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Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Horticulture Research 2021年第1期8卷 1618-1631页

作者： Xiao-Li Hu Haiwei Lu Md Mahmudul Hassan jin Zhang Guoliang Yuan Paul E.Abraham Him K.Shrestha Manuel I.Villalobos Solis jin-Gui Chen timothy j.tschaplinski Mitchel j.Doktycz Gerald A.Tuskan Zong-Ming(Max)Cheng Xiaohan Yang Department of Plant Sciences University of TennesseeKnoxvilleTNUSA Biosciences Division Oak Ridge National LaboratoryOak RidgeTNUSA State Key Laboratory of Subtropical Silviculture School of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouZhejiangChina The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTNUSA Department of Genome Science and Technology University of TennesseeKnoxvilleTNUSA College of Horticulture Nanjing Agricultural UniversityNanjingJiangsuChina

Small secreted proteins(SSPs)are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion *** plants,SSPs have been found to play important roles in various processes,including plant growth and development,plant response to abiotic and biotic stresses,and beneficial plant–microbe *** the past 10 years,substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture,bioenergy,and ***,there are potentially a lot of SSPs that have not been discovered in plant genomes,which is largely due to limitations of existing computational *** advances in genomics,transcriptomics,and proteomics research,as well as the development of new computational algorithms based on machine learning,provide unprecedented capabilities for genome-wide discovery of novel SSPs in *** this review,we summarize known SSPs and their functions in various plant *** we provide an update on the computational and experimental approaches that can be used to discover new ***,we discuss strategies for elucidating the biological functions of SSPs in plants.

关键词： species functional dating

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Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

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BioDesign Research 2021年第1期2021卷 17-38页

作者： Xiaohan Yang Degao Liu Haiwei Lu David j.Weston jin-Gui Chen Wellington Muchero Stanton Martin Yang Liu Md Mahmudul Hassan Guoliang Yuan Udaya C.Kalluri timothy j.tschaplinski julie C.Mitchell Stan D.Wullschleger Gerald A.Tuskan Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Genetics Cell Biology and DevelopmentCenter for Precision Plant Genomicsand Center for Genome EngineeringUniversity of MinnesotaSaint PaulMN 55108USA Department of Academic Education Central Community College-HastingsHastingsNE 68902USA Environmental Sciences Division and Climate Change Science Institute Oak Ridge National LaboratoryOak RidgeTN 37831USA

A grand challenge facing society is climate change caused mainly by rising CO_(2) concentration in Earth’s *** plants are linchpins in global carbon cycling,with a unique capability of capturing CO_(2) via photosynthesis and translocating captured carbon to stems,roots,and soils for long-term ***,many researchers postulate that existing land plants cannot meet the ambitious requirement for CO_(2) removal to mitigate climate change in the future due to low photosynthetic efficiency,limited carbon allocation for long-term storage,and low suitability for the *** address these limitations,there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design(or biodesign).Here,we summarize validated biological parts(e.g.,protein-encoding genes and noncoding RNAs)for biological engineering of carbon dioxide removal(CDR)traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant ***,we first summarize the framework of plant-based CDR(e.g.,CO_(2) capture,translocation,storage,and conversion to value-added products).Then,we highlight some representative biological parts,with experimental evidence,in this ***,we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

关键词： dioxide roots locating

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Reconfiguring Plant Metabolism for Biodegradable Plastic Production

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BioDesign Research 2020年第1期2020卷 111-123页

作者： Haiwei Lu Guoliang Yuan Steven H.Strauss timothy j.tschaplinski Gerald A.Tuskan jin-Gui Chen Xiaohan Yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Forest Ecosystems and Society Oregon State UniversityCorvallisOR 97331USA

For decades,plants have been the subject of genetic engineering to synthesize novel,value-added ***(PHAs),a large class of biodegradable biopolymers naturally synthesized in eubacteria,are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic *** was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic ***,after three decades of effort synthesizing PHAs,and in particular the simplest form polyhydroxybutyrate(PHB),and seeking to improve their production in plants,it has proven very difficult to reach a commercially profitable rate in a normally growing *** seems to be due to the growth defects associated with PHA production and accumulation in plant ***,we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been ***,from the point of view of plant synthetic biology,we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production,with the goal of maximizing PHA yield while minimizing growth ***,we suggest genetic elements that can be considered in genetic circuit design,approaches for nuclear genome and plastome modification,and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.

