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Ma X, Xing Y, Zhai R, Du Y, Yan H. Development and advancements in rodent MRI-based brain atlases. Heliyon 2024; 10:e27421. [PMID: 38510053 PMCID: PMC10950579 DOI: 10.1016/j.heliyon.2024.e27421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/15/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Rodents, particularly mice and rats, are extensively utilized in fundamental neuroscience research. Brain atlases have played a pivotal role in this field, evolving from traditional printed histology atlases to digital atlases incorporating diverse imaging datasets. Magnetic resonance imaging (MRI)-based brain atlases, also known as brain maps, have been employed in specific studies. However, the existence of numerous versions of MRI-based brain atlases has impeded their standardized application and widespread use, despite the consensus within the academic community regarding their significance in mice and rats. Furthermore, there is a dearth of comprehensive and systematic reviews on MRI-based brain atlases for rodents. This review aims to bridge this gap by providing a comprehensive overview of the advancements in MRI-based brain atlases for rodents, with a specific focus on mice and rats. It seeks to explore the advantages and disadvantages of histologically printed brain atlases in comparison to MRI brain atlases, delineate the standardized methods for creating MRI brain atlases, and summarize their primary applications in neuroscience research. Additionally, this review aims to assist researchers in selecting appropriate versions of MRI brain atlases for their studies or refining existing MRI brain atlas resources, thereby facilitating the development and widespread adoption of standardized MRI-based brain atlases in rodents.
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Affiliation(s)
- Xiaoyi Ma
- Department of Geriatrics, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yao Xing
- School of Information Science and Technology, Fudan University, Shanghai, 200433, China
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Renkuan Zhai
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Yingying Du
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Huanhuan Yan
- Shenzhen United Imaging Research Institute of Innovative Medical Equipment, Shenzhen, 518048, China
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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2
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Mitchell B, Mu E, Currey L, Whitehead D, Walters S, Thor S, Kasherman M, Piper M. A protocol for high-resolution episcopic microscopy and 3D volumetric analyses of the adult mouse brain. Neurosci Lett 2024; 824:137675. [PMID: 38355003 DOI: 10.1016/j.neulet.2024.137675] [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: 09/15/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
The rapid evolution of different imaging modalities in the last two decades has enabled the investigation of the role of different genes in development and disease to be studied in a range of model organisms. However, selection of the appropriate imaging technique depends on a number of constraints, including cost, time, image resolution, size of the sample, computational complexity and processing power. Here, we use the adult mouse central nervous system to investigate whether High-Resolution Episcopic Microscopy (HREM) can provide an effective means to study the volume of individual subregions within the brain. We find that HREM can provide precise volume quantification of different structures within the mouse brain, albeit with limitations regarding the time involved for analysis and the necessity of some estimations.
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Affiliation(s)
- Benjamin Mitchell
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Mu
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Laura Currey
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Darryl Whitehead
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shaun Walters
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefan Thor
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maria Kasherman
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia; Katharina Gaus Light Microscopy Facility, Division of Research, Lowy Cancer Research Center C25, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Michael Piper
- The School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia.
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Papaioannou VE, Behringer RR. Analysis of Mid- to Late-Gestation Phenotypes in Mice. Cold Spring Harb Protoc 2024; 2024:107973. [PMID: 37932082 DOI: 10.1101/pdb.over107973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Mid- to late gestation is characterized by tissue differentiation, maturation, organogenesis, and growth, and many mutant genes have detrimental effects during this phase of development. The outcome may be lethal before birth or may be compatible with life but result in birth defects. Some of the common causes of death during late gestation are hematopoietic defects, cardiovascular problems, and placental insufficiency. Many morphological abnormalities, lethal or not, can be investigated with gross and histological analyses or by visualization of the developing skeleton. Molecular characterization of mutant phenotypes, guided by the expression pattern of the mutant gene, can reveal disruptions in gene expression patterns of known developmental genes. Cell proliferation and cell death assays will reveal disruptions in cellular dynamics. Various modalities of 3D imaging of intact embryos can provide volumetric information about mutant phenotypes.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Saleh MAA, Gülave B, Campagne O, Stewart CF, Elassaiss-Schaap J, de Lange ECM. Using the LeiCNS-PK3.0 Physiologically-Based Pharmacokinetic Model to Predict Brain Extracellular Fluid Pharmacokinetics in Mice. Pharm Res 2023; 40:2555-2566. [PMID: 37442882 PMCID: PMC10733198 DOI: 10.1007/s11095-023-03554-5] [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: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
INTRODUCTION The unbound brain extracelullar fluid (brainECF) to plasma steady state partition coefficient, Kp,uu,BBB, values provide steady-state information on the extent of blood-brain barrier (BBB) transport equilibration, but not on pharmacokinetic (PK) profiles seen by the brain targets. Mouse models are frequently used to study brain PK, but this information cannot directly be used to inform on human brain PK, given the different CNS physiology of mouse and human. Physiologically based PK (PBPK) models are useful to translate PK information across species. AIM Use the LeiCNS-PK3.0 PBPK model, to predict brain extracellular fluid PK in mice. METHODS Information on mouse brain physiology was collected from literature. All available connected data on unbound plasma, brainECF PK of 10 drugs (cyclophosphamide, quinidine, erlotonib, phenobarbital, colchicine, ribociclib, topotecan, cefradroxil, prexasertib, and methotrexate) from different mouse strains were used. Dosing regimen dependent plasma PK was modelled, and Kpuu,BBB values were estimated, and provided as input into the LeiCNS-PK3.0 model to result in prediction of PK profiles in brainECF. RESULTS Overall, the model gave an adequate prediction of the brainECF PK profile for 7 out of the 10 drugs. For 7 drugs, the predicted versus observed brainECF data was within two-fold error limit and the other 2 drugs were within five-fold error limit. CONCLUSION The current version of the mouse LeiCNS-PK3.0 model seems to reasonably predict available information on brainECF from healthy mice for most drugs. This brings the translation between mouse and human brain PK one step further.
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Affiliation(s)
- Mohammed A A Saleh
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Gorlaeus laboratorium, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Berfin Gülave
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Gorlaeus laboratorium, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Olivia Campagne
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, USA
| | - Clinton F Stewart
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, USA
| | | | - Elizabeth C M de Lange
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Gorlaeus laboratorium, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Villalobos D, Reese M, Wright MC, Wong M, Syed A, Park J, Hall A, Browndyke JN, Martucci KT, Devinney MJ, Acker L, Moretti EW, Talbot L, Colin B, Ohlendorf B, Waligorska T, Shaw LM, Whitson HE, Cohen HJ, Mathew JP, Berger M. Perioperative changes in neurocognitive and Alzheimer's disease-related cerebrospinal fluid biomarker in older patients randomised to isoflurane or propofol for anaesthetic maintenance. Br J Anaesth 2023:S0007-0912(23)00194-0. [PMID: 37271721 PMCID: PMC10375507 DOI: 10.1016/j.bja.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Animal studies have shown that isoflurane and propofol have differential effects on Alzheimer's disease (AD) pathology and memory, although it is unclear whether this occurs in humans. METHODS This was a nested randomised controlled trial within a prospective cohort study; patients age ≥60 yr undergoing noncardiac/non-neurological surgery were randomised to isoflurane or propofol for anaesthetic maintenance. Cerebrospinal fluid (CSF) was collected via lumbar puncture before, 24 h, and 6 weeks after surgery. Cognitive testing was performed before and 6 weeks after surgery. Nonparametric methods and linear regression were used to evaluate CSF biomarkers and cognitive function, respectively. RESULTS There were 107 subjects (54 randomised to isoflurane and 53 to propofol) who completed the 6-week follow-up and were included in the analysis. There was no significant effect of anaesthetic treatment group, time, or group-by-time interaction for CSF amyloid-beta (Aβ), tau, or phospho-tau181p levels, or on the tau/Aβ or p-tau181p/Aβ ratios (all P>0.05 after Bonferroni correction). In multivariable-adjusted intention-to-treat analyses, there were no significant differences between the isoflurane and propofol groups in 6-week postoperative change in overall cognition (mean difference [95% confidence interval]: 0.01 [-0.12 to 0.13]; P=0.89) or individual cognitive domains (P>0.05 for each). Results remained consistent across as-treated and per-protocol analyses. CONCLUSIONS Intraoperative anaesthetic maintenance with isoflurane vs propofol had no significant effect on postoperative cognition or CSF Alzheimer's disease-related biomarkers within 6 weeks after noncardiac, non-neurological surgery in older adults. CLINICAL TRIAL REGISTRATION NCT01993836.
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Affiliation(s)
| | - Melody Reese
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA; Center for the Study of Aging and Human Development, Duke University Medical Centre, Durham, NC, USA
| | - Mary Cooter Wright
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Megan Wong
- Duke University School of Medicine, Durham, NC, USA
| | - Ayesha Syed
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA; Trinity College, Duke University, Durham, NC, USA
| | - John Park
- Duke University School of Medicine, Durham, NC, USA; Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Ashley Hall
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Jeffrey N Browndyke
- Department of Psychiatry and Behavioural Medicine, Division of Behavioral Medicine & Neurosciences, Duke University Medical Center, Durham, NC, USA; Center for Cognitive Neuroscience, Duke University, Durham, NC, USA; Duke Brain Imaging and Analysis Center, Durham, NC, USA; Duke Institute for Brain Sciences, Durham, NC, USA
| | - Katherine T Martucci
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA; Center for Cognitive Neuroscience, Duke University, Durham, NC, USA; Duke Brain Imaging and Analysis Center, Durham, NC, USA; Duke Institute for Brain Sciences, Durham, NC, USA
| | - Michael J Devinney
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Leah Acker
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Eugene W Moretti
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Leonard Talbot
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Brian Colin
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Brian Ohlendorf
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Teresa Waligorska
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Heather E Whitson
- Center for the Study of Aging and Human Development, Duke University Medical Centre, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Harvey J Cohen
- Center for the Study of Aging and Human Development, Duke University Medical Centre, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Joseph P Mathew
- Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA
| | - Miles Berger
- Duke University School of Medicine, Durham, NC, USA; Department of Anaesthesiology, Duke University Medical Centre, Durham, NC, USA; Center for the Study of Aging and Human Development, Duke University Medical Centre, Durham, NC, USA; Center for Cognitive Neuroscience, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Durham, NC, USA.
