Name: september 2016-this month in jove: introducing jove genetics, jove biochemistry, and jove cancer research
Uploaded: 2016-09-01T15:15:00.000+00:00
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Description: Watch this Scientific Journal Video about September 2016-This Month in JoVE: Introducing JoVE Genetics, JoVE Biochemistry, and JoVE Cancer Research at JoVE.com

<h2 class="jove_title"><a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54529">Identification of Small Molecule-binding Proteins in a Native Cellular Environment by Live-cell Photoaffinity Labeling</a></h2>Sarah A. Head1, Jun O. Liu1,21Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 2Department of Oncology, Johns Hopkins University School of MedicineWe describe here a method for identification of small molecule-binding proteins using photoaffinity labeling. The advantage of this technique is that binding and covalent labeling of the target proteins occurs within the live cellular environment, removing the risk of disrupting native protein structure and binding conditions upon cell lysis. <h2 class="jove_title"><a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54402">Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry</a></h2>Hajime MiyaguchiNational Research Institute of Police ScienceAn improved polymerase chain reaction-restriction fragment length polymorphism method for genotyping pufferfish species by liquid chromatography/ mass spectrometry is described. A reverse-phase silica monolith column is employed for separating digested amplicons. This method can elucidate the monoisotopic masses of oligonucleotides, which is useful for identifying base composition.<h2 class="jove_title"><a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54429">A Mimic of the Tumor Microenvironment: A Simple Method for Generating Enriched Cell Populations and Investigating Intercellular Communication</a></h2>Jason D. Domogauer, Sonia M. de Toledo, Edouard I. AzzamDepartment of Radiology, New Jersey Medical School, Rutgers UniversityWe adapted a permeable microporous membrane insert to mimic the tumor microenvironment (TME). The model consists of a mixed cell culture, allows simplified generation of highly enriched individual cell populations without using fluorescent tagging or cell sorting, and permits studying intercellular communication within the TME under normal or stress conditions.<h2 class="jove_title"><a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54315">A Method of Targeted Cell Isolation via Glass Surface Functionalization</a></h2>Ali Ansari1, Reema Patel2, Kinsey Schultheis1, Vesna Naumovski3, P. I. Imoukhuede11Department of Bioengineering, University of Illinois at Urbana-Champaign, 2Department of Liberal Arts &amp; Sciences, University of Illinois at Urbana-Champaign, 3Department of Biomedical Engineering, Illinois Institute of TechnologyThis protocol describes customizable surface functionalization of the desthiobiotin, streptavidin, and APTES system in order to isolate specific cell types of interest. In addition, this manuscript covers the applications, optimization, and verification of this process. <h2 class="jove_title"><a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54371">Genetic Engineering of an Unconventional Yeast for Renewable Biofuel and Biochemical Production</a></h2>Ai-Qun Yu1,2, Nina Pratomo1,2, Tee-Kheang Ng1,2, Hua Ling1,2, Han-Saem Cho1,2, Susanna Su Jan Leong1,2,3, Matthew Wook Chang1,21Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 2NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 3Food Science and Chemical Engineering, Singapore Institute of TechnologyWe herein report methods on the molecular genetic manipulation of the Yarrowia lipolytica Po1g strain for improved gene deletion efficiency. The resulting engineered Y. lipolytica strains have potential applications in biofuel and biochemical production.<h2 class="jove_title"><a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54420">Species Determination and Quantitation in Mixtures Using MRM Mass Spectrometry of Peptides Applied to Meat Authentication</a></h2>Yvonne Gunning1, Andrew D. Watson1, Neil M. Rigby2, Mark Philo1, Joshua K. Peazer1,3, E. Kate Kemsley11Analytical Sciences Unit, Institute of Food Research, 2Institute of Food Research, 3School of Chemistry, University of East AngliaWe present a protocol for identifying and quantifying the components in mixtures of species possessing similar proteins. Mass spectrometry detects peptides for identification, and gives relative quantitation by ratios of peak areas. As a tool food for fraud detection, the method can detect 1% horse in beef.

september 2016-this month in jove: introducing jove genetics, jove biochemistry, and jove cancer research

