From 4888a31d6b75819ef5a1764b98203a83c471546d Mon Sep 17 00:00:00 2001 From: Quarto GHA Workflow Runner Date: Sun, 25 Feb 2024 08:13:31 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- atlases.html | 12 +++---- atlases/2021-carpentier-34618370/index.html | 2 +- atlases/2021-walsh-33843587/index.html | 2 +- atlases/2024-lucas-38194268/index.html | 2 +- index.html | 30 ++++++++-------- investigators.html | 10 +++--- projects.html | 40 ++++++++++----------- pubs.html | 27 +++++++------- search.json | 10 +++--- site_libs/bootstrap/bootstrap-dark.min.css | 2 +- site_libs/bootstrap/bootstrap.min.css | 2 +- sitemap.xml | 40 ++++++++++----------- timeline.json | 2 +- 14 files changed, 92 insertions(+), 91 deletions(-) diff --git a/.nojekyll b/.nojekyll index 02f2be3..39a93df 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -8078f164 \ No newline at end of file +e6b5c896 \ No newline at end of file diff --git a/atlases.html b/atlases.html index dbc036e..46b5124 100644 --- a/atlases.html +++ b/atlases.html @@ -229,7 +229,7 @@

Atlases

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Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
-Atlas + Atlas
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MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination
-Atlas + Atlas
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Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node
-Atlas + Atlas
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MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination

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Atlas

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Atlas

Project-1
Project-2
diff --git a/atlases/2021-walsh-33843587/index.html b/atlases/2021-walsh-33843587/index.html index 0cc18b6..fab4eb6 100644 --- a/atlases/2021-walsh-33843587/index.html +++ b/atlases/2021-walsh-33843587/index.html @@ -148,7 +148,7 @@

Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node

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Atlas

+

Atlas

Project-2
Core-C
diff --git a/atlases/2024-lucas-38194268/index.html b/atlases/2024-lucas-38194268/index.html index 3ef0128..78bf064 100644 --- a/atlases/2024-lucas-38194268/index.html +++ b/atlases/2024-lucas-38194268/index.html @@ -146,7 +146,7 @@

Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO

-

Atlas

+

Atlas

Project-1
Project-2
diff --git a/index.html b/index.html index 1416153..15a72d8 100644 --- a/index.html +++ b/index.html @@ -154,29 +154,29 @@

Projects

Cores

diff --git a/investigators.html b/investigators.html index 4d73998..3acf274 100644 --- a/investigators.html +++ b/investigators.html @@ -168,7 +168,7 @@

Investigators

Thomas Morrison, PhD

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Publications Website Email Project-1

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Publications Website Email Project-1

My laboratory investigates mechanisms of infectious disease pathogenesis and immunity. We use genetic, molecular, cellular, and immunological approaches to define molecular mechanisms of pathogenesis, to elucidate immunological mechanisms that dictate viral clearance, including antibodies and B cells, and to evaluate novel therapeutic interventions. My laboratory has developed mouse models of chikungunya virus (CHIKV) and Ross River virus (RRV)-induced rheumatic disease that recapitulate important aspects of acute and chronic CHIKV and RRV disease in humans. In addition, we also investigate mechanisms of neurological disease associated with neurotropic viruses such as Venezuelan equine encephalitis virus (VEEV), West Nile virus, and Zika virus. I also have extensive experience working with human coronaviruses and other highly pathogenic respiratory viruses.

@@ -176,7 +176,7 @@

Beth Tamburini, PhD

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Publications Website Email Project-2

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Publications Website Email Project-2

The overarching goal of my research program is to understand how the lymphatic stroma recognize and react to stimuli within the lymph to guide the immune response. My initial studies of lymphatic stroma were focused on understanding the mechanisms by which lymphatic endothelial cells acquire and retain antigens as well as recruit and interact with immune cells in different organs. Currently my research program is focused on understanding the immunologic consequence of interaction between lymphatic stroma and components of the immune system within different organ systems. We have been working to dissect how the lymphatics respond to stimuli such as proteins, small molecules, fat, cholesterol, alcohol, infectious material and cytokine. We have experience with a number of techniques including flow cytometry, immunohistochemistry, immunofluorescence, live molecular imaging, and a number of therapeutic treatments to target and identify lymphatic endothelial cells as well as experience in several mouse models and assays. In addition, my expertise and the expertise of a wide range of collaborators at the University of Colorado in the fields of Gastroenterology, Hepatology and Immunology have been critical in developing this research program. This collaborative research program as proven to be well suited for the training and success of the graduate students and post-docs in my laboratory.

