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Sun Z, Chu X, Adams C, Ilina TV, Guerrero M, Lin G, Chen C, Jelev D, Ishima R, Li W, Mellors JW, Calero G, Dimitrov DS. Preclinical assessment of a novel human antibody VH domain targeting mesothelin as an antibody-drug conjugate. Mol Ther Oncolytics 2023; 31:100726. [PMID: 37771390 PMCID: PMC10522976 DOI: 10.1016/j.omto.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
Mesothelin (MSLN) has been a validated tumor-associated antigen target for several solid tumors for over a decade, making it an attractive option for therapeutic interventions. Novel antibodies with high affinity and better therapeutic properties are needed. In the current study, we have isolated and characterized a novel heavy chain variable (VH) domain 3C9 from a large-size human immunoglobulin VH domain library. 3C9 exhibited high affinity (KD [dissociation constant] <3 nM) and binding specificity in a membrane proteome array (MPA). In a mouse xenograft model, 3C9 fused to human IgG1 Fc was detected at tumor sites as early as 8 h post-infusion and remained at the site for over 10 days. Furthermore, 3C9 fused to a human Fc domain drug conjugate effectively inhibited MSLN-positive tumor growth in a mouse xenograft model. The X-ray crystal structure of full-length MSLN in complex with 3C9 reveals interaction of the 3C9 domains with two distinctive residue patches on the MSLN surface. This newly discovered VH antibody domain has a high potential as a therapeutic candidate for MSLN-expressing cancers.
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Affiliation(s)
- Zehua Sun
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Xiaojie Chu
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Cynthia Adams
- Abound Bio, 1401 Forbes Avenue, Pittsburgh, PA 15219, USA
| | - Tatiana V. Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Michel Guerrero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Chuan Chen
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Dontcho Jelev
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - John W. Mellors
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
- Abound Bio, 1401 Forbes Avenue, Pittsburgh, PA 15219, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
- Abound Bio, 1401 Forbes Avenue, Pittsburgh, PA 15219, USA
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El Jaddaoui I, Ghazal H, Bennett JW. Mold in Paradise: A Review of Fungi Found in Libraries. J Fungi (Basel) 2023; 9:1061. [PMID: 37998867 PMCID: PMC10672585 DOI: 10.3390/jof9111061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Libraries contain a large amount of organic material, frequently stored with inadequate climate control; thus, mold growth represents a considerable threat to library buildings and their contents. In this essay, we review published papers that have isolated microscopic fungi from library books, shelving, walls, and other surfaces, as well as from air samples within library buildings. Our literature search found 54 published studies about mold in libraries, 53 of which identified fungi to genus and/or species. In 28 of the 53 studies, Aspergillus was the single most common genus isolated from libraries. Most of these studies used traditional culture and microscopic methods for identifying the fungi. Mold damage to books and archival holdings causes biodeterioration of valuable educational and cultural resources. Exposure to molds may also be correlated with negative health effects in both patrons and librarians, so there are legitimate concerns about the dangers of contact with high levels of fungal contamination. Microbiologists are frequently called upon to help librarians after flooding and other events that bring water into library settings. This review can help guide microbiologists to choose appropriate protocols for the isolation and identification of mold in libraries and be a resource for librarians who are not usually trained in building science to manage the threat molds can pose to library holdings.
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Affiliation(s)
- Islam El Jaddaoui
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, University Mohammed V, Rabat 10000, Morocco
- Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat 10000, Morocco
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA;
| | - Hassan Ghazal
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences, Casablanca 82403, Morocco;
- Royal Institute of Sports, Royal Institute for Managerial Training in Youth and Sport, Department of Sports Sciences, Laboratory of Sports Sciences and Performance Optimization, Salé 10102, Morocco
| | - Joan W. Bennett
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA;
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Takács G, Havasi D, Sándor M, Dohánics Z, Balogh GT, Kiss R. DIY Virtual Chemical Libraries - Novel Starting Points for Drug Discovery. ACS Med Chem Lett 2023; 14:1188-1197. [PMID: 37736187 PMCID: PMC10510501 DOI: 10.1021/acsmedchemlett.3c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
The advancement of in silico technologies such as library enumeration and synthetic feasibility prediction has made drug discovery pipelines rely more and more on virtual libraries, which provide a significantly larger pool of compounds than in-stock supplier catalogs. Virtual libraries from external sources, however, may be associated with long delivery time and high cost. In this study, we present a Do-It-Yourself (DIY) combinatorial chemistry library containing over 14 million almost completely novel products built from 1000 low-cost building blocks based on robust reactions frequently applied at medicinal chemistry laboratories. The applicability of the DIY library for various drug discovery approaches is demonstrated by extensive physicochemical property, structural diversity profiling, and the generation of focused libraries. We found that internally built DIY chemical libraries present a viable alternative of external virtual catalogs by providing access to a large number of low-cost and quickly accessible potential chemical starting points for drug discovery.
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Affiliation(s)
- Gergely Takács
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Dávid Havasi
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Márk Sándor
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Zsolt Dohánics
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - György T. Balogh
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Department
of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Semmelweis University, Hőgyes Endre utca 7-9, Budapest 1092, Hungary
| | - Róbert Kiss
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
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Kim YM, Chin EM, Fahey M, Gelineau-Morel R, Himmelmann K, O'Malley J, Oskoui M, Shapiro B, Shevell M, Wilson JL, Wiznitzer M, Aravamuthan B. SIGnature Libraries: A roadmap for the formation of special interest group libraries. Ann Child Neurol Soc 2023; 1:218-227. [PMID: 37795255 PMCID: PMC10550070 DOI: 10.1002/cns3.20021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/19/2023] [Indexed: 10/06/2023]
Abstract
Objective "SIGnature Libraries" channel the dynamism of academic society-based special interest groups (SIG) to systematically identify and provide user-oriented access to essential literature for a subspecialty field in a manner that keeps pace with the field's continuing evolution. The libraries include literature beyond clinical trial data to encompass historical context, diagnostic conceptualization, and community organization materials to foster a holistic understanding of how neurologic conditions affect individuals, their community, and their lived experience. Methods Utilizing a modified-Delphi approach, Child Neurology Society's Cerebral Palsy (CP) SIG (n = 75) administered two rounds of literature submissions and ratings. A final review by an 11-member international advisory group determined threshold ratings for resource inclusion and the library's final structure. Results Seventy-nine articles were submitted for the first Delphi round and 22 articles for the second Delphi round. Survey response rates among SIG members were 29/75 for the first round and 24/75 for the second round. The advisory board added additional articles in the final review process in view of the overall project goal. A total of 60 articles were included in the final library, and articles were divided into seven sections and stratified by rating scores. A process for ongoing revisions of the library was determined. The library will be published on the Child Neurology Society website and made publicly accessible. Conclusions The CP SIGnature Library offers learners an unprecedented resource that provides equitable access to latest consensus guidelines, existing seminal datasets, up-to-date review articles, and other patient care tools. A distinctive feature of the library is its intentional large scope and depth, presented in a stratified fashion relative to the consensus-determined importance of each article. Learners can efficiently navigate the library based on individual interests and goals, and the library can be used as core curriculum for CP education.
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Affiliation(s)
- Young-Min Kim
- Department of Neurology and Pediatrics, Loma Linda University, Loma Linda, California, USA
| | - Eric M Chin
- Department of Neurology and Pediatrics, Phelps Center for Cerebral Palsy and Neurodevelopmental Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Fahey
- Department of Paediatrics, Monash University, Monash, Australia
| | - Rose Gelineau-Morel
- Division of Neurology, Children's Mercy Hospital, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Kate Himmelmann
- Department of Pediatrics, Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jennifer O'Malley
- Department of Neurology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Maryam Oskoui
- Department of Pediatrics, Department of Neurology & Neurosurgery, Centre for Outcomes Research and Evaluation, McGill University Health Center Research Institute, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Bruce Shapiro
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Emeritus Vice President, Training, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Michael Shevell
- Departments of Pediatrics & Neurology/Neurosurgery, McGill University, Montreal, Canada
- Division of Pediatric Neurology, Montreal Children's Hospital, Montreal, Canada
| | - Jenny L Wilson
- Division of Pediatric Neurology, Oregon Health & Science University, Portland, Oregon, USA
| | - Max Wiznitzer
- Department of Neurology, Case Western Reserve University School of Medicine, Rainbow Babies & Children's Hospital, Cleveland, Ohio, USA
| | - Bhooma Aravamuthan
- Department of Neurology and Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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Stevenson ZC, Moerdyk-Schauwecker MJ, Banse SA, Patel DS, Lu H, Phillips PC. High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS). eLife 2023; 12:RP84831. [PMID: 37401921 PMCID: PMC10328503 DOI: 10.7554/elife.84831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.
