Johnathon Walls - Profile on Academia.edu (original) (raw)

Papers by Johnathon Walls

Comparison of transcriptional differences between IL-4Ra and IL-5 blockade in a mouse model of asthma

Molecular pathology and functional genomics

Genome-wide association study of liver fat, iron, and extracellular fluid fraction in the UK Biobank

Abdominal magnetic resonance imaging (MRI) represents a non-invasive approach allowing the extrac... more Abdominal magnetic resonance imaging (MRI) represents a non-invasive approach allowing the extraction of clinically informative phenotypes. We developed an automated pipeline to segment liver pixels from abdominal MRI images and apply published models to approximate fat fraction, extracellular fluid fraction and iron content in 40,058 MRIs from the UK Biobank. We then conducted a genome-wide association of these traits using imputed variants (N=37,250 individuals, 11,914,698 variants) and exome sequence data (N=35,274 individuals, 8,287,315 variants). For liver fat we identified 8 novel loci in or near genes MARC1, GCKR, ADH1B, MTTP, TRIB1, GPAM, PNPLA2 and APOH. For liver iron we identified 1 novel locus between the genes ASNSD1 and SLC40A1, an iron transporter involved in hemochromatosis. For extracellular fluid fraction we identified 6 novel loci in or near genes AGMAT, NAT2, MRPL4-S1PR2, FADS1, ABO and HFE, with almost all having prior associations to obesity, liver, iron, or li...

European Journal of Human Genetics

Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) mis... more Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles...

Biology of Reproduction

The A disintegrin and metalloprotease domain-containing (ADAM) family of proteins is involved in ... more The A disintegrin and metalloprotease domain-containing (ADAM) family of proteins is involved in cell adhesion, migration, proteolysis, and signaling. Many ADAMs are required for reproduction; however, the role of Adam6 has remained largely unknown. In the course of humanizing the mouse immunoglobulin heavy chain (IgH) locus, we generated Adam6-deficient mice that demonstrate severe subfertility. We decided to elucidate the role of ADAM6 in fertility and explore the underlying mechanisms. Despite normal sperm development and motility, Adam6-deficient mice display diminished male fertility, have abnormal sperm adhesion, and most importantly cannot transition from uterus to oviduct. To test whether ADAM6 is required for sperm's binding to extracellular matrix (ECM) components, we used a panel of ECM components and showed that unlike normal sperm, Adam6-deficient sperm cannot bind fibronectin, laminin, and tenascin. Reintroduction of Adam6 into these deficient mice repaired sperm interaction with ECM, restored male fertility, and corrected the sperm transport deficit. Together, our data suggest that ADAM6, either alone or in complex with other proteins, aids sperm transport through the female reproductive tract by providing a temporary site of attachment of sperm to ECM components prior to ascent into the oviduct. ADAM6, a testis-specific protein, is required for sperm ascent into the oviduct and its deletion results in deficits in both sperm-sperm and sperm-extracellular matrix associations.

Axial molecular-beam mid-infrared diode laser spectrometer

SPIE Proceedings, 2002

A novel molecular beam spectrometer for the purpose of trace gas sensing is described. Sensitivit... more A novel molecular beam spectrometer for the purpose of trace gas sensing is described. Sensitivity is greatly enhanced and absorption interference by atmospheric H2O and CO2 is greatly reduced by using a molecular expansion. The expansion results in rotational cooling and population enhancement of low-lying energy levels. The instrument employs a tunable mid-infrared lead salt diode, which operates in single mode from 2348.5 to 2351.1 cm-1, and a 36 m Herriott multipass cell. The sample gas is injected axially through a coupling hole in one of the spherical mirrors. The result is an increase of the residence time of the molecular beam in the sampling region. Pulsed operation of the nozzle allows background subtracted spectra to be acquired. The spectrometer can either be operated in fast scan mode, in which the laser frequency is rapidly scanned over the absorption feature of interest, or in frequency modulation mode with 2f-detection. A special adaptation of frequency modulation to the axial sampling system is described. Sample data of CO2 are presented.

PLoS ONE, 2013

Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered... more Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm 3 . This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop.