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Arefin TM, Lee CH, Liang Z, Rallapalli H, Wadghiri YZ, Turnbull DH, Zhang J. Towards reliable reconstruction of the mouse brain corticothalamic connectivity using diffusion MRI. Neuroimage 2023; 273:120111. [PMID: 37060936 PMCID: PMC10149621 DOI: 10.1016/j.neuroimage.2023.120111] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023] Open
Abstract
Diffusion magnetic resonance imaging (dMRI) tractography has yielded intriguing insights into brain circuits and their relationship to behavior in response to gene mutations or neurological diseases across a number of species. Still, existing tractography approaches suffer from limited sensitivity and specificity, leading to uncertain interpretation of the reconstructed connections. Hence, in this study, we aimed to optimize the imaging and computational pipeline to achieve the best possible spatial overlaps between the tractography and tracer-based axonal projection maps within the mouse brain corticothalamic network. We developed a dMRI-based atlas of the mouse forebrain with structural labels imported from the Allen Mouse Brain Atlas (AMBA). Using the atlas and dMRI tractography, we first reconstructed detailed node-to-node mouse brain corticothalamic structural connectivity matrices using different imaging and tractography parameters. We then investigated the effects of each condition for accurate reconstruction of the corticothalamic projections by quantifying the similarities between the tractography and the tracer data from the Allen Mouse Brain Connectivity Atlas (AMBCA). Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain. Furthermore, tractography in mouse brain gray matter still face challenges and need improved imaging and tractography methods.
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Affiliation(s)
- Tanzil Mahmud Arefin
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States; Center for Neurotechnology in Mental Health Research, Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Choong Heon Lee
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States
| | - Zifei Liang
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States
| | - Harikrishna Rallapalli
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States
| | - Youssef Z Wadghiri
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States
| | - Daniel H Turnbull
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States
| | - Jiangyang Zhang
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York City, NY, United States.
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Perens J, Salinas CG, Roostalu U, Skytte JL, Gundlach C, Hecksher-Sørensen J, Dahl AB, Dyrby TB. Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System. Neuroinformatics 2023; 21:269-286. [PMID: 36809643 DOI: 10.1007/s12021-023-09623-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 02/23/2023]
Abstract
Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that enable non-disruptive 3-dimensional imaging of whole mouse brains. A combination of complementary information from both modalities is desirable for studying neuroscience in general, disease progression and drug efficacy. Although both technologies rely on atlas mapping for quantitative analyses, the translation of LSFM recorded data to MRI templates has been complicated by the morphological changes inflicted by tissue clearing and the enormous size of the raw data sets. Consequently, there is an unmet need for tools that will facilitate fast and accurate translation of LSFM recorded brains to in vivo, non-distorted templates. In this study, we have developed a bidirectional multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen's Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, Hørsholm, Denmark.,Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | | | | | | | - Carsten Gundlach
- Neutrons and X-rays for Materials Physics, Department of Physics, Technical University Denmark, Kongens Lyngby, Denmark
| | | | - Anders Bjorholm Dahl
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
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Galvano E, Pandit H, Sepulveda J, Ng CAS, Becher MK, Mandelblatt JS, Van Dyk K, Rebeck GW. Behavioral and transcriptomic effects of the cancer treatment tamoxifen in mice. Front Neurosci 2023; 17:1068334. [PMID: 36845433 PMCID: PMC9951777 DOI: 10.3389/fnins.2023.1068334] [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: 10/12/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Tamoxifen is a common treatment for estrogen receptor-positive breast cancer. While tamoxifen treatment is generally accepted as safe, there are concerns about adverse effects on cognition. Methods We used a mouse model of chronic tamoxifen exposure to examine the effects of tamoxifen on the brain. Female C57/BL6 mice were exposed to tamoxifen or vehicle control for six weeks; brains of 15 mice were analyzed for tamoxifen levels and transcriptomic changes, and an additional 32 mice were analyzed through a battery of behavioral tests. Results Tamoxifen and its metabolite 4-OH-tamoxifen were found at higher levels in the brain than in the plasma, demonstrating the facile entry of tamoxifen into the CNS. Behaviorally, tamoxifen-exposed mice showed no impairment in assays related to general health, exploration, motor function, sensorimotor gating, and spatial learning. Tamoxifen-treated mice showed a significantly increased freezing response in a fear conditioning paradigm, but no effects on anxiety measures in the absence of stressors. RNA sequencing analysis of whole hippocampi showed tamoxifen-induced reductions in gene pathways related to microtubule function, synapse regulation, and neurogenesis. Discussion These findings of the effects of tamoxifen exposure on fear conditioning and on gene expression related to neuronal connectivity suggest that there may be CNS side effects of this common breast cancer treatment.
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Affiliation(s)
- Elena Galvano
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, United States
| | - Harshul Pandit
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, United States
| | - Jordy Sepulveda
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, United States
| | - Christi Anne S. Ng
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, United States
| | - Melanie K. Becher
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, United States
| | - Jeanne S. Mandelblatt
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Kathleen Van Dyk
- Department of Psychiatry, UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, United States
| | - G. William Rebeck
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, United States,*Correspondence: G. William Rebeck,
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Effects of Chronic Caffeine Consumption on Synaptic Function, Metabolism and Adenosine Modulation in Different Brain Areas. Biomolecules 2023; 13:biom13010106. [PMID: 36671491 PMCID: PMC9855869 DOI: 10.3390/biom13010106] [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: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Adenosine receptors mainly control synaptic function, and excessive activation of adenosine receptors may worsen the onset of many neurological disorders. Accordingly, the regular intake of moderate doses of caffeine antagonizes adenosine receptors and affords robust neuroprotection. Although caffeine intake alters brain functional connectivity and multi-omics analyses indicate that caffeine intake modifies synaptic and metabolic processes, it is unclear how caffeine intake affects behavior, synaptic plasticity and its modulation by adenosine. We now report that male mice drinking caffeinated water (0.3 g/L) for 2 weeks were behaviorally indistinguishable (locomotion, mood, memory) from control mice (drinking water) and displayed superimposable synaptic plasticity (long-term potentiation) in different brain areas (hippocampus, prefrontal cortex, amygdala). Moreover, there was a general preservation of the efficiency of adenosine A1 and A2A receptors to control synaptic transmission and plasticity, although there was a tendency for lower levels of endogenous adenosine ensuring A1 receptor-mediated inhibition. In spite of similar behavioral and neurophysiological function, caffeine intake increased the energy charge and redox state of cortical synaptosomes. This increased metabolic competence likely involved a putative increase in the glycolytic rate in synapses and a prospective greater astrocyte-synapse lactate shuttling. It was concluded that caffeine intake does not trigger evident alterations of behavior or of synaptic plasticity but increases the metabolic competence of synapses, which might be related with the previously described better ability of animals consuming caffeine to cope with deleterious stimuli triggering brain dysfunction.
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11
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Mendez-Gonzalez D, Lifante J, Zabala Gutierrez I, Marin R, Ximendes E, Sanz-de Diego E, Iglesias-de la Cruz MC, Teran FJ, Rubio-Retama J, Jaque D. Optomagnetic nanofluids for controlled brain hyperthermia: a critical study. NANOSCALE 2022; 14:16208-16219. [PMID: 36281691 DOI: 10.1039/d2nr03413a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Optomagnetic nanofluids (OMNFs) are colloidal dispersions of nanoparticles (NPs) with combined magnetic and optical properties. They are especially appealing in biomedicine since they can be used as minimally invasive platforms for controlled hyperthermia treatment of otherwise difficultly accessible tumors such as intracranial ones. On the one hand, magnetic NPs act as heating mediators when subjected to alternating magnetic fields or light irradiation. On the other hand, suitably tailored luminescent NPs can provide a precise and remote thermal readout in real time. The combination of heating and thermometric properties allows, in principle, to precisely monitor the increase in the temperature of brain tumors up to the therapeutic level, without causing undesired collateral damage. In this work we demonstrate that this view is an oversimplification since it ignores the presence of relevant interactions between magnetic (γ-Fe2O3 nanoflowers) and luminescent nanoparticles (Ag2S NPs) that result in a detrimental alteration of their physicochemical properties. The magnitude of such interactions depends on the interparticle distance and on the surface properties of nanoparticles. Experiments performed in mouse brains (phantoms and ex vivo) revealed that OMNFs cannot induce relevant heating under alternating magnetic fields and fail to provide reliable temperature reading. In contrast, we demonstrate that the use of luminescent nanofluids (containing only Ag2S NPs acting as both photothermal agents and nanothermometers) stands out as a better alternative for thermally monitored hyperthermia treatment of brain tumors in small animal models.
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Affiliation(s)
- Diego Mendez-Gonzalez
- Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramon y Cajal 2, Madrid, 28040, Spain.
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
| | - José Lifante
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain
| | - Irene Zabala Gutierrez
- Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramon y Cajal 2, Madrid, 28040, Spain.
| | - Riccardo Marin
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
- NanoBIG, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, Madrid, 28049, Spain
| | - Erving Ximendes
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
- NanoBIG, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, Madrid, 28049, Spain
| | - Elena Sanz-de Diego
- IMDEA Nanociencia, Campus Universitario de Cantoblanco, Calle Faraday 9, 28049 Madrid, Spain
| | - M Carmen Iglesias-de la Cruz
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, 28029, Spain
| | - Francisco J Teran
- IMDEA Nanociencia, Campus Universitario de Cantoblanco, Calle Faraday 9, 28049 Madrid, Spain
- Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Jorge Rubio-Retama
- Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramon y Cajal 2, Madrid, 28040, Spain.
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
| | - Daniel Jaque
- Nanobiology Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. De Colmenar Viejo, Km. 9100, Madrid, 28034, Spain.
- NanoBIG, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, Madrid, 28049, Spain
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12
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Lee JY, You T, Woo CW, Kim SG. Optogenetic fMRI for Brain-Wide Circuit Analysis of Sensory Processing. Int J Mol Sci 2022; 23:ijms232012268. [PMID: 36293125 PMCID: PMC9602603 DOI: 10.3390/ijms232012268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/12/2022] [Accepted: 10/12/2022] [Indexed: 11/20/2022] Open
Abstract
Sensory processing is a complex neurological process that receives, integrates, and responds to information from one's own body and environment, which is closely related to survival as well as neurological disorders. Brain-wide networks of sensory processing are difficult to investigate due to their dynamic regulation by multiple brain circuits. Optogenetics, a neuromodulation technique that uses light-sensitive proteins, can be combined with functional magnetic resonance imaging (ofMRI) to measure whole-brain activity. Since ofMRI has increasingly been used for investigating brain circuits underlying sensory processing for over a decade, we systematically reviewed recent ofMRI studies of sensory circuits and discussed the challenges of optogenetic fMRI in rodents.
