David Q Matus

David Q Matus
Stony Brook University | Stony Brook · Department of Biochemistry and Cell Biology

M.S., PhD

About

133
Publications
19,967
Reads
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4,743
Citations
Introduction
I am interested in the intersection of evolutionary, developmental and cell biology studying the transcriptional regulation of cell cycle and morphogenesis.
Additional affiliations
September 2007 - present
Duke University
August 1999 - December 2007
University of Hawaiʻi at Mānoa
Description
  • Kewalo Marine Laboratory

Publications

Publications (133)
Article
Full-text available
Large gaps in basement membrane (BM) occur during organ remodelling and cancer cell invasion. Whether dividing cells, which temporarily reduce their attachment to BM, influence these breaches is unknown. Here we analyse uterine-vulval attachment during development across 21 species of rhabditid nematodes and find that the BM gap that forms between...
Article
Full-text available
Cell invasion through basement membranes during development, immune surveillance, and metastasis remains poorly understood. To gain further insight into this key cellular behavior, we performed an in vivo screen for regulators of cell invasion through basement membranes, using the simple model of Caenorhabditis elegans anchor cell invasion, and ide...
Article
Full-text available
Many breast cancer (BC) patients suffer from complications of metastatic disease. To form metastases, cancer cells must become migratory and coordinate both invasive and proliferative programs at distant organs. Here, we identify srGAP1 as a regulator of a proliferative-to-invasive switch in BC cells. High-resolution light-sheet microscopy demonstr...
Preprint
Light sheet fluorescence microscopy (LSFM) has become a method of choice for live imaging because of its fast acquisition and reduced photobleaching and phototoxicity. Despite the strengths and growing availability of LSFM systems, no generalized LSFM mounting protocol has been adapted for live imaging of post-embryonic stages of C. elegans. A majo...
Article
Full-text available
Notch signaling mediates cell-cell interactions during development and homeostasis. Methods for visualizing and manipulating Notch activity in vivo are essential to elucidate how the Notch pathway functions. Here, we provide new tools for use in C. elegans to visualize and perturb Notch signaling in vivo using endogenously tagged alleles of the Not...
Article
Full-text available
Notch/Delta signaling regulates numerous cell-cell interactions that occur during development, homeostasis, and in disease states. In many cases, the Notch/Delta pathway mediates lateral inhibition between cells to specify alternative fates. Here, we provide new tools for use in C. elegans to investigate feedback between the Notch receptor LIN-12 a...
Preprint
Centrosomes are membraneless organelles that nucleate microtubules. At their core is a pair of centrioles that recruit pericentriolar material (PCM), a phase-separated condensate. In many cell types, including human cells, centrosomes are surrounded by endoplasmic reticulum-derived membranes of unknown structure and function. Using volume electron...
Article
Cyclin-dependent kinase (CDK) sensors have facilitated investigations of the cell cycle in living cells. These genetically encoded fluorescent biosensors change their subcellular location upon activation of CDKs. Activation is primarily regulated by their association with cyclins, which in turn trigger cell-cycle progression. In the absence of CDK...
Article
Full-text available
Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as hist...
Article
Full-text available
The auxin-inducible degradation system in C. elegans allows for spatial and temporal control of protein degradation via heterologous expression of a single Arabidopsis thaliana F-box protein, transport inhibitor response 1 (AtTIR1). In this system, exogenous auxin (Indole-3-acetic acid; IAA) enhances the ability of AtTIR1 to function as a substrate...
Article
Full-text available
The helix-loop-helix transcription factor hlh-2 (E/Daughterless) has been shown to play an important role in regulating cell fate patterning, cell cycle, and basement membrane invasion in the context of the development of the C. elegans somatic gonad. Here, using CRISPR/Cas9 genome engineering, we generated a new hlh-2 allele (hlh-2(Δ-1303-702)) in...
Preprint
The auxin-inducible degradation system in C. elegans allows for spatial and temporal control of protein degradation via heterologous expression of a single Arabidopsis thaliana F-box protein, transport inhibitor response 1 ( At TIR1). In this system, exogenous auxin (Indole-3-acetic acid; IAA) enhances the ability of At TIR1 to function as a substr...
