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SSRN 2024年

作者： Kim, Jua Gilbert, Jeremy L. Lv, William W. Pan, Haobo Du, Ping Center for Human Tissues and Organs Degeneration China Shenzhen Key Laboratory of Marine Biomaterials CAS-HK Joint Lab of Biomaterials The Key Laboratory of Biomedical Imaging Science System Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen University Town 1068 Xueyuan Avenue Shenzhen518055 China Syracuse Biomaterials Institute Syracuse University Syracuse University 318 Bowne Hall SyracuseNY13244 United States Clemson- Medical University of South Carolina Bioengineering Program Department of Bioengineering Clemson University 68 Presidents St CharlestonSC39425 United States Department of Orthopaedics and Traumatology Li Ka Shing Faculty of Medicine The University of Hong Kong 999077 Hong Kong Shenzhen Healthemes Biotechnology Co. Ltd Shenzhen518102 China

Magnesium (Mg) alloys are popular biodegradable metals studied for orthopedic and cardiovascular applications, mainly because Mg ions are essential trace elements known to promote angiogenesis and osteogenesis. However, all metal corrosion, including Mg alloys, consists of oxidation and reduction reactions, where oxidation of metal is inevitably accompanied by reduction of water, oxygen, and other biomolecules nearby. It is still unclear how all these by-products and Mg ions concomitantly alter the microenvironment and cell behaviors spatially and temporally. By-products produced from reduction reactions like alkaline pH, hydrogen, and ROS/RNS are generally unwanted side effects;however, reduction reactions are inevitable. Depending on the rate, reduction reactions exhibit biphasic effects that can induce discrete biological responses. This study shows that Mg corrosion produces ROS both in vitro and in vivo, and ROS significantly affects HIF1A expression and signaling pathways like WNT and PI3K/AKT/mTOR, related to BMSC proliferation and differentiation. Furthermore, cells may respond to Mg ions and oxidative stress differently at different pH levels, which can vary in different pathological conditions. Therefore, this study provides a fundamental insight into the importance of reduction reactions in all metallic biomaterials. © 2024, The Authors. All rights reserved.

关键词： Magnesium alloys

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Author Correction: Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

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Light, science & applications 2023年第1期12卷 93页

作者： Kyrollos Yanny Nick Antipa William Liberti Sam Dehaeck Kristina Monakhova Fanglin Linda Liu Konlin Shen Ren Ng Laura Waller UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley CA 94720 USA. kyrollosyanny@***. Department of Electrical Engineering & Computer Sciences University of California Berkeley CA 94720 USA. naantipa@***. Department of Electrical Engineering & Computer Sciences University of California Berkeley CA 94720 USA. TIPs Department Université libre de Bruxelles (ULB) 1050 Brussels Belgium. UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley CA 94720 USA.

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RNA-seq based transcription characterization of fusion breakpoints as a potential estimator for its oncogenic potential

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BioMed Research International 2017年第1期2017卷 9829175页

作者： Gu, Jian-Lei Chukhman, Morris Lu, Yao Liu, Cong Liu, Shi-Yi Lu, Hui Shanghai Institute of Medical Genetics Shanghai Children's Hospital Shanghai Jiao Tong University Shanghai 200040 China Department of Bioinformatics SJTU-Yale Joint Center for Biostatistics Shanghai Jiao Tong University Shanghai 200240 China Key Laboratory of Molecular Embryology Ministry of Health Shanghai Key Laboratory of Embryo and Reproduction Engineering Shanghai 200040 China Department of Bioengineering Bioinformatics Program University of Illinois at Chicago Chicago 60607 IL United States

Based on high-throughput sequencing technology, the detection of gene fusions is no longer a big challenge but estimating the oncogenic potential of fusion genes remains challenging. Recent studies successfully applied machine learning methods and gene structural and functional features of fusion mutation to predict their oncogenic potentials. However, the transcription characterizations features of fusion genes have not yet been studied. In this study, based on the clonal evolution theory, we hypothesized that a fusion gene is more likely to be an oncogenic genomic alteration, if the neoplastic cells harboring this fusion mutation have larger clonal size than other neoplastic cells in a *** proposed a novel method, called iFCR (internal Fusion Clone Ratio), given an estimation of oncogenic potential for fusion *** have evaluated the iFCR method in three public cancer transcriptome sequencing datasets;the results demonstrated that the fusion mutations occurring in tumor samples have higher internal fusion clone ratio than normal samples. And the most frequent prostate cancer fusion mutation, TMPRSS2-ERG, appears to have a remarkably higher iFCR value in all three independent patients. The preliminary results suggest that the internal fusion clone ratio might potentially advantage current fusion mutation oncogenic potential prediction methods. © 2017 Jian-lei Gu et al.