An axial molecular-beam diode laser spectrometer

Review of Scientific Instruments, 2004

A mid-infrared tunable diode laser molecular-beam spectrometer for the purpose of trace gas sensi... more A mid-infrared tunable diode laser molecular-beam spectrometer for the purpose of trace gas sensing and the study of van der Waals complexes is described. The spectrometer employs a Herriott multipass cell with up to 72 passes. The sample gas is injected parallel to the optical axis through a hole at the center of the far mirror. The molecular absorption is Doppler split, resulting from the laser beam propagating parallel and antiparallel to the molecular-beam expansion. The axial expansion leads to narrower line widths and increased sensitivity, compared to the traditional vertical injection method, as a result of selective sampling of the central part of the molecular expansion with reduced Doppler broadening and longer residence time of the molecular sample in the laser beam. The molecular expansion leads also to selective signal enhancement of low-J transitions, as demonstrated for the nu3 antisymmetric stretch vibration of CO2. A microwave horn antenna was implemented into the spectrometer to enable microwave-infrared double-resonance experiments. The spectrometer performance was evaluated by recording spectra of the CO2-Ar, (CO2)2, CO2-He, and CO2-SO2 van der Waals complexes near the R(0) transition of the nu3 band of CO2 around 2349 cm-1. The feasibility of using a pulsed molecular expansion for trace gas sensing is explored.

Proceedings of the National Academy of Sciences, 2011

The vasculature of the CNS is structurally and functionally distinct from that of other organ sys... more The vasculature of the CNS is structurally and functionally distinct from that of other organ systems and is particularly prone to developmental abnormalities and hemorrhage. Although other embryonic tissues undergo primary vascularization, the developing nervous system is unique in that it is secondarily vascularized by sprouting angiogenesis from a surrounding perineural plexus. This sprouting angiogenesis requires the TGF-β and Wnt pathways because ablation of these pathways results in aberrant sprouting and hemorrhage. We have genetically deleted Gpr124, a member of the large family of long N-terminal group B G protein-coupled receptors, few members of which have identified ligands or well-defined biologic functions in mammals. We show that, in the developing CNS, Gpr124 is specifically expressed in the vasculature and is absolutely required for proper angiogenic sprouting into the developing neural tube. Embryos lacking Gpr124 exhibit vascular defects characterized by delayed v...

PLoS ONE, 2008

Key vasculogenic (de-novo vessel forming) and angiogenic (vessel remodelling) events occur in the... more Key vasculogenic (de-novo vessel forming) and angiogenic (vessel remodelling) events occur in the mouse embryo between embryonic days (E) 8.0 and 10.0 of gestation, during which time the vasculature develops from a simple circulatory loop into a complex, fine structured, three-dimensional organ. Interpretation of vascular phenotypes exhibited by signalling pathway mutants has historically been hindered by an inability to comprehensively image the normal sequence of events that shape the basic architecture of the early mouse vascular system. We have employed Optical Projection Tomography (OPT) using frequency distance relationship (FDR)-based deconvolution to image embryos immunostained with the endothelial specific marker PECAM-1 to create a high resolution, three-dimensional atlas of mouse vascular development between E8.0 and E10.0 (5 to 30 somites). Analysis of the atlas has provided significant new information regarding normal development of intersomitic vessels, the perineural vascular plexus, the cephalic plexus and vessels connecting the embryonic and extraembryonic circulation. We describe examples of vascular remodelling that provide new insight into the mechanisms of sprouting angiogenesis, vascular guidance cues and artery/vein identity that directly relate to phenotypes observed in mouse mutants affecting vascular development between E8.0 and E10.0. This atlas is freely available at . mouseimaging.ca/research/mouse_atlas.html and will serve as a platform to provide insight into normal and abnormal vascular development.

