1
|
Brettner L, Geiler-Samerotte K. Single-cell heterogeneity in ribosome content and the consequences for the growth laws. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590370. [PMID: 38895328 PMCID: PMC11185559 DOI: 10.1101/2024.04.19.590370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Previous work has suggested that the ribosome content of a cell is optimized to maximize growth given the nutrient availability. The resulting correlation between ribosome number and growth rate appears to be independent of the rate limiting nutrient and has been reported in many organisms. The robustness and universality of this observation has given it the classification of a "growth law." These laws have had powerful impacts on many biological disciplines. They have fueled predictions about how organisms evolve to maximize reproduction, and informed models about how cells regulate growth. Due to methodological limitations, this growth law has rarely been studied at the level of individual cells. While populations of fast-growing cells tend to have more ribosomes than populations of slow-growing cells, it is unclear if individual cells tightly regulate their ribosome content to match their environment. Here, we use recent ground-breaking single-cell RNA sequencing techniques to study this growth law at the single-cell level in two different microbes, S. cerevisiae (a single-celled yeast and eukaryote) and B. subtilis (a bacterium and prokaryote). In both species, we find enormous variation in the ribosomal content of single cells that is not predictive of growth rate. Fast-growing populations include cells showing transcriptional signatures of slow growth and stress, as do cells with the highest ribosome content we survey. Broadening our focus to the levels of non-ribosomal transcripts reveals subpopulations of cells in unique transcriptional states suggestive of divergent growth strategies. These results suggest that single-cell ribosome levels are not finely tuned to match population growth rates or nutrient availability, at least not in a way that can be captured by a unifying law that applies to all cell types. Overall, this work encourages the expansion of these "laws" and other models that predict how growth rates are regulated or how they evolve to consider single-cell heterogeneity.
Collapse
Affiliation(s)
- Leandra Brettner
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Kerry Geiler-Samerotte
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
2
|
Banse SA, Jackson EG, Sedore CA, Onken B, Hall D, Coleman-Hulbert A, Huynh P, Garrett T, Johnson E, Harinath G, Inman D, Guo S, Morshead M, Xue J, Falkowski R, Chen E, Herrera C, Kirsch AJ, Perez VI, Guo M, Lithgow GJ, Driscoll M, Phillips PC. The coupling between healthspan and lifespan in Caenorhabditis depends on complex interactions between compound intervention and genetic background. Aging (Albany NY) 2024; 16:5829-5855. [PMID: 38613792 PMCID: PMC11042945 DOI: 10.18632/aging.205743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/11/2024] [Indexed: 04/15/2024]
Abstract
Aging is characterized by declining health that results in decreased cellular resilience and neuromuscular function. The relationship between lifespan and health, and the influence of genetic background on that relationship, has important implications in the development of pharmacological anti-aging interventions. Here we assessed swimming performance as well as survival under thermal and oxidative stress across a nematode genetic diversity test panel to evaluate health effects for three compounds previously studied in the Caenorhabditis Intervention Testing Program and thought to promote longevity in different ways - NP1 (nitrophenyl piperazine-containing compound 1), propyl gallate, and resveratrol. Overall, we find the relationships among median lifespan, oxidative stress resistance, thermotolerance, and mobility vigor to be complex. We show that oxidative stress resistance and thermotolerance vary with compound intervention, genetic background, and age. The effects of tested compounds on swimming locomotion, in contrast, are largely species-specific. In this study, thermotolerance, but not oxidative stress or swimming ability, correlates with lifespan. Notably, some compounds exert strong impact on some health measures without an equally strong impact on lifespan. Our results demonstrate the importance of assessing health and lifespan across genetic backgrounds in the effort to identify reproducible anti-aging interventions, with data underscoring how personalized treatments might be required to optimize health benefits.
Collapse
Affiliation(s)
- Stephen A. Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - E. Grace Jackson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Christine A. Sedore
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Brian Onken
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David Hall
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | | | - Phu Huynh
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Theo Garrett
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Erik Johnson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Girish Harinath
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Delaney Inman
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Suzhen Guo
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Jian Xue
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ron Falkowski
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christopher Herrera
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Allie J. Kirsch
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Viviana I. Perez
- Division of Aging Biology, National Institute on Aging, Bethesda, MD 20892, USA
| | - Max Guo
- Division of Aging Biology, National Institute on Aging, Bethesda, MD 20892, USA
| | | | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
3
|
Banse SA, Sedore CA, Johnson E, Coleman-Hulbert AL, Onken B, Hall D, Jackson EG, Huynh P, Foulger AC, Guo S, Garrett T, Xue J, Inman D, Morshead ML, Plummer WT, Chen E, Bhaumik D, Chen MK, Harinath G, Chamoli M, Quinn RP, Falkowski R, Edgar D, Schmidt MO, Lucanic M, Guo M, Driscoll M, Lithgow GJ, Phillips PC. Antioxidants green tea extract and nordihydroguaiaretic acid confer species and strain-specific lifespan and health effects in Caenorhabditis nematodes. GeroScience 2024; 46:2239-2251. [PMID: 37923874 PMCID: PMC10828308 DOI: 10.1007/s11357-023-00978-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/08/2023] [Indexed: 11/06/2023] Open
Abstract
The Caenorhabditis Intervention Testing Program (CITP) is an NIH-funded research consortium of investigators who conduct analyses at three independent sites to identify chemical interventions that reproducibly promote health and lifespan in a robust manner. The founding principle of the CITP is that compounds with positive effects across a genetically diverse panel of Caenorhabditis species and strains are likely engaging conserved biochemical pathways to exert their effects. As such, interventions that are broadly efficacious might be considered prominent compounds for translation for pre-clinical research and human clinical applications. Here, we report results generated using a recently streamlined pipeline approach for the evaluation of the effects of chemical compounds on lifespan and health. We studied five compounds previously shown to extend C. elegans lifespan or thought to promote mammalian health: 17α-estradiol, acarbose, green tea extract, nordihydroguaiaretic acid, and rapamycin. We found that green tea extract and nordihydroguaiaretic acid extend Caenorhabditis lifespan in a species-specific manner. Additionally, these two antioxidants conferred assay-specific effects in some studies-for example, decreasing survival for certain genetic backgrounds in manual survival assays in contrast with extended lifespan as assayed using automated C. elegans Lifespan Machines. We also observed that GTE and NDGA impact on older adult mobility capacity is dependent on genetic background, and that GTE reduces oxidative stress resistance in some Caenorhabditis strains. Overall, our analysis of the five compounds supports the general idea that genetic background and assay type can influence lifespan and health effects of compounds, and underscores that lifespan and health can be uncoupled by chemical interventions.
Collapse
Affiliation(s)
- Stephen A Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Christine A Sedore
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Erik Johnson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | | | - Brian Onken
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - David Hall
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - E Grace Jackson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Phu Huynh
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - Anna C Foulger
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Suzhen Guo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - Theo Garrett
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Jian Xue
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - Delaney Inman
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | | | - W Todd Plummer
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - Dipa Bhaumik
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Michelle K Chen
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Girish Harinath
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - Manish Chamoli
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Rose P Quinn
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Ron Falkowski
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA
| | - Daniel Edgar
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Madeline O Schmidt
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Mark Lucanic
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA
| | - Max Guo
- Division of Aging Biology, National Institute On Aging, Bethesda, MD, 20892-9205, USA
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Gordon J Lithgow
- The Buck Institute for Research On Aging, Novato, CA, 94945, USA.
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
| |
Collapse
|
4
|
Baran JK, Kosztyła P, Antoł W, Labocha MK, Sychta K, Drobniak SM, Prokop ZM. Reproductive system, temperature, and genetic background effects in experimentally evolving populations of Caenorhabditis elegans. PLoS One 2024; 19:e0300276. [PMID: 38557670 PMCID: PMC10984399 DOI: 10.1371/journal.pone.0300276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/25/2024] [Indexed: 04/04/2024] Open
Abstract
Experimental evolution (EE) is a powerful research framework for gaining insights into many biological questions, including the evolution of reproductive systems. We designed a long-term and highly replicated EE project using the nematode C. elegans, with the main aim of investigating the impact of reproductive system on adaptation and diversification under environmental challenge. From the laboratory-adapted strain N2, we derived isogenic lines and introgressed the fog-2(q71) mutation, which changes the reproductive system from nearly exclusive selfing to obligatory outcrossing, independently into 3 of them. This way, we obtained 3 pairs of isogenic ancestral populations differing in reproductive system; from these, we derived replicate EE populations and let them evolve in either novel (increased temperature) or control conditions for over 100 generations. Subsequently, fitness of both EE and ancestral populations was assayed under the increased temperature conditions. Importantly, each population was assayed in 2-4 independent blocks, allowing us to gain insight into the reproducibility of fitness scores. We expected to find upward fitness divergence, compared to ancestors, in populations which had evolved in this treatment, particularly in the outcrossing ones due to the benefits of genetic shuffling. However, our data did not support these predictions. The first major finding was very strong effect of replicate block on populations' fitness scores. This indicates that despite standardization procedures, some important environmental effects were varying among blocks, and possibly compounded by epigenetic inheritance. Our second key finding was that patterns of EE populations' divergence from ancestors differed among the ancestral isolines, suggesting that research conclusions derived for any particular genetic background should never be generalized without sampling a wider set of backgrounds. Overall, our results support the calls to pay more attention to biological variability when designing studies and interpreting their results, and to avoid over-generalizations of outcomes obtained for specific genetic and/or environmental conditions.
Collapse
Affiliation(s)
- Joanna K. Baran
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University in Krakow, Krakow, Poland
| | - Paulina Kosztyła
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University in Krakow, Krakow, Poland
| | - Weronika Antoł
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University in Krakow, Krakow, Poland
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Marta K. Labocha
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University in Krakow, Krakow, Poland
| | - Karolina Sychta
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Szymon M. Drobniak
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University in Krakow, Krakow, Poland
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Zofia M. Prokop
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University in Krakow, Krakow, Poland
| |
Collapse
|
5
|
Fanara JJ, Sassi PL, Goenaga J, Hasson E. Genetic basis and repeatability for desiccation resistance in Drosophila melanogaster (Diptera: Drosophilidae). Genetica 2024; 152:1-9. [PMID: 38102503 DOI: 10.1007/s10709-023-00201-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
Dehydration is a stress factor for organisms inhabiting natural habitats where water is scarce. Thus, it may be expected that species facing arid environments will develop mechanisms that maximize resistance to desiccation. Insects are excellent models for studying the effects of dehydration as well as the mechanisms and processes that prevent water loss since the effect of desiccation is greater due to the higher area/volume ratio than larger animals. Even though physiological and behavioral mechanisms to cope with desiccation are being understood, the genetic basis underlying the mechanisms related to variation in desiccation resistance and the context-dependent effect remain unsolved. Here we analyze the genetic bases of desiccation resistance in Drosophila melanogaster and identify candidate genes that underlie trait variation. Our quantitative genetic analysis of desiccation resistance revealed sexual dimorphism and extensive genetic variation. The phenotype-genotype association analyses (GWAS) identified 71 candidate genes responsible for total phenotypic variation in desiccation resistance. Half of these candidate genes were sex-specific suggesting that the genetic architecture underlying this adaptive trait differs between males and females. Moreover, the public availability of desiccation data analyzed on the same lines but in a different lab allows us to investigate the reliability and repeatability of results obtained in independent screens. Our survey indicates a pervasive micro-environment lab-dependent effect since we did not detect overlap in the sets of genes affecting desiccation resistance identified between labs.
