Category Archives: Important Concepts

Hacking Time Management for the Bench Scientist

This article originally appeared on Gradhacker.org on August 9th, 2013.CC use via Flickr user archer10

Many of us in the sciences begin graduate school not only with classes, but with extensive lab rotations that center upon completing bench science as well. This is the real classroom for many scientists-in-training and is an invaluable training experience. However, for some students it can be difficult to be productive during such a short time (some rotations last only a few weeks), so learning good time management skills at the bench will aid you now in your rotations and down the road in your dissertation lab.

I worked on my time management as a research assistant prior to graduate school and still struggled to balance classes and significant hours in the lab. I’ve come to refer to my time management method for lab work as the “Russian nesting  doll approach.” These basic principles can be widely applied in a variety of research situations. Continue reading Hacking Time Management for the Bench Scientist

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Opening Pandora’s Box to find the largest virus on Earth

法国发现新巨型病毒 可能来自外太空(图)
Colorized Pandoravirus electron microscopy(图) (Photo credit: 禁书网中国禁闻)

This last year has had many important developments in the field of microbiology, but by far one of the most interesting is the publication discovery of the Pandoravirus genus of viruses. Published in the July 19th 2013 issue of Science Magazine, it is undeniably the biggest virus ever discovered; both in terms of its genome (2.5 MILLION base pairs in length) and it’s physical size ( at 1 micrometer in length it can be seen with a LIGHT microscope!).

So why do these new viruses matter? Why is it so groundbreaking to find a virus of this size? Read on to learn more about the importance of the discovery of these giant viruses. Continue reading Opening Pandora’s Box to find the largest virus on Earth

A newly discovered means for controlling viral infection

This image shows a 0.1 x 0.03 inch (2.5 x 0.8 ...
A  small Drosophila melanogaster fly. (Photo credit: Wikipedia)

The first moment a virus infects a cell it has to deal with multiple cellular defenses. From surviving highly acidic conditions in endosomes  to evading the host enzymes that can digest its very genetic code, an invading virus must navigate and eventually subvert the functions of a host cell. This intricate molecular dance has played out time and again for millions of years and modern science is just beginning to understand and appreciate the intricacy of these steps.

A recent paper published in Nature Immunology suggests that there may be even more steps in the virus-host dance than we had imagined. Outside of science fiction, I would have dismissed this mechanism until I read the paper  “RNA-mediated interference and reverst transcription control the persistence of RNA viruses in the insect model Drosophila” by Goic and others (1).

Keep reading to find out more about this new exciting mechanism of viral defense. Continue reading A newly discovered means for controlling viral infection

Microbe Matters Book Club: The Coming Plague by Laurie Garret

Cover of "The Coming Plague: Newly Emergi...For this installment of book club I am happy to introduce The Coming Plague: Newly Emerging Diseases in a World out of Balance by Laurie Garret.

Written in 1994, this is an impressively well researched work on the current microbiological topics of the time. While this book is almost 20 years old, I was very impressed by how many of our current problems in health care were covered in these 620 pages and how well the content has held up to the passage of time.

What is even more impressive is how the author narrates the stories, giving a more human side to the factual recounting of disease outbreaks that most of us in the microbiology community are familiar with.

This book is arranged so that each chapter covers a specific disease or theme. Notable chapters on exotic pathogens include those on Bolivian Hemorrhagic fever, the Ebola virus, Lassa fever, the Legionnaires’ disease outbreak in 1976, and the Hantavirus outbreak in the 4 corners region of the United States. These are all fascinating chapters as many of the people who were present for these events were interviewed and there is a real sense of the fear and confusion that accompanies the outbreak of unknown diseases.

These chapters also show “disease cowboys” in action during these outbreaks, scrambling to find out the causative agent or vector for these diseases. As someone who has just learned how to work in a Biosafety level 3 lab I can only imagine the difficulty involved in doing any kind or research in the field, let alone in with diseases that are known to be highly lethal.

The author does an excellent job of showing how environmental, social, and political factors drive the emergence of disease in human population. No other chapter covers this intersection quite as well as well as her work on the early years of the HIV epidemic. With 30 years separating me from this period in time it is easy to not think about how we got to where we are today with HIV; during my life it has always been here. It was eye-opening to see just how badly the epidemic was handled by politicians of the day or how distinguished scientists could fight so readily over discoveries relating to this new viral plague.

Overall, I highly recommend this book to anyone looking for a more in-depth and extremely well written take on the challenges we face against the invisible armies of microbes that continually surround us.

The Concept of Quasispecies

RNA Polymerase
RNA Polymerase (Photo credit: ynse)

Today’s topic is directly related to my own research with RNA viruses and is what I consider a very interesting topic: quasispecies.

Many of us are familiar with the concept of a species at the macro (visible) scale. Dogs are dogs; pigs are pigs, and so on. Each is a distinct species based on the fact that they can only reproduce and generate fertile offspring with other members of the same species. Over the course of many generations mutations may arise in these populations which lead to different genotypes in the species. Left long enough, these two subpopulations may keep mutating to the point where they can no longer interbreed and become their own genetically distinct species. However, when you get down to the viral scale species becomes a much more difficult concept. Viruses don’t have sex in the traditional sense, so how can they be a species?

Continue reading The Concept of Quasispecies