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Affiliation(s)
- Jeong-Yun Lee
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea
| | - Taeyi You
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon 16419, Korea
| | - Choong-Wan Woo
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon 16419, Korea
| | - Seong-Gi Kim
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon 16419, Korea
- Correspondence: ; Tel.: +82-31-299-4350; Fax: +82-31-299-4506
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13
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Lopes van den Broek S, Shalgunov V, García Vázquez R, Beschorner N, Bidesi NSR, Nedergaard M, Knudsen GM, Sehlin D, Syvänen S, Herth MM. Pretargeted Imaging beyond the Blood–Brain Barrier—Utopia or Feasible? Pharmaceuticals (Basel) 2022; 15:ph15101191. [PMID: 36297303 PMCID: PMC9612205 DOI: 10.3390/ph15101191] [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] [Received: 08/01/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Pretargeting is a promising nuclear imaging technique that allows for the usage of antibodies (Abs) with enhanced imaging contrast and reduced patient radiation burden. It is based on bioorthogonal chemistry with the tetrazine ligation—a reaction between trans-cyclooctenes (TCOs) and tetrazines (Tzs)—currently being the most popular reaction due to its high selectivity and reactivity. As Abs can be designed to bind specifically to currently ‘undruggable’ targets such as protein isoforms or oligomers, which play a crucial role in neurodegenerative diseases, pretargeted imaging beyond the BBB is highly sought after, but has not been achieved yet. A challenge in this respect is that large molecules such as Abs show poor brain uptake. Uptake can be increased by receptor mediated transcytosis; however, it is largely unknown if the achieved brain concentrations are sufficient for pretargeted imaging. In this study, we investigated whether the required concentrations are feasible to reach. As a model Ab, we used the bispecific anti-amyloid beta (Aβ) anti-transferrin receptor (TfR) Ab 3D6scFv8D3 and conjugated it to a different amount of TCOs per Ab and tested different concentrations in vitro. With this model in hand, we estimated the minimum required TCO concentration to achieve a suitable contrast between the high and low binding regions. The estimation was carried out using pretargeted autoradiography on brain sections of an Alzheimer’s disease mouse model. Biodistribution studies in wild-type (WT) mice were used to correlate how different TCO/Ab ratios alter the brain uptake. Pretargeted autoradiography showed that increasing the number of TCOs as well as increasing the TCO-Ab concentration increased the imaging contrast. A minimum brain concentration of TCOs for pretargeting purposes was determined to be 10.7 pmol/g in vitro. Biodistribution studies in WT mice showed a brain uptake of 1.1% ID/g using TCO-3D6scFv8D3 with 6.8 TCO/Ab. According to our estimations using the optimal parameters, pretargeted imaging beyond the BBB is not a utopia. Necessary brain TCO concentrations can be reached and are in the same order of magnitude as required to achieve sufficient contrast. This work gives a first estimate that pretargeted imaging is indeed possible with antibodies. This could allow the imaging of currently ‘undruggable’ targets and therefore be crucial to monitor (e.g., therapies for intractable neurodegenerative diseases).
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Affiliation(s)
- Sara Lopes van den Broek
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Vladimir Shalgunov
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Rocío García Vázquez
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Natalie Beschorner
- Center for Translational Neuromedicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Natasha S. R. Bidesi
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Gitte M. Knudsen
- Neurobiology Research Unit, Rigshospitalet Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Dag Sehlin
- Rudbeck Laboratory, Department of Public Health and Caring Sciences, University of Uppsala, Dag Hammarskjölds väg 20, 75185 Uppsala, Sweden
| | - Stina Syvänen
- Rudbeck Laboratory, Department of Public Health and Caring Sciences, University of Uppsala, Dag Hammarskjölds väg 20, 75185 Uppsala, Sweden
| | - Matthias M. Herth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Correspondence:
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14
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Singh A, Kusunose J, Phipps MA, Wang F, Chen LM, Caskey CF. Guiding and monitoring focused ultrasound mediated blood-brain barrier opening in rats using power Doppler imaging and passive acoustic mapping. Sci Rep 2022; 12:14758. [PMID: 36042266 PMCID: PMC9427847 DOI: 10.1038/s41598-022-18328-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
The blood-brain barrier (BBB) prevents harmful toxins from entering brain but can also inhibit therapeutic molecules designed to treat neurodegenerative diseases. Focused ultrasound (FUS) combined with microbubbles can enhance permeability of BBB and is often performed under MRI guidance. We present an all-ultrasound system capable of targeting desired regions to open BBB with millimeter-scale accuracy in two dimensions based on Doppler images. We registered imaging coordinates to FUS coordinates with target registration error of 0.6 ± 0.3 mm and used the system to target microbubbles flowing in cellulose tube in two in vitro scenarios (agarose-embedded and through a rat skull), while receiving echoes on imaging transducer. We created passive acoustic maps from received echoes and found error between intended location in imaging plane and location of pixel with maximum intensity after passive acoustic maps reconstruction to be within 2 mm in 5/6 cases. We validated ultrasound-guided procedure in three in vivo rat brains by delivering MRI contrast agent to cortical regions of rat brains after BBB opening. Landmark-based registration of vascular maps created with MRI and Doppler ultrasound revealed BBB opening inside the intended focus with targeting accuracy within 1.5 mm. Combined use of power Doppler imaging with passive acoustic mapping demonstrates an ultrasound-based solution to guide focused ultrasound with high precision in rodents.
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Affiliation(s)
- Aparna Singh
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - Jiro Kusunose
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - M Anthony Phipps
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - Feng Wang
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - Li Min Chen
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - Charles F Caskey
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA.
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15
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Ouyang F, Chen X, Liang J, Li J, Jiang Z, Chen Y, Yan Z, Zeng J, Xing S. Population-Average Brain Templates and Application to Automated Voxel-Wise Analysis Pipelines for Cynomolgus Macaque. Neuroinformatics 2022; 20:613-626. [PMID: 34523062 DOI: 10.1007/s12021-021-09545-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 12/31/2022]
Abstract
The growing number of neuroimaging studies of cynomolgus macaques require extending existing templates to facilitate species-specific application of voxel-wise neuroimaging methodologies. This study aimed to create population-averaged structural magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) templates for the cynomolgus macaques and apply the templates in fully automated voxel-wise analyses. We presented the development of symmetric and asymmetric MRI and DTI templates from a sample of 63 young male cynomolgus monkeys with the use of optimized template creation approaches. We also generated the associated average tissue probability maps and Diffeomorphic Anatomical Registration using Exponentiated Lie Algebra templates for use with the Statistical Parametric Mapping (SPM), as well as the average fractional anisotropy/skeleton targets for incorporation into tract-based spatial statistics (TBSS) framework. Both asymmetric and symmetric templates in a standardized coordinate space demonstrated low bias and high contrast. Fully automated processing using SPM was accomplished for all native MRI datasets and demonstrated outstanding performance regarding skull-stripping, segmentation, and normalization when using the MRI templates. Automated normalization to the DTI template was excellently achieved for all native DTI images using the TBSS pipeline. The cynomolgus MRI and DTI templates are anticipated to provide a common platform for precise single-subject data analysis and facilitate comparison of neuroimaging findings in cynomolgus monkeys across studies and sites. It is also hoped that the procedures of template creation and fully-automated voxel-wise frameworks will provide a straightforward avenue for investigating brain function, development, and neuro-psychopathological disorders in non-human primate models.
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Affiliation(s)
- Fubing Ouyang
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Xinran Chen
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Jiahui Liang
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Jianle Li
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Zimu Jiang
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Yicong Chen
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Zhicong Yan
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China
| | - Jinsheng Zeng
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China.
| | - Shihui Xing
- Department of Neurology and Stroke Center, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, National Key Clinical Department and Key Discipline of Neurology, No. 58 Zhongshan Road 2, Guangzhou, 510080, China.
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16
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Uselman TW, Medina CS, Gray HB, Jacobs RE, Bearer EL. Longitudinal manganese-enhanced magnetic resonance imaging of neural projections and activity. NMR IN BIOMEDICINE 2022; 35:e4675. [PMID: 35253280 PMCID: PMC11064873 DOI: 10.1002/nbm.4675] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Manganese-enhanced magnetic resonance imaging (MEMRI) holds exceptional promise for preclinical studies of brain-wide physiology in awake-behaving animals. The objectives of this review are to update the current information regarding MEMRI and to inform new investigators as to its potential. Mn(II) is a powerful contrast agent for two main reasons: (1) high signal intensity at low doses; and (2) biological interactions, such as projection tracing and neural activity mapping via entry into electrically active neurons in the living brain. High-spin Mn(II) reduces the relaxation time of water protons: at Mn(II) concentrations typically encountered in MEMRI, robust hyperintensity is obtained without adverse effects. By selectively entering neurons through voltage-gated calcium channels, Mn(II) highlights active neurons. Safe doses may be repeated over weeks to allow for longitudinal imaging of brain-wide dynamics in the same individual across time. When delivered by stereotactic intracerebral injection, Mn(II) enters active neurons at the injection site and then travels inside axons for long distances, tracing neuronal projection anatomy. Rates of axonal transport within the brain were measured for the first time in "time-lapse" MEMRI. When delivered systemically, Mn(II) enters active neurons throughout the brain via voltage-sensitive calcium channels and clears slowly. Thus behavior can be monitored during Mn(II) uptake and hyperintense signals due to Mn(II) uptake captured retrospectively, allowing pairing of behavior with neural activity maps for the first time. Here we review critical information gained from MEMRI projection mapping about human neuropsychological disorders. We then discuss results from neural activity mapping from systemic Mn(II) imaged longitudinally that have illuminated development of the tonotopic map in the inferior colliculus as well as brain-wide responses to acute threat and how it evolves over time. MEMRI posed specific challenges for image data analysis that have recently been transcended. We predict a bright future for longitudinal MEMRI in pursuit of solutions to the brain-behavior mystery.