Collapse
Affiliation(s)
- Juan Jose Fanara
- Laboratorio de Evolución, Departamento de Ecología Genética y Evolución, Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), CONICET-UBA, FCEN, Buenos Aires, Argentina.
| | - Paola Lorena Sassi
- Grupo de Ecología Integrativa de Fauna Silvestre, Instituto Argentino de Investigaciones de Zonas Áridas, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Julieta Goenaga
- Quality Control & NIR Scientist, Biomar Group, Aarhus, Denmark
| | - Esteban Hasson
- Laboratorio de Evolución, Departamento de Ecología Genética y Evolución, Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), CONICET-UBA, FCEN, Buenos Aires, Argentina
| |
Collapse
|
6
|
Bonuccelli G, Brooks DR, Shepherd S, Sotgia F, Lisanti MP. Antibiotics that target mitochondria extend lifespan in C. elegans. Aging (Albany NY) 2023; 15:11764-11781. [PMID: 37950722 PMCID: PMC10683609 DOI: 10.18632/aging.205229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/13/2023]
Abstract
Aging is a continuous degenerative process caused by a progressive decline of cell and tissue functions in an organism. It is induced by the accumulation of damage that affects normal cellular processes, ultimately leading to cell death. It has been speculated for many years that mitochondria play a key role in the aging process. In the aim of characterizing the implications of mitochondria in aging, here we used Caenorhabditis elegans (C. elegans) as an organismal model treated a panel of mitochondrial inhibitors and assessed for survival. In our study, we assessed survival by evaluating worm lifespan, and we assessed aging markers by evaluating the pharyngeal muscle contraction, the accumulation of lipofuscin pigment and ATP levels. Our results show that treatment of worms with either doxycycline, azithromycin (inhibitors of the small and the large mitochondrial ribosomes, respectively), or a combination of both, significantly extended median lifespan of C. elegans, enhanced their pharyngeal pumping rate, reduced their lipofuscin content and their energy consumption (ATP levels), as compared to control untreated worms, suggesting an aging-abrogating effect for these drugs. Similarly, DPI, an inhibitor of mitochondrial complex I and II, was capable of prolonging the median lifespan of treated worms. On the other hand, subjecting worms to vitamin C, a pro-oxidant, failed to extend C. elegans lifespan and upregulated its energy consumption, revealing an increase in ATP level. Therefore, our longevity study reveals that mitochondrial inhibitors (i.e., mitochondria-targeting antibiotics) could abrogate aging and extend lifespan in C. elegans.
Collapse
Affiliation(s)
- Gloria Bonuccelli
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Darren R. Brooks
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Sally Shepherd
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Federica Sotgia
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Michael P. Lisanti
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| |
Collapse
|
7
|
Lin Y, Lin C, Cao Y, Chen Y. Caenorhabditis elegans as an in vivo model for the identification of natural antioxidants with anti-aging actions. Biomed Pharmacother 2023; 167:115594. [PMID: 37776641 DOI: 10.1016/j.biopha.2023.115594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023] Open
Abstract
Natural antioxidants have recently emerged as a highly exciting and significant topic in anti-aging research. Diverse organism models present a viable protocol for future research. Notably, many breakthroughs on natural antioxidants have been achieved in the nematode Caenorhabditis elegans, an animal model frequently utilized for the study of aging research and anti-aging drugs in vivo. Due to the conservation of signaling pathways on oxidative stress resistance, lifespan regulation, and aging disease between C. elegans and multiple high-level organisms (humans), as well as the low and controllable cost of time and labor, it gradually develops into a trustworthy in vivo model for high-throughput screening and validation of natural antioxidants with anti-aging actions. First, information and models on free radicals and aging are presented in this review. We also describe indexes, detection methods, and molecular mechanisms for studying the in vivo antioxidant and anti-aging effects of natural antioxidants using C. elegans. It includes lifespan, physiological aging processes, oxidative stress levels, antioxidant enzyme activation, and anti-aging pathways. Furthermore, oxidative stress and healthspan improvement induced by natural antioxidants in humans and C. elegans are compared, to understand the potential and limitations of the screening model in preclinical studies. Finally, we emphasize that C. elegans is a useful model for exploring more natural antioxidant resources and uncovering the mechanisms underlying aging-related risk factors and diseases.
Collapse
Affiliation(s)
- Yugui Lin
- Microbiology Laboratory, Zhongshan Bo'ai Hospital, Southern Medical University, Zhongshan 528400, China; Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Chunxiu Lin
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Yunjiao Chen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China.
| |
Collapse
|
8
|
Mendez Q, Driscoll HA, Mirando GR, Acca F, Chapados CD, Jones KS, Weiner M, Li X, Ferguson MR. MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation. J Immunol Methods 2023; 521:113540. [PMID: 37597727 PMCID: PMC10568614 DOI: 10.1016/j.jim.2023.113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.
Collapse
Affiliation(s)
- Qiana Mendez
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Holland A Driscoll
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Gregory R Mirando
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Felicity Acca
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Cassandra D Chapados
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Kezzia S Jones
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Michael Weiner
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Xiaofeng Li
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Mary R Ferguson
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| |
Collapse
|
9
|
Palka JK, Dyba A, Brzozowska J, Antoł W, Sychta K, Prokop ZM. Evolution of fertilization ability in obligatorily outcrossing populations of Caenorhabditis elegans. PeerJ 2023; 11:e15825. [PMID: 37701823 PMCID: PMC10494835 DOI: 10.7717/peerj.15825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
In species reproducing by selfing, the traits connected with outcrossing typically undergo degeneration, a phenomenon called selfing syndrome. In Caenorhabditis elegans nematodes, selfing syndrome affects many traits involved in mating, rendering cross-fertilization highly inefficient. In this study, we investigated the evolution of cross-fertilization efficiency in populations genetically modified to reproduce by obligatory outcrossing. Following the genetic modification, replicate obligatorily outcrossing were maintained for over 100 generations, at either optimal (20 °C) or elevated (24 °C) temperatures, as a part of a broader experimental evolution program. Subsequently, fertilization rates were assayed in the evolving populations, as well as their ancestors who had the obligatory outcrossing introduced but did not go through experimental evolution. Fertilization effectivity was measured by tracking the fractions of fertilized females in age-synchronized populations, through 8 h since reaching adulthood. In order to check the robustness of our measurements, each evolving population was assayed in two or three independent replicate blocks. Indeed, we found high levels of among-block variability in the fertilization trajectories, and in the estimates of divergence between evolving populations and their ancestors. We also identified five populations which appear to have evolved increased fertilization efficiency, relative to their ancestors. However, due to the abovementioned high variability, this set of populations should be treated as candidate, with further replications needed to either confirm or disprove their divergence from ancestors. Furthermore, we also discuss additional observations we have made concerning fertilization trajectories.
Collapse
Affiliation(s)
- Joanna K. Palka
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Cracow, Cracow, Poland
| | - Alicja Dyba
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Cracow, Cracow, Poland
| | - Julia Brzozowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Cracow, Cracow, Poland
| | - Weronika Antoł
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Cracow, Cracow, Poland
| | - Karolina Sychta
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Cracow, Cracow, Poland
| | - Zofia M. Prokop
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Cracow, Cracow, Poland
| |
Collapse
|
10
|
Kinsler G, Schmidlin K, Newell D, Eder R, Apodaca S, Lam G, Petrov D, Geiler-Samerotte K. Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch. J Mol Evol 2023; 91:293-310. [PMID: 37237236 PMCID: PMC10276131 DOI: 10.1007/s00239-023-10114-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
The phrase "survival of the fittest" has become an iconic descriptor of how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.
Collapse
Affiliation(s)
| | - Kara Schmidlin
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Daphne Newell
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Rachel Eder
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Sam Apodaca
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | | | | | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA.
- School of Life Sciences, Arizona State University, Tempe, USA.
| |
Collapse
|
11
|
Hughes RL, Frankenfeld CL, Gohl DM, Huttenhower C, Jackson SA, Vandeputte D, Vogtmann E, Comstock SS, Kable ME. Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]. Nutrients 2023; 15:nu15112451. [PMID: 37299414 DOI: 10.3390/nu15112451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The microbial cells colonizing the human body form an ecosystem that is integral to the regulation and maintenance of human health. Elucidation of specific associations between the human microbiome and health outcomes is facilitating the development of microbiome-targeted recommendations and treatments (e.g., fecal microbiota transplant; pre-, pro-, and post-biotics) to help prevent and treat disease. However, the potential of such recommendations and treatments to improve human health has yet to be fully realized. Technological advances have led to the development and proliferation of a wide range of tools and methods to collect, store, sequence, and analyze microbiome samples. However, differences in methodology at each step in these analytic processes can lead to variability in results due to the unique biases and limitations of each component. This technical variability hampers the detection and validation of associations with small to medium effect sizes. Therefore, the American Society for Nutrition (ASN) Nutritional Microbiology Group Engaging Members (GEM), sponsored by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), hosted a satellite session on methods in nutrition and gut microbiome research to review currently available methods for microbiome research, best practices, as well as tools and standards to aid in comparability of methods and results. This manuscript summarizes the topics and research discussed at the session. Consideration of the guidelines and principles reviewed in this session will increase the accuracy, precision, and comparability of microbiome research and ultimately the understanding of the associations between the human microbiome and health.