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Jenna Guthmiller, PhD

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Publications Website Email Project-3

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Publications Website Email Project-3

My long-term scientific goals are to understand the complex interactions between pathogens and the immune response mounted against them, with the objective of identifying and developing interventions to limit global infectious disease burdens. Fitting within these goals, my independent laboratory studies how preexisting immunity influences future immune responses against rapidly evolving viruses. My major contributions to science are understanding how protective humoral immunity is generated following infection and vaccination and how vaccination can harness broadly protective humoral immunity. During my postdoctoral studies, I investigated how preexisting immunity against influenza viruses shapes the recall of memory B cells in humans. I found that in the absence of preexisting immunity against the variable epitopes of the hemagglutinin (HA) head domain, humans could recall memory B cells against broadly protective epitopes of HA. These studies identified several novel classes of broadly neutralizing antibodies and a new highly conserved epitope where HA ‘anchors’ itself into the viral membrane. My research also identified that the first in-human universal influenza vaccine, which is intended to circumvent preexisting antibodies, robustly induced antibodies against broadly protective epitopes, including the anchor epitope. Lastly, I identified influenza vaccination and infection in humans differentially recalled discrete memory B cell specificities, with infection recalling memory B cells primed during childhood against highly conserved, albeit non-protective antigens. Together, these studies highlight the importance of understanding how preexisting antibodies influence the generation of broadly protective immunity.

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Jay Hesselberth, PhD

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Publications Website Email Core-C Core-D

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Publications Website Email Core-C Core-D

I am an RNA biochemist and computational biologist with extensive experience in developing new high- throughput methods and associated bioinformatic analysis software. My RNA biology program spans classical and modern approaches to address outstanding questions in RNA damage and repair. Over the past ten years my group has developed new sequencing approaches to identify damaged RNAs and new model systems with which to understand the causes and consequences of RNA damage. Our studies have led to new concepts in post-transcriptional regulation that have broad implications for understanding the role of RNA damage in biology. Recently we have been focused on understanding how RNA damage and repair events are coupled to control RNA fate after stress-induced RNA cleavage. More recently, we have applied nanopore RNA sequencing to characterize the landscape of RNA repair events in budding yeast.

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Jennifer Matsuda, PhD

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Publications Email Core-B

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Publications Email Core-B

In 2008, following my graduate studies and post-doctoral training, I became the Director of the Mouse Genetics Core Facility at National Jewish Health. Given my years at the bench, it was critical to me that the facility I established enabled all investigators, regardless of prior experience, with the support necessary to make mouse models. To this end, in addition to classic services like ES cell targeting, blastocyst and pronuclear microinjections, embryo and sperm cryopreservation, in vitro fertilization, and rederivation, we have developed additional areas of expertise. We generate complex DNA constructs, using BAC recombineering, markerless recombineering, and classic cloning methodologies. We also train graduate students and post-doctoral fellows in our laboratory to make their own constructs. We have also gained the expertise to identify homologous recombinant ES cell clones by Loss of Allele (LOA). In addition, we successfully use engineered nucleases (ZFNs, TALENs, and more recently CRISPR/Cas9) to generate knockout mice by NHEJ as well as relying upon homology directed repair (HDR) to introduce genetic modifications. This technology has been further improved upon by our capacity to make mouse models directly on a variety of backgrounds by using IVF, including but not limited to: C57BL/6, FVB, NOD, 129S4, and NSGS backgrounds as well genetically modified strains of mice. Due to the core’s consistently high quality of work, we have recently been designated as the Regional Mouse Genetics Core Facility to support investigators at the University of Colorado Denver, in addition to the investigators at NJH.

diff --git a/projects.html b/projects.html index 0c7d0e9..30357d0 100644 --- a/projects.html +++ b/projects.html @@ -156,54 +156,54 @@

On this page

Projects

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Define protective and pathogenic roles of LNSCs during viral infection

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Thomas Morrison, PhD Publications Atlases

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We hypothesize that inflammatory responses, cell trafficking, and development of protective adaptive immune responses are regulated by discrete populations of LNSCs during viral infection

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Thomas Morrison, PhD Publications Atlases

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We hypothesize that inflammatory responses, cell trafficking, and development of protective adaptive immune responses are regulated by discrete populations of LNSCs during viral infection

-

Project 1 will define how viral targeting of distinct LNSCs regulates viral dissemination, LN organization and inflammation, and development of adaptive immunity. Project 1 and Project 2 will establish how viral targeting of LNSCs impacts antigen archiving and immune memory to archived antigens. Finally, Project 1 coordinates with Project 3 to study how isotype-specific immune complexes (ICs) promote chronic viral infection of follicular dendritic cells (FDCs). This project will use novel mouse models and human tissues and advanced spatial and single-cell RNA approaches. This project will define how LNSCs shape antiviral immune responses and how viruses manipulate LNSCs to evade immunity.

+

Project 1 will define how viral targeting of distinct LNSCs regulates viral dissemination, LN organization and inflammation, and development of adaptive immunity. Project 1 will establish how viral targeting of LNSCs impacts antigen archiving and immune memory to archived antigens. Finally, Project 1 will study how isotype-specific immune complexes (ICs) promote chronic viral infection of follicular dendritic cells (FDCs). This project will use novel mouse models and human tissues and advanced spatial and single-cell RNA approaches. This project will define how LNSCs shape antiviral immune responses and how viruses manipulate LNSCs to evade immunity.