关键词： breakthrough seeking Plant

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Kinetics of glyphosate and aminomethylphosphonic acid sorption onto montmorillonite clays in soil and their translocation to genetically modified corn

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journal of Environmental Sciences 2024年第1期135卷 669-680页

作者： Meichen Wang Kelly j Rivenbark timothy D Phillips Veterinary Physiology and Pharmacology College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityTX 77845USA

The co-occurrence of glyphosate(GLP)and aminomethylphosphonic acid(AMPA)in contaminated water,soil,sediment and plants is a cause for concern due to potential threats to the ecosystem and human health.A major route of exposure is through contact with contaminated soil and consumption of crops containing GLP and AMPA ***,clay-based sorption strategies for mixtures of GLP and AMPA in soil,plants and garden produce have been very *** this study,in vitro soil and in vivo genetically modified corn models were used to establish the proof of concept that the inclusion of clay sorbents in contaminated soils will reduce the bioavailability of GLP and AMPA in soils and their adverse effects on plant *** of chemical concentration(1–10 mg/kg),sorbent dose(0.5%-3%in soil and 0.5%-1%in plants)and duration(up to 28 days)on sorption kinetics were *** time course results showed a continuous GLP degradation to *** inclusion of calcium montmorillonite(CM)and acid processed montmorillonite(APM)clays at all doses significantly and consistently reduced the bioavailability of both chemicals from soils to plant roots and leaves in a dose-and time-dependent manner without detectable *** treated with 0.5%and 1%APM inclusion showed the highest growth rate(p≤0.05)and lowest chemical bioavailability with up to 76%reduction in roots and57%reduction in *** indicated that montmorillonite clays could be added as soil supplements to reduce hazardous mixtures of GLP and AMPA in soils and plants.

关键词： Glyphosate AMPA Adsorption Soil remediation Plant Hydroponic system

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Biological and Molecular Components for Genetically Engineering Biosensors in Plants

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BioDesign Research 2022年第1期2022卷 19-37页

作者： Yang Liu Guoliang Yuan Md MahmudulHassan Paul E.Abraham julie C.Mitchell Daniel jacobson Gerald A.Tuskan Arjun Khakhar june Medford Cheng Zhao Chang-jun Liu Carrie A.Eckert Mitchel j.Doktycz timothy j.tschaplinski Xiaohan Yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTennessee37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTennessee37831USA Department of Genetics and Plant Breeding Patuakhali Science and Technology UniversityDumkiPatuakhali8602Bangladesh Departmentof Biology Colorado State UniversityFort CollinsColorado80523USA Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese A cademy of Agriculural SciencesShenzhen 518120China Biology Department Brookhaven National LaboratoryUptonNew York 11973USA

Plants adapt to their changing environments by sensing and responding to physical,biological,and chemical *** to their sessile lifestyles,plants experience a vast array of external stimuli and selectively perceive and respond to specific *** repurposing the logic circuitry and biological and molecular components used by plants in nature,genetically encoded plant-based biosensors(GEPBs)have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily *** allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and *** are also useful for environmental monitoring,plant abiotic and biotic stress management,and accelerating design-build-test-learn cycles of plant *** the advent of synthetic biology,biological and molecular components derived from alternate natural organisms(e.g.,microbes)and/or de novo parts have been used to build *** this review,we summarize the framework for engineering different types of *** then highlight representative validated biological components for building plant-based biosensors,along with various applications of plant-based biosensors in basic and applied plant science ***,we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.

