。这些缺点为国外愈演愈烈的对中国反倾销及其它指责提供了口实。中美有各自的优势,两者的合作,将不仅能够促进中国产业集群的转型升级,而且将大大缓解中美间的贸易摩擦。

关键词：中美贸易摩擦产业集群产业转型

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博弈论视角下的可持续发展问题研究

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科技管理研究 2010年第23期30卷 243-246页

作者：孙卫东 William j.lawrence 江苏大学财经学院江苏镇江212013 纽约理工大学管理学院美国纽约10023

可持续发展是属于外部不经济的"公共地"问题。从历史上看,造成目前一系列全球环境问题的主要责任在发达国家,所以,在可持续发展问题上,国际社会形成了"共同但有区别"的责任分摊原则。通过博弈模型分析发现,目前发达国家与发展中国家之... 详细信息

可持续发展是属于外部不经济的"公共地"问题。从历史上看,造成目前一系列全球环境问题的主要责任在发达国家,所以,在可持续发展问题上,国际社会形成了"共同但有区别"的责任分摊原则。通过博弈模型分析发现,目前发达国家与发展中国家之所以谈判一再陷入僵局,是因为双方合作还缺乏适当的条件和机制,可持续发展问题的妥善解决,至少需要三个先决条件,但目前还没有一个条件已经满足。

关键词：博弈论可持续发展先决条件创新机制

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