Collapse
Affiliation(s)
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Curtis Huttenhower
- Department of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott A Jackson
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Doris Vandeputte
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Mary E Kable
- USDA-ARS Western Human Nutrition Research Center, University of California-Davis, Davis, CA 95616, USA
| |
Collapse
|
12
|
Herbicides widely used in the world: an investigation of toxic effects on Caenorhabditis elegans. Biol Futur 2023:10.1007/s42977-023-00152-9. [PMID: 36639591 DOI: 10.1007/s42977-023-00152-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023]
Abstract
Dicamba, paraquat, picloram, clopyralid and linuron are herbicides widely used in agriculture. The aim of the present study is to evaluate the toxicity effects of the herbicides used on survival, fertility and length of Caenorhabditis elegans. Kaplan-Meier Survival Analysis method was used to identify the toxicity effect of herbicides on survival, and ANOVA and Post Hoc tests were used to determine the toxicity effects on fertility and length. In the study, C. elegans was exposed to 5 different concentrations (62.5, 125, 250, 500, 1000 µM) of each herbicide. When the results were evaluated, it was observed that survival (life span) and length (physical growth) were more affected, respectively, by paraquat, dicamba, linuron, picloram and clopyralid herbicides, fertility (egg productivity) were more affected, respectively, by paraquat, linuron, dicamba, picloram and clopyralid herbicides. As a result, it was determined that increasing the dose amounts of herbicides caused many toxic reactions on C. elegans, affecting survival, egg productivity and length.
Collapse
|
13
|
Hines WC, Hines WC. Lost in transduction: Critical considerations when using viral vectors. Front Cell Dev Biol 2023; 10:1080265. [PMID: 36684429 PMCID: PMC9849944 DOI: 10.3389/fcell.2022.1080265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
The application of retroviral vectors in the laboratory requires considerations that often go overlooked but are often easy to circumvent. Here, we discuss the relationship between the observed transduction efficiency of a cell population and per-cell viral insertions-and describe how differential cell-type susceptibilities can confound results. We consider the math underlying this problem and review an alternative approach to the commonly used "multiplicity of infection" (MOI) method of titering and using viral vectors in the biomedical research laboratory.
Collapse
Affiliation(s)
| | - William C. Hines
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, University of NM, Albuquerque, NM, United States,*Correspondence: William C. Hines III,
| |
Collapse
|
14
|
Weinkove D, Zavagno G. Applying C. elegans to the Industrial Drug Discovery Process to Slow Aging. FRONTIERS IN AGING 2022; 2:740582. [PMID: 35821999 PMCID: PMC9261450 DOI: 10.3389/fragi.2021.740582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/29/2021] [Indexed: 01/29/2023]
Abstract
The increase in our molecular understanding of the biology of aging, coupled with a recent surge in investment, has led to the formation of several companies developing pharmaceuticals to slow aging. Research using the tiny nematode worm Caenorhabditis elegans was the first to show that mutations in single genes can extend lifespan, and subsequent research has shown that this model organism is uniquely suited to testing interventions to slow aging. Yet, with a few notable exceptions, C. elegans is not in the standard toolkit of longevity companies. Here we discuss the paths to overcome the barriers to using C. elegans in industrial drug discovery. We address the predictive power of C. elegans for human aging, how C. elegans research can be applied to specific challenges in the typical drug discovery pipeline, and how standardised and quantitative assays will help C. elegans fulfil its potential in the biotech and pharmaceutical industry. We argue that correct application of this model and its knowledge base will significantly accelerate progress to slow human aging.
Collapse
Affiliation(s)
- David Weinkove
- Department of Biosciences, Durham University, Durham, United Kingdom.,Magnitude Biosciences Ltd., NETpark Plexus, Sedgefield, United Kingdom
| | - Giulia Zavagno
- Department of Biosciences, Durham University, Durham, United Kingdom.,Magnitude Biosciences Ltd., NETpark Plexus, Sedgefield, United Kingdom
| |
Collapse
|
15
|
Feeney MA, Newitt JT, Addington E, Algora-Gallardo L, Allan C, Balis L, Birke AS, Castaño-Espriu L, Charkoudian LK, Devine R, Gayrard D, Hamilton J, Hennrich O, Hoskisson PA, Keith-Baker M, Klein JG, Kruasuwan W, Mark DR, Mast Y, McHugh RE, McLean TC, Mohit E, Munnoch JT, Murray J, Noble K, Otani H, Parra J, Pereira CF, Perry L, Pintor-Escobar L, Pritchard L, Prudence SMM, Russell AH, Schniete JK, Seipke RF, Sélem-Mojica N, Undabarrena A, Vind K, van Wezel GP, Wilkinson B, Worsley SF, Duncan KR, Fernández-Martínez LT, Hutchings MI. ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria. Microb Genom 2022; 8. [PMID: 35775972 PMCID: PMC9455695 DOI: 10.1099/mgen.0.000824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.
Collapse
Affiliation(s)
- Morgan Anne Feeney
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jake Terry Newitt
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Emily Addington
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Lis Algora-Gallardo
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Craig Allan
- Swansea University Institute of Life Science, College of Medicine, Swansea, Wales, UK
| | - Lucas Balis
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anna S Birke
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Laia Castaño-Espriu
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jacob Hamilton
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Oliver Hennrich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Paul A Hoskisson
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Molly Keith-Baker
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Worarat Kruasuwan
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - David R Mark
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Yvonne Mast
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rebecca E McHugh
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Thomas C McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Elmira Mohit
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - John T Munnoch
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jordan Murray
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
| | - Katie Noble
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hiroshi Otani
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA 94720, USA
| | - Jonathan Parra
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Camila F Pereira
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Louisa Perry
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Leighton Pritchard
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Samuel M M Prudence
- School of Biological and Behavioral Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | | | - Jana K Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nelly Sélem-Mojica
- Universidad Nacional Autónoma de México, Centro de Ciencias Matemáticas, en Morelia, Michoacán, Mexico
| | - Agustina Undabarrena
- Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Valparaíso, 2340000, Chile
| | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Rapenburg, The Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| |
Collapse
|
16
|
Fischer I, Martinez-Dominguez MV, Hänggi D, Kahlert U. Reducing sources of variance in experimental procedures in in vitro research. F1000Res 2022; 10:1037. [PMID: 35035893 PMCID: PMC8749900 DOI: 10.12688/f1000research.73497.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Lack of reproducibility in preclinical research poses ethical and economic challenges for biomedical science. Various institutional activities by society stakeholders of leading industrialised nations are currently underway with the aim of improving the situation. Such initiatives are usually concerned with high-level organisational issues and typically do not focus on improving experimental approaches per se. Addressing these is necessary in order to increase consistency and success rates of lab-to-lab repetitions. Methods: In this project, we statistically evaluated repetitive data of a very basic and widely applied lab procedure, namely quantifying the number of viable cells. The purpose of this was to assess the impact of different parameters and instrumentations which may constitute sources of variance in this procedure. Conclusion: By comparing the variability of data acquired under two different procedures, featuring improved stringency of protocol adherence, our project attempts to identify the sources and propose guidelines on how to reduce such fluctuations. We believe our work can contribute to tackling the repeatability crisis in biomedical research.
Collapse
Affiliation(s)
- Igor Fischer
- Department of Neurosurgery, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | | | - Daniel Hänggi
- Department of Neurosurgery, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Ulf Kahlert
- Department of Neurosurgery, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany.,Clinic for General, Visceral, Vascular, and Transplant Surgery, Otto-von-Guericke-Universität Magdeburg, Magdeburg, 39106, Germany
| |
Collapse
|
17
|
Onken B, Sedore CA, Coleman‐Hulbert AL, Hall D, Johnson E, Jones EG, Banse SA, Huynh P, Guo S, Xue J, Chen E, Harinath G, Foulger A, Chao EA, Hope J, Bhaumik D, Plummer T, Inman D, Morshead M, Guo M, Lithgow G, Phillips PC, Driscoll M. Metformin treatment of diverse Caenorhabditis species reveals the importance of genetic background in longevity and healthspan extension outcomes. Aging Cell 2022; 21:e13488. [PMID: 34837316 PMCID: PMC8761014 DOI: 10.1111/acel.13488] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/31/2021] [Accepted: 09/19/2021] [Indexed: 11/30/2022] Open
Abstract
Metformin, the most commonly prescribed anti‐diabetes medication, has multiple reported health benefits, including lowering the risks of cardiovascular disease and cancer, improving cognitive function with age, extending survival in diabetic patients, and, in several animal models, promoting youthful physiology and lifespan. Due to its longevity and health effects, metformin is now the focus of the first proposed clinical trial of an anti‐aging drug—the Targeting Aging with Metformin (TAME) program. Genetic variation will likely influence outcomes when studying metformin health effects in human populations. To test for metformin impact in diverse genetic backgrounds, we measured lifespan and healthspan effects of metformin treatment in three Caenorhabditis species representing genetic variability greater than that between mice and humans. We show that metformin increases median survival in three C. elegans strains, but not in C. briggsae and C. tropicalis strains. In C. briggsae, metformin either has no impact on survival or decreases lifespan. In C. tropicalis, metformin decreases median survival in a dose‐dependent manner. We show that metformin prolongs the period of youthful vigor in all C. elegans strains and in two C. briggsae strains, but that metformin has a negative impact on the locomotion of C. tropicalis strains. Our data demonstrate that metformin can be a robust promoter of healthy aging across different genetic backgrounds, but that genetic variation can determine whether metformin has positive, neutral, or negative lifespan/healthspan impact. These results underscore the importance of tailoring treatment to individuals when testing for metformin health benefits in diverse human populations.
Collapse
Affiliation(s)
- Brian Onken
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | | | | | - David Hall
- The Buck Institute for Research on Aging Novato California USA
| | - Erik Johnson
- Institute of Ecology and Evolution University of Oregon Eugene Oregon USA
| | | | - Stephen A. Banse
- Institute of Ecology and Evolution University of Oregon Eugene Oregon USA
| | - Phu Huynh
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Suzhen Guo
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Jian Xue
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Esteban Chen
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Girish Harinath
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Anna C. Foulger
- The Buck Institute for Research on Aging Novato California USA
| | | | - June Hope
- The Buck Institute for Research on Aging Novato California USA
| | - Dipa Bhaumik
- The Buck Institute for Research on Aging Novato California USA
| | - Todd Plummer
- The Buck Institute for Research on Aging Novato California USA
| | - Delaney Inman
- The Buck Institute for Research on Aging Novato California USA
| | | | - Max Guo
- Division of Aging Biology National Institute on Aging Bethesda Maryland USA
| | | | | | - Monica Driscoll
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| |
Collapse
|
18
|
Jones KS, Chapman AE, Driscoll HA, Fuller EP, Kelly M, Li X, Mansour S, McBride SL, Zhao Q, Weiner M, Ferguson MR. MILKSHAKE: novel validation method for antibodies to post-translationally modified targets by surrogate Western blot. Biotechniques 2022; 72:11-20. [PMID: 34841898 PMCID: PMC10568613 DOI: 10.2144/btn-2021-0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibody (Ab) validation is the procedure in which an Ab is thoroughly assayed for sensitivity and specificity in a given application. Validation of Abs against post-translationally modified (PTM) targets is particularly challenging because it requires specifically prepared antigen. Here we describe a novel validation method using surrogate proteins in a Western blot. The surrogate protein, which we termed 'MILKSHAKE,' is a modified maltose binding protein enzymatically conjugated to a peptide from the chosen target that is either modified or nonmodified at the residue of interest. The certainty of the residue's modification status can be used to confirm Ab specificity. This method also allows for Ab validation even in the absence or limited availability of treated cell lysates.