关键词： Plants Molecular monitoring

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Biosystems Design to Accelerate C3-to-CAM Progression

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BioDesign Research 2020年第1期2020卷 18-33页

作者： Guoliang Yuan MdMahmudul Hassan Degao Liu Sung Don Lim Won Cheol Yim john C.Cushman Kasey Markel Patrick M.Shih Haiwei Lu David j.Weston jin-Gui Chen timothy j.tschaplinski Gerald A.Tuskan Xiaohan Yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Genetics and Plant Breeding Patuakhali Science and Technology UniversityDumkiPatuakhali 8602Bangladesh Department of Genetics Cell Biology and DevelopmentCenter for Precision Plant Genomicsand Center for Genome EngineeringUniversity of MinnesotaSaint PaulMN 55108USA Department of Applied Plant Sciences Kangwon National UniversityChuncheon 24341Republic of Korea Department of Biochemistry and Molecular Biology University of NevadaRenoNVUSA Department of Plant Biology University of CaliforniaDavisDavisCAUSA Feedstocks Division Joint BioEnergy InstituteEmeryvilleCAUSA

Global demand for food and bioenergy production has increased rapidly,while the area of arable land has been declining for decades due to damage caused by erosion,pollution,sea level rise,urban development,soil salinization,and water scarcity driven by global climate *** order to overcome this conflict,there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency(WUE).Crassulacean acid metabolism(CAM)species have substantially higher WUE than species performing C3 or C4 *** plants are derived from C3 photosynthesis ***,it is extremely unlikely that the C3 or C4 crop plants would evolve rapidly into CAM photosynthesis without human ***,there is growing interest in improving WUE through transferring CAM into C3 ***,engineering a major metabolic plant pathway,like CAM,is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C3 and CAM photosynthesis,as well as overcoming physiometabolic limitations such as diurnal stomatal *** advances in CAM evolutionary genomics research,genome editing,and synthetic biology have increased the likelihood of successful acceleration of C3-to-CAM ***,we first summarize the systems biology-level understanding of the molecular processes in the CAM ***,we review the principles of CAM engineering in an evolutionary ***,we discuss the technical approaches to accelerate the C3-to-CAM transition in plants using synthetic biology toolboxes.

关键词： overcome acceleration evolve

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Cultural Exclusion and the Transformation of the Cultural Landscape: The Origins of Anti-Chinese Racism in Canada

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Social Sciences in China 2024年第3期45卷 181-202页

作者： timothy j.Stanley Faculty of Education University of Ottawa

Anti-Chinese racism in Canada is a social structure of racialized exclusion that over time came to be built into the settler colonialism that continues to shape the *** of European,and especially of British and French origins,have consequently created the cultural landscapes that constitute the country(i.e.,its material constructions and dominant cultural overlays).When read against these landscapes,people of Chinese origins and members of other racialized groups continue to be positioned as aliens who do not belong in the country in way in which people racialized as white are *** on British Columbia(BC),Canada's westernmost province,and the historical activity of people of Chinese origins,this paper traces the history of anti-Chinese racism and its links to Anglo-Canadian settler *** has long been linked to China,and the Chinese entered BC at the same time as Europeans before the country *** this,Chinese people have repeatedly been positioned as threats to Anglo-Canadian dominance,and especially to control over the land and its *** Canadian resistance to racist exclusions,along with that of other groups,has led to the elimination of legislated ***,historic exclusions continue to shape cultural landscapes and popular understandings of who belongs and who does *** these landscapes requires an antiracist project of pursuing common projects that cross over racialized differences to remake the territory in ways that affirm the presence of all the peoples of Canada.

关键词： Chinese Canadians cultural exclusion white supremacy racism

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Machine learning-guided accelerated discovery of structure-property correlations in lean magnesium alloys for biomedical applications

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journal of Magnesium and Alloys 2024年第6期12卷 2267-2283页

作者： Sreenivas Raguraman Maitreyee Sharma Priyadarshini Tram Nguyen Ryan McGovern Andrew Kim Adam j.Griebel Paulette Clancy timothy P.Weihs Department of Materials Science and Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Hopkins Extreme Materials Institute Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Department of Chemical and Biomolecular Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Translational Tissue Engineering Center Johns Hopkins School of Medicine400 N BroadwayBaltimore21231MDU.S.A Department of Biomedical Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Research and Development Fort Wayne Metals Research ProductsLLC9609 Ardmore AveFort Wayne46809INU.S.A Department of Mechanical Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A

