Friday, December 26, 2014

Look What I Found! - Smallpox and Friends Edition

I don't want to spend a lot of time on this post because most everything that can, has been said about the situation. However, there is a particular point that I really want to make and some venting that I feel like doing.

On 01 July 2014, the National Institutes of Health (NIH) notified the Division of Select Agents and Toxins (DSAT) and the Center for Disease Control and Prevention (CDC) (When are they going to change their name to the CDCP? Branding nightmare.) that employees discovered vials labeled "variola" in an unused portion of a storage room (how can part of a storage room be unused? I get what they are trying to say, but calling the place where they found smallpox "unused" sort of undercuts the fact that THERE WAS SMALLPOX IN THE ROOM!) at the FDA lab on the NIH campus which was opened in 1972. The vials appear to date from the 1950's.

This here is my main point. How the hell did this happen?!? I can't f'ing stand dirty, unorganized lab space. Most of this is my personality, but part of it is training. The first lab that I worked in was at Aldevron, a biotechnology start up in Fargo, ND. They had just moved into a warehouse at the time so they were still in the process of setting up lab space and organizing. Then I worked in some labs on campus at NDSU, mostly new faculty which again were clean and organized. Fast forward to my PhD again with a new faculty member in a new lab space.
Point being, most of the time I was a large part of the initial setup and organization, and there wasn't a lot of old junk to worry about throwing out, organizing, or worrying about.

Then I worked at a public health lab and it was a completely different story. They kept everything; it was a science hoarders dream. A single drawer in some cases could outfit a science museum. And it was there I understood. People save stuff, all the time. I was zero surprised when they found smallpox, and I will be zero surprised in 20 years when they find polio, or rinderpest, or whatever other eradicated disease is out there. Dirty little secret is that scientists are not clean and organized. Maybe their data, maybe their desk, but certainly not the lab. Very few of them clean the lab space, and keep it organized and most of it is rationalized as a time issue, or "this is taxpayer money so we can't throw it out".

Human nature is definitely something to consider when discussing the "should we destroy the remaining vials or not" topic. Not only is there the potential for it to be used as a weapon (which I think is extremely small) but there is the more likely chance that someone wasn't careful and has it stashed somewhere forgotten. I personally don't think we should destroy the stocks until we can reliably reproduce the virus from DNA sequence, but even if the decision to destroy the last remaining stocks occurs, it probably won't be "the last remaining stocks".
The other thing I find fascinating is the idea that an invasion of another country was justified by selling the idea Iraq had weapons of mass destruction. My guess is 99% of all the other countries in the world have less bioweapons than what has been lost in storage rooms at the NIH and other labs around the country.

Another amazing aspect of this whole ordeal, is the discovery of multiple other substances including ricin, yersinia pestis, staphylococcal enterotoxin, burkholderia pseudomallei, and francessella tuleremia. As if smallpox wasn't bad enough. Ugh. I hate the idea that people can't even be held responsible for knowing what is in their lab. It's YOUR lab. You work with smallpox, etc. how do you not know exactly what is in the lab, and where? It isn't that hard people. But clearly it is.

Last but not least was the string of tweets that occurred once the story broke. I won't go into them here, but I would highly recommend visiting the link.
  • I have a PhD in microbiology and immunology and I am a clinical/public health laboratorian.
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Post Doc Happy Thoughts

Recently, a manuscript was published in the journal Stress and Health. The primary finding of the study suggested that post docs who experience high levels of positive emotions are less likely to suffer from stress-associated anxiety or depression than other post docs. This was according to a recent study of 200 University of Texas (UT) Austin postdoctoral fellows, 79% of whom work in the sciences.

That's right. You heard it here first post docs; think happy thoughts and everything will be A-Okay!

One apparent link between positive thoughts and reduced anxiety and depression is resilience. More positive emotion was correlated with high resilience, which in turn was linked to less anxiety and depression.

