New Integrated Software for Biologists

Oftentimes scientists are slowed down by software that isn’t intuitive or localized. Taking the first step to solve this problem, PerkinElmer Inc. launched a new informatics suite designed to help bypass these difficulties. The Ensemble for Biology platform is “an integrated suite of informatics solutions that focuses on the complex and varied needs of biological research,” as classified by the company’s website.

The software replaces Excel as a data input software, and offers its own data processing environment by reducing the necessity of spreadsheet experts. Useful formulae and data analysis tasks specific to biological sciences are built into the software. All of the data is also stored in a collaborative manner, allowing multiple users to edit data at different stages of the workflow. Ultimately, Ensemble for Biology could prove to be crucial software for laboratories in the fast paced research environment we live in. To find out more about the software, you can download a White Paper highlighting the software here.

Domo arigato, Mr. Roboto: Using Robots to Treat Cardiac Arrhythmias.

Arrhythmias refer to an abnormal heart rate or heart rhythm, the electrical impulses that may be too slow (bradycardia), too fast (tachycardia), or erratic. These are caused by problems with the heart’s electrical conductance system.

In a normal heartbeat, the electrical signal spreads from the sinoatrial (SA) node (the heart’s natural pacemaker) and spreads through the atria, passes to the atrioventricular (AV) node and finally makes its way to the lower chambers, the ventricles. These signals translate messages in order to orchestrate a highly coordinated sequence of contractions in each of the chambers to pump blood; glitches at any of these points can cause arrhythmias.

Catheter ablation is one way to treat specific arrhythmias or those arrhythmias that have not responded to medication, i.e. elimination of accessory pathways (APs), atrial flutter (AFL), or atrial-fibrillation (AF). Catheters (thin, flexible wires) are implanted into the blood vessel and guided into the heart to deliver radiofrequency (RF) energy to destroy the tissue responsible for these irregularities. According to the American Heart Association (AHA), this form of treatment is successful in over 90% of arrhythmias, eliminating the need for open-heart surgery or long-term drug therapy. However, while manual catheter ablation is quite successful, there are still many limitations including catheter manipulation in ‘hard-to-reach’ areas, less catheter stability, and efficiency/effectiveness of the ablation burn.

Enter the robotic remote-controlled catheter technology. Robotically-steerable catheters offer increased maneuverability, stability, as well as better suitability in unpredictable anatomy and possible reduction in vessel trauma. Using a computerized workstation, the physician is able to, via remote control, guide the steerable catheter into place. Two types of remote catheter navigation systems are being used currently, an electromechanical guidance and magnetic steering, making use of a permanent magnetic field to align the catheter.

Advances like robot technology in the field of interventional cardiology offer many exciting possibilities within the field of healthcare and robotics. The 2012 Heart Rhythm Society Meeting is highlighting these cutting edge robotics techniques in their upcoming scientific sessions at the annual meeting here in Boston May 9 – 12.

Welcome to the Future of Online Publishing

Since it was founded in October of 2006, The Journal of Visualized Experiments, JoVE, has spearheaded a new frontier in peer-reviewed scientific publishing by producing methods papers as methods videos. Our CEO, Moshe Pritsker, founded JoVE with two goals in mind: increase transparency and reproducibility of biological experiments, and streamline the time-intensive process of learning new experimental techniques. With the help of Aaron Kolski-Andreaco, Director of Content, and others JoVE has expanded to a monthly publication with nearly 1700 video articles published and counting.

Today (April 17, 2012 for those of you in the future) JoVE re-launches its website with a brand new design.  In the words of Cory Goodale, Chief Technology Officer, “JoVE is excited to bring a new face to our innovative video protocols. We believe these features will make JoVE even more useful for our authors and subscribers.” The new site features:

  • A larger video player bringing our articles to more video players on a wider variety of computers and mobile devices.
  • Larger previews on the homepage allowing scientists to easier find the articles that will most help them.
  • A clear and accessible navigation pane providing a clear, organized platform of our article’s data like PDF’s, and electronic citations.
  • Video recommendations to guide scientists to other procedures that may be relevant to their labs.

