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Sanders LM, Scott RT, Yang JH, Qutub AA, Garcia Martin H, Berrios DC, Hastings JJA, Rask J, Mackintosh G, Hoarfrost AL, Chalk S, Kalantari J, Khezeli K, Antonsen EL, Babdor J, Barker R, Baranzini SE, Beheshti A, Delgado-Aparicio GM, Glicksberg BS, Greene CS, Haendel M, Hamid AA, Heller P, Jamieson D, Jarvis KJ, Komarova SV, Komorowski M, Kothiyal P, Mahabal A, Manor U, Mason CE, Matar M, Mias GI, Miller J, Myers JG, Nelson C, Oribello J, Park SM, Parsons-Wingerter P, Prabhu RK, Reynolds RJ, Saravia-Butler A, Saria S, Sawyer A, Singh NK, Snyder M, Soboczenski F, Soman K, Theriot CA, Van Valen D, Venkateswaran K, Warren L, Worthey L, Zitnik M, Costes SV. Biological research and self-driving labs in deep space supported by artificial intelligence. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00618-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. CELL REPORTS METHODS 2022; 2:100325. [PMID: 36452864 PMCID: PMC9701605 DOI: 10.1016/j.crmeth.2022.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.
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Affiliation(s)
- Eliah G. Overbey
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca Klotz
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German
- yuri GmbH, Meckenbeuren, Germany
| | | | - Ryan T. Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher E. Mason
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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Zhang Y, Wang J, Yu C, Xia K, Yang B, Zhang Y, Ying L, Wang C, Huang X, Chen Q, Shen L, Li F, Liang C. Advances in single-cell sequencing and its application to musculoskeletal system research. Cell Prolif 2022; 55:e13161. [PMID: 34888976 PMCID: PMC8780907 DOI: 10.1111/cpr.13161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/30/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022] Open
Abstract
In recent years, single-cell sequencing (SCS) technologies have continued to advance with improved operating procedures and reduced cost, leading to increasing practical adoption among researchers. These emerging technologies have superior abilities to analyse cell heterogeneity at a single-cell level, which have elevated multi-omics research to a higher level. In some fields of research, application of SCS has enabled many valuable discoveries, and musculoskeletal system offers typical examples. This article reviews some major scientific issues and recent advances in musculoskeletal system. In addition, combined with SCS technologies, the research of cell or tissue heterogeneity in limb development and various musculoskeletal system clinical diseases also provides new possibilities for treatment strategies. Finally, this article discusses the challenges and future development potential of SCS and recommends the direction of future applications of SCS to musculoskeletal medicine.
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Affiliation(s)
- Yongxiang Zhang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Jingkai Wang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Chao Yu
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Kaishun Xia
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Biao Yang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Yuang Zhang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Liwei Ying
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Chenggui Wang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Xianpeng Huang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Qixin Chen
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Li Shen
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhouChina
- Hangzhou Innovation CenterZhejiang UniversityHangzhouChina
| | - Fangcai Li
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
| | - Chengzhen Liang
- Department of Orthopedics SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
- Zhejiang Key Laboratory of Bone and Joint Precision and Department of OrthopedicsResearch Institute of Zhejiang UniversityHangzhouZhejiangChina
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Hong X, Ratri A, Choi SY, Tash JS, Ronca AE, Alwood JS, Christenson LK. Effects of spaceflight aboard the International Space Station on mouse estrous cycle and ovarian gene expression. NPJ Microgravity 2021; 7:11. [PMID: 33712627 PMCID: PMC7954810 DOI: 10.1038/s41526-021-00139-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/17/2021] [Indexed: 12/24/2022] Open
Abstract
Ovarian steroids dramatically impact normal homeostatic and metabolic processes of most tissues within the body, including muscle, bone, neural, immune, cardiovascular, and reproductive systems. Determining the effects of spaceflight on the ovary and estrous cycle is, therefore, critical to our understanding of all spaceflight experiments using female mice. Adult female mice (n = 10) were exposed to and sacrificed on-orbit after 37 days of spaceflight in microgravity. Contemporary control (preflight baseline, vivarium, and habitat; n = 10/group) groups were maintained at the Kennedy Space Center, prior to sacrifice and similar tissue collection at the NASA Ames Research Center. Ovarian tissues were collected and processed for RNA and steroid analyses at initial carcass thaw. Vaginal wall tissue collected from twice frozen/thawed carcasses was fixed for estrous cycle stage determinations. The proportion of animals in each phase of the estrous cycle (i.e., proestrus, estrus, metestrus, and diestrus) did not appreciably differ between baseline, vivarium, and flight mice, while habitat control mice exhibited greater numbers in diestrus. Ovarian tissue steroid concentrations indicated no differences in estradiol across groups, while progesterone levels were lower (p < 0.05) in habitat and flight compared to baseline females. Genes involved in ovarian steroidogenic function were not differentially expressed across groups. As ovarian estrogen can dramatically impact multiple non-reproductive tissues, these data support vaginal wall estrous cycle classification of all female mice flown in space. Additionally, since females exposed to long-term spaceflight were observed at different estrous cycle stages, this indicates females are likely undergoing ovarian cyclicity and may yet be fertile.