Personally, I fall into the Viktor Frankl - Man's Search for Meaning side of things. I have always sort of approached things as a "hope for the best, plan for the worst".

Another blog post I stumbled upon this week mentions a similar finding.

I have a thought. You know what would help lower post doc stress levels? Money. Stability. Upward mobility. 

Ask any post doc out there and I guarantee in five minutes you will have a long list of problems that need fixing. I think a lot of people in science know there is a problem and probably have a few ideas to fix it. Action is slow, I get it. However, I am extremely tired of the lack of progress, and more so the "apologists". Usually they are long-tenured professors that "when they were post docs got a paper in Nature, their first RO1, and their first job all by the time they were 30".

Here's to hoping for the best, but planning for the worst.
  • I have a PhD in microbiology and immunology and I am a clinical/public health laboratorian.
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Saturday, November 1, 2014

Chagas in Virginia and Texas; and Using Dogs as Sentinels for Parasite Spread

Chagas disease or American Trypanosomiasis is a disease that makes me cringe. Not only because of the high potential it increases its endemic range in the next 20 years, but because of the vector that trasmits it.

Health officials in Texas are becoming concerned about the rise of a "new to the region" blood sucking insect with a deadly bite known as the "kissing bug". Trust me, they are gross. Also, trust me that you don't want to know how big they are, or why they are called the kissing bug.

Kissing/Triatomid Bug - They come in at night and bite you in the face (kissing). The parasite is spread through their feces, so once they bite you, the rub their abdomen on you and the parasite enters the wound. Gross right?
The kissing bug or triatomid bug carries a potentially deadly parasite that can cause Chagas disease. The bugs originiated in Central and South America as well as Mexico. There are growing numbers of reports about cases being discovered in the United States, especially Virginia and Texas.

Virginia seems like a strange place for Chagas to pop up, but Northern Virginia has a large number of Bolivian immigrants currently living there, and continuing to immigrate there. Texas on the other hand makes perfect sense based on geography, and researchers at Texas A and M have apparently discovered the vector in Dallas, TX.

If you have questions, please use the comments section below!

A person infected with Chagas can live for many years without showing any signs. Similiar to HIV or Hepatitis infections, Chagas can be"latent" for many years. Approximately 30% of patients will suffer from cardiac disorders, and roughly 10% will suffer from digestive tract issues. In later years, the infection can lead to sudden death or heart failure which is caused by progressive destruction of cardiac muscle.

Screening in the blood supply began in 2007 and physicans began paying more attention after the increases in incidence and prevalance in the U.S. It is estimated that Chagas affects 8 million people across Mexico, Central and South America. In the United States infection estimates range from 300,000 to 1 million.

Recently, an interesting dispatch came out in Emerging Infectious Diseases from a group at Texas A and M; "Shelter Dogs as Sentinels for Tyrpanosoma cruzi Transmission across Texas"and it raised some interesting points:

  1. Enzoonotic cycles involving infected wildlife reservoirs and domestic dogs occur in the southern United States. Beyond the vector transmission via bite from the kissing bug, the parasite can also be spread via consumption of infected bugs or contaminated food products, blood transfusions, and "congenitally".
  2. Dogs manifest similar symptoms to humans.
  3. No vaccine avvailable for humans or dogs
  4. Texas is a high-risk state for transmission of T. cruzi to dogs
The study established a network of seven canine shelters across Texas and collected blood samples from roughly 30 dogs at each shelter. Detection of T. cruzi was done by Chagas STAT-PAK (link). A total of 205 blood samples were collected and 18 (8.8%) were seropositive for T. cruzi antibodies. Seroprevelence ranged from 6.7% to 13.8%. The authors went on to explain that based on some testing anomalies, this is most likely a conservative (low) estimation.

Thursday, October 30, 2014

Lab Acquired Salmonella

An interesting bit of lab saftey news came out awhile back that I think hasn't gotten quite enough attention.
Since November 2013, 41 people in 13 states have been sickened by a Salmonella typhimurium outbreak (enterica serotype).