JoVE is excited about the new site and proud of the fruit of our hard working IT team’s labor:

Cory Goodale, Director of Information Technology

Chris Macdonald, Deputy Director of Information Technology

Chuck McCallum, Software Engineer

Andres Alfonso, Graphic Design and Web Design

Jack Payette, Assistant Developer

Come see JoVE @ EB 2012

Continuing our travels across the country, the JoVE booth is shipping out to San Diego for the annual Experimental Biology Conference. On April 22 the JoVE team will be joining the conference and more than 14,000 scientists, exhibitors and other registered guests in attending this year’s conference. We are looking forward to an amazing program, full of the latest discoveries in experimental biology, spanning the fields of anatomy, physiology, pathology, biochemistry, nutrition, and pharmacology.

The official Banner for EB 2012, taken from the conference's home page.

As always, we are eager to learn more about this year’s most cutting edge discoveries. In addition to the numerous posters and keynote speakers, the conference program notably features great career services for scientists at every stage of education and employment.

So, if you are at the Experimental Biology Conference, come and visit JoVE at booth #446. Here, you can sign up for a one-month personal subscription to all sections of JoVE and enter for the chance to win an iPad. Also, make sure you follow @Jovejournal on twitter for updates about the conference, and tweet at us with the hash tag #EB2012 to find us at the conference.

Check back here for some of JoVE’s favorite research during the meeting!

Doctors Treat Gynecological Cancer 92% Faster

Approximately 71,500 women in the United States are diagnosed with gynecological cancer every year, according to the Centers for Disease Control. Researchers from University Hospitals Case Medical Center have developed a more effective way to treat gynecological cancers, shortening radiation treatment time from five weeks to three days.

The new method, stereotactic body radiotherapy (SBRT) has been used on other types of cancer, but Case Medical Center is the first treatment facility to apply it to gynecological cancers. Dr. Charles Kunos, who co-authored the article, said the radiation therapy machine “looks like a robot you would make cars with, and targets specific cancer cells.”

Unlike traditional radiation therapy, SBRT uses focused radiation beams and targets well-defined tumors. In order to focus in on the region, the tumors need to be imaged and marked (using fiduciary markers) in advance. During treatment with the Cyberknife system (from Accuray), patients need to be immobilized, and even the patient’s breathing needs to be taken into account.

The highly specific nature of the procedure not only shortens treatment time, it limits the effect of the radiation on healthy tissues.

“SBRT holds great promise for treating persistent or recurrent gynecological cancers,” said JoVE Science Editor, Dr. Nandita Singh. “SBRT can deliver radiation with high precision and is particularly effective in delivering reduced radiation to cancer targets that are refractory to chemotherapy and conventional radiation.”

Dr. Kunos said he is very pleased with his article, and felt that it was critical to high-quality video of the protocol for people to see when he and his team launch a nationwide clinical trial. To learn more about how a video in JoVE Medicine can help you, please click here.

JoVE returns from AACR!

This post was co-authored by JoVE Editorial Director, Dr. Beth Hovey.

The JoVE team is back in Cambridge, MA after a successful trip to the annual AACR meeting in Chicago last week.  We set up camp in the exhibitor’s hall at booth 4821, and a steady stream of you came by to visit. It was great to meet you all!

We also attended a wide range of posters, symposia and other special sessions, and got to hear about novel research on the cancer field.

Closely associated with the meeting was the Stand Up To Cancer (SUTC) campaign, for which AACR is the sole scientific partner. SUTC funds “Dream Teams”—collaborative, multi-disciplinary teams of scientists whose aim is to ultimately translate cutting edge scientific discoveries into advances in cancer prevention and treatment.

At this year’s AACR meeting, Dr. Bert Vogelstein, SUTC’s Genomics Advisory Committee Leader, announced the publication of his work on the use of whole genome screens for the prediction of disease.  While he noted that whole genome sequencing is important and informational following diagnosis of disease, he suggested that clinicians do not use this technology as a risk assessment tool.

JoVE author, Dr. Charles Sawyers and his colleague Dr. Arul Chinnaiyan were named as the leaders of the latest SUTC’s list of Dream Teams.  The Prostate Cancer Dream team will first focus on finding a cure for advanced (metastatic) prostate cancer.

The next stop on the conference calendar is the Experimental Biology Meeting in San Diego from April 21-25th. Maybe we’ll see you there!

Transparency, Results and Fraud

Every so often, the scientific community finds cases where fraudulent data or results are used to help publish articles in journals and advance a scientist’s career. With grant money, tenure, and career advancement at risk for scientists it is no surprise that individuals in high pressure environments make ethically void decisions without regard to the effects of these practices on the scientific community as a whole. Recently, Fei Wang of the Kanazawa University in Japan admitted to altering data in his 2010 paper published in the Journal of Clinical Investigation.

