Zero Order


From Lab To Leash: 5 Science Lab Lessons I Applied to Dog Walking

Posted in Uncategorized by Amy Ross on March 11, 2012

A couple months ago, I took a part time job dog walking and cat sitting for a local company.  There’s a few reasons for this. One, sitting around the house all day reading the job boards and watching TV is really, really boring after a while. It was fine for a couple of weeks, but then I started getting antsy. Two, I like dogs and cats. Three, this type of job gives me the flexibility to look for full time work in science and go on interviews. Though I’m not at a bench or a desk, I’m still applying what I’ve learned to  my new daily routine. These traits of course, aren’t unique to a scientific career, but still valuable.

1. Working independently. Although my boss comes with me on the first visit with a new client, I’m usually working by myself. If I have questions or am not sure about something, I have to figure it out and use my best judgment.  In the lab, I had several group members that were working on projects related to my own, and I found it helpful to talk to them about my progress and toss around ideas. Much of the time, I was working on my own experiments. And of course, thesis writing and defending is a solo task!

2. Creative problem solving. How do I give medicine to a cat that’s hiding under the bed? Or convince a pup to go back in her crate when she won’t move, not even for a treat?

The keys to problem solving are knowledge and preparation. General knowledge of dogs and specific knowledge of the pet go a long way.  Last week I had a new doggie client that wouldn’t let me put a leash on her. She barked and jumped out of arm’s length every time I approached her. I sat down on the floor to get down on her level. She walked around me a few times and sniffed, and eventually was convinced to let me take her for a walk.  When I first started, I was assigned a deaf dog. I’d never been around a deaf dog, so I Googled for some information on how to best handle her.

Preparation:  I always come to a doggie’s home prepared. In my backpack, I carry extra plastic bags, a leash, paper towels, a flashlight, and treats.

In science of course, there’s plenty of problems to solve, from methodology to equipment. Time, money, and manpower are limited, and your superiors can’t hold your hand every step of the way.

3. Attention to detail.  Are paws wiped? Dishes cleaned? Crates secure? Doors locked?  These tasks may be small, but are essential to the client’s wishes and the pet’s well-being. Of course, attention to detail is important at the bench to ensure protocols are being followed correctly and experiments are being replicated accurately. When I worked in the lab, I would meet with my PI periodically to discuss what I was working on. I’m under closer scrutiny now; my clients are evaluating my work every day.

4. Good communication skills. I rarely see my clients in person, but I communicate with them every day through notes. I have to be clear and concise while giving a full picture of what occurred during my visit. In the long run, writing that we saw a squirrel during our walk isn’t that important. But if there’s a change in eating habits or behavior, the owners need to know. One of the clients has a young puppy being housebroken, so it was important to keep them updated on her progress.

Likewise, communication  is essential in science, whether updating a lab notework or writing a publication. In writing a protocol, you’re writing for future employees or grad students that will be reading it after you’ve left that position.

5. Having fun.   I try to enjoy each visit with a pet, whether it’s a cat chasing after a toy or a dog walk in the sunshine.  Even though I take my work seriously,  I do want to have fun relaxing with colleagues after a long day.

I hope dog walking will keep me busy until I can get the research job I’m looking for. Until then, I’ll keep a steady supply of doggie treats on hand.

 

On-screen women in STEM: Nerd edition

Posted in Uncategorized by Amy Ross on February 28, 2012

Today the American Association for University Women (AAUW) posted “Our Favorite On-screen Women in STEM”.  While they had some good choices,  I found a few of them questionable.  Hermione Granger? She was a wizard.  Are there really so few female scientists they had to name Sandy from Spongebob Squarepants?

So with that, I give you my top five onscreen women in STEM. I will warn you it’s going to be heavily sci-fi biases. This not geeking out thing on the blog isn’t going well at the moment…

1. Martha Jones, Doctor Who

Martha met the Doctor when she was a med student. Through her travels in time and space, she was able to get out of scrapes by thinking on her feet, solving problems, and occasionally, treating a dislocation in a humanoid fish. Oh, and she saved the world.

2. Toshiko “Tosh” Sato, Torchwood

Tosh was the computer and technology expert for Torchwood, a secret alien-fighting agency. Access to government databases? Alien technology? No problem.

3. Leslie Winkle,  The Big Bang Theory

Leslie is an experimental physicist who uses likes to use lab equipment to prepare her breakfast. Although Amy Farrah Fowler gets more attention, I’ve always like Leslie. She had decent social skills and didn’t hesitate to put Sheldon in his place.

4. B’Elanna Torres, Star Trek: Voyager


Flunking out of Starfleet Academy didn’t stop B’Elanna from becoming Chief Engineer when Voyager was flung to the Delta Quadrant. She was tough and could fix anything. And don’t laugh; Voyager had some good episodes.

