Archive
R.I.P. Christina Takanishi
Recently we learned that a former BMCDB student (originally enrolled in CDB before the merger from the Wood lab) Christina Takanishi has died last Wednesday (2012-01-25).
Goodbye, Chris. You will be missed.
PS:
From her former lab as can be read in the comments:
“A memorial service for Christina in Sacramento is in the works and I will pass along that information to the BMCDB GG when I receive it.
- Matt Wood”
Wish we had a graduate student community center here at UCD? Here’s your chance to be heard!
Winter Dialogue with Dean Gibeling
“Envisioning a Graduate Student Community Center”
Wednesday February 1st
Noon-2:00pm
Lunch will be provided
Student Community Center (across from Silo) - Meeting Room D
Moderators note: Unfortunately I will be unable to attend this day because of a wine sensory work shop, however we desperately need members of the BMCDB graduate group to go and talk to Dean Gibeling about creating a common space exclusive to graduate and professional students here at UCD. It is absurd that we have 5000+ graduate students and hardly any specific services for us on campus. It is time for us to stand up and demand facilities that will serve our graduate community for the future. You can make a real change and get a chance to discuss things with the actual dean of graduate studies – plus you get free lunch! Let me know if you are interesting in going, I can update you on the plans I have already drawn up for the community center. Thanks!
-Gordon
Entering Mentoring Seminars – sign up today!
Greetings BMCDB!
Learn how to be a better mentor and teacher! Next week will be the first Entering Mentoring seminar for the Winter quarter. This seminar is open to graduate students, postdocs, and even professors that want to enhance their abilities as a mentor. This Winter we will hold 6 weekly 1-hour seminars covering topics common to all mentoring relationships.
Here are just a few benefits of participating in the Mentoring Seminar:
1. Enhance your mentoring abilities through awareness and learn tools for effective mentoring
2. Gain perspective on all mentoring relationships, including your own student/PI relationship
3. Put on your CV that you took a HHMI Entering Mentoring Seminar
4. Free coffee and bagels on Wednesday mornings!
Details:
Time: Wednesday mornings from 9:00am to 10:00am
Dates: February 2nd through March 7th (6 weeks long)
Place: 148 Briggs Hall
Our tentative weekly schedule will focus on the following topics:
1. Establishing a good mentoring relationship, and elements of a good research project
2. Learning to communicate effectively and adaptively
3. Setting goals and expectations, and developing trust
4. Identifying and resolving challenges in mentoring
5. Evaluating your progress as a mentor
6. Developing a mentoring philosophy and drawing parallels in mentoring
To sign up, subscribe to the EnteringMentoring listserve at: https://lists.ucdavis.edu/sympa/info/enteringmentoring or email Brandon Zipp (bjzipp@ucdavis.edu) or Kristi Bezold (kristi.bezold@gmail.com) for more information.
Feel free to email with any questions that you might have. I look forward to seeing you next Wednesday!
Brandon
Cancer vaccine trials underway
From the Roswell Park Cancer Institute
Dendritic cell vaccine, manufactured in unique RPCI facility, trains body’s defenses to remember, destroy cancer cell.
The Center for Immunotherapy at Roswell Park Cancer Institute (RPCI) has launched a phase I clinical research study of a dendritic cell vaccine designed to both eradicate cancer cells and prevent disease relapse. Developed at RPCI, the NY-ESO-1 dendritic cell vaccine will be manufactured in the Institute’s new Therapeutic Cell Production Facility using a unique FDA-approved process — making RPCI the first research facility in the U.S. to use a custom-made barrier isolator for vaccine cell production, and the first in the world to use this system in an approved, government-regulated study.
Dendritic cells are the gatekeepers of the human immune system, defending against invaders like bacteria, viruses and cancer. The vaccine to be produced at RPCI will be the first to incorporate a particular form of NY-ESO-1, antiDEC205-NY-ESO-1. “Armed with this specialized protein, the treated cells are then given back to the patient as a vaccine designed to recruit an army of killer immune cells that seek out and destroy cancer,” explains Kunle Odunsi, MD, PhD, Director of RPCI’s Center for Immunotherapy (CFI) and the study’s Principal Investigator.
The new study is also unique in that it’s the first to test a dendritic vaccine given in combination with rapamycin, a compound used to prevent rejection of solid-organ transplant. The study just launched will capitalize on a striking recent scientific discovery by Protul Shrikant, PhD, of the Department of Immunology at RPCI, who found that in low doses, rapamycin confers a previously unknown benefit — it prevents the immune system from using up its cancer-killing T-cells in one quick burst. “We have shown for the first time that rapamycin has the capacity to produce immune cells that have memory attributes,” explains Dr. Odunsi, who is also Chair of RPCI’s Department of Gynecologic Oncology. “The immune cells are trained to live longer and to always remember that cancer cells are bad and should be attacked and killed.”
