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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 repositories.However,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)compliance.In 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 elements.Moreover,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,respectively.Additionally,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 scripts.We 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 required.Here we present a novel yeast-based platform for biosynthesis of bacterial aromatic polyketides.The 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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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 events.The calcium sensor calmodulin picks up the change in calcium concentration and relays this information to its more than 300 downstream interaction partners.In this way,calmodulin affects cellular processes such as fertilization,muscle contraction,neuronal firing,and apoptosis.That 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 types.Moreover,throughout vertebrate evolution,the protein sequence has remained completely unchanged.

关键词： consequences unchanged calmodulin

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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 columns.They are named after their ability to synthesize internal magnetic particles that allow them to align and swim along the Earth’s magnetic field lines.Here,we show that two magnetotactic species,Magnetospirillum magneticum strain AMB-1 and Magnetospirillum gryphiswaldense strain MSR-1,are electroactive.Both M.magneticum and M.gryphiswaldense were able to generate current in microbial fuel cells with maximum power densities of 27 and 11μW/m^(2),respectively.In the presence of the electron shuttle resazurin both species were able to reduce the crystalline iron oxide hematite(Fe_(2)O_(3)).In addition,M.magneticum could reduce poorly crystalline iron oxide(FeOOH).Our study adds M.magneticum and M.gryphiswaldense 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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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 areas.However,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 location.Here,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 location.After 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 field.The 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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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 consumption.This study investigated the impact of radiative properties of materials,façade orientation,and morphological parameters on energy consumption in six typical residential neighborhoods in Nanjing,China.The neighborhood energy consumption of 16 application schemes considering the façade orientation factor is compared to determine the best energy-saving scheme.Seasonal and annual energy-saving rates,savings in electricity costs,and the price ceiling for materials per unit area are analyzed.The 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%,respectively.Using cool materials on the south façade of buildings is not recommended due to significant heat loss in winter.Considering 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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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 N-acetyl-alpha-glucosaminidase.This results in the aggregation of heparan sulfate polysaccharides within cell lysosomes that leads to progressive and severe debilitating neurological dysfunction.Current treatment options are expensive,limited,and presently there are no approved cures for mucopolysaccharidoses typeⅢB.Adeno-associated virus gene therapy has significantly advanced the field forward,allowing researchers to successfully design,enhance,and improve potential cures.Our 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 mice.Here,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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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 networks.In 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 sources.Firstly,a deterministic reactive power scheduling(DRPS)model and an RRPS model are formulated.Secondly,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 errors.To represent all possible scenarios,point prediction values and prediction errors are combined to construct two worst-case scenarios in the RRPS model.Finally,the RRPS model is solved to find a scheduling scheme,which ensures the security of distribution networks for all possible scenarios in theory.Simulation results show that the worst-case scenarios constructed by the modified bootstrap technique outperform popular baselines.Besides,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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Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez Laura M.jensen Raluca G.Mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied Systems Biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production.Results Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were identified.Conclusions In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the develo

关键词： Beef cattle Fertility GWAS QTL

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The global regulation of c-di-GMP and cAMP in bacteria

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mLife 2024年第1期3卷 42-56页

作者： Cong Liu Rui Shi Marcus S.jensen Jingrong Zhu Jiawen Liu Xiaobo Liu Di Sun Weijie Liu Jiangsu key Laboratory of Phylogenomics&Comparative Genomics School of Life SciencesJiangsu Normal UniversityXuzhouChina key Laboratory of Metabolic Engineering and Biosynthesis Technology Ministry of Industry and Information TechnologyNanjing University of Science and TechnologyNanjingChina

Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in bacteria.The best-studied examples are cyclic AMP(cAMP)and bis-(3'-5')-cyclic dimeric guanosine monophosphate(c-di-GMP),which both act as global regulators.Global regulatory frameworks of c-di-GMP and cAMP in bacteria show several parallels but also significant variances.In this review,we llustrate the global regulatory models of the two nucleotide second messengers,compare the different regulatory frameworks between c-di-GMP and cAMP,and discuss the mechanisms and physiological significance of cross-regulation between c-di-GMP and cAMP.c-di-GMP responds to numerous signals de-pendent on a great number of metabolic enzymes,and it regulates various signal transduction pathways through its huge number of effectors with varying activities.In contrast,due to the limited quantity,the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse signals.cAMP performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein(CRP)in most bacteria.This review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes,providing theoretical guidelines for future research.

关键词： bacteria cAMP c-di-GMP cross-regulation CRP

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