19 Jan

I’ve Been M.I.A.

I must apologize for being missing for the past several months. I have been dealing with a lot of personal stress as well as school stress and took a break from blogging to address most of the issues.

I took this time to re-evaluate what I want to get out of this blog. Mostly, I want to have a place to vent about being a graduate student, but I also want to have a forum to educate the masses about the wonders that are science! I am starting the new year with the goal to write a post twice a week. We’ll see if the chaos allows more.

One of the biggest stressors but also my greatest passion has been that I was elected to the inaugural Outreach Officer to our graduate student association. My job is to decide what exactly the position will be responsible for as well as coordinate the outreach events our organization takes part. My biggest problem, in general, is the ability to say “no” to tasks that I cannot complete (whether it is because I don’t know how or, the more likely, that I already have too much on my plate). This position has allowed me to expand as a person by becoming comfortable with saying “No” to things I can’t/don’t want to do.

In the fall semester, I coordinated volunteers and activities for three events at local elementary and middle schools. I also developed and executed a workshop that was designed for our local Women in Science and Engineering “Expanding Your Horizons” workshop for sixth-grade girls. All of these events were successful and tons of fun!

The best part happened today.

I received contact from a local eighth-grade science teacher to coordinate demos starting in March at a local middle school. I also received contact from a science instructional coach (here is a good job posting that describes what a SIC does). I will hopefully be meeting with her soon to discuss what our group can contribute to the local school system.

As I’ve become more and more involved, I’ve realized I have a very large passion for outreach and science education. I think I have finally found what I want to be when I grow up! Now to figure out how to get there.

Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world. Science is the highest personification of the nation because that nation will remain the first which carries the furthest the works of thought and intelligence. – Louis Pasteur

7 Sep

Designing an Undergraduate Research Project

With the start of the semester comes new undergraduate students who are required to do research as part of their Biochemistry degree at Big State University. I am taking on my first undergrad and have been tasked with designing her project for the next two semesters.

When I’m thinking about what the goals should be when designing her project, a few jump to mind.

Obviously, to learn HOW research is done. How do you perform a literature search and how do you read to understand the articles you select? Leaning to try different things when something isn’t working. Making mistakes, and learning from them. And learning how to ask good questions.

Secondly, to learn science!! After all, we are a STEM field. I would think that by the end of a project the undergrad would understand the concepts and theory behind the techniques that they are performing in the lab.

Ideally, the undergrad will have an opportunity to interact with a range of scientist. My lab only has grad students and the professor (PI) but other labs generally have post-docs and/or technicians.

Finally, I hope that an undergrad that performs research will experience the joys and the frustrations that come with doing science.

An undergad should NOT be slave labor!!

With these goals in mind, I started to think about what a good project would be. Here is what I came up with:

  • as simple as possible: they should be able to complete the project on their own and in a semester (or two if you are lucky)
  • illustrate important concepts: the whole point of them doing research is to gain hands-on experience of concepts they learn in class
  • it should allow the student to actually understand what is going on: the concepts shouldn’t be out of the grasp of the student
  • connect the theory they learn in class to the experiments they are doing in the lab
  • challenge the individual student: the project should be adaptable to accommodate the level of the student; a weaker student can still achieve the goal while there is potential for more layers for an advanced student.

With these in mind, I go to contempt what I will have my first student do for her project.

Do you have any tips for designing undergraduate projects? I look forward to reading your comments below.

25 Aug

How do you plan crazy?

Whew, what a crazy summer I had! And this fall is going to be even crazier. I am teaching two lab sections that are three hours each plus the extra time to prep lectures and grade assignments. I am also taking a genomics course that is a three credit hour course (meaning we meet in class three hours a week) and don’t really know how much work that is going to take. I have also been elected the outreach officer for the 2015-16 Biochemistry Graduate Association at my school (brand new position so I have no guidance). So far this entails officer meetings of about an hour in length at least once a month, putting together a weekly email of events coming up the following week, and planning our participation in local outreach activities. I am attempting to finish a teaching certificate that our university offers to prepare grad students for a tenure-track teaching position. For this, I have to attend several seminars throughout the year, audit a couple of classes and fill out evaluations, as well as write a teaching philosophy statement, CV and a syllabus.