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Affiliation(s)
- Xiaoman Hong
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anamika Ratri
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Joseph S Tash
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - April E Ronca
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, CA, USA.,Department of Obstetrics & Gynecology, Wake Forest Medical School, Winston-Salem, NC, USA
| | - Joshua S Alwood
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, CA, USA
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
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Lai Polo SH, Saravia-Butler AM, Boyko V, Dinh MT, Chen YC, Fogle H, Reinsch SS, Ray S, Chakravarty K, Marcu O, Chen RB, Costes SV, Galazka JM. RNAseq Analysis of Rodent Spaceflight Experiments Is Confounded by Sample Collection Techniques. iScience 2020; 23:101733. [PMID: 33376967 PMCID: PMC7756143 DOI: 10.1016/j.isci.2020.101733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/04/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
To understand the physiological changes that occur in response to spaceflight, mice are transported to the International Space Station (ISS) and housed for variable periods of time before euthanasia on-orbit or return to Earth. Sample collection under such difficult conditions introduces confounding factors that need to be identified and addressed. We found large changes in the transcriptome of mouse tissues dissected and preserved on-orbit compared with tissues from mice euthanized on-orbit, preserved, and dissected after return to Earth. Changes due to preservation method eclipsed those between flight and ground samples, making it difficult to identify spaceflight-specific changes. Follow-on experiments to interrogate the roles of euthanasia methods, tissue and carcass preservation protocols, and library preparation methods suggested that differences due to preservation protocols are exacerbated when coupled with polyA selection. This has important implications for the interpretation of existing datasets and the design of future experiments. Experimentation is necessary to understand how organisms respond to space Specialized protocols are used for preserving biological samples on the ISS RNAseq datasets are impacted by preservation protocols used on the ISS Impacts can be alleviated with improved carcass preservation protocols
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Affiliation(s)
- San-Huei Lai Polo
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Amanda M Saravia-Butler
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,Logyx, LLC, Mountain View, CA 94043, USA
| | - Valery Boyko
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Marie T Dinh
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,Logyx, LLC, Mountain View, CA 94043, USA
| | - Yi-Chun Chen
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Homer Fogle
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | | | - Oana Marcu
- Carl Sagan Center, SETI Institute, Mountain View, CA 94043, USA
| | - Rick B Chen
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
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Validation of a New Rodent Experimental System to Investigate Consequences of Long Duration Space Habitation. Sci Rep 2020; 10:2336. [PMID: 32047211 PMCID: PMC7012842 DOI: 10.1038/s41598-020-58898-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Animal models are useful for exploring the health consequences of prolonged spaceflight. Capabilities were developed to perform experiments in low earth orbit with on-board sample recovery, thereby avoiding complications caused by return to Earth. For NASA’s Rodent Research-1 mission, female mice (ten 32 wk C57BL/6NTac; ten 16 wk C57BL/6J) were launched on an unmanned vehicle, then resided on the International Space Station for 21/22d or 37d in microgravity. Mice were euthanized on-orbit, livers and spleens dissected, and remaining tissues frozen in situ for later analyses. Mice appeared healthy by daily video health checks and body, adrenal, and spleen weights of 37d-flight (FLT) mice did not differ from ground controls housed in flight hardware (GC), while thymus weights were 35% greater in FLT than GC. Mice exposed to 37d of spaceflight displayed elevated liver mass (33%) and select enzyme activities compared to GC, whereas 21/22d-FLT mice did not. FLT mice appeared more physically active than respective GC while soleus muscle showed expected atrophy. RNA and enzyme activity levels in tissues recovered on-orbit were of acceptable quality. Thus, this system establishes a new capability for conducting long-duration experiments in space, enables sample recovery on-orbit, and avoids triggering standard indices of chronic stress.