Physics in Medicine and Biology, 2005

A new imaging technique called optical projection tomography (OPT), essentially an optical versio... more A new imaging technique called optical projection tomography (OPT), essentially an optical version of x-ray computed tomography (CT), provides molecular specificity, cellular resolution and larger specimen coverage (≈1 cubic centimetre) than was previously possible with other imaging techniques. It is ideally suited to gene expression studies in small animals. Reconstructed OPT images demonstrate several artefacts which reduce the overall image quality. In this paper, we describe methods to prevent smear artefacts due to illumination intensity fluctuation, ring artefacts due to CCD pixel sensitivity variation and a new 'detector edge' artefact caused by non-zero background signal. We also present an automated method to align the position of the rotational axis during image reconstruction. Finally, we propose a method to eliminate bowl artefacts due to projection truncation using a lower resolution OPT scan of the same specimen. This solution also provides OPT with the ability to obtain a high-resolution reconstruction from a region of interest of a specimen that is larger than the field of view. Implementation of these corrections and modifications increases the accuracy of the OPT imaging technique and extends its capabilities to obtain higher resolution data from within a whole specimen.

Physics in Medicine and Biology, 2007

A new imaging technique called emission optical projection tomography (eOPT), essentially an opti... more A new imaging technique called emission optical projection tomography (eOPT), essentially an optical version of single-photon emission computed tomography (SPECT), provides molecular specificity, resolution on the order of microns to tens of microns, and large specimen coverage (≈ 1 cubic centimetre). It is ideally suited to gene expression studies in embryos. Reconstructed eOPT images suffer from blurring that worsens as the distance from the axis of rotation increases. This blur is caused in part by the defocusing of the lens' point-spread function, which increases with object distance from the focal plane. In this paper, we describe a frequency space filter based on the frequency-distance relationship of sinograms to deconvolve the distance-dependent point-spread function and exclude highly defocused data from the eOPT sinograms prior to reconstruction. The method is shown to reduce the volume at half-maximum of the reconstructed point-spread function to approximately 20% the original, and the volume at 10% maximum to approximately 6% the original. As an illustration, the visibility of fine details in the vasculature of a 9.5 day old mouse embryo is dramatically improved.

Journal of Cell Science, 2012

Blood vessels deliver oxygen, nutrients, hormones and immunity factors throughout the body. To pe... more Blood vessels deliver oxygen, nutrients, hormones and immunity factors throughout the body. To perform these vital functions, vascular cords branch, lumenize and interconnect. Yet, little is known about the cellular, molecular and physiological mechanisms that control how circulatory networks form and interconnect. Specifically, how circulatory networks merge by interconnecting in parallel along their boundaries remains unexplored. To examine this process we studied the formation and functional maturation of the plexus that forms between the Dorsal Longitudinal Anastomotic Vessels (DLAVs) in the zebrafish. We find that the migration and proliferation of endothelial cells within the DLAVs and their Segmental (Se) vessel precursors drives DLAV plexus formation. Remarkably, the presence of Se vessels containing only endothelial cells of the arterial lineage is sufficient for DLAV plexus morphogenesis, suggesting that endothelial cells from the venous lineage make a dispensable or null ...

ILAR Journal, 2006

Considerable progress has been made in adapting existing and developing new technologies to enabl... more Considerable progress has been made in adapting existing and developing new technologies to enable increasingly detailed phenotypic information to be obtained in embryonic and newborn mice. Sophisticated methods for imaging mouse embryos and newborns are available and include ultrasound and magnetic resonance imaging (MRI) for in vivo imaging, and MRI, vascular corrosion casts, microcomputed tomography, and optical projection tomography (OPT) for postmortem imaging. In addition, Doppler and M-mode ultrasound are useful noninvasive tools to monitor cardiac and vascular hemodynamics in vivo in embryos and newborns. The developmental stage of the animals being phenotyped is an important consideration when selecting the appropriate technique for anesthesia or euthanasia and for labeling animals in longitudinal studies. Study design also needs to control for possible differences between interand intralitter variability, and for possible long-term developmental effects caused by anesthesia and/or procedures. Noninvasive or minimally invasive intravenous or intracardiac injections or blood sampling, and arterial pressure and electrocardiography (ECG) measurements are feasible in newborns. Whereas microinjection techniques are available for embryos as young as 6.5 days of gestation, further advances are required to enable minimally invasive fluid or tissue samples, or blood pressure or ECG measurements, to be obtained from mouse embryos in utero. The growing repertoire of techniques available for phenotyping mouse embryos and newborns promises to accelerate knowledge gained from studies using genetically engineered mice to understand molecular regulation of morphogenesis and the etiology of congenital diseases.