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Identify mechanisms of vaccine antigen localization and retention by LNSCs that drive and enhance cellular and humoral immunity

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Beth Tamburini, PhD Publications Atlases

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We hypothesize that LNSC targeting improves and extends the cellular and humoral responses required for vaccine mediated immunity

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Beth Tamburini, PhD Publications Atlases

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We hypothesize that LNSC targeting improves and extends the cellular and humoral responses required for vaccine mediated immunity

-

Project 2 will work with Project 3 to define mechanisms of vaccine antigen acquisition and retention by different LNSCs. Project 2 will work with Projects 1 and 3 to determine if manipulation of antigen duration in LNSCs improves vaccine protection against arboviruses and influenza virus. Finally, Project 2 will work with Project 1 to define the consequences of virus induced cell death on LEC “training” and the impact on vaccine immunity. This project will distinguish functions of specific LNSC populations and create novel vaccine strategies (e.g., mRNA, virus-like particles, and lipid nanoparticles) and apply sophisticated spatial and single-cell transcriptomic approaches to evaluate antigen levels within infrequent and transcriptionally defined LNSC subsets. This project will determine how specific LNSC subsets shape vaccine immunity and the consequences of viral infection of LNSCs to vaccine immunity.

+

Project 2 will define mechanisms of vaccine antigen acquisition and retention by different LNSCs. Project 2 will determine if manipulation of antigen duration in LNSCs improves vaccine protection against arboviruses and influenza virus. Finally, Project 2 will define the consequences of virus induced cell death on LEC ‘training’ and the impact on vaccine immunity. This project will distinguish functions of specific LNSC populations and create novel vaccine strategies (e.g., mRNA, virus-like particles, and lipid nanoparticles) and apply sophisticated spatial and single-cell transcriptomic approaches to evaluate antigen levels within infrequent and transcriptionally defined LNSC subsets. This project will determine how specific LNSC subsets shape vaccine immunity and the consequences of viral infection of LNSCs to vaccine immunity.

-

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Investigate the role of immune complexes in antigen acquisition and retention by LNSCs to modulate cellular and humoral immunity

Jenna Guthmiller, PhD

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We hypothesize that antibody isotype in an IC regulates protective immunity by determining which LNSC populations acquire and retain antigen via isotype-specific interactions with complement and Fc receptors (FcRs)

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We hypothesize that antibody isotype in an IC regulates protective immunity by determining which LNSC populations acquire and retain antigen via isotype-specific interactions with complement and Fc receptors (FcRs)

-

Project 3 will engineer monoclonal antibodies (mAbs) with fixed antigen specificity on discrete antibody isotypes and subclasses. Using stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen complexes to determine the spatial and cellular localization of ICs in comparison with free antigen. Project 3 also investigates how FcR expression by LNSCs impacts IC acquisition and will work with Project 1 to determine viral antigen retention and define consequences to protective humoral and cellular immunity. This project will use mouse models engineered to manipulate complement receptor and FcR expression by discrete LNSC populations and will define how different LNSC populations use antibody to determine antigen uptake and localization.

+

Project 3 will engineer monoclonal antibodies (mAbs) with fixed antigen specificity on discrete antibody isotypes and subclasses. Using stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen complexes to determine the spatial and cellular localization of ICs in comparison with free antigen. Project 3 also investigates how FcR expression by LNSCs impacts IC acquisition and will work with Project 1 to determine viral antigen retention and define consequences to protective humoral and cellular immunity. This project will use mouse models engineered to manipulate complement receptor and FcR expression by discrete LNSC populations and will define how different LNSC populations use antibody to determine antigen uptake and localization.

Cores

-

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Mouse transgenics and tissue characterization

-

Jennifer Matsuda, PhD Publications

-

The goal of the mouse transgenics and tissue core is to generate novel genetic mouse models and to develop a tissue and cell repository, this includes the following key tasks.

+

Jennifer Matsuda, PhD Publications

+

Core B will generate novel genetic mouse models and develop a tissue and cell repository, this includes the following tasks.

Task 1. Generation of novel mouse lines

Task 2. Provide a mouse colony for LNSC biology

Task 3. Provide a resource for maintenance and distribution of human and mouse LNSCs and lymphoid tissues -

+

Molecular technologies

-

Jay Hesselberth, PhD Publications Atlases

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The molecular technologies cores will apply new molecular tools to understand the contributions of lymph node stromal cells to immune responses, this includes the following key tasks.

+

Jay Hesselberth, PhD Publications Atlases

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Core C will apply new molecular tools to understand the contributions of lymph node stromal cells to immune responses, this includes the following tasks.

Task 1. Generate validated reagents for and execute single-cell and spatial transcriptomic experiments to probe LNSC biology

Task 2. Production of customized lipid nanoparticles with mRNA and siRNA cargo

Task 3. Expression and purification of antibodies, antigens, and immune complexes -

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Bioinformatics

-

Jay Hesselberth, PhD Ryan Sheridan, PhD Publications Atlases

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The bioinformatics core will apply new informatics approaches to understand the contributions of LNSCs to immune responses, this includes the following tasks.

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Jay Hesselberth, PhD Ryan Sheridan, PhD Publications Atlases

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Core D will apply new informatics approaches to understand the contributions of LNSCs to immune responses, this includes the following tasks.

