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Article ; Online: Live Imaging Transverse Sections of Zebrafish Embryo Explants.

Paulissen, Eric / Martin, Benjamin L

2024 Volume 14, Issue 3, Page(s) e4928

Abstract: Vertebrate embryogenesis is a highly dynamic process involving coordinated cell and tissue movements that generate the final embryonic body plan. Many of these movements are difficult to image at high resolution because they occur deep within the embryo ... ...

Abstract	Vertebrate embryogenesis is a highly dynamic process involving coordinated cell and tissue movements that generate the final embryonic body plan. Many of these movements are difficult to image at high resolution because they occur deep within the embryo along the midline, causing light scattering and requiring longer working distances. Here, we present an explant-based method to image transverse cross sections of living zebrafish embryos. This method allows for the capture of all cell movements at high-resolution throughout the embryonic trunk, including hard-to-image deep tissues. This technique offers an alternative to expensive or computationally difficult microscopy methods. Key features • Generates intact zebrafish explants with minimal tissue disturbance. • Allows for live imaging of deep tissues normally obscured by common confocal microscopy techniques. • Immobilizes tissues for extended periods required for time-lapse imaging. • Utilizes readily available reagents and tools, which can minimize the time and cost of the procedure.
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.4928
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Article ; Online: A Chemically Inducible Muscle Ablation System for the Zebrafish.

Paulissen, Eric / Martin, Benjamin L

Zebrafish

2024

Abstract: An effective method for tissue-specific ablation in zebrafish is the nitroreductase (NTR)/metronidazole (MTZ) system. Expressing bacterial NTR in the presence of nitroimidazole compounds causes apoptotic cell death, which can be useful for understanding ... ...

Abstract	An effective method for tissue-specific ablation in zebrafish is the nitroreductase (NTR)/metronidazole (MTZ) system. Expressing bacterial NTR in the presence of nitroimidazole compounds causes apoptotic cell death, which can be useful for understanding many biological processes. However, this requires tissue-specific expression of the NTR enzyme, and many tissues have yet to be targeted with transgenic lines that express NTR. We generated a transgenic zebrafish line expressing NTR in differentiated skeletal muscle. Treatment of embryos with MTZ caused muscle specific cell ablation. We demonstrate this line can be used to monitor muscle regeneration in whole embryos and in transplanted transgenic cells.
Language	English
Publishing date	2024-03-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2156020-1
ISSN	1557-8542 ; 1545-8547
ISSN (online)	1557-8542
ISSN	1545-8547
DOI	10.1089/zeb.2023.0102
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Article ; Online: Mesoderm induction and patterning: Insights from neuromesodermal progenitors.

Martin, Benjamin L

Seminars in cell & developmental biology

2021 Volume 127, Page(s) 37–45

Abstract: The discovery of mesoderm inducing signals helped usher in the era of molecular developmental biology, and today the mechanisms of mesoderm induction and patterning are still intensely studied. Mesoderm induction begins during gastrulation, but recent ... ...

Abstract	The discovery of mesoderm inducing signals helped usher in the era of molecular developmental biology, and today the mechanisms of mesoderm induction and patterning are still intensely studied. Mesoderm induction begins during gastrulation, but recent evidence in vertebrates shows that this process continues after gastrulation in a group of posteriorly localized cells called neuromesodermal progenitors (NMPs). NMPs reside within the post-gastrulation embryonic structure called the tailbud, where they make a lineage decision between ectoderm (spinal cord) and mesoderm. The majority of NMP-derived mesoderm generates somites, but also contributes to lateral mesoderm fates such as endothelium. The discovery of NMPs provides a new paradigm in which to study vertebrate mesoderm induction. This review will discuss mechanisms of mesoderm induction within NMPs, and how they have informed our understanding of mesoderm induction more broadly within vertebrates as well as animal species outside of the vertebrate lineage. Special focus will be given to the signaling networks underlying NMP-derived mesoderm induction and patterning, as well as emerging work on the significance of partial epithelial-mesenchymal states in coordinating cell fate and morphogenesis.
MeSH term(s)	Animals ; Body Patterning ; Cell Differentiation ; Gastrulation ; Gene Expression Regulation, Developmental ; Mesoderm ; Somites
Language	English
Publishing date	2021-11-25
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2021.11.010
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Article ; Online: The art of equity: critical health humanities in practice.