The European Physical Journal D, 2003

The lithium D lines were studied using a diode laser that was frequency modulated by an electroop... more The lithium D lines were studied using a diode laser that was frequency modulated by an electrooptic modulator, to excite an atomic beam. The transmission of part of the laser beam through an etalon was monitored to correct for the nonlinearity of the laser scan. The results for the 6,7 Li 2S 1/2 and 2P 1/2 hyperfine splittings agree very well with the best existing data while those for the D1 isotope shift and 6,7 Li fine structure splittings disagree significantly from data obtained by a previous laser atomic beam experiment. Our result for the D1 isotope shift is very close to the latest value computed using Hylleraas variational theory.

Developmental Cell, 2004

which is the most common form of birth defect in humans (Harvey, 2002a; Olson and Schneider, 2003... more which is the most common form of birth defect in humans (Harvey, 2002a; Olson and Schneider, 2003). Initiation of heart development occurs in the cardiac crescent,

Development, 2012

The goal of the International Mouse Phenotyping Consortium (IMPC) is to phenotype targeted knocko... more The goal of the International Mouse Phenotyping Consortium (IMPC) is to phenotype targeted knockout mouse strains throughout the whole mouse genome (23,000 genes) by 2021. A significant percentage of the generated mice will be embryonic lethal; therefore, phenotyping methods tuned to the mouse embryo are needed. Methods that are robust, quantitative, automated and high-throughput are attractive owing to the numbers of mice involved. Three-dimensional (3D) imaging is a useful method for characterizing morphological phenotypes. However, tools to automatically quantify morphological information of mouse embryos from 3D imaging have not been fully developed. We present a representative mouse embryo average 3D atlas comprising micro-CT images of 35 individual C57BL/6J mouse embryos at 15.5 days post-coitum. The 35 micro-CT images were registered into a consensus average image with our automated image registration software and 48 anatomical structures were segmented manually. We report th...

Imaging for Mouse Phenotyping

PLoS ONE, 2013

Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered... more Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm 3 . This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop.

Comparison of transcriptional differences between IL-4Ra and IL-5 blockade in a mouse model of asthma

Molecular pathology and functional genomics

Genome-wide association study of liver fat, iron, and extracellular fluid fraction in the UK Biobank

Abdominal magnetic resonance imaging (MRI) represents a non-invasive approach allowing the extrac... more Abdominal magnetic resonance imaging (MRI) represents a non-invasive approach allowing the extraction of clinically informative phenotypes. We developed an automated pipeline to segment liver pixels from abdominal MRI images and apply published models to approximate fat fraction, extracellular fluid fraction and iron content in 40,058 MRIs from the UK Biobank. We then conducted a genome-wide association of these traits using imputed variants (N=37,250 individuals, 11,914,698 variants) and exome sequence data (N=35,274 individuals, 8,287,315 variants). For liver fat we identified 8 novel loci in or near genes MARC1, GCKR, ADH1B, MTTP, TRIB1, GPAM, PNPLA2 and APOH. For liver iron we identified 1 novel locus between the genes ASNSD1 and SLC40A1, an iron transporter involved in hemochromatosis. For extracellular fluid fraction we identified 6 novel loci in or near genes AGMAT, NAT2, MRPL4-S1PR2, FADS1, ABO and HFE, with almost all having prior associations to obesity, liver, iron, or li...

European Journal of Human Genetics

Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) mis... more Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles...