Oh, and I am also guest lecturing for my advisor towards the end of the semester.

On top of all this, I had a “come to Jesus” meeting with The Boss today and he informed me he wants me writing by next December. This means I should have all my research done by the end of next year.

Yikes!!!

I’m obviously needing to plan out what I want/need to accomplish. I’ve decided that I want to break it down in the following way:

  • Long term: Completing my project by December 2016
  • Long, mid-term: Plan out what I need to complete by the end of each semester
  • Short, mid-term: Plan out what I need to complete by the end of each month
  • Short-term: Plan out what I need to complete by the end of the week

After making this decision, my next step was to head to Google. And boy was I overwhelmed with articles and templates on time management and planning (over 502 million results for “time management” and over 54 million results for “planning dissertation research”). Trying to sort through what is helpful and what isn’t relevant is turning into a task of its own.

As I investigate further, my question to you is this: How do you plan your tasks? What do you use to lay out your goals? Please leave your tips and suggestions, all are welcome!!!

27 Jul

Electronic Lab Notebooks (ELNs)

In today’s technology-driven world, replacing the old trusty paper lab notebook with an electronic version is quite appealing. I’ve often thought it odd that I would take my digital data and print it out to tape into the composition book that served as my lab notebook. I then bought a Galaxy Note 8.0 to take notes during my classes. That is when I decided to switch to an electronic lab notebook or ELN.

An article by Jim Giles in Nature highlighted some of the benefits of going paperless in the lab – more detailed records, more accessible data sharing, improved efficiency, and even the potential to extract results from data due to improved methods of searching and analyzing. It’s also great if, like me, you often find yourself struggling to read what you wrote last week, you’re constantly flipping through pages looking for that one experiment you did that one time, or if you find that your lab notebook is starting to shed papers like your dog sheds hair.

There are several options for ELNs. Lab Archives and eCAT are two options that are designed specifically for laboratories. They both offer free versions, but you need to upgrade to access all of their functions. Many people are also adapting note taking software such as Microsoft OneNote and Evernote to their needs. Again, there are free versions of both of these available.

After checking them all out, I chose Evernote.

Evernote is an extremely versatile note-taking software that seamlessly syncs between devices. It allows for the transition from the old paper and tape to the new digital rather seamlessly. Rather than using scissors and tape to cut and paste images or tables to a notebook, you use control/command-c and -v. You paste the attachments right into the note or attach a file that can be quickly viewed or opened for further analysis.

The program also allows for efficient searching – the search function will even find text within images – and multiple levels of organization. I’m currently in the process of trying to optimize my layout within the program. I am thinking of organizing by experiment with all procedures, results, and analysis on a single page. Each experiment will be labeled with all samples involved in that experiment so I can quickly view the history of a particular sample.

Some other handy features are the “insert date/time” shortcuts (alt-shift-D in Windows or command-shift-D on a Mac) and the “copy note links” function that allows for a quickly made table of contents and page linking. There is also the added advantage of directly importing snapshots taken with Evernote. You can use Evernote’s WebClipper to capture entire web pages, a particular article on the web you found or save it as a PDF to attach to a note. You can also forward emails directly to Evernote if you upgrade to the Plus/Premium package.

I have noticed that the editing features within a note are limited. As such, I am linking to files rather than pasting images directly in the note. In addition, picture resizing isn’t possible, nor is it possible to use symbols or superscripts/subscripts within the text.

Another advantage is that you can group notebooks together into stacks. I have several “stacks”: my main research project which contains notebooks dedicated to each of the aims of my dissertation project, a school stack where I keep class notes and related files, and a personal stack.

One thing I have discovered is that you want your notebooks to be as discrete as possible. You never want to wonder which notebook a particular note belongs to. If you end up with two notebooks with similar function, you can merge them together.