Mathieu, Irène P / Martin, Benjamin J

Philosophy, ethics, and humanities in medicine : PEHM

2023 Volume 18, Issue 1, Page(s) 19

Abstract: Background: The American Association of Medical Colleges has called for incorporation of the health humanities into medical education, and many medical schools now offer formal programs or content in this field. However, there is growing recognition ... ...

Abstract	Background: The American Association of Medical Colleges has called for incorporation of the health humanities into medical education, and many medical schools now offer formal programs or content in this field. However, there is growing recognition among educators that we must expand beyond empathy and wellness and apply the health humanities to questions of social justice - that is, critical health humanities. In this paper we demonstrate how this burgeoning field offers us tools for integrating social justice into medical education, utilizing the frameworks of critical consciousness and structural competency. Practice of health humanities: Critical health humanities can be applied at multiple levels of learners, and in a variety of contexts. We are two physician-writers who have developed several educational programs that demonstrate this. We taught a seminar that introduced first-year and second-year undergraduates to concepts such as social determinants of health, intergenerational trauma, intersectionality, resilience, and cross-cultural care through works of fiction, poetry, film, podcasts, stand-up comedy, and more. Through creative projects and empathic reflection, students engaged with the complexities of structural forces that create and maintain health disparities. Medical students in their clinical years can engage in critical health humanities learning experiences as well. We teach several multidisciplinary electives that address social (in)justice in medicine, as well as mentor fourth-year students engaged in independent electives that foster critical awareness around health equity and ethics. Beyond the classroom, we have actively engaged in critical health humanities practices through story slams, literary journal clubs, conference presentations, and Grand Rounds. Through these activities we have included learners at GME and CME levels. These examples also demonstrate how community engagement and multidisciplinary partnerships can contribute to the practice of critical health humanities. Conclusion: In this paper, we explore the growing field of critical health humanities and its potential for teaching health equity through narrative practices. We provide concrete examples of educational activities that incorporate critical consciousness and structural competency - frameworks we have found useful for conceptualizing critical health humanities as a pedagogical practice. We also discuss the strengths and challenges of this work and suggest future directions.
MeSH term(s)	Humans ; Curriculum ; Humanities/education ; Education, Medical ; Learning ; Medicine ; Education, Medical, Undergraduate
Language	English
Publishing date	2023-12-13
Publishing country	England
Document type	Letter
ZDB-ID	2229777-7
ISSN	1747-5341 ; 1747-5341
ISSN (online)	1747-5341
ISSN	1747-5341
DOI	10.1186/s13010-023-00149-1
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Article ; Online: Gene expression flux analysis reveals specific regulatory modalities of gene expression.

Martin, Benjamin / Suter, David M

iScience

2023 Volume 26, Issue 10, Page(s) 107758

Abstract: The level of a given protein is determined by the synthesis and degradation rates of its mRNA and protein. While several studies have quantified the contribution of different gene expression steps in regulating protein levels, these are limited by using ... ...

Abstract	The level of a given protein is determined by the synthesis and degradation rates of its mRNA and protein. While several studies have quantified the contribution of different gene expression steps in regulating protein levels, these are limited by using equilibrium approximations in out-of-equilibrium biological systems. Here, we introduce gene expression flux analysis to quantitatively dissect the dynamics of the expression level for specific proteins and use it to analyze published transcriptomics and proteomics datasets. Our analysis reveals distinct regulatory modalities shared by sets of genes with clear functional signatures. We also find that protein degradation plays a stronger role than expected in the adaptation of protein levels. These findings suggest that shared regulatory strategies can lead to versatile responses at the protein level and highlight the importance of going beyond equilibrium approximations to dissect the quantitative contribution of different steps of gene expression to protein dynamics.
Language	English
Publishing date	2023-08-28
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107758
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Article ; Online: An out-of-equilibrium definition of protein turnover.

