One of many research initiatives in the Matthews' lab focuses on the role of extracellular matrix and cell surface glycoproteins in the developing nervous system and in learning, memory, plasticity and diseases. This slide shows extracellular matrix (ECM) staining on a glioma initiating cell.

Neuroscience Program Faculty

Barry E Knox, PhD

Barry E Knox, PhD
Appointed 07/12/90
3613 Institute For Human Performance (IHP)
505 Irving Ave.
Syracuse, NY 13210

315 464-8719

Current Appointments

Hospital Campus

  • Downtown

Research Programs and Affiliations

  • Biochemistry and Molecular Biology
  • Biomedical Sciences Program
  • Neuroscience Program
  • Neuroscience and Physiology
  • Ophthalmology

Education & Fellowships

  • Postdoctoral Fellow: Massachusetts Institute of Technology
  • PhD: Johns Hopkins University School of Medicine, 1984

Research Interests

  • Visual transduction, Gene Expression, Membrane proteins

Web Resources


Link to PubMed External Icon (Opens new window. Close the PubMed window to return to this page.)


Our laboratory is studying light transduction and development in the retina using molecular biological, biochemical and physiological approaches. Light transduction is carried out in specialized cells (rods and cones) that express a group of proteins designed to efficiently capture photons and transmit the information as a change in the conductance of the plasma membrane. The visual pigments (opsins) are a large family of proteins that absorb light and initiate the intracellular signal transduction pathway through a G-protein cascade. Opsins differ from each other in their wavelength of maximum absorbance (permitting color detection), their conformational changes after light activation and in retinal expression patterns. These issues are crucial for shaping a photoreceptor's characteristic response properties. We have a long standing research effort to understand thare studying how photoreceptors develop and the molecular basis of rod/cone opsin functional differences.

The control of retinal gene transcription involves numerous cis-acting DNA elements in the proximal promoter, as well as more distant sequences. A complete understanding of the mechanism of transcriptional control that leads to cell-specific expression will require detailed experiments in vivo. We have developed transient transfections assays of embryos and transgenic Xenopus approaches that are ideally suited to answer these questions.

Photopic vision is mediated by cone cells, which express a protein, calleda color or cone opsin, that determines its spectral sensitivity and response characteristics. The molecular mechanisms that produce the unique properties of cone pigments are not understood. The overall goal of this project is to understand the molecular mechanisms of 11-cis-retinal/short wavelength opsin interactions that bring about their unique absorbance properties and photobleaching/ regeneration behavior; in particular, to determine how specific amino acid residues contribute to spectral tuning and phototransduction. We are biochemically characterizing the bleaching /regeneration pathway and studying the physiologically active conformation of short wavelength cone opsins using low temperature and time-resolved (>10 ns) UV-visible spectroscopy. We are investigating the role specific amino acids in violet cone opsin have in retinal interactions, photobleaching and regeneration using molecular models coupled to site-directed mutagenesis. New structural approaches to elucidate the function of these proteins are under development and to investigate structural basis of retinal disease.

Selected Publications:

Baker SA, Haeri M, Yoo P, Gospe SM 3rd, Skiba NP, Knox BE, Arshavsky VY. The outer segment serves as a default destination for the trafficking of membrane proteins in photoreceptors. J Cell Biol. 2008 Nov 3;183(3):485-98.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM. Bioinformatic identification of novel putative photoreceptor specific cis-elements. BMC Bioinformatics. 2007 Oct 22;8:407.

Ramos LS, Chen MH, Knox BE, Birge RR. Regulation of photoactivation in vertebrate short wavelength visual pigments: protonation of the retinylidene Schiff base and a counterion switch. Biochemistry. 2007 May 8;46(18):5330-40. Epub 2007 Apr 18.

McIlvain VA, Knox BE. Nr2e3 and Nrl can reprogram retinal precursors to the rod fate in Xenopus retina. Dev Dyn. 2007 Jul;236(7):1970-9.
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Additional Collaborators

  • Paul Gold, PhD External Icon
    Professor, Biology (Syracuse University)
    Research Interests: Aging, Cell Signaling and Communication, Learning, Memory, and Plasticity, Neurological and Psychiatric Conditions.
  • James Hewett, PhD External Icon
    Associate Professor, Biology (Syracuse University)
    Research Interests: Neuroscience and Central Nervous System Neurobiology and Pathology: Neuromodulators and Epilepsy: Arachidonic Acid Metabolism and Cyclooxygenase-2: Cytokines and Interleukin-1beta: Signal Transduction and Gene Expression.
  • Sandra Hewett, PhD External Icon
    Professor, Neuroscience, Biology (Syracuse University)
    Research Interests: Mechanisms underlying cell death in the central nervous system: the interplay between excitotoxicity and inflammation.
  • Donna Korol, PhD External Icon
    Associate Professor, Biology (Syracuse University)
    Research Interests: Neural mechanisms of learning and memory across the lifespan.
  • Katharine (Kate) Lewis, PhD External Icon
    Associate Professor, Biology (Syracuse University)
    Research Interests: Specification and patterning of spinal cord interneurons; Formation of functional neuronal circuitry; Evolution of spinal cord patterning and function; Dorsal-ventral neural tube patterning; zebrafish development.