Collapse
Affiliation(s)
- Kezzia S Jones
- AxioMx, an Abcam Company, Branford, CT, USA
- Abbratech Inc., Branford, CT, USA
| | | | - Holland A Driscoll
- AxioMx, an Abcam Company, Branford, CT, USA
- Abbratech Inc., Branford, CT, USA
| | | | | | - Xiaofeng Li
- AxioMx, an Abcam Company, Branford, CT, USA
- Abbratech Inc., Branford, CT, USA
| | | | | | - Qi Zhao
- AxioMx, an Abcam Company, Branford, CT, USA
- Enrich Therapeutics Inc., Branford, CT, USA
| | - Michael Weiner
- AxioMx, an Abcam Company, Branford, CT, USA
- Abbratech Inc., Branford, CT, USA
| | - Mary R Ferguson
- AxioMx, an Abcam Company, Branford, CT, USA
- Abbratech Inc., Branford, CT, USA
| |
Collapse
|
19
|
Caron M, Gely L, Garvis S, Adrait A, Couté Y, Palladino F, Fabrizio P. Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans. Life Sci Alliance 2021; 5:5/3/e202101140. [PMID: 34893559 PMCID: PMC8675910 DOI: 10.26508/lsa.202101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/06/2023] Open
Abstract
Changes in histone post-translational modifications are associated with aging through poorly defined mechanisms. Histone 3 lysine 4 (H3K4) methylation at promoters is deposited by SET1 family methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans SET1 homolog. We show that set-2(syb2085) animals retain the ability to form COMPASS, but have a marked global loss of H3K4 di- and trimethylation (H3K4me2/3). Reduced H3K4 methylation was accompanied by loss of fertility, as expected; however, in contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks the SET1/COMPASS chromatin-targeting component. These results challenge previously held views and establish that WT H3K4me2/3 levels are essential for normal lifespan in C. elegans.
Collapse
Affiliation(s)
- Matthieu Caron
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Loïc Gely
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Steven Garvis
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Annie Adrait
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Yohann Couté
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Francesca Palladino
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Paola Fabrizio
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| |
Collapse
|
20
|
Workflow for Segmentation of Caenorhabditis elegans from Fluorescence Images for the Quantitation of Lipids. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112311420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The small and transparent nematode Caenorhabditis elegans is increasingly employed for phenotypic in vivo chemical screens. The influence of compounds on worm body fat stores can be assayed with Nile red staining and imaging. Segmentation of C. elegans from fluorescence images is hereby a primary task. In this paper, we present an image-processing workflow that includes machine-learning-based segmentation of C. elegans directly from fluorescence images and quantifies their Nile red lipid-derived fluorescence. The segmentation is based on a J48 classifier using pixel entropies and is refined by size-thresholding. The accuracy of segmentation was >90% in our external validation. Binarization with a global threshold set to the brightness of the vehicle control group worms of each experiment allows a robust and reproducible quantification of worm fluorescence. The workflow is available as a script written in the macro language of imageJ, allowing the user additional manual control of classification results and custom specification settings for binarization. Our approach can be easily adapted to the requirements of other fluorescence image-based experiments with C. elegans.
Collapse
|
21
|
Bonello J, Cachia E, Alfino N. AutoFAIR-A portal for automating FAIR assessments for bioinformatics resources. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1865:194767. [PMID: 34749004 DOI: 10.1016/j.bbagrm.2021.194767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 10/06/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Research in Bioinformatics generates tools and datasets in Bioinformatics at a very fast rate. Meanwhile, a lot of effort is going into making these resources findable and reusable to improve resource discovery by researchers in the course of their work. PURPOSE This paper proposes a semi-automated tool to assess a resource according to the Findability, Accessibility, Interoperability and Reusability (FAIR) criteria. The aim is to create a portal that presents the assessment score together with a report that researchers can use to gauge a resource. METHOD Our system uses internet searches to automate the process of generating FAIR scores. The process is semi-automated in that if a particular property of the FAIR scores has not been captured by AutoFAIR, a user is able to amend and supply the information to complete the assessment. RESULTS We compare our results against FAIRshake that was used as the benchmark tool for comparing the assessments. The results show that AutoFAIR was able to match the FAIR criteria in FAIRshake with minimal intervention from the user. CONCLUSIONS We show that AutoFAIR can be a good repository for storing metadata about tools and datasets, together with comprehensive reports detailing the assessments of the resources. Moreover, AutoFAIR is also able to score workflows, giving an overall indication of the FAIRness of the resources used in a scientific study.
Collapse
Affiliation(s)
- Joseph Bonello
- Department of Computer Information Systems, Faculty of ICT, University of Malta, Malta.
| | - Ernest Cachia
- Department of Computer Information Systems, Faculty of ICT, University of Malta, Malta.
| | - Nigel Alfino
- Department of Computer Information Systems, Faculty of ICT, University of Malta, Malta.
| |
Collapse
|
22
|
|
23
|
Osier ND, Bramlett HM, Shear DA, Mondello S, Carlson SW, Dietrich WD, Deng-Bryant Y, Wang KKW, Hayes RL, Yang Z, Empey PE, Poloyac SM, Lafrenaye AD, Povlishock JT, Gilsdorf JS, Kochanek PM, Dixon CE. Kollidon VA64 Treatment in Traumatic Brain Injury: Operation Brain Trauma Therapy. J Neurotrauma 2021; 38:2454-2472. [PMID: 33843262 DOI: 10.1089/neu.2021.0089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Loss of plasmalemmal integrity may mediate cell death after traumatic brain injury (TBI). Prior studies in controlled cortical impact (CCI) indicated that the membrane resealing agent Kollidon VA64 improved histopathological and functional outcomes. Kollidon VA64 was therefore selected as the seventh therapy tested by the Operation Brain Trauma Therapy consortium, across three pre-clinical TBI rat models: parasagittal fluid percussion injury (FPI), CCI, and penetrating ballistic-like brain injury (PBBI). In each model, rats were randomized to one of four exposures (7-15/group): (1) sham; (2) TBI+vehicle; (3) TBI+Kollidon VA64 low-dose (0.4 g/kg); and (4) TBI+Kollidon VA64 high-dose (0.8 g/kg). A single intravenous VA64 bolus was given 15 min post-injury. Behavioral, histopathological, and serum biomarker outcomes were assessed over 21 days generating a 22-point scoring matrix per model. In FPI, low-dose VA64 produced zero points across behavior and histopathology. High-dose VA64 worsened motor performance compared with TBI-vehicle, producing -2.5 points. In CCI, low-dose VA64 produced intermediate benefit on beam balance and the Morris water maze (MWM), generating +3.5 points, whereas high-dose VA64 showed no effects on behavior or histopathology. In PBBI, neither dose altered behavior or histopathology. Regarding biomarkers, significant increases in glial fibrillary acidic protein (GFAP) levels were seen in TBI versus sham at 4 h and 24 h across models. Benefit of low-dose VA64 on GFAP was seen at 24 h only in FPI. Ubiquitin C-terminal hydrolase-L1 (UCH-L1) was increased in TBI compared with vehicle across models at 4 h but not at 24 h, without treatment effects. Overall, low dose VA64 generated +4.5 points (+3.5 in CCI) whereas high dose generated -2.0 points. The modest/inconsistent benefit observed reduced enthusiasm to pursue further testing.
Collapse
Affiliation(s)
- Nicole D Osier
- Holistic Adult Health Division, University of Texas at Austin, School of Nursing, Austin, Texas, USA
- Department of Neurology, University of Texas at Austin, Dell Medical School, Austin Texas, USA
| | - Helen M Bramlett
- Department of Neurological Surgery, The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, Florida, USA
- Bruce W. Carter Department of Veterans Affairs Medical Center, Miami, Florida, USA
| | - Deborah A Shear
- Brain Trauma Neuroprotection Program, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Shaun W Carlson
- Department of Neurological Surgery, Brain Trauma Research Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - W Dalton Dietrich
- Department of Neurological Surgery, The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Ying Deng-Bryant
- Brain Trauma Neuroprotection Program, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Kevin K W Wang
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, McKnight Brain Institute of the University of Florida, Gainesville, Florida, USA
| | - Ronald L Hayes
- Center for Innovative Research, Center for Proteomics and Biomarkers Research, Banyan Biomarkers, Inc., Alachua, Florida, USA
| | - Zhihui Yang
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, McKnight Brain Institute of the University of Florida, Gainesville, Florida, USA
| | - Philip E Empey
- Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Samuel M Poloyac
- University of Texas Austin School of Pharmacy, Austin, Texas, USA
| | - Audrey D Lafrenaye
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - John T Povlishock
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Janice S Gilsdorf
- Brain Trauma Neuroprotection Program, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick M Kochanek
- Safar Center for Resuscitation Research, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Departments of Pediatrics, Anesthesiology, and Clinical and Translational Science, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh Pennsylvania, USA
| | - C Edward Dixon
- Department of Neurological Surgery, Brain Trauma Research Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| |
Collapse
|
24
|
Vihinen M. Measuring and interpreting pervasive heterogeneity, poikilosis. FASEB Bioadv 2021; 3:611-625. [PMID: 34377957 PMCID: PMC8332472 DOI: 10.1096/fba.2021-00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 11/11/2022] Open
Abstract
Measurements are widely used in science, engineering, industry, and trade. They form the basis for experimental scientific research, approach, and progress; however, their foundations are seldom thought or questioned. Recently poikilosis, pervasive heterogeneity ranging from subatomic level to biosphere, was introduced. Poikilosis makes single point measurements and estimates obsolete and irrelevant as measurands display intervals of magnitudes. Consideration of poikilosis requires new lines of thinking in experimental design, conduction of studies, data analysis and interpretation. Measurements of poikilosis must consider lagom, normal, variation extent. Measurements, measures, and measurands as well as the measuring systems and uncertainties are discussed from the perspective of poikilosis. New systematics is introduced for description of uncertainty in measurements and for types of experimental designs. Poikilosis-aware experimenting, data analysis and interpretation are discussed. Instructions are provided for how to measure lagom and non-lagom effects of poikilosis. Consideration of poikilosis can solve scientific controversies and enigmas and can allow novel insight into systems, processes, mechanisms, and reactions and their interpretation, understanding, and manipulation. Furthermore, it will increase reproducibility of measurements and studies.