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Affiliation(s)
- Taylor W. Uselman
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | | | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, California, USA
| | - Russell E. Jacobs
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Elaine L. Bearer
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
- Beckman Institute, California Institute of Technology, Pasadena, California, USA
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17
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Xu N, LaGrow TJ, Anumba N, Lee A, Zhang X, Yousefi B, Bassil Y, Clavijo GP, Khalilzad Sharghi V, Maltbie E, Meyer-Baese L, Nezafati M, Pan WJ, Keilholz S. Functional Connectivity of the Brain Across Rodents and Humans. Front Neurosci 2022; 16:816331. [PMID: 35350561 PMCID: PMC8957796 DOI: 10.3389/fnins.2022.816331] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Resting-state functional magnetic resonance imaging (rs-fMRI), which measures the spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, is increasingly utilized for the investigation of the brain's physiological and pathological functional activity. Rodents, as a typical animal model in neuroscience, play an important role in the studies that examine the neuronal processes that underpin the spontaneous fluctuations in the BOLD signal and the functional connectivity that results. Translating this knowledge from rodents to humans requires a basic knowledge of the similarities and differences across species in terms of both the BOLD signal fluctuations and the resulting functional connectivity. This review begins by examining similarities and differences in anatomical features, acquisition parameters, and preprocessing techniques, as factors that contribute to functional connectivity. Homologous functional networks are compared across species, and aspects of the BOLD fluctuations such as the topography of the global signal and the relationship between structural and functional connectivity are examined. Time-varying features of functional connectivity, obtained by sliding windowed approaches, quasi-periodic patterns, and coactivation patterns, are compared across species. Applications demonstrating the use of rs-fMRI as a translational tool for cross-species analysis are discussed, with an emphasis on neurological and psychiatric disorders. Finally, open questions are presented to encapsulate the future direction of the field.
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Affiliation(s)
- Nan Xu
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Theodore J. LaGrow
- Electrical and Computer Engineering, Georgia Tech, Atlanta, GA, United States
| | - Nmachi Anumba
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Azalea Lee
- Neuroscience Graduate Program, Emory University, Atlanta, GA, United States
- Emory University School of Medicine, Atlanta, GA, United States
| | - Xiaodi Zhang
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Behnaz Yousefi
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Yasmine Bassil
- Neuroscience Graduate Program, Emory University, Atlanta, GA, United States
| | - Gloria P. Clavijo
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | | | - Eric Maltbie
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Lisa Meyer-Baese
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Maysam Nezafati
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Wen-Ju Pan
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
| | - Shella Keilholz
- Biomedical Engineering, Emory University and Georgia Tech, Atlanta, GA, United States
- Neuroscience Graduate Program, Emory University, Atlanta, GA, United States
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18
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Manno FAM, Kumar R, An Z, Khan MS, Su J, Liu J, Wu EX, He J, Feng Y, Lau C. Structural and Functional Hippocampal Correlations in Environmental Enrichment During the Adolescent to Adulthood Transition in Mice. Front Syst Neurosci 2022; 15:807297. [PMID: 35242015 PMCID: PMC8886042 DOI: 10.3389/fnsys.2021.807297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 01/13/2023] Open
Abstract
Environmental enrichment is known to induce neuronal changes; however, the underlying structural and functional factors involved are not fully known and remain an active area of study. To investigate these factors, we assessed enriched environment (EE) and standard environment (SE) control mice over 30 days using structural and functional MRI methods. Naïve adult male mice (n = 30, ≈20 g, C57BL/B6J, postnatal day 60 initial scan) were divided into SE and EE groups and scanned before and after 30 days. Structural analyses included volumetry based on manual segmentation as well as diffusion tensor imaging (DTI). Functional analyses included seed-based analysis (SBA), independent component analysis (ICA), the amplitude of low-frequency fluctuation (ALFF), and fractional ALFF (fALFF). Structural results indicated that environmental enrichment led to an increase in the volumes of cornu ammonis 1 (CA1) and dentate gyrus. Structural results indicated changes in radial diffusivity and mean diffusivity in the visual cortex and secondary somatosensory cortex after EE. Furthermore, SBA and ICA indicated an increase in resting-state functional MRI (rsfMRI) functional connectivity in the hippocampus. Using parallel structural and functional analyses, we have demonstrated coexistent structural and functional changes in the hippocampal subdivision CA1. Future research should map alterations temporally during environmental enrichment to investigate the initiation of these structural and functional changes.
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Affiliation(s)
- Francis A M Manno
- Center for Imaging Science, Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States.,Department of Physics, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Rachit Kumar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Medical Scientist Training Program, University of Pennsylvania, Philadelphia, PA, United States
| | - Ziqi An
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, China
| | - Muhammad Shehzad Khan
- Department of Physics, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Junfeng Su
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Harvard University, Boston, MA, United States
| | - Jiaming Liu
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, China
| | - Ed X Wu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong SAR, China.,Laboratory of Biomedical Imaging and Signal Processing, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jufang He
- Department of Neuroscience, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yanqiu Feng
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, China
| | - Condon Lau
- Department of Physics, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
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19
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Visual and structural feature combination in an interactive machine learning system for medical image segmentation. MACHINE LEARNING WITH APPLICATIONS 2022. [DOI: 10.1016/j.mlwa.2022.100294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Janiak FK, Bartel P, Bale MR, Yoshimatsu T, Komulainen E, Zhou M, Staras K, Prieto-Godino LL, Euler T, Maravall M, Baden T. Non-telecentric two-photon microscopy for 3D random access mesoscale imaging. Nat Commun 2022; 13:544. [PMID: 35087041 PMCID: PMC8795402 DOI: 10.1038/s41467-022-28192-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/04/2022] [Indexed: 01/07/2023] Open
Abstract
Diffraction-limited two-photon microscopy permits minimally invasive optical monitoring of neuronal activity. However, most conventional two-photon microscopes impose significant constraints on the size of the imaging field-of-view and the specific shape of the effective excitation volume, thus limiting the scope of biological questions that can be addressed and the information obtainable. Here, employing a non-telecentric optical design, we present a low-cost, easily implemented and flexible solution to address these limitations, offering a several-fold expanded three-dimensional field of view. Moreover, rapid laser-focus control via an electrically tunable lens allows near-simultaneous imaging of remote regions separated in three dimensions and permits the bending of imaging planes to follow natural curvatures in biological structures. Crucially, our core design is readily implemented (and reversed) within a matter of hours, making it highly suitable as a base platform for further development. We demonstrate the application of our system for imaging neuronal activity in a variety of examples in zebrafish, mice and fruit flies.
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Affiliation(s)
- F K Janiak
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK.
| | - P Bartel
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - M R Bale
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - T Yoshimatsu
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - E Komulainen
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - M Zhou
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - K Staras
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | | | - T Euler
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | - M Maravall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - T Baden
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK.
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany.
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21
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Accurate Localization of Linear Probe Electrode Arrays across Multiple Brains. eNeuro 2021; 8:ENEURO.0241-21.2021. [PMID: 34697075 PMCID: PMC8597948 DOI: 10.1523/eneuro.0241-21.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Recently developed probes for extracellular electrophysiological recordings have large numbers of electrodes on long linear shanks. Linear electrode arrays, such as Neuropixels probes, have hundreds of recording electrodes distributed over linear shanks that span several millimeters. Because of the length of the probes, linear probe recordings in rodents usually cover multiple brain areas. Typical studies collate recordings across several recording sessions and animals. Neurons recorded in different sessions and animals thus have to be aligned to each other and to a standardized brain coordinate system. Here, we evaluate two typical workflows for localization of individual electrodes in standardized coordinates. These workflows rely on imaging brains with fluorescent probe tracks and warping 3D image stacks to standardized brain atlases. One workflow is based on tissue clearing and selective plane illumination microscopy (SPIM), whereas the other workflow is based on serial block-face two-photon (SBF2P) microscopy. In both cases electrophysiological features are then used to anchor particular electrodes along the reconstructed tracks to specific locations in the brain atlas and therefore to specific brain structures. We performed groundtruth experiments, in which motor cortex outputs are labeled with ChR2 and a fluorescence protein. Light-evoked electrical activity and fluorescence can be independently localized. Recordings from brain regions targeted by the motor cortex reveal better than 0.1-mm accuracy for electrode localization, independent of workflow used.
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22
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Kang HG, Tashima H, Nishikido F, Akamatsu G, Wakizaka H, Higuchi M, Yamaya T. Initial results of a mouse brain PET insert with a staggered 3-layer DOI detector. Phys Med Biol 2021; 66. [PMID: 34666328 DOI: 10.1088/1361-6560/ac311c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/19/2021] [Indexed: 11/11/2022]
Abstract
Objective.Small animal positron emission tomography (PET) requires a submillimeter resolution for better quantification of radiopharmaceuticals. On the other hand, depth-of-interaction (DOI) information is essential to preserve the spatial resolution while maintaining the sensitivity. Recently, we developed a staggered 3-layer DOI detector with 1 mm crystal pitch and 15 mm total crystal thickness, but we did not demonstrate the imaging performance of the DOI detector with full ring geometry. In this study we present initial imaging results obtained for a mouse brain PET prototype developed with the staggered 3-layer DOI detector.Approach.The prototype had 53 mm inner diameter and 11 mm axial field-of-view. The PET scanner consisted of 16 DOI detectors each of which had a staggered 3-layer LYSO crystal array (4/4/7 mm) coupled to a 4 × 4 silicon photomultiplier array. The physical performance was evaluated in terms of the NEMA NU 4 2008 protocol.Main Results.The measured spatial resolutions at the center and 15 mm radial offset were 0.67 mm and 1.56 mm for filtered-back-projection, respectively. The peak absolute sensitivity of 0.74% was obtained with an energy window of 400-600 keV. The resolution phantom imaging results show the clear identification of a submillimetric rod pattern with the ordered-subset expectation maximization algorithm. The inter-crystal scatter rejection using a narrow energy window could enhance the resolvability of a 0.75 mm rod significantly.Significance.In an animal imaging experiment, the detailed mouse brain structures such as cortex and thalamus were clearly identified with high contrast. In conclusion, we successfully developed the mouse brain PET insert prototype with a staggered 3-layer DOI detector.
