Thursday, March 20, 2014

NCAA March Madness Blot

I mean really?!?
My first thought was that it looks like a DNA blot, but I guess it really could be any blot. Either way, GO SCIENCE!

I encourage everyone to use the comments section below! 

Lance D. Presser has a PhD in Microbiology and Immunology and currently is a Public Health Laboratorian.

Follow Lance @ldpsci

Hire Lance for any of your microbiology, virology, or public health consulting needs.

Hepatitis C Virus Infectious for Six Weeks on Surfaces?

Giant Microbes - HCV

A group of researchers from the Yale Schools of Medicine and Public Health demonstrated that hepatitis C virus (HCV) can remain infectious for up to six weeks on surfaces at room temperature. Previously, it was thought that HCV could survive for up to four days on surfaces outside the body, this new research extends that number by a month and a half

The implications of these findings are far reaching, including safety of patients and workers in healthcare settings, as well as reducing viral hepatitis transmission associated with drug use.

The study, which was funded by the National Institute on Drug Abuse (NIDA), and was designed to assess the risk of HCV transmission after infectious material dried on environmental surfaces.

This study reinforces previous findings indicating strict adherence to infection control standards and universal precautions are essential to prevent transmission of HCV in healthcare settings.

HCV has been transmitted via intravenous catheters, blood lancets, and blood glucose monitors (and now, potentially insulin pens). This new study highlights the importance of education when dealing with healthcare staff, as well as others who might come in contact with infected blood. The researchers confirmed that common commercial antiseptics (e.g. bleach, CaviCide, alcohol, etc.) reduce HCV infectiousness when used at the recommended concentrations, but not when diluted.

Brett D. Lindenbach was also a co-author on this manuscript, as he engineered the strain of HCV that was essential for the experiments. I never met Dr. Lindenbach, but I read many of his papers for my PhD, and paid close attention to his excellent work.

The HCV used for this study was Jc1/GLuc2A reporter virus. Which is an engineered virus using the chimeric genotype 2a FL-J6/JFH with a luciferase gene from Gaussia princeps (copepod) inserted between the p7 and NS2 genes.

HCV Genome - Note GLuc2A inserted between p7 and NS2 gene
2a FL-J6/JFH is a very common HCV strain used in the lab, as it is one of the only strains that replicates well enough to work with. Initially the JFH (Japanese Fulminant Hepatitis) strain was what was used, until the J6/JFH chimera was constructed, which increased the virus' replication. The luciferase gene inserted into the HCV genome is extremely useful as a way to determine infectivity or HCV presence.

If you have questions, use the comments section below! 

The authors suggest that the most likely circumstances in which healthcare workers or patients will come into contact with HCV dried on surfaces are following spillage of HCV-contaminated blood, serum, or plasma during the course of preparing blood samples for analysis or removing a venous line.

The authors simulated these types of accidents by obtaining EDTA-anticoagulated blood from HIV and HCV seronegative donors. The procedure was done twice in a biosafety cabinet where a foil mat was used to collect "accidental" drops of plasma.

To determine how quickly the plasma would dry on a surface, 24-well tissue culture plates were seeded with "accidental" drops and observed at refrigerator temperature (4 degrees Celsius), room temperature (22 degrees C), and human body temperature (37 degrees C).

24-well culture plate
Samples of plasma spiked with HCV were dropped onto the 24-well plates in a similar manner and after six weeks, Huh-7.5 cells (susceptible to HCV) were seeded in a 96-well cell culture plate, dried blood/plasma spots were rehydrated and reconstituted with culture media and then incubated with the Huh-7.5 cells. Three days later, cells were lysed and examined for luciferase (light) activity (provided by engineered HCV genome). So, if there was measurable light coming from the lysed cells (measurable by machine, not naked eye) then those cells were considered infected.

Figure 1 - A. Showing viable HCV at 40+ days at refrigerator and room temperatures
I am okay with the idea of 33ul being a droplet. I would think that is a pretty good small-average size droplet.

Overall this paper states the obvious, drops of blood or plasma containing HCV can be infectious, for how long depends on temperature, humidity, and drying as well as drop size and amount of virus contained in the drop.

It also states that common disinfectants (bleach, 70% ethanol, Cavicide) are useful, but only optimal when used at recommended concentrations, not when they are diluted.