Collapse
Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical ScienceLund UniversityLundSweden
| |
Collapse
|
25
|
Romila CA, Townsend S, Malecki M, Kamrad S, Rodríguez-López M, Hillson O, Cotobal C, Ralser M, Bähler J. Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:146-160. [PMID: 34250083 PMCID: PMC8246024 DOI: 10.15698/mic2021.07.754] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022]
Abstract
Ageing-related processes are largely conserved, with simple organisms remaining the main platform to discover and dissect new ageing-associated genes. Yeasts provide potent model systems to study cellular ageing owing their amenability to systematic functional assays under controlled conditions. Even with yeast cells, however, ageing assays can be laborious and resource-intensive. Here we present improved experimental and computational methods to study chronological lifespan in Schizosaccharomyces pombe. We decoded the barcodes for 3206 mutants of the latest gene-deletion library, enabling the parallel profiling of ~700 additional mutants compared to previous screens. We then applied a refined method of barcode sequencing (Bar-seq), addressing technical and statistical issues raised by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to screen for mutants showing altered lifespan during stationary phase. This screen identified 341 long-lived mutants and 1246 short-lived mutants which point to many previously unknown ageing-associated genes, including 46 conserved but entirely uncharacterized genes. The ageing-associated genes showed coherent enrichments in processes also associated with human ageing, particularly with respect to ageing in non-proliferative brain cells. We also developed an automated colony-forming unit assay to facilitate medium- to high-throughput chronological-lifespan studies by saving time and resources compared to the traditional assay. Results from the Bar-seq screen showed good agreement with this new assay. This study provides an effective methodological platform and identifies many new ageing-associated genes as a framework for analysing cellular ageing in yeast and beyond.
Collapse
Affiliation(s)
- Catalina A. Romila
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- These authors contributed equally
| | - StJohn Townsend
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- These authors contributed equally
| | - Michal Malecki
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- Current address: Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Stephan Kamrad
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- Current address: Charité Universitätsmedizin Berlin, Department of Biochemistry, Germany
| | - María Rodríguez-López
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Olivia Hillson
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Cristina Cotobal
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- Charité Universitätsmedizin Berlin, Department of Biochemistry, Germany
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| |
Collapse
|
26
|
Dato S, Crocco P, Rambaldi Migliore N, Lescai F. Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging. Front Genet 2021; 12:689824. [PMID: 34178042 PMCID: PMC8225294 DOI: 10.3389/fgene.2021.689824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Aging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration. Recent Advances In this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today. Critical Issues Although the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types. Future Directions We critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.
Collapse
Affiliation(s)
- Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | | | - Francesco Lescai
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| |
Collapse
|
27
|
Admasu TD, Barardo D, Ng LF, Batchu KC, Cazenave-Gassiot A, Wenk MR, Gruber J. A small-molecule Psora-4 acts as a caloric restriction mimetic to promote longevity in C. elegans. GeroScience 2021; 44:1029-1046. [PMID: 33988831 DOI: 10.1007/s11357-021-00374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/20/2021] [Indexed: 10/21/2022] Open
Abstract
In populations around the world, the fraction of humans aged 65 and above is increasing at an unprecedented rate. Aging is the main risk factor for the most important degenerative diseases and this demographic shift poses significant social, economic, and medical challenges. Pharmacological interventions directly targeting mechanisms of aging are an emerging strategy to delay or prevent age-dependent diseases. Successful application of this approach has the potential to yield dramatic health, social, and economic benefits. Psora-4 is an inhibitor of the voltage-gated potassium channel, Kv1.3, that has previously been shown to increase longevity and health span in the nematode Caenorhabditis elegans (C. elegans). Our recent discovery that Psora-4 lifespan benefits in C. elegans are synergistic with those of several other lifespan-extending drugs has motivated us to investigate further the mechanism by which Psora-4 extends lifespan. Here, we report that Psora-4 increases the production of free radicals and modulates genes related to stress response and that its effect intersects closely with the target set of caloric restriction (CR) genes, suggesting that it, in part, acts as CR mimetic. This effect may be related to the role of potassium channels in energy metabolism. Our discovery of a potassium channel blocker as a CR mimetic suggests a novel avenue for mimicking CR and extending a healthy lifespan.
Collapse
Affiliation(s)
- Tesfahun Dessale Admasu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117608, Singapore
- SENS Research Foundation Research Center, Mountain View, CA, 94041, USA
| | - Diogo Barardo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117608, Singapore
- Science Divisions, Yale-NUS College, Singapore, 138527, Singapore
| | - Li Fang Ng
- Science Divisions, Yale-NUS College, Singapore, 138527, Singapore
| | | | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117608, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117608, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117608, Singapore.
- Science Divisions, Yale-NUS College, Singapore, 138527, Singapore.
| |
Collapse
|
28
|
Webb A, Knoblauch J, Sabankar N, Kallur AS, Hey J, Sethuraman A. The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses. Mol Biol Evol 2021; 38:3478-3485. [PMID: 33950197 PMCID: PMC8321520 DOI: 10.1093/molbev/msab113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The Pop-Gen Pipeline Platform (PPP) is a software platform for population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including input preparation, file format conversion, various population genomic analyses, and output generation. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.
Collapse
Affiliation(s)
- Andrew Webb
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Jared Knoblauch
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Nitesh Sabankar
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
| | - Apeksha Sukesh Kallur
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
| | - Jody Hey
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Arun Sethuraman
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA.,Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
| |
Collapse
|
29
|
Bennett HL, McClanahan PD, Fang-Yen C, Kalb RG. Preconditioning of Caenorhabditis elegans to anoxic insult by inactivation of cholinergic, GABAergic and muscle activity. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12713. [PMID: 33155386 DOI: 10.1111/gbb.12713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/19/2020] [Accepted: 11/04/2020] [Indexed: 11/26/2022]
Abstract
For most metazoans, oxygen deprivation leads to cell dysfunction and if severe, death. Sublethal stress prior to a hypoxic or anoxic insult ("preconditioning") can protect cells from subsequent oxygen deprivation. The molecular mechanisms by which sublethal stress can buffer against a subsequent toxic insult and the role of the nervous system in the response are not well understood. We studied the role of neuronal activity preconditioning to oxygen deprivation in Caenorhabditis elegans. Animals expressing the histamine gated chloride channels (HisCl1) in select cell populations were used to temporally and spatially inactivate the nervous system or tissue prior to an anoxic insult. We find that inactivation of the nervous system for 3 h prior to the insult confers resistance to a 48-h anoxic insult in 4th-stage larval animals. Experiments show that this resistance can be attributed to loss of activity in cholinergic and GABAergic neurons as well as in body wall muscles. These observations indicate that the nervous system activity can mediate the organism's response to anoxia.
Collapse
Affiliation(s)
- Heather L Bennett
- Department of Pediatrics, Division of Neurology, Research Institute, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biology, Reem-Kayden Center for Science and Computation, Bard College, New York, New York, USA
| | - Patrick D McClanahan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert G Kalb
- Department of Pediatrics, Division of Neurology, Research Institute, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| |
Collapse
|
30
|
Janero DR. Tackling the reproducibility problem to empower translation of preclinical academic drug discovery: is there an answer? Expert Opin Drug Discov 2021; 16:595-600. [PMID: 33617734 DOI: 10.1080/17460441.2021.1893690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- David R Janero
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences; and Health Sciences Entrepreneurs; Northeastern University, Boston, MA, USA
| |
Collapse
|
31
|
Setting Up an Automated Biomanufacturing Laboratory. Methods Mol Biol 2021; 2229:137-155. [PMID: 33405219 DOI: 10.1007/978-1-0716-1032-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Laboratory automation is a key enabling technology for genetic engineering that can lead to higher throughput, more efficient and accurate experiments, better data management and analysis, decrease in the DBT (Design, Build, and Test) cycle turnaround, increase of reproducibility, and savings in lab resources. Choosing the correct framework among so many options available in terms of software, hardware, and skills needed to operate them is crucial for the success of any automation project. This chapter explores the multiple aspects to be considered for the solid development of a biofoundry project including available software and hardware tools, resources, strategies, partnerships, and collaborations in the field needed to speed up the translation of research results to solve important society problems.
Collapse
|
32
|
Santos L, Oliveira C, Vasconcelos BM, Vilela D, Melo L, Ambrósio L, da Silva A, Murback L, Kurissio J, Cavalcante J, Cassaro CV, Barros L, Barraviera B, Ferreira RS. Good management practices of venomous snakes in captivity to produce biological venom-based medicines: achieving replicability and contributing to pharmaceutical industry. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2021; 24:30-50. [PMID: 33308037 DOI: 10.1080/10937404.2020.1855279] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
One of the factors responsible for lack of reproducible findings may be attributed to the raw material used. To date, there are no apparent studies examining reproducibility using venoms for the development of new toxin-based drugs with respect to regulatory agencies' policies. For this reason, protocols were implemented to produce animal toxins with quality, traceability, and strict compliance with Good Manufacturing Practices. This required validation of the production chain from the arrival of the animal to the vivarium, followed by handling, housing, as well as compliance with respect to extraction, freeze-drying, and, finally, storage protocols, aimed at generating compounds to serve as candidate molecules applicable in clinical trials. Currently, to produce quality snake venoms to support reproductive studies, the Center for the Study of Venoms and Venomous Animals (CEVAP) from São Paulo State University (UNESP), São Paulo, Brazil has 449 microchipped snakes through rigid and standardized operating procedures for safety, health, and welfare of animals. Snakes were frequently subjected to vet clinical examination, anthelmintic, and antiparasitic treatment. Venom milk used to destroy prey was collected from each animal in individual plastic microtubes to avoid contamination and for traceability. In addition, venoms were submitted to microbiological, and biochemical toxicological analyses. It is noteworthy that investigators are responsible for caring, maintaining, and manipulating snakes and ensuring their health in captivity. This review aimed to contribute to the pharmaceutical industry the experimental experience and entire snake venom production chain required to generate quality products for therapeutic human consumption.