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The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges

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BioDesign Research 2020年第1期2020卷 1-8页

作者： Charles DeLisi Aristides Patrinos Michael MacCracken Dan Drell George Annas Adam Arkin George Church Robert Cook-Deegan Henry Jacoby Mary Lidstrom Jerry Melillo Ron Milo Keith Paustian John Reilly Richard J.Roberts Daniel Segrè Susan Solomon Dominic Woolf Stan D.Wullschleger Xiaohan Yang Department of Biomedical Engineering and Program in Bioinformatics College of EngineeringBoston UniversityBoston MA 02215USA The NOVIM Group Kohn HallUC Santa BarbaraCA 93106USA Climate Institute WashingtonDCUSA Department of Energy WashingtonDCUSA Center for Health Law Ethics&Human Rights at the Boston University School of Public HealthSchool of MedicineBoston UniversityUSA Department of Bioengineering University of CaliforniaBerkeley CAUSA Department of Genetics Harvard Medical SchoolCambridge MAUSA School for the Future of Innovation in Society Arizona State UniversityBarrett&O’Connor Washington Center1800 I StreetNWWashingtonDC 20006USA Sloan School of Management MITCambridge MAUSA Department of Chemical Engineering University of WashingtonSeattle WashingtonUSA The Ecosystems Center of the Marine Biological Laboratory in Woods Hole MAUSA Department of Plant and Environmental Sciences Weizmann Institute of ScienceRehovotIsrael Department of Soil and Crop Sciences Colorado State UniversityFort Collins CO 80523USA MIT Joint Program on the Science and Policy of Global Change MITCambridge MAUSA New England Biolabs Beverly MAUSA Department of Biology and Program in Bioinformatics Boston UniversityBoston MA 02215USA Department of Earth Atmospheric and Planetary SciencesMITCambridge MAUSA Soil and Crop Sciences Section School of Integrated Plant SciencesCornell UniversityIthaca NYUSA Environmental Sciences Division Oak Ridge National LaboratoryOak Ridge TNUSA Biosciences Division Oak Ridge National LaboratoryOak RidgeTNUSA

The long atmospheric residence time of CO2 creates an urgent need to add atmospheric carbon drawdown to CO2 regulatory *** and systems biology(SSB),which enables manipulation of cellular phenotypes,offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric *** participants(in attendance:Christina Agapakis,George Annas,Adam Arkin,George Church,Robert Cook-Deegan,Charles DeLisi,Dan Drell,Sheldon Glashow,Steve Hamburg,Henry Jacoby,Henry Kelly,Mark Kon,Todd Kuiken,Mary Lidstrom,Mike MacCracken,June Medford,Jerry Melillo,Ron Milo,Pilar Ossorio,Ari Patrinos,Keith Paustian,Kristala Jones Prather,Kent Redford,David Resnik,John Reilly,Richard ***,Daniel Segre,Susan Solomon,Elizabeth Strychalski,Chris Voigt,Dominic Woolf,Stan Wullschleger,and Xiaohan Yang)identified a range of possibilities by which SSB might help reduce greenhouse gas concentrations and which might also contribute to environmental sustainability and *** include,among other possibilities,engineering plants to convert CO2 produced by respiration into a stable carbonate,designing plants with an increased root-to-shoot ratio,and creating plants with the ability to self-fertilize.A number of serious ecological and societal challenges must,however,be confronted and resolved before any such application can be fully assessed,realized,and deployed.

关键词： Synthetic Roberts enable

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Bioelectronic Interfaces: Inkjet‐Printed Flexible Gold Electrode Arrays for Bioelectronic Interfaces (Adv. Funct. Mater. 7/2016)

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Advanced Functional Materials 2016年第7期26卷

作者： Yasser Khan Felippe J. Pavinatto Monica C. Lin Amy Liao Sarah L. Swisher Kaylee Mann Vivek Subramanian Michel M. Maharbiz Ana C. Arias Department of Electrical Engineering and Computer Sciences University of California Berkeley CA 94720 USA Physics Institute of São Carlos University of São Paulo CEP: 13566‐590 São Carlos SP Brazil Joint Graduate Program in Bioengineering University of California Berkeley CA 94720 USA