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Affiliation(s)
- Han Gyu Kang
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
| | - Hideaki Tashima
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
| | - Fumihiko Nishikido
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
| | - Go Akamatsu
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
| | - Hidekazu Wakizaka
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
| | - Makoto Higuchi
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
| | - Taiga Yamaya
- National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, Japan
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23
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Perens J, Salinas CG, Skytte JL, Roostalu U, Dahl AB, Dyrby TB, Wichern F, Barkholt P, Vrang N, Jelsing J, Hecksher-Sørensen J. An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy. Neuroinformatics 2021; 19:433-446. [PMID: 33063286 PMCID: PMC8233272 DOI: 10.1007/s12021-020-09490-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen’s Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, 2970, Hørsholm, Denmark.,Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | | | | | | | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, 2650, Hvidovre, Denmark
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24
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Perens J, Salinas CG, Skytte JL, Roostalu U, Dahl AB, Dyrby TB, Wichern F, Barkholt P, Vrang N, Jelsing J, Hecksher-Sørensen J. An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy. Neuroinformatics 2021. [PMID: 33063286 DOI: 10.1007/s12021-020-09490-8/figures/5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen's Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, 2970, Hørsholm, Denmark
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | | | | | | | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, 2650, Hvidovre, Denmark
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25
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Naseri Kouzehgarani G, Feldsien T, Engelhard HH, Mirakhur KK, Phipps C, Nimmrich V, Clausznitzer D, Lefebvre DR. Harnessing cerebrospinal fluid circulation for drug delivery to brain tissues. Adv Drug Deliv Rev 2021; 173:20-59. [PMID: 33705875 DOI: 10.1016/j.addr.2021.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/10/2021] [Accepted: 03/01/2021] [Indexed: 12/31/2022]
Abstract
Initially thought to be useful only to reach tissues in the immediate vicinity of the CSF circulatory system, CSF circulation is now increasingly viewed as a viable pathway to deliver certain therapeutics deeper into brain tissues. There is emerging evidence that this goal is achievable in the case of large therapeutic proteins, provided conditions are met that are described herein. We show how fluid dynamic modeling helps predict infusion rate and duration to overcome high CSF turnover. We posit that despite model limitations and controversies, fluid dynamic models, pharmacokinetic models, preclinical testing, and a qualitative understanding of the glymphatic system circulation can be used to estimate drug penetration in brain tissues. Lastly, in addition to highlighting landmark scientific and medical literature, we provide practical advice on formulation development, device selection, and pharmacokinetic modeling. Our review of clinical studies suggests a growing interest for intra-CSF delivery, particularly for targeted proteins.
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26
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27
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MRI- and histologically derived neuroanatomical atlas of the Ambystoma mexicanum (axolotl). Sci Rep 2021; 11:9850. [PMID: 33972650 PMCID: PMC8110773 DOI: 10.1038/s41598-021-89357-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
Amphibians are an important vertebrate model system to understand anatomy, genetics and physiology. Importantly, the brain and spinal cord of adult urodels (salamanders) have an incredible regeneration capacity, contrary to anurans (frogs) and the rest of adult vertebrates. Among these amphibians, the axolotl (Ambystoma mexicanum) has gained most attention because of the surge in the understanding of central nervous system (CNS) regeneration and the recent sequencing of its whole genome. However, a complete comprehension of the brain anatomy is not available. In the present study we created a magnetic resonance imaging (MRI) atlas of the in vivo neuroanatomy of the juvenile axolotl brain. This is the first MRI atlas for this species and includes three levels: (1) 82 regions of interest (ROIs) and a version with 64 ROIs; (2) a division of the brain according to the embryological origin of the neural tube, and (3) left and right hemispheres. Additionally, we localized the myelin rich regions of the juvenile brain. The atlas, the template that the atlas was derived from, and a masking file, can be found on Zenodo at https://doi.org/10.5281/zenodo.4595016 . This MRI brain atlas aims to be an important tool for future research of the axolotl brain and that of other amphibians.
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28
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MRI of Capn15 Knockout Mice and Analysis of Capn 15 Distribution Reveal Possible Roles in Brain Development and Plasticity. Neuroscience 2021; 465:128-141. [PMID: 33951504 DOI: 10.1016/j.neuroscience.2021.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/03/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022]
Abstract
The Small Optic Lobe (SOL) family of calpains are intracellular cysteine proteases that are expressed in the nervous system and play an important role in neuronal development in both Drosophila, where loss of this calpain leads to the eponymous small optic lobes, and in mouse and human, where loss of this calpain leads to eye anomalies. Some human individuals with biallelic variants in CAPN15 also have developmental delay and autism. However, neither the specific effect of the loss of the Capn15 protein on brain development nor the brain regions where this calpain is expressed in the adult is known. Here we show using small animal MRI that mice with the complete loss of Capn15 have smaller brains overall with larger decreases in the thalamus and subregions of the hippocampus. These losses are not seen in Capn15 conditional knockout (KO) mice where Capn15 is knocked out only in excitatory neurons in the adult. Based on β-galactosidase expression in an insert strain where lacZ is expressed under the control of the Capn15 promoter, we show that Capn15 is expressed in adult mice, particularly in neurons involved in plasticity such as the hippocampus, lateral amygdala and Purkinje neurons, and partially in other non-characterized cell types. The regions of the brain in the adult where Capn15 is expressed do not correspond well to the regions of the brain most affected by the complete knockout suggesting distinct roles of Capn15 in brain development and adult brain function.
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29
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Constructing the rodent stereotaxic brain atlas: a survey. SCIENCE CHINA-LIFE SCIENCES 2021; 65:93-106. [PMID: 33860452 DOI: 10.1007/s11427-020-1911-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/03/2021] [Indexed: 12/22/2022]
Abstract
The stereotaxic brain atlas is a fundamental reference tool commonly used in the field of neuroscience. Here we provide a brief history of brain atlas development and clarify three key conceptual elements of stereotaxic brain atlasing: brain image, atlas, and stereotaxis. We also refine four technical indices for evaluating the construction of atlases: the quality of staining and labeling, the granularity of delineation, spatial resolution, and the precision of spatial location and orientation. Additionally, we discuss state-of-the-art technologies and their trends in the fields of image acquisition, stereotaxic coordinate construction, image processing, anatomical structure recognition, and publishing: the procedures of brain atlas illustration. We believe that the use of single-cell resolution and micron-level location precision will become a future trend in the study of the stereotaxic brain atlas, which will greatly benefit the development of neuroscience.
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30
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Takata N, Sato N, Komaki Y, Okano H, Tanaka KF. Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy. Sci Rep 2021; 11:6234. [PMID: 33737651 PMCID: PMC7973786 DOI: 10.1038/s41598-021-85807-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
A brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher's necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.
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Affiliation(s)
- Norio Takata
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.
- Central Institute for Experimental Animals (CIEA), 3-25-12, Tonomachi, Kawasaki, Kanagawa, 210-0821, Japan.
| | - Nobuhiko Sato
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Yuji Komaki
- Central Institute for Experimental Animals (CIEA), 3-25-12, Tonomachi, Kawasaki, Kanagawa, 210-0821, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Kenji F Tanaka
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
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31
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Badea A, Schmalzigaug R, Kim W, Bonner P, Ahmed U, Johnson GA, Cofer G, Foster M, Anderson RJ, Badea C, Premont RT. Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging. Magn Reson Imaging 2021; 76:26-38. [PMID: 33010377 PMCID: PMC7802083 DOI: 10.1016/j.mri.2020.09.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 01/06/2023]
Abstract
G Protein-Coupled Receptor Kinase-Interacting Protein-1 (GIT1) regulates neuronal functions, including cell and axon migration and synapse formation and maintenance, and GIT1 knockout (KO) mice exhibit learning and memory deficits. We noted that male and female GIT1-KO mice exhibit neuroimaging phenotypes including microcephaly, and altered cortical layering, with a decrease in neuron density in cortical layer V. Micro-CT and magnetic resonance microscopy (MRM) were used to identify morphometric phenotypes for the skulls and throughout the GIT1-KO brains. High field MRM of actively-stained mouse brains from GIT1-KO and wild type (WT) controls (n = 6 per group) allowed segmenting 37 regions, based on co-registration to the Waxholm Space atlas. Overall brain size in GIT1-KO mice was ~32% smaller compared to WT controls. After correcting for brain size, several regions were significantly different in GIT1-KO mice relative to WT, including the gray matter of the ventral thalamic nuclei and the rest of the thalamus, the inferior colliculus, and pontine nuclei. GIT1-KO mice had reduced volume of white matter tracts, most notably in the anterior commissure (~26% smaller), but also in the cerebral peduncle, fornix, and spinal trigeminal tract. On the other hand, the basal ganglia appeared enlarged in GIT1-KO mice, including the globus pallidus, caudate putamen, and particularly the accumbens - supporting a possible vulnerability to addiction. Volume based morphometry based on high-resolution MRM (21.5 μm isotropic voxels) was effective in detecting overall, and local differences in brain volumes in GIT1-KO mice, including in white matter tracts. The reduced relative volume of specific brain regions suggests a critical, but not uniform, role for GIT1 in brain development, conducive to brain microcephaly, and aberrant connectivity.
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Affiliation(s)
- Alexandra Badea
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, United States of America; Department of Neurology, Duke University Medical Center, Durham, NC 27710, United States of America; Departments of Biomedical Engineering, Duke University Medical Center, Durham, NC 27710, United States of America; Brain Imaging and Analysis Center, Duke University Medical Center, Durham, NC 27710, United States of America.
| | - Robert Schmalzigaug
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Woojoo Kim
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Pamela Bonner
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Umer Ahmed
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States of America
| | - G Allan Johnson
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, United States of America; Departments of Biomedical Engineering, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Gary Cofer
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Mark Foster
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Robert J Anderson
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Cristian Badea
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, United States of America; Departments of Biomedical Engineering, Duke University Medical Center, Durham, NC 27710, United States of America
| | - Richard T Premont
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States of America.
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32
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Brain orchestration of pregnancy and maternal behavior in mice: A longitudinal morphometric study. Neuroimage 2021; 230:117776. [PMID: 33516895 DOI: 10.1016/j.neuroimage.2021.117776] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 01/10/2023] Open
Abstract
Reproduction induces changes within the brain to prepare for gestation and motherhood. However, the dynamic of these central changes and their relationships with the development of maternal behavior remain poorly understood. Here, we describe a longitudinal morphometric neuroimaging study in female mice between pre-gestation and weaning, using new magnetic resonance imaging (MRI) resources comprising a high-resolution brain template, its associated tissue priors (60-µm isotropic resolution) and a corresponding mouse brain atlas (1320 regions of interest). Using these tools, we observed transient hypertrophies not only within key regions controlling gestation and maternal behavior (medial preoptic area, bed nucleus of the stria terminalis), but also in the amygdala, caudate nucleus and hippocampus. Additionally, unlike females exhibiting lower levels of maternal care, highly maternal females developed transient hypertrophies in somatosensory, entorhinal and retrosplenial cortices among other regions. Therefore, coordinated and transient brain modifications associated with maternal performance occurred during gestation and lactation.
