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Rockefeller University

8 ARTICLES PUBLISHED IN JoVE

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Biology

MALDI Sample Preparation: the Ultra Thin Layer Method
David Fenyo 1, Qingjun Wang 1, Jeffrey A. DeGrasse 1, Julio C. Padovan 1, Martine Cadene 1, Brian T. Chait 1
1Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS).

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Biology

High-resolution Measurement of Odor-Driven Behavior in Drosophila Larvae
Matthieu Louis 1, Silvia Piccinotti 1, Leslie B. Vosshall 1
1Laboratory of Neurogenetics and Behavior, Rockefeller University

In this video article, we describe a new method allowing the construction of odorant gradients with stable and controllable geometries. We briefly illustrate how these gradients can be used to screen for olfactory defects (full and partial anosmia) and to study more subtle features of chemotaxis behavior.

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Neuroscience

Single Sensillum Recordings in the Insects Drosophila melanogaster and Anopheles gambiae
Maurizio Pellegrino 1, Takao Nakagawa 1, Leslie B. Vosshall 1
1Laboratory of Neurogenetics and Behavior, Rockefeller University

Electrophysiological responses of olfactory sensory neurons to odorants can be measured in insects using single sensillum recordings. In this video article we will demonstrate how to perform single sensillum recordings in the antennae of the vinegar fly (Drosophila melanogaster) and the maxillary palps of the malaria mosquito (Anopheles gambiae).

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Biology

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
Richard T. Pomerantz 1, Mike O'Donnell 1
1Howard Hughes Medical Institute, Rockefeller University

The fate of the replisome following a collision with a head-on RNA polymerase (RNAP) is unknown. We find that the replisome stalls upon collision with a head-on RNAP, but resumes elongation after displacing the RNAP from DNA. Mfd promotes replication restart by facilitating displacement of the RNAP after the collision.

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Biology

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Markus Hafner 1, Markus Landthaler 2, Lukas Burger 3, Mohsen Khorshid 3, Jean Hausser 4, Philipp Berninger 4, Andrea Rothballer 1, Manuel Ascano 1, Anna-Carina Jungkamp 2, Mathias Munschauer 2, Alexander Ulrich 1, Greg S. Wardle 1, Scott Dewell 5, Mihaela Zavolan 3, Thomas Tuschl 1
1Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, 2Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 3Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 4Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 5Genomics Resource Center, Rockefeller University

RNA transcripts are subject to extensive posttranscriptional regulation that is mediated by a multitude of trans-acting RNA-binding proteins (RBPs). Here we present a generalizable method to identify precisely and on a transcriptome-wide scale the RNA binding sites of RBPs.

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Immunology and Infection

Detection of Trypanosoma brucei Variant Surface Glycoprotein Switching by Magnetic Activated Cell Sorting and Flow Cytometry
Danae Schulz 1,2, Monica R. Mugnier 1, Catherine E. Boothroyd 1,3, F. Nina Papavasiliou 1
1Laboratory of Lymphocyte Biology, Rockefeller University, 2Department of Biology, Harvey Mudd College, 3Masters School

African trypanosomes grown in vitro undergo antigenic variation at a low rate, such that populations are made up of parasites expressing a dominant variant surface glycoprotein (VSG) type and a small population of "switched" variants. This protocol describes a fast method for detecting and quantifying these populations.

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Biochemistry

Analysis of β-Amyloid-induced Abnormalities on Fibrin Clot Structure by Spectroscopy and Scanning Electron Microscopy
Pradeep K. Singh *1, Hanna E. Berk-Rauch *1, Nadine Soplop 2, Kunihiro Uryu 2, Sidney Strickland 1, Hyung Jin Ahn 1
1Patricia and John Rosenwald Laboratory of Neurobiology and Genetics, Rockefeller University, 2Electron Microscopy Resource Center, Rockefeller University

Presented here are two methods that can be used individually or in combination to analyze the effect of beta-amyloid on fibrin clot structure. Included is a protocol for creating an in vitro fibrin clot, followed by clot turbidity and scanning electron microscopy methods.

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Education

Investigation into Deep Breathing through Measurement of Ventilatory Parameters and Observation of Breathing Patterns
Masami Yokogawa 1, Tomoyo Kurebayashi 2, Kazuki Soma 3, Hiroichi Miaki 1, Takao Nakagawa 4
1Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 2Rehabilitation Section, Higashimatsuyama Municipal Hospital, 3Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, 4Department of Physical and Rehabilitation Medicine, Kanazawa Medical University

Here, we present a protocol to assess two deep breathing patterns of natural and diaphragmatic breathing for their effectiveness and ease of execution. Fifteen participants were selected, utilizing an electrocardiograph and expired gas analyzer for measurement of the ventilatory parameters, together with visual assessment by video capture of thoracoabdominal movement.

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