Investigating the Origins of Life

Miller-Urey experiments study the abiotic synthesis of organic compounds by creating an environment similar to that of the early earth. An electric discharge is applied to a mixture of gases representing the early earth’s atmosphere and lightening. This is done in the presence of a liquid water reservoir, representing the early oceans, as well as with an apparatus simulating evaporation and precipitation.

JoVE introduces a 21st century adaptation of the Miller-Urey origin of life experiments.

Earlier this week, we published a modern approach to the famous 1953 experiment by Dr. Stanley Miller (then a graduate student at the University of Chicago) and Dr. Harold Urey that explored one of the most intriguing research questions facing scientists today—the origin of life on earth. Read more…

New JoVE Articles 03/11/2013

JoVE General

Rapid Genetic Analysis of Epithelial-Mesenchymal Signaling During Hair Regeneration
Article 4344 Wei-Meng Woo*, Scott X. Atwood*, Hanson H. Zhen, Anthony E. OroProgram in Epithelial Biology, Stanford University School of MedicinePublished February 28, 2013 | 417 Views

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Rapid and Efficient Generation of Neurons from Human Pluripotent Stem Cells in a Multititre Plate Format
Miao Zhang1, Hans R. Schöler1,2, Boris Greber11Max Planck Institute for Molecular Biomedicine, 2Medical Faculty, University of MünsterPublished March 5, 2013 | 321 Views

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Article 4335

Generation of Stable Human Cell Lines with Tetracycline-inducible (Tet-on) shRNA or cDNA Expression
Article 50171 Marta Gomez-Martinez1, Debora Schmitz2, Alexander Hergovich11UCL Cancer Institute, 2Friedrich Miescher Institute for Biomedical ResearchPublished March 5, 2013 | 330 Views

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JoVE Neuroscience

Labeling of Single Cells in the Central Nervous System of Drosophila melanogaster
Christof Rickert1, Thomas Kunz1, Kerri-Lee Harris2, Paul Whitington2, Gerhard Technau11Institute of Genetics, University of Mainz, 2Department of Anatomy and Neuroscience, University of MelbournePublished March 4, 2013 | 336 Views

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Article 50150

Mitochondria-associated ER Membranes (MAMs) and Glycosphingolipid Enriched Microdomains (GEMs): Isolation from Mouse Brain
Article 50215 Ida Annunziata*, Annette Patterson*, Alessandra d’AzzoDepartment of Genetics, St Jude Children’s Research HospitalPublished March 4, 2013 | 326 Views

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JoVE Immunology and Infection

Separation of Plasmodium falciparum Late Stage-infected Erythrocytes by Magnetic Means
Lorena Michelle Coronado1,2, Nicole Michelle Tayler1,2, Ricardo Correa1,2, Rita Marissa Giovani3, Carmenza Spadafora11Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), 2Acharya Nagarjuna University, 3Departamento de Medios y Creativo, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP)Published March 2, 2013 | 257 Views

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Article 50342

JoVE Clinical and Translational Medicine

A Zebrafish Model of Diabetes Mellitus and Metabolic Memory
Article 50232 Robert V. Intine1, Ansgar S. Olsen1, Michael P. Sarras Jr.21Dr. William M. Scholl College of Podiatric Medicine, Rosalind Franklin University of Medicine and Science, 2Chicago Medical School, Rosalind Franklin University of Medicine and SciencePublished February 28, 2013 | 425 Views

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Murine Spinotrapezius Model to Assess the Impact of Arteriolar Ligation on Microvascular Function and Remodeling
Alexander Michael Guendel*1, Kyle S. Martin*1, Joshua Cutts2, Patricia L. Foley3, Alexander M. Bailey1, Feilim Mac Gabhann4, Trevor R. Cardinal2, Shayn M. Peirce11Department of Biomedical Engineering, University of Virginia, 2Department of Biomedical Engineering, California Polytechnic State University, 3Office of Animal Welfare, University of Virginia, 4Department of Biomedical Engineering & Institute for Computational Medicine, Johns Hopkins UniversityPublished March 3, 2013 | 250 Views

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Article 50218

JoVE Bioengineering

Evaluation of Polymeric Gene Delivery Nanoparticles by Nanoparticle Tracking Analysis and High-throughput Flow Cytometry
Article 50176 Ron B. Shmueli1,2, Nupura S. Bhise1,2, Jordan J. Green1,2,3,41Biomedical Engineering Department, Johns Hopkins University School of Medicine, 2Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, 3Wilmer Eye Institute, Johns Hopkins University School of Medicine, 4Institute for Nanobiotechnology, Johns Hopkins University School of MedicinePublished March 1, 2013 | 224 Views