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33
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De Feo R, Shatillo A, Sierra A, Valverde JM, Gröhn O, Giove F, Tohka J. Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases. Neuroimage 2021; 229:117734. [PMID: 33454412 DOI: 10.1016/j.neuroimage.2021.117734] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/09/2020] [Accepted: 01/07/2021] [Indexed: 12/27/2022] Open
Abstract
Skull-stripping and region segmentation are fundamental steps in preclinical magnetic resonance imaging (MRI) studies, and these common procedures are usually performed manually. We present Multi-task U-Net (MU-Net), a convolutional neural network designed to accomplish both tasks simultaneously. MU-Net achieved higher segmentation accuracy than state-of-the-art multi-atlas segmentation methods with an inference time of 0.35 s and no pre-processing requirements. We trained and validated MU-Net on 128 T2-weighted mouse MRI volumes as well as on the publicly available MRM NeAT dataset of 10 MRI volumes. We tested MU-Net with an unusually large dataset combining several independent studies consisting of 1782 mouse brain MRI volumes of both healthy and Huntington animals, and measured average Dice scores of 0.906 (striati), 0.937 (cortex), and 0.978 (brain mask). Further, we explored the effectiveness of our network in the presence of different architectural features, including skip connections and recently proposed framing connections, and the effects of the age range of the training set animals. These high evaluation scores demonstrate that MU-Net is a powerful tool for segmentation and skull-stripping, decreasing inter and intra-rater variability of manual segmentation. The MU-Net code and the trained model are publicly available at https://github.com/Hierakonpolis/MU-Net.
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Affiliation(s)
- Riccardo De Feo
- Sapienza Università di Roma, Rome 00184, Italy; Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, Rome 00184, Italy; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70210, Finland.
| | | | - Alejandra Sierra
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70210, Finland
| | - Juan Miguel Valverde
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70210, Finland
| | - Olli Gröhn
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70210, Finland
| | - Federico Giove
- Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, Rome 00184, Italy; Fondazione Santa Lucia IRCCS, Rome 00179, Italy
| | - Jussi Tohka
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70210, Finland
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Hosseini S, Laursen K, Rashidi A, Mondal T, Corbett B, Moradi F. S-MRUT: Sectored-Multiring Ultrasonic Transducer for Selective Powering of Brain Implants. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2021; 68:191-200. [PMID: 32746178 DOI: 10.1109/tuffc.2020.3001084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One of the main challenges of the current ultrasonic transducers for powering brain implants is the complexity of focusing ultrasonic waves in various axial and lateral directions. The available transducers usually use electrically controlled phased array for beamforming the ultrasonic waves, which increases the complexity of the system even further. In this article, we propose a straightforward solution for selective powering of brain implants to remove the complexity of conventional phased arrays. Our approach features a Sectored-Multiring Ultrasonic Transducer (S-MRUT) on a single piezoelectric sheet, specifically designed for powering implantable devices for optogenetics in freely moving animals. The proposed unidirectional S-MRUT is capable of focusing the ultrasonic waves on brain implants located at different depths and regions of the brain. The S-MRUT is designed based on Fresnel Zone Plate (FZP) theory, simulated in COMSOL, and fabricated with the microfabrication process. The acoustic profile of the seven different configurations of the S-MRUT was measured using a hydrophone with the total number of 7436 grid points. The measurements show the ability of the proposed S-MRUT to sweep the focus point of the acoustic waves in the axial direction in depths of 1 - 3 mm, which is suitable for powering implants in the striatum of the mouse. Furthermore, the proposed S-MRUT demonstrates a steering area with an average radius of 0.862 mm and 0.678 mm in experiments and simulations, respectively. The S-MRUT is designed with the size of 3.8×3.8×0.5 mm3 and the weight of 0.054gr , showing that it is compact and light enough to be worn by a mouse. Finally, the S-MRUT was tested in our measurement setup, where it successfully transfers sufficient power to a 2.8-mm3 optogentic stimulator to turn on a micro-LED on the stimulator.
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Sinha A, Ahmed S, George C, Tsagaris M, Naufer A, von Both I, Tkachyova I, van Eede M, Henkelman M, Schulze A. Magnetic resonance imaging reveals specific anatomical changes in the brain of Agat- and Gamt-mice attributed to creatine depletion and guanidinoacetate alteration. J Inherit Metab Dis 2020; 43:827-842. [PMID: 31951021 DOI: 10.1002/jimd.12215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/30/2019] [Accepted: 01/09/2020] [Indexed: 11/07/2022]
Abstract
Arginine:glycine amidinotransferase- and guanidinoacetate methyltransferase deficiency are severe neurodevelopmental disorders. It is not known whether mouse models of disease express a neuroanatomical phenotype. High-resolution magnetic resonance imaging (MRI) with advanced image analysis was performed in perfused, fixed mouse brains encapsulated with the skull from male, 10-12 week old Agat -exc and B6J.Cg-Gamt tm1Isb mice (n = 48; n = 8 per genotype, strain). T2-weighted MRI scans were nonlinearly aligned to a 3D atlas of the mouse brain with 62 structures identified. Local differences in brain shape related to genotype were assessed by analysis of deformation fields. Creatine (Cr) and guanidinoacetate (GAA) were measured with high-performance liquid chromatography (HPLC) in brain homogenates (n = 24; n = 4 per genotype, strain) after whole-body perfusion. Cr was decreased in the brain of Agat- and Gamt mutant mice. GAA was decreased in Agat-/- and increased in Gamt-/- . Body weight and brain volume were lower in Agat-/- than in Gamt-/- . The analysis of entire brain structures revealed corpus callosum, internal capsule, fimbria and hypothalamus being different between the genotypes in both strains. Eighteen and fourteen significant peaks (local areas of difference in relative size) were found in Agat- and Gamt mutants, respectively. Comparing Agat-/- with Gamt-/- , we found changes in three brain regions, lateral septum, amygdala, and medulla. Intra-strain differences in four brain structures can be associated with Cr deficiency, while the inter-strain differences in three brain structures of the mutant mice may relate to GAA. Correlating these neuroanatomical findings with gene expression data implies the role of Cr metabolism in the developing brain and the importance of early intervention in patients with Cr deficiency syndromes.
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Affiliation(s)
- Ankit Sinha
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sohail Ahmed
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chris George
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melina Tsagaris
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amriya Naufer
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ingo von Both
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ilona Tkachyova
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthijs van Eede
- Mouse Imaging Centre, Toronto Center of Phenogenomics, Toronto, Ontario, Canada
| | - Mark Henkelman
- Mouse Imaging Centre, Toronto Center of Phenogenomics, Toronto, Ontario, Canada
- Neurosciences and Mental Health Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andreas Schulze
- Genetics and Genome Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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Celestine M, Nadkarni NA, Garin CM, Bougacha S, Dhenain M. Sammba-MRI: A Library for Processing SmAll-MaMmal BrAin MRI Data in Python. Front Neuroinform 2020; 14:24. [PMID: 32547380 PMCID: PMC7270712 DOI: 10.3389/fninf.2020.00024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 04/23/2020] [Indexed: 11/23/2022] Open
Abstract
Small-mammal neuroimaging offers incredible opportunities to investigate structural and functional aspects of the brain. Many tools have been developed in the last decade to analyse small animal data, but current softwares are less mature than the available tools that process human brain data. The Python package Sammba-MRI (SmAll-MaMmal BrAin MRI in Python; http://sammba-mri.github.io) allows flexible and efficient use of existing methods and enables fluent scriptable analysis workflows, from raw data conversion to multimodal processing.
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Affiliation(s)
- Marina Celestine
- UMR9199 Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France.,MIRCen, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses, France
| | - Nachiket A Nadkarni
- UMR9199 Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France.,MIRCen, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses, France
| | - Clément M Garin
- UMR9199 Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France.,MIRCen, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses, France
| | - Salma Bougacha
- UMR9199 Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France.,MIRCen, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses, France.,UMR-S U1237 Physiopathologie et imagerie des troubles Neurologiques (PhIND), INSERM, Université de Caen-Normandie, GIP Cyceron, Caen, France.,Normandie Université, UNICAEN, PSL Research University, EPHE, Inserm, U1077, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Caen, France
| | - Marc Dhenain
- UMR9199 Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France.,MIRCen, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses, France
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Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell 2020; 181:936-953.e20. [PMID: 32386544 PMCID: PMC8152789 DOI: 10.1016/j.cell.2020.04.007] [Citation(s) in RCA: 454] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/12/2019] [Accepted: 04/03/2020] [Indexed: 01/25/2023]
Abstract
Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/).
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Affiliation(s)
- Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Josh Royall
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nile Graddis
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Maitham Naeemi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Benjamin Facer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anh Ho
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Seung Wook Oh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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Li B, Ohtomo R, Thunemann M, Adams SR, Yang J, Fu B, Yaseen MA, Ran C, Polimeni JR, Boas DA, Devor A, Lo EH, Arai K, Sakadžić S. Two-photon microscopic imaging of capillary red blood cell flux in mouse brain reveals vulnerability of cerebral white matter to hypoperfusion. J Cereb Blood Flow Metab 2020; 40:501-512. [PMID: 30829101 PMCID: PMC7026840 DOI: 10.1177/0271678x19831016] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/15/2023]
Abstract
Despite the importance of understanding the regulation of microvascular blood flow in white matter, no data on subcortical capillary blood flow parameters are available, largely due to the lack of appropriate imaging methods. To address this knowledge gap, we employed two-photon microscopy using a far-red fluorophore Alexa680 and photon-counting detection to measure capillary red blood cell (RBC) flux in both cerebral gray and white matter, in isoflurane-anesthetized mice. We have found that in control animals, baseline capillary RBC flux in the white matter was significantly higher than in the adjacent cerebral gray matter. In response to mild hypercapnia, RBC flux in the white matter exhibited significantly smaller fractional increase than in the gray matter. Finally, during global cerebral hypoperfusion, RBC flux in the white matter was reduced significantly in comparison to the controls, while RBC flux in the gray matter was preserved. Our results suggest that blood flow in the white matter may be less efficiently regulated when challenged by physiological perturbations as compared to the gray matter. Importantly, the blood flow in the white matter may be more susceptible to hypoperfusion than in the gray matter, potentially exacerbating the white matter deterioration in brain conditions involving global cerebral hypoperfusion.