Preprint
Full-text available
Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as hist...
Article
Full-text available
The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, muscle, pharynx, hypodermis...
Article
Full-text available
Cell proliferation and quiescence are intimately coordinated during metazoan development. Here, we adapt a cyclin-dependent kinase (CDK) sensor to uncouple these key events of the cell cycle in C. elegans and zebrafish through live-cell imaging. The CDK sensor consists of a fluorescently tagged CDK substrate that steadily translocates from the nucl...
Preprint
Full-text available
Scientific research experiences are beneficial to students allowing them to gain laboratory and problem-solving skills, as well as foundational research skills in a team-based setting. We designed a laboratory module to provide a guided research experience to stimulate curiosity, introduce students to experimental techniques, and provide students w...
Preprint
Full-text available
The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell-types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, muscle, hypodermis, seam ce...
Article
The auxin-inducible degron (AID) technology was recently adapted for use in the nematode Caenorhabditis elegans. Rapid degradation of C. elegans proteins tagged with an AID is mediated by a plant-specific F-box protein, transport inhibitor response 1 (TIR1), and occurs only in the presence of the phytohormone auxin. The first iteration of this tech...
Preprint
Full-text available
During organismal development, differential regulation of the cell cycle is critical to many cell biological processes, including cell fate specification and differentiation. While the mechanisms of cell cycle regulation are well studied, how control of the cell cycle is linked to differentiated cellular behavior remains poorly understood, mostly d...
Article
Full-text available
Cellular invasion is a key part of development, immunity, and disease. Using the in vivo model of C. elegans anchor cell invasion, we characterize the gene regulatory network that promotes cell invasion. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified four conse...
Article
Full-text available
As developmental biologists in the age of genome editing, we now have access to an ever-increasing array of tools to manipulate endogenous gene expression. The auxin-inducible degradation system allows for spatial and temporal control of protein degradation via a hormone-inducible Arabidopsis F-box protein, transport inhibitor response 1 (TIR1). In...
Preprint
Full-text available
As developmental biologists in the age of genome editing, we now have access to an ever-increasing array of tools to manipulate endogenous gene expression. The auxin-inducible degradation system, allows for spatial and temporal control of protein degradation, functioning through the activity of a hormone-inducible Arabidopsis F-box protein, transpo...
Preprint
Full-text available
Cellular invasion is a key part of development, immunity, and disease. Using the in vivo model of C. elegans anchor cell invasion, we characterize the gene regulatory network that promotes invasive differentiation. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified...
Article
Matrix metalloproteinases (MMPs) are associated with decreased patient prognosis but have failed as anti-invasive drug targets despite promoting cancer cell invasion. Through time-lapse imaging, optical highlighting, and combined genetic removal of the five MMPs expressed during anchor cell (AC) invasion in C. elegans, we find that MMPs hasten inva...
Article
True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resol...
Preprint
Full-text available
True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution...
Article
Full-text available
Cell invasion is a specialized cell behavior that likely co-evolved with the emergence of basement membranes in metazoans as a mechanism to break down the barriers that separate tissues. A variety of conserved and lineage-specific biological processes that occur during development and homeostasis rely on cell invasive behavior. Recent innovations i...
Article
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Mesoderm induction begins during gastrulation. Recent evidence from several vertebrate species indicates mesoderm induction continues after gastrulation in neuromesodermal progenitor cells (NMPs) within the posterior-most embryonic structure called the tailbud. It is unclear to what extent the molecular mechanisms of mesoderm induction are conserve...
Article
The specification of individual cells into differentiated cell types is a hallmark of multicellular organisms and driving force underlying body-plan diversity. The molecular underpinnings of cell fate acquisition during embryogenesis, adult homeostasis and following injury have been the subject of intense focus for many years. Advances in the abili...