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Graphene Coatings for Biomedical Implants
Ramakrishna Podila1,2, Thomas Moore3, Frank Alexis3, Apparao Rao1,41Department of Physics, Clemson University, 2Department of Pharmacology and Toxicology, East Carolina University, 3Department of Bioengineering, Clemson University, 4Center for Optical Materials Science and Engineering Technologies, Clemson UniversityPublished March 1, 2013 | 317 Views

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Article 50276

JoVE Applied Physics

Determining 3D Flow Fields via Multi-camera Light Field Imaging
Article 4325 Tadd T. Truscott1, Jesse Belden2, Joseph R. Nielson1, David J. Daily1, Scott L. Thomson11Department of Mechanical Engineering, Brigham Young University, 2Naval Undersea Warfare Center, Newport, RIPublished March 6, 2013 | 322 Views

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JoVE Chemistry

Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies
Pooja Sharma1,2, Mariam Kaywan-Lutfi1, Logesvaran Krshnan1,2, Eamon F. X. Byrne1,2, Melissa Joy Call1,2, Matthew Edwin Call1,21Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 2The University of MelbournePublished March 6, 2013 | 256 Views

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Article 50141

New Articles 3/4/2013

JoVE General

Design and Use of Multiplexed Chemostat Arrays
Article 50262 Aaron W. Miller, Corrie Befort, Emily O. Kerr, Maitreya J. DunhamDepartment of Genome Sciences, University of WashingtonPublished February 23, 2013 | 340 Views

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Enrichment of Spermatogonial Stem and Progenitor Cells (SSCs) in
Culture for Derivation of Long-term Adult Mouse SSC Lines
Laura A. Martin, Marco SeandelDepartment of Surgery, Weill Cornell Medical CollegePublished February 25, 2013 | 230 Views

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Article 50017

Trajectory Data Analyses for Pedestrian Space-time Activity Study
Article 50130 Feng Qi1, Fei Du21School of Environmental and Life Sciences, Kean University, 2Department of Geography, University of Wisconsin-MadisonPublished February 25, 2013 | 305 Views

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JoVE Neuroscience

Identification of Olfactory Volatiles using Gas Chromatography-Multi-unit Recordings (GCMR) in the Insect Antennal Lobe
Kelsey J. R. P. Byers, Elischa Sanders, Jeffrey A. RiffellDepartment of Biology, University of WashingtonPublished February 24, 2013 | 273 Views

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Article 4381

JoVE Clinical and Translational Medicine

Utilizing a Cranial Window to Visualize the Middle Cerebral Artery During Endothelin-1 Induced Middle Cerebral Artery Occlusion
Article 50015 Robert W. Regenhardt1, Saeed Ansari2, Hassan Azari3, Kenneth J. Caldwell2, Adam P. Mecca11Department of Physiology and Functional Genomics, University of Florida, 2Department of Neurosurgery, McKnight Brain Institute, University of Florida, 3Department of Anatomical Sciences, Shiraz University of Medical Sciences, Shiraz, IranPublished February 22, 2013 | 280 Views

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In vivo Measurement of the Mouse Pulmonary Endothelial Surface Layer
Yimu Yang, Gaoqing Yang, Eric P. SchmidtDivision of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of MedicinePublished February 22, 2013 | 298 Views

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Article 50322

Vein Isolation by Radiofrequency Ablation followed by Implantation of a
WATCHMAN Left Atrial Appendage Occlusion Device
Article 3818 Martin J. Swaans, Benno J.W.M. Rensing, Lucas V.A. BoersmaDepartment of Cardiology, St. Antonius Hospital, The NetherlandsPublished February 26, 2013 | 455 Views

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Direct Pressure Monitoring Accurately Predicts Pulmonary Vein Occlusion During Cryoballoon Ablation
Ioanna Kosmidou1, Shannnon Wooden1, Brian Jones2, Thomas Deering1, Andrew Wickliffe1, Dan Dan11Department of Cardiac Electrophysiology, Piedmont Heart Institute, 2Cardiac Rhythm, Medtronic Inc.Published February 26, 2013 | 181 Views

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Article 50247

JoVE Bioengineering

Quantitative FRET (Förster Resonance Energy Transfer) Analysis for SENP1 Protease Kinetics Determination
Article 4430 Yan Liu, Jiayu LiaoDepartment of Bioengineering, Bourns College of Engineering, University of California, RiversidePublished February 21, 2013 | 234 Views