As reported by BioTechniques today, “In less than two years, the paper has been cited by more than 20 times, according to Google Scholar. As a result of the paper, S1P has become a new potential therapeutic target…”meaning that thousands of dollars have been spent on research based in part on this paper’s findings. Furthermore, there should now be a legitimate evaluation of whether this research should be continued or abandoned.

Read more…

A Better Tool to Diagnose Tuberculosis

Up to 30 percent of the world’s population is infected with Tuberculosis (TB), but in many areas of the world, TB diagnosis still relies on insensitive, poorly standardized, and time-consuming methods. A new diagnostic tool, endorsed by the World Health Organization (WHO), may change that. Dr. Thomas Bodmer from the University of Bern, Switzerland, shows how it’s done in the April issue of JoVE.

Currently, TB is diagnosed through either a skin test, which produces a small bump on the patient’s arm when administered and needs to be checked after 72 hours, and through smear microscopy, a method that was developed over a century ago. The new test is fully automated and takes about an hour and a half to give results. It is also able to determine if the patient is infected with a multidrug-resistant strain of the bacteria.

“The Xpert MTB/RIF assay is intended for use with specimens from patients for whom there is suspicion of pulmonary tuberculosis and who fulfill the criteria outlined in the accompanied text,” said Dr. Bodmer, who co-authored the article.

WHO endorsed the test in 2010, and is working to roll it out across tuberculosis-affected countries. An important aspect of this is training people to use the device, and the JoVE video-article will help with standardization.

“TB is one of the most deadly infectious diseases worldwide and accurate and rapid diagnosis is essential for timely and proper treatment. This test is expected to dramatically improve the diagnosis of TB,” said JoVE Science Editor, Dr. Charlotte Frank Sage. “Publication of the protocol in JoVE allows researchers around the world to see a detailed demonstration of this diagnostic tool and will aid in establishing this technology in their laboratories and clinics.”

To see the full video-article, please click here.

Vampires and Science!

Let’s face it: vampires rock! Turn on any American Television and you’re sure to be inundated by the Twilights, Underworlds, and True Bloods of the world. Ever since Dracula was written by Bram Stoker in 1897, our culture has been fascinated by creatures of the night drinking the blood of unsuspecting maidens. How could vampires serve as an inspiration for science? JoVE provides the answer!

An example of the vampiric withdrawal of fluid

Back in March, Dr. Stephen Banse published an article with JoVE titled Vampiric Isolation of Extracellular Fluid from Caenorhabditis elegans. Spooky right? Banse took the novel concept of Vampirism, or draining the blood from a person, and applied it to develop a technique called Vampiric Isolation of Extracellular Fluid to drain blood from C. elegans. The lesson to take away is the use of one of our culture’s myths as inspiration for an innovative technological technique. Strictly the title of Banse’s article sparks the reader’s imagination by putting all of our knowledge of vampires in the forefront of our mind. The visualization of the procedure then shows a needle doing the iconic vampire action, draining the extracellular fluid from one organism and then injecting it in another.

Who knows what other aspects of our cultural mythos could provide inspiration for a new discovery. Could someone inspired by zombies develop a new method for drug administration, or could Frankenstein’s monster inspire a new technique for flesh grafts? Who knows- but in the meantime check out the full article here. Don’t have full access to JoVE? Recommend JoVE to your institution’s librarian here!

How Fat Are Your Lab Mice?

Researchers are increasingly aware that fat in some parts of the body is more harmful than fat in other places. To help determine how obesity works, scientists turn to animal models and now, they are able to visualize how much fat their lab rats are carrying and where it is stored.

“One of the key benefits of this technique versus existing methods, like ex vivo analysis, is that this technique allows for non-invasive and longitudinal assessment of fat in small animal disease models,” said paper-author Dr. Todd Sasser.

Traditionally, researchers have had to use either invasive techniques, which provide more insight into where fat is being stored specifically but result in the death of the mouse, or less specific, non-invasive imaging techniques. Here, they use dedicated small animal X-ray computed tomography (CT) and customized analytics to see how the fat is distributed inside the animal.

The process is highly visual, resulting in three-dimensional images of the fat within the mouse, which is why the researchers chose to publish their method in JoVE, the only peer reviewed, PubMed-indexed science journal to publish all of its content in both text and video format.

“Generally, individuals new to this method will struggle, because the segmentation and visualization protocol includes several steps that must be completed in succession,” said co-author Sarah Chapman, from the University of Notre Dame.

To see the full video-article, please click here.