The ability to stretch out the attack for a long-term, durable response suggests that the vaccine may be effective in preventing disease recurrence. The new NY-ESO-1 dendritic cell vaccine is expected to show great promise in patients with bladder, brain, breast, esophageal, gastrointestinal, hepatocellular, kidney, lung, melanoma, ovarian, prostate, sarcoma and uterine tumors.
The NY-ESO-1 vaccine, tailor-made for each patient, will be produced in RPCI’s Therapeutic Cell Production Facility (TCPF) under the direction of Yeong “Christopher” Choi, PhD, who notes: “We believe that our facility’s custom-made barrier isolator, the unit in which the vaccines are manufactured, is the first of its kind.” The barrier isolator — an Xvivo System processing chamber designed to RPCI’s specifications by BioSpherix, Ltd., Lacona, NY — maintains strict control of the unit’s temperature and atmospheric gases, critical for optimal production of dendritic cell vaccines.
“Those conditions, and the sterile vaccine-manufacturing environment, are rigidly maintained throughout the entire process,” says Dr. Choi. “The Xvivo — which at about 70 square feet is basically a clean room in a box — acts as a physical barrier that protects the cell-therapy product from outside contaminants, resulting in a safer, more predictable manufacturing process.”
Read the complete article here.
Self assembling cell-membrane created at UCSD
A recent press release from UC San Diego by Susan Brown:
Neal Devaraj watches as undergraduate student Weilong Li works on a next step in their quest to create an entirely artificial cell.
Chemists have taken an important step in making artificial life forms from scratch. Using a novel chemical reaction, they have created self-assembling cell membranes, the structural envelopes that contain and support the reactions required for life.
Neal Devaraj, assistant professor of chemistry at the University of California, San Diego, and Itay Budin, a graduate student at Harvard University, report their success in the Journal of the American Chemical Society.
“One of our long term, very ambitious goals is to try to make an artificial cell, a synthetic living unit from the bottom up – to make a living organism from non-living molecules that have never been through or touched a living organism,” Devaraj said. “Presumably this occurred at some point in the past. Otherwise life wouldn’t exist.”
By assembling an essential component of earthly life with no biological precursors, they hope to illuminate life’s origins.
“We don’t understand this really fundamental step in our existence, which is how non-living matter went to living matter,” Devaraj said. “So this is a really ripe area to try to understand what knowledge we lack about how that transition might have occurred. That could teach us a lot – even the basic chemical, biological principles that are necessary for life.”
Molecules that make up cell membranes have heads that mix easily with water and tails that repel it. In water, they form a double layer with heads out and tails in, a barrier that sequesters the contents of the cell.
Devaraj and Budin created similar molecules with a novel reaction that joins two chains of lipids. Nature uses complex enzymes that are themselves embedded in membranes to accomplish this, making it hard to understand how the very first membranes came to be.
“In our system, we use a sort of primitive catalyst, a very simple metal ion,” Devaraj said. “The reaction itself is completely artificial. There’s no biological equivalent of this chemical reaction. This is how you could have a de novo formation of membranes.”
Read the complete article here.
Wanna win some cash? Of you do! Apply to the IGPS today!
The Interdisciplinary Graduate and Professional Symposium (IGPS) http://gradstudies.ucdavis.edu/about/igps.html. is a chance for you to show off your research to the rest of campus, and to folks from industry. This is a great chance to present your work, make meaningful connections, and best of all – win some cash!
Prizes for the best:
$5000 – best talk
$1000 – best poster
$1000 – best visual or performing art
$2500 – best Student-run Session
And there will be more!
Apply before Feb 1st – be careful to read the detailed SmartSite instructions for uploading your application (must be completed in Adode Acrobat Reader, also label your Abstract as your Kerebros user name)
Good luck!
Staying Productive
The best way to maintain a good work/life balance is to be as productive as possible during work time, but distracting websites can often get in the way. No longer.
Several plugins for your favorite web browser allow you to set time limits for the time you spend on time-wasting websites. When time is up for the day, you can’t visit those websites anymore. Once such plugin is StayFocused for Google Chrome, but similar programs exist for other browsers.
Storer Lectures: Luke O’Neill – Jan 26 @ 16h10 in ARC Ballroom Room B
MCB Joint Seminar series- Dr. Gary Ward-Thursday, January 26, 2012
Dr. Gary Ward
Professor
Department of Microbiology and Molecular Genetics
University of Vermont
“Invade and Conquer: How the parasite Toxoplasma gondii forces its way into host cells”
Thursday, January 26, 2012
4:10 p.m.
1022 Life Sciences
Faculty Host: Jim Trimmer (jtrimmer@ucdavis.edu)
(If you wish an appointment with the invited speaker, please contact their host.)
