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A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

Synthetic and Systems Biotechnology 2022年第2期7卷 657-663页

作者： Vasil D’Ambrosio Lea G.Hansen Jie Zhang Emil D.jensen Dushica Arsovska Marcos Laloux Tadas Jakociunas Pernille Hjort Davide De Lucrezia Serena Marletta Jay D.keasling michael k.jensen Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKgs.LyngbyDenmark Explora Biotech Srl Italy Joint BioEnergy Institute EmeryvilleCAUSA Biological Systems and Engineering Division Lawrence Berkeley National LaboratoryBerkeleyCAUSA Department of Chemical and Biomolecular Engineering Department of BioengineeringUniversity of CaliforniaBerkeleyCAUSA Center for Synthetic Biochemistry Institute for Synthetic BiologyShenzhen Institutes of Advanced TechnologiesShenzhenChina

The synthetic biology toolkit for baker’s yeast,Saccharomyces cerevisiae,includes extensive genome engineering toolkits and parts ***,with the increasing complexity of engineering tasks and versatile applications of this model eukaryote,there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR(findable,accessible,interoperable,and reproducible)*** this study,we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded ***,we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements,***,all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own *** expect the data,parts,and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

关键词： gRNA Promoter Terminator Yeast Standardization

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Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast

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Synthetic and Systems Biotechnology 2020年第1期5卷 11-18页

作者： Tadas Jakočiūnas Andreas k.klitgaard Eftychia Eva kontou Julie Bang Nielsen Emil Thomsen David Romero-Suarez kai Blin Christopher J.Petzold Jennifer W.Gin Yaojun Tong Charlotte Held Gotfredsen Pep Charusanti Rasmus J.N.Frandsen Tilmann Weber Sang Yup Lee michael k.jensen Jay D.keasling The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKgs.LyngbyDenmark Joint BioEnergy Institute EmeryvilleCAUSA Biological Systems&Engineering Division Lawrence Berkeley National LaboratoryBerkeleyCAUSA Department of Chemical and Biomolecular Engineering&Department of Bioengineering University of California BerkeleyCAUSA Center for Synthetic Biochemistry Institute for Synthetic BiologyShenzhen Institutes for Advanced TechnologiesShenzhenChina Department of Chemistry Technical University of DenmarkKgs.LyngbyDenmark Department of Biotechnology and Biomedicine Technical University of DenmarkKgs.LyngbyDenmark Department of Chemical and Biomolecular Engineering(Bk21 Plus Program) Korea Advanced Institute of Science and Technology(KAIST)291 Daehak-roYuseong-guDaejeon34141Republic of Korea

To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms,development of new,versatile,bio-based production platforms is *** we present a novel yeast-based platform for biosynthesis of bacterial aromatic *** platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.

关键词： Natural products Synthetic biology Aromatic polyketides CRISPR/Cas9 Polyketide Production platform in eukaryotes Metabolic engineering Biotechnology

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Electroactivity of the magnetotactic bacteria Magnetospirillum magneticum AMB-1 and Magnetospirillum gryphiswaldense MSR-1

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Frontiers of Environmental Science & Engineering 2024年第4期18卷 103-110页

作者： Mathias Fessler Qingxian Su Marlene Mark.jensen Yifeng Zhang Department of Environmental and Resource Engineering Technical University of DenmarkCopenhagenDK-2800Denmark

Magnetotactic bacteria reside in sediments and stratified water *** are named after their ability to synthesize internal magnetic particles that allow them to align and swim along the Earth’s magnetic field ***,we show that two magnetotactic species,Magnetospirillum magneticum strain AMB-1 and Magnetospirillum gryphiswaldense strain MSR-1,are *** *** and *** were able to generate current in microbial fuel cells with maximum power densities of 27 and 11μW/m^(2),*** the presence of the electron shuttle resazurin both species were able to reduce the crystalline iron oxide hematite(Fe_(2)O_(3)).In addition,*** could reduce poorly crystalline iron oxide(FeOOH).Our study adds *** and *** to the growing list of known electroactive bacteria,and implies that electroactivity might be common for bacteria within the Magnetospirillum genus.

关键词： Magnetotactic bacteria Magnetospirillum magneticum Magnetospirillum gryphiswaldense Extracellular electron transfer Microbial fuel cells

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The effects of cool materials,façade orientation,and morphological parameters on energy consumption at the residential neighborhood scale

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Building Simulation 2024年第4期17卷 525-542页

作者： Fusuo Xu Dongdong Tian Zhi Gao Jianshun jensen Zhang Department of Mechanical and Aerospace Engineering Syracuse UniversitySyracuseNY13210USA School of Architecture and Urban Planning Nanjing University22 Hankou RoadNanjingJiangsu Province210093China

Building surface cool materials are novel materials that can reduce urban heat island intensity and decrease building energy *** study investigated the impact of radiative properties of materials,façade orientation,and morphological parameters on energy consumption in six typical residential neighborhoods in Nanjing,*** neighborhood energy consumption of 16 application schemes considering the façade orientation factor is compared to determine the best energy-saving *** and annual energy-saving rates,savings in electricity costs,and the price ceiling for materials per unit area are *** results show that for low-rise buildings,using cool materials only on the roof can reduce the annual energy consumption by 1%.When cool or super cool materials are also used on the building façade,the annual energy saving rate can be up to 3.4%and 4.3%,*** cool materials on the south façade of buildings is not recommended due to significant heat loss in *** savings in electricity costs and the price ceiling for materials per unit area,the price of cool and super cool materials should be less than 3.0 and 3.7 RMB/m2,respectively,assuming a lifespan of eight years in Nanjing.