Martin, Benjamin / Suter, David M

BioEssays : news and reviews in molecular, cellular and developmental biology

2023 Volume 45, Issue 6, Page(s) e2200209

Abstract: Protein turnover (PT) has been formally defined only in equilibrium conditions, which is ill-suited to quantify PT during dynamic processes that occur during embryogenesis or (extra) cellular signaling. In this Hypothesis, we propose a definition of PT ... ...

Abstract	Protein turnover (PT) has been formally defined only in equilibrium conditions, which is ill-suited to quantify PT during dynamic processes that occur during embryogenesis or (extra) cellular signaling. In this Hypothesis, we propose a definition of PT in an out-of-equilibrium regime that allows the quantification of PT in virtually any biological context. We propose a simple mathematical and conceptual framework applicable to a broad range of available data, such as RNA sequencing coupled with pulsed-SILAC datasets. We apply our framework to a published dataset and show that stimulation of mouse dendritic cells with LPS leads to a proteome-wide change in PT. This is the first quantification of PT out-of-equilibrium, paving the way for the analysis of biological systems in other contexts.
MeSH term(s)	Animals ; Mice ; Proteolysis ; Proteome
Chemical Substances	Proteome
Language	English
Publishing date	2023-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202200209
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Article ; Online: An out‐of‐equilibrium definition of protein turnover

Martin, Benjamin / Suter, David M.

BioEssays. 2023 June, v. 45, no. 6 p.e2200209-

2023

Abstract: Protein turnover (PT) has been formally defined only in equilibrium conditions, which is ill‐suited to quantify PT during dynamic processes that occur during embryogenesis or (extra) cellular signaling. In this Hypothesis, we propose a definition of PT ... ...

Abstract	Protein turnover (PT) has been formally defined only in equilibrium conditions, which is ill‐suited to quantify PT during dynamic processes that occur during embryogenesis or (extra) cellular signaling. In this Hypothesis, we propose a definition of PT in an out‐of‐equilibrium regime that allows the quantification of PT in virtually any biological context. We propose a simple mathematical and conceptual framework applicable to a broad range of available data, such as RNA sequencing coupled with pulsed‐SILAC datasets. We apply our framework to a published dataset and show that stimulation of mouse dendritic cells with LPS leads to a proteome‐wide change in PT. This is the first quantification of PT out‐of‐equilibrium, paving the way for the analysis of biological systems in other contexts.
Keywords	RNA ; data collection ; embryogenesis ; mice ; protein metabolism
Language	English
Dates of publication	2023-06
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202200209
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Article ; Online: Myogenic regulatory factors Myod and Myf5 are required for dorsal aorta formation and angiogenic sprouting.

Paulissen, Eric / Martin, Benjamin L

Developmental biology

2022 Volume 490, Page(s) 134–143

Abstract: The vertebrate embryonic midline vasculature forms in close proximity to the developing skeletal muscle, which originates in the somites. Angioblasts migrate from bilateral positions along the ventral edge of the somites until they meet at the midline, ... ...

Abstract	The vertebrate embryonic midline vasculature forms in close proximity to the developing skeletal muscle, which originates in the somites. Angioblasts migrate from bilateral positions along the ventral edge of the somites until they meet at the midline, where they sort and differentiate into the dorsal aorta and the cardinal vein. This migration occurs at the same time that myoblasts in the somites are beginning to differentiate into skeletal muscle, a process which requires the activity of the basic helix loop helix (bHLH) transcription factors Myod and Myf5. Here we examined vasculature formation in myod and myf5 mutant zebrafish. In the absence of skeletal myogenesis, angioblasts migrate normally to the midline but form only the cardinal vein and not the dorsal aorta. The phenotype is due to the failure to activate vascular endothelial growth factor ligand vegfaa expression in the somites, which in turn is required in the adjacent angioblasts for dorsal aorta specification. Myod and Myf5 cooperate with Hedgehog signaling to activate and later maintain vegfaa expression in the medial somites, which is required for angiogenic sprouting from the dorsal aorta. Our work reveals that the early embryonic skeletal musculature in teleosts evolved to organize the midline vasculature during development.
MeSH term(s)	Animals ; Aorta/metabolism ; Gene Expression Regulation, Developmental ; Hedgehog Proteins/genetics ; Hedgehog Proteins/metabolism ; Muscle Proteins/genetics ; Muscle, Skeletal ; MyoD Protein/genetics ; MyoD Protein/metabolism ; Myogenic Regulatory Factor 5/genetics ; Myogenic Regulatory Factor 5/metabolism ; Myogenic Regulatory Factors/genetics ; Myogenic Regulatory Factors/metabolism ; Vascular Endothelial Growth Factor A/metabolism ; Zebrafish/genetics ; Zebrafish/metabolism
Chemical Substances	Hedgehog Proteins ; Muscle Proteins ; MyoD Protein ; Myogenic Regulatory Factor 5 ; Myogenic Regulatory Factors ; Vascular Endothelial Growth Factor A
Language	English
Publishing date	2022-07-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2022.07.009
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Article ; Online: A fishy tail: Insights into the cell and molecular biology of neuromesodermal cells from zebrafish embryos.