Collapse
Affiliation(s)
- Lucilene Santos
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Clinical Research, Botucatu Medical School (FMB) and CEVAP, São Paulo State University (UNESP) , Botucatu, Brazil
| | - Cristiano Oliveira
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Barbara Marques Vasconcelos
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Daniela Vilela
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Leonardo Melo
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Clinical Research, Botucatu Medical School (FMB) and CEVAP, São Paulo State University (UNESP) , Botucatu, Brazil
| | - Lívia Ambrósio
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Amanda da Silva
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Leticia Murback
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Jacqueline Kurissio
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Joeliton Cavalcante
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Claudia Vilalva Cassaro
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Luciana Barros
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
| | - Benedito Barraviera
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Clinical Research, Botucatu Medical School (FMB) and CEVAP, São Paulo State University (UNESP) , Botucatu, Brazil
| | - Rui Seabra Ferreira
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP) , Botucatu, Brazil
- Graduate Program in Clinical Research, Botucatu Medical School (FMB) and CEVAP, São Paulo State University (UNESP) , Botucatu, Brazil
| |
Collapse
|
33
|
Torres-Sánchez M. Variation under domestication in animal models: the case of the Mexican axolotl. BMC Genomics 2020; 21:827. [PMID: 33228551 PMCID: PMC7685626 DOI: 10.1186/s12864-020-07248-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864. RESULTS Using gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations. CONCLUSIONS Awareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.
Collapse
Affiliation(s)
- María Torres-Sánchez
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center & Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA.
- Present address: Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.
| |
Collapse
|
34
|
Kochanek PM, Jackson TC, Jha RM, Clark RS, Okonkwo DO, Bayır H, Poloyac SM, Wagner AK, Empey PE, Conley YP, Bell MJ, Kline AE, Bondi CO, Simon DW, Carlson SW, Puccio AM, Horvat CM, Au AK, Elmer J, Treble-Barna A, Ikonomovic MD, Shutter LA, Taylor DL, Stern AM, Graham SH, Kagan VE, Jackson EK, Wisniewski SR, Dixon CE. Paths to Successful Translation of New Therapies for Severe Traumatic Brain Injury in the Golden Age of Traumatic Brain Injury Research: A Pittsburgh Vision. J Neurotrauma 2020; 37:2353-2371. [PMID: 30520681 PMCID: PMC7698994 DOI: 10.1089/neu.2018.6203] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
New neuroprotective therapies for severe traumatic brain injury (TBI) have not translated from pre-clinical to clinical success. Numerous explanations have been suggested in both the pre-clinical and clinical arenas. Coverage of TBI in the lay press has reinvigorated interest, creating a golden age of TBI research with innovative strategies to circumvent roadblocks. We discuss the need for more robust therapies. We present concepts for traditional and novel approaches to defining therapeutic targets. We review lessons learned from the ongoing work of the pre-clinical drug and biomarker screening consortium Operation Brain Trauma Therapy and suggest ways to further enhance pre-clinical consortia. Biomarkers have emerged that empower choice and assessment of target engagement by candidate therapies. Drug combinations may be needed, and it may require moving beyond conventional drug therapies. Precision medicine may also link the right therapy to the right patient, including new approaches to TBI classification beyond the Glasgow Coma Scale or anatomical phenotyping-incorporating new genetic and physiologic approaches. Therapeutic breakthroughs may also come from alternative approaches in clinical investigation (comparative effectiveness, adaptive trial design, use of the electronic medical record, and big data). The full continuum of care must also be represented in translational studies, given the important clinical role of pre-hospital events, extracerebral insults in the intensive care unit, and rehabilitation. TBI research from concussion to coma can cross-pollinate and further advancement of new therapies. Misconceptions can stifle/misdirect TBI research and deserve special attention. Finally, we synthesize an approach to deliver therapeutic breakthroughs in this golden age of TBI research.
Collapse
Affiliation(s)
- Patrick M. Kochanek
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Travis C. Jackson
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ruchira M. Jha
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert S.B. Clark
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David O. Okonkwo
- Department of Neurological Surgery, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania, USA
| | - Hülya Bayır
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Samuel M. Poloyac
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Amy K. Wagner
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Philip E. Empey
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Yvette P. Conley
- Health Promotion and Development, University of Pittsburgh School of Nursing, Pittsburgh, Pennsylvania, USA
| | - Michael J. Bell
- Department of Critical Care Medicine, Children's National Medical Center, Washington, DC, USA
| | - Anthony E. Kline
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Corina O. Bondi
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dennis W. Simon
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Shaun W. Carlson
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ava M. Puccio
- Department of Neurological Surgery, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania, USA
| | - Christopher M. Horvat
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alicia K. Au
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jonathan Elmer
- Departments of Emergency Medicine and Critical Care Medicine, University of Pittsburgh School of Medicine, UPMC Presbyterian Hospital, Pittsburgh, Pennsylvania, USA
| | - Amery Treble-Barna
- Safar Center for Resuscitation Research, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Milos D. Ikonomovic
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lori A. Shutter
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - D. Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Andrew M. Stern
- Drug Discovery Institute, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven H. Graham
- Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Valerian E. Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Edwin K. Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen R. Wisniewski
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - C. Edward Dixon
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
35
|
Kumar S, Peterson TR. Moonshots for aging. ACTA ACUST UNITED AC 2020; 5:239-246. [PMID: 33344796 PMCID: PMC7740370 DOI: 10.3233/nha-190064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
As the global population ages, there is increased interest in living longer and improving one’s quality of life in later years. However, studying aging – the decline in body function – is expensive and time-consuming. And despite research success to make model organisms live longer, there still aren’t really any feasible solutions for delaying aging in humans. With space travel, scientists and engineers couldn’t know what it would take to get to the moon. They had to extrapolate from theory and shorter-range tests. Perhaps with aging, we need a similar moonshot philosophy. And though “shot” might imply medicine, perhaps we need to think beyond medical interventions. Like the moon once was, we seem a long way away from provable therapies to increase human healthspan (the healthy period of one’s life) or lifespan (how long one lives). This review therefore focuses on radical proposals. We hope it might stimulate discussion on what we might consider doing significantly differently than ongoing aging research.
Collapse
Affiliation(s)
- Sandeep Kumar
- Department of Internal Medicine, Division of Bone and Mineral Diseases, Department of Genetics, Institute for Public Health, Washington University School of Medicine, BJC Institute of Health, MO, USA
| | - Timothy R Peterson
- Department of Internal Medicine, Division of Bone and Mineral Diseases, Department of Genetics, Institute for Public Health, Washington University School of Medicine, BJC Institute of Health, MO, USA
| |
Collapse
|
36
|
Berry C. Frameworks for evaluation and integration of data in regulatory evaluations: The need for excellence in regulatory toxicology. TOXICOLOGY RESEARCH AND APPLICATION 2020. [DOI: 10.1177/2397847320951377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Following a number of published expressions of concern about the reliability of experimental science and the implications of non-reproducibility for regulatory toxicology, the European Risk Forum undertook to consider what practises might improve the basis on which regulatory decisions might be made. Guidelines which may be useful in assessments are presented. The document acknowledges the value of the experimental standards used in most regulatory studies but indicates how these may fail to provide the ‘best outcome’ and how imperfect studies based on outdated views of pathophysiology of disease in H. Sapiens may offer little of predictive value.
Collapse
Affiliation(s)
- Colin Berry
- Professor Emeritus of Pathology, Queen Mary and Westfield College, London, UK
| |
Collapse
|
37
|
Abbott M, Banse SA, Melentijevic I, Jarrett CM, Ange JS, Sedore CA, Falkowski R, Blue BW, Coleman-Hulbert AL, Johnson E, Guo M, Lithgow GJ, Phillips PC, Driscoll M. A simplified design for the C. elegans lifespan machine. J Biol Methods 2020; 7:e137. [PMID: 33204740 PMCID: PMC7666331 DOI: 10.14440/jbm.2020.332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 02/02/2023] Open
Abstract
Caenorhabditis elegans (C. elegans) lifespan assays constitute a broadly used approach for investigating the fundamental biology of longevity. Traditional C. elegans lifespan assays require labor-intensive microscopic monitoring of individual animals to evaluate life/death over a period of weeks, making large-scale high throughput studies impractical. The lifespan machine developed by Stroustrup et al. (2013) adapted flatbed scanner technologies to contribute a major technical advance in the efficiency of C. elegans survival assays. Introducing a platform in which large portions of a lifespan assay are automated enabled longevity studies of a scope not possible with previous exclusively manual assays and facilitated novel discovery. Still, as initially described, constructing and operating scanner-based lifespan machines requires considerable effort and expertise. Here we report on design modifications that simplify construction, decrease cost, eliminate certain mechanical failures, and decrease assay workload requirements. The modifications we document should make the lifespan machine more accessible to interested laboratories.
Collapse
Affiliation(s)
- Mark Abbott
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA
| | - Stephen A. Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Ilija Melentijevic
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA
| | - Cody M. Jarrett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Jonathan St. Ange
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA
| | - Christine A. Sedore
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Ron Falkowski
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA
| | - Benjamin W. Blue
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | | | - Erik Johnson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Max Guo
- Division of Aging Biology, National Institute on Aging, Bethesda, MD, 20892, USA
| | | | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Monica Driscoll
- Rutgers University, Department of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA,*Corresponding author: Monica Driscoll,
| |
Collapse
|
38
|
Marqués G, Pengo T, Sanders MA. Imaging methods are vastly underreported in biomedical research. eLife 2020; 9:55133. [PMID: 32780019 PMCID: PMC7434332 DOI: 10.7554/elife.55133] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
A variety of microscopy techniques are used by researchers in the life and biomedical sciences. As these techniques become more powerful and more complex, it is vital that scientific articles containing images obtained with advanced microscopes include full details about how each image was obtained. To explore the reporting of such details we examined 240 original research articles published in eight journals. We found that the quality of reporting was poor, with some articles containing no information about how images were obtained, and many articles lacking important basic details. Efforts by researchers, funding agencies, journals, equipment manufacturers and staff at shared imaging facilities are required to improve the reporting of experiments that rely on microscopy techniques.