Task 1. Provide a bioinformatics resource for rigorous and reproducible analysis of sequencing experiments

Task 2. Develop pipelines for large scale meta-analysis of single-cell and spatial transcriptomic data

Task 3. Curate a public-facing LNSC atlas to allow for interactive exploration of published datasets

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Publications

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Publications

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diff --git a/search.json b/search.json index ae10801..ac9050f 100644 --- a/search.json +++ b/search.json @@ -4,7 +4,7 @@ "href": "atlases.html", "title": "Atlases", "section": "", - "text": "Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO\n\n\nAtlas\n\n\n\nProject-1\n\n\nProject-2\n\n\nCore-C\n\n\nCore-D\n\n\n2024\n\n\n\n\nJan 9, 2024\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination\n\n\nAtlas\n\n\n\nProject-1\n\n\nProject-2\n\n\nCore-C\n\n\nCore-D\n\n\n2021\n\n\n\n\nNov 15, 2021\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMolecular tracking devices quantify antigen distribution and archiving in the murine lymph node\n\n\nAtlas\n\n\n\nProject-2\n\n\nCore-C\n\n\nCore-D\n\n\n2021\n\n\n\n\nApr 12, 2021\n\n\n\n\n\n\n\n\nNo matching items", + "text": "Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO\n\n\n Atlas\n\n\n\nProject-1\n\n\nProject-2\n\n\nCore-C\n\n\nCore-D\n\n\n2024\n\n\n\n\nJan 9, 2024\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination\n\n\n Atlas\n\n\n\nProject-1\n\n\nProject-2\n\n\nCore-C\n\n\nCore-D\n\n\n2021\n\n\n\n\nNov 15, 2021\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMolecular tracking devices quantify antigen distribution and archiving in the murine lymph node\n\n\n Atlas\n\n\n\nProject-2\n\n\nCore-C\n\n\nCore-D\n\n\n2021\n\n\n\n\nApr 12, 2021\n\n\n\n\n\n\n\n\nNo matching items", "crumbs": [ "Atlases" ] @@ -14,7 +14,7 @@ "href": "projects.html", "title": "Projects", "section": "", - "text": "Projects\n\nDefine protective and pathogenic roles of LNSCs during viral infection\n\nThomas Morrison, PhD Publications Atlases\nWe hypothesize that inflammatory responses, cell trafficking, and development of protective adaptive immune responses are regulated by discrete populations of LNSCs during viral infection\n\n Project 1 will define how viral targeting of distinct LNSCs regulates viral dissemination, LN organization and inflammation, and development of adaptive immunity. Project 1 and Project 2 will establish how viral targeting of LNSCs impacts antigen archiving and immune memory to archived antigens. Finally, Project 1 coordinates with Project 3 to study how isotype-specific immune complexes (ICs) promote chronic viral infection of follicular dendritic cells (FDCs). This project will use novel mouse models and human tissues and advanced spatial and single-cell RNA approaches. This project will define how LNSCs shape antiviral immune responses and how viruses manipulate LNSCs to evade immunity.\n\n\nIdentify mechanisms of vaccine antigen localization and retention by LNSCs that drive and enhance cellular and humoral immunity\n\nBeth Tamburini, PhD Publications Atlases\nWe hypothesize that LNSC targeting improves and extends the cellular and humoral responses required for vaccine mediated immunity\n\n Project 2 will work with Project 3 to define mechanisms of vaccine antigen acquisition and retention by different LNSCs. Project 2 will work with Projects 1 and 3 to determine if manipulation of antigen duration in LNSCs improves vaccine protection against arboviruses and influenza virus. Finally, Project 2 will work with Project 1 to define the consequences of virus induced cell death on LEC “training” and the impact on vaccine immunity. This project will distinguish functions of specific LNSC populations and create novel vaccine strategies (e.g., mRNA, virus-like particles, and lipid nanoparticles) and apply sophisticated spatial and single-cell transcriptomic approaches to evaluate antigen levels within infrequent and transcriptionally defined LNSC subsets. This project will determine how specific LNSC subsets shape vaccine immunity and the consequences of viral infection of LNSCs to vaccine immunity.\n\n\nInvestigate the role of immune complexes in antigen acquisition and retention by LNSCs to modulate cellular and humoral immunity\n\nJenna Guthmiller, PhD\nWe hypothesize that antibody isotype in an IC regulates protective immunity by determining which LNSC populations acquire and retain antigen via isotype-specific interactions with complement and Fc receptors (FcRs)\n\n Project 3 will engineer monoclonal antibodies (mAbs) with fixed antigen specificity on discrete antibody isotypes and subclasses. Using stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen complexes to determine the spatial and cellular localization of ICs in comparison with free antigen. Project 3 also investigates how FcR expression by LNSCs impacts IC acquisition and will work with Project 1 to determine viral antigen retention and define consequences to protective humoral and cellular immunity. This project will use mouse models engineered to manipulate complement receptor and FcR expression by discrete LNSC populations and will define how different LNSC populations use antibody to determine antigen uptake and localization.\n\n\n\nCores\n\nMouse transgenics and tissue characterization\n\nJennifer Matsuda, PhD Publications\nThe goal of the mouse transgenics and tissue core is to generate novel genetic mouse models and to develop a tissue and cell repository, this includes the following key tasks.\nTask 1. Generation of novel mouse lines\nTask 2. Provide a mouse colony for LNSC biology\nTask 3. Provide a resource for maintenance and distribution of human and mouse LNSCs and lymphoid tissues\n\nMolecular technologies\n\nJay Hesselberth, PhD Publications Atlases\nThe molecular technologies cores will apply new molecular tools to understand the contributions of lymph node stromal cells to immune responses, this includes the following key tasks.\nTask 1. Generate validated reagents for and execute single-cell and spatial transcriptomic experiments to probe LNSC biology\nTask 2. Production of customized lipid nanoparticles with mRNA and siRNA cargo\nTask 3. Expression and purification of antibodies, antigens, and immune complexes\n\nBioinformatics\n\nJay Hesselberth, PhD Ryan Sheridan, PhD Publications Atlases\nThe bioinformatics core will apply new informatics approaches to understand the contributions of LNSCs to immune responses, this includes the following tasks.\nTask 1. Provide a bioinformatics resource for rigorous and reproducible analysis of sequencing experiments\nTask 2. Develop pipelines for large scale meta-analysis of single-cell and spatial transcriptomic data\nTask 3. Curate a public-facing LNSC atlas to allow for interactive exploration of published datasets", + "text": "Projects\n\nDefine protective and pathogenic roles of LNSCs during viral infection\n\nThomas Morrison, PhD Publications Atlases\nWe hypothesize that inflammatory responses, cell trafficking, and development of protective adaptive immune responses are regulated by discrete populations of LNSCs during viral infection\n\n Project 1 will define how viral targeting of distinct LNSCs regulates viral dissemination, LN organization and inflammation, and development of adaptive immunity. Project 1 will establish how viral targeting of LNSCs impacts antigen archiving and immune memory to archived antigens. Finally, Project 1 will study how isotype-specific immune complexes (ICs) promote chronic viral infection of follicular dendritic cells (FDCs). This project will use novel mouse models and human tissues and advanced spatial and single-cell RNA approaches. This project will define how LNSCs shape antiviral immune responses and how viruses manipulate LNSCs to evade immunity.\n\n\nIdentify mechanisms of vaccine antigen localization and retention by LNSCs that drive and enhance cellular and humoral immunity\n\nBeth Tamburini, PhD Publications Atlases\nWe hypothesize that LNSC targeting improves and extends the cellular and humoral responses required for vaccine mediated immunity\n\n Project 2 will define mechanisms of vaccine antigen acquisition and retention by different LNSCs. Project 2 will determine if manipulation of antigen duration in LNSCs improves vaccine protection against arboviruses and influenza virus. Finally, Project 2 will define the consequences of virus induced cell death on LEC ‘training’ and the impact on vaccine immunity. This project will distinguish functions of specific LNSC populations and create novel vaccine strategies (e.g., mRNA, virus-like particles, and lipid nanoparticles) and apply sophisticated spatial and single-cell transcriptomic approaches to evaluate antigen levels within infrequent and transcriptionally defined LNSC subsets. This project will determine how specific LNSC subsets shape vaccine immunity and the consequences of viral infection of LNSCs to vaccine immunity.\n\n\nInvestigate the role of immune complexes in antigen acquisition and retention by LNSCs to modulate cellular and humoral immunity\n\nJenna Guthmiller, PhD\nWe hypothesize that antibody isotype in an IC regulates protective immunity by determining which LNSC populations acquire and retain antigen via isotype-specific interactions with complement and Fc receptors (FcRs)\n\n Project 3 will engineer monoclonal antibodies (mAbs) with fixed antigen specificity on discrete antibody isotypes and subclasses. Using stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen complexes to determine the spatial and cellular localization of ICs in comparison with free antigen. Project 3 also investigates how FcR expression by LNSCs impacts IC acquisition and will work with Project 1 to determine viral antigen retention and define consequences to protective humoral and cellular immunity. This project will use mouse models engineered to manipulate complement receptor and FcR expression by discrete LNSC populations and will define how different LNSC populations use antibody to determine antigen uptake and localization.\n\n\n\nCores\n\nMouse transgenics and tissue characterization\n\nJennifer Matsuda, PhD Publications\nCore B will generate novel genetic mouse models and develop a tissue and cell repository, this includes the following tasks.\nTask 1. Generation of novel mouse lines\nTask 2. Provide a mouse colony for LNSC biology\nTask 3. Provide a resource for maintenance and distribution of human and mouse LNSCs and lymphoid tissues\n\nMolecular technologies\n\nJay Hesselberth, PhD Publications Atlases\nCore C will apply new molecular tools to understand the contributions of lymph node stromal cells to immune responses, this includes the following tasks.\nTask 1. Generate validated reagents for and execute single-cell and spatial transcriptomic experiments to probe LNSC biology\nTask 2. Production of customized lipid nanoparticles with mRNA and siRNA cargo\nTask 3. Expression and purification of antibodies, antigens, and immune complexes\n\nBioinformatics\n\nJay Hesselberth, PhD Ryan Sheridan, PhD Publications Atlases\nCore D will apply new informatics approaches to understand the contributions of LNSCs to immune responses, this includes the following tasks.