Biology of Reproduction

The A disintegrin and metalloprotease domain-containing (ADAM) family of proteins is involved in ... more The A disintegrin and metalloprotease domain-containing (ADAM) family of proteins is involved in cell adhesion, migration, proteolysis, and signaling. Many ADAMs are required for reproduction; however, the role of Adam6 has remained largely unknown. In the course of humanizing the mouse immunoglobulin heavy chain (IgH) locus, we generated Adam6-deficient mice that demonstrate severe subfertility. We decided to elucidate the role of ADAM6 in fertility and explore the underlying mechanisms. Despite normal sperm development and motility, Adam6-deficient mice display diminished male fertility, have abnormal sperm adhesion, and most importantly cannot transition from uterus to oviduct. To test whether ADAM6 is required for sperm's binding to extracellular matrix (ECM) components, we used a panel of ECM components and showed that unlike normal sperm, Adam6-deficient sperm cannot bind fibronectin, laminin, and tenascin. Reintroduction of Adam6 into these deficient mice repaired sperm interaction with ECM, restored male fertility, and corrected the sperm transport deficit. Together, our data suggest that ADAM6, either alone or in complex with other proteins, aids sperm transport through the female reproductive tract by providing a temporary site of attachment of sperm to ECM components prior to ascent into the oviduct. ADAM6, a testis-specific protein, is required for sperm ascent into the oviduct and its deletion results in deficits in both sperm-sperm and sperm-extracellular matrix associations.

Axial molecular-beam mid-infrared diode laser spectrometer

SPIE Proceedings, 2002

A novel molecular beam spectrometer for the purpose of trace gas sensing is described. Sensitivit... more A novel molecular beam spectrometer for the purpose of trace gas sensing is described. Sensitivity is greatly enhanced and absorption interference by atmospheric H2O and CO2 is greatly reduced by using a molecular expansion. The expansion results in rotational cooling and population enhancement of low-lying energy levels. The instrument employs a tunable mid-infrared lead salt diode, which operates in single mode from 2348.5 to 2351.1 cm-1, and a 36 m Herriott multipass cell. The sample gas is injected axially through a coupling hole in one of the spherical mirrors. The result is an increase of the residence time of the molecular beam in the sampling region. Pulsed operation of the nozzle allows background subtracted spectra to be acquired. The spectrometer can either be operated in fast scan mode, in which the laser frequency is rapidly scanned over the absorption feature of interest, or in frequency modulation mode with 2f-detection. A special adaptation of frequency modulation to the axial sampling system is described. Sample data of CO2 are presented.

PLoS ONE, 2013

Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered... more Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm 3 . This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop.

An axial molecular-beam diode laser spectrometer

Review of Scientific Instruments, 2004

A mid-infrared tunable diode laser molecular-beam spectrometer for the purpose of trace gas sensi... more A mid-infrared tunable diode laser molecular-beam spectrometer for the purpose of trace gas sensing and the study of van der Waals complexes is described. The spectrometer employs a Herriott multipass cell with up to 72 passes. The sample gas is injected parallel to the optical axis through a hole at the center of the far mirror. The molecular absorption is Doppler split, resulting from the laser beam propagating parallel and antiparallel to the molecular-beam expansion. The axial expansion leads to narrower line widths and increased sensitivity, compared to the traditional vertical injection method, as a result of selective sampling of the central part of the molecular expansion with reduced Doppler broadening and longer residence time of the molecular sample in the laser beam. The molecular expansion leads also to selective signal enhancement of low-J transitions, as demonstrated for the nu3 antisymmetric stretch vibration of CO2. A microwave horn antenna was implemented into the spectrometer to enable microwave-infrared double-resonance experiments. The spectrometer performance was evaluated by recording spectra of the CO2-Ar, (CO2)2, CO2-He, and CO2-SO2 van der Waals complexes near the R(0) transition of the nu3 band of CO2 around 2349 cm-1. The feasibility of using a pulsed molecular expansion for trace gas sensing is explored.

Proceedings of the National Academy of Sciences, 2011

The vasculature of the CNS is structurally and functionally distinct from that of other organ sys... more The vasculature of the CNS is structurally and functionally distinct from that of other organ systems and is particularly prone to developmental abnormalities and hemorrhage. Although other embryonic tissues undergo primary vascularization, the developing nervous system is unique in that it is secondarily vascularized by sprouting angiogenesis from a surrounding perineural plexus. This sprouting angiogenesis requires the TGF-β and Wnt pathways because ablation of these pathways results in aberrant sprouting and hemorrhage. We have genetically deleted Gpr124, a member of the large family of long N-terminal group B G protein-coupled receptors, few members of which have identified ligands or well-defined biologic functions in mammals. We show that, in the developing CNS, Gpr124 is specifically expressed in the vasculature and is absolutely required for proper angiogenic sprouting into the developing neural tube. Embryos lacking Gpr124 exhibit vascular defects characterized by delayed v...