Davis – Bicycle Capital of California, but what can it learn from the Dutch?
by Daniël Melters
Everyone who comes to Davis will notice that there a lot of bikes everywhere and people actually use them on a regular basis. Davis is fairly small town and it is also flat. This makes Davis a prime location for easy cycling. One reason why Davis is only one of three communities in the US that has a platinum rating [PDF] according to the League of American Bicyclists. Add to the equation the favorable climate: there is not too much wind (compared to coastal region), the summers are warm (or hot, depending on your perspective) and the winter very mild (a bit of rain with moderate cold at worst (if you even call it a winter)). All of this resulted in a true bicylce-culture in Davis. There are several bike-clubs and even more bike events, including the Foxy’s Fall century (50 km / 100 km / 100 miles). Around campus there are many pumps and repair stations locations, in case you get a flat. There is even an iPhone app with Davis bike routes on it. Of course a bicycle advocacy group (advocacy blog) have to be included as well and there are three in Davis alone. Not bad for a town with only 65,000 inhabitants.
This does not mean that there no problem associated with bicycles. Of course bike theft is a real concern (100s per year) and it would serve you well to have two locks on your bike to secure both your wheel to your frame, which in turn is secured to a solid, unmovable object. A more serious issue is that bicyclist are weak participants in traffic. Not physically weak as in no muscle strength, but they tend to do not particularly well in an accident. When a car and bicyclist collide, it is the bicyclist that will almost always lose. Even though is a very bike friendly town, accident do happen, as this heat map, made by UC Davis graduate student Russell Neches (his blog and the story why he made the heatmap), shows.
Car-Bike crashes in Davis 2004-2008 by Russell Neches
What to do to limit the accidents from happening? There are three things that are important: one and two, the drivers of both the car and the bicycle, and three, the road design.
Driver:
Well, as a driver, always be aware of cyclist. They are much narrower and much more agile than you in your car, so they can slip in small spaces, which they will do especially in slow traffic or at traffic lights. Also keep in mind that it is rather strenuous for a cyclist to come to a complete stop at a stop sign and get going again. All you do is roll out the car, press the brakes. Come to a stop and press the throttle to keep going again. In addition, cyclists don’t have a cage around their heads, so they can see more, besides the fact that they sit higher. Their slower speed also gives them more time to assess the traffic at a given intersection. As a result, a cyclist will be inclined to not come to a complete stop at a stop sign, but rather ride through them while watching for traffic. Illegal? Yes, bicycles are legally equal to cars, even though they lack two wheels, a front- and rear-bumper, and an engine. Of course, this does not stop UC Davis police or Davis police to stop and fine cyclists who don’t come to a complete stop at a stop sign. This effort is especially intensified at the beginning of every quarter.
Cyclist:
Assume that every driver of a car or truck hasn’t seen you, as this is most likely true. Also, every car has a blind spot. If you are in there, the driver cannot see you. Period. The higher the vehicle, the less the driver can and thus will see. In you collide with a car, you will probably lose, so wear a helmet for your own protection. But by wearing a helmet, drivers are more inclined to drive past you at a closer distance than if you were not wearing a helmet. The fact that you drive slower than a car, means that you have more time to look around you and thus more time to anticipate your surrounding. This difference is intensified when it is dark. Always cycle with front and rear lights that are bright. If you blend in the dark background, no driver can see you and thus consider you when (s)he makes a decision. Finally, as traffic participants cyclist are still not appreciated as much compared to some other countries, such as Denmark or the Netherlands.
Speaking about the Netherlands. This country has a lot of similarities to Davis. It is flat and very bike friendly (18+ millions bike used by 16 million people and about 750,000 bikes are stolen each year). In total there are 29,000 km dedicated bicycles paths in the Netherlands, whereas there are only 5,012 km highways and 7,899 km country roads. In comparison, Davis has over 100 miles (160 km) of bicycles paths and lanes. In comparison, about 15-20% of people in Davis commute by bike. In Amsterdam, this number is ~40%. How did an entire country build such a large bicycle path network and what effect did this have on bicycle use? Here is a video that explains a few things:
Road design:
A good road design takes into consideration all traffic participants: pedestrians, cyclists and motorists. In the Netherlands a new road within city limits includes a sidewalk on both sides of the street, followed by cycling paths on both sides of the street and in the center the main roadway for motorist. To prevent motorist and cyclist (or pedestrians for that matter) to use the same road, means that there is less change that they can actually physically meet. Davis is on its way to improve this, but from a Dutch perspective they have a long way to go. What would happen to the number of bicycle-car accidents if at the main driving corridors in Davis, bicyclists were driving on bicycle paths that are physically separated from the road used by cars? And what would happen if at the traffic lights (roundabouts can handle 50% more traffic, but that on the side) bicycles are given their own time for crossing without cars being allowed to cross? My bet: fewer accidents between bicycles and cars.
Davis is doing well compared to its US counterparts and Davis can be proud of that. As it stands now, it can only improve for the better, with Amsterdam and Copenhagen as possible examples. For now, share the road and be extra cautious/considerate with the those traffic participants who are more vulnerable. Drive safe.