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Corrigendum: Rapid and visual Chlamydia trachomatis detection using loop-mediated isothermal amplification and hydroxynaphthol blue

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Letters in applied microbiology 2017年第4期65卷 343页

作者： I Choopara N Arunrut W Kiatpathomchai D Dean N Somboonna Program in Biotechnology Faculty of Science Chulalongkorn University Bangkok Thailand. Bioengineering and Sensing Technology Laboratory National Center for Genetic Engineering and Biotechnology Khlong Nueng Khlong Luang Pathum Thani Thailand. Center for Immunobiology and Vaccine Development UCSF Benioff Children's Hospital Oakland Research Institute Oakland CA USA. Department of Medicine University of California San Francisco CA USA. Joint Graduate Program in Bioengineering University of California Berkeley CA USA. Department of Microbiology Faculty of Science Chulalongkorn University Bangkok Thailand.

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General Formation of Macro-/Mesoporous Nanoshells from Interfacial Assembly of Irregular Mesostructured Nanounits

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Angewandte Chemie 2020年第44期132卷

作者： Chen G. Yan Y. Wang J. Ok Y.S. Zhong G. Guan B.Y. Yamauchi Y. State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 China International Center for Materials Nanoarchitechtonics (WPI-MANA) National Institute for Materials Science 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan Korea Biochar Research Center APRU Sustainable Waste Management Program and Division of Environmental Science and Ecological Engineering Korea University Seoul 02841 South Korea Joint Research Center for Future Materials International Center of Future Science Jilin University Qianjin Street 2699 Changchun 130012 China School of Chemical Engineering and Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane QLD 4072 Australia

Mesoporous core–shell nanostructures with controllable ultra-large open channels in their nanoshells are of great interest. However, soft template-directed cooperative assembly to mesoporous nanoshells with highly accessible pores larger than 30 nm, or even above 50 nm into macroporous range, remains a significant challenge. Herein we report a general approach for precisely tailored coating of hierarchically macro-/mesoporous polymer and carbon shells, possessing highly accessible radial channels with extremely wide pore size distribution from ca. 10 nm to ca. 200 nm, on diverse functional materials. This strategy creates opportunities to tailor the interfacial assembly of irregular mesostructured nanounits on core materials and generate various core–shell nanomaterials with controllable pore architectures. The obtained Fe,N-doped macro-/mesoporous carbon nanoshells show enhanced electrochemical performance for the oxygen reduction reaction in alkaline condition. © 2020 Wiley-VCH GmbH

关键词： carbon core–shell nanostructures electrocatalysis macro-/mesoporous nanoshells polydopamine

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Correction for Thompson et al., "Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing"

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Applied and Environmental Microbiology 2021年第8期87卷 1-1页

作者： Thompson, Mitchell G. Incha, Matthew R. Pearson, Allison N. Schmidt, Matthias Sharpless, William A. Eiben, Christopher B. Cruz-Morales, Pablo Blake-Hedges, Jacquelyn M. Liu, Yuzhong Adams, Catharine A. Haushalter, Robert W. Krishna, Rohith N. Lichtner, Patrick Blank, Lars M. Mukhopadhyay, Aindrila Deutschbauer, Adam M. Shih, Patrick M. Keasling, Jay D. Joint BioEnergy Institute EmeryvilleCalifornia United States Biological Systems and Engineering Division Lawrence Berkeley National Laboratory BerkeleyCalifornia United States Department of Plant Biology University of California DavisCalifornia United States Department of Plant and Microbial Biology University of California BerkeleyCalifornia United States RWTH Aachen University Aachen Germany Joint Program in Bioengineering University of California BerkeleyCalifornia United States Centro de Biotecnología FEMSA Instituto Tecnológico y de Estudios Superiores de Monterrey Monterrey Mexico Department of Chemistry University of California BerkeleyCalifornia United States Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory BerkeleyCalifornia United States Environmental and Genomics and Systems Biology Division Lawrence Berkeley National Laboratory BerkeleyCalifornia United States Department of Chemical and Biomolecular Engineering University of California BerkeleyCalifornia United States Institute for Quantitative Biosciences University of California BerkeleyCalifornia United States The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Lyngby Denmark Center for Synthetic Biochemistry Institute for Synthetic Biology Shenzhen Institutes for Advanced Technologies Shenzhen China

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Theoretical design and evaluation of endoluminal ultrasound applicators for thermal therapy of pancreatic cancer under image guidance

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AIP Conference Proceedings 2017年第1期1821卷