Article
Cell invasion through the basement membrane (BM) occurs during normal embryonic development and is a fundamental feature of cancer metastasis. The underlying cellular and genetic machinery required for invasion has been difficult to identify, due to a lack of adequate in vivo models to accurately examine invasion in single cells at subcellular reso...
Article
Full-text available
Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge. It improves the 3D imaging ability of SPIM in r...
Data
An incoherent seven Bessel beam array tiled at seven positions in dye solution (NAOD=0.35, NAID=0.14).
Data
(Continue from Supplementary Movie 3) Volume rendering and orthogonal slices of a C. elegans embryo (OD 95) imaged by TLS-SPIM every 30 minutes for 5 hours (time point 6-10).
Data
XZ axial slices of the same C. elegans embryo (Supplementary Movie 8) at the selected time points (green channel). Associated with Figure 3, 4 and Supplementary Figure 17.
Data
Volume rendering of two mesodermal cells in a ~15 hpf zebrafish embryo tailbud imaged by TLS-SPIM alternated between a low spatial resolution, high imaging speed mode (NAOD=0.2, NAID=0.05, tiled at two positions) and a high spatial resolution, low imaging speed mode (NAOD=0.35, NAID=0.14, tiled at seven positions). Upper left and lower left: volume...
Data
Volume renderings of another two mesodermal cells in a ~15 hpf zebrafish embryo tailbud imaged by TLS-SPIM alternated between the two modes.
Data
XZ axial slices of two C. elegans embryos (OD95) imaged by regular Lattice light sheet microscopy (left), TLS-SPIM with a tiling Lattice light sheet (middle) and TLS-SPIM (right) with a tiling light sheet generated by dithering an incoherent Bessel beam array. Associated with Supplementary Figure 14.
Data
Volume rendering and orthogonal slices of a ~15 hpf nuclei-labeled zebrafish embryo tailbud. Upper left: 3D volume rendering, upper right: XY slice, lower left: YZ slice, lower right: XZ slice. Scale bar 20 μm. Associated with Figure 1 and Supplementary Figure 16.
Data
Volume renderings of a C. elegans embryo (LP162) expressing GFP-tagged myosin II viewed from different directions. Associated with Figure 2 (NAOD=0.35, NAID=0.14, tiled at three positions).
Data
Volume renderings of a C. elegans embryo (OD95) imaged every half-minute in two colors, viewed from two orthogonal directions. Left: lateral, right: axial. Scale bar 10 μm. Associated with Figure 3, 4 and Supplementary Figure 17 (NAOD=0.35, NAID=0.14, tiled at three positions).
Data
Volume rendering of the same C. elegans embryo (Supplementary Movie 8) at the first 61 time points with all cells segmented and viewed from four orthogonal directions. Associated with Figure 3, 4.
Data
A coherent Bessel beam array tiled at seven positions in dye solution (NAOD=0.35, NAID=0.14).
Data
XZ axial slices of three C. elegans embryos (OD95 and RW10029) imaged by regular SPIM (left, middle) and TLS-SPIM (right). Associated with Supplementary Figure 12 and 13.
Data
Volume renderings of the two mesodermal cells imaged in the two modes showing the different spatial resolution. Associated with Supplementary Movie 13 and Figure 5.
Data
Volume rendering and orthogonal slices of a C. elegans embryo (OD 95) imaged by TLS-SPIM every 30 minutes for 5 hours (time point 1-5). Upper left: 3D volume rendering, upper right: XY slice, lower left: XZ slice, lower right: YZ slice. Associated with Figure 1 (NAOD=0.35, NAID=0.14, tiled at three positions).
Data
Volume rendering of all cells of the same C. elegans embryo (Supplementary Movie 8) at two selected time points of 1.5 minutes apart at the 8 to 12 cell stage. Associated with Figure 4.
Data
Volume renderings of the ABa and ABp cells of the same embryo (Supplementary Movie 7) showing the unaligned contractile rings during cytokinesis and the counter flow of two myosin II particle groups on the ABa cell. Different colormaps were used in left panels and right panels. Associated with Figure 2.