关键词： cool materials building energy saving neighborhood morphology façade orientation

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Magnetic field regression using artificial neural networks for cold atom experiments

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Chinese Physics B 2024年第2期33卷 46-51页

作者：陈子霆黃建陶 Bojeong Seo 黄明琛 Mithilesh k.Parit 何逸飞甄浩廷 jensen Li Gyu-Boong Jo Department of Physics The Hong Kong University of Science and TechnologyKowloon 999077China

Accurately measuring magnetic fields is essential for magnetic-field sensitive experiments in areas like atomic,molecular,and optical physics,condensed matter experiments,and other ***,since many experiments are often conducted in an isolated environment that is inaccessible to experimentalists,it can be challenging to accurately determine the magnetic field at the target ***,we propose an efficient method for detecting magnetic fields with the assistance of an artificial neural network(NN).Instead of measuring the magnetic field directly at the desired location,we detect fields at several surrounding positions,and a trained NN can accurately predict the magnetic field at the target *** training,we achieve a below 0.3%relative prediction error of magnetic field magnitude at the center of the vacuum chamber,and successfully apply this method to our erbium quantum gas apparatus for accurate calibration of magnetic field and long-term monitoring of environmental stray magnetic *** demonstrated approach significantly simplifies the process of determining magnetic fields in isolated environments and can be applied to various research fields across a wide range of magnetic field magnitudes.

关键词： ultracold gases trapped gases measurement methods and instrumentation

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Neurological consequences of human calmodulin mutations

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Neural Regeneration Research 2024年第5期19卷 943-944页

作者： Helene H.jensen Anders Olsen Medical Biotechnology Department of Chemistry and BiosciencesAalborg UniversityAalborgDenmark

When calcium ions enter the cytosol,it is a stimulatory signal for cellular *** calcium sensor calmodulin picks up the change in calcium concentration and relays this information to its more than 300 downstream interaction *** this way,calmodulin affects cellular processes such as fertilization,muscle contraction,neuronal firing,and *** is,calmodulin is involved in(nearly)everything!The significance of calmodulin is emphasized by the fact that we all carry three different genes(CALM1,2,3)on different chromosomes that encode the exact same calmodulin protein,and these are all expressed in all cell ***,throughout vertebrate evolution,the protein sequence has remained completely unchanged.

关键词： consequences unchanged calmodulin

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Robust Reactive Power Scheduling of Distribution Networks Based on Modified Bootstrap Technique

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Journal of Modern Power Systems and Clean Energy 2024年第1期12卷 154-166页

作者： Wenlong Liao Shouxiang Wang Birgitte Bak.jensen Jayakrishnan Radhakrishna Pillai Zhe Yang the AAU Energy Aalborg UniversityAalborg 9220Denmark the key Laboratory of Smart Grid Ministry of EducationSchool of Electrical and Information EngineeringTianjin UniversityTianjin 300072China

The uncertainties of the power load,wind power,and photovoltaic power lead to errors between point prediction values and real values,which challenges the safe operation of distribution *** this paper,a robust reactive power scheduling(RRPS)model based on a modified bootstrap technique is proposed to consider the uncertainties of power loads and renewable energy ***,a deterministic reactive power scheduling(DRPS)model and an RRPS model are ***,a modified bootstrap technique is proposed to estimate prediction errors of power loads and renewable energy sources without artificially assuming the probability density function of prediction *** represent all possible scenarios,point prediction values and prediction errors are combined to construct two worst-case scenarios in the RRPS ***,the RRPS model is solved to find a scheduling scheme,which ensures the security of distribution networks for all possible scenarios in *** results show that the worst-case scenarios constructed by the modified bootstrap technique outperform popular ***,the RRPS model based on the modified bootstrap technique balances economics and security well.