Here are some additional Evernote resources:

Evernote is free up to a monthly usage of 60 MB/month. If you have large files that you’d regularly like to upload, as well as access to a few premium features such as searching within uploaded files, there is the possibility of upgrading to a premium account for $49.99/year.

Have you tried experimenting with an electronic lab notebook? If so, what tools do you use? How do you integrate them into your workflow and method of organization?

20 Jul

Fake it till you make it!!

Mental health issues are not something to take lightly. According to the ADAA, anxiety disorders affect over 40 million American adults. In addition, it is common for someone with an anxiety disorder to suffer from depression or vice versa.

Anxiety is a normal biological response that helps us get out of danger and prepare for important events. It is Mother Nature’s way of telling us we need to take action. However, problems arise when we experience anxiety that is persistent, seemingly uncontrollable, and overwhelming. If it’s an excessive, irrational dread of everyday situations, it can be disabling. When anxiety interferes with daily activities, you may have an anxiety disorder.

Most people feel depressed at times. Losing a loved one, getting fired from a job, and other difficult situations can lead to a person feeling sad and lonely. These feelings are a normal reaction to life’s stressors. Some people experience these feeling daily, or nearly daily, for no apparent reason, making it difficult to carry on with normal, everyday functioning. Depression is a condition in which a person feels discouraged, sad, hopeless, unmotivated, or disinterested in life in general. When these feelings start interfering with daily activities such as taking care of family, spending time with friends, or going to work or school, it is likely a major depressive episode.

Both of these conditions are treatable illnesses that only roughly one-third of those suffering seek help. If you have mild cases of anxiety or depression, the following tips may help. The Anxiety and Depression Association of American has some great resources for finding help if you need it.

If you are having thoughts of harming yourself or others, please seek professional help immediately. 

Here are some tips to stay positive and move forward.

Don’t be ashamed or embarrassed by your feelings. Depression and anxiety are NOT weaknesses. Very often they are treatable medical conditions. Talk about what you are going through with supportive people.

Foster supportive relationships. At the very least, spend time with one or two other people. Have lunch with a friend, email your sister, Skype with your parents. Make time to have dinner with your significant other each night.

Challenge negative thinking and your own limiting beliefs. Performing experiments can be very self-depreciating. How many times has your experiment failed before it finally worked? In STEM fields, our work is constantly be scrutinized by other scientists, our manuscripts are rejected from journals, and there always seems that answers to our questions just bring more questions. Remember to not be too hard on yourself. Do not measure your value based on the results you do (or don’t) achieve in the lab or the number of papers you publish.

Take care of yourself. As a grad student, work often requires long hours in the lab, sleep deprivation and little to no time for eating and exercise. Remember to do one thing for yourself each day. Whether its that yoga class in the afternoon at the student recreational center, going for a run in the morning, cooking dinner, or joining a sports team, taking a little time for yourself each day will go a long ways.

Celebrate successes, no matter how small. Keep a gratitude journal and write down at least one thing you are thankful for each day. Corny, but it works. Keeping the journal makes you more creative and helps you sleep better. Here are some iOS and Android apps to start and keep a gratitude journal on your tablet or phone. Also, keep finding small wins to show off to yourself and other people. Hang that western blot you finally succeeded in performing by your desk. Go out for dinner and drinks with your lab mates when you had a breakthrough.

Try new things, take the unbeaten path. Just because everyone else is going to do a postdoc doesn’t mean you have to as well. Create your own path. Don’t worry about what other people may think about your decisions.

Seek Professional Help. Most universities have student counseling services available for their students. The counselor you will see can help you decided if you need long-term guidance or just short-term help to get through a rough patch. They can provide you with coping mechanisms as well as a place for you to talk about your concerns without being judged.

Two final things to remember:

Follow Dory’s advice:

And Muhammad Ali’s:

ali

 

Have you dealt with anxiety and/or depression while in grad school (or other stressful situation)? What advice would you give someone going through the same thing? Please leave your comments below!