PLoS ONE, 2008

Key vasculogenic (de-novo vessel forming) and angiogenic (vessel remodelling) events occur in the... more Key vasculogenic (de-novo vessel forming) and angiogenic (vessel remodelling) events occur in the mouse embryo between embryonic days (E) 8.0 and 10.0 of gestation, during which time the vasculature develops from a simple circulatory loop into a complex, fine structured, three-dimensional organ. Interpretation of vascular phenotypes exhibited by signalling pathway mutants has historically been hindered by an inability to comprehensively image the normal sequence of events that shape the basic architecture of the early mouse vascular system. We have employed Optical Projection Tomography (OPT) using frequency distance relationship (FDR)-based deconvolution to image embryos immunostained with the endothelial specific marker PECAM-1 to create a high resolution, three-dimensional atlas of mouse vascular development between E8.0 and E10.0 (5 to 30 somites). Analysis of the atlas has provided significant new information regarding normal development of intersomitic vessels, the perineural vascular plexus, the cephalic plexus and vessels connecting the embryonic and extraembryonic circulation. We describe examples of vascular remodelling that provide new insight into the mechanisms of sprouting angiogenesis, vascular guidance cues and artery/vein identity that directly relate to phenotypes observed in mouse mutants affecting vascular development between E8.0 and E10.0. This atlas is freely available at . mouseimaging.ca/research/mouse_atlas.html and will serve as a platform to provide insight into normal and abnormal vascular development.

Physics in Medicine and Biology, 2005

A new imaging technique called optical projection tomography (OPT), essentially an optical versio... more A new imaging technique called optical projection tomography (OPT), essentially an optical version of x-ray computed tomography (CT), provides molecular specificity, cellular resolution and larger specimen coverage (≈1 cubic centimetre) than was previously possible with other imaging techniques. It is ideally suited to gene expression studies in small animals. Reconstructed OPT images demonstrate several artefacts which reduce the overall image quality. In this paper, we describe methods to prevent smear artefacts due to illumination intensity fluctuation, ring artefacts due to CCD pixel sensitivity variation and a new 'detector edge' artefact caused by non-zero background signal. We also present an automated method to align the position of the rotational axis during image reconstruction. Finally, we propose a method to eliminate bowl artefacts due to projection truncation using a lower resolution OPT scan of the same specimen. This solution also provides OPT with the ability to obtain a high-resolution reconstruction from a region of interest of a specimen that is larger than the field of view. Implementation of these corrections and modifications increases the accuracy of the OPT imaging technique and extends its capabilities to obtain higher resolution data from within a whole specimen.

Physics in Medicine and Biology, 2007

A new imaging technique called emission optical projection tomography (eOPT), essentially an opti... more A new imaging technique called emission optical projection tomography (eOPT), essentially an optical version of single-photon emission computed tomography (SPECT), provides molecular specificity, resolution on the order of microns to tens of microns, and large specimen coverage (≈ 1 cubic centimetre). It is ideally suited to gene expression studies in embryos. Reconstructed eOPT images suffer from blurring that worsens as the distance from the axis of rotation increases. This blur is caused in part by the defocusing of the lens' point-spread function, which increases with object distance from the focal plane. In this paper, we describe a frequency space filter based on the frequency-distance relationship of sinograms to deconvolve the distance-dependent point-spread function and exclude highly defocused data from the eOPT sinograms prior to reconstruction. The method is shown to reduce the volume at half-maximum of the reconstructed point-spread function to approximately 20% the original, and the volume at 10% maximum to approximately 6% the original. As an illustration, the visibility of fine details in the vasculature of a 9.5 day old mouse embryo is dramatically improved.