关键词： Distribution network worst-case scenario robust programming prediction error bootstrap technique

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Mucopolysaccharidosis typeⅢB:a current review and exploration of the AAV therapy landscape

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Neural Regeneration Research 2024年第2期19卷 355-359页

作者： Courtney J.Rouse Victoria N.jensen Coy D.Heldermon Lacerta Therapeutics AlachuaFLUSA University of Florida College of Medicine GainesvilleFLUSA

Mucopolysaccharidoses typeⅢB is a rare genetic disorder caused by mutations in the gene that encodes for *** results in the aggregation of heparan sulfate polysaccharides within cell lysosomes that leads to progressive and severe debilitating neurological *** treatment options are expensive,limited,and presently there are no approved cures for mucopolysaccharidoses typeⅢ***-associated virus gene therapy has significantly advanced the field forward,allowing researchers to successfully design,enhance,and improve potential *** group recently published an effective treatment using a codon-optimized triple mutant adeno-associated virus 8 vector that restores N-acetyl-alpha-glucosaminidase levels,auditory function,and lifespan in the murine model for mucopolysaccharidoses typeⅢB to that seen in healthy ***,we review the current state of the field in relation to the capsid landscape,adeno-associated virus gene therapy and its successes and challenges in the clinic,and how novel adenoassociated virus capsid designs have evolved research in the mucopolysaccharidoses typeⅢB field.

关键词： adeno-associated virus central nervous system gene therapy heparan sulfate immune response mucopolysaccharidoses type IIIB N-acetyl-alpha-glucosaminidase newborn screening

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Spatial relationship of tertiary lymphoid structures and tumor-associated neutrophils in bladder cancer and prognostic potential for anti-PD-L1 immunotherapy

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Cancer Communications 2024年第4期44卷 499-503页

作者： Xuechun Wang Anna Juncker-jensen Gang Huang Mate Levente Nagy Xuemin Lu Liang Cheng Xin Lu Department of Biological Sciences Boler-Parseghian Center for Rare and Neglected DiseasesHarper Cancer Research InstituteUniversity of Notre DameNotre DameINUSA NeoGenomics Laboratories Inc.Aliso ViejoCAUSA Department of Pathology and Laboratory Medicine Brown University Warren Alpert Medical SchoolLifespan Academic Medical CenterLegorreta Cancer Center at Brown UniversityProvidenceRIUSA Tumor Microenvironment and Metastasis Program Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisINUSA

Dear Editor,Tertiary lymphoid structures(TLSs)are organized clus-ters of immune cells found in non-lymphoid tissues of chronic inflammation,including solid tumors[1].High endothelial venules(HEVs)positive for peripheral node addressin(PNAd)are present in TLSs and may pro-vide highway entry for ***-residing TLSs may be formed by the concerted actions of cytokines and chemokines,a finding supported by the relation between a 12-chemokine signature and TLSs[2].

关键词： bladder lymphoid inflammation

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Formation of RRR-a-tocopherol in rumen and intestinal digestibility of tocopherols in dairy cows

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Animal Nutrition 2023年第4期15卷 350-363页

作者： Saman Lashkari Farhad M.Panah Martin R.Weisbjerg Søren k.jensen Department of Animal and Veterinary Sciences Aarhus UniversityDenmark

Tocopherol sources in diets are often a combination of all-rac-a-tocopheryl acetate(synthetic a-tocopherol)from vitamin supplements and natural tocopherols and 2R-(4’R,8’R)-5,7,8-trimethyltocotrienol(a-tocotrienols)from the feed *** a-tocopherol consists of 8 different stereoisomers including 2R-(4’R,8’R)-5,7,8-trimethyltocol(RRR-a-tocopherol),2R-(4’S,8’R)-5,7,8-trimethyltocol(RSR-a-tocopherol),2R-(4’R,8’S)-5,7,8-trimethyltocol(RRS-a-tocopherol),2R-(4’S,8’S)-5,7,8-trimethyltocol(RSS-a-tocopherol),2S-(4’S,8’S)-5,7,8-trimethyltocol(SSS-a-tocopherol),2S-(4’R,8’S)-5,7,8-trimethyltocol(SRS-a-tocopherol),2S-(4’S,8’R)-5,7,8-trimethyltocol(SSR-a-tocopherol),and2S-(4’R,8’R)-5,7,8-trimethyltocol(SRR-a-tocopherol).The pre-absorption metabolism of tocopherols and tocotrienols in ruminants differs from monogastric animals due to the extensive microbial fermentation in the anaerobic *** current study investigated the impact of toasting and decortication of oats on metabolism in the digestive tract(synthesis,digestion),and intestinal digestibility of tocopherols in dairy cows by using 4 ruminal and intestinal cannulated Danish Holstein cows in a 4×4 Latin square design for 4 *** were fed a total mixed ration ad libitum containing different forms of oats:whole oat,decorticated oat,toasted oat,and decorticated toasted oat,all rolled before mixed *** means across 4 treatments were statistically analyzed,testing whether overall means were different from *** or toasting did not affect the balance or digestibility of a-tocopherols in *** across treatments showed the ruminal degradation of synthetic a-tocopherol(279 mg/d,P=0.02;P-value shows that average across treatments is different from zero),synthetic 2R-a-tocopherol(133 mg/d,P<0.01;summation of RRS-,RSR-and RSS-a-tocopherol),and 2S-a-tocopherol(190 mg/d;P<0.01,summation of SSS-,SRS-,SSR,and SRR-a-tocopherol),while RRR-a-tocopherol was formed in the rumen(221 mg/d,P=0.1

关键词： Vitamin E a-Tocopherol stereoisomers Toasting Decortication Cow

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