17 Jul

This Week in Science 07-17-2015

Mosquitos are not only are a nuisance, they also can carry numerous diseases. But good luck outsmarting them. The carbon dioxide you exhale, the look of high-contrast objects, and the warmth of bitable bodies all attract mosquitos, but in interacting ways that make it difficult for us to beat them. A recent study concludes that the independent and repetitive nature of the sensory-motor reflexes renders mosquitoes’ host-seeking strategy annoyingly robust.

A mosquito (far left) mixes strategies and clues as it homes in on its next blood meal.

 

For those with chronic pain, a new hope of a potential long-lasting treatment may be in the future. As reported in the Journal of Clinical Investigation, scientists injected mice with a spinal cord injury with cells extracted from mouse bone marrow. These cells flocked to the injured cells and produced a pain-relieving protein, called transforming growth factor beta 1 (TGFB1). The specialized cells found their ultimate destination by following chemical signals released by the injured cells. The cells were able to relieve pain in less than one day and the effects lasted for over a month.

lump-sugar-548647_1280

It turns out that sugar is the culprit of making us want a nap after those large meals. A recent study in the Journal of Neuroscience shows that an increase in glucose (a simple sugar found in most everything) leads to “amping up” of specialized neurons that act as sleep-inducing cells in the brain. These neurons can directly sense the glucose in their neighborhood, other experiments revealed. And the more glucose the neurons detected, the more they fired their sleep-inducing signals. There might even be a good reason to feel drowsy after a large meal. By sleeping, an animal, or human, will stay close to a good food source.

Imagine when someone gets out of hand in a bar. A very burly guy (usually) will appear from seemingly thin air and ask the no-good-doer to leave. This guy is called a bouncer and it is his job it is to keep the party from getting out of control. Scientists have shown that the gene Apc acts as the cellular bouncer. By switching Apc on, researchers turned mouse cancer cells back into normal intestinal tissue. This provides optimism for a genetic approach to beat cancer.

Other randomness:

A 50-million-year-old fossil sperm was discovered in Antarctica.

A handful of studies are linking shift work with not only disruption of our circadian clocks but also affects our metabolic function leading to higher body mass index and increased risks of metabolic syndrome, cancer, and sleep disorders.

And in case you were under a rock the last few days, NASA’s New Horizons flew by Pluto and was able to capture some amazing images (see below). You can see more here and here.

tn-p_lorri_fullframe_color
Pluto is dominated by the feature that is informally named the “Heart”. The Heart is approximately 1,000 miles (1,600 kilometers) across.
pluto-and-charon-01
Full-frame images of Pluto and its moon Charon. This image is a composite image to show the relative reflectivity, size, separation, and orientations of Pluto and Charon.
14 Jul

The Science of Tattoos

With some fresh ink on my arm, I thought I’d take a moment and explain the science behind a tattoo’s permanence.

As this fascinating video from TED explains, tattoos are actually a complicated inflammatory process—a delicate balancing act between your body and the dye that’s invading it.

It turns out my fierce samurai is kind of like an infection—and the reason it’s permanent is because your body keeps on fighting it forever.

Tattoo needles punch through the epidermis, the outer layer of skin, and drive the ink into the dermis, the deeper layer that’s mottled with nerves and blood vessels. “Every time the needle penetrates, it causes a wound that alerts the body to begin the inflammatory process,” the video explains.

That signal sends immune system cells racing to the site of the wound (or multiple wounds, in the case of the five-inch dragon breathing fire across your chest). Special cells called macrophages come to the rescue, eating up the dye in an attempt to “clean up” the inflammation it’s causing. The rest of the dye gets soaked up by skin cells called fibroblasts. The fibroblasts, along with many of the macrophages, stay suspended in the dermis in perpetuity. The dye in the bellies of the trapped macrophages and fibroblasts shows through the skin, projecting your Chinese word for “love” or constellation of tiny blue stars to the outside world.

Oh, and just in case you have “ragrets” about your choice, the video explains how you can get that fixed.

“You have no regrets? Like, not even a single letter?”
26 Jun

This week in Science 06-26-2015

Sorry for the lack of posts, my schedule suddenly got chaotic. My husband and his co-workers found four three-week-old kittens at his work with no mama in sight. 🙁 Between them, my research, and my new position as outreach officer in our Biochemistry Graduate Association, my week has been filled up.

Anywho, on to the science!!!!

When a rat is resting, it dreams of journeys that will lead to a desired future, such as that big block of cheese. In a recent study, scientist studied the brain activity in the hippocampus of rats as they observed a treat they were unable to reach, while they were resting, and then when they were allowed to reach the treat. During rest, the data suggests that the rats stimulating walking to the treat. This study could help explain why some people with damage to the hippocampus are unable to imagine the future.

A recent study tested the memory and thinking skills of participants every three years for 18 years. Of the participants studied, those who scored lower overall on the memory and thinking tests had an increased risk of developing the Alzheimer’s disease. During the first year of the study, people with lower test scores were about 10 times more likely to be diagnosed with Alzheimer’s disease than people with higher scores, with the odds increasing by 10 for every standard deviation that the score was lower than the average. “A general current concept is that in the development of Alzheimer’s disease, certain physical and biologic changes precede memory and thinking impairment. If this is so, then these underlying processes may have a very long duration. Efforts to successfully prevent the disease may well require a better understanding of these processes near middle age,” study author Kumar B. Rajan, Ph.D., with Rush University Medical Center in Chicago.

A team of scientists from The University of Texas at Austin, the Australian Institute of Marine Science and Oregon State University has found that some coral populations already have genetic variants necessary to tolerate warm ocean waters, and humans can help to spread these genes. “Coral larvae can move across oceans naturally, but humans could also contribute, relocating adult corals to jump-start the process,” said Mikhail Matz, an associate professor of integrative biology at The University of Texas at Austin. Reef-building corals from species in the northern Pacific Ocean and the Caribbean Sea are similar to those used in the study. These reefs may benefit from conservation and restoration efforts that protect the most heat-tolerant corals and prioritize them for any restoration initiatives involving artificial propagation.

It has been five years since the Deepwater Horizon oil spill in the Gulf of Mexico. Many of the delicate marshes along the Gulf’s coast were in dire need of cleaning up, and soil microbes stepped up to the plate. Populations of oil-degrading microbes have boomed in some of Louisiana’s most heavily oiled marsh soils. These invisible-to-the-eye janitors are breaking down the goopy brown oil faster than expected, scientists report, hinting at a relatively speedy ecological recovery.

Last year’s flu vaccine was a dud, and now scientists know why.The vaccine targeted a flu strain that didn’t look like most of the strains traveling around the Northern Hemisphere during the 2014-2015 flu season, researchers report. Much like wearing a hat and glasses or a fake mustache, tiny changes to the strains’ appearance let the virus disguise itself from the immune systems of vaccinated people. The finding explains the U.S. Centers for Disease Control and Prevention’s lackluster estimate of the vaccine’s efficiency: It was only about 20 percent effective at preventing flu-related trips to the doctor. These findings will help researchers formulate better vaccines for future flu seasons.

A new test can rapidly and accurately diagnose Ebola virus within minutes.

Google is testing out a self-driving car in California. Check out the video here.

The first commercial jetpack is set to be available next year.

 

18 Jun

C.A.: Coffee-addict Anonymous

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Addiction to caffeine is a pretty easy one to have. There are dealers on every corner and it can be really cheap (unless you drink those fancy Starbucks drinks). In general, it’s also not a bad one to have. Research shows that there aren’t too many health risks and even some evidence of health benefits (supposedly black coffee is great pre-workout). While caffeine can be found in many forms, my personal favorite source is coffee.

Within the top drinking professions are scientists (number one!), writers, and professors—pretty much exactly what many of us grad students are working on becoming. Since all signs point to our coffee drinking being a life-long habit, it makes sense to consider how we’re drinking it.

Where Are You Getting It?