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Quantifying the Mechanical Properties of the Endothelial Glycocalyx with Atomic Force Microscopy
Graham Marsh, Richard E. WaughDepartment of Biomedical Engineering, University of RochesterPublished February 21, 2013 | 297 Views

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Article 50163

JoVE Applied Physics

of Surface Modifications by White Light Interferometry: Applications in
Ion Sputtering, Laser Ablation, and Tribology Experiments
Article 50260 Sergey V. Baryshev1, Robert A. Erck2, Jerry F. Moore3, Alexander V. Zinovev1, C. Emil Tripa1, Igor V. Veryovkin11Materials Science Division, Argonne National Laboratory, 2Energy Systems Division, Argonne National Laboratory, 3MassThink LLCPublished February 27, 2013 | 192 Views

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Fabrication of Nano-engineered Transparent Conducting Oxides by Pulsed Laser Deposition
Paolo Gondoni1, Matteo Ghidelli1, Fabio Di Fonzo1,2, Andrea Li Bassi1,2, Carlo S. Casari11Department of Energy and NEMAS – Center for NanoEngineered Materials and Surfaces, Politecnico di Milano, 2Center for Nano Science and Technology, Instituto Italiano di TecnologiaPublished February 27, 2013 | 206 Views

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Article 50297

New Advances In Celiac Disease Treatment

According to the University of Chicago Celiac Disease Center, over 3 million people in the United States currently suffer from celiac disease, an intestinal inflammatory disease with auto-immune features. The ingestion of gluten triggers immune system responses in the human body, generally causing severe gastrointestinal pain, as well as other long-term problems including malnutrition and fatigue. Although these symptoms and further intestinal damage can be avoided by maintaining a strict gluten-free diet, this can be difficult and present a financial burden. Because of this, many scientists are searching for treatment methods for celiac disease. Significant advances have been made in this field recently, including an intestinal medicine, a vaccine, and a microbial therapeutic approach.

Read more…

The Macro-Micro World through CellScope

Dr. Eva Schmid, Postdoctoral Fellow at Dr. Daniel Fletcher’s laboratory at the Department of Bioengineering, University of California, Berkeley, presented her work on developing CellScope at the annual ASCB 2012 meeting in San Francisco. CellScope is a rugged hand held microscope that can be mounted on a cell phone, or even an iPad, and uses its optics to generate a high resolution picture. The microscope is designed to generate high resolution images that are capable of disease diagnosis outside of a traditional laboratory. In fact this was the reason for developing CellScope; as a tool for disease diagnosis in developing countries.

The CellScope Microscope in Action

However, a serendipitous meeting with Saber Khan, a middle school teacher at Friends School in San Francisco, evolved this into a fun and an exciting teaching tool for school kids. The middle school students got engaged in completing a Micro-Macro project where they took macroscopic and microscopic pictures of objects around their homes and neighborhood like leavers, petals, pets, pet- hair, etc. “The response of the students was phenomenal,” says Mr. Saber Khan. The students also realize that this fun learning tool has the ability to be used as a real diagnostic instrument capable of impacting global health.

Who knew, a cell phone would become a teacher’s friend.

Another application is, of course, using this very portable device for research in the field. University of Hawaii researchers have used CellScope to monitor plankton diversity. CellScope has also been used to monitor coral reefs for coral bleaching. At the end of the day, it’s just really cool and a regular old microscope just won’t do under the Christmas tree anymore. I wish I had a CellScope to bring on my next wilderness hike.

Sleeping Flies and Feeding Slugs

Sleeping Flies and Feeding Slugs

Welcome to your weekly update on some of the latest cutting edge articles from JoVE! Last week we told you about home-made 3D Printers and mice grown from stem cells. This week, two of our most innovative articles come from the University of Pennsylvania Perelman School of Medicine and Case Western Reserve University.

Do sleeping flies have better immune response?

Drosophila being put to sleep ahead of assay

As anyone who has ever been sick knows, a lot of sleep is an important part of the healing process. It is no surprise that sleep helps our mammalian cousins heal, but who would have thought that sleep is also an integral part of the fly immune system? In order to better understand how sleep helps flies heal, scientists from the University of Pennsylvania Perelman School of Medicine have developed a technique to quantitatively measure the immune response of genetically modified Drosophila melanogaster. Using this assay, scientists can use phenotypically distinct flies to understand which aspect of sleep is most valuable to the immune system.