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Affiliation(s)
| | | | - Stephen A Banse
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
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Yadav MP, Kundra V. Chromatin immunoprecipitation and library preparation: a powerful tool to unravel the epigenome. Biotechniques 2023. [PMID: 37386860 DOI: 10.2144/btn-2022-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Affiliation(s)
| | - Vikas Kundra
- University of Maryland, School of Medicine, Baltimore, MD 21201, USA
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Egbewande FA, Schwartz BD, Duffy S, Avery VM, Davis RA. Synthesis and Antimalarial Evaluation of Halogenated Analogues of Thiaplakortone A. Mar Drugs 2023; 21:md21050317. [PMID: 37233511 DOI: 10.3390/md21050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
The incorporation of bromine, iodine or fluorine into the tricyclic core structure of thiaplakortone A (1), a potent antimalarial marine natural product, is reported. Although yields were low, it was possible to synthesise a small nine-membered library using the previously synthesised Boc-protected thiaplakortone A (2) as a scaffold for late-stage functionalisation. The new thiaplakortone A analogues (3-11) were generated using N-bromosuccinimide, N-iodosuccinimide or a Diversinate™ reagent. The chemical structures of all new analogues were fully characterised by 1D/2D NMR, UV, IR and MS data analyses. All compounds were evaluated for their antimalarial activity against Plasmodium falciparum 3D7 (drug-sensitive) and Dd2 (drug-resistant) strains. Incorporation of halogens at positions 2 and 7 of the thiaplakortone A scaffold was shown to reduce antimalarial activity compared to the natural product. Of the new compounds, the mono-brominated analogue (compound 5) displayed the best antimalarial activity with IC50 values of 0.559 and 0.058 μM against P. falciparum 3D7 and Dd2, respectively, with minimal toxicity against a human cell line (HEK293) observed at 80 μM. Of note, the majority of the halogenated compounds showed greater efficacy against the P. falciparum drug-resistant strain.
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Affiliation(s)
- Folake A Egbewande
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Brett D Schwartz
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Sandra Duffy
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
- Discovery Biology, Centre for Cellular Phenomics, Griffith University, Nathan, QLD 4111, Australia
| | - Vicky M Avery
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
- Discovery Biology, Centre for Cellular Phenomics, Griffith University, Nathan, QLD 4111, Australia
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
- NatureBank, Griffith University, Nathan, QLD 4111, Australia
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Zvezdanova ME, de Aledo MG, López-Mirones JI, Ortega J, Canut A, Castro C, Gomez C, Hernáez S, Oviaño M, Ercibengoa M, Alkorta M, Muñoz P, Rodriguez-Temporal D, Rodríguez-Sánchez B. Validation of an expanded, in-house library and an optimized preparation method for the identification of fungal isolates using MALDI-TOF mass spectrometry. Med Mycol 2023; 61:myad038. [PMID: 37102224 DOI: 10.1093/mmy/myad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/17/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
The goal of this study was to validate an optimized sample preparation method for filamentous fungal isolates coupled with the use of an in-house library for the identification of moulds using Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in a multicenter context. For that purpose, three Spanish microbiology laboratories participated in the identification of 97 fungal isolates using MALDI-TOF MS coupled with the Filamentous Fungi library 3.0 (Bruker Daltonics) and an in-house library containing 314 unique fungal references. The isolates analyzed belonged to 25 species from the genus Aspergillus, Fusarium, Scedosporium/Lomentospora, the Mucorales order and the Dermatophytes group. MALDI-TOF MS identification was carried out from hyphae resuspended in water and ethanol. After a high-speed centrifugation step, the supernatant was discarded and the pellet submitted to a standard protein extraction step. The protein extract was analyzed with the MBT Smart MALDI Biotyper system (Bruker Daltonics). The rate of accurate, species-level identification obtained ranged between 84.5% and 94.8% and the score values were 1.8 for 72.2-94.9% of the cases. Two laboratories failed to identify only one isolate of Syncephalastrum sp. and Trichophyton rubrum, respectively and three isolates could not be identified in the third center (F. proliferatum, n = 1; T.interdigitale, n = 2). In conclusion, the availability of an effective sample preparation method and an extended database allowed high rates of correct identification of fungal species using MALDI-TOF MS. Some species, such as Trichophyton spp. are still difficult to identify. Although further improvements are still required, the developed methodology allowed the reliable identification of most fungal species.
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Affiliation(s)
- Margarita Estreya Zvezdanova
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
| | - Manuel González de Aledo
- Clinical Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña 15006, Spain
| | | | - Jesús Ortega
- Clinical Microbiology Department, Hospital Universitario Virgen de Valme, Seville 41014, Spain
| | - Andrés Canut
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Carmen Castro
- Clinical Microbiology Department, Hospital Universitario Virgen de Valme, Seville 41014, Spain
| | - Carmen Gomez
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Silvia Hernáez
- Clinical Microbiology Department, Hospital Universitario de Álava, Vitoria-Gasteiz 01009, Spain
| | - Marina Oviaño
- Clinical Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña 15006, Spain
| | - María Ercibengoa
- Biodonostia Institute, Department of respiratory diseases and antimicrobial resistance, San Sebastián 20014, Spain
| | - Miriam Alkorta
- Biodonostia Institute, Department of diseases preventable by vaccination, San Sebastián 20014, Spain
- Clinical Microbiology Department, Hospital Universitario Donostia, San Sebastian 20014, Spain
- Microbiology Department, Faculty of Medicine, Universidad del País Vasco/ EHU-Donostia, San Sebastian 20014, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid 28007, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - David Rodriguez-Temporal
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
| | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón -IiSGM-, Madrid 28007, Spain
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10
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Puius YA, Azar MM, Tsai H, Vergidis P, Harris CE, Anjan S, Barros N, Belga S, Chuang ST, Czeresnia JM, Goel S, Ince D, Luk A, Majeed A, Multani A, Obeid KM, Swaminathan N. Transplantid.net: A Pilot Crowdsourced, Living, Online Library of Resources for the Teaching and Practice of Transplant Infectious Diseases. Open Forum Infect Dis 2023; 10:ofad081. [PMID: 36861087 PMCID: PMC9969731 DOI: 10.1093/ofid/ofad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The field of transplant infectious diseases is rapidly evolving, presenting a challenge for clinical practice and trainee education. Here we describe the construction of transplantid.net, a free online library, crowdsourced and continuously updated for the dual purpose of point-of-care evidence-based management and teaching.
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Affiliation(s)
- Yoram A Puius
- Correspondence: Yoram A. Puius, MD, PhD, Division of Infectious Diseases, Montefiore Medical Center, 111 E 210th St, Bronx, NY 10467 ()
| | - Marwan M Azar
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Helen Tsai
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA
| | - Paschalis Vergidis
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Courtney E Harris
- Division of Infectious Diseases, Brigham and Women’s Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Shweta Anjan
- Division of Infectious Disease, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Nicolas Barros
- Division of Infectious Diseases, Indiana University Health, Indianapolis, Indiana, USA
| | - Sara Belga
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sally T Chuang
- Division of Infectious Diseases, Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jonathan M Czeresnia
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA
| | - Shipra Goel
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Dilek Ince
- Division of Infectious Diseases, Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Alfred Luk
- Section of Infectious Diseases, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Aneela Majeed
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ashrit Multani
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Karam M Obeid
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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11
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Brown Epstein HA. Come aboard the Magnet Journey. Med Ref Serv Q 2023; 42:38-46. [PMID: 36862615 DOI: 10.1080/02763869.2023.2160130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In 2007, Diane Ream Rourke published in this journal, the history and explanation for Baptist Hospital in Florida to include its library on its successful Magnet journey. This article draws heavily from American Nursing Credentialing Center (ANCC) Magnet Information pages. It begins with a quick review of the history of the Program, further suggestions for a librarian's contribution to obtain Magnet Recognition and a brief current literature review on the values Magnet Recognition brings to a hospital's economics, patient care, and nursing staff. The quick history review and suggestions on the librarian contribution to the Magnet journey are based on an invited CE course by this author. The literature review on the values Magnet Recognition brings to a hospital's economics, patient care, and nursing staff was part of a presentation this author prepared for the Chief of Nursing. This author was a Magnet Champion and Magnet exemplar when Virtua Health first earned its first Magnet designation.
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12
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Kashkin KN, Kotova ES, Alekseenko IV, Bulanenkova SS, Akopov SB, Kopantzev EP, Nikolaev LG, Chernov IP, Didych DA. Efficient Selection of Enhancers and Promoters from MIA PaCa-2 Pancreatic Cancer Cells by ChIP-lentiMPRA. Int J Mol Sci 2022; 23:ijms232315011. [PMID: 36499347 PMCID: PMC9740945 DOI: 10.3390/ijms232315011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
A library of active genome regulatory elements (putative promoters and enhancers) from MIA PaCa-2 pancreatic adenocarcinoma cells was constructed using a specially designed lentiviral vector and a massive parallel reporter assay (ChIP-lentiMPRA). Chromatin immunoprecipitation of the cell genomic DNA by H3K27ac antibodies was used for primary enrichment of the library for regulatory elements. Totally, 11,264 unique genome regions, many of which are capable of enhancing the expression of the CopGFP reporter gene from the minimal CMV promoter, were identified. The regions tend to be located near promoters. Based on the proximity assay, we found an enrichment of highly expressed genes among those associated with three or more mapped distal regions (2 kb distant from the 5'-ends of genes). It was shown significant enrichment of genes related to carcinogenesis or Mia PaCa-2 cell identity genes in this group. In contrast, genes associated with 1-2 distal regions or only with proximal regions (within 2 kbp of the 5'-ends of genes) are more often related to housekeeping functions. Thus, ChIP-lentiMPRA is a useful strategy for creating libraries of regulatory elements for the study of tumor-specific gene transcription.