This manuscript does have value in that it gives an upper limit to how long some of these drops could potentially remain infectious. It is a very artificial system, and I would argue using cultured cells that are specifically engineered to be susceptible to HCV infection, is not the same as exposure to a dried droplet in a clinical setting. I think six weeks is probably WAY to long to be concerned in a real-life setting.

When I was younger, I hunted a lot. I was taught to treat every gun as if it was loaded. I think it would be wise to view every drop of blood or plasma in a similar fashion, especially in the clinical or research setting.

I encourage everyone to use the comments section below! 

Lance D. Presser has a PhD in Microbiology and Immunology and currently is a Public Health Laboratorian.

Follow Lance @ldpsci

Hire Lance for any of your microbiology, virology, or public health consulting needs.

Sunday, March 16, 2014

Potential HIV, Hepatitis B and C Exposure at Long Island Hospital

South Nassau Communities Hospital is sending out 4000+ letters to patients recommending they be tested for hepatitis B, C, and HIV due to a potential risk of infection from an insulin pen.

If you have questions, use the comments section below! 

An insulin pen is typically used for people with diabetes and is a pre-filled syringe meant to dispense insulin in a single patient. Because of potential backflow of a patient's blood into the pen cartridge after injection, using a pen or cartridge on multiple patients may expose them to blood-borne infections.

The hospital spokesman said no one was observed re-using the insulin pen reservoir on more than one patient, but a nurse was heard saying it was all right to do so. A report was then sent to the New York Department of Public Health. The hospital has stated the risk of infection is "extremely low."

Out of an abundance of caution, the hospital is recommending that patients receiving the notification be tested for HBV, HCV, and HIV. While the testing is voluntary, it is recommended.
Hepatitis C Awareness Ribbon
The hospital said it has since banned the use of insulin pens and permits only the use of single-patient-use vials.

The state Department of Health said that in 2013, three health facilities reported potential insulin pen re-use: two state-regulated facilities and the Veterans Administration's medical center in Buffalo.

It sounds to me that this is a pretty minimal risk. I would imagine the hospital took a very firm stance with the nurse when they over heard her say that it was acceptable use. Hopefully she told the truth and she (or any of the nurses) hadn't actually done it.

The situation is worth monitoring however, as anytime there is a potential hospital blood exposure to 4000+ people.

I encourage everyone to use the comments section below! 

Lance D. Presser has a PhD in Microbiology and Immunology and currently is a Public Health Laboratorian.

Follow Lance @ldpsci

Hire Lance as a consultant using Zintro. 

Wednesday, March 12, 2014

Post #2 My Background - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

I grew up on a small family farm near Turtle Lake, ND. With 2010 census numbers showing a population of 581 people, 95.5% white, most people have a firm grip of what my childhood was probably like. 
File:ND McLean County Turtle Lake.svg
Circle indicates Turtle Lake. Located in McLean County, ND
The best way I can describe geographically how isolated Turtle Lake is;
  • I was 60+ miles from the nearest McDonald's
  • I was 60+ miles away from the nearest interstate highway
  • The closest city of 100,000 people was Fargo, 230 miles away
  • The closest city of 500,000 people was Winnipeg, 323 miles away
Rusty the Turtle - Turtle Lake, ND (It was spend money on this or a public pool...good call Turtle Lake)
There was nothing spectacular about my childhood. I wasn't a child prodigy. I wasn't in any special classes. I was above average academically, but what does that really mean coming from Turtle Lake, ND? I don't want to spend a lot of time going through my entire life, but some of these points are relevant to the decisions I made about my academic career, and could be relevant to yours as well.

The summer before starting high school (9th grade), my family moved 110 miles due east to Grace City, ND and I would start high school in nearby Carrington, ND. Carrington was bigger (roughly 2,100 people), the high school had better teachers, and there were more extracurricular opportunities than Turtle Lake. That being said, there were no AP classes, no real upper level courses what-so-ever. I was one of eight in a class of roughly 55 who took physics (which was taught by the earth sciences, chemistry, basketball coach).

Chieftain CafĂ© - Carrington, ND (Yes, it is the defining landmark.) 
What I am trying to get at is, I had no idea how many opportunities I was missing out on, or how far behind I was, compared to many kids in large high schools in urban or suburban settings, that I would be competing with later on.