This month we are pleased to introduce three new sections of the JoVE family: Genetics, Biochemistry, and Cancer Research.
JoVE Genetics contains methodologies for exploring all aspects of genes and heredity-from human genetics to model organisms, epigenetics to evolutionary genetics, and gene editing to gene therapy. This section features a method for genotyping pufferfish species by liquid chromatography/mass spectrometry, described by <a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54402/">Miyaguchi</a>. This technique can aid in the appropriate identification and differentiation of toxic species, which is not only important for public health but also for forensics and investigations of food fraud. Also in JoVE Genetics, <a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54371/">Yu et al.</a> report methods for genetically engineering the unconventional yeast Yarrowia lipolytica with improved gene deletion efficiency. The engineered Y. lipolytica strains have potential applications in biofuel and biochemical production.
JoVE Biochemistry comprises methods that advance our understanding of biomolecule structure and function, as well as their interactions and transformations during biological processes. This month, <a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54420">Gunning et al.</a> present a method of meat authentication using multiple reaction monitoring (MRM) mass spectrometry, which identifies peptides and gives relative quantitation for detecting adulterant species in meat mixtures. This method is sensitive enough to detect 1% horsemeat in beef products. Also in JoVE Biochemistry, <a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54529/">Head and Liu</a> describe a method for identifying small molecule-binding proteins using photoaffinity labeling. The target proteins are bound and covalently labeled within the live cellular environment, which helps preserve native protein structure and binding conditions.
JoVE Cancer Research encompasses a broad range of techniques used to advance the understanding and treatment of cancer. This includes methodologies for studying carcinogenesis, developing innovative diagnostics and therapeutics, and uncovering the mechanisms of drug resistance. This month in JoVE Cancer Research, <a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54315">Ansari et al.</a> report a method of targeted cell isolation via glass surface functionalization. This method can identify biomarkers of resistance or susceptibility to anti-angiogenic therapies. Also in this section, <a href="https://www-jove-com.remotexs.ntu.edu.sg/video/54429/">Domogauer et al.</a> present a mixed cell culture model that mimics the tumor microenvironment. With this model, the intercellular communication within the tumor microenvironment can be studied under various conditions.
You've just had a sneak peek of the articles in the newest sections of JoVE. Visit the website to see the full-length articles, plus many more, in <a href="https://www-jove-com.remotexs.ntu.edu.sg/">JoVE: The Journal of Visualized Experiments</a>.

Watch this Scientific Journal Video about September 2016-This Month in JoVE: Introducing JoVE Genetics, JoVE Biochemistry, and JoVE Cancer Research at JoVE.com

September 2016-This Month in JoVE: Introducing JoVE Genetics, JoVE Biochemistry, and JoVE Cancer Research

This month we are pleased to introduce three new sections of the JoVE family: Genetics, Biochemistry, and Cancer Research.
JoVE Genetics contains ...

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Video: September 2016-This Month in JoVE: Introducing JoVE Genetics, JoVE Biochemistry, and JoVE Cancer Research