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Affiliation(s)
- Baoqiang Li
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Ryo Ohtomo
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Martin Thunemann
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jing Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Buyin Fu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Mohammad A Yaseen
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - David A Boas
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Anna Devor
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Eng H Lo
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Ken Arai
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Sava Sakadžić
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
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Niesen J, Ohli J, Sedlacik J, Dührsen L, Hellwig M, Spohn M, Holsten T, Schüller U. Pik3ca mutations significantly enhance the growth of SHH medulloblastoma and lead to metastatic tumour growth in a novel mouse model. Cancer Lett 2020; 477:10-18. [PMID: 32112900 DOI: 10.1016/j.canlet.2020.02.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022]
Abstract
Medulloblastoma (MB) is the most frequent malignant brain tumour in children with a poor outcome. Divided into four molecular subgroups, MB of the Sonic hedgehog (SHH) subgroup accounts for approximately 25% of the cases and is driven by mutations within components of the SHH pathway, such as its receptors PTCH1 or SMO. A fraction of these cases additionally harbour PIK3CA mutations, the relevance of which is so far unknown. To unravel the role of Pik3ca mutations alone or in combination with a constitutively activated SHH signalling pathway, transgenic mice were used. These mice show mutated variants within Smo, Ptch1 or Pik3ca genes in cerebellar granule neuron precursors, which represent the cellular origin of SHH MB. Our results show that Pik3ca mutations alone are insufficient to cause developmental alterations or to initiate MB. However, they significantly accelerate the growth of Shh MB, induce tumour spread throughout the cerebrospinal fluid, and result in lower survival rates of mice with a double Pik3caH1047R/SmoM2 or Pik3caH1047R/Ptch1 mutation. Therefore, PIK3CA mutations in SHH MB may represent a therapeutic target for first and second line combination treatments.
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Affiliation(s)
- Judith Niesen
- Department of Pediatric Hematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Research Institute Children's Cancer Centre Hamburg, Hamburg, Germany
| | - Jasmin Ohli
- Centre for Neuropathology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Jan Sedlacik
- Department of Neuroradiology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Hellwig
- Department of Pediatric Hematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Research Institute Children's Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Centre Hamburg, Hamburg, Germany
| | - Till Holsten
- Department of Pediatric Hematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Research Institute Children's Cancer Centre Hamburg, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany; Research Institute Children's Cancer Centre Hamburg, Hamburg, Germany; Institute of Neuropathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
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40
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Unno K, Sumiyoshi A, Konishi T, Hayashi M, Taguchi K, Muguruma Y, Inoue K, Iguchi K, Nonaka H, Kawashima R, Hasegawa-Ishii S, Shimada A, Nakamura Y. Theanine, the Main Amino Acid in Tea, Prevents Stress-Induced Brain Atrophy by Modifying Early Stress Responses. Nutrients 2020; 12:nu12010174. [PMID: 31936294 PMCID: PMC7019546 DOI: 10.3390/nu12010174] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/30/2019] [Accepted: 01/04/2020] [Indexed: 11/16/2022] Open
Abstract
Chronic stress can impair the health of human brains. An important strategy that may prevent the accumulation of stress may be the consumption of functional foods. When senescence-accelerated mice prone 10 (SAMP10), a stress-sensitive strain, were loaded with stress using imposed male mouse territoriality, brain volume decreased. However, in mice that ingested theanine (6 mg/kg), the main amino acid in tea leaves, brain atrophy was suppressed, even under stress. On the other hand, brain atrophy was not clearly observed in a mouse strain that aged normally (Slc:ddY). The expression level of the transcription factor Npas4 (neuronal PAS domain protein 4), which regulates the formation and maintenance of inhibitory synapses in response to excitatory synaptic activity, decreased in the hippocampus and prefrontal cortex of stressed SAMP10 mice, but increased in mice that ingested theanine. Lipocalin 2 (Lcn2), the expression of which increased in response to stress, was significantly high in the hippocampus and prefrontal cortex of stressed SAMP10 mice, but not in mice that ingested theanine. These data suggest that Npas4 and Lcn2 are involved in the brain atrophy and stress vulnerability of SAMP10 mice, which are prevented by the consumption of theanine, causing changes in the expression of these genes.
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Affiliation(s)
- Keiko Unno
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan;
- Correspondence: ; Tel.: +81-54-264-5822
| | - Akira Sumiyoshi
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; (A.S.); (H.N.); (R.K.)
- National Institutes for Quantum and Radiological Science and Technology, 4-9-1, Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Tomokazu Konishi
- Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjo Nakano, Akita 010-0195, Japan;
| | - Michiko Hayashi
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
| | - Kyoko Taguchi
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
| | - Yoshio Muguruma
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (Y.M.); (K.I.)
| | - Koichi Inoue
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (Y.M.); (K.I.)
| | - Kazuaki Iguchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan;
| | - Hiroi Nonaka
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; (A.S.); (H.N.); (R.K.)
| | - Ryuta Kawashima
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; (A.S.); (H.N.); (R.K.)
| | - Sanae Hasegawa-Ishii
- Faculty of Health Sciences, Kyorin University, 5-4-1 Shimorenjaku, Mitaka, Tokyo 181-8612, Japan; (S.H.-I.); (A.S.)
| | - Atsuyoshi Shimada
- Faculty of Health Sciences, Kyorin University, 5-4-1 Shimorenjaku, Mitaka, Tokyo 181-8612, Japan; (S.H.-I.); (A.S.)
| | - Yoriyuki Nakamura
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.H.); (K.T.); (Y.N.)
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41
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Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R. Toward a Common Coordinate Framework for the Human Body. Cell 2019; 179:1455-1467. [PMID: 31835027 PMCID: PMC6934046 DOI: 10.1016/j.cell.2019.11.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/30/2019] [Accepted: 11/13/2019] [Indexed: 01/21/2023]
Abstract
Understanding the genetic and molecular drivers of phenotypic heterogeneity across individuals is central to biology. As new technologies enable fine-grained and spatially resolved molecular profiling, we need new computational approaches to integrate data from the same organ across different individuals into a consistent reference and to construct maps of molecular and cellular organization at histological and anatomical scales. Here, we review previous efforts and discuss challenges involved in establishing such a common coordinate framework, the underlying map of tissues and organs. We focus on strategies to handle anatomical variation across individuals and highlight the need for new technologies and analytical methods spanning multiple hierarchical scales of spatial resolution.
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Affiliation(s)
- Jennifer E Rood
- Klarman Cell Observatory, Broad Institute, Cambridge, MA 02142, USA
| | - Tim Stuart
- New York Genome Center, New York, NY 10013, USA
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | | | - Eyal Fisher
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Andrew Butler
- New York Genome Center, New York, NY 10013, USA; New York University, Center for Genomics and Systems Biology, New York, NY 10012, USA
| | - Anna Hupalowska
- Klarman Cell Observatory, Broad Institute, Cambridge, MA 02142, USA
| | - Leslie Gaffney
- Klarman Cell Observatory, Broad Institute, Cambridge, MA 02142, USA
| | - William Mauck
- New York Genome Center, New York, NY 10013, USA; New York University, Center for Genomics and Systems Biology, New York, NY 10012, USA
| | - Gökçen Eraslan
- Klarman Cell Observatory, Broad Institute, Cambridge, MA 02142, USA
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA 02142, USA.
| | - Rahul Satija
- New York Genome Center, New York, NY 10013, USA; New York University, Center for Genomics and Systems Biology, New York, NY 10012, USA.
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42
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Imaging of Mouse Brain Fixated in Ethanol in Micro-CT. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2054262. [PMID: 31392208 PMCID: PMC6662504 DOI: 10.1155/2019/2054262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/07/2019] [Accepted: 06/20/2019] [Indexed: 12/25/2022]
Abstract
Micro-CT imaging is a well-established morphological method for the visualization of animal models. We used ethanol fixation of the mouse brains to perform high-resolution micro-CT scans showing in great details brain grey and white matters. It was possible to identify more than 50 neuroanatomical structures on the 5 selected coronal sections. Among white matter structures, we identified fornix, medial lemniscus, crossed tectospinal pathway, mammillothalamic tract, and the sensory root of the trigeminal ganglion. Among grey matter structures, we identified basal nuclei, habenular complex, thalamic nuclei, amygdala, subparts of hippocampal formation, superior colliculi, Edinger-Westphal nucleus, and others. We suggest that micro-CT of the mouse brain could be used for neurohistological lesions evaluation as an alternative to classical neurohistology because it does not destroy brain tissue.
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Feo R, Giove F. Towards an efficient segmentation of small rodents brain: A short critical review. J Neurosci Methods 2019; 323:82-89. [DOI: 10.1016/j.jneumeth.2019.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 01/27/2023]
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Chang HY, Wu S, Meno-Tetang G, Shah DK. A translational platform PBPK model for antibody disposition in the brain. J Pharmacokinet Pharmacodyn 2019; 46:319-338. [PMID: 31115858 DOI: 10.1007/s10928-019-09641-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022]
Abstract
In this manuscript, we have presented the development of a novel platform physiologically-based pharmacokinetic (PBPK) model to characterize brain disposition of mAbs in the mouse, rat, monkey and human. The model accounts for known anatomy and physiology of the brain, including the presence of distinct blood-brain barrier and blood-cerebrospinal fluid (CSF) barrier. CSF and interstitial fluid turnover, and FcRn mediated transport of mAbs are accounted for. The model was first used to characterize published and in-house pharmacokinetic (PK) data on the disposition of mAbs in rat brain, including the data on PK of mAb in different regions of brain determined using microdialysis. Majority of model parameters were fixed based on literature reported values, and only 3 parameters were estimated using rat data. The rat PBPK model was translated to mouse, monkey, and human, simply by changing the values of physiological parameters corresponding to each species. The translated PBPK models were validated by a priori predicting brain PK of mAbs in all three species, and comparing predicted exposures with observed data. The platform PBPK model was able to a priori predict all the validation PK profiles reasonably well (within threefold), without estimating any parameters. As such, the platform PBPK model presented here provides an unprecedented quantitative tool for prediction of mAb PK at the site-of-action in the brain, and preclinical-to-clinical translation of mAbs being developed against central nervous system (CNS) disorders. The proposed model can be further expanded to account for target engagement, disease pathophysiology, and novel mechanisms, to support discovery and development of novel CNS targeting mAbs.