作者： Matthew Adams Serena Scott Vasant Salgaonkar Graham Sommer Chris Diederich 1Thermal Therapy Research Group University of California San Francisco 2340 Sutter Street S341 San Francisco CA 94109 USA 2Joint Graduate Program in Bioengineering UC Berkeley and UC San Francisco USA 3Stanford Medical Center 300 Pasteur Drive Stanford CA 94305 USA

An image-guided endoluminal ultrasound applicator has been proposed for palliative and potential curative thermal therapy of pancreatic tumors. By considering a directional transducer array of planar, tubular, or curvilinear transducers, this design offers the potential for fast volumetric therapy and 3D spatial control over the energy deposition profile. Treatment of pancreatic tumor tissue would be performed in a minimally invasive fashion with the applicator positioned in the gastrointestinal (GI) lumen, and sparing of the luminal wall would be achieved with a water-cooled balloon surrounding the transducers. A theoretical evaluation of this design was performed by developing a 3D acoustic and bioheat transfer model, with temperature and thermal dose solutions obtained using a FEM solver (COMSOL Multiphysics). Parametric studies were performed on a generalized anatomical model of the pancreas, tumor, and adjacent luminal wall to determine preferred transducer configurations and frequencies for maximizing lesion volume and penetration while sparing the luminal wall. Patient-specific models of pancreatic tumors were generated from CT studies and used to assess the feasibility of performing thermal ablation or hyperthermia on small (∼2 cm diameter) pancreatic head tumors with an endoluminal applicator positioned within the duodenum. Simulation results indicate lower transducer operating frequencies (1-3 MHz) are necessary to mitigate damage to the luminal wall, and a tradeoff between penetration depth and lesion volume emerges as the degree of focusing increases. For patient-specific ablation modeling of tumors within 30 mm of the luminal wall, approximately 95% of the volume could be ablated within 15 min using a planar or lightly focused transducer configuration without duodenal damage. Over 90% of the volume could be elevated above 40°C at steady state for hyperthermia applications (e.g., radiation sensitization, drug delivery) using a tubular transducer. For tum

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Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer

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Metabolic Engineering Communications 2019年 9卷 e00098页

作者： Thompson, Mitchell G. Valencia, Luis E. Blake-Hedges, Jacquelyn M. Cruz-Morales, Pablo Velasquez, Alexandria E. Pearson, Allison N. Sermeno, Lauren N. Sharpless, William A. Benites, Veronica T. Chen, Yan Baidoo, Edward E.K. Petzold, Christopher J. Deutschbauer, Adam M. Keasling, Jay D. Joint BioEnergy Institute 5885 Hollis Street Emeryville 94608 CA United States Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley 94720 CA United States Department of Plant and Microbial Biology University of California Berkeley 94720 CA United States Joint Program in Bioengineering University of California Berkeley/San Francisco 94720 CA United States Department of Chemistry University of California Berkeley 94720 CA United States Centro de Biotecnologia FEMSA Instituto Tecnologico y de Estudios Superiores de Monterrey Mexico Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA United States Department of Chemical and Biomolecular Engineering University of California Berkeley 94720 CA United States The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Denmark Center for Synthetic Biochemistry Institute for Synthetic Biology Shenzhen Institutes for Advanced Technologies Shenzhen China

Pseudomonas putida is a promising bacterial chassis for metabolic engineering given its ability to metabolize a wide array of carbon sources, especially aromatic compounds derived from lignin. However, this omnivorous metabolism can also be a hindrance when it can naturally metabolize products produced from engineered pathways. Herein we show that P. putida is able to use valerolactam as a sole carbon source, as well as degrade caprolactam. Lactams represent important nylon precursors, and are produced in quantities exceeding one million tons per year (Zhang et al., 2017). To better understand this metabolism we use a combination of Random Barcode Transposon Sequencing (RB-TnSeq) and shotgun proteomics to identify the oplBA locus as the likely responsible amide hydrolase that initiates valerolactam catabolism. Deletion of the oplBA genes prevented P. putida from growing on valerolactam, prevented the degradation of valerolactam in rich media, and dramatically reduced caprolactam degradation under the same conditions. Deletion of oplBA, as well as pathways that compete for precursors L-lysine or 5-aminovalerate, increased the titer of valerolactam from undetectable after 48 h of production to ~90 mg/L. This work may serve as a template to rapidly eliminate undesirable metabolism in non-model hosts in future metabolic engineering efforts. © 2019

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