Salmonella typhimurium (pink)
The Salmonella was linked to clinical and university teaching laboratories according to the CDC investigation.
Cases have been reported in Illinois, Indiana, Kentucky, Maine, Massachusetts, Missouri, New Hampshire, New Jersey, Ohio, Pennsylvania, Virginia, Washington, and Wisconsin. The CDC investigation (probably performed mostly by the PulseNet group) revealed via laboratory testing (pulsed-field gel electrophoresis) sequence from commercially available S. typhimurium strains used in laboratory settings for teaching or quality control purposes. Basically, the S. typhimurium strain infecting people and making them ill was identified by PFGE (seperating DNA in a gel matrix based on a changing electric field), and it was similar to the S. typhimurium that could be acquired commercially.

The S. typhimurium strains are known to be present in several teaching laboratories that were associated with ill people. Epidemiological information gathered showed that 18 of the 21 people infected (86%) were enrolled in either a human biology or microbiology course. 15 of those 18 ill persons were students, and three (22%) were employees.
This is not the first outbreak linked to a college laboratory class, in 2011 a total of 109 illnesses were linked to clinical and microbiology teaching laboratories.
These outbreaks of Salmonella and other lab-associated organisms bring up important points about lab safety in teaching labs.
  • Some of the bacteria you work with can make you and others near you sick. Most of the time, lab-bacterial strains are weak and non pathogenic. However, it is possible that they can still cause illness.
  • It is possible to spread bacteria via contaminated lab coats, pens, keys, phones, mp3 players, notebooks, and other items that go in and out of the laboratory. Avoid taking things in and out of the lab.
  • People who work with infectious agents should be careful to handle samples properly and to wash hands appropriately, especially before you prepare any food, baby bottles, before eating, or contacting young children.
  • Non-pathogenic or attenuated bacterial strains should be used when possible in teaching laboratories.
This is what a microbiology teaching lab looks like.
I am guilty of breaking on some occasion most of these rules. I wear an ipod most days (albeit inside my lab coat). I have definitely eaten and drank in the lab, etc. The main thing to consider is handwashing, and proper handling of organisms. And if you are unsure, it is always better to be safe than sorry. 

Sunday, October 19, 2014

Post #7 Ebola, Career Ambition, and Coming Up Short - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

With all the discussion about the Ebola outbreak that is going on in Africa, I can't help but think about my brushes with Ebola research. Ideally, I would have had more than "brushes" with Ebola by now, however I haven't been able to get a position (postdoc, fellowship, or other) where BSL-4 work is required.

When I was in college, Joseph McCormick and Susan Fisher-Hoch came to my undergraduate school (North Dakota State University) to give a talk and to promote their book "Level 4: Virus Hunters of the CDC". It was a wonderful opportunity to talk with them about their careers. I was always enthralled with the idea of working in BSL-4 conditions, ideally in the field. So I took advantage of a willing group of faculty who let me sit with them for when they talked with the guests (I was the only student). I don't remember specifics, but it had an effect. Plus, I got a signed copy of their book out of the deal!

If you have questions, please use the comments section below!

The options at my undergrad didn't exist for BSL-4 research, nor did it happen during my MS. I applied to UTMB-Galveston for my PhD, but didn't get accepted. I applied and interviewed for a post doc at Texas Biomedical Research Institute (TBRI) in an Ebola lab. Didn't get it (the lab hired someone with previous BSL-4 experience). I applied and interviewed for a fellowship at USAMRIID in an Ebola lab. Didn't get it (got really good, better than expected reviews on my grant application, but DTRA didn't fund it, no go.) I applied for the CDC EIS program three years in a row. Never got an interview. I am certainly not done applying.

Below are two links. The first is for the grant I wrote, "Generation of a Gold Nanorod Vaccine against Ebolavirus and Marburgvirus". The second link is to the reviewer's comments.

