Elemental, My Dear Watson

As I was studying for the MCAT yesterday (General Chemistry), doing the Examkrackers practice problems, I kept having to refer back to the periodic table at the beginning of the book. Now, I know quite a bit of the periodic table information - the molar masses of oxygen (~16), carbon (~12), and nitrogen (~14), for example. But if a problem comes up about nickel, I'm gonna be in a pickle.

Thankfully, I discovered today, we DO get a periodic table on the MCAT, which includes atomic numbers and atomic weights (whew!). Otherwise, I thought I was going to have to memorize this song ...

It's All Coming Back To Me Now

Finally, after some hemming and hawing, I have begun studying for the MCAT. "M"-Day for me is March 23, 2013. So I've got a bit of time. But given that I took Physics, General Biology, and General Chemistry two years ago (2010-2011), and Organic Chem one year ago (2011-2012), I feel the need to do some hard-core review. That, and the fact that the average MD/PhD matriculant's MCAT score is a 35 puts a bit of pressure on.

To put that score in perspective, the mean MCAT score for 2011, according to the American Association of Medical Colleges, was a 25.1. That's out of a best-possible 45. Not a single person got a 45 in 2011. The highest score was a 42. To get a 35, I would have to be in the 94th percentile. Yikes. (See the full score report from the AAMC here.)

My strategy is to use the Examkrackers review books series, both the subject matter review books and the "1,001" questions books. I have started Gen Chem, Orgo, and Gen Bio. Today I will venture into the world of Physics. I am making flashcards on Quizlet, which I can study anywhere using their iPhone app. With all of these resources, along with taking (and re-taking) the available AAMC practice tests, I believe I will be as prepared as I can be.

That said, I was a bit worried, when I first opened the review books, that I would have forgotten ... EVERYTHING. Not so. And thus, the song "It's All Coming Back To Me Now" has been cycling through my head. And of course, like most songs that play in my head over and over again, I had forgotten most of the lyrics. Solution: YouTube. So here, I present Glee performing this song, in celebration of the fact that my science knowledge is ... all coming back to me now.

Stupid Google! (and some HTML resources)

Dear Google: Your Dynamic layout series is wonderful, in many respects. It is interactive, reader-friendly, and attractive. However, there is one major problem: The inability to change the HTML coding stifles creativity, and seems to go against the philosophy of Google itself. I hope you will fix this problem. In the meantime, I am sadly restricted to one of your lesser templates, simply because it affords me the ability to customize my pages. Were it not for my followers (however few they may be), I would consider changing blogging platforms. For now, though, I will hold out hope for your listening to the many complaints online about this omission in your template design. Sincerely, Lorien Menhennett mybedsidemanner.blogspot.com

For those of you who may have visited my blog in the last few days, you may have noticed that it has been a revolving door of layouts and templates. For this, I apologize. I realize this can be disorienting and confusing to readers ... I know it is to the author.

The reason for this is as follows: I found a very wonderful template, called the Dynamic series. However, I wanted to customize it by changing the HTML coding. After about an hour of frustration on both my blog and other blogs dedicated to helping bloggers blog, I discovered that this template series does not allow you to edit the HTML code. It is fixed, so to speak. I find this very frustrating. Hence my faux open letter to Google in my faux version of The New York Times (at right).

I find it humorous that this was a problem for me (at 5 a.m. on a Saturday, especially). I never would have dreamed that I would be editing HTML code. But I have learned bits and pieces of it, through different Web sites and others' blogs. This post is a shout-out to those of you who are experts at this foreign language, which I am slowly learning. This post is also a complaint to Google for not making it possible to speak this language in the Dynamic template series, which aside from this issue is pretty darn cool.

With that said, here are two sites I have found helpful in learning HTML code. Just in case, ya know, you want to try it out too ...

http://www.quackit.com/html/
This site is great. It offers tons of code HTML code resources. One of my favorite things about this site is that it has "code generators." I know, I know ... the purists will call me lazy, but I really like that I can just specify the number of columns, rows, background color, etc. in a table and have the site churn out the whole table's code for me, which I can then copy and paste into my blog. (Here is the specific table generator link: http://www.quackit.com/html/html_table_generator.cfm.)

http://blogger-hints-and-tips.blogspot.com
There are blogs about everything. Including blogs about blogging. This is a great one if you need tips on technical things (I have found it quite useful).

IFLS Helps Make Facebook Worth the Trouble

IFLS: The Facts Founder: Elise Andrew (employed by LabX Media Group, which owns LabWrench and publishes Lab Manager Magazine and The Scientist) Description: A community built for the posting and sharing of scientific updates, quotes, cartoons, jokes and photographs. We're dedicated to bringing the amazing world of science straight to your newsfeed in an amusing and accessible way. Tell us what makes you say "wow!" Facebook Page "Likes": 1.6 million Alternate site: If our name bothers you, please see our mirror page here:  http://www.facebook.com/ ScienceIsSeriouslyAwesome Source: IFLS FB page

Like many people, I have mixed feelings about Facebook. There are definitely pros and cons associated with this social networking site.

But, like hundreds of millions of other people in the world, I have decided it's worth the trouble. I love keeping up with old friends, yes, espeically the ones who live far away and now have little kiddos I never get to see. But also in great part because of one single FB page: I f***ing Love Science, aka "IFLS." (Note: There most definitely is an expletive in that title, which I have asterisked out. Not that doing so hides it very well ... )

With so many FB pages out there, so many people posting photos and status updates, why do I care about this particular one? Because it appeals to the scientist in me. In so many ways.

IFLS posts are sometimes hilarious, sometimes poignant, sometimes thought-provoking, sometimes informational, sometimes ridiculous (or a mix thereof).

I don't pay heed to every single post from IFLS - there are quite a few every day - but I make sure to at least glance through them when I'm taking a study break and in need of a hearty laugh or some inspiration.

In this blog post, I present a few recent photos posted by IFLS. Happy viewing ...

The Kinky World of Bacterial "Sex" (and why we should care)

An image of Clostridium difficile,
a potentially deadly bacteria.

C. diff. It's a name that may not mean much to the layperson, but to any health care worker, it causes shuddering and trembling.

Just ask my mom, who is a hospice nurse. She has a patient who has been afflicted with this nasty (and sometimes deadly) bacterial infection for weeks now. It can be resistant to most antibiotics, and is also quite resistant to destruction. Killing it requires bleach; soap and water or alcohol-based hand rub don't do a thing. C. diff is also very infectious, so my mom's patient has unfortunately had to be under isolation precautions this whole time. Which for anyone would be awful, but if you are in your last days of life, being isolated from the world - and having anyone who entered your world have to gown up and wear gloves - would be terrible. (At least I think so.)

So what exactly is C. diff, and what makes it so evil (to us at least)? Here is a bit about this robust bacteria, from the Mayo Clinic's Web site:

"Clostridium difficile (klos-TRID-e-uhm dif-uh-SEEL), often called C. difficile or C. diff, is a bacterium that can cause symptoms ranging from diarrhea to life-threatening inflammation of the colon. Illness from C. difficile most commonly affects older adults in hospitals or in long term care facilities and typically occurs after use of antibiotic medications." (Source: Mayo Clinic)

Bacteria can be beautiful -
and also dangerous.

That all said, bacteria are fascinating little buggers. (Not to mention beautiful under the microscope, as you can see from the picture at left.) And they are not all bad. There are bacteria in our bodies that are quite helpful to us, in fact. Bacteria can also be highly adaptive, which makes them all the more interesting - and potentially dangerous, when it comes to certain species.

One of the major issues facing health care today is MDROs - Multi-Drug Resistant Organisms. This includes several kinds of bacteria (such as Vancomycin-Resistant Enterococci, or VRE; and Methicillin-Resistant Staphylococcus aureus, or MRSA; as well as C. diff). As you can probably tell from the names, these organisms are resistant to specific drug treatments - the antibiotics vancomycin and methicillin, respectively, in the cases of VRE and MRSA.

But let's step back for a moment. How do antibiotics work? Or rather, how are they supposed to work? Antibiotics are separated into different classes depending on how they affect bacteria. For example, antibiotics can target a bacteria's:
1. Cell wall
2. Cell membrane
3. Essential enzymes

Antibiotics, when they work, cause destruction of the bacteria via one of these targeting mechanisms. Which is how they make us well again.

As I said, though, bacteria are highly adaptive. They can undergo "evolution" - favorable DNA changes - very rapidly, enabling them to resist an antibiotic's targeting mechanism. Examples of these rapid adaptations include:

1. No longer relying on a glycoprotein cell wall
2. Enzymatic deactivation of antibiotics
3. Decreased cell wall permeability to antibiotics
4. Altered target sites of antibiotic
5. Efflux mechanisms to remove antibiotics
6. Increased mutation rate as a stress response

(Thank you, Wikipedia, for the very succinct list above.)

Anyone who has read much about evolution, though, knows that this process is usually a very slow one: favorable DNA mutations gradually accumulate over time via reproduction and the passage of these favorable mutations down to offspring.

But bacteria are a little, well, different in terms of their DNA-transferring and reproductive capabilities. And these differences are what enable them to rapidly exchange DNA mutations in an expedited manner. How does this work? Well, let me explain.

Bacteria have not one, not two, but THREE methods for sharing DNA. This is in addition to an extremely rapid method of asexual reproduction called binary fission. I will explore each of these in detail (with pictures, of course).

Enter the world of bacterial "sex" ...

1. Conjugation. (See images, and explanation, below.)

Diagram of bacterial conjugation.

Bacterial Conjugation:
An image of the sex pilus

Conjugation is the closest that bacteria get to mating (i.e., sex). What happens is that one bacterial cell, termed the "donor," produces a cellular protrusion called a sex pilus. The sex pilus attaches to the "recipient" cell, and brings the two cells together. DNA is then replicated and transferred across the cell membranes, from the donor to the recipient. (Note: the donor possesses what is called an "F factor" - this is what enables it to transfer its DNA to the recipient. This F factor can also be transmitted, allowing both cells to then be donors.) This method of gene transfer can transmit antibiotic resistance from one bacterial cell to another. 

2. Transformation. This is the process by which a bacterial cell basically absorbs DNA from the environment through its membrane, incorporates the exogenous (outside) DNA into its own, and then expresses those new genes. The new DNA can either be incorporated into the bacteria's circular chromosome, or as a separate circular piece of DNA called a "plasmid." (See the diagram below.)

Diagram of bacterial transformation.

An electron micrograph, and a diagram, of a bacteriophage.
This is called a T4 bacteriophage.

3. Transduction. This process is a bit more complicated to explain, as it involves not only bacteria, but bacteriophages (aka "phages"). Phages are little viruses that infect bacteria. (Yes, bacteria are subject to infection, too.) What happens is that these bacteriophages attach to the bacteria, inject their phage DNA, and the phage DNA takes over the cellular machinery of the bacterial cell. Rather than meet its own needs (i.e., produce bacterial proteins), the bacterial cell begins to express the phage genes, producing new bacteriophage components. These phage components are assembled, again with the help of the bacteria's cellular machinery. Eventually, the bacteria lyses (breaks open), releasing the little viruses. Those new viruses can then go infect other bacterial cells. Sometimes, a piece of bacterial DNA gets "stuck" in a baby bacteriophage. So that when that bacteriophage goes on to infect another bacterial cell, the previous (and now lysed) bacteria's DNA gets injected and incorporated into the new bacterial cell. To complicate matters, there are two different cycles of bacteriophage infection: lytic and lysogenic. In the lytic cycle, the bacterial cell is immediately destroyed (lysed) and the new baby phages are released. In the lysogenic cycle, the phage DNA is incorporated into the bacteria and remains dormant until activated by certain environmental or stress conditions. So in order for a bacterial cell to share its newly incorporated DNA (from the phage infection), it must be in the lysogenic cycle. (For a graphic explanation of transduction, see the diagram below. Note that in Step 5, this is a second bacterial cell which is being infected.)

Diagram of bacterial transduction.

E. coli cells, some of which
are undergoing binary fission.

4. Binary Fission. So let's assume a bacterial cell has gotten a piece of DNA that gives it antibiotic resistance. It could transmit that DNA via one of the mechanisms above, to one bacteria at a time. But bacteria also reproduce, albeit asexually. And they are quite efficient at it. In a very simplified explanation, a bacterial cell replicates its DNA (which is in the form of one circular chromosome), the two chromosomes move toward opposite "poles" of the cell, and then the cell splits in half, forming two new cells. These divisions are measured in "generation times," which can be quite rapid. For example, under optimal conditions, E. coli's generation time is about 17 minutes. For Staphylococcus aureus, it's about 27-30 minutes. For S. aureus, that means that in 30 minutes, you go from 1 to 2 cells. After an hour, you have 4, then 8, 16, 32, and so on. It doesn't take long, then, to develop a sizeable colony. (Source: Online Textbook of Bacteriology)

So what does this mean? In essence, once one bacteria (or a few) accumulate DNA mutations that confer antibiotic resistance, there are myriad ways - conjugation, transformation, and transduction - to spread that DNA around. And then those bacterial cells "reproduce" (asexually) via binary fission and a whole host of nasty, antibiotic-resistant bacteria results. So when someone is given an antibiotic, the bacteria that are NOT resistant will die, but those that ARE resistant will live, and continue to reproduce. Not good. (At least, not for us. Good for the bacteria, obviously!)

The misure and overuse of antibiotics contribute to this problem by helping antibiotic-resistant bacteria survive, proliferate, and then spread to other people. This is especially an issue in hospitals and other health care facilities, such as nursing homes, where people are in close contact with each other (or contaminated objects come into contact with people) and patients are often immune compromised to begin with. 

Unfortunately, many of these so-called "superbugs" are resistant to multiple drugs, and are very virulent (infectious and harmful). And while there was a time several decades ago that saw wild discovery and development of new antibiotics, that has trailed off in recent years. In part because antibiotics are not seen as the "cash cows" that other drugs may be, and in part because the low fruit of antibiotic development has been plucked, it seems.

There is now an effort (at least of some sorts) to search for new sources of antibiotics, both natural and synthetic, as well as to curtail unnecessary use of antibiotics. But the "superbugs" are here to stay. For a good while, at least. And it's all thanks to the kinky world of bacterial "sex."

Survey Says!

Picture an episode of the game show "Family Feud." The question: One hundred health care workers were asked, "Name the first feeling you have when you hear the words 'The Joint Commission.' " 

Chances are, when the show's host shouts his famous "Survey says!" line, TERROR will be the top answer on the six-item list. (Followed by fear, anxiety, dread, panic, and shock.)

The Joint Commission (http://www.jointcommission.org) is the organization that accredits most hospitals and many other health care facilities in the United States via so-called "surveys" (a nice phrase for "inspections"). Accreditation is the key to Medicare reimbursement, as well as a generally recognized standard of patient care. So organizations desperately want to comply with The Joint Commission's standards, for both financial and public relations reasons. Complying with these standards, though, can be a challenge, due to the sheer volume of requirements. The updated 2012 version of the CAMH (Comprehensive Accreditation Manual for Hospitals) is more than 750 pages long. No joke; I've got a PDF of it on my laptop. So this terror response to an impending Joint Commission survey is somewhat understandable.

But I believe in The Joint Commission, and its mission statement:

To continuously improve health care for the public, in collaboration with other stakeholders, by evaluating health care organizations and inspiring them to excel in providing safe and effective care of the highest quality and value. 

Maybe that sounds corny, and naive (given that I am not yet in the trenches of health care work). But I am currently doing freelance editing and writing for Joint Commission Resources, the publishing arm of The Joint Commission. And the materials I have been exposed to have convinced me that overall, The Joint Commission isn't out to punish people, it's out to protect patients, and ensure the best possible care for them. And isn't that what physicians, nurses, and other health care professions should strive for as well?

I am both a journalist and a scientist, and out of service to both of these roles, I will provide evidence to support my claim. Others may or may not agree with me, but I hope that this post will at least provoke some thought, and perhaps some discussion.

First of all, most of The Joint Commission standards I have seen - while complex and extensive - make sense and have a purpose. For example, organizations are required to have a formal, written "Emergency Operations Plan" (EOP) that takes what is called an "all-hazards" approach to emergencies. Basically, what this means is that a hospital (or other facility) has to be prepared for whatever may happen, along with having specific steps and procedures in place for dealing with certain types of more likely situations such as fires. The EM (Emergency Management) standards and related EPs (Elements of Performance, which are basically broken out objectives) literally comprise 20 pages of the CAMH. There are standards related to evacuation, utilities management, licensing of independent practitioners in event of a disaster, and many other scenarios and issues. That's a lot to keep track of, obviously. But think of it this way - if you were a patient, or had an ill family member in the hospital, wouldn't you want a hospital to have such a plan in place and ready to initiate at a moment's notice? Without such a plan, an emergency or disaster would cause absolute mayhem. Of this I am completely convinced. 

One of the things I have enjoyed most (and also benefited from) with regard to my freelance work for Joint Commission Resources is reading case studies related to implementation of certain standards. For example, one of the case studies I read involved a small community hospital that faced a major hurricane. The hospital lost power, and risked losing generator capability as well, so was forced to evacuate all of its patients to surrounding facilities. Without electricity, though, such an endeavor is a feat. Consider that the hospital was several stories tall, and the elevators were out of service. So non-ambulatory patients had to be carried down the stairs on gurneys. Remember also that without electricity, photocopy machines were not working. Which meant it was impossible to copy patients' charts prior to their transfer elsewhere. The solution to this problem was that hospital staff accompanied patients to the transfer locations, copied the charts there, and brought the original charts back to the community hospital (because both locations needed the patients' records). While the case study (and the hospital administrators) acknowledged room for improvement, and a few hiccups in the process, for the most part this complicated evacuation went pretty smoothly. And that was because the hospital had a detailed EOP. 

Second, The Joint Commission genuinely (in my opinion) tries to provide resources to help hospitals better comply with all of these standards (via Joint Commission Resources publications). Many of these resources are articles and books that specifically address complex standards. Some of them are best-practice examples from organizations that have gone above and beyond in developing a particular policy, procedural checklist, etc. I have been working with Joint Commission Resources to secure permissions for some of these best-practice examples, and have seen how Joint Commission standards can inspire organizations to improve their own workflow, procedures, and policies with the ultimate goal of providing improved patient care. 

Third, I have been inspired. I know I'm not even in medical school yet, much less a practicing physician facing a Joint Commission survey. But some of the case studies, and responses to Joint Commission standards, have given me ideas on how to better provide patient care in my capacity as a Spanish medical translator, as well as ideas for patient care practices in my future as a doctor. For example, one case study I read referenced the development and use of something called a "Patient Care Notebook." This was in response to miscommunications and accidental gaps in care, especially after a patient was discharged from the hospital and went into the outpatient setting (or vice versa). The Patient Care Notebook is just that - a notebook (rather, a three-ring binder) with dividers for different types of information, medication logs, doctor's visit logs, space for patients to write down their own questions (and the practitioners' answers), important contact information, discharge papers, care plans, etc. This helped organize a patient's medical information in one place, and provided a tool for both the patient and his or her practitioners. It was something the patient could bring to every visit, hospital stay, etc., and add (or remove) information (medications, etc.) as time went on. 

As I came across this, I thought to myself, "How brilliant!" I immediately e-mailed the community outreach coordinator at the clinic where I volunteer, to see whether she might be interested in incorporating this tool into the patient health literacy initiative she is working on (and I am helping with). I also realized that this type of tool is something I could develop and customize for my own patients in the future, as it is not readily commercially available. (Which does not make sense to me at all, given how beneficial it has the potential to be.)

So if I were one of the health care survey respondents, and was asked that question I posed at the beginning of this post, my answer would be different: "Gratitude."

Long-Overdue Update

Well, it seems it's been 2 months since I last posted. How time flies, doesn't it? But I've been keeping myself out of trouble, I promise. Here is a bit about what I've been up to ...

I wrote in a previous post that I had a tentative part-time job at the University of Illinois-Chicago Anesthesiology lab where I worked as an unpaid assistant for two summers (2010 and 2011). I started that job (paid this time!) back in mid-August. Working there, being paid to do what I do, and having so many more responsibilities than I ever did before, I feel just a little bit more like a "scientist." If that makes sense. I'll see if I can explain.

When I was a summer lab assistant at UIC, I worked with a wonderful post-doc named Olga who has become something of a mentor to me. She still works in the same department, and her lab room is actually next to mine now. When I have a question about something, I usually go ask Olga. Not only will she help me (or help me figure out where to find the answer to my question, if she doesn't know), but she does so happily and willingly. Not everyone is like that. Olga taught me to pipette, to set up PCR, to run gels, to culture cells. It was while I worked with her that I discovered my love of bench science and research.

With the wonderful background Olga provided me, as well as what I learned in my post-bac coursework and research at Dominican, I felt I was ready for a position with more responsibility and autonomy. Well, I got it! While there was a bit of a rough start, things are going quite well now. And in that rough start, I learned a great deal about the scientific process, and my aptitude for it.

I was hired at UIC to genotype mice. My department is trying to breed double knockouts (DKOs, for short) of several genes in order to study these genes' combinatorial roles in lung diseases. Genotyping mice, at least the way we are doing it, involves (in part) two techniques that are quite familiar to me: PCR and gel electrophoresis. I did both of these with Olga, as well as in my Research Methods course at Dominican. But genotyping involves many more steps as well, steps which were new to me. In addition, while I had done both PCR and gels, I had never done them completely from start to finish. By that, I mean from ordering primers to taking the gel photo in the dark room. I had done the middle part - the actual PCR and the gel - but not the initial and final steps. So I definitely had a lot to learn when I started this new position.

So here is the basic outline of the genotyping process:

1. Cut small pieces (about 0.5 cm) of mice tails
2. Digest mice tails to extract DNA
3. Run two rounds of competitive PCR (one for each gene) to amplify the DNA
4. Run a gel to determine whether each mouse is a wild type, knockout, or heterozygote for each gene
5. Analyze results, and hopefully set up new breeding pairs if you get any DKOs

Steps 1 and 2 were brand new to me. But I am proud to say that I am now a mouse anesthesiologist and surgeon! On one of my first days at the lab, my supervisor took me down to the animal facility and taught me how to anesthetize the mice, tag their ears, and snip of a bit of tail into an eppendorf tube (being careful to wipe with ETOH in between each mouse to avoid DNA contamination).

One of my gels, from last week. Pardon
the over-exposure and the line of dNTPs
at the bottom. I'm still working out the
kinks with my primer concentrations
and still getting the hang of working
the darkroom camera ... it's a work in
progress, but I'm getting there!

The tail digestion step was a bit of a debacle to begin with. I started out with a complex and time-intensive protocol that was handed down to me by another post-doc at the lab. It involved using proteinase K and several other reagents, heating the tail tubes in a 55°C water bath for four hours, and then inactivating the proteinase at 95°C for 10 minutes. When you counted prep time (thawing reagents, pipetting, labeling tubes, etc.), the whole process lasted somewhere between five and six hours. And I was getting very inconsistent results. But honestly, I wasn't sure whether it was the tail digestion or the PCR that was the problem. For example, my primers could have been bad, or I could have been over- (or under-) digesting the tails. I literally worked with this protocol for a month, to no avail. Then my supervisor suggested I go talk to the woman, Debbie, who runs the Molecular Core, where the PCR machines are. I asked her how long she incubated her tails for.

"Oh, I use a kit," she said, nonchalantly. "Why, what are you doing?" After I gave a brief outline of my method, her co-worker literally busted out laughing and said, "Wow, you're really doing it old school!"

This "kit" is a miracle: while my protocol was taking five to six hours, the kit takes 30 to 45 minutes. And, as if that weren't enough, the kit comes with a pre-made PCR master mix that contains a Taq JumpStart antibody which prevents the Taq from activating at room temperature ... meaning you can set up PCR on the lab bench rather than on ice! It's absolutely amazing.

Debbie let me borrow her kit to try it out, and it worked beautifully. My results are now consistent, and I even determined last week that we indeed did have several DKO mice - three males and one female.

While it's obviously exciting to get results, what's also exciting to me is the process of science. I faced frustration, and I didn't give up - I worked on figuring out what was going wrong. Also, one of the things that always amazed me about Olga (when I worked with her those first two summers) was that she always had several experiments running simultaneously, and somehow the timing all worked out. I am learning how to do that as well - how to time my agarose melting, reagent thawing, and PCR and gel running (along with meticulous notebook note-taking) so that I get the most out of my time there.

I work at the UIC lab three days a week. This past Thursday I was working from home on freelance writing. When I woke up that morning, I felt a little sad, and thought to myself, "I wish I were going to the lab today."

I think that's a good sign.