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Bertoni APS, Iser IC, de Campos RP, Wink MR. Normalization in Human Glioma Tissue. Methods Mol Biol 2019; 2065:175-190. [PMID: 31578695 DOI: 10.1007/978-1-4939-9833-3_13] [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: 02/22/2023]
Abstract
For tissues obtained from glioma samples with/without nonneoplastic brain there is no consensus for universal reference gene but there are some potential genes that might have good stability, under certain conditions. Considering all points described in this work, the care with tissue collection, until gene amplification, directly impacts on the reliable characterization of its mRNA levels. Moreover, it is clear the importance of selecting the most appropriate reference genes for each experimental situation, to allow the accurate normalization of target genes, especially for genes that are subtly regulated.
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Affiliation(s)
- Ana Paula Santin Bertoni
- Laboratório de Biologia Celular, Departamento de Ciências Básicas da Saúde (DCBS), Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
| | - Isabele Cristiana Iser
- Laboratório de Biologia Celular, Departamento de Ciências Básicas da Saúde (DCBS), Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Rafael Paschoal de Campos
- Laboratório de Biologia Celular, Departamento de Ciências Básicas da Saúde (DCBS), Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.,Laboratório de Sinalização e Plasticidade Celular, Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcia Rosangela Wink
- Laboratório de Biologia Celular, Departamento de Ciências Básicas da Saúde (DCBS), Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
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Abstract
PURPOSE OF REVIEW The goal of this paper is to review state-of-the-art transcriptome profiling methods and their recent applications in the field of skeletal biology. RECENT FINDINGS Next-generation sequencing of mRNA (RNA-seq) methods have been established and routinely used in skeletal biology research. RNA-seq has led to the identification of novel genes and transcription factors involved in skeletal development and disease, through its application in small and large animal models, as well as human tissue and cells. With the availability of advanced techniques such as single-cell RNA-seq, novel cell types in skeletal tissues are being identified. As the sequencing technologies are rapidly evolving, the exciting discoveries supported by transcriptomics will continue to emerge and improve our understanding of the biology of the skeleton.
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Affiliation(s)
- Ugur Ayturk
- Musculoskeletal Integrity Program, Hospital for Special Surgery, 515 East 71st St. Suite 403, New York, NY, 10021, USA.
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Passow CN, Kono TJY, Stahl BA, Jaggard JB, Keene AC, McGaugh SE. Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods. Mol Ecol Resour 2018; 19:456-464. [PMID: 30447171 DOI: 10.1111/1755-0998.12965] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/19/2018] [Accepted: 11/08/2018] [Indexed: 01/30/2023]
Abstract
RNA sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30-day-old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at -80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.
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Affiliation(s)
- Courtney N Passow
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Bethany A Stahl
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - James B Jaggard
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
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Beheshti A, Miller J, Kidane Y, Berrios D, Gebre SG, Costes SV. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies. Radiat Res 2018; 189:553-559. [DOI: 10.1667/rr15062.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Afshin Beheshti
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Jack Miller
- Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Yared Kidane
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Daniel Berrios
- USRA, NASA Ames Research Center, Moffett Field, Calfornia 94035
| | - Samrawit G. Gebre
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, California 94035
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11
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Vrentas CE, Boggiatto PM, Schaut RG, Olsen SC. Collection and Processing of Lymph Nodes from Large Animals for RNA Analysis: Preparing for Lymph Node Transcriptomic Studies of Large Animal Species. J Vis Exp 2018. [PMID: 29863658 DOI: 10.3791/57195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Large animals (both livestock and wildlife) serve as important reservoirs of zoonotic pathogens, including Brucella, Mycobacterium bovis, Salmonella, and E. coli, and are useful for the study of pathogenesis and/or spread of the bacteria in natural hosts. With the key function of lymph nodes in the host immune response, lymph node tissues serve as a potential source of RNA for downstream transcriptomic analyses, in order to assess the temporal changes in gene expression in cells over the course of an infection. This article presents an overview of the process of lymph node collection, tissue sampling, and downstream RNA processing in livestock, using cattle (Bos taurus) as a model, with additional examples provided from the American bison (Bison bison). The protocol includes information about the location, identification, and removal of lymph nodes from multiple key sites in the body. Additionally, a biopsy sampling methodology is presented that allows for a consistency of sampling across multiple animals. Several considerations for sample preservation are discussed, including the generation of RNA suitable for downstream methodologies like RNA-sequencing and RT-PCR. Due to the long delays inherent in large animal vs. mouse time course studies, representative results from bison and bovine lymph node tissues are presented to describe the time course of the degradation in this tissue type, in the context of a review of previous methodological work on RNA degradation in other tissues. Overall, this protocol will be useful to both veterinary researchers beginning transcriptome projects on large animal samples and to molecular biologists interested in learning techniques for in vivo tissue sampling and in vitro processing.
