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  1. Article: IST1 regulates select endosomal recycling pathways.

    Clippinger, Amy K / Naismith, Teresa V / Yoo, Wonjin / Jansen, Silvia / Kast, David / Hanson, Phyllis I

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ESCRTs (Endosomal Sorting Complex Required for Transport) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intralumenal vesicles (ILVs) to generate multivesicular endosomes. While most ... ...

    Abstract ESCRTs (Endosomal Sorting Complex Required for Transport) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intralumenal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome.
    Language English
    Publishing date 2023-08-19
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.31.551359
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: IST1 regulates select recycling pathways.

    Clippinger, Amy K / Naismith, Teresa V / Yoo, Wonjin / Jansen, Silvia / Kast, David J / Hanson, Phyllis I

    Traffic (Copenhagen, Denmark)

    2023  Volume 25, Issue 1, Page(s) e12921

    Abstract: ESCRTs (Endosomal Sorting Complex Required for Transports) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intraluminal vesicles (ILVs) to generate multivesicular endosomes. While most ... ...

    Abstract ESCRTs (Endosomal Sorting Complex Required for Transports) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intraluminal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Functionally, depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy, we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome.
    MeSH term(s) Endosomal Sorting Complexes Required for Transport/metabolism ; Protein Transport ; Endosomes/metabolism ; Multivesicular Bodies/metabolism ; Biological Transport
    Chemical Substances Endosomal Sorting Complexes Required for Transport
    Language English
    Publishing date 2023-11-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 1483852-7
    ISSN 1600-0854 ; 1398-9219
    ISSN (online) 1600-0854
    ISSN 1398-9219
    DOI 10.1111/tra.12921
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Increasing the use of animal-free recombinant antibodies.

    Groff, Katherine / Allen, David / Casey, Warren / Clippinger, Amy

    ALTEX

    2020  Volume 37, Issue 2, Page(s) 309–311

    Abstract: Antibodies are used in a range of research, diagnostic, and regulatory applications. Traditional methods for producing such reagents involve the immunization of animals, which introduces variability into the methods that use them and is not aligned with ... ...

    Abstract Antibodies are used in a range of research, diagnostic, and regulatory applications. Traditional methods for producing such reagents involve the immunization of animals, which introduces variability into the methods that use them and is not aligned with efforts to replace and reduce animal use. Experts from academia, biotechnology, government, and animal protection organizations met December 3, 2019, at the National Institutes of Health in Bethesda, MD, USA to discuss the status of development and use of animal-free recombinant antibodies and their potential to replace antibodies derived from animals. This paper summarizes the discussion and the actions that resulted to facilitate increased production and use of animal-free recombinant antibodies.
    MeSH term(s) Animal Testing Alternatives ; Animals ; Antibodies/chemistry ; Antibodies/immunology ; Recombinant Proteins
    Chemical Substances Antibodies ; Recombinant Proteins
    Language English
    Publishing date 2020-01-08
    Publishing country Germany
    Document type Editorial
    ZDB-ID 165707-0
    ISSN 1868-596X ; 1018-4562 ; 0946-7785
    ISSN 1868-596X ; 1018-4562 ; 0946-7785
    DOI 10.14573/altex.2001071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: An approach to identifying quality research antibodies.

    Groff, Katherine / Allen, David / Fiebig, Michael / Cosson, Pierre / Casey, Warren / Clippinger, Amy J

    BioTechniques

    2022  Volume 73, Issue 4, Page(s) 167–170

    MeSH term(s) Antibodies, Monoclonal
    Chemical Substances Antibodies, Monoclonal
    Language English
    Publishing date 2022-09-23
    Publishing country England
    Document type Editorial
    ZDB-ID 48453-2
    ISSN 1940-9818 ; 0736-6205
    ISSN (online) 1940-9818
    ISSN 0736-6205
    DOI 10.2144/btn-2022-0071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Maximizing the relevance and reproducibility of A549 cell culture using FBS-free media.

    Chary, Aline / Groff, Katherine / Stucki, Andreas O / Contal, Servane / Stoffels, Charlotte / Cambier, Sébastien / Sharma, Monita / Gutleb, Arno C / Clippinger, Amy J

    Toxicology in vitro : an international journal published in association with BIBRA

    2022  Volume 83, Page(s) 105423

    Abstract: Scientists are using in vitro methods to answer important research questions and implementing strategies to maximize the reliability and human relevance of these methods. One strategy is to replace the use of fetal bovine serum (FBS)-an undefined and ... ...