I love my Keurig! It makes a great cup of coffee with tons of flavor choices, it’s also saved me a ton of money. That $2 (minimum!) spent every morning at the building café may not seem like much, but it adds up—two cups a day during the week (only because my café isn’t open on the weekend) will set you back just over $1000 a year! Compare that with making your own coffee, which easily costs under $0.50 per cup, and you’re looking at over $700 in savings every year. Not too bad, right? If you are buying those fancy-schmancy Starbucks coffees, the savings is even more!

The other nice thing about making your own coffee is the choice. You can choose how it tastes—light and fruity, deep and chocolaty… The choices can be overwhelming, but if you’re drinking it every day, you have time to figure out what you like. Also, you can choose where it comes from: locally roasted? fair-trade? sustainable?

So making your own coffee might work for the morning, but what about that coffee after lunch? My choice is to make my own coffee on campus. My labmate and I bought a cheap 4-cup coffee make and take turns buying coffee, filter, creamers, etc. It’s amazing how big a motivator the smell of brewing coffee can be.

As a self-proclaimed coffee addict, I will quickly admit that bad coffee is better than no coffee, but given the choice, I’d rather drink the good stuff, especially if it also means spending less!

When Are You Drinking It?

Check out this infographic on the best time to drink coffee, based on this post. The idea is that our bodies produce different amounts of cortisol—a hormone that, among other things, makes you feel awake and alert—in a natural rhythm throughout the day. According to the posts, the ideal times to drink coffee for maximum buzz are when your cortisol levels are lower and you’re not being “naturally caffeinated,” which tends to occur from 9:30-11:30am and from 1:30-5:00pm. Are you drinking coffee at the time of day when you really need it?

How Does It Make You Feel?

Do you ever feel like this?

by The Awkward Yeti
by The Awkward Yeti

If so, it might be time to cut back. On the other hand, some people claim to just not be affected by coffee. There aren’t too many guidelines regarding how much you, as an individual, should be drinking. Pay attention to how you feel and adjust accordingly. That first cup might seem to double your efficiency, but if the second cup makes your mind race, note it and avoid it next time.

Do you drink coffee? What is your favorite kind? I look forward to your comments below!

15 Jun

Women respond beautifully to Tim Hunt’s comments about “Girls” in the lab

In case you missed it last week, Nobel prize winner Sir Tim Hunt made some comments about the problems with girls in the lab.

The problem with girls in the lab is that they fall in love with you, you fall in love with them, and when you criticize them, they cry.

Being a woman in science, this comment made me angry but didn’t surprise me. While it is sad that in 2015, there are still prominent men who think that women are just a ball of emotions and we don’t know how to “behave” in a lab, I’ve met discouragement from the moment I started high school.

I grew up in the south. My parents always taught me I could be whatever I wanted to be and encouraged me to do what I loved and what I excelled at: Science! The discouragement occurred at school. I was constantly asked why I was interested in science and math instead of cosmetology. Why did I want to go to college and grad school instead of having a family? For some reason, as a woman in the south, I should be a teacher, nurse, or stay-at-home mom. I was thankful that I had a handful of strong women role models. My 5th-grade science and math teacher was amazing, while most of the boys and girls thought she was tough. My high school biology teacher encouraged me to pursue biology when I told her how much it intrigued me, stating that I should never stop learning.

Now that I’m in grad school, I am aware of the fact that even though we seem to out-number the men, the number of tenure-track professors who are women are few and far between. I am also aware of the salary differences once I graduate.

Instead of giving in, I’ve buckled down and I work harder. I seek out women mentors. I take part in the Women in Science and Engineering (WISE) group on campus. My goal is to keep pushing “the norm” until the idea of a little girl wanting to do chemistry or becoming an engineering doesn’t cause anyone to second guess them. Instead of asking why they want to do science or math, we need to encourage them. We need to make them feel as if they aren’t weird for wanting to be smart.

I’m not the only woman who feels this way and many took to social media to hit back. Now I give you some of my favorite #distractinglysexy tweets!

 

Have you ever met discouragement? How did you respond? How can you help encourage our little girls to become our future science and engineers? I look forward to reading all your comments below!!!