Collapse
Affiliation(s)
- Guillermo Marqués
- University Imaging Centers and Department of Neuroscience, University of Minnesota, Minneapolis, United States
| | - Thomas Pengo
- University of Minnesota Informatics Institute , University of Minnesota, Minneapolis, United States
| | - Mark A Sanders
- University Imaging Centers and Department of Neuroscience, University of Minnesota, Minneapolis, United States
| |
Collapse
|
39
|
Bulterijs S, Braeckman BP. Phenotypic Screening in C. elegans as a Tool for the Discovery of New Geroprotective Drugs. Pharmaceuticals (Basel) 2020; 13:E164. [PMID: 32722365 PMCID: PMC7463874 DOI: 10.3390/ph13080164] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/10/2023] Open
Abstract
Population aging is one of the largest challenges of the 21st century. As more people live to advanced ages, the prevalence of age-related diseases and disabilities will increase placing an ever larger burden on our healthcare system. A potential solution to this conundrum is to develop treatments that prevent, delay or reduce the severity of age-related diseases by decreasing the rate of the aging process. This ambition has been accomplished in model organisms through dietary, genetic and pharmacological interventions. The pharmacological approaches hold the greatest opportunity for successful translation to the clinic. The discovery of such pharmacological interventions in aging requires high-throughput screening strategies. However, the majority of screens performed for geroprotective drugs in C. elegans so far are rather low throughput. Therefore, the development of high-throughput screening strategies is of utmost importance.
Collapse
Affiliation(s)
- Sven Bulterijs
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Bart P. Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| |
Collapse
|
40
|
Oren S, Sela T, Levy DJ, Schonberg T. Item Features Interact With Item Category in Their Influence on Preferences. Front Psychol 2020; 11:988. [PMID: 32793016 PMCID: PMC7391002 DOI: 10.3389/fpsyg.2020.00988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/21/2020] [Indexed: 11/25/2022] Open
Abstract
Low-level visual features are known to play a role in value-based decision-making. However, most previous studies focused on the role of only a single low-level feature or only for one type of item. These studies also used only one method of measurement and provided a theory accounting for those specific findings. We aimed to utilize a different more robust approach. We tested the contribution of low-level visual features to value-based decision-making of three item types: fractal-art images, faces, and snack food items. We used two techniques to estimate values: subjective ratings and actual choices. We found that low-level visual features contribute to value-based decision-making even after controlling for higher level features relevant for each item category (for faces, features like eye distance and for food snacks, features like price and calories). Importantly, we show that, overall, while low-level visual features consistently contribute to value-based decision-making as was previously shown, different features distinctively contribute to preferences of specific item types, as was evident when we estimated values using both techniques. We claim that theories relying on the role of single features for individual item types do not capture the complexity of the contribution of low-level visual features to value-based decision-making. Our conclusions call for future studies using multiple item types and various measurement methods for estimating value in order to modify current theories and construct a unifying framework regarding the relationship between low-level visual features and choice.
Collapse
Affiliation(s)
- Shiran Oren
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tal Sela
- Department of Behavioral Sciences, School of Social Sciences and Humanities, Kinneret Academic College on the Sea of Galilee, Zemach, Israel
| | - Dino J. Levy
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Coller School of Management, Tel Aviv University, Tel Aviv, Israel
| | - Tom Schonberg
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
41
|
Reproducibility of animal research in light of biological variation. Nat Rev Neurosci 2020; 21:384-393. [PMID: 32488205 DOI: 10.1038/s41583-020-0313-3] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 12/16/2022]
Abstract
Context-dependent biological variation presents a unique challenge to the reproducibility of results in experimental animal research, because organisms' responses to experimental treatments can vary with both genotype and environmental conditions. In March 2019, experts in animal biology, experimental design and statistics convened in Blonay, Switzerland, to discuss strategies addressing this challenge. In contrast to the current gold standard of rigorous standardization in experimental animal research, we recommend the use of systematic heterogenization of study samples and conditions by actively incorporating biological variation into study design through diversifying study samples and conditions. Here we provide the scientific rationale for this approach in the hope that researchers, regulators, funders and editors can embrace this paradigm shift. We also present a road map towards better practices in view of improving the reproducibility of animal research.
Collapse
|
42
|
Reproducibility issues with correlating Beall-listed publications and research awards at a small Canadian business school. Scientometrics 2020. [DOI: 10.1007/s11192-020-03353-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
43
|
Wat LW, Chao C, Bartlett R, Buchanan JL, Millington JW, Chih HJ, Chowdhury ZS, Biswas P, Huang V, Shin LJ, Wang LC, Gauthier MPL, Barone MC, Montooth KL, Welte MA, Rideout EJ. A role for triglyceride lipase brummer in the regulation of sex differences in Drosophila fat storage and breakdown. PLoS Biol 2020; 18:e3000595. [PMID: 31961851 PMCID: PMC6994176 DOI: 10.1371/journal.pbio.3000595] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 01/31/2020] [Accepted: 01/03/2020] [Indexed: 01/26/2023] Open
Abstract
Triglycerides are the major form of stored fat in all animals. One important determinant of whole-body fat storage is whether an animal is male or female. Here, we use Drosophila, an established model for studies on triglyceride metabolism, to gain insight into the genes and physiological mechanisms that contribute to sex differences in fat storage. Our analysis of triglyceride storage and breakdown in both sexes identified a role for triglyceride lipase brummer (bmm) in the regulation of sex differences in triglyceride homeostasis. Normally, male flies have higher levels of bmm mRNA both under normal culture conditions and in response to starvation, a lipolytic stimulus. We find that loss of bmm largely eliminates the sex difference in triglyceride storage and abolishes the sex difference in triglyceride breakdown via strongly male-biased effects. Although we show that bmm function in the fat body affects whole-body triglyceride levels in both sexes, in males, we identify an additional role for bmm function in the somatic cells of the gonad and in neurons in the regulation of whole-body triglyceride homeostasis. Furthermore, we demonstrate that lipid droplets are normally present in both the somatic cells of the male gonad and in neurons, revealing a previously unrecognized role for bmm function, and possibly lipid droplets, in these cell types in the regulation of whole-body triglyceride homeostasis. Taken together, our data reveal a role for bmm function in the somatic cells of the gonad and in neurons in the regulation of male–female differences in fat storage and breakdown and identify bmm as a link between the regulation of triglyceride homeostasis and biological sex. An investigation of the genetic and physiological mechanisms underlying sex differences in fat storage and breakdown in the fruit fly Drosophila identifies previously unrecognized sex- and cell type-specific roles for the conserved triglyceride lipase brummer.
Collapse
Affiliation(s)
- Lianna W. Wat
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte Chao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachael Bartlett
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Justin L. Buchanan
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jason W. Millington
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Hui Ju Chih
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Zahid S. Chowdhury
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Puja Biswas
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vivian Huang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Leah J. Shin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lin Chuan Wang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marie-Pierre L. Gauthier
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Maria C. Barone
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Kristi L. Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Michael A. Welte
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Elizabeth J. Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
44
|
Sorkin BC, Kuszak AJ, Bloss G, Fukagawa NK, Hoffman FA, Jafari M, Barrett B, Brown PN, Bushman FD, Casper S, Chilton FH, Coffey CS, Ferruzzi MG, Hopp DC, Kiely M, Lakens D, MacMillan JB, Meltzer DO, Pahor M, Paul J, Pritchett-Corning K, Quinney SK, Rehermann B, Setchell KD, Sipes NS, Stephens JM, Taylor DL, Tiriac H, Walters MA, Xi D, Zappalá G, Pauli GF. Improving natural product research translation: From source to clinical trial. FASEB J 2020; 34:41-65. [PMID: 31914647 PMCID: PMC7470648 DOI: 10.1096/fj.201902143r] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/12/2019] [Accepted: 10/21/2019] [Indexed: 12/28/2022]
Abstract
While great interest in health effects of natural product (NP) including dietary supplements and foods persists, promising preclinical NP research is not consistently translating into actionable clinical trial (CT) outcomes. Generally considered the gold standard for assessing safety and efficacy, CTs, especially phase III CTs, are costly and require rigorous planning to optimize the value of the information obtained. More effective bridging from NP research to CT was the goal of a September, 2018 transdisciplinary workshop. Participants emphasized that replicability and likelihood of successful translation depend on rigor in experimental design, interpretation, and reporting across the continuum of NP research. Discussions spanned good practices for NP characterization and quality control; use and interpretation of models (computational through in vivo) with strong clinical predictive validity; controls for experimental artefacts, especially for in vitro interrogation of bioactivity and mechanisms of action; rigorous assessment and interpretation of prior research; transparency in all reporting; and prioritization of research questions. Natural product clinical trials prioritized based on rigorous, convergent supporting data and current public health needs are most likely to be informative and ultimately affect public health. Thoughtful, coordinated implementation of these practices should enhance the knowledge gained from future NP research.
Collapse
Affiliation(s)
- Barbara C. Sorkin
- Office of Dietary Supplements, National Institutes of Health (NIH), Bethesda, MD, US
| | - Adam J. Kuszak
- Office of Dietary Supplements, National Institutes of Health (NIH), Bethesda, MD, US
| | - Gregory Bloss
- National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, US
| | | | | | | | | | - Paula N. Brown
- British Columbia Institute of Technology, Burnaby, British Columbia, Canada
| | | | - Steven Casper
- Office of Dietary Supplement Programs, Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), Hyattsville, MD, US
| | - Floyd H. Chilton
- Department of Nutritional Sciences and the BIO5 Institute, University of Arizona, Tucson, AZ, US
| | | | - Mario G. Ferruzzi
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, US
| | - D. Craig Hopp
- National Center for Complementary and Integrative Health, NIH, Bethesda, MD, US
| | - Mairead Kiely
- Cork Centre for Vitamin D and Nutrition Research, School of Food and Nutritional Sciences, University College Cork, Ireland
| | - Daniel Lakens
- Eindhoven University of Technology, Eindhoven, Netherlands
| | | | | | | | - Jeffrey Paul
- Drexel Graduate College of Biomedical Sciences, College of Medicine, Evanston, IL, US
| | | | | | - Barbara Rehermann
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, US
| | | | - Nisha S. Sipes
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, US
| | | | | | - Hervé Tiriac
- University of California, San Diego, La Jolla, CA, US]
| | - Michael A. Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, US
| | - Dan Xi
- Office of Cancer Complementary and Alternative Medicine, National Cancer Institute, NIH, Shady Grove, MD, US
| | | | - Guido F. Pauli
- CENAPT and PCRPS, University of Illinois at Chicago College of Pharmacy, Chicago, IL, US
| |
Collapse
|
45
|
|
46
|
Deutschmann C, Roggenbuck D, Schierack P, Rödiger S. Autoantibody testing by enzyme-linked immunosorbent assay-a case in which the solid phase decides on success and failure. Heliyon 2020; 6:e03270. [PMID: 31993528 PMCID: PMC6971389 DOI: 10.1016/j.heliyon.2020.e03270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/12/2019] [Accepted: 01/16/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The enzyme-linked immunosorbent assay (ELISA) is an indispensable tool for clinical diagnostics to identify or differentiate diseases such as autoimmune illnesses, but also to monitor their progression or control the efficacy of drugs. One use case of ELISA is to differentiate between different states (e.g. healthy vs. diseased). Another goal is to quantitatively assess the biomarker in question, like autoantibodies. Thus, the ELISA technology is used for the discovery and verification of new autoantibodies, too. Of key interest, however, is the development of immunoassays for the sensitive and specific detection of such biomarkers at early disease stages. Therefore, users have to deal with many parameters, such as buffer systems or antigen-autoantibody interactions, to successfully establish an ELISA. Often, fine-tuning like testing of several blocking substances is performed to yield high signal-to-noise ratios. METHODS We developed an ELISA to detect IgA and IgG autoantibodies against chitinase-3-like protein 1 (CHI3L1), a newly identified autoantigen in inflammatory bowel disease (IBD), in the serum of control and disease groups (n = 23, respectively). Microwell plates with different surface modifications (PolySorp and MaxiSorp coating) were tested to detect reproducibility problems. RESULTS We found a significant impact of the surface properties of the microwell plates. IgA antibody reactivity was significantly lower, since it was in the range of background noise, when measured on MaxiSorp coated plates (p < 0.0001). The IgG antibody reactivity did not differ on the diverse plates, but the plate surface had a significant influence on the test result (p = 0.0005). CONCLUSION With this report, we want to draw readers' attention to the properties of solid phases and their effects on the detection of autoantibodies by ELISA. We want to sensitize the reader to the fact that the choice of the wrong plate can lead to a false negative test result, which in turn has serious consequences for the discovery of autoantibodies.