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Affiliation(s)
- Kirill Nikitich Kashkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Elena Sergeevna Kotova
- Laboratory of Human Molecular Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Street, 1a, 119435 Moscow, Russia
| | - Irina Vasilievna Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Svetlana Sergeevna Bulanenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Sergey Borisovich Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Eugene Pavlovich Kopantzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Lev Grigorievich Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Igor Pavlovich Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Dmitry Alexandrovich Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-919-777-4620
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13
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Zinn E, Unzu C, Schmit PF, Turunen HT, Zabaleta N, Sanmiguel J, Fieldsend A, Bhatt U, Diop C, Merkel E, Gurrala R, Peacker B, Rios C, Messemer K, Santos J, Estelien R, Andres-Mateos E, Wagers AJ, Tipper C, Vandenberghe LH. Ancestral library identifies conserved reprogrammable liver motif on AAV capsid. Cell Rep Med 2022; 3:100803. [PMID: 36327973 PMCID: PMC9729830 DOI: 10.1016/j.xcrm.2022.100803] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/18/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
Gene therapy is emerging as a modality in 21st-century medicine. Adeno-associated viral (AAV) gene transfer is a leading technology to achieve efficient and durable expression of a therapeutic transgene. However, the structural complexity of the capsid has constrained efforts to engineer the particle toward improved clinical safety and efficacy. Here, we generate a curated library of barcoded AAVs with mutations across a variety of functionally relevant motifs. We then screen this library in vitro and in vivo in mice and nonhuman primates, enabling a broad, multiparametric assessment of every vector within the library. Among the results, we note a single residue that modulates liver transduction across all interrogated models while preserving transduction in heart and skeletal muscles. Moreover, we find that this mutation can be grafted into AAV9 and leads to profound liver detargeting while retaining muscle transduction-a finding potentially relevant to preventing hepatoxicities seen in clinical studies.
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Affiliation(s)
- Eric Zinn
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Carmen Unzu
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Pauline F Schmit
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Heikki T Turunen
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Julio Sanmiguel
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Allegra Fieldsend
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Urja Bhatt
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Cheikh Diop
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Erin Merkel
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Rakesh Gurrala
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Bryan Peacker
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Rios
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen Messemer
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer Santos
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Reynette Estelien
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Eva Andres-Mateos
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Amy J Wagers
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA; Joslin Diabetes Center, Boston, MA 02215, USA
| | - Christopher Tipper
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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14
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Tunahan GI, Altamirano H. Seating Behaviour of Students before and after the COVID-19 Pandemic: Findings from Occupancy Monitoring with PIR Sensors at the UCL Bartlett Library. Int J Environ Res Public Health 2022; 19:13255. [PMID: 36293841 PMCID: PMC9602605 DOI: 10.3390/ijerph192013255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Since the first case of COVID-19 was confirmed in China, social and physical distancing has been promoted worldwide as an effective community mitigation strategy. However, our understanding remains limited regarding how students would resume their activities and use of libraries when the restrictions to manage the spread of coronavirus were lifted. Understanding students' seating behaviour in libraries is required to guarantee that the libraries meet the needs and preferences of students and promote students' health and well-being and satisfaction with the library. This paper aims to explore the changes in the use of study spaces before and after the pandemic. Occupancy data from the UCL Bartlett Library collected at 10-min intervals from motion sensors located underneath desks was used to assess the occupancy within the library and which was then compared to characteristics of the space. This study revealed that the COVID-19 pandemic significantly impacted students' use of the library as well as how much time they spent there. While seats with a good combination of daylight, outdoor view and privacy were in most demand before the pandemic, distance from other students seems to be the priority after the pandemic. Students' seating preferences appear to be also influenced by the position of desk dividers after COVID-19. Future research should focus on assessing and proposing new seating arrangements and developing strategies to promote students' satisfaction with libraries in response to changes in students' seating behaviours.
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15
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Cecchi T. Scent of knowledge: The molecular fingerprint of volatiles in an emblematic historical library in Italy. Indoor Air 2022; 32:e13139. [PMID: 36305069 DOI: 10.1111/ina.13139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Heritage guidelines recognize odors as a value associated with a place. This study aims to clarify the connection between heritage and volatile organic compounds at the molecular level. At variance with previous studies, usually focused only on book-related compounds from accelerated degradation tests, the whole air of one of the most significant historical libraries in Italy was studied. A sampling of the volatiles off-gassing from the two most iconic rooms, respectively open and forbidden to visitors, was performed via a non-invasive, nondestructive green method, solid-phase-micro-extraction. The gas-chromatographic analyses resulted in the appraisal of olfactory contributions from books, storage environment, and, for the first time, anthropic activities and pollution.Concerning the paper decay process, for the very first time, the presence of 2-ethyl-1-hexanol in the chromatographic signature of the library air is rationalized according to the Guerbet reaction. The presence of all other compounds is explained by the paper decay process, anthropic sources, and pollution. Indoor air comprises analytes related to paper decay, identified by previous studies, and additional compounds never found before.Most volatile compounds are aliphatic and aromatic hydrocarbons, aldehydes, alcohols, terpenes, and terpenoids. Odor contributions from a selected number of analytes were pinpointed. Alkanes dominate the volatiles chromatographic signature, and impart a slight hydrocarbon smell. Aromatics supplement their characteristic aromatic odor. Aldehydes' very low odor threshold makes them strongly contribute to both fruity and fatty descriptors. Benzaldehyde, furfural, vanillin, and camphor add, respectively, an hint of almond, bread, vanilla, and camphor. Alcohols such as 2-ethyl hexanol have a floral scent. Wood-related terpenes and terpenoids contribute to the woody smell of the library.The digital molecular fingerprint of the "scent of knowledge" enables documentation, conservation, and future chemical reproduction of the historical library odor.
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16
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Tognetti M, Sklodowski K, Müller S, Kamber D, Muntel J, Bruderer R, Reiter L. Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area. J Proteome Res 2022; 21:1718-1735. [PMID: 35605973 PMCID: PMC9251764 DOI: 10.1021/acs.jproteome.2c00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The plasma proteome
has the potential to enable a holistic analysis
of the health state of an individual. However, plasma biomarker discovery
is difficult due to its high dynamic range and variability. Here,
we present a novel automated analytical approach for deep plasma profiling
and applied it to a 180-sample cohort of human plasma from lung, breast,
colorectal, pancreatic, and prostate cancers. Using a controlled quantitative
experiment, we demonstrate a 257% increase in protein identification
and a 263% increase in significantly differentially abundant proteins
over neat plasma. In the cohort, we identified 2732 proteins. Using
machine learning, we discovered biomarker candidates such as STAT3
in colorectal cancer and developed models that classify the diseased
state. For pancreatic cancer, a separation by stage was achieved.
Importantly, biomarker candidates came predominantly from the low
abundance region, demonstrating the necessity to deeply profile because
they would have been missed by shallow profiling.
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Affiliation(s)
| | | | | | | | - Jan Muntel
- Biognosys, Schlieren, Zurich 8952, Switzerland
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17
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Castillo JJ, Couture G, Bacalzo NP Jr, Chen Y, Chin EL, Blecksmith SE, Bouzid YY, Vainberg Y, Masarweh C, Zhou Q, Smilowitz JT, German JB, Mills DA, Lemay DG, Lebrilla CB. The Development of the Davis Food Glycopedia-A Glycan Encyclopedia of Food. Nutrients 2022; 14:1639. [PMID: 35458202 DOI: 10.3390/nu14081639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/03/2022] [Accepted: 04/12/2022] [Indexed: 12/17/2022] Open
Abstract
The molecular complexity of the carbohydrates consumed by humans has been deceptively oversimplified due to a lack of analytical methods that possess the throughput, sensitivity, and resolution required to provide quantitative structural information. However, such information is becoming an integral part of understanding how specific glycan structures impact health through their interaction with the gut microbiome and host physiology. This work presents a detailed catalogue of the glycans present in complementary foods commonly consumed by toddlers during weaning and foods commonly consumed by American adults. The monosaccharide compositions of over 800 foods from diverse food groups including Fruits, Vegetables, Grain Products, Beans, Peas, Other Legumes, Nuts, Seeds; Sugars, Sweets and Beverages; Animal Products, and more were obtained and used to construct the “Davis Food Glycopedia” (DFG), an open-access database that provides quantitative structural information on the carbohydrates in food. While many foods within the same group possessed similar compositions, hierarchical clustering analysis revealed similarities between different groups as well. Such a Glycopedia can be used to formulate diets rich in specific monosaccharide residues to provide a more targeted modulation of the gut microbiome, thereby opening the door for a new class of prophylactic or therapeutic diets.
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18
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Stokes AM. Disruption of Library Services Due to Hospital Cyberattack: A Case Study. Med Ref Serv Q 2022; 41:204-212. [PMID: 35511424 DOI: 10.1080/02763869.2022.2054198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyberattacks on healthcare organizations increased dramatically in 2020 and 2021. The University of Vermont Medical Center suffered an attack in October 2020, during the second wave of the COVID-19 pandemic. The disruption to hospital computer systems had wide-ranging impacts, including loss of online access to the medical library for nearly three months. Library staff worked to reduce impacts and increase access for hospital employees until full access was restored. This case study offers lessons learned and resources for health sciences libraries planning for a potential cyberattack.
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Affiliation(s)
- Alice M Stokes
- Dana Medical Library, University of Vermont, Burlington, USA
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19
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Lokmic-Tomkins Z, Cochrane L, Celeste T, Burnie M. An Interdisciplinary Partnership Approach to Improving the Digital Literacy Skills of Nursing Students to Become Digitally Fluent, Work-Ready Graduates. Stud Health Technol Inform 2021; 284:103-107. [PMID: 34920484 DOI: 10.3233/shti210679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Digital transformation and the development of a digitally fluent nursing workforce are necessary for engagement with digital technologies in healthcare settings. For this purpose, educators aim to develop workforce-ready graduates equipped with disciplinary knowledge, expertise, and digital capabilities supportive of further professional development. Having identified a subset of nursing students with low levels of digital literacy, the nursing faculty engaged with library services and the academic skills unit to develop and embed a sustainable Nursing Digital Literacy Module in the graduate entry to practice nursing program. This paper reports on the model created and early evaluation of the student uptake of the module.