1. Generation of a Gold Nanorod Vaccine against Ebolavirus and Marburgvirus
2. Reviewer's comments

I am more than likely not done applying to BSL-4 positions. At this point, I have a pretty diverse resume, and I have found I am happy doing a variety of jobs. Therefore, it may not happen. I am not going to focus only on BSL-4 jobs just because they are too few and geographically sparse. However, if the right opportunity presents itself, I would be all over it.

Good luck to everyone in the field working on the Ebola outbreak. It is a dream of mine.

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
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  • INSPIRE Excelencia!

    I know sometimes I come off a bit negative about things, especially as it relates to my PhD experience. However, it wasn't all bad and recently I was reminded of one of the better experiences.

    A few weeks back the INfluence Student Potential and Increase Representation in Education (INSPIRE) program at Rosalind Franklin University of Medicine and Science (RFUMS) received national recognition as a pathway for Latino students interested in graduate education and possible careers in the health and biomedical sciences.

    INSPIRE was one of the 14 finalists from a pool of 217 competitors for the 2014 Examples of Excelencia award. The award recognizes programs from across the nation that increase academic opportunities and achievement for Latino students.

    I would never want to oversell, but I would like to think I had a fairly major hand in developing the INSPIRE program. Along with Dr. Rasgado-Flores and Christina Lopez (who were the brains behind the organization, and who recruited me to help) we developed the program, and set about recruiting faculty, and graduate students to participate. We then set about spreading the word to local high schools and began interviewing students. We also did some fundraising, community outreach, etc. It was a great experience and I was proud to be the GSEO (graduate student executive officer - yes i just made that title up).

    INSPIRE was designed as an eight-week mentoring and research program which provides an opportunity for hands-on biomedical research. A mentoring/tutoring aspect is provided as well. Lunch-philosophy sessions with mentors, course-work review, college and career planning, etc. are all part of the INSPIRE program.

    We want to increase the number of qualified students from underrepresented populations who complete advanced-degree health programs and serve their community as practicing health professionals,” said Hector Rasgado-Flores, PhD, faculty advisor and RFUMS associate professor of physiology. “INSPIRE is about removing barriers to higher education.” (Side note: Dr. Rasgado-Flores is an inspiration himself. An incredibly charismatic and gifted speaker, he is always a student favorite lecturer. He is also a gifted pianist and composer)

    According to the U.S. Department of Education, just four percent of Latinos attain a master’s or higher degree. FOUR PERCENT! This video is a presentation that Dr. Rasgado-Flores has given. In it are some amazing statistics higher education and the Latino population.

    And now the victory lap!

    As one of this year’s finalists, Rosalind Franklin University of Medicine and Science is at the forefront of meeting the challenge of improving higher educational achievement for Latino students,” said Sarita Brown, president of Excelencia in Education. “No longer should policymakers and institutional leaders ask how to improve college success for Latinos — we have the largest accumulation of proven examples and tested strategies that show them how. Today’s question is do leaders have the will to put these practices into action?”

    Thank you Excelencia in Education for the recognition. Thank you Dr. Rasgado-Flores and Ms. Lopez for the opportunity to help out. Good luck in the future!


    Check out the new YouTube Video!

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
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  • Sunday, September 28, 2014

    When Scientists Give Up (On Academic Science)

    A couple of recent articles published by NPR and Nature really hit home with me as well as with friends of mine.

    The NPR article titled "When Scientists Give Up", I thought was a great piece. I know titles are tough, and I am certainly not without fault, but I thought it was a bit ridiculous (which is why I changed it to the title above).

    In my opinion, "giving up" on research science (especially, but not limited to academic science) at this point in time is probably the smart move. The quotes by Glomski are meaningful, "You actually have to be much more conservative these days than you used to...and being that conservative I think ultimately hurts the scientific enterprise." "Society is losing out on the cutting-edge research that really is what pushes science forward." Eventually, this having to be conservative, and his more aggressive research not getting funded, drove him out of science at the age of 41 and he is planning on starting a distillery.