Journal of Cell Science, 2012

Blood vessels deliver oxygen, nutrients, hormones and immunity factors throughout the body. To pe... more Blood vessels deliver oxygen, nutrients, hormones and immunity factors throughout the body. To perform these vital functions, vascular cords branch, lumenize and interconnect. Yet, little is known about the cellular, molecular and physiological mechanisms that control how circulatory networks form and interconnect. Specifically, how circulatory networks merge by interconnecting in parallel along their boundaries remains unexplored. To examine this process we studied the formation and functional maturation of the plexus that forms between the Dorsal Longitudinal Anastomotic Vessels (DLAVs) in the zebrafish. We find that the migration and proliferation of endothelial cells within the DLAVs and their Segmental (Se) vessel precursors drives DLAV plexus formation. Remarkably, the presence of Se vessels containing only endothelial cells of the arterial lineage is sufficient for DLAV plexus morphogenesis, suggesting that endothelial cells from the venous lineage make a dispensable or null ...

ILAR Journal, 2006

Considerable progress has been made in adapting existing and developing new technologies to enabl... more Considerable progress has been made in adapting existing and developing new technologies to enable increasingly detailed phenotypic information to be obtained in embryonic and newborn mice. Sophisticated methods for imaging mouse embryos and newborns are available and include ultrasound and magnetic resonance imaging (MRI) for in vivo imaging, and MRI, vascular corrosion casts, microcomputed tomography, and optical projection tomography (OPT) for postmortem imaging. In addition, Doppler and M-mode ultrasound are useful noninvasive tools to monitor cardiac and vascular hemodynamics in vivo in embryos and newborns. The developmental stage of the animals being phenotyped is an important consideration when selecting the appropriate technique for anesthesia or euthanasia and for labeling animals in longitudinal studies. Study design also needs to control for possible differences between interand intralitter variability, and for possible long-term developmental effects caused by anesthesia and/or procedures. Noninvasive or minimally invasive intravenous or intracardiac injections or blood sampling, and arterial pressure and electrocardiography (ECG) measurements are feasible in newborns. Whereas microinjection techniques are available for embryos as young as 6.5 days of gestation, further advances are required to enable minimally invasive fluid or tissue samples, or blood pressure or ECG measurements, to be obtained from mouse embryos in utero. The growing repertoire of techniques available for phenotyping mouse embryos and newborns promises to accelerate knowledge gained from studies using genetically engineered mice to understand molecular regulation of morphogenesis and the etiology of congenital diseases.

The European Physical Journal D, 2003

The lithium D lines were studied using a diode laser that was frequency modulated by an electroop... more The lithium D lines were studied using a diode laser that was frequency modulated by an electrooptic modulator, to excite an atomic beam. The transmission of part of the laser beam through an etalon was monitored to correct for the nonlinearity of the laser scan. The results for the 6,7 Li 2S 1/2 and 2P 1/2 hyperfine splittings agree very well with the best existing data while those for the D1 isotope shift and 6,7 Li fine structure splittings disagree significantly from data obtained by a previous laser atomic beam experiment. Our result for the D1 isotope shift is very close to the latest value computed using Hylleraas variational theory.

Developmental Cell, 2004

which is the most common form of birth defect in humans (Harvey, 2002a; Olson and Schneider, 2003... more which is the most common form of birth defect in humans (Harvey, 2002a; Olson and Schneider, 2003). Initiation of heart development occurs in the cardiac crescent,

Development, 2012

The goal of the International Mouse Phenotyping Consortium (IMPC) is to phenotype targeted knocko... more The goal of the International Mouse Phenotyping Consortium (IMPC) is to phenotype targeted knockout mouse strains throughout the whole mouse genome (23,000 genes) by 2021. A significant percentage of the generated mice will be embryonic lethal; therefore, phenotyping methods tuned to the mouse embryo are needed. Methods that are robust, quantitative, automated and high-throughput are attractive owing to the numbers of mice involved. Three-dimensional (3D) imaging is a useful method for characterizing morphological phenotypes. However, tools to automatically quantify morphological information of mouse embryos from 3D imaging have not been fully developed. We present a representative mouse embryo average 3D atlas comprising micro-CT images of 35 individual C57BL/6J mouse embryos at 15.5 days post-coitum. The 35 micro-CT images were registered into a consensus average image with our automated image registration software and 48 anatomical structures were segmented manually. We report th...

Imaging for Mouse Phenotyping

PLoS ONE, 2013

Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered... more Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm 3 . This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop.