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!!!

10 Jun

Troubleshooting experiments, or how to waste your time.

I’ve been doing really well with getting over my mid-Ph.D. crisis (post here) and have been getting in the lab every day to get work done. I have recently begun doing quantitative RT-PCR. I extract messenger RNA from zebrafish embryos, reverse transcribe it into cDNA and then perform specific PCR looking to see if there is a difference in transcript levels of the mRNA.

Anyone who has done qRT-PCR knows how much work goes into setting up the experiment. You have to determine the quality and quantity of RNA you have extracted, determine if there are any inhibitory  components in the sample, design your primers, pick a template for standards and optimization, determine what primer concentration is best and analyze the primer performance in the assay, validate the assay efficiency and sensitivity, and finally perform the RT and qPCR steps. Follow all this up with data analysis and qRT-PCR is quite an extensive process.

I set up my first reaction and my melt curves are off. I run a general PCR and run the product on a gel to see what is going on. Low and behold I have primer dimers. This is where my primers anneal to each other and form products instead of the template and forming amplicons. Big problem if you want to quantitate the amount of template present in a sample. So back to the primer design I go.

In addition to this, I also discovered that either our enzyme or primers are contaminated with DNA as my “no template control” produced a product. I had a just soaked my pipettes, UV’d my bench, and opened a fresh bottle of nuclease-free water. That leaves only enzyme and primers as being the culprit. I guess I’ll find out with the new primers.

Sorry for the very specific rant about lab work. Do you have any tips on setting up qPCR?? If so, I’d love to see your comments below!

8 Jun

Becoming an intrinsic motivator

Recently, my personal trainer mentioned that I need to work on becoming a fitness intrinsic motivator. I had no idea what she was talking about so I, of course, had to do some research.

In psychology, there are two type of motivation: extrinsic and intrinsic. Extrinsic motivation occurs when we are motivated to perform a certain behavior or activity to receive an outside award or avoid punishment. Intrinsic Motivation involves engaging in behaviors or activities because it is personally rewarding, aka you do it because you want to do it not for some external reward.

Some examples of extrinsic motivation include competing in a contest in order to win an award or cleaning your room to avoid being punished by your parents. Some examples of intrinsic motivation are participating in a sport/activity because you find the activity enjoyable or solving a word puzzle because you enjoy the challenge.

This got me thinking, I need to find my intrinsic motivation in all aspects of my life, not just my physical fitness (I plan to write a separate post on that journey soon:)) So how exactly can I do this? I found an interesting article (here) that discusses intrinsic motivation and some factors that can lead to an increase in this form of motivation. Here is a brief recap as well as how I plan to adapt these to my research.

  • Challenge: The whole idea of something being a challenge, whether it is mastering something I don’t understand or setting a new personal record with my running or lifting, is a big motivator for me. The article states that people are more likely to be motivated when there is personal meaning to their goals. For my research, I am diving into molecular genetics, developmental biology, and bioinformatics for my project. These are all concepts that are foreign to me and that I am slowly building my understanding. The fact that this is something I don’t understand challenges me but also leads to the next point.
  • Curiosity: It peaks my curiosity! If something grabs an individual’s attention and stimulates their want to understand more, their intrinsic motivation increases. I’ve always been a curious person and love learning new things (hence while I’m still in school ;)). Sometimes the fact that I will be learning something new is enough to get me to do something.
  • Control: Who doesn’t want to control their situation? Being able to control one’s self and their environment will lead to an increase in intrinsic motivation. Since I’ve started meeting with The Boss and planning my weeks, I feel I have more control over my time and have become more motivated to get things done.
  • Cooperation and Competition: Intrinsic motivation can also be increased in cases where a person gets joy out of helping others as well as in cases where they are able to compare their own performance to that of others. For me, the competition aspect is a big part of my motivation. I compete against myself in my fitness regime a lot! As I’m getting back into running, the first thing that comes to mind is can I beat my PR for a mile? In the gym, it is “dang, look at that girl working out with 300 lbs in the squat rack! I want to do that!!!”. I’ve decided I want to try and go to a conference a year to keep my competition in research going also. By having a deadline where I will go present my work to other researchers, I feel this will keep me on track.
  • Recognition: Who doesn’t like being told that they are doing a good job? When I received my Graduate Teaching Reward, this just made me work harder to become a better TA. For me, recognition is being told my work is very interesting by fellow students after my student seminar talk or being selected to give a talk at a university-wide research competition. All of these tell me that I am doing good and interesting work and help motivate me to keep going.

How do you keep motivated? Are you intrinsically motivated? Please comment below to start a discussion!

5 Jun

This Week in Science 06-05-2015

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It’s been a long week for me. I’ve had a lot on my plate and getting back into the lab after vacation is always hard. But it is FRIDAY!!! And with that, here is this week’s science tidbits.

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In a recent report in the June 4th issue of Cell, scientists discuss the strange concept of the nose being able to control behavior in mice. The researchers found that neurons in the nose of female mice turned off the ability to smell potential mates during periods of infertility, known as diestrus. The scientists were looking into why female mice were indifferent to male mice during diestrus. They were expecting to be looking at the brain when they discovered that the neurons in the nose essentially act as information gatekeepers.

Epigenetics is the study of external or environmental factors that turn genes on and off and affect how cells read genes. Modifications to the DNA of genes or proteins in which the DNA is wrapped around alter whether a gene is marked for expression or repression. It has readily believed that at these modifications are passed onto our children. However, three recent studies has revealed that this may not be the case (1, 2, 3). In these report, researchers reveal that during the first few weeks after conception, some of the cells in the embryo have their genetic blueprint wiped clean and these cells will then become the embryos sperm or egg cells. This means that, for the most part, the child’s offspring will not be affected by the grandparent’s environmental factors. One of these studies found that some small areas avoided this scrubbing, implying that some DNA notes that people gather during their lives could potentially pass from generation to generation, possibly transmitting risks for diseases such as schizophrenia far down the family tree.

The antidepressant Zoloft may protect against the Ebloa virus. Researchers tested roughly 2,600 compounds and found that 30 already FDA approved drugs may confer protection against Ebola infection. Seven out of 10 mice inoculated with Zoloft and then exposed to the virus survived. In addition to Zoloft, the researchers also tested the calcium channel blocker Vascor, used in patients with heart problems. In the case of Vascor, all 10 mice survived.

As anyone has ever heard, women tend to outlive men. An interesting fact is that 95% of all people that live to 110 are women. But why? Scientists have known for a while that there is a difference in the way men and women age, but the exact reason women live longer is still elusive. A recent review in Cell Stem Cell discusses how estrogen may play a role. Studies have shown that estrogen directly affects stem cells including increasing the number of blood stem cells and enhancing the regenerative capacity of brain stem cells. If this has a direct effect on lifespan still needs to be investigated. In addition, estrogen supplements have been shown to increase the lifespan of male mice.

Escherichia coli
Escherichia coli

New research introduces a promising new tool to combat the rapid, extensive spread of antibiotic resistance around the world. It places an antibiotic resistance in selected bacteria and renders other bacteria more sensitive to antibiotics. The research, if ultimately applied to pathogens on hospital surfaces or medical personnel’s hands, could turn the tide on untreatable, often lethal bacterial infections

Other random things:

Lastly, for my fellow STEM peeps, The Society for Science & the Public announced the launch of a pilot mini-grant program in 2015.

 

3 Jun

Grading and feedback, how to make them meaningful

I received news that my hiatus from teaching will be over this fall and I’m torn on how I feel. On one hand, I enjoy teaching. On the other hand, this means less time in the lab. As I mentioned in my recent post about goal-setting vs. goal achieving, I’ve struggled to multi-task and have recently laid out my goals. Now I will have to adjust these goals to take into account the time needed for teaching.

If I had to state the one thing that I believe takes up the most time for teaching, it is hands-down grading (and most other grad student TAs will give the same answer. Multiple choice questions are easy, its right or not. In science, asking multiple choice doesn’t help the student learn so we tend not to use these types of questions. That means most of what I’m grading is short answer questions. I’ve always been a TA that likes to give feedback when a student misses a question. With a new semester fast approaching and me wanting to spend more time in the lab and less time grading, I’ve decided to look at ways to reframe my approach to grading.

1. Prioritize and write feedback that will have the most impact. This is probably the most important lesson. I’ve decided that I will grade without corrections/feedback first to look for common mistakes amongst my students. Generally speaking, they usually seem to miss the same questions. I can save tons of time by recognizing where my students are struggling as a whole and addressing this in class rather than writing the same comments 15-25 times on their papers. In addition, I will list what my priorities are for what I want out of their answers. Are there keywords that they should include? Is there a particular concept I was wanting them to use? My addressing my priorities first, I can get a large chunk of the feedback out-of-the-way.

2. Feedback is all about Socialization. Most of the students I teach have taken laboratory classes but have not worked in a formal lab. The way we expect them to record data and answer questions in my lab is the same way they would if they were performing research in a lab. I try to explain to my students that, up until this point, they probably have not done much technical writing. They need to be precise. When keeping their lab notebooks, they must write it like a user’s manual. I tell them that I should be able to take their notebook to someone in the hall that has never taken the course and that person should be able to understand why they did the experiment they did and how to perform it. I try to help them “learn the ropes” and guide them rather than act as a gatekeeper meant to keep them out (or passing the course). Keeping this in mind, I plan to be upfront in how I expect them to write their answers and lab notebooks and hopefully remove some of the minor corrections.

3. Work with the student, not just the assignment. Something I’ve been proud of myself for doing in the past is being able to recognize when a student is struggling with concepts. Sure, you have the kids that just don’t put forth the effort but I’m talking about the kids that pay attention during lecture, ask you questions during the experiment but still seem to struggle when it comes around to quiz time. Here are some things that I plan to implement to try to help my students even more:

  • Take a long look at the student’s development in my course and use my feedback as a means of having a conversation about their progress.
  • Make sure I match my feedback to the goals of the assignment. No point wasting my time and confusing the students if what I write doesn’t line up.

What strategies do you find helpful when you sit down to grade student assignments? Please share your thoughts and ideas in the comments below!

1 Jun

Goal-Setting Vs. Goal Achieving

In an open-ended project that is a PhD., important to make consistent progress towards major milestones. This is overwhelming for most students, including myself as I’m a first-generation student (there is a really good article over at GradHacker about first-gen grad student here). It is very easy to get lost in day-to-day and find yourself a 6th year with no publications and no conference presentations. So how do you stay on track? Or find the right track in the first place?

I am not a strong multi-tasker and as I mentioned in my recent post, I’ve become lost in my program this year. As a result, I have not made much progress. Being a first-generation graduate student, I decided that I need more guidance and had a sit down with The Boss. We agreed to have a weekly planning meeting. I would come to the meeting with my goals for the week and a rough day-to-day plan to achieve these goals. He would offer advice on how to juggle multiple tasks and help set realistic goals.

Going into these meeting I have three basic questions: How do you identify important goals? How do you then set realistic goals? How do you track your progress in order to achieve your major goals?

Identifying Goals: The first step here is to look at the program requirements. Is there a certain number of publications required? When do you need to take major exams? Do you need to apply for a grant? These are specific to a STEM field, but the idea for any field is the same. You need to find out what requirements your program has and these will become your important goals.

Setting Goals: I’ve begun to realize here that the trick is working backward. What components are required? When do they need to be achieved? Do you need to perform sub-projects in a specific sequence? By taking a project management approach to setting goals, you can break big projects into minor components, estimate the time to completion, set realistic milestones, and adjust your timelines as you move forward. This is important as things rarely go as planned in science.

Achieving Goals: After meeting with The Boss, I’ve decided to use a weekly goal audit to track my progress. Every Sunday, I’m going to sit down with my major to-do list with my long-, mid-, and short-term goals and their associated tasks for the week ahead. I will determine which short-term goals need to be completed in the coming week (usually experiments, data analysis, protocol optimizations, etc), and what steps need to be completed for each of those projects. I also need to plan for my mid- and long-range projects such as manuscript and dissertation writing (say by setting aside blocks of time each week to work on these). When we have our meeting on Mondays, we will review what I accomplished and what I did not get done over the last week. I’m hoping these meetings will help me identify where I succeed and where I struggle.

One thing I’m realizing is that details are key when it comes to setting up goals. I’m hoping this summer I learn to structure my day so that I am as productive as possible.

How do you set and obtain goals? Do you think your process is discipline-specific? Why or why not? Is there something you have learned that boosts productivity? Share your knowledge in the comments!

30 May

This Week In Science! 05-30-15

After a brief hiatus, here are this week’s science facts.

In the first long-term study of what effects long periods of time in weightless conditions have on skin, scientists observed that mice who spent three months in space have thinner skin. Not much of a surprise to scientists as astronauts often reported skin injuries after extended periods in space.

In what is probably the world’s oldest murder, researchers report on the double-blow to a 430,000-year-old school.

Researchers estimate that Everest could lose the majority of its ice by 2100. While the seasonal ice melts supply much-needed water for people in the region, the disappearing ice poses to be a natural hazard. The melt water can pile up behind debris before breaking over dams and leading to deadly flooding.

Finally, we can lay to rest the old nature vs nurture question. In the May 18 issue of Nature Genetics, researchers conclude that, while all traits are inheritable to a degree, overall they had a 49% heritability rate. This means that genetic makeup, as well as the environment, have an equal influence on human traits.

Some changes in the PRDM12 gene, a previously unscrutinized gene, can rob people of the ability to feel pain. This would leave the person prone to unintentional injuries such as scarred tongues, scratched corneas, and missing digits. Understanding how these changes block pain sensation can lead to better treatment of patients who suffer from chronic pain.

Finally, as reported over at Sciencenews.org, a brain implant gives a paralyzed man the ability to operate a robotic arm.