\nTask 1. Provide a bioinformatics resource for rigorous and reproducible analysis of sequencing experiments\nTask 2. Develop pipelines for large scale meta-analysis of single-cell and spatial transcriptomic data\nTask 3. Curate a public-facing LNSC atlas to allow for interactive exploration of published datasets", "crumbs": [ "Projects" ] @@ -73,14 +73,14 @@ "href": "index.html#projects", "title": "\nLymph Node Stromal Cell Browser\n", "section": "Projects", - "text": "Projects\n\nDefine protective and pathogenic roles of LNSCs during viral infection\nThomas Morrison, PhD Publications Atlases\nProject 1 will define how viral targeting of distinct LNSCs regulates viral dissemination, LN organization and inflammation, and development of adaptive immunity\nIdentify mechanisms of vaccine antigen localization and retention by LNSCs that drive and enhance cellular and humoral immunity\nBeth Tamburini, PhD Publications Atlases\nProject 2 will define mechanisms of vaccine antigen acquisition and retention by different LNSCs\nInvestigate the role of immune complexes in antigen acquisition and retention by LNSCs to modulate cellular and humoral immunity\nJenna Guthmiller, PhD\nProject 3 will use stabilized DNA conjugates to track antibody:antigen complexes to determine the spatial and cellular localization of immune complexes" + "text": "Projects\n\nDefine protective and pathogenic roles of LNSCs during viral infection\nThomas Morrison, PhD Publications Atlases\nProject 1 will define how viral targeting of distinct LNSCs regulates viral dissemination, LN organization and inflammation, and development of adaptive immunity\nIdentify mechanisms of vaccine antigen localization and retention by LNSCs that drive and enhance cellular and humoral immunity\nBeth Tamburini, PhD Publications Atlases\nProject 2 will define mechanisms of vaccine antigen acquisition and retention by different LNSCs\nInvestigate the role of immune complexes in antigen acquisition and retention by LNSCs to modulate cellular and humoral immunity\nJenna Guthmiller, PhD\nProject 3 will use stabilized DNA conjugates to track antibody:antigen complexes to determine the spatial and cellular localization of immune complexes" }, { "objectID": "index.html#cores", "href": "index.html#cores", "title": "\nLymph Node Stromal Cell Browser\n", "section": "Cores", - "text": "Cores\n\nMouse transgenics and tissue characterization\nJennifer Matsuda, PhD Publications\nThe goal of the animal and tissue core is to generate novel genetic mouse models and to develop a tissue and cell repository\nMolecular technologies\nJay Hesselberth, PhD Publications Atlases\nThe molecular technologies core will apply new molecular tools to understand the contributions of lymph node stromal cells to immune responses\nBioinformatics\nJay Hesselberth, PhD Ryan Sheridan, PhD Publications Atlases\nThe bioinformatics core will apply new informatics approaches to understand the contributions of lymph node stromal cells (LN SC) to immune responses" + "text": "Cores\n\nMouse transgenics and tissue characterization\nJennifer Matsuda, PhD Publications\nCore B will generate novel genetic mouse models and develop a tissue and cell repository\nMolecular technologies\nJay Hesselberth, PhD Publications Atlases\nCore C will apply new molecular tools to understand the contributions of lymph node stromal cells to immune responses\nBioinformatics\nJay Hesselberth, PhD Ryan Sheridan, PhD Publications Atlases\nCore D will apply new informatics approaches to understand the contributions of LNSCs to immune responses" }, { "objectID": "atlases/2021-walsh-33843587/index.html", @@ -160,7 +160,7 @@ "href": "investigators.html", "title": "Investigators", "section": "", - "text": "Thomas Morrison, PhD\n\nPublications Website Email Project-1\nMy laboratory investigates mechanisms of infectious disease pathogenesis and immunity. We use genetic, molecular, cellular, and immunological approaches to define molecular mechanisms of pathogenesis, to elucidate immunological mechanisms that dictate viral clearance, including antibodies and B cells, and to evaluate novel therapeutic interventions. My laboratory has developed mouse models of chikungunya virus (CHIKV) and Ross River virus (RRV)-induced rheumatic disease that recapitulate important aspects of acute and chronic CHIKV and RRV disease in humans. In addition, we also investigate mechanisms of neurological disease associated with neurotropic viruses such as Venezuelan equine encephalitis virus (VEEV), West Nile virus, and Zika virus. I also have extensive experience working with human coronaviruses and other highly pathogenic respiratory viruses.\n\n\n\n\nBeth Tamburini, PhD\n\nPublications Website Email Project-2\nThe overarching goal of my research program is to understand how the lymphatic stroma recognize and react to stimuli within the lymph to guide the immune response. My initial studies of lymphatic stroma were focused on understanding the mechanisms by which lymphatic endothelial cells acquire and retain antigens as well as recruit and interact with immune cells in different organs. Currently my research program is focused on understanding the immunologic consequence of interaction between lymphatic stroma and components of the immune system within different organ systems. We have been working to dissect how the lymphatics respond to stimuli such as proteins, small molecules, fat, cholesterol, alcohol, infectious material and cytokine. We have experience with a number of techniques including flow cytometry, immunohistochemistry, immunofluorescence, live molecular imaging, and a number of therapeutic treatments to target and identify lymphatic endothelial cells as well as experience in several mouse models and assays. In addition, my expertise and the expertise of a wide range of collaborators at the University of Colorado in the fields of Gastroenterology, Hepatology and Immunology have been critical in developing this research program. This collaborative research program as proven to be well suited for the training and success of the graduate students and post-docs in my laboratory.