Magnesium alloys are emerging as promising alternatives to traditional orthopedic implant materials thanks to their biodegradability,biocompatibility,and impressive mechanical ***,their rapid in-vivo degradation presents challenges,notably in upholding mechanical integrity over *** study investigates the impact of high-temperature thermal processing on the mechanical and degradation attributes of a lean Mg-Zn-Ca-Mn alloy,*** rapid,cost-efficient characterization methods like X-ray diffraction and optical microscopy,we swiftly examine microstructural changes post-thermal *** Pearson correlation coefficient analysis,we unveil the relationship between microstructural properties and critical targets(properties):hardness and corrosion ***,leveraging the least absolute shrinkage and selection operator(LASSO),we pinpoint the dominant microstructural factors among closely correlated *** findings underscore the significant role of grain size refinement in strengthening and the predominance of the ternary Ca_(2)Mg_(6)Zn_(3)phase in corrosion *** suggests that achieving an optimal blend of strength and corrosion resistance is attainable through fine grains and reduced concentration of ternary *** thorough investigation furnishes valuable insights into the intricate interplay of processing,structure,and properties in magnesium alloys,thereby advancing the development of superior biodegradable implant materials.

关键词： Magnesium alloys Machine learning Corrosion Mechanical properties Rapid characterization

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The Regional Economic Impacts of Coal Mining: A Case Study of Signal Peak Energy

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Natural Resources 2024年第8期15卷 211-223页

作者： timothy j. Considine School of Energy Resources University of Wyoming Laramie USA

This paper quantifies the regional economic contributions of coal exports from the US using a case study of Signal Peak Energy in Montana. Two methods of estimating economic contributions are compared, contribution and impact analysis. The latter is adopted because the industry impact analysis is more accurate, especially since it is based upon accounting records from Signal Peak. Our estimates of regional economic and fiscal impacts do not vary significantly with the price of coal because we explicitly account for swings in royalty income. Our analysis finds that Signal Peak Energy supports 678 jobs, over $55 million in tax revenues, more than $90 million in royalties, $111.7 million in value added, and $62.3 million in labor income. Curtailing or halting Signal Peak’s coal production for environmental reasons as some environmental groups have argued would eliminate these economic contributions.

关键词： Coal Regional Economic Exports Fiscal

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In vivo measurement of NADH fluorescence lifetime in skeletal muscle via -ber-coupled time-correlated single photon counting

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journal of Innovative Optical Health Sciences 2024年第1期17卷 121-134页

作者： Kathryn M.Priest jacob V.Schluns Nathania Nischal Colton L.Gattis jeffrey C.Wolchok timothy j.Muldoon Department of Biomedical Engineering University of Arkansas FayettevilleARUSA

Nicotinamide adenine dinucleotide(NADH)is a cofactor that serves to shuttle electrons during metabolic processes such as glycolysis,the tricarboxylic acid cycle,and oxidative phosphorylation(OXPHOS).NADH is autofluorescent,and itsfluorescence lifetime can be used to infer metabolic dynamics in living ***-coupled time-correlated single photon counting(TCSPC)equipped with an implantable needle probe can be used to measure NADH lifetime in vivo,enabling investigation of changing metabolic demand during muscle contraction or tissue *** study illustrates a proof of concept for point-based,minimally-invasive NADHfluorescence lifetime measurement in *** muscle loss(VML)injuries were created in the left tibialis anterior(TA)muscle of male Sprague Dawley *** lifetime measurements were collected before,during,and after a 30 s tetanic contraction in the injured and uninjured TA muscles,which was subsequently-t to a biexponential decay model to yield a metric of NADH utilization(cytoplasmic vs protein-bound NADH,the A11/A22 ratio).On average,this ratio was higher during and after contraction in uninjured muscle compared to muscle at rest,suggesting higher levels of free NADH in contracting and recovering muscle,indicating increased rates of *** injured muscle,this ratio was higher than uninjured muscle overall but decreased over time,which is consistent with current knowledge of inflammatory response to injury,suggesting tissue regeneration has *** data suggest that-ber-coupled TCSPC has the potential to measure changes in NADH binding in vivo in a minimally invasive manner that requires further investigation.

关键词： Glycolysis oxidative phosphorylation energy metabolism volumetric muscle loss

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