5. Lisbeth Salander, The Girl With the Dragon Tattoo and lesser known sequels

Although she never graduated high school, Lisbeth is a brilliant computer hacker. She’s curious, strong willed, and insists on justice, even if she has to take drastic measures.

Honorable Mentions:
Jean Grey, X-Men movies
Jordan Cochran, Real Genius
Kaylee Frye, Firefly
Liz Shaw, Classic Doctor Who

What was interesting about coming up with this list was how few women were eligible and how long it took to think of them.  There are over 100 recurring characters on The Simpsons; not one is a woman in a STEM field.  There’s no shortage of women executives, lawyers, or politicians on TV, but scientists? Not so much.

On the upside, I had a much easier time thinking of actual women in STEM. Marie Curie. Rosalind Franklin. Maud Lenora Menten. Barbara McClintock. Danica McKellar. And of course, there’s all the women faculty members and industry people who aren’t famous.

Publications and easy caffeine

Posted in Uncategorized by Amy Ross on February 19, 2012
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Hello there.  I haven’t had a whole lot to write about. I’ve been focusing on the job search and some home repair things that unfortunately, keep jumping in price. It’s so much fun to find out the previous owner installed something wrong!

I do have a little exciting news:  A paper I co-authored has been accepted for publication! The paper examines cell viability when encapsulated in superporous hydrogels. This paper was originally written by a previous Master’s student, but had been rejected for publication. I rewrote the intro and conclusion, and one of my labmates rewrote some of the methods and discussion in addition to improving the quality of the images.  “Macroporous Hydrogel Scaffolds: A Platform for Cell Encapsulation” will be published in Biomedical Materials in April.

In the news:

Pharmacy on a chip gets closer: Researchers at MIT performed a clinical trial with an implantable drug delivery device for osteoporosis patients. This is the first implantable drug delivery device I’ve read about that uses electronics; typically the release is governed by diffusion or degradation. Externally programmable pacemakers exist, so why not a drug delivery chip?

FDA to review inhalable caffeine: Aeroshot was actually developed by a bioengineering professor at Harvard. As a Diet Coke addict, I approve of this development :)  At $2.99 a tube, it’s cheaper than a cup of coffee at Starbucks.

 

Quick links: Biocapsules and 3-D printing

Posted in Uncategorized by Amy Ross on February 9, 2012
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The folks at Gizmodo were impressed by a controlled drug delivery system using carbon nanotubes. The nanotube capsule is implanted under the skin and releases a drug or protein when exposed to a stimulus. For example, a capsule for a diabetic would release insulin in response to high blood sugar. The creator also proposed putting cells in the nanotubes that would secrete a necessary protein.

There are a number of examples of stimulus responsive drug delivery systems in the literature. The cell angle is unique, but I think there’s a lot of challenges to this sort of system. Can cells secrete enough of the protein to have a therapeutic impact? Is the trigger for release sufficiently sensitive?  I also wondered about the long term viability of the cells, but the system’s creator, Dr. Loftus, addresses this in an update to the article.

Next up: New jaw for woman fabricated using 3-D printer. I’ve always been fascinated by 3-D printing, and I’ve read predictions that someday we’ll be using 3-D printers to create vital organs. I am worried about what happens to body parts when you’re printing and run low on toner!

 

Targeting MMPs in Crohn’s disease

Posted in Uncategorized by Amy Ross on February 5, 2012

I’ve been meaning to write about this article for a few weeks: Synthetic Molecules Treat Autoimmune Disease in Mice. The synthetic molecule in question is an antibody to the enzyme matrix metalloproteinase-9 (MMP-9). Since my research project involved manipulating MMPs in controlled drug delivery, I make it a point to check out related topics.

This particular article is about a treatment for Crohn’s disease. Crohn’s is a disorder in which the body’s own immune system (hence, autoimmune) attacks the intestines, causing inflammation and lots of unpleasant symptoms I’m not going to mention in case you’re eating.  The exact cause of Crohn’s disease is unknown.  Crohn’s can be treated with lifestyle changes and medications, but some cases are severe and refractory to all known treatments. I saw a few severe cases  in my old job as a medical records coder. Severe or mild, this is Not Fun.

Now a little about MMPs. MMPs are a family of enzymes that degrade the extracellular matrix (ECM), the proteins in your body between the cells. Collagen is one type of ECM protein.  They’re all identified by numbers, so MMP-1, MMP-2, MMP-3, and so forth.  In normal function, MMPs contribute to many normal body functions, such as growth and wound healing. In certain diseases, including cancer and Crohn’s disease, MMP expression and activation is well above normal levels. In inflammatory bowel diseases such as Crohn’s, the overactive MMPs  (namely, MMP-2, 9, and 13) have been suggested in the breakdown of the intestinal walls, leading to the ulceration or fibrosis (1). So, by stopping the MMPs, we should have a treatment for the disease, right?

Well, yes and no. MMP inhibitors were examined in the 1990s as a cancer treatment. Since MMPs contribute role to the growth of cancer by creating space for tumors to grow, aiding the formation of new blood vessels, and being involved in metastasis, inhibition seemed like a good route to pursue. The MMP inhibitors did well in studies with animals, but poorly in trials with humans.  The actual picture of the relationship between MMPs and tumors was much more complicated than previously thought; some MMPs had a protective effect against cancer (2). Also, the MMP inhibitors stopped the spread of cancer, but weren’t able to attack the tumor that was already present (3).

This particular paper seems more promising. The research group developed molecules that when injected, would cause the body to develop antibodies to MMP-9 (which they dubbed metallobodies).  The researchers tried this in a mouse model of Crohn’s disease and were able to detect metallobodies in the mice’s blood and prevent the symptoms of Crohn’s. The metallobodies bound to MMP-2 and MMP-9, which isn’t surprising since MMP-2 and MMP-9 are very similar in structure and function (The enzyme I worked with for my research was MMP-2, so I’m well acquainted with both).  The specificity is encouraging, as the inhibitor won’t interfere with the normal functions of the other MMPs.

Other questions remain to be answered: the human immune system is more complex than that of a mouse, will this molecule have the same effect? What effect will the molecule or the metallobodies have on the rest of the Crohn’s disease process? We’ll see how this pans out.

References:

1. Altadill, et. al. “Comparative Analysis of the Expression of Metalloproteases and Their Inhibitors in Resected Crohn’s Disease and Complicated Diverticular Disease ” Inflammatory Bowel Diseases, 2012, 18 (1) 120-130.

2. Martin and Matrisian. “The other side of MMP: Protective Roles in Tumor Progression” Cancer Metastasis Reviews, 2007, 26(3-4), 717-724

3. Coussens et. al. “Matrix Metalloproteinase Inhibitors and Cancer: Trials and Tribulations” Science, 2002,  295(5564): 2387

Diving Head First into the World of Skeptics

Posted in Uncategorized by Amy Ross on January 29, 2012

Things went pretty well at Chicago Skepticamp yesterday.

The event was held at Streetside Bar and Grill in Logan Square. Between 50 and 70 people came out to hear short presentations on a variety of topics and socialize.  Camps are informal events, as noted when the organizers showed the program could be made into a paper hat! The bar was open, but I waited until after my talk to drink.

Beth proudly wears her program/hat! Photo by Ivan Phillips

As I mentioned before, my talk was on stem cell facts and misconceptions. There’s enough material on bogus stem cell information to fill a few hours, but I focused on one particular claim: that embryonic stem cells are useless or not as useful as adult stem cells for clinical applications. These claims are typically made by people who have an ideological opposition to embryonic stem cell research (ESCR). If someone has  a moral opposition to ESCR, I can deal with that, they’re entitled to their opinion. But when ESCR opponents start distorting the science, I get angry.  So I discussed the different stem cell categories, advantages and disadvantages to each in research for disease treatment, and argued that all categories were valuable in further research.

While putting together this talk, I actually learned a lot, particularly about hematopoieitic (blood-forming) stem cells (HSCs). We didn’t talk about HSCs as much in class, but they’ve been used in therapy for years and still being investigated for experimental treatments.   I prepared the talk assuming my audience, being interested in science, already knew quite a bit about stem cells, but didn’t know a lot of details, such as the different types of adult stem cells (e.g., HSCs versus mesenchymal stem cells).  I tried not to get overly technical, so no qPCR results, no graphs, only diagrams of stem cell sources or differentiation.

Chicago Skepticamp attendees wave hello to Skepticamp Madrid, joining us via Skype! Photo by Ivan Phillips.

When the event started, I got a little worried my content was going to be too dry and technical. I hadn’t attended a Skepticamp before, and I wasn’t entirely sure what to expect.  One of the early speakers, Ashley, gave a lighthearted talk about bogus anti-aging treatments-all involving lasers, for some reason. The audience got a kick out of the crazy things people will do to get rid of cellulite. I was thinking “Crap, I hope everyone isn’t bored during my talk. The funniest thing I have is a quote from the Institute for Creation Research.”

Despite a little adjustment in speaking in front of such a large audience (and using a microphone-I’m not used to that!) the talk went over well. I had a lot of questions at the end, everything from cost differences to the different phases of FDA clinical trials. During lunch and breaks, many people approached me with additional questions. Unfortunately I wasn’t able to answer all the questions I got, but I did provide resources for more information in my presentation slides.

Overall I had a lot of fun at Skepticamp, although I felt worn out my the end of the day. Everything ran smoothly; very few technical

My talk! The image on the slide is a megakaryoycyte, the cell responsible for producing platelets. Photo by Ivan Phillips.

problems and events didn’t get too far off schedule. My favorite talk was “Canine Aggression and Dominance: Myths and Misunderstandings” by Lynn Liliedahl.  This is a topic I’ve never seen discussed in a skeptical context, but the topic is important because handling an aggressive dog incorrectly could result in physical harm. As much as I enjoy a bizarre conspiracy theory, has anyone been injured from believing the moon landing was faked? Highly unlikely.  I also got a lot out of listening to Ali Marie’s talk “Fostering Curiosity”, focused on encouraging preteen and teen interest in science.

Today I’ve been thinking about what I’d like to do with this talk in a longer format. I’d like to go into more detail about the complexity of engineering solid tissues, which I only touched on in this talk. I’d also like to delve into stem cell quackery-charlatans offering stem cell injections (usually outside the U.S.) that don’t actually do anything. What other topics could I bring to Chicago skepticism? Myths about nanotechnology? Studies about belief? The possibilities are numerous!

Short update

Posted in Uncategorized by Amy Ross on January 23, 2012

-I’ve put together my Skepticamp presentation.  The last three slides are more text heavy than I like to go in a PowerPoint, but there’s no way around that. I could discuss incorrect information and scams regarding stem cells for hours, but since I only a short time, I’m going to focus on the belief that one (or more) categories of stem cells is useless in human therapies.  I’m a little nervous I’m going to get a question I can’t answer, and I won’t have a professor to  bail me out. I have given a couple presentations for interviews, and overall those went well. I plan to do lots of reading about stem cells and try to keep my cool.

-I recently finished James Watson’s memoir Avoid Boring People: Lessons Learned From a Life In Science. Watson writes a lot about the people he associated with from childhood through his resignation from Harvard. To be honest, most of the cast of characters were indistinguishable aside from the ones I’d heard of before. Every chapter has a set of lessons learned. Favorite lessons?  Choose a young graduate advisor (young scientists are more likely to be accepting of new ideas). Surround yourself with intellectual equals-someone who can tell you if your ideas are completely wrong. And of course, don’t have a fit if someone turns down your request for funding.

Speaking at Skepticamp

Posted in Uncategorized by Amy Ross on January 16, 2012

A little exciting news: I’ve signed up to speak at Chicago Skepticamp later this month.

What is a skeptic? I like this definition from Brainyquote.com, which  defines a skeptic as “One who is yet undecided as to what is true; one who is looking or inquiring for what is true; an inquirer after facts or reasons. ” We’re interested in exposing false information about   a variety of topics:

-ESP/Paranormal powers

-Ghosts

-Cryptozoology (e.g., Bigfoot)

-Alternative medicine

-Conspiracy theories

EDIT: Well, that’s odd. WordPress ate half my post. Short recap: my talk is titled “Stem Cells: Facts and Misconceptions”. I’m a little nervous since this is my first time at a skeptical event, but I did plenty of presentations in grad school and have a lot of practice speaking and thinking on my feet.  If you’re in the Chicago area and you’re interested in attending, there are spots open-and registration is free!

Bad Depictions of Science in the Media

Posted in Uncategorized by Amy Ross on January 12, 2012

We’ve been watching the reimagined Battlestar Galactica for the past few months. At the risk of geeking out,  I was very upset by the season 2.5 episode “Epiphanies” . Not merely for the absurd plot twist, but for the bad example how to conduct research.  I am distressed by the lack of scientific literacy in our society. I don’t blame TV shows, and I accept that science fiction takes liberties with principles and technology, but science basics should remain intact. Besides, this episode just bugged me. Spoilers ahead!

 

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Quick articles of interest:

Posted in Uncategorized by Amy Ross on January 6, 2012

A quick update on the Pompe disease post I wrote a couple weeks ago.

The  enzyme replacement therapy (Myozyme) I discussed previously decreases in effectiveness if the patient develops antigens to the enzyme. A small clinical trial found patients who receive a low dose of  chemotherapy drugs decreased the immune response and improved the patients’ functioning.

Via one of my FB friends: USF Study links autism to abnormal immune characteristics, novel protein fragment. Researchers found a protein fragment in circulating blood at higher levels in an autistic mouse model compared to nonautistic mice. More testing needs to be done, but perhaps this could lead to a blood test for autism.

That’s all I’ve got for now. Have a good weekend!

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