    The Kenny Rogers song "The Gambler" comes to mind. "You've got to know when to hold them, no when to fold them, know when to walk away, and know when to run." In the case of academic science careers, I would recommend running.

    If you have questions, please use the comments section below!

    Personally, there were numerous times during my PhD that I thought about running. At one point I was considering quitting and moving back home, taking a few college courses and becoming a high school or community college science teacher (I already had a MS at that point). I considered becoming a brewer (I think a lot of people have this "dream" now days). I considered getting more involved in community/charity work at places like this, where I already volunteered.

    The problem in my mind with all this nonsense is that overall in the very long run the effect of numerous smart, motivated people scattering to the wind in an ivory tower diaspora should be positive. More science educators with more science education, more science people in brewing, distilling, art, film, business, etc. In the short term though, it is difficult, painful, and depressing to the people going through it.

    The flip side of the NPR story is Randen Patterson, who once worked at a prestigious neuroscience lab before getting a tenure-track assistant professorship at Penn State University and then UC-Davis. Patterson is the more frightening of the two stories. A prodigy that dedicated himself to only the hardest and most cutting edge questions, he had the pedigree, the brain, the drive and never could secure funding as his research was deemed "too risky". He left to own/operate a small grocery store.

    The NPR article suggests that there are no national statistics about how many people are giving up on academic science, but an NPR analysis of NIH data found that 3,400 scientists lost their sustaining grants between 2012 and 2013. I have mentioned this on the blog before, but I hate the idea that there is no measurables here.

    At Rosalind Franklin University of Medicine and Science, where I received my PhD, they claimed that they were successfully training PhDs and Postdocs, had a great track record of training, etc. They didn't even have an alumni association! They didn't adequately keep track of their alumni, so how on earth could you claim that you were successful in their training?!?Every single one of them could have dropped out of academic science and the University wouldn't have known. PhD mills are real, and they are a problem.

    The second article, published in Nature is an interesting spin on the concept of quitting academic science as well. It discusses researchers that got away, with the bend that it is not always the weakest that gets culled from the herd, but often it is the best that leaves the herd to find a better life.

    The article cites a study of doctorate recipients conducted by the US National Science Foundation, nearly one-fifth of employed people with science and engineering PhDs were no longer working in science in 2010. Partially, this is due to lack of room at the top, but also things like money, family, or other opportunities for freedom, and self-fulfillment exist outside of science.

    I left academic science research. I have taught, and worked in a public health/clinical setting, and I don't think I ever want to go back to an academic research setting. If I do go back to research, a government setting (NIH, USAMRIID, etc.) or industry setting would be preferred. The last thing I want, is to be locked into the ivory London tower of academic science.

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
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  • HCV in Minot

    The North Dakota Department of Health has been dealing with an outbreak of  hepatitis C virus (HCV) in Minot, North Dakota. The outbreak was first noticed at a local nursing home, and all but two cases are related to ManorCare. Most recently, two cases have been identified outside of ManorCare at Somerset Court. Thus far, the total case number is at 47, 45 at ManorCare and two at Somerset Court. Since the investigation began last August 2013, the Health Department has tested at least 500 people for exposure to the virus.

    The ND Department of Health has stated that the HCV isolated from infected persons is genetically related and epidemiologically linked to the nursing home. The data coming from the investigation is minimal at this point, and I haven't seen anything reported on what they think the source is.

    If you have questions, please use the comments section below!

    HCV is typically transmitted by blood contact via transfusion or shared needle/sharps exposure. There have been past cases of HCV or HBV, hospital-acquired infections (iatrogenic) relating to glucose point of care testing, dialysis centers, or medication contamination by drug-abusing health care workers.

    I will definitely be watching this outbreak closely. Hopefully a source can be determined.

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
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  • Friday, September 12, 2014

    Kitteh Rabies in North Dakota

    A kitten purchased from Amy's Pet Parade pet store in Minot, North Dakota tested positive for rabies last Friday (05 September 2014).
    Giles - Kitteh Model
    This has the potential to get really ugly. There were six kittens in the litter that were anonymously dropped off at the pet store 29 August 2014. Amy's Pet parade put the kittens on display the same day and the last kitten was sold this week.
    The number of people potentially exposed is very high. All six kittens were exposed (assuming the infection and initial exposure happened before they were dropped off at the store). If they were on display, numerous people probably handled them, including store workers. They were sold, which means that multiple families were potentially exposed, the list goes on and on.

    If you have questions, use the comments section below!

    The North Dakota Health Department is asking anyone who may have been exposed to saliva from the kittens by being bitten, licked, or scratched to contact the department's after-hours number at 701-220-0819.

    Rabies was a recent topic of discussion, as my father-in-law was visiting this week (he was a veterinarian in ND for 30+ years). We were discussing his "worst" case which was very similar to this one, only it was puppies. Apparently a puppy in a litter had been exposed and eventually developed rabies and died, all the other puppies had been sold or given away, there was a miscommunicaiton with the lab, and eventually it ended in some lawsuits and many people having to get vaccinated or tested.

    Rabies is a very nasty virus. 100% fatal in humans (I think there have been a handful of survivors, four due to the Milwaukee, or Modified Milwaukee Protocol). Luckily, in the United States, there are very few human fatalities due to great prevention and vaccination efforts. In countries like India however, roughly 20,000 people die of rabies yearly (world wide total is 50-60k yearly).

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
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  • Thursday, September 11, 2014

    Department of Health Fulton County Georgia

    I wanted to quickly post two photos from the Department of Health and Wellness in Fulton County, Georgia. Two gorgeous pieces of art on the building. Nothing to say with this post besides how cool I think they look.

    • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
    • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
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    Post #6 Control Your Image (Social vs. Reality) - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

    You had one job!
    I am not a big "image" guy. I wasn't someone who cared too much about my appearance (I can rock a flannel shirt with the best of them). I certainly didn't care much what people thought. Okay, not entirely true. I cared what people thought, I worked very hard to please people and to make them think I was a hard worker, trustworthy, etc. Basically I tried my best to be a great person and I wanted people to see that. What I should clarify, is that I was horrible at self-promotion. Probably like most people, especially true for most graduate students who work in the life sciences, or any science for that matter. 

    I will paraphrase a Jack White quote; I don't necessarily feel like you deserve to know shit about me. I am a private person. That lack of presence makes it easy for people to fill in the blanks however they want.
    Jack White's Recording Studio - Very cool.
    The Microbiology Department at Rosalind Franklin University of Medicine and Science was extremely homogeneous. The other issue was, the tenured faculty that were there had zero cache. They weren't remotely up to date on research, or life outside of their four-walled office. 

    A student such as myself, who liked to get involved with organizations, who liked to be social, who liked to be athletic and be involved with intramural sports was constantly looked down upon because I was "distracted". No way could I possibly be a good student, or a good researcher if I was spending time on these other "foolish pursuits". I completely understand that there is a line. I do know some students who spent way too much time outside the lab, or when they were in the lab, they were using it as a home office. I know a lot of graduate students (and faculty) that are poor at time management and have terrible organizational skills. I am by no means perfect. But if I can be in the lab 8+ hours every day (and weekends), publish multiple first author and middle author papers, mentor numerous summer students, go the the gym, play intramural football, etc. all while being a good researcher, then what is the problem? 

    Haters gonna hate.

    This led to inevitable problems. To this day (two-plus years after finishing my PhD) when people ask me "how's it going" I still have to fight the urge to put my head down and respond with a brusque "busy".

    This concept is currently somewhat of a cultural phenomenon. Numerous articles or opinion pieces on the work-ethic/culture in this country have suggested that a "cult of busy" exists, and is unhealthy.
    1. New York Times Opinion Piece - The Busy Trap
    2. Lifehacker - How to Escape the Cult of Busy
    3. Worksmart - Why You Need to stop Bragging About How Busy You Are
    The culture of busy was instilled in us students at RFUMS in the Microbiology department. There wasn't supposed to be breaks, vacations, or weekends. There also wasn't supposed to be lives, hobbies, significant others, etc. 