\n\n\n\n\nJenna Guthmiller, PhD\n\nPublications Website Email Project-3\nMy long-term scientific goals are to understand the complex interactions between pathogens and the immune response mounted against them, with the objective of identifying and developing interventions to limit global infectious disease burdens. Fitting within these goals, my independent laboratory studies how preexisting immunity influences future immune responses against rapidly evolving viruses. My major contributions to science are understanding how protective humoral immunity is generated following infection and vaccination and how vaccination can harness broadly protective humoral immunity. During my postdoctoral studies, I investigated how preexisting immunity against influenza viruses shapes the recall of memory B cells in humans. I found that in the absence of preexisting immunity against the variable epitopes of the hemagglutinin (HA) head domain, humans could recall memory B cells against broadly protective epitopes of HA. These studies identified several novel classes of broadly neutralizing antibodies and a new highly conserved epitope where HA ‘anchors’ itself into the viral membrane. My research also identified that the first in-human universal influenza vaccine, which is intended to circumvent preexisting antibodies, robustly induced antibodies against broadly protective epitopes, including the anchor epitope. Lastly, I identified influenza vaccination and infection in humans differentially recalled discrete memory B cell specificities, with infection recalling memory B cells primed during childhood against highly conserved, albeit non-protective antigens. Together, these studies highlight the importance of understanding how preexisting antibodies influence the generation of broadly protective immunity.\n\n\n\n\nJay Hesselberth, PhD\n\nPublications Website Email Core-C Core-D\nI am an RNA biochemist and computational biologist with extensive experience in developing new high- throughput methods and associated bioinformatic analysis software. My RNA biology program spans classical and modern approaches to address outstanding questions in RNA damage and repair. Over the past ten years my group has developed new sequencing approaches to identify damaged RNAs and new model systems with which to understand the causes and consequences of RNA damage. Our studies have led to new concepts in post-transcriptional regulation that have broad implications for understanding the role of RNA damage in biology. Recently we have been focused on understanding how RNA damage and repair events are coupled to control RNA fate after stress-induced RNA cleavage. More recently, we have applied nanopore RNA sequencing to characterize the landscape of RNA repair events in budding yeast.\n\n\n\n\nJennifer Matsuda, PhD\n\nPublications Email Core-B\nIn 2008, following my graduate studies and post-doctoral training, I became the Director of the Mouse Genetics Core Facility at National Jewish Health. Given my years at the bench, it was critical to me that the facility I established enabled all investigators, regardless of prior experience, with the support necessary to make mouse models. To this end, in addition to classic services like ES cell targeting, blastocyst and pronuclear microinjections, embryo and sperm cryopreservation, in vitro fertilization, and rederivation, we have developed additional areas of expertise. We generate complex DNA constructs, using BAC recombineering, markerless recombineering, and classic cloning methodologies. We also train graduate students and post-doctoral fellows in our laboratory to make their own constructs. We have also gained the expertise to identify homologous recombinant ES cell clones by Loss of Allele (LOA). In addition, we successfully use engineered nucleases (ZFNs, TALENs, and more recently CRISPR/Cas9) to generate knockout mice by NHEJ as well as relying upon homology directed repair (HDR) to introduce genetic modifications. This technology has been further improved upon by our capacity to make mouse models directly on a variety of backgrounds by using IVF, including but not limited to: C57BL/6, FVB, NOD, 129S4, and NSGS backgrounds as well genetically modified strains of mice. Due to the core’s consistently high quality of work, we have recently been designated as the Regional Mouse Genetics Core Facility to support investigators at the University of Colorado Denver, in addition to the investigators at NJH.", + "text": "Thomas Morrison, PhD\n\n Publications Website Email Project-1\nMy laboratory investigates mechanisms of infectious disease pathogenesis and immunity. We use genetic, molecular, cellular, and immunological approaches to define molecular mechanisms of pathogenesis, to elucidate immunological mechanisms that dictate viral clearance, including antibodies and B cells, and to evaluate novel therapeutic interventions. My laboratory has developed mouse models of chikungunya virus (CHIKV) and Ross River virus (RRV)-induced rheumatic disease that recapitulate important aspects of acute and chronic CHIKV and RRV disease in humans. In addition, we also investigate mechanisms of neurological disease associated with neurotropic viruses such as Venezuelan equine encephalitis virus (VEEV), West Nile virus, and Zika virus. I also have extensive experience working with human coronaviruses and other highly pathogenic respiratory viruses.