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Affiliation(s)
- Catherine E Vrentas
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture;
| | - Paola M Boggiatto
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture
| | - Robert G Schaut
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture
| | - Steven C Olsen
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture
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12
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Kheravii SK, Swick RA, Choct M, Wu SB. Upregulation of genes encoding digestive enzymes and nutrient transporters in the digestive system of broiler chickens by dietary supplementation of fiber and inclusion of coarse particle size corn. BMC Genomics 2018; 19:208. [PMID: 29558897 PMCID: PMC5859539 DOI: 10.1186/s12864-018-4592-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/09/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Measures to improve bird performance have been sought due to the imminent phase out of in-feed antibiotics in poultry and continued demand for higher poultry feeding efficiency. Increasing grain particle size and dietary fibre may improve gizzard function, digestive efficiency and nutrient absorption. This study was conducted to evaluate the effect increased particle size of corn and inclusion of sugarcane bagasse (SB) on mRNA expression of genes encoding digestive enzymes and nutrient transporters in broilers. RESULTS A total of 336 day-old Ross 308 males were assigned in a 2 × 2 factorial arrangement of treatments with corn particle size - coarse 3576 μm or fine 1113 μm geometric mean diameter, and SB - 0 or 2% inclusion. Feed conversion ratio (FCR), weight gain and feed intake were measured from d 0-10 and d 10-24. The relative gizzard weight and mRNA expression of genes encoding digestive enzymes and intestinal nutrient transporters were measured on d 24. During d 10-24, a particle size × SB interaction was observed for FCR (P < 0.01), where birds fed coarsely ground corn (CC) with 2% SB had lower FCR than those fed CC without SB. A particle size × SB interaction was observed for both expression of pepsinogen A and C (P < 0.01) which were negatively correlated with FCR on d 24. Addition of 2% SB upregulated pepsinogen A and C only in CC fed birds. Further, 2% SB also upregulated pancreatic amylase (AMY2A) and intestinal cationic amino acid transporter-1 (CAT1). Inclusion of dietary CC upregulated duodenal amino peptidase N (APN), jejunal alanine, serine, cysteine and threonine transporter-1 (ASCT1), and ileal peptide transporter-2 (PepT2). CONCLUSION These results suggest that both SB and coarse particle size modulate expression of genes encoding important digestive enzymes and nutrient transporters and thus are directly related to bird performance. These findings provide insights into the combination effects of dietary fiber and particle size in the future management of broiler feeding.
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Affiliation(s)
- Sarbast K Kheravii
- Animal Science, School of Environmental and Rural Science, University of New England, Elm Avenue, Armidale, NSW, 2351, Australia.,Animal production, Faculty of Agriculture and Forestry, University of Duhok, Duhok, Kurdistan, 42003, Iraq
| | - Robert A Swick
- Animal Science, School of Environmental and Rural Science, University of New England, Elm Avenue, Armidale, NSW, 2351, Australia
| | - Mingan Choct
- Animal Science, School of Environmental and Rural Science, University of New England, Elm Avenue, Armidale, NSW, 2351, Australia
| | - Shu-Biao Wu
- Animal Science, School of Environmental and Rural Science, University of New England, Elm Avenue, Armidale, NSW, 2351, Australia.
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