August 2012: This Month in JoVE

Traditional microscopy requires lens objectives to magnify specimens, and can involve numerous optical components like additional objectives, filters, and mirrors to refract and direct light to optical sensors. The August 2012 issue of JoVE (Journal of Visualized Experiments) is marked by the third publication from the Ozcan Lab (University of California, Los Angeles) on their lens free lens-free "on-chip" microscopy platform, which they have pioneered.
Back in 2009, the Ozcan lab published their first article, which demonstrated the use of a lens-free imaging platform that could image cells within whole blood. This imaging technique involves placing a sample directly on an optoelectric sensor array, like the CCD or CMOS chips found in the standard camcorder. Then, LED illumination from above the sample casts shadows on the chip, which are recorded as digital holograms that can be subjected to image processing. Not only does this lensless imaging system allow for an extremely large field of view (FOV of 0.6-8 cm2), the lack of bulky optical components makes it excellent for microfluidic applications. The Ozcan group demonstrates this in their follow-up 2011 JoVE article, in which fluorescently labeled white blood cells are imaged within a microfluidic chip.
This August in JoVE, the Ozcan group demonstrates further advancements to their lens-free microscopy platform by applying it to tomographic imaging of the nematode, C. elegans. By changing the angle of illumination, using a motorized rotation stage, the Ozcan group shows how multiple holographic slices may be generated for a sample-which, following processing, can be combined into tomograms. The Ozcan group confirms that their 3D reconstruction of the worm is successful by citing that the pharyngeal tube, a 5-micron-thick structure, is only visible in a single slice and in a 3D reconstructed cross section.
The compact and inexpensive nature of the lens-free imaging systems - designed and assembled by the Ozcan group - make them well suited for point-of-care diagnostic applications, or even cell phone based microscopy that can be performed in the field.
At the Ernest Gallo Clinic and Research Center at University of California, San Francisco JoVE learns how to visualize morphological changes in single cells using three-dimensional fluorescence microscopy and computer analysis. In this procedure, cells are given agonist, antagonist plus agonist, or no treatment, and prepared for immunofluorescence microscopy. Three-dimensional images are acquired with the help of a two-photon laser system, and the fluorescence data are processed on the computer using Imaris and Matlab.
To demonstrate the power of this technique, our authors quantify single-cell phenotypic changes in transfected HEK293 cells. Three-dimensional morphometric analysis shows dramatic changes in cells treated with agonist. These changes are not always apparent when using conventional 2D analysis. This technique allows morphological changes in single cells to be quantified and characterized in response to pharmacologic stimuli, offering a powerful new assessment tool to the arsenal of drug discovery research.
This month, in JoVE Applied Physics, we travel to South Carolina to visit the School of Materials Science and Engineering at Clemson University. Here, researchers show us how to construct lithium batteries for laboratory research.
The basic components of a lithium coin cell are the working electrode, the lithium electrolyte, and a lithium foil counter electrode. The different components of the coin cell are carefully assembled and sealed with a crimping machine. The finished coin cell can then be characterized in a battery tester. Using their homemade coin cells, our researchers can experiment with using different materials to make the cathodes of lithium coin cells.
This month in JoVE Immunology and Infection, we head to Basel, Switzerland to witness two techniques for diagnosing helminth infections. We also see how investigators perform the shuttle run test in children, in order to assess the effects of these infections on physical fitness.
Helminths are parasitic worms that can live inside humans and animals. Many species infect the intestinal tract, and may be transmitted through soil. Our authors demonstrate the Kato-Katz technique, which is used for diagnosing several common soil-transmitted helminths. They also demonstrate the Baermann technique, which uses light to stimulate the migration of certain types of phototactic helminths out of sample preparations. The various types of helminth species can subsequently be determined based on morphology.
Our authors then demonstrate how to set up and perform a 20-meter shuttle run test for children, and to measure the impact of helminth infections on physical fitness. This method can help determine the true burden of soil-transmitted helminth infections on overall health.
This brief summary highlights but a few notable video-articles that will be released in August. We'll also feature articles that demonstrate how to express genes in the midbrain of the chick embryo, study neutrophil transmigration in parallel flow chambers lined with endothelial cells, and precisely measure proteolytic degradation of the extracellular matrix.

Traditional microscopy requires lens objectives to magnify specimens, and can involve numerous optical components like additional objectives, filters, and mirrors to refract and direct light to optical sensors. The August 2012 issue of JoVE (Journal of Visualized Experiments) is marked by the third publication from the Ozcan Lab (University of California, Los Angeles) on their lens-free "on-chip" microscopy platform, which they have pioneered.

Traditional microscopy requires lens objectives to magnify specimens, and can involve numerous optical components like additional objectives, filters, and ...