\n\n\n\n\nBeth Tamburini, PhD\n\n Publications Website Email Project-2\nThe overarching goal of my research program is to understand how the lymphatic stroma recognize and react to stimuli within the lymph to guide the immune response. My initial studies of lymphatic stroma were focused on understanding the mechanisms by which lymphatic endothelial cells acquire and retain antigens as well as recruit and interact with immune cells in different organs. Currently my research program is focused on understanding the immunologic consequence of interaction between lymphatic stroma and components of the immune system within different organ systems. We have been working to dissect how the lymphatics respond to stimuli such as proteins, small molecules, fat, cholesterol, alcohol, infectious material and cytokine. We have experience with a number of techniques including flow cytometry, immunohistochemistry, immunofluorescence, live molecular imaging, and a number of therapeutic treatments to target and identify lymphatic endothelial cells as well as experience in several mouse models and assays. In addition, my expertise and the expertise of a wide range of collaborators at the University of Colorado in the fields of Gastroenterology, Hepatology and Immunology have been critical in developing this research program. This collaborative research program as proven to be well suited for the training and success of the graduate students and post-docs in my laboratory.\n\n\n\n\nJenna Guthmiller, PhD\n\n Publications Website Email Project-3\nMy long-term scientific goals are to understand the complex interactions between pathogens and the immune response mounted against them, with the objective of identifying and developing interventions to limit global infectious disease burdens. Fitting within these goals, my independent laboratory studies how preexisting immunity influences future immune responses against rapidly evolving viruses. My major contributions to science are understanding how protective humoral immunity is generated following infection and vaccination and how vaccination can harness broadly protective humoral immunity. During my postdoctoral studies, I investigated how preexisting immunity against influenza viruses shapes the recall of memory B cells in humans. I found that in the absence of preexisting immunity against the variable epitopes of the hemagglutinin (HA) head domain, humans could recall memory B cells against broadly protective epitopes of HA. These studies identified several novel classes of broadly neutralizing antibodies and a new highly conserved epitope where HA ‘anchors’ itself into the viral membrane. My research also identified that the first in-human universal influenza vaccine, which is intended to circumvent preexisting antibodies, robustly induced antibodies against broadly protective epitopes, including the anchor epitope. Lastly, I identified influenza vaccination and infection in humans differentially recalled discrete memory B cell specificities, with infection recalling memory B cells primed during childhood against highly conserved, albeit non-protective antigens. Together, these studies highlight the importance of understanding how preexisting antibodies influence the generation of broadly protective immunity.\n\n\n\n\nJay Hesselberth, PhD\n\n Publications Website Email Core-C Core-D\nI am an RNA biochemist and computational biologist with extensive experience in developing new high- throughput methods and associated bioinformatic analysis software. My RNA biology program spans classical and modern approaches to address outstanding questions in RNA damage and repair. Over the past ten years my group has developed new sequencing approaches to identify damaged RNAs and new model systems with which to understand the causes and consequences of RNA damage. Our studies have led to new concepts in post-transcriptional regulation that have broad implications for understanding the role of RNA damage in biology. Recently we have been focused on understanding how RNA damage and repair events are coupled to control RNA fate after stress-induced RNA cleavage. More recently, we have applied nanopore RNA sequencing to characterize the landscape of RNA repair events in budding yeast.\n\n\n\n\nJennifer Matsuda, PhD\n\n Publications Email Core-B\nIn 2008, following my graduate studies and post-doctoral training, I became the Director of the Mouse Genetics Core Facility at National Jewish Health. Given my years at the bench, it was critical to me that the facility I established enabled all investigators, regardless of prior experience, with the support necessary to make mouse models. To this end, in addition to classic services like ES cell targeting, blastocyst and pronuclear microinjections, embryo and sperm cryopreservation, in vitro fertilization, and rederivation, we have developed additional areas of expertise. We generate complex DNA constructs, using BAC recombineering, markerless recombineering, and classic cloning methodologies. We also train graduate students and post-doctoral fellows in our laboratory to make their own constructs. We have also gained the expertise to identify homologous recombinant ES cell clones by Loss of Allele (LOA). In addition, we successfully use engineered nucleases (ZFNs, TALENs, and more recently CRISPR/Cas9) to generate knockout mice by NHEJ as well as relying upon homology directed repair (HDR) to introduce genetic modifications. This technology has been further improved upon by our capacity to make mouse models directly on a variety of backgrounds by using IVF, including but not limited to: C57BL/6, FVB, NOD, 129S4, and NSGS backgrounds as well genetically modified strains of mice. Due to the core’s consistently high quality of work, we have recently been designated as the Regional Mouse Genetics Core Facility to support investigators at the University of Colorado Denver, in addition to the investigators at NJH.", "crumbs": [ "Investigators" ] diff --git a/site_libs/bootstrap/bootstrap-dark.min.css b/site_libs/bootstrap/bootstrap-dark.min.css index eeb04b0..b954779 100644 --- a/site_libs/bootstrap/bootstrap-dark.min.css +++ b/site_libs/bootstrap/bootstrap-dark.min.css @@ -9,4 +9,4 @@ * we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since * that seems to be what ansi_up emits * 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