The full title of the article is “Quantitative Measurement of the Immune Response and Sleep in Drosophila” and can be found here.

Time to feed the Sea Slugs

An Aplysia buccal mass biting

Aplysia californica, or the California Sea Slug, have been a valuable animal in the laboratory since Eric Kandel won the 2000 Nobel Prize in Physiology or Medicine for his research using Aplysia neurons to understand the physiological basis of memory. Because of their characteristically large neurons, which are up to 1 mm in width, Aplysia are valuable for neuroscientists interested in a wide range of mechanisms. In this study, scientists at Case Western Reserve University remove the slug’s feeding organ, the buccal mass, from the animal to study how neural input allows this organ to have multiple functions for the animal: biting, swallowing and rejection of food. This allows scientists to record neural activity in these organs clearly while the organs form naturally occurring movements.

The article, titled “An In Vitro Preparation for Eliciting and Recording Feeding Motor Programs with Physiological Movements in Aplysia californica” can be found here.

Want to learn more about JoVE? See what our authors have to say about us!

How do you cure superbugs?

When Alexander Fleming discovered the first naturally occurring antibiotic, penicillin, in 1928 he changed the world of medicine, and because of this discovery he earned the 1945 Nobel Prize in Medicine alongside Ernst Chain and Howard Florey. Penicillin’s development allowed patients to be cured of deadly diseases like syphilis, or those caused by staphylococci or streptococci. Due to this discovery, over the last century, our society’s lifespan has increased and the world’s population has exploded.

Bacteria as seen in a microscope. Taken from Jove article found below

Unfortunately, many species of bacteria are now evolving to be antibiotic-resistant “superbugs.” Fighting superbugs requires unconventional treatments, which would cost the worlds’ government’s billions of dollars in additional healthcare expenses. To make matters worse, any methods we currently have to kill superbugs often have painful side effects such as vomiting or organ damage.

Luckily, researchers are working on ways to get around antibiotic-resistance. Dr. Qi Zhou, an academic researcher in the Faculty of Pharmacy at the University of Sydney, is working on a technique to deliver nano-sized antibiotics via an inhaler to target respiratory superbugs. According to this press release, upper and lower respiratory tract infections caused by superbugs cost the Australian taxpayers over $150 million and accounts for nearly seven million doctor visits per year. This effectively allows antibiotics to be delivered directly to the infected site. This reduces potential side-effects such as damaging other organs. “These new inhaled nanomedicines will target the antibiotics directly at the respiratory tract” Dr. Zhou’s colleague Professor Hak-Kim Chan says. “The new inhaled nanoantibiotic therapy will be pivotal in the fight to reduce drug resistance and adverse effects for combating respiratory superbugs.”

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Image source can be found here.

Home-made 3d Printers and Mice from Stem Cells

With so many great video-articles coming out in JoVE each week, it’s hard to make sure you catch all of the interesting science. This week, two of our most innovative articles come from MIT and The Scripps Research Institute. Check them out:

3D Printing from a Digital Projector?

3D structure produced with MIT's home-made 3D printer.

In an article published on November 27, mechanical engineers at Massachusetts Institute of Technology demonstrate how to make a 3D printer from a commercially available digital projector. Using a few external mirrors and lenses, the engineers project each layer of the structure they are fabricating into a pool of photosensitive resin, which polymerizes into the desired shape. The process is known as projection micro-stereolithography, and is being used to study buckling mechanisms commonly found in nature.

The full title of the article is “Micro 3D Printing Using a Digital Projector and its Application in the Study of Soft Materials Mechanics” and can be found here.

Life from stem cells?

Stem cells have been in the news lately, particularly as The 2012 Nobel Prize in Physiology or Medicine was awarded to Sir John B. Gurdon and Shinya Yamanaka for their work in stem cells. These Nobel Prize Winners discovered techniques to produce induced pluripotent stem cells from adult cells. This is a significant breakthrough for researchers as stem cells are hard to study in adults or come from embryos, where collection of stem cells have political and ethical implications. In this JoVE article, researchers at The Scripps Research Institute demonstrate how to produce mice from induced pluripotent stem cells, a valuable demonstration of the viability of stem cells to grow into any necessary tissue.

The article, titled “Generation of Mice from Induced Pluripotent Stem Cells,” will be published on November 29, 2012 and can be found here.

Want to check out more JoVE articles? Get a free trial to Journal of Visualized Experiments!