Article
Despite critical roles in development and cancer, the mechanisms that specify invasive cellular behavior are poorly understood. Through a screen of transcription factors in Caenorhabditis elegans, we identified G1 cell-cycle arrest as a precisely regulated requirement of the anchor cell (AC) invasion program. We show that the nuclear receptor nhr-6...
Article
Full-text available
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, D...
Article
The primary axis of cnidarians runs from the oral pole to the apical tuft and defines the major body axis of both the planula larva and adult polyp. In the anthozoan cnidarian Nematostella vectensis, the primary oral-aboral (O-Ab) axis first develops during the early embryonic stage. Here, we present evidence that pharmaceutical activators of canon...
Article
This is a conversation with David Matus and David Sherwood about a Research Article published in the 4 May 2010 issue of Science Signaling.
Article
The gonad in Caenorhabditis elegans is an important model system for understanding complex morphogenetic processes including cellular movement, cell fusion, cell invasion and cell polarity during development. One class of signaling proteins known to be critical for the cellular events underlying morphogenesis is the Rho family GTPases, particularly...
Article
Nematostella vectensis, an anthozoan cnidarian, whose genome has been sequenced and is suitable for developmental and ecological studies, has a complex neural morphology that is modified during development from the larval to adult form. N. vectensis' nervous system is a diffuse nerve net with both ectodermal sensory and effector cells and endoderma...
Data
Neighbor-joining bootstrap consensus tree. A neighbor-joining (NJ) bootstrap consensus tree (using mean amino acid distances) was constructed using PAUP* v4.0b10 [29] with 1,000 iterations, using a 72-AA alignment of representative bilaterian Hox and Parahox genes (see Figure S1), including the 60-AA homeodomain as well as the 12 AAs immeditately f...
Data
Full-text available
Nexus alignment used in phylogenetic analyses. A 72-amino acid alignment was constructed using the 60 amino acids of the homeodomain and the 12 amino acids immediately 3′ of the homeodomain from representative bilaterian taxa representing all of the Hox and Parahox PGs. Cc indicates Capitella sp. I; Nv, Nereis virens; Es, Euprymna scolopes; Tc, Tri...
Data
Maximum likelihood bootstrap consensus tree. A maximum likelihood (ML) bootstrap consensus tree was constructed using RAXML v2.2.1 [31] using the rtrev+G model of protein evolution, selected via ProtTest [30]. An initial search of 500 iterations was conducted to determine consistency of recovering the most likely tree (unpublished data). An additio...
Article
Phylogenetic analyses of 150 genes from 77 widely sampled metazoans (including 29 taxa for which we collected new expressed sequence tag data) corroborate important nodes that have been supported in most recent studies (such as Ecdysozoa and Spiralia), resolve multiple relationships that had conflicting support across smaller previous datasets (suc...
Article
Full-text available
Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many re...
Article
Full-text available
Hox genes define regional identities along the anterior-posterior axis in many animals. In a number of species, Hox genes are clustered in the genome, and the relative order of genes corresponds with position of expression in the body. Previous Hox gene studies in lophotrochozoans have reported expression for only a subset of the Hox gene complemen...
Article
Hedgehog signaling is an important component of cell-cell communication during bilaterian development, and abnormal Hedgehog signaling contributes to disease and birth defects. Hedgehog genes are composed of a ligand ("hedge") domain and an autocatalytic intein ("hog") domain. Hedgehog (hh) ligands bind to a conserved set of receptors and activate...
Article
Full-text available
Chaetognaths are transparent marine animals that are ubiquitous and abundant members of oceanic zooplanktonic communities. Their phylogenetic position within the Metazoa, however, has remained obscure since their discovery. Morphology and embryology have traditionally allied chaetognaths with deuterostomes, but molecular evidence suggests otherwise...
Article
Animal development is orchestrated largely by diffusible ligands of the Wnt, TGF-β, hedgehog (Hh) and FGF signaling pathways, as well as cell-surface molecules, such as Notch, cadherins, integrins and the immunoglobulin-like proteins 1 and 2. Here, we show that Hh proteins are likely to have evolved very early in metazoan evolution by domain shuffl...