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Affiliation(s)
- Zerina Lokmic-Tomkins
- Department of Nursing, The University of Melbourne, Australia.,Centre for Digital Transformation of Health, The University of Melbourne, Australia
| | - Lindy Cochrane
- Library Services, The University of Melbourne, Australia
| | - Tania Celeste
- Library Services, The University of Melbourne, Australia
| | - Morag Burnie
- Academic Skills Unit, The University of Melbourne, Australia
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20
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Abstract
Current antiviral drugs are limited because of their adverse side effects and increased rate of resistance. In recent decades, much scientific effort has been invested in the discovery of new synthetic and natural compounds with promising antiviral properties. Among this new generation of compounds, antimicrobial peptides with antiviral activity have been described and are attracting attention due to their mechanism of action and biological properties. To understand the potential of antiviral peptides (AVPs), we analyse the antiviral activity of well-known AVP families isolated from different natural sources, discuss their physical-chemical properties, and demonstrate how AVP databases can guide us to design synthetic AVPs with better therapeutic properties. All considerations in this sphere of antiviral therapy clearly demonstrate the remarkable contribution that AVPs may make in conquering old as well as newly emerging viruses that plague humanity.
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Affiliation(s)
- Hovakim Zakaryan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, 0014, Yerevan, Armenia
- Denovo Sciences CJSC, 0033, Yerevan, Armenia
| | - Garri Chilingaryan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, 0014, Yerevan, Armenia
| | - Erik Arabyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, 0014, Yerevan, Armenia
| | | | - Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5900, USA
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21
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Kim DM, Go MJ, Lee J, Na D, Yoo SM. Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies. Molecules 2021; 26:molecules26175187. [PMID: 34500620 PMCID: PMC8434002 DOI: 10.3390/molecules26175187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.
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Affiliation(s)
- Dong-Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea;
| | - Myeong-June Go
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
- Correspondence: (D.N.); (S.-M.Y.)
| | - Seung-Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
- Correspondence: (D.N.); (S.-M.Y.)
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22
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Teh R, Azimi A, Ali M, Mann G, Fernández-Peñas P. Specialised skin cancer spectral library for use in data-independent mass spectrometry. Proteomics 2021; 21:e2100128. [PMID: 34374218 DOI: 10.1002/pmic.202100128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Rachel Teh
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, 2145, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, Westmead, New South Wales, 2145, Australia
| | - Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, 2145, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, Westmead, New South Wales, 2145, Australia
| | - Marina Ali
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, 2145, Australia
| | - Graham Mann
- Centre for Cancer Research, Westmead Institute for Medical Research, Westmead, New South Wales, 2145, Australia.,The John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, ACT, 2601, Australia
| | - Pablo Fernández-Peñas
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, 2145, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, Westmead, New South Wales, 2145, Australia
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23
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Carle V, Kong XD, Comberlato A, Edwards C, Díaz-Perlas C, Heinis C. Generation of a 100-billion cyclic peptide phage display library having a high skeletal diversity. Protein Eng Des Sel 2021; 34:6333815. [PMID: 34341825 DOI: 10.1093/protein/gzab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Phage display is a powerful technique routinely used for the generation of peptide- or protein-based ligands. The success of phage display selections critically depends on the size and structural diversity of the libraries, but the generation of large libraries remains challenging. In this work, we have succeeded in developing a phage display library comprising around 100 billion different (bi)cyclic peptides and thus more structures than any previously reported cyclic peptide phage display library. Building such a high diversity was achieved by combining a recently reported library cloning technique, based on whole plasmid PCR, with a small plasmid that facilitated bacterial transformation. The library cloned is based on 273 different peptide backbones and thus has a large skeletal diversity. Panning of the peptide repertoire against the important thrombosis target coagulation factor XI enriched high-affinity peptides with long consensus sequences that can only be found if the library diversity is large.
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Affiliation(s)
- Vanessa Carle
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Alice Comberlato
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Chelsea Edwards
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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24
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Lavarello C, Barco S, Bartolucci M, Panfoli I, Magi E, Tripodi G, Petretto A, Cangemi G. Development of an Accurate Mass Retention Time Database for Untargeted Metabolomic Analysis and Its Application to Plasma and Urine Pediatric Samples. Molecules 2021; 26:molecules26144256. [PMID: 34299531 PMCID: PMC8303579 DOI: 10.3390/molecules26144256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 07/09/2021] [Indexed: 01/17/2023] Open
Abstract
Liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is currently the method of choice for untargeted metabolomic analysis. The availability of established protocols to achieve a high confidence identification of metabolites is crucial. The aim of this work is to describe the workflow that we have applied to build an Accurate Mass Retention Time (AMRT) database using a commercial metabolite library of standards. LC-HRMS analysis was carried out using a Vanquish Horizon UHPLC system coupled to a Q-Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Milan, Italy). The fragmentation spectra, obtained with 12 collision energies, were acquired for each metabolite, in both polarities, through flow injection analysis. Several chromatographic conditions were tested to obtain a protocol that yielded stable retention times. The adopted chromatographic protocol included a gradient separation using a reversed phase (Waters Acquity BEH C18) and a HILIC (Waters Acquity BEH Amide) column. An AMRT database of 518 compounds was obtained and tested on real plasma and urine samples analyzed in data-dependent acquisition mode. Our AMRT library allowed a level 1 identification, according to the Metabolomics Standards Initiative, of 132 and 124 metabolites in human pediatric plasma and urine samples, respectively. This library represents a starting point for future metabolomic studies in pediatric settings.
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Affiliation(s)
- Chiara Lavarello
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (C.L.); (M.B.)
- Department of Chemistry and Industrial Chemistry, University of Genoa, 16146 Genoa, Italy;
| | - Sebastiano Barco
- Chromatography and Mass Spectrometry Section, Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.B.); (G.T.); (G.C.)
| | - Martina Bartolucci
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (C.L.); (M.B.)
| | - Isabella Panfoli
- DIFAR-Biochemistry Laboratory, University of Genoa, 16132 Genova, Italy;
| | - Emanuele Magi
- Department of Chemistry and Industrial Chemistry, University of Genoa, 16146 Genoa, Italy;
| | - Gino Tripodi
- Chromatography and Mass Spectrometry Section, Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.B.); (G.T.); (G.C.)
| | - Andrea Petretto
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (C.L.); (M.B.)
- Correspondence: ; Tel.: +39-01056362911
| | - Giuliana Cangemi
- Chromatography and Mass Spectrometry Section, Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.B.); (G.T.); (G.C.)
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25
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Liu Y, Ye Q, Zeng F, Jiang X, Cai B, Lv W, Wen J. Library-driven approach for fast implementation of the voxel spread function to correct magnetic field inhomogeneity artifacts for gradient-echo sequences. Med Phys 2021; 48:3714-3720. [PMID: 33914914 DOI: 10.1002/mp.14904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Previously developed Voxel Spread Function (VSF) method (Yablonskiy, et al, MRM, 2013;70:1283) provides solution to correct artifacts induced by macroscopic magnetic field inhomogeneity in the images obtained by multi-Gradient-Recalled-Echo (mGRE) techniques. The goal of this study was to develop a library-driven approach for fast VSF implementation. METHODS The VSF approach describes the contribution of the magnetic field inhomogeneity effects on the mGRE signal decay in terms of the F-function calculated from mGRE phase and magnitude images. A pre-calculated library accounting for a variety of background field gradients caused by magnetic field inhomogeneity was used herein to speed up the calculation of F-function. Quantitative R2* maps from the mGRE data collected from two healthy volunteers were generated using the library as validation. RESULTS As compared with direct calculation of the F-function based on a voxel-wise approach, the new library-driven method substantially reduces computational time from several hours to few minutes, while, at the same time, providing similar accuracy of R2* mapping. CONCLUSION The new procedure proposed in this study provides a fast post-processing algorithm that can be incorporated in the quantitative analysis of mGRE data to account for background field inhomogeneity artifacts, thus can facilitate the applications of mGRE-based quantitative techniques in clinical practices.
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Affiliation(s)
- Ying Liu
- Department of Radiology, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiong Ye
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Feiyan Zeng
- Department of Radiology, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaohua Jiang
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bin Cai
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO, USA
| | - Weifu Lv
- Department of Radiology, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jie Wen
- Department of Radiology, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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26
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Göttl VL, Schmitt I, Braun K, Peters-Wendisch P, Wendisch VF, Henke NA. CRISPRi- Library-Guided Target Identification for Engineering Carotenoid Production by Corynebacterium glutamicum. Microorganisms 2021; 9:microorganisms9040670. [PMID: 33805131 PMCID: PMC8064071 DOI: 10.3390/microorganisms9040670] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 01/24/2023] Open
Abstract
Corynebacterium glutamicum is a prominent production host for various value-added compounds in white biotechnology. Gene repression by dCas9/clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) allows for the identification of target genes for metabolic engineering. In this study, a CRISPRi-based library for the repression of 74 genes of C. glutamicum was constructed. The chosen genes included genes encoding enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle, regulatory genes, as well as genes of the methylerythritol phosphate and carotenoid biosynthesis pathways. As expected, CRISPRi-mediated repression of the carotenogenesis repressor gene crtR resulted in increased pigmentation and cellular content of the native carotenoid pigment decaprenoxanthin. CRISPRi screening identified 14 genes that affected decaprenoxanthin biosynthesis when repressed. Carotenoid biosynthesis was significantly decreased upon CRISPRi-mediated repression of 11 of these genes, while repression of 3 genes was beneficial for decaprenoxanthin production. Largely, but not in all cases, deletion of selected genes identified in the CRISPRi screen confirmed the pigmentation phenotypes obtained by CRISPRi. Notably, deletion of pgi as well as of gapA improved decaprenoxanthin levels 43-fold and 9-fold, respectively. The scope of the designed library to identify metabolic engineering targets, transfer of gene repression to stable gene deletion, and limitations of the approach were discussed.