Interfacing Man and Machine with Biofabrication Techniques

Think back to the last time you had to work in a group. Maybe it was in high school, maybe college, more than likely, it was last week in your staff meeting. Do you remember how difficult it was (and is!) to get anything done when someone in the group either didn’t seem to be speaking the same language, had a different set of priorities or just couldn’t communicate what they were thinking? This is a problem that persists beyond human interaction and into technological spheres. Everyday, bioengineers and computer scientists deal with communication issues when attempting to interface two opposing programs or materials. They must ask how two materials interface and communicate in such a way that a desired step is taken. For the bioengineer, the more specific question is: how can we make electronics and biological materials combine and work together? A JoVE article, “Bridging the Bio-Electronic Interface with Biofabrication”, published on June 6th, 2012 shows one such way, via a biological microelectrochemical system (bioMEMS).

In research funded by the U.S. Government’s Defense Threat Reduction Agency (DTRA), University of Maryland faculty Dr. Gregory Payne and Dr. William Bentley describe their method for bridging the gap between electronics and biological components in JoVE. Their biofabrication technique uses electrodeposition to attach bio-compatible polymer films to electrodes. The polymer films act as an intermediate between the electrodes and biological materials, which is step one in creating a productive interface between man and machine. The films are then functionalized with biological components by covalently bonding proteins or whole cells to the primary amine groups of the polymer films.

See the Video and read more here

Publication Bias and the Scientific Process

The future of the scientific process is now open for debate. On May 10th, Daniel Sarewitz published a column in Nature (Nature 485,149 (10 May 2012) doi:10.1038/485149a) decrying the recent trend towards positive publishing bias in the biomedical sciences. This means that more often than not, studies that fail to find positive results are not reported, while any hint of a statistically significant positive result is published. This positive publication bias is substantiated by the now famous Amgen study (C. G. Begley & L. M. Ellis Nature 483, 531–533; 2012) that reported the inability to reproduce 47 of 53 landmark cancer studies.

Calle et al. (2011) - 'A Procedure for Lung Engineering'

Calle et al. (2011) - 'A Procedure for Lung Engineering' -a novel technique published in a visualized format

One possible explanation for this lack of reproducibility is that positive results are actually false positives, (i.e. not actually true). Another explanation is supported by a 2005 paper by John Ioannidis (also cited by Sarewitz), titled ‘Why Most Published Research Findings Are False’ (PLoS Med. 2, e124; 2005). Here, Ioannidis (2005) asserts that research results are less likely to be true when the studies have greater ‘flexibility in designs, definitions, outcomes, and analytical modes’. Simply put, your method of study is extremely important in producing un-biased, true research. However, in the current state of most scientific publishing, transparency of methods is embarrassingly poor. If you open any of the highest impact journals, methods sections are relegated to the end of the paper, often in trimmed down and difficult to decipher versions. We exist in a scientific culture that places exceeding importance on positive results, without fully describing, or showing, how these results were obtained.

If Ioannidis (2005) is correct, then reducing variability amongst methods for similar experiments by increasing transparency is one key solution for reducing bias and providing faster verification and falsification of findings. This self-correction is at the heart of the scientific method. By keeping methodology in a diminished form, and not highlighting verified, accurately executed techniques, we fail to control for one highly significant variable in producing unbiased research. The scientific process is at stake here, so we must ask ourselves: how are we going to move forward? We can begin by publishing highly transparent and visible methodology, both novel and ‘gold standard’.

Lee et al (2012)- Gel Electrophoresis

Lee et al. (2012) showing proper technique for loading and running agarose gels

Here, it’s important for novel methods to garner high visibility so that the scientific process can hone, correct and apply them in the appropriate circumstances. For example, in March 2011, Dr. Laura Nicklason published her laboratory’s tissue engineering technique (Calle, E. A., Petersen, T. H., Niklason, L. E. J. Vis. Exp. (49), e2651, DOI: 10.3791/2651 (2011)), which is difficult to reproduce without visualization of the apparatus and methodology. Presented in the multimedia format of a JoVE publication, this complicated technique is now more easily reproduced. Concurrently, it’s critical that the time honored, ‘gold standard’ techniques continue to be executed correctly. For example, a recent JoVE publication, Agarose Gel Electrophoresis for the Separation of DNA Fragments (Lee, P. Y., Costumbrado, J., Hsu, C., Kim, Y. H. J. Vis. Exp. (62), e3923, DOI: 10.3791/3923 (2012), shows best practices for a standard biological technique. In both of these cases, visualizing techniques allows for better execution of experiments, which will improve reproducibility and, hopefully, decrease publication bias.