    Abstract Scientists are using in vitro methods to answer important research questions and implementing strategies to maximize the reliability and human relevance of these methods. One strategy is to replace the use of fetal bovine serum (FBS)-an undefined and variable mixture of biomolecules-in cell culture media with chemically defined or xeno-free medium. In this study, A549 cells, a human lung alveolar-like cell line commonly used in respiratory research, were transitioned from a culture medium containing FBS to media without FBS. A successful transition was determined based on analysis of cell morphology and functionality. Following transition to commercially available CnT-Prime Airway (CELLnTEC) or X-VIVO™ 10 (Lonza) medium, the cells were characterized by microscopic evaluation and calculation of doubling time. Their genotype, morphology, and functionality were assessed by monitoring the expression of gene markers for lung cell types, surfactant production, cytokine release, the presence of multilamellar bodies, and cell viability following sodium dodecyl sulphate exposure. Our results showed that A549 cells successfully transitioned to FBS-free media under submerged and air-liquid-interface conditions. Cells grown in X-VIVO™ 10 medium mimicked cellular characteristics of FBS-supplemented media while those grown in CnT-Prime Airway medium demonstrated characteristics possibly more reflective of normal human alveolar epithelial cells.
    MeSH term(s) A549 Cells ; Cell Culture Techniques/methods ; Cells, Cultured ; Culture Media/chemistry ; Culture Media, Serum-Free ; Humans ; Reproducibility of Results ; Serum Albumin, Bovine
    Chemical Substances Culture Media ; Culture Media, Serum-Free ; Serum Albumin, Bovine (27432CM55Q)
    Language English
    Publishing date 2022-06-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 639064-x
    ISSN 1879-3177 ; 0887-2333
    ISSN (online) 1879-3177
    ISSN 0887-2333
    DOI 10.1016/j.tiv.2022.105423
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Cryopreserved human precision-cut lung slices provide an immune competent pulmonary test system for "on-demand" use and long-term cultures.

    Patel, Vivek S / Amin, Khalid / Wahab, Adam / Marimoutou, Méry / Ukishima, Lindsey / Alvarez, Jose / Battle, Kelley / Stucki, Andreas O / Clippinger, Amy J / Behrsing, Holger P

    Toxicological sciences : an official journal of the Society of Toxicology

    2023  Volume 191, Issue 2, Page(s) 253–265

    Abstract: Human precision-cut lung slices (hPCLS), considered a highly relevant ex vivo model of the lung, offer native architecture and cells of the lung tissue including respiratory parenchyma, small airways, and immune competent cells. However, the irregular ... ...

    Abstract Human precision-cut lung slices (hPCLS), considered a highly relevant ex vivo model of the lung, offer native architecture and cells of the lung tissue including respiratory parenchyma, small airways, and immune competent cells. However, the irregular availability of donor lungs has limited the accessibility of this system. As described here, thousands of hPCLS can be created from 1 lung, cryopreserved, and used "on demand" by applying slicing and cryopreservation methodology improvements. Fresh and cryopreserved (∼7 and ∼34 weeks; F&C) hPCLS from 1 donor lung were cultured for up to 29 days and evaluated for biomass, viability, tissue integrity, and inflammatory markers in response to lipopolysaccharide (LPS; 5 µg/ml) and Triton X-100 (TX100; 0.1%) challenge (24 h) at days 1, 8, 15, 22, and 29 following culture initiation. The F&C hPCLS retained biomass, viability, and tissue integrity throughout the 29 days and demonstrated immune responsiveness with up to ∼30-fold LPS-induced cytokine increases. Histologically, more than 70% of normal cytomorphological features were preserved in all groups through day 29. Similar retention of tissue viability and immune responsiveness post cryopreservation (4-6 weeks) and culture (up to 14 days) was observed in hPCLS from additional 3 donor lungs. Banking cryopreserved hPCLS from various donors (and disease states) provides a critical element in researching human-derived pulmonary tissue. The retention of viability and functional responsiveness (≥4 weeks) allows evaluation of long-term, complex endpoints reflecting key events in Adverse Outcome Pathways and positions hPCLS as a valuable human-relevant model for use in regulatory applications.
    MeSH term(s) Humans ; Lipopolysaccharides/toxicity ; Immune System ; Cryopreservation/methods ; Lung/pathology
    Chemical Substances Lipopolysaccharides
    Language English
    Publishing date 2023-01-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1420885-4
    ISSN 1096-0929 ; 1096-6080
    ISSN (online) 1096-0929
    ISSN 1096-6080
    DOI 10.1093/toxsci/kfac136
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Modern affinity reagents: Recombinant antibodies and aptamers.

    Groff, Katherine / Brown, Jeffrey / Clippinger, Amy J

    Biotechnology advances

    2015  Volume 33, Issue 8, Page(s) 1787–1798

    Abstract: Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of ...

    Abstract Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.
    MeSH term(s) Animals ; Antibodies/immunology ; Antibodies/metabolism ; Aptamers, Nucleotide/biosynthesis ; Aptamers, Nucleotide/genetics ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/immunology ; SELEX Aptamer Technique
    Chemical Substances Antibodies ; Aptamers, Nucleotide ; Recombinant Proteins
    Language English
    Publishing date 2015-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 47165-3
    ISSN 1873-1899 ; 0734-9750
    ISSN (online) 1873-1899
    ISSN 0734-9750
    DOI 10.1016/j.biotechadv.2015.10.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Mind the gaps: Prioritizing activities to meet regulatory needs for acute systemic lethality

    Sullivan, Kristie / Allen, David G / Clippinger, Amy J / Wilson, Daniel M / Edwards, Stephen W / Glover, Kyle / Mansouri, Kamel / Settivari, Raja / Wijeyesakere, Sanjeeva J / Casey, Warren

    ALTEX

    2021  Volume 38, Issue 2, Page(s) 327–335

    Abstract: Efforts are underway to develop and implement nonanimal approaches which can characterize acute systemic lethality. A workshop was held in October 2019 to discuss developments in the prediction of acute oral lethality for chemicals and mixtures, as well ... ...