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27
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Rampler E, Hermann G, Grabmann G, El Abiead Y, Schoeny H, Baumgartinger C, Köcher T, Koellensperger G. Benchmarking Non-Targeted Metabolomics Using Yeast-Derived Libraries. Metabolites 2021; 11:metabo11030160. [PMID: 33802096 PMCID: PMC7998801 DOI: 10.3390/metabo11030160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Non-targeted analysis by high-resolution mass spectrometry (HRMS) is an essential discovery tool in metabolomics. To date, standardization and validation remain a challenge. Community-wide accepted cost-effective benchmark materials are lacking. In this work, we propose yeast (Pichia pastoris) extracts derived from fully controlled fermentations for this purpose. We established an open-source metabolite library of >200 identified metabolites based on compound identification by accurate mass, matching retention times, and MS/MS, as well as a comprehensive literature search. The library includes metabolites from the classes of (1) organic acids and derivatives (2) nucleosides, nucleotides, and analogs, (3) lipids and lipid-like molecules, (4) organic oxygen compounds, (5) organoheterocyclic compounds, (6) organic nitrogen compounds, and (7) benzoids at expected concentrations ranges of sub-nM to µM. As yeast is a eukaryotic organism, key regulatory elements are highly conserved between yeast and all annotated metabolites were also reported in the human metabolome database (HMDB). Orthogonal state-of-the-art reversed-phase (RP-) and hydrophilic interaction chromatography mass spectrometry (HILIC-MS) non-targeted analysis and authentic standards revealed that 104 out of the 206 confirmed metabolites were reproducibly recovered and stable over the course of three years when stored at −80 °C. Overall, 67 out of these 104 metabolites were identified with comparably stable areas over all three yeast fermentation and are the ideal starting point for benchmarking experiments. The provided yeast benchmark material enabled not only to test for the chemical space and coverage upon method implementation and developments but also allowed in-house routines for instrumental performance tests. Transferring the quality control strategy of proteomics workflows based on the number of protein identification in HeLa extracts, metabolite IDs in the yeast benchmarking material can be used as metabolomics quality control. Finally, the benchmark material opens new avenues for batch-to-batch corrections in large-scale non-targeted metabolomics studies.
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Affiliation(s)
- Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
- ISOtopic Solutions, Währinger Str. 38, 1090 Vienna, Austria
| | - Gerlinde Grabmann
- Metabolomics Core Facility, Vienna BioCenter Core Facilities, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria; (G.G.); (T.K.)
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
| | - Christoph Baumgartinger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
| | - Thomas Köcher
- Metabolomics Core Facility, Vienna BioCenter Core Facilities, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria; (G.G.); (T.K.)
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; (E.R.); (G.H.); (Y.E.A.); (H.S.); (C.B.)
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Correspondence:
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Abstract
Facing increasing caseloads and an everchanging drug landscape, forensic laboratories have been implementing new analytical tools. Direct analysis in real time mass spectrometry (DART-MS) is often one of these tools because it provides a wealth of information from a rapid, simple analysis. The data produced by these systems, while extremely useful, can be difficult to interpret, especially in the case of complex mixtures, and therefore, mass spectral databases are often used to assist in interpretation of data. Development of these databases can be expensive and time-consuming and often relies on manual evaluation of the underlying data. The National Institute of Standards and Technology (NIST) released an initial DART-MS in-source collisional-induced dissociation mass spectral database for seized drugs in the early 2010s but it has not been updated to reflect the increasing prevalence of novel psychoactive substances. Recently, efforts to update the database have been undertaken. To assist in development of the database, an automated data evaluation process was also created. This manuscript describes the new NIST DART-MS Forensics Database and the steps taken to automate the data evaluation process.
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Affiliation(s)
- Edward Sisco
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Arun S Moorthy
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Laura M Watt
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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Mazure ES, Colburn JL, Wallace E, Justice EM, Shaw S, Stigleman S. Librarian Contributions to a Regional Response in the COVID-19 Pandemic in Western North Carolina. Med Ref Serv Q 2021; 40:79-89. [PMID: 33625326 DOI: 10.1080/02763869.2021.1873626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
At the start of the COVID-19 pandemic, the Mountain Area Health Education Center formed a response team with the goal of building capacity across Western North Carolina health systems to collectively identify needs, coordinate resources to fill gaps, and strategically manage the regional threats of the pandemic. The library team collaborated on interprofessional projects by gathering information and using LibGuides to quickly and easily organize and share resources. The team met challenges, including moving to telecommuting, balancing a growing workload, and navigating a changing information landscape, and in doing so, strengthened relationships across the organization and the region.
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Affiliation(s)
- Emily S Mazure
- UNC Health Sciences at MAHEC, University of North Carolina, Asheville, USA
| | - Joan L Colburn
- UNC Health Sciences at MAHEC, University of North Carolina, Asheville, USA
| | - Elisabeth Wallace
- UNC Health Sciences at MAHEC, University of North Carolina, Asheville, USA
| | - Ellen M Justice
- UNC Health Sciences at MAHEC, University of North Carolina, Asheville, USA
| | - Scout Shaw
- UNC Health Sciences at MAHEC, University of North Carolina, Asheville, USA
| | - Sue Stigleman
- UNC Health Sciences at MAHEC, University of North Carolina, Asheville, USA
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30
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Pierre R, Brethon A, Jacques SA, Blond A, Chambon S, Talano S, Raffin C, Musicki B, Bouix-Peter C, Tomas L, Ouvry G, Morgentin R, Hennequin LF, Harris CS. Novel library synthesis of 3,4-disubstituted pyridin-2(1 H)-ones via cleavage of pyridine-2-oxy-7-azabenzotriazole ethers under ionic hydrogenation conditions at room temperature. Beilstein J Org Chem 2021; 17:156-165. [PMID: 33564326 PMCID: PMC7849264 DOI: 10.3762/bjoc.17.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/24/2020] [Indexed: 11/23/2022] Open
Abstract
In our hands, efficient access to the 4-amino-3-carboxamide disubstituted pyridine-2(1H)-one kinase hinge-binder motif proved to be more challenging than anticipated requiring a significant investment in route scouting and optimization. This full paper focuses on the synthesis issues that we encountered during our route exploration and the original solutions we found that helped us to identify two optimized library-style processes to prepare our large kinase inhibitor library.
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Affiliation(s)
- Romain Pierre
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
| | - Anne Brethon
- Edelris, 60, Avenue Rockefeller, Bioparc, Bioserra 1 Building, 69008 Lyon, France
| | - Sylvain A Jacques
- Edelris, 60, Avenue Rockefeller, Bioparc, Bioserra 1 Building, 69008 Lyon, France
| | - Aurélie Blond
- Edelris, 60, Avenue Rockefeller, Bioparc, Bioserra 1 Building, 69008 Lyon, France
| | - Sandrine Chambon
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
| | - Sandrine Talano
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
| | - Catherine Raffin
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
| | | | | | - Loic Tomas
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
| | - Gilles Ouvry
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
| | - Rémy Morgentin
- Edelris, 60, Avenue Rockefeller, Bioparc, Bioserra 1 Building, 69008 Lyon, France
| | | | - Craig S Harris
- Galderma SA, Rue d'Entre-deux-Villes 10, 1814 Vevey, Switzerland
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31
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Lee HW, Jeon JI, Lim HB, Lee KB, Park SY, Lee CM. A Preliminary Research Study for Distribution Characteristics and Sources of Indoor Air Pollutants in the Valuable Archive of the National Library of Korea. Int J Environ Res Public Health 2021; 18:ijerph18041715. [PMID: 33578932 PMCID: PMC7916716 DOI: 10.3390/ijerph18041715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 11/16/2022]
Abstract
Important records can be damaged directly and indirectly. Their restoration, if possible, is difficult as it is very time-consuming and costly. Although measures have been taken to permanently preserve records, most studies focus on preventing short-term damage from physical or biological factors and not on preventive measures against chemical damage from long-term polluted air exposure. This study investigated the types, concentrations, and distribution characteristics of hazardous chemicals present in the valuable archive of the National Library of Korea (NLK) and identified the sources of these pollutants. Mean SO2, NOX, CO, CO2, and total volatile organic compound (TVOC) concentrations were 1.49 ± 0.44 ppb, 30.52 ± 19.70 ppb, 0.75 ± 0.21 ppm, 368.91 ± 32.23 ppm, and 320.03 ± 44.20 µg/m3, respectively, meeting the Ministry of the Interior and Safety (MOIS) of Korea standards. Toluene (66.43 ± 10.69 µg/m3) and acetaldehyde (157.23 ± 6.43 µg/m3) were present at the highest concentrations, respectively. Two principal components were extracted via a principal component analysis; the primary component (66%) was closely related to outdoor pollution sources and the secondary component (33%) to indoor sources. Results contribute to establishing air quality standards and management measures for preservation of this archive.