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Affiliation(s)
- Hsueh-Yuan Chang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, 455 Kapoor Hall, Buffalo, NY, 14214-8033, USA
| | - Shengjia Wu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, 455 Kapoor Hall, Buffalo, NY, 14214-8033, USA
| | - Guy Meno-Tetang
- Quantitative Clinical Pharmacology/PK-PD, Modeling & Simulation, Immunology/Inflammation, UCB Pharmaceuticals, Brussels, Belgium
| | - Dhaval K Shah
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, 455 Kapoor Hall, Buffalo, NY, 14214-8033, USA.
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Linninger A, Hartung G, Badr S, Morley R. Mathematical synthesis of the cortical circulation for the whole mouse brain-part I. theory and image integration. Comput Biol Med 2019; 110:265-275. [PMID: 31247510 DOI: 10.1016/j.compbiomed.2019.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/25/2019] [Accepted: 05/04/2019] [Indexed: 12/19/2022]
Abstract
Microcirculation plays a significant role in cerebral metabolism and blood flow control, yet explaining and predicting functional mechanisms remains elusive because it is difficult to make physiologically accurate mathematical models of the vascular network. As a precursor to the human brain, this paper presents a computational framework for synthesizing anatomically accurate network models for the cortical blood supply in mouse. It addresses two critical deficiencies in cerebrovascular modeling. At the microscopic length scale of individual capillaries, we present a novel synthesis method for building anatomically consistent capillary networks with loops and anastomoses (=microcirculatory closure). This overcomes shortcomings in existing algorithms which are unable to create closed circulatory networks. A second critical innovation allows the incorporation of detailed anatomical features from image data into vascular growth. Specifically, computed tomography and two photon laser scanning microscopy data are input into the novel synthesis algorithm to build the cortical circulation for the entire mouse brain in silico. Computer predictions of blood flow and oxygen exchange executed on synthetic large-scale network models are expected to elucidate poorly understood functional mechanisms of the cerebral circulation.
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Affiliation(s)
- Andreas Linninger
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA.
| | - Grant Hartung
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Shoale Badr
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Ryan Morley
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
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Breu M, Reisinger D, Tao L, Wu D, Zhang Y, Budde MD, Fatemi A, Pathak AP, Zhang J. In vivo high-resolution diffusion tensor imaging of the developing neonatal rat cortex and its relationship to glial and dendritic maturation. Brain Struct Funct 2019; 224:1815-1829. [PMID: 31011813 DOI: 10.1007/s00429-019-01878-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/11/2019] [Indexed: 12/25/2022]
Abstract
Diffusion tensor imaging (DTI) is increasingly utilized as a sensitive tool for studying brain maturation and injuries during the neonatal period. In this study, we acquired high resolution in vivo DTI data from neonatal rat brains from postnatal day 2 (P2) to P10 and correlated temporal changes in DTI derived markers with microstructural organization of glia, axons, and dendrites during this critical period of brain development. Group average images showed dramatic temporal changes in brain morphology, fractional anisotropy (FA) and mean diffusivity (MD). Most cortical regions showed a monotonous decline in FA and an initial increase in MD from P2 to P8 that declined slightly by P10. Qualitative histology revealed rapid maturation of the glial and dendritic networks in the developing cortex. In the cingulate and motor cortex, the decreases in FA over time significantly correlated with structural anisotropy values computed from histological sections stained with glial and dendritic markers. However, in the sensory and visual cortex, other factors probably contributed to the observed decreases in FA. We did not observe any significant correlations between FA and structural anisotropy computed from the axonal histological marker.
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Affiliation(s)
- Markus Breu
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Dominik Reisinger
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Liangcheng Tao
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Wu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yajing Zhang
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew D Budde
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ali Fatemi
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Arvind P Pathak
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiangyang Zhang
- Department of Radiology, New York University School of Medicine, 660 First Avenue, Room 207, New York, NY, 10016, USA.
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Volumes of brain structures in captive wild-type and laboratory rats: 7T magnetic resonance in vivo automatic atlas-based study. PLoS One 2019; 14:e0215348. [PMID: 30973956 PMCID: PMC6459519 DOI: 10.1371/journal.pone.0215348] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 03/27/2019] [Indexed: 11/19/2022] Open
Abstract
Selective breeding of laboratory rats resulted in changes of their behavior. Concomitantly, the albino strains developed vision related pathologies. These alterations certainly occurred on the background of modifications in brain morphology. The aim of the study was to assess and compare volumes of major structures in brains of wild-captive, laboratory albino and laboratory pigmented rats. High resolution T2-weighted images of brains of adult male Warsaw Wild Captive Pisula-Stryjek rats (WWCPS, a model of wild type), laboratory pigmented (Brown Norway strain, BN) and albino rats (Wistar strain, WI) were obtained with a 7T small animal-dedicated magnetic resonance tomograph. Volume quantification of whole brains and 50 brain structures within each brain were performed with the digital Schwarz rat brain atlas and a custom-made MATLAB/SPM8 scripts. Brain volumes were scaled to body mass, whereas volumes of brain structures were normalized to individual brain volumes. Normalized brain volume was similar in WWCPS and BN, but lower in WI. Normalized neocortex volume was smaller in both laboratory strains than in WWCPS and the visual cortex was smaller in albino WI rats than in WWCPS and BN. Relative volumes of phylogenetically older structures, such as hippocampus, amygdala, nucleus accumbens and olfactory nuclei, also displayed certain strain-related differences. The present data shows that selective breeding of laboratory rats markedly affected brain morphology, the neocortex being most significantly altered. In particular, albino rats display reduced volume of the visual cortex, possibly related to retinal degeneration and the development of blindness.
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Percival CJ, Devine J, Darwin BC, Liu W, van Eede M, Henkelman RM, Hallgrimsson B. The effect of automated landmark identification on morphometric analyses. J Anat 2019; 234:917-935. [PMID: 30901082 DOI: 10.1111/joa.12973] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/20/2023] Open
Abstract
Morphometric analysis of anatomical landmarks allows researchers to identify specific morphological differences between natural populations or experimental groups, but manually identifying landmarks is time-consuming. We compare manually and automatically generated adult mouse skull landmarks and subsequent morphometric analyses to elucidate how switching from manual to automated landmarking will impact morphometric analysis results for large mouse (Mus musculus) samples (n = 1205) that represent a wide range of 'normal' phenotypic variation (62 genotypes). Other studies have suggested that the use of automated landmarking methods is feasible, but this study is the first to compare the utility of current automated approaches to manual landmarking for a large dataset that allows the quantification of intra- and inter-strain variation. With this unique sample, we investigated how switching to a non-linear image registration-based automated landmarking method impacts estimated differences in genotype mean shape and shape variance-covariance structure. In addition, we tested whether an initial registration of specimen images to genotype-specific averages improves automatic landmark identification accuracy. Our results indicated that automated landmark placement was significantly different than manual landmark placement but that estimated skull shape covariation was correlated across methods. The addition of a preliminary genotype-specific registration step as part of a two-level procedure did not substantially improve on the accuracy of one-level automatic landmark placement. The landmarks with the lowest automatic landmark accuracy are found in locations with poor image registration alignment. The most serious outliers within morphometric analysis of automated landmarks displayed instances of stochastic image registration error that are likely representative of errors common when applying image registration methods to micro-computed tomography datasets that were initially collected with manual landmarking in mind. Additional efforts during specimen preparation and image acquisition can help reduce the number of registration errors and improve registration results. A reduction in skull shape variance estimates were noted for automated landmarking methods compared with manual landmarking. This partially reflects an underestimation of more extreme genotype shapes and loss of biological signal, but largely represents the fact that automated methods do not suffer from intra-observer landmarking error. For appropriate samples and research questions, our image registration-based automated landmarking method can eliminate the time required for manual landmarking and have a similar power to identify shape differences between inbred mouse genotypes.
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Affiliation(s)
| | - Jay Devine
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Benjamin C Darwin
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Liu
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Matthijs van Eede
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, AB, Canada.,The McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
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Economo MN, Winnubst J, Bas E, Ferreira TA, Chandrashekar J. Single‐neuron axonal reconstruction: The search for a wiring diagram of the brain. J Comp Neurol 2019; 527:2190-2199. [DOI: 10.1002/cne.24674] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 12/16/2022]
Affiliation(s)
| | - Johan Winnubst
- Janelia Research CampusHoward Hughes Medical Institute Ashburn Virginia
| | - Erhan Bas
- Janelia Research CampusHoward Hughes Medical Institute Ashburn Virginia
| | - Tiago A. Ferreira
- Janelia Research CampusHoward Hughes Medical Institute Ashburn Virginia
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Lay FY, Chen PY, Cheng HF, Kuo YM, Huang CC. Ex Vivo Evaluation of Mouse Brain Elasticity Using High-Frequency Ultrasound Elastography. IEEE Trans Biomed Eng 2019; 66:3426-3435. [PMID: 30892196 DOI: 10.1109/tbme.2019.2905551] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE Most neurodegenerative diseases are highly linked with aging. The mechanical properties of the brain should be determined for predicting and diagnosing age-related brain diseases. A preclinical animal study is crucial for neurological disease research. However, estimation of the elasticity properties of different regions of mouse brains remains difficult because of the size of the brain. In this paper, high-frequency ultrasound elastography (HFUSE) based on shear wave imaging was proposed for mapping the stiffness of the mouse brain at different ages ex vivo. METHODS For HFUSE, a 40-MHz ultrasound array transducer with an ultrafast ultrasound imaging system was used in this paper. The accuracy and resolution during HFUSE were determined through a mechanical testing system and by conducting phantom experiments. RESULTS In the experiments, the error in the elastic modulus measurement was approximately 10% on average, and the axial resolution was 248 μm. Animal testing was conducted using mice that were 4 (young aged) and 11 (middle aged) months old. The elasticity distributions of the cortex and hippocampus in the mouse brains were obtained through HFUSE. CONCLUSION The average shear moduli of the cortex and hippocampus were 3.84 and 2.33 kPa for the 4-month-old mice and 3.77 and 1.94 kPa for the 11-month-old mice, respectively. No statistical difference was observed in the cortex stiffness of mice of different ages. However, the hippocampus significantly softened with aging.
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