    Abstract Efforts are underway to develop and implement nonanimal approaches which can characterize acute systemic lethality. A workshop was held in October 2019 to discuss developments in the prediction of acute oral lethality for chemicals and mixtures, as well as progress and needs in the understanding and modeling of mechanisms of acute lethality. During the workshop, each speaker led the group through a series of charge questions to determine clear next steps to progress the aims of the workshop. Participants concluded that a variety of approaches will be needed and should be applied in a tiered fashion. Non-testing approaches, including waiving tests, computational models for single chemicals, and calculating the acute lethality of mixtures based on the LD50 values of mixture components, could be used for some assessments now, especially in the very toxic or non-toxic classification ranges. Agencies can develop policies indicating contexts under which mathematical approaches for mixtures assessment are acceptable; to expand applicability, poorly predicted mixtures should be examined to understand discrepancies and adapt the approach. Transparency and an understanding of the variability of in vivo approaches are crucial to facilitate regulatory application of new approaches. In a replacement strategy, mechanistically based in vitro or in silico models will be needed to support non-testing approaches especially for highly acutely toxic chemicals. The workshop discussed approaches that can be used in the immediate or near term for some applications and identified remaining actions needed to implement approaches to fully replace the use of animals for acute systemic toxicity testing.
    MeSH term(s) Animals ; Computer Simulation ; Humans ; Toxicity Tests, Acute
    Language English
    Publishing date 2021-01-21
    Publishing country Germany
    Document type Editorial
    ZDB-ID 165707-0
    ISSN 1868-596X ; 1018-4562 ; 0946-7785
    ISSN 1868-596X ; 1018-4562 ; 0946-7785
    DOI 10.14573/altex.2012121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Using the monocyte activation test as a stand-alone release test for medical devices.

    Brown, Jeffrey / Clippinger, Amy J / Fritz Briglia, Claire / Casey, Warren / Coleman, Kelly / Fritsch, Anja / Hartung, Thomas / Maouyo, Djik / Muller, Thierry / Reich, Johannes / Robert, Laure / Roeder, Ruth / Sanchez, Guillermo / Sawyer, Anita Y / Solati, Shabnam / Tirumalai, Radhakrishna / Zwisler, Walter / Allen, David

    ALTEX

    2021  Volume 38, Issue 1, Page(s) 151–156

    Abstract: Monocyte activation tests (MAT) are widely available but rarely used in place of animal-based pyrogen tests for safety assessment of medical devices. To address this issue, the National Toxicology Program Interagency Center for the Evaluation of ... ...

    Abstract Monocyte activation tests (MAT) are widely available but rarely used in place of animal-based pyrogen tests for safety assessment of medical devices. To address this issue, the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods and the PETA International Science Consortium Ltd. convened a workshop at the National Institutes of Health on September 18-19, 2018. Participants included representatives from MAT testing laboratories, medical device manufacturers, the U.S. Food and Drug Administration's Center for Devices and Radiologic Health (CDRH), the U.S. Pharmacopeia, the International Organization for Standardization, and experts in the development of MAT protocols. Discussions covered industry experiences with the MAT, remaining challenges, and how CDRH's Medical Device Development Tools (MDDT) Program, which qualifies tools for use in evaluating medical devices to streamline device development and regulatory evaluation, could be a pathway to qualify the use of MAT in place of the rabbit pyrogen test and the limulus amebocyte lysate test for medical device testing. Workshop outcomes and follow-up activities are discussed.
    MeSH term(s) Animal Testing Alternatives ; Animals ; Endotoxins ; Equipment and Supplies/adverse effects ; Monocytes/physiology ; Pyrogens ; Rabbits ; Toxicity Tests/methods
    Chemical Substances Endotoxins ; Pyrogens
    Language English
    Publishing date 2021-01-15
    Publishing country Germany
    Document type Editorial
    ZDB-ID 165707-0
    ISSN 1868-596X ; 1018-4562 ; 0946-7785
    ISSN 1868-596X ; 1018-4562 ; 0946-7785
    DOI 10.14573/altex.2012021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Modern affinity reagents: Recombinant antibodies and aptamers

    Groff, Katherine / Amy J. Clippinger / Jeffrey Brown

    Biotechnology Advances. 2015 Dec., v. 33

    2015  

    Abstract: Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of ...

    Abstract Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.
    Keywords animals ; antibody formation ; monoclonal antibodies ; oligonucleotides ; recombinant antibodies
    Language English
    Dates of publication 2015-12
    Size p. 1787-1798.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 47165-3
    ISSN 0734-9750
    ISSN 0734-9750
    DOI 10.1016/j.biotechadv.2015.10.004
    Database NAL-Catalogue (AGRICOLA)

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