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Affiliation(s)
- Hye-Won Lee
- Department of Health Science, Korea University, Seoul 02841, Korea;
- Institute of Risk Assessment, SeoKyeong University, Seoul 02713, Korea
| | - Jeong-In Jeon
- Department of Nano & Biological Engineering, SeoKyeong University, Seoul 02713, Korea; (J.-I.J.); (H.-B.L.)
| | - Hui-Been Lim
- Department of Nano & Biological Engineering, SeoKyeong University, Seoul 02713, Korea; (J.-I.J.); (H.-B.L.)
| | - Kwi-Bok Lee
- Research Center of the Records Preservation, National Library of Korea, Seoul 06579, Korea; (K.-B.L.); (S.-Y.P.)
| | - So-Yeon Park
- Research Center of the Records Preservation, National Library of Korea, Seoul 06579, Korea; (K.-B.L.); (S.-Y.P.)
| | - Cheol-Min Lee
- Institute of Risk Assessment, SeoKyeong University, Seoul 02713, Korea
- Department of Nano & Biological Engineering, SeoKyeong University, Seoul 02713, Korea; (J.-I.J.); (H.-B.L.)
- Correspondence: ; Tel.: +82-940-2924
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32
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Martinez-Martin E, Ferrer E, Vasilev I, del Pobil AP. The UJI Aerial Librarian Robot: A Quadcopter for Visual Library Inventory and Book Localisation. Sensors (Basel) 2021; 21:s21041079. [PMID: 33557363 PMCID: PMC7915268 DOI: 10.3390/s21041079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Over time, the field of robotics has provided solutions to automate routine tasks in different scenarios. In particular, libraries are awakening great interest in automated tasks since they are semi-structured environments where machines coexist with humans and several repetitive operations could be automatically performed. In addition, multirotor aerial vehicles have become very popular in many applications over the past decade, however autonomous flight in confined spaces still presents a number of challenges and the use of small drones has not been reported as an automated inventory device within libraries. This paper presents the UJI aerial librarian robot that leverages computer vision techniques to autonomously self-localize and navigate in a library for automated inventory and book localization. A control strategy to navigate along the library bookcases is presented by using visual markers for self-localization during a visual inspection of bookshelves. An image-based book recognition technique is described that combines computer vision techniques to detect the tags on the book spines, followed by an optical character recognizer (OCR) to convert the book code on the tags into text. These data can be used for library inventory. Misplaced books can be automatically detected, and a particular book can be located within the library. Our quadrotor robot was tested in a real library with promising results. The problems encountered and limitation of the system are discussed, along with its relation to similar applications, such as automated inventory in warehouses.
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Affiliation(s)
- Ester Martinez-Martin
- RoViT, Department of Computer Science and Artificial Intelligence, University of Alicante, 03690 Alicante, Spain
- Correspondence:
| | - Eric Ferrer
- Robotic Intelligence Lab (RobInLab), Department of Engineering and Computer Science, Universitat Jaume I, 12071 Castellón, Spain; (E.F.); (I.V.); (A.P.d.P.)
| | - Ilia Vasilev
- Robotic Intelligence Lab (RobInLab), Department of Engineering and Computer Science, Universitat Jaume I, 12071 Castellón, Spain; (E.F.); (I.V.); (A.P.d.P.)
| | - Angel P. del Pobil
- Robotic Intelligence Lab (RobInLab), Department of Engineering and Computer Science, Universitat Jaume I, 12071 Castellón, Spain; (E.F.); (I.V.); (A.P.d.P.)
- Department of Interaction Science, Sungkyunkwan University, Seoul 110-745, Korea
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33
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Abstract
BACKGROUND According to ergonomic researches regarding a good sitting posture, it is essential to ensure a natural back-curve in order to prevent musculoskeletal disorders. A brief observation among the Scientific Technology Library inside the University of Salerno showed that students used to complain about neck and lumbar pain, especially after a study day. OBJECTIVE On the light of this background, a sitting posture comfort analysis had been performed on chairs inside the library to check the critical factors that influence the postural comfort and, consequently, the learning. METHODS A prolonged sitting posture, that is common during the daily study activity, had been simulated with fifteen volunteer students performing 1-hour tests (divided into four 15-minutes tasks). Subjective perceptions had been gathered through questionnaires rating on a 5-point Comfort scale, both the expected comfort at the beginning of the experiment and the Localized Postural Comfort at the end of each task have been investigated. Then, postural angles had been gathered through photographic acquisition and Kinovea®. CaMAN software had been used to calculate the objective (dis)comfort indexes. Finally, subjective and objective data had been statistically processed and compared. RESULTS Lumbar area scored the lowest perceived comfort while the perceived comfort was independent of participants and tasks, but dependent on time. CONCLUSIONS After this comfort-driven analysis, critical factors of the chair-design were checked, and a proposal for a future re-design was hypothesized.
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34
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Kim T, Cho S, Oh H, Hur J, Kim H, Choi YH, Jeon S, Yang YD, Kim SH. Design of Anticancer 2,4-Diaminopyrimidines as Novel Anoctamin 1 (ANO1) Ion Channel Blockers. Molecules 2020; 25:E5180. [PMID: 33172169 DOI: 10.3390/molecules25215180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Pyrimidine is a privileged scaffold in many synthetic compounds exhibiting diverse pharmacological activities, and is used for therapeutic applications in a broad spectrum of human diseases. In this study, we prepared a small set of pyrimidine libraries based on the structure of two hit compounds that were identified through the screening of an in-house library in order to identify an inhibitor of anoctamin 1 (ANO1). ANO1 is amplified in various types of human malignant tumors, such as head and neck, parathyroid, and gastrointestinal stromal tumors, as well as in breast, lung, and prostate cancers. After initial screening and further structure optimization, we identified Aa3 as a dose-dependent ANO1 blocker. This compound exhibited more potent anti-cancer activity in the NCI-H460 cell line, expressing high levels of ANO1 compared with that in A549 cells that express low levels of ANO1. Our results open a new direction for the development of small-molecule ANO1 blockers composed of a pyrimidine scaffold and a nitrogen-containing heterocyclic moiety, with drug-like properties.
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35
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Abstract
Collaboration between several College of Medicine departments, including the library, resulted in a creation of a new service for faculty during the COVID-19 pandemic crisis. By combining efforts, support for teaching online became a united effort and much less daunting for faculty, who could consult one group for online teaching support, rather than three or four different entities. The resulting endeavor led to a website FAQ and consulting email address that is accessible to all faculty to provide focused and timely technology and education assistance to faculty.
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Affiliation(s)
- Michael P Cote
- Harrell Health Sciences Library Research and Learning Commons, Pennsylvania State University College of Medicine, Hershey, USA
| | - Eliza M Donne
- Harrell Health Sciences Library Research and Learning Commons, Pennsylvania State University College of Medicine, Hershey, USA
| | - Benjamin D Hoover
- Harrell Health Sciences Library Research and Learning Commons, Pennsylvania State University College of Medicine, Hershey, USA
| | - Kelly Thormodson
- Harrell Health Sciences Library Research and Learning Commons, Pennsylvania State University College of Medicine, Hershey, USA
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36
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Hajeri PB, Sharma NS, Yamamoto M. Oncolytic Adenoviruses: Strategies for Improved Targeting and Specificity. Cancers (Basel) 2020; 12:E1504. [PMID: 32526919 DOI: 10.3390/cancers12061504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is a major health problem. Most of the treatments exhibit systemic toxicity, as they are not targeted or specific to cancerous cells and tumors. Adenoviruses are very promising gene delivery vectors and have immense potential to deliver targeted therapy. Here, we review a wide range of strategies that have been tried, tested, and demonstrated to enhance the specificity of oncolytic viruses towards specific cancer cells. A combination of these strategies and other conventional therapies may be more effective than any of those strategies alone.
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37
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Abstract
In this unit, we describe a set of protocols and recommendations for Illumina library preparation. We review best practices in template quantitation methods; template fragmentation methodologies; solid-phase reverse-immobilization cleanup, including buffer exchange and size selection; end repair, A-tailing, and adapter ligation; indexing strategies; considerations regarding whether to use polymerase chain reaction; final library quantification methodologies; and normalization and pooling strategies. These workflows are applicable to both high-throughput and low-throughput Illumina library preparation and should help reduce bias, increase cost effectiveness, and produce high library yields. This is an extensive update of the previous version of this unit. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Iraad F Bronner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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38
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Lei T, Xiao B, He Y, Qu J, Sun Z, Li L. [Development and applications of CRISPR/Cas9 library screening technology in cancer research]. Nan Fang Yi Ke Da Xue Xue Bao 2019; 39:1381-1386. [PMID: 31852637 DOI: 10.12122/j.issn.1673-4254.2019.11.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The CRISPR/Cas9 technology has developed rapidly in recent years with fast, simple and accurate editing functions to allow gene knockout, knock in, activation and interference. It has become a powerful genetic screening tool and been widely used in various models including cell lines, mice and zebrafish. The application of CRISPR system in constructing genome library for high-throughput screening is the main strategy for target gene research of diseases, especially neoplasms. Here we summarize the rationales and recent development of CRISPR/Cas9 library screening technology, the strategies for improving the off-target effects, the basic workflow of library screening and the application of this technology in tumor research.