Collapse
Affiliation(s)
- Claudia Deutschmann
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane, The University of Potsdam, Senftenberg, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane, The University of Potsdam, Senftenberg, Germany
| |
Collapse
|
47
|
Macleod M, Mohan S. Reproducibility and Rigor in Animal-Based Research. ILAR J 2019; 60:17-23. [PMID: 31687758 PMCID: PMC7275809 DOI: 10.1093/ilar/ilz015] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/06/2019] [Accepted: 07/24/2019] [Indexed: 11/13/2022] Open
Abstract
Increasing focus on issues of research reproducibility affords us the opportunity to review some of the key issues related in vivo research. First, we set out some key definitions, to guide the reader through the rest of the paper. Next we consider issues of epistemology, of how animal experiments lead to changes in our understanding of biomedicine and, potentially, to the development of new therapeutics. Here we consider the meaning of statistical significance; the importance of understanding whether findings have general truth; and the advances in knowledge which can result from 'failed' replication. Then, we consider weaknesses in the design, conduct and reporting of experiments, and review evidence for this from systematic reviews and from experimental studies addressing these issues. We consider the impact that these weaknesses have on the development of new treatments for human disease, and reflect on the response to these issues from the biomedical research community. Finally, we consider strategies for improvement including increased use of brief, pre-registered study protocols; pre-registration, open publication and open data; and the central importance of education in improving research performance.
Collapse
Affiliation(s)
- Malcolm Macleod
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Swapna Mohan
- National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland (previously in the Division of Policy and Education at the NIH Office of Laboratory Animal Welfare, NIH)
| |
Collapse
|
48
|
Banse SA, Lucanic M, Sedore CA, Coleman-Hulbert AL, Plummer WT, Chen E, Kish JL, Hall D, Onken B, Presley MP, Jones EG, Blue BW, Garrett T, Abbott M, Xue J, Guo S, Johnson E, Foulger AC, Chamoli M, Falkowski R, Melentijevic I, Harinath G, Huynh P, Patel S, Edgar D, Jarrett CM, Guo M, Kapahi P, Lithgow GJ, Driscoll M, Phillips PC. Automated lifespan determination across Caenorhabditis strains and species reveals assay-specific effects of chemical interventions. GeroScience 2019; 41:945-960. [PMID: 31820364 PMCID: PMC6925072 DOI: 10.1007/s11357-019-00108-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 02/01/2023] Open
Abstract
The goal of the Caenorhabditis Intervention Testing Program is to identify robust and reproducible pro-longevity interventions that are efficacious across genetically diverse cohorts in the Caenorhabditis genus. The project design features multiple experimental replicates collected by three different laboratories. Our initial effort employed fully manual survival assays. With an interest in increasing throughput, we explored automation with flatbed scanner-based Automated Lifespan Machines (ALMs). We used ALMs to measure survivorship of 22 Caenorhabditis strains spanning three species. Additionally, we tested five chemicals that we previously found extended lifespan in manual assays. Overall, we found similar sources of variation among trials for the ALM and our previous manual assays, verifying reproducibility of outcome. Survival assessment was generally consistent between the manual and the ALM assays, although we did observe radically contrasting results for certain compound interventions. We found that particular lifespan outcome differences could be attributed to protocol elements such as enhanced light exposure of specific compounds in the ALM, underscoring that differences in technical details can influence outcomes and therefore interpretation. Overall, we demonstrate that the ALMs effectively reproduce a large, conventionally scored dataset from a diverse test set, independently validating ALMs as a robust and reproducible approach toward aging-intervention screening.
Collapse
Affiliation(s)
- Stephen A. Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Mark Lucanic
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Christine A. Sedore
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | | | - W. Todd Plummer
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Jason L. Kish
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - David Hall
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Brian Onken
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | | | - E. Grace Jones
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Benjamin W. Blue
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Theo Garrett
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Mark Abbott
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Jian Xue
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Suzhen Guo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Erik Johnson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Anna C. Foulger
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Manish Chamoli
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Ron Falkowski
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Ilija Melentijevic
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Girish Harinath
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Phu Huynh
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Shobhna Patel
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Daniel Edgar
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | - Cody M. Jarrett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Max Guo
- Division of Aging Biology, National Institute on Aging, Bethesda, MD 20892-9205 USA
| | - Pankaj Kapahi
- The Buck Institute for Research on Aging, Novato, CA 94945 USA
| | | | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08854 USA
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| |
Collapse
|
49
|
Pillai-Kastoori L, Heaton S, Shiflett SD, Roberts AC, Solache A, Schutz-Geschwender AR. Antibody validation for Western blot: By the user, for the user. J Biol Chem 2019; 295:926-939. [PMID: 31819006 PMCID: PMC6983856 DOI: 10.1074/jbc.ra119.010472] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
Well-characterized antibody reagents play a key role in the reproducibility of research findings, and inconsistent antibody performance leads to variability in Western blotting and other immunoassays. The current lack of clear, accepted standards for antibody validation and reporting of experimental details contributes to this problem. Because the performance of primary antibodies is strongly influenced by assay context, recommendations for validation and usage are unique to each type of immunoassay. Practical strategies are proposed for the validation of primary antibody specificity, selectivity, and reproducibility using Western blot analysis. The antibody should produce reproducible results within and between Western blotting experiments and the observed effect confirmed with a complementary or orthogonal method. Routine implementation of standardized antibody validation and reporting in immunoassays such as Western blotting may promote improved reproducibility across the global life sciences community.
Collapse
Affiliation(s)
| | - Sam Heaton
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, United Kingdom
| | | | - Annabelle C Roberts
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, United Kingdom
| | - Alejandra Solache
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, United Kingdom
| | | |
Collapse
|
50
|
Gulinello M, Mitchell HA, Chang Q, Timothy O'Brien W, Zhou Z, Abel T, Wang L, Corbin JG, Veeraragavan S, Samaco RC, Andrews NA, Fagiolini M, Cole TB, Burbacher TM, Crawley JN. Rigor and reproducibility in rodent behavioral research. Neurobiol Learn Mem 2019; 165:106780. [PMID: 29307548 PMCID: PMC6034984 DOI: 10.1016/j.nlm.2018.01.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023]
Abstract
Behavioral neuroscience research incorporates the identical high level of meticulous methodologies and exacting attention to detail as all other scientific disciplines. To achieve maximal rigor and reproducibility of findings, well-trained investigators employ a variety of established best practices. Here we explicate some of the requirements for rigorous experimental design and accurate data analysis in conducting mouse and rat behavioral tests. Novel object recognition is used as an example of a cognitive assay which has been conducted successfully with a range of methods, all based on common principles of appropriate procedures, controls, and statistics. Directors of Rodent Core facilities within Intellectual and Developmental Disabilities Research Centers contribute key aspects of their own novel object recognition protocols, offering insights into essential similarities and less-critical differences. Literature cited in this review article will lead the interested reader to source papers that provide step-by-step protocols which illustrate optimized methods for many standard rodent behavioral assays. Adhering to best practices in behavioral neuroscience will enhance the value of animal models for the multiple goals of understanding biological mechanisms, evaluating consequences of genetic mutations, and discovering efficacious therapeutics.
Collapse
Affiliation(s)
- Maria Gulinello
- IDDRC Behavioral Core Facility, Neuroscience Department, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Heather A Mitchell
- IDD Models Core, Waisman Center, University of Wisconsin Madison, Madison, WI 53705, USA
| | - Qiang Chang
- IDD Models Core, Waisman Center, University of Wisconsin Madison, Madison, WI 53705, USA
| | - W Timothy O'Brien
- IDDRC Preclinical Models Core, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zhaolan Zhou
- IDDRC Preclinical Models Core, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ted Abel
- IDDRC Preclinical Models Core, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current affiliation: Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Li Wang
- IDDRC Neurobehavioral Core, Center for Neuroscience Research, Children's National Health System, Washington, DC 20010, USA
| | - Joshua G Corbin
- IDDRC Neurobehavioral Core, Center for Neuroscience Research, Children's National Health System, Washington, DC 20010, USA
| | - Surabi Veeraragavan
- IDDRC Neurobehavioral Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rodney C Samaco
- IDDRC Neurobehavioral Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nick A Andrews
- IDDRC Neurodevelopmental Behavior Core, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michela Fagiolini
- IDDRC Neurodevelopmental Behavior Core, Boston Children's Hospital, Boston, MA 02115, USA
| | - Toby B Cole
- IDDRC Rodent Behavior Laboratory, Center on Human Development and Disability, University of Washington, Seattle, WA 98195, USA
| | - Thomas M Burbacher
- IDDRC Rodent Behavior Laboratory, Center on Human Development and Disability, University of Washington, Seattle, WA 98195, USA
| | - Jacqueline N Crawley
- IDDRC Rodent Behavior Core, MIND Institute, University of California Davis School of Medicine, Sacramento, CA 95817, USA.
| |
Collapse
|