State University of New York

12 articles published in JoVE

• Biology

  
  Investigating Interactions Between Histone Modifying Enzymes and Transcription Factors in vivo by Fluorescence Resonance Energy Transfer Mi Sa Vo Phan¹, Phu Tri Tran¹, Vitaly Citovsky^{1 1}Department of Biochemistry and Cell Biology, State University of New York Fluorescence resonance energy transfer (FRET) is an imaging technique for detecting protein interactions in living cells. Here, a FRET protocol is presented to study the association of histone-modifying enzymes with transcription factors that recruit them to the target promoters for epigenetic regulation of gene expression in plant tissues.

• Developmental Biology

  
  Primary Cell Cultures to Study the Regeneration Potential of Murine Müller Glia after MicroRNA Treatment Seoyoung Kang¹, Stefanie G. Wohl^{1 1}Department of Biological and Vision Sciences, College of Optometry, The State University of New York Müller glia primary cultures obtained from mouse retinas represent a very robust and reliable tool to study the glial conversion into retinal progenitor cells after microRNA treatment. Single molecules or combinations can be tested before their subsequent application of in vivo approaches.

• Chemistry

  
  ARL Spectral Fitting as an Application to Augment Spectral Data via Franck-Condon Lineshape Analysis and Color Analysis William R. Roberts^1,2, Thomas N. Rohrabaugh¹, Ryan M. O'Donnell^{1 1}DEVCOM Army Research Laboratory (ARL), ²Department of Chemistry, State University of New York at Buffalo This protocol introduces Franck-Condon Lineshape Analyses (FCLSA) of emission spectra and serves as a tutorial for the use of ARL Spectral Fitting software. The open-source software provides an easy and intuitive way to perform advanced analysis of emission spectra including excited state energy calculations, CIE color coordinate determination, and FCLSA.

• Bioengineering

  
  Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning Minakshi Mukherjee*¹, Emily Caroll*¹, Zhen Q. Wang^{1 1}Department of Biological Sciences, University at Buffalo, State University of New York The goal of this protocol is to provide a detailed, step-by-step guide for assembling multi-gene constructs using the modular cloning system based on Golden Gate cloning. It also gives recommendations on critical steps to ensure optimal assembly based on our experiences.

• Immunology and Infection

  
  Identification of Plasmodesmal Localization Sequences in Proteins In Planta Cheng Yuan¹, Sondra G. Lazarowitz², Vitaly Citovsky^{1 1}Department of Biochemistry and Cell Biology, State University of New York, ²Department of Plant Pathology and Plant-Microbe Biology, Cornell University Plant intercellular connections, the plasmodesmata (Pd), play central roles in plant physiology and plant-virus interactions. Critical to Pd transport are sorting signals that direct proteins to Pd. However, our knowledge about these sequences is still in its infancy. We describe a strategy to identify Pd localization signals in Pd-targeted proteins.

• Engineering

  
  Fabrication of Uniform Nanoscale Cavities via Silicon Direct Wafer Bonding Stephen R. D. Thomson¹, Justin K. Perron^2,3, Mark O. Kimball⁴, Sarabjit Mehta⁵, Francis M. Gasparini^{1 1}Department of Physics, The State University of New York at Buffalo, ²Joint Quantum Institute, University of Maryland, ³The National Institute of Standards and Technology, ⁴Cryogenics and Fluids Branch, NASA Goddard Space Flight Center, ⁵HRL Laboratories A method for permanently bonding two silicon wafers so as to realize a uniform enclosure is described. This includes wafer preparation, cleaning, RT bonding, and annealing processes. The resulting bonded wafers (cells) have uniformity of enclosure ~1%^1,2. The resulting geometry allows for measurements of confined liquids and gasses.

• Biology

  
  Preparation of the Mgm101 Recombination Protein by MBP-based Tagging Strategy Xiaowen Wang¹, MacMillan Mbantenkhu¹, Sara Wierzbicki¹, Xin Jie Chen^{1 1}Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University The yeast mitochondrial nucleoid protein, Mgm101, is a Rad52-type recombination protein that forms large oligomeric rings. A protocol is described to prepare soluble recombinant Mgm101 using the Maltose Binding Protein (MBP)-tagging strategy coupled with cation exchange and size exclusion chromatography.

• Biology

  
  Genetic Modification and Recombination of Salivary Gland Organ Cultures Sharon J. Sequeira*¹, Elise M. Gervais*¹, Shayoni Ray¹, Melinda Larsen^{1 1}Department of Biological Sciences, University at Albany, SUNY A technique to genetically manipulate epithelial cells within whole ex vivo cultured embryonic mouse submandibular glands (SMGs) using viral gene transfer is described. This method takes advantage of the innate ability of SMG epithelium and mesenchyme to spontaneously recombine after separation and infection of epithelial rudiments with adenoviral vectors.

• Neuroscience

  
  Hippocampal Insulin Microinjection and In vivo Microdialysis During Spatial Memory Testing Ewan C. McNay¹, Leslie A. Sandusky¹, Jiah Pearson-Leary^{1 1}Behavioral Neuroscience, University at Albany Modulation of hippocampally-dependent spatial working memory by direct intrahippocampal microinjection, accompanied and followed by in vivo microdialysis for metabolites in conscious, behaving animals.

• Neuroscience

  
  Recording Human Electrocorticographic (ECoG) Signals for Neuroscientific Research and Real-time Functional Cortical Mapping N. Jeremy Hill¹, Disha Gupta^1,2, Peter Brunner^1,2, Aysegul Gunduz^1,2, Matthew A. Adamo³, Anthony Ritaccio², Gerwin Schalk^{1,2,4,5,6,7 1}Wadsworth Center, New York State Department of Health, ²Department of Neurology, Albany Medical College, ³Department of Neurosurgery, Albany Medical College, ⁴Department of Neurosurgery, Washington University, ⁵Department of Biomed. Eng., Rensselaer Polytechnic Institute, ⁶Department of Biomed. Sci., State University of New York at Albany, ⁷Department of Elec. and Comp. Eng., University of Texas at El Paso We present a method for collecting electrocorticographic signals for research purposes from humans who are undergoing invasive epilepsy monitoring. We show how to use the BCI2000 software platform for data collection, signal processing and stimulus presentation. Specifically, we demonstrate SIGFRIED, a BCI2000-based tool for real-time functional brain mapping.

• Biology

  
  Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro Shoko Ueki¹, Benoît Lacroix¹, Vitaly Citovsky^{1 1}Department of Biochemistry and Cell Biology, State University of New York Testing protein-protein interaction is indispensable for dissection of protein functionality. Here, we introduce an in vitro protein-protein binding assay to probe a membrane-immobilized protein with a soluble protein. This assay provides a reliable method to test interaction between an insoluble protein and a protein in solution.

• Biology

  
  Insulin Injection and Hemolymph Extraction to Measure Insulin Sensitivity in Adult Drosophila melanogaster Aaron T. Haselton¹, Yih-Woei C. Fridell^{2 1}Department of Biology, State University of New York, ²Allied Health Sciences, University of Connecticut Conserved insulin signaling pathways found in the fruit fly Drosophila melanogaster make this organism a potential tool for modeling metabolic disorders including type II diabetes. To this end, it is critical to establish physiological assays to effectively measure systemic insulin action in peripheral glucose disposal in the adult fly.