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Affiliation(s)
- Ting Lei
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China.,Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Bin Xiao
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Yongyin He
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China.,Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jing Qu
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Zhaohui Sun
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Linhai Li
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
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39
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Schmit PF, Pacouret S, Zinn E, Telford E, Nicolaou F, Broucque F, Andres-Mateos E, Xiao R, Penaud-Budloo M, Bouzelha M, Jaulin N, Adjali O, Ayuso E, Vandenberghe LH. Cross-Packaging and Capsid Mosaic Formation in Multiplexed AAV Libraries. Mol Ther Methods Clin Dev 2019; 17:107-121. [PMID: 31909084 PMCID: PMC6938944 DOI: 10.1016/j.omtm.2019.11.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022]
Abstract
Generation and screening of libraries of adeno-associated virus (AAV) variants have emerged as a powerful method for identifying novel capsids for gene therapy applications. For the majority of libraries, vast population diversity requires multiplexed production, in which a library of inverted terminal repeat (ITR)-containing plasmid variants is transfected together into cells to generate the viral library. This process has the potential to be confounded by cross-packaging and mosaicism, in which particles are comprised of genomes and capsid monomers derived from different library members. Here, we investigate the prevalence of cross-packaging and mosaicism in simplified, minimal libraries using novel assays designed to assess capsid composition and packaging fidelity. We show that AAV library variants are prone to cross-packaging and capsid mosaic formation when produced at high plasmid levels, although to a lesser extent than in a recombinant context. We also provide experimental evidence that dilution of input library DNA significantly increases capsid monomer homogeneity and increases capsid:genome correlation in AAV libraries. Lastly, we determine that similar dilution methods yield higher-quality libraries when used for in vivo screens. Together, these findings quantitatively characterized the prevalence of cross-packaging and mosaicism in AAV libraries and established conditions that minimize related noise in subsequent screens.
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Affiliation(s)
- Pauline F Schmit
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA
| | - Simon Pacouret
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA.,INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Eric Zinn
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA
| | - Elizabeth Telford
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA
| | - Fotini Nicolaou
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA
| | - Frédéric Broucque
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Eva Andres-Mateos
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA
| | - Ru Xiao
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA
| | - Magalie Penaud-Budloo
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Mohammed Bouzelha
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Nicolas Jaulin
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Oumeya Adjali
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Eduard Ayuso
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA 02114, USA.,Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
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40
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Egbewande FA, Coster MJ, Jenkins ID, Davis RA. Reaction of Papaverine with Baran Diversinates TM. Molecules 2019; 24:molecules24213938. [PMID: 31683610 PMCID: PMC6864744 DOI: 10.3390/molecules24213938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/24/2019] [Accepted: 10/28/2019] [Indexed: 12/01/2022] Open
Abstract
The reaction of papaverine with a series of Baran DiversinatesTM is reported. Although the yields were low, it was possible to synthesize a small biodiscovery library using this plant alkaloid as a scaffold for late-stage C–H functionalization. Ten papaverine analogues (2–11), including seven new compounds, were synthesized. An unexpected radical-induced exchange reaction is reported where the dimethoxybenzyl group of papaverine was replaced by an alkyl group. This side reaction enabled the synthesis of additional novel fragments based on the isoquinoline scaffold, which is present in numerous natural products. Possible reasons for the poor yields in the DiversinateTM reactions with this particular scaffold are discussed.
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Affiliation(s)
- Folake A Egbewande
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Mark J Coster
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Ian D Jenkins
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
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41
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Abstract
In experimental psychology, subjects are often confronted with computer-based experimental paradigms. Creating such paradigms can require a lot of effort. PyParadigm is a newly developed Python library to ease the development of such paradigms by employing a declarative approach to build user interfaces (UIs). Paradigm specifications in this approach requires much less code and training than in alternative libraries. Although PyParadigm was initially developed for the creation of experimental paradigms, it is generally suited to build UIs that display or interact with 2D objects.
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Affiliation(s)
- Felix G Knorr
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - Johannes Petzold
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
| | - Michael Marxen
- Department of Psychiatry and Neuroimaging Center, Technische Universität Dresden, Dresden, Germany
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42
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Seth-Smith HMB, Bonfiglio F, Cuénod A, Reist J, Egli A, Wüthrich D. Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation. Front Public Health 2019; 7:241. [PMID: 31508405 PMCID: PMC6719548 DOI: 10.3389/fpubh.2019.00241] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022] Open
Abstract
Whole genome sequencing (WGS) has become the new gold standard for bacterial outbreak investigation, due to the high resolution available for typing. While sequencing is currently predominantly performed on Illumina devices, the preceding library preparation can be performed using various protocols. Enzymatic fragmentation library preparation protocols are fast, have minimal hands-on time, and work with small quantities of DNA. The aim of our study was to compare three library preparation protocols for molecular typing: Nextera XT (Illumina); Nextera Flex (Illumina); and QIAseq FX (Qiagen). We selected 12 ATCC strains from human Gram-positive and Gram-negative pathogens with %G+C-content ranging from 27% (Fusobacterium nucleatum) to 73% (Micrococcus luteus), each having a high quality complete genome assembly available, to allow in-depth analysis of the resulting Illumina sequence data quality. Additionally, we selected isolates from previously analyzed cases of vancomycin-resistant Enterococcus faecium (VRE) (n = 7) and a local outbreak of Klebsiella aerogenes (n = 5). The number of protocol steps and time required were compared, in order to test the suitability for routine laboratory work. Data analyses were performed with standard tools commonly used in outbreak situations: Ridom SeqSphere+ for cgMLST; CLC genomics workbench for SNP analysis; and open source programs. Nextera Flex and QIAseq FX were found to be less sensitive than Nextera XT to variable %G+C-content, resulting in an almost uniform distribution of read-depth. Therefore, low coverage regions are reduced to a minimum resulting in a more complete representation of the genome. Thus, with these two protocols, more alleles were detected in the cgMLST analysis, producing a higher resolution of closely related isolates. Furthermore, they result in a more complete representation of accessory genes. In particular, the high data quality and relative simplicity of the workflow of Nextera Flex stood out in this comparison. This thorough comparison within an ISO/IEC 17025 accredited environment will be of interest to those aiming to optimize their clinical microbiological genome sequencing.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,DBM Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ferdinando Bonfiglio
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Personalized Health Basel, University of Basel, Basel, Switzerland
| | - Aline Cuénod
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josiane Reist
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Daniel Wüthrich
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,DBM Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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43
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Vázquez Bernat N, Corcoran M, Hardt U, Kaduk M, Phad GE, Martin M, Karlsson Hedestam GB. High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis. Front Immunol 2019; 10:660. [PMID: 31024532 PMCID: PMC6459949 DOI: 10.3389/fimmu.2019.00660] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing (NGS) of immunoglobulin (Ig) repertoires (Rep-seq) enables examination of the adaptive immune system at an unprecedented level. Applications include studies of expressed repertoires, gene usage, somatic hypermutation levels, Ig lineage tracing and identification of genetic variation within the Ig loci through inference methods. All these applications require starting libraries that allow the generation of sequence data with low error rate and optimal representation of the expressed repertoire. Here, we provide detailed protocols for the production of libraries suitable for human Ig germline gene inference and Ig repertoire studies. Various parameters used in the process were tested in order to demonstrate factors that are critical to obtain high quality libraries. We demonstrate an improved 5'RACE technique that reduces the length constraints of Illumina MiSeq based Rep-seq analysis but allows for the acquisition of sequences upstream of Ig V genes, useful for primer design. We then describe a 5' multiplex method for library preparation, which yields full length V(D)J sequences suitable for genotype identification and novel gene inference. We provide comprehensive sets of primers targeting IGHV, IGKV, and IGLV genes. Using the optimized protocol, we produced IgM, IgG, IgK, and IgL libraries and analyzed them using the germline inference tool IgDiscover to identify expressed germline V alleles. This process additionally uncovered three IGHV, one IGKV, and six IGLV novel alleles in a single individual, which are absent from the IMGT reference database, highlighting the need for further study of Ig genetic variation. The library generation protocols presented here enable a robust means of analyzing expressed Ig repertoires, identifying novel alleles and producing individualized germline gene databases from humans.
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Affiliation(s)
- Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Uta Hardt
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ganesh E. Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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44
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Heidrich J, Sperl LE, Boeckler FM. Embracing the Diversity of Halogen Bonding Motifs in Fragment-Based Drug Discovery-Construction of a Diversity-Optimized Halogen-Enriched Fragment Library. Front Chem 2019; 7:9. [PMID: 30834240 PMCID: PMC6387937 DOI: 10.3389/fchem.2019.00009] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/07/2019] [Indexed: 12/30/2022] Open
Abstract
Halogen bonds have recently gained attention in life sciences and drug discovery. However, it can be difficult to harness their full potential, when newly introducing them into an established hit or lead structure by molecular design. A possible solution to overcome this problem is the use of halogen-enriched fragment libraries (HEFLibs), which consist of chemical probes that provide the opportunity to identify halogen bonds as one of the main features of the binding mode. Initially, we have suggested the HEFLibs concept when constructing a focused library for finding p53 mutant stabilizers. Herein, we broaden and extent this concept aiming for a general HEFLib comprising a huge diversity of binding motifs and, thus, increasing the applicability to various targets. Using the construction principle of feature trees, we represent each halogenated fragment by treating all simple to complex substituents as modifiers of the central (hetero)arylhalide. This approach allows us to focus on the proximal binding interface around the halogen bond and, thus, its integration into a network of interactions based on the fragment's binding motif. As a first illustrative example, we generated a library of 198 fragments that unifies a two-fold strategy: Besides achieving a diversity-optimized basis of the library, we have extended this "core" by structurally similar "satellite compounds" that exhibit quite different halogen bonding interfaces. Tuning effects, i.e., increasing the magnitude of the σ-hole, can have an essential influence on the strength of the halogen bond. We were able to implement this key feature into the diversity selection, based on the rapid and efficient prediction of the highest positive electrostatic potential on the electron isodensity surface, representing the σ-hole, by VmaxPred.