    I have quoted the line before, but our Department Chair told us graduate students (four males) at the start of our second year "Keep your balls in the freezer, graduate school is no time for relationships." 

    This was the culture of busy that was instilled in us. It always bothered me. I couldn't help but think of the great stories about great moments in science that were thought up on a night at the pub, or when Kary Mullis thought up PCR when driving down the California coastline one night. 
    If you have questions, use the comments section below!
    Numerous people talk about how they have their best ideas in the shower, or when they are gardening etc. Scientists need to relax, it isn't healthy to constantly work or to be constantly, actively thinking about their product. You need to reset, refocus, find your zen, whatever you want to call it sometimes things click into place when you aren't so focused.

    This is where the image control comes in. How do you do these things, when your "higher-ups" don't condone them?

    I don't know. That is the best answer I have. I hid. I blended in. I blocked or hid everyone on social media. I went silent. I didn't give them anything. That strategy didn't work, and it goes back to the Jack White quote. People filled in whatever they thought since I wasn't giving them any information.
    I think what can work is; 1. Not going into a lab or department where this is an issue. 2. If you must, or already are in the situation, get out in front of it. 
    1. Brag about how much you love the lab, your project, your lab mates, everything. Positive spin as much as possible.
    2. Bring up your project or science anytime you are in a conversation.
    3. Talk about how much you love science.
    4. Be a nerd about everything, about the school, about the department, about your project, etc.
    5. Drink the Kool-Aid, or at least pretend as best you can.
    6. Give people something to hang onto, but not too much. For example, when people ask what you do outside the lab, have some hobby that is respectable or understandable. I played sports, had friends and went to bars and concerts, etc. My adviser and department chair were of a different cultural background and had no understanding of my behavior. Initially, I should have told them I like to run, or garden, or photography, or play piano. That's it. Keep it simple, keep it limited to something they can respect, but maybe don't themselves do. 
    7. Don't discuss how much fun you have with your friends or family. Don't discuss how much you drank last weekend, or how you watched football all day. Don't say that you went to a baseball game, or spent the day at the beach. People will resent you, as I said above; haters gonna hate. You can flaunt it all you want, but in most situations, be prepared for the consequences. Department chairs who say things like "You are lucky I am giving you time off to go home for a funeral" or the "balls in the freezer" quote, aren't playing. Don't tempt them by showing them your amazing day at the beach. They hate joy, fun, and all things good and they are out to crush your soul. (Slight exaggeration...maybe.)
    Gus Presser - Livin'
    Above is a picture of an alternative mindst. You can just say "screw it" and do your thing, justify it by saying "those people don't know me, they don't control me, as long as I am getting my work done, they can't punish me, etc." Sometimes they do though. I have seen a lot of PhD students not finish, for various reasons, but some of them were precisely because they didn't understand that if they upset the wrong person, they would lose.

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
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  • Thursday, August 28, 2014

    Carbapenem-Resistant Enterobacter cloacae Isolates Producing KPC-3 in North Dakota, USA.

    A recent letter in the Emerging Infectious Diseases journal discussed the emerging threat of Carbapenem-Resistant Enterobacter cloacae (CRE) in the "far-flung" land of North Dakota (ND).

    CRE infections are usually mediated by acquisition of Klebsiella pneumoniae carbapenemase (KPC) expressed by Klebsiella spp.

    Klebsiella pneumoniae on a MacConkey Agar Plate
    After reporting of CRE infections became mandatory in ND in 2011, 20 CRE cases were noted in 12 of 53 counties. Most cases occurred in Cass County, where ND's largest city (Fargo) is located.