Martin, Benjamin L / Steventon, Benjamin

Developmental biology

2022 Volume 487, Page(s) 67–73

Abstract: Vertebrate embryos establish their primary body axis in a conserved progressive fashion from the anterior to the posterior. During this process, a posteriorly localized neuromesodermal cell population called neuromesodermal progenitors (NMps) plays a ... ...

Abstract	Vertebrate embryos establish their primary body axis in a conserved progressive fashion from the anterior to the posterior. During this process, a posteriorly localized neuromesodermal cell population called neuromesodermal progenitors (NMps) plays a critical role in contributing new cells to the spinal cord and mesoderm as the embryo elongates. Defects in neuromesodermal population development can cause severe disruptions to the formation of the body posterior to the head. Given their importance during development and their potential, some of which has already been realized, for revealing new methods of in vitro tissue generation, there is great interest in better understanding NMp biology. The zebrafish model system has been instrumental in advancing our understanding of the molecular and cellular attributes of the NM cell population and its derivatives. In this review, we focus on our current understanding of the zebrafish NM population and its contribution to body axis formation, with particular emphasis on the lineage potency, morphogenesis, and niche factors that promote or inhibit differentiation.
MeSH term(s)	Animals ; Body Patterning/genetics ; Gene Expression Regulation, Developmental ; Mesoderm ; Molecular Biology ; Neural Stem Cells ; Zebrafish/genetics
Language	English
Publishing date	2022-05-02
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2022.04.010
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Article: Myogenic regulatory factors Myod and Myf5 are required for dorsal aorta formation and angiogenic sprouting

Paulissen, Eric / Martin, Benjamin L.

Developmental biology. 2022 Oct., v. 490

2022

Abstract	The vertebrate embryonic midline vasculature forms in close proximity to the developing skeletal muscle, which originates in the somites. Angioblasts migrate from bilateral positions along the ventral edge of the somites until they meet at the midline, where they sort and differentiate into the dorsal aorta and the cardinal vein. This migration occurs at the same time that myoblasts in the somites are beginning to differentiate into skeletal muscle, a process which requires the activity of the basic helix loop helix (bHLH) transcription factors Myod and Myf5. Here we examined vasculature formation in myod and myf5 mutant zebrafish. In the absence of skeletal myogenesis, angioblasts migrate normally to the midline but form only the cardinal vein and not the dorsal aorta. The phenotype is due to the failure to activate vascular endothelial growth factor ligand vegfaa expression in the somites, which in turn is required in the adjacent angioblasts for dorsal aorta specification. Myod and Myf5 cooperate with Hedgehog signaling to activate and later maintain vegfaa expression in the medial somites, which is required for angiogenic sprouting from the dorsal aorta. Our work reveals that the early embryonic skeletal musculature in teleosts evolved to organize the midline vasculature during development.
Keywords	Danio rerio ; Erinaceidae ; aorta ; ligands ; muscle development ; mutants ; myoblasts ; phenotype ; skeletal muscle ; vascular endothelial growth factors ; vertebrates
Language	English
Dates of publication	2022-10
Size	p. 134-143.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2022.07.009
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