As a sophomore or junior in high school, I asked my career councilor about being an epidemiologist, to which he replied, "I have no idea what that is" and left it at that.

My senior year, a few Carrington H.S. alumni came back and gave a talk about career-type things. One of which had gone to North Dakota State University (NDSU) and graduated with a degree in biotechnology and had started Aldevron, a small biotech startup in Fargo, ND. 
Aldevron - Fargo, ND
Michael Chambers (CEO and Founder of Aldevron) was super nice and inspiring, and I was very interested in biotechnology as well. Those were some of the big reasons I chose NDSU and decided to double major in biotechnology and microbiology. It was the only school I applied to. The idea of going to a "name-brand" university didn't even strike me as something I should consider. NDSU was close, cheap, and had what I needed. I will always defend my choice to go to NDSU, but even though it worked out for me, I feel that there are rural ND students who don't feel empowered to explore other options outside of the local colleges and universities, and are therefore not reaching their full potential.

NDSU was great. I will continue to insist that it is highly underrated. The coursework is top notch. I still think the research aspect of things (specifically Microbiology-related) is lacking, but efforts have, and are being made to improve. I was persistent enough to convince Dr. Lynn Rust to let me volunteer my time in her lab, and when she moved to take another position, her replacement Dr. Penelope Gibbs continued mentoring me. I spent a lot of time in the lab as an undergrad, and while I learned a lot (technically, culturally, maturity, etc.) my undergraduate lab experience is the source of one of my biggest regrets/career blunders.

The biggest thing that I regret as an undergraduate researcher was not being more organized and goal driven. In the lab, I was so excited to be learning techniques and doing science that I neglected to think about publishing papers, and without anyone telling me otherwise, I was content to "just learn". What I got out of my undergraduate research was a lot of technical knowledge, thousands of hours of practice, and a great mentor in Dr. Rust and Dr. Gibbs. What I didn't get was proof that I could be productive, in the form of publications or grants.

At the end of my undergraduate, numerous friends went directly into PhD or MD programs, but I wasn't ready for that kind of commitment yet and I applied to Emory, Tulane, Boston University, and the University of Pittsburgh Infectious Disease MPH programs. I got into all of them (although not exactly with Emory), and ended up choosing the University of Pittsburgh, based almost entirely on the efforts of Robin Leaf and Dr. Todd Reinhart to recruit me there. I wanted to go to Tulane, it was my first choice, but Pitt got to me first and it worked out for the best because I started my MS in the fall of 2005 and Hurricane Katrina struck Tulane shortly after.

Use the comments section to ask questions!!!
The University of Pittsburgh was great. I loved it there, I loved the people, I thought they were all incredibly bright and talented. Again, I got a lot out of it, but what I failed to get were publications. Nothing. So now I had six good years of lab work, two BS degrees, a MS degree, and not a lot to show for it.

Just a note here. I often debate on what I would have been better off with, an MS or an MPH. I don't think even in hindsight that question has been answered yet, but for people who go this route, it is something to consider.

I think the lack of manuscripts is what doomed my PhD application. I think my lack of publications was the difference between UW-Madison, UM-Minneapolis, or UW-Seattle. Instead the only school I was accepted to was Rosalind Franklin University of Medicine and Science (RFUMS).

Note: One of the most important things I did before applying to PhD programs, especially with the rise of "interdisciplinary programs" was to directly email professors I was interested in working with and asking if they had time, space, money, etc. Many of them were very honest and either had a firm yes or no. One professor at Northwestern mentioned she wasn't taking students any longer because she was retiring. Most would say they had space, and were impressed by the CV, get into the program first, and then we will talk.

As funding has stagnated and dropped over the years, the amount of faculty that have funding for a student has also dropped. The number of students being admitted into PhD programs has not dropped. Therefore, if you don't do your homework, you may end up in an interdisciplinary program and not like any of your options for mentors. I saw this at the University of Pittsburgh, and again at RFUMS. It sucks to all of a sudden realize that the one person you wanted to work with doesn't have space in their lab.

Use the comments section to ask questions!!!

I started at RFUMS in the fall of 2007, and was honestly excited about it. It was significantly smaller than the schools I had previously attended. It was more focused and specific than the schools I had previously attended. Geographically, it was a great fit for me. The longer I was there, the more problems I started to notice, and eventually came to understand the absolute failings of the microbiology department, graduate school, and administration (the medical school has been put on probation by the LCME TWICE! in the last 10 years). I won't get into all of them now, or in some cases ever. I will be detailing some of them in certain sections because I learned a lot by watching these failings, or actively trying to change them.

When I arrived, there was no alumni association for the graduate school, no organized teaching opportunities for those who wanted teaching experience, and they didn't actively recruit or advertise (while sitting in a hotbed of large Big-10 universities) undergraduates interested in graduate school. They had/have an extremely limited footprint

RFUMS was located near Abbott Laboratories, Takeda, and Baxter and had minimal relations with any of them, and since I started there (roughly seven years), no graduate or postdoc that I know of has gotten a job at any of those companies.

Not only were there institutional failings, but I will be sharing numerous stories of mistreatment by my mentor and the microbiology department chair at RFUMS, with the intention of warning, and helping others who have had to or will go through similar situations. I developed a lot of coping/defense mechanisms that in the end were very effective. I plan on sharing them throughout the posts.

After a very rough PhD, I ended up with two first-author manuscripts that I am very proud of, multiple semesters of great teaching experience, some wonderful extracurricular activities, and thicker skin. I left knowing that I wanted very little to do with academia in its current state. 

It took me a while to find a job after finishing my PhD. I was teaching at the time and considered it a nice "working vacation". I eventually interviewed for a postdoc and my current position in a public health department. I took the public health job and I love it. I love everything about it. So, as always, if you have questions, use the comments section and check back roughly weekly for updates

I encourage everyone to use the comments section below! 

Lance D. Presser has a PhD in Microbiology and Immunology and currently is a Public Health Laboratorian.

Follow Lance @ldpsci

Hire Lance as a consultant using Zintro. 

Thursday, March 6, 2014

Post #1 Introduction - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

Welcome to My PhD Process.

More than likely you are a current PhD student, or maybe you are thinking about starting a PhD program. You are reading this because you have heard that a PhD is difficult and you want information, hints on how to be successful, or maybe you are a sponge (which is great if you want to earn a higher degree) and are trying to ingest every bit of information you possibly can.

Whatever the reason that led you here, it was a good one. Not that this series is going to be the greatest document ever written, but I have been through a PhD program, and it didn't go well. That being said, I was extremely active in understanding the process, trying to change the process, and eventually mastering the process. Many of my close friends over the years have also completed their PhDs at numerous other institutions (University of Pittsburgh, Michigan, Chicago, Wisconsin, Colorado, and Northwestern University, etc.) and some of them have failed in their attempt to earn a PhD. I have tried my best to learn from them and understand what made their experience different than my own.

The current attrition (dropout) rate for PhDs is accepted to be at about 50%. Half of all PhD students quit. Personally, I am surprised the attrition rate isn't higher. I am also surprised that so many people are still willing to enter a system that has steadily over time failed to live up to the standards it had over history maintained.

There were numerous times when I felt the urge to quit. After my second year, around qualification time was a very rough period in the lab. It didn't get any better afterward. I will discuss my background in more detail in the next entry, but I will say that quitting is a very personal choice, and isn't always a bad one. Every situation is unique, but I will say, even if it doesn't seem like it at the time, a PhD is valuable. It has value in the real world. It may not be "worth" what you are going through, and it may not be "worth" what you thought it was going to be, but it does have value and they can't take it away from you.

Through this series of blog posts, I am going to take you through my thoughts and observations on a number of topics including
  • The unwritten rules of graduate school
  • Frustration
  • Understanding your department and lab
  • Expectations vs. potential
  • Controlling your image
  • Just-in-time learning
  • Hints and tips along the way that will save you time, energy, and anguish
I also plan on discussing how I approached the surprisingly terrifying idea of "I am finished with my dissertation and defending what?"

I hope that these posts can stimulate discussion, answer questions, entertain, and most of all help people get through what is for most people, at this point in time in history, a difficult time.

I encourage everyone to use the comments section below!

Lance D. Presser has a PhD in Microbiology and Immunology and currently is a Public Health Laboratorian.

Follow Lance @ldpsci

Hire Lance as a consultant using Zintro.