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Affiliation(s)
- Johannes Heidrich
- Lab for Molecular Design & Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Laura E. Sperl
- Lab for Molecular Design & Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Frank M. Boeckler
- Lab for Molecular Design & Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
- Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Tübingen, Germany
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45
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Liu X, Yang X, Sun W, Wu Q, Song Y, Yuan L, Yang G. Systematic Evolution of Ligands by Exosome Enrichment: A Proof-of-Concept Study for Exosome-Based Targeting Peptide Screening. ACTA ACUST UNITED AC 2018; 3:e1800275. [PMID: 32627374 DOI: 10.1002/adbi.201800275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/04/2018] [Indexed: 11/10/2022]
Abstract
Selection of a peptide that binds preferentially to targeted cells or tissues is a prerequisite for targeted therapy. Although in vivo phage display is a high-throughput method, it is restricted in identifying target ligands specific for different vascular beds. In this study, the exosomes are repurposed for targeting peptide screening. Briefly, the signal peptide region of Lamp2b (a membrane protein on the exosomes) in the N-terminus is engineered to fuse with 10 aa long random peptides, while the C-terminus of Lamp2b is fused with the MS2 coating protein (MCP). Then, the whole Lamp2b-MCP open reading frame (ORF) is further engineered to harbor a 3'UTR sequence consisting of MS2. The resultant exosomes from engineered Lamp2b-MCP expressing cells display the 10 aa peptides on the outside while containing the genetic information inside. By proof-of-principle experiments, the exosomes with different peptides could preferentially distribute to different tissues besides the spleen and liver. Furthermore, detailed target sequences for different tissues are enriched by rounds of selection. In summary, the established novel targeted peptide screening strategy, namely, "exosome display," has broad applicability, especially for displaying and screening targeted peptides for the cells outside the capillary with condense barriers, like the neurons in the brain.
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Affiliation(s)
- Xiangwei Liu
- Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture Department of Implant Dentistry, State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases, Fourth Military Medical University, Xi'an, 710032, China
| | - Xuekang Yang
- Department of Burn Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Wenqi Sun
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xinshi Road NO. 569th, Xi'an, 710038, China
| | - Qi Wu
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yingliang Song
- Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture Department of Implant Dentistry, State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases, Fourth Military Medical University, Xi'an, 710032, China
| | - Lijun Yuan
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xinshi Road NO. 569th, Xi'an, 710038, China
| | - Guodong Yang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
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46
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Cabanes-Creus M, Ginn SL, Amaya AK, Liao SHY, Westhaus A, Hallwirth CV, Wilmott P, Ward J, Dilworth KL, Santilli G, Rybicki A, Nakai H, Thrasher AJ, Filip AC, Alexander IE, Lisowski L. Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality. Mol Ther Methods Clin Dev 2018; 12:71-84. [PMID: 30534580 PMCID: PMC6279885 DOI: 10.1016/j.omtm.2018.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/29/2018] [Indexed: 12/22/2022]
Abstract
Adeno-associated virus (AAV) vectors have become one of the most widely used gene transfer tools in human gene therapy. Considerable effort is currently being focused on AAV capsid engineering strategies with the aim of developing novel variants with enhanced tropism for specific human cell types, decreased human seroreactivity, and increased manufacturability. Selection strategies based on directed evolution rely on the generation of highly variable AAV capsid libraries using methods such as DNA-family shuffling, a technique reliant on stretches of high DNA sequence identity between input parental capsid sequences. This identity dependence for reassembly of shuffled capsids is inherently limiting and results in decreased shuffling efficiency as the phylogenetic distance between parental AAV capsids increases. To overcome this limitation, we have developed a novel codon-optimization algorithm that exploits evolutionarily defined codon usage at each amino acid residue in the parental sequences. This method increases average sequence identity between capsids, while enhancing the probability of retaining capsid functionality, and facilitates incorporation of phylogenetically distant serotypes into the DNA-shuffled libraries. This technology will help accelerate the discovery of an increasingly powerful repertoire of AAV capsid variants for cell-type and disease-specific applications.
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Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Sophia H Y Liao
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Adrian Westhaus
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Patrick Wilmott
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jason Ward
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kimberley L Dilworth
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgia Santilli
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Arkadiusz Rybicki
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hiroyuki Nakai
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adrian C Filip
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2145, Australia
| | - Leszek Lisowski
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, 24-100 Puławy, Poland
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Millán-Esteban D, Reyes-García D, García-Casado Z, Bañuls J, López-Guerrero JA, Requena C, Rodríguez-Hernández A, Traves V, Nagore E. Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests. Biotechniques 2018; 65:79-85. [PMID: 30091391 DOI: 10.2144/btn-2018-0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of melanoma FFPE samples for an amplicon-based NGS custom panel analysis. DNA was extracted from unstained melanoma samples and wide local excision samples. Amplicon-based libraries were constructed and tested using time and quality parameters as variables. Time elapsed from sample retrieval >7 years, a quality control value > 5.63 and a DNA integrity value < 2.05 indicated samples were not suitable. A decision tree is provided with rate of samples suitable for analysis according to the combination of these parameters.
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48
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Butkovic M. History of the CMCC Health Science Library 1945 - present. J Can Chiropr Assoc 2018; 62:62-71. [PMID: 30270929 PMCID: PMC6160899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This paper traces the development of the CMCC Health Sciences Library from its humble beginning in 1945 to the present day. In the early years of its development the library grew and prospered thanks to the support of early pioneers, the believers in the importance of the library to chiropractic education. In the later years of its growth and in spite of some challenges, with the support of CMCC presidents Dr. Ian Coulter and Dr. Jean Moss, and the academic deans Dr. Al Adams and Dr. John Mrozek, the library prospered. The Library at the new campus is a hub of intellectual life for our students and faculty, and a source of information for chiropractors and other healthcare professionals.
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Abstract
The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .
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Affiliation(s)
- Andrew Collins
- Department of Functional and Comparative Genomics, Institute of Integrated Biology, University of Liverpool , Liverpool, L69 7ZB, United Kingdom
| | - Andrew R Jones
- Department of Functional and Comparative Genomics, Institute of Integrated Biology, University of Liverpool , Liverpool, L69 7ZB, United Kingdom
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50
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Paulk NK, Pekrun K, Zhu E, Nygaard S, Li B, Xu J, Chu K, Leborgne C, Dane AP, Haft A, Zhang Y, Zhang F, Morton C, Valentine MB, Davidoff AM, Nathwani AC, Mingozzi F, Grompe M, Alexander IE, Lisowski L, Kay MA. Bioengineered AAV Capsids with Combined High Human Liver Transduction In Vivo and Unique Humoral Seroreactivity. Mol Ther 2018; 26:289-303. [PMID: 29055620 PMCID: PMC5763027 DOI: 10.1016/j.ymthe.2017.09.021] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/17/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
Existing recombinant adeno-associated virus (rAAV) serotypes for delivering in vivo gene therapy treatments for human liver diseases have not yielded combined high-level human hepatocyte transduction and favorable humoral neutralization properties in diverse patient groups. Yet, these combined properties are important for therapeutic efficacy. To bioengineer capsids that exhibit both unique seroreactivity profiles and functionally transduce human hepatocytes at therapeutically relevant levels, we performed multiplexed sequential directed evolution screens using diverse capsid libraries in both primary human hepatocytes in vivo and with pooled human sera from thousands of patients. AAV libraries were subjected to five rounds of in vivo selection in xenografted mice with human livers to isolate an enriched human-hepatotropic library that was then used as input for a sequential on-bead screen against pooled human immunoglobulins. Evolved variants were vectorized and validated against existing hepatotropic serotypes. Two of the evolved AAV serotypes, NP40 and NP59, exhibited dramatically improved functional human hepatocyte transduction in vivo in xenografted mice with human livers, along with favorable human seroreactivity profiles, compared with existing serotypes. These novel capsids represent enhanced vector delivery systems for future human liver gene therapy applications.
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Affiliation(s)
- Nicole K Paulk
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Katja Pekrun
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erhua Zhu
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Sean Nygaard
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Bin Li
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jianpeng Xu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kirk Chu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Allison P Dane
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Annelise Haft
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Yue Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chris Morton
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Marcus B Valentine
- Cytogenetic Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amit C Nathwani
- Department of Haematology, UCL Cancer Institute, London, UK; Department of Haematology and Katharine Dormandy Haemophilia Centre & Thrombosis Unit, Royal Free London NHS Foundation Trust Hospital, London, UK; National Health Services Blood and Transplant, Watford, UK
| | - Federico Mingozzi
- Genethon and INSERM U951, Evry, France; University Pierre and Marie Curie, Paris, France
| | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ian E Alexander
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Leszek Lisowski
- Translational Vectorology Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia; Military Institute of Hygiene and Epidemiology (MIHE), Puławy, Poland
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.
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