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JoVE Journal

Biology

2012: A Year In Review

Here's a look at some of the milestones and highlights of the year 2012 in Journal of Visualized Experiments (JoVE).
At the start of 2012, JoVE reached a major milestone by publishing our 1500th article. In this publication, in JoVE Bioengineering, Yu et al. described a method for analyzing the free radical composition of cigarette smoke. This method simulated cigarette puffing with a single-port smoking device, and combined it with electron spin resonance (ESR) spectroscopy to measure the degree to which antioxidant compounds can scavenge free radicals in cigarette smoke. A possible outcome of this research is the creation of less harmful cigarettes.
JoVE Bioengineering also contained the most-viewed article of 2012. Owczarczak et al. described a method for hacking a standard inkjet printer, loading ink cartridges with a cell-suspension "bioink," and printing lines of live cells onto glass slides. The thermal inkjet printing process creates temporary pores in the cell membrane, visualized by the incorporation of fluorescently labeled actin monomers. This concept, called "bioprinting," has many potential applications in cell and tissue engineering.
Also in 2012, JoVE Bioengineering featured a protocol by Hsia et al. for isolating and purifying spider silk protein, spinning it into fibers, and assessing the fiber strength. This protocol for laboratory-scale production of spider silk, which is stronger than tensile steel, can potentially be extended to large-scale manufacturing.
In JoVE Clinical and Translational Medicine, we featured a number of articles related to stroke, one of which. In one article, M&ouml;bius-Winkler et al. demonstrated placement of the WATCHMAN left atrial appendage occlusion device from Boston Scientific. This device is designed to prevent strokes by trapping clots within the left atrial appendage of the heart before they exit. Our authors demonstrated how to insert the guide wire through the femoral artery into the heart, advance the device into the left atrium, and deploy the device in the left atrial appendage.
Another article focused on stroke, Hamel et al. described the use of a driving simulator to study how patients compensate for visual field defects following stroke. By analyzing the compensatory gaze behavior of patients as they navigated through virtual driving courses with varying degrees of complexity, our authors see great potential for the use of driving simulators in stroke rehabilitation.
In JoVE Immunology and Infection, we published an article by Keyel et al. describing the real-time kinetics of immune cell responses to bacterial toxins using live cell microscopy. Combined with high-speed 3D confocal microscopy, this technique can also visualize the cellular repair response.
Also in JoVE Immunology and Infection, we featured an article by Yap et al. describing methods for diagnosing helminth infections in children. Helminths are parasitic worms that can infect the intestinal tract of humans and animals, and may be distinguished based on their morphology. The same article demonstrated how to measure the impact of helminth infections on physical fitness in children, which is a measure of overall health.
In JoVE Neuroscience, we featured a method by Hoffmann et al., who used tiny headphones to alter the auditory feedback in songbirds, and analyzed the computational and neurophysiological basis of vocal learning in birds when they adjust their singing in response to altered acoustic signals.
Also in JoVE Neuroscience, we moved from birds to bees with a method that assesses associative and non-associative tactile learning in honeybees. This method, by Mujagi&#263; et al., allowed bees to scan different metal surfaces with their antennae, then conditioned them to expect sugar water when their antennae touched particular surfaces, and analyzed the corresponding changes in antennal movement.
In 2012, we launched a brand-new section: JoVE Applied Physics, which features articles on subjects ranging from plasma physics to material science. The Applied Physics section also contained JoVE's 2000th video article, filmed in a synchrotron radiation facility, where Borisenko et al. showed how to determine the electronic structure of complex materials using angle-resolved photoemission spectroscopy.
In the JoVE General section, we published an article by Artioli et al. demonstrating the use of a portable gas analyzer to measure oxygen consumption during complex exercise - such as judo. By analyzing oxygen consumption and collecting blood for measuring plasma lactate concentration, this method can determine the relative contributions of different energy systems to specific aspects of complex exercise.
Finally, JoVE followed Dolhi et al. to a permanently ice-covered saline lake in Antarctica. There, scientists drilled through the ice to study single-celled microorganisms called protists that live in the harsh conditions of Antarctica.
This Year in Review was just a brief glimpse of a few of over 600 video articles that JoVE offered in 2012. Browse the JoVE archives to see thousands of other videos, and stay tuned for what's coming up this year in JoVE: The Journal of Visualized Experiments.

Here's a look at some of the milestones and highlights of the year 2012 in Journal of Visualized Experiments (JoVE).

 
 
Here's a look at some of the milestones and highlights of the year 2012 in Journal of Visualized Experiments (JoVE).
At the start of 2012, JoVE ...

September 2016-This Month in JoVE: Introducing JoVE Genetics, JoVE Biochemistry, and JoVE Cancer Research

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