    Sanford Health is a 538-bed, acute-care facility that represents roughly 70% of acute-care beds in Fargo. Sanford Health is currently in the process of attempting to bring a quality healthcare product to rural areas of ND, SD and MN. Sanford has been slowly working its way west, buying out healthcare facilities and attempting to revamp healthcare in rural areas.

    According to the letter, during the period between December 2011 and December 2012, all isolates of Enterobacteriacea (a large family of Gram-negative bacteria that include normal gut microbiota, pathogens, and normal gut microbiota that can become pathogens in certain circumstances) with reduced susceptibility to ertapenem (MIC > 1 ug/mL) identified at the hospital's clinical microbiology laboratory were screened for carbapenemase production using the modified Hodge tests (mHT)

    Ertapenem is a carbapenem antibiotic (broad-spectrum beta-lactam) marketed by Merck as Invanz. Ertapenem has been designed to be effective against both Gram-negative and Gram-positive bacteria. It is not active against Methycillin-resistant Staphylococcus aureus (MRSA), ampicillin-resistant enterococci, Pseudomonas aeruginosa, or Acinetobacter species.

    If you have questions, use the comments section below!

    Identification and sensitivity testing were done with the MicroScan system and MICs of carbapenems were done with Etest.

    MicroScan System

    Etest - Biomerieux

    The 20 patients from whom KPC-producing CRE isolates were obtained had been hospitalized at Sanford Health during the three months before CRE isolation; of the 20, 13 were admitted to intensive care. 13 was also the number of patients that had been admitted to the long-term care facility during the year before CRE isolation. Co-colonization with multi-drug resistant bacteria was documented in 16 patients, including extended-spectrum beta-lactamase producing and carbapenem-resistant organisms in four and two patients respectively. Seven of the documented patients died with three of those deaths being attributed to the CRE infection.

    If you have questions, use the comments section below!

    The authors end with...

    "This outbreak of KPC-producing E. cloacae infections in a health care system in North Dakota highlights the infection control challenges of long-term care facilities and the potential role they play in CRE dissemination."

    CRE's have been identified in almost every state in the U.S. and with rising rates, figure to be an important factor for every infectious disease practitioner.

    • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
    • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
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    Saturday, August 9, 2014

    New Smallpox Relative Discovered in Georgia (the country).

    Smallpox Virus - False colored to demonstrate structure
    Smallpox. It has been in the news a lot lately due to the recent discovery of viable virus tucked away in storage at a government facility in Maryland.

    Smallpox killed an estimated 300 to 500 million people in the 1900's until it was eradicated in the late 1970's by an aggressive worldwide vaccination campaign.

    Smallpox relatives are also particularly virulent. Other members of the orthopoxvirus family include cowpox, monkeypox, vaccinia, etc.

    Recently, the CDC has announced a new orthopoxvirus that was discovered in three people from the nation of Georgia in Western Asia. Two of which were herdsmen who had daily contact with cows and other livestock.

    Both men had painful blisters covering their body, swollen lymph nodes, and high fevers. 

    If you have questions, use the comments section below!

    It is believed that the new poxvirus spread to the two men from cattle. Most of the orthopoxviruses typically infect animals, then jump to humans who have close contact with animals carrying viruses. The new poxvirus is as yet unnamed since little is known about it, however thus far, no human to human spread has been documented.

    The CDC interviewed 55 people who had contact with the herdsmen or their cattle. It was found that of nine interviewees (who were not previously vaccinated for smallpox) five had orthopoxvirus antibodies. It was also discovered that some of the herdsmen's cows had previously been exposed, more than likely by the rodents that live in the area.
    Johann Friedrich Voltz - Herdsman and cows, in the distance a village
    Issues like these continue to pop up. Nature can be difficult to predict. Not to be reactionary, but what if an "as virulent" relative of smallpox emerged? People are notorious for being terrible at risk-assessment and while I understand why people overreact to Ebola or Influenza, I don't understand why those overreactions don't translate to proper scientific research. 

    I encourage everyone to use the comments section below!
    • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
    • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
    • Follow Lance @ldpsci