Microorganisms: Infectious Disease and Ecology

Blog entries about bacteria, viruses, fungi and other microorganisms.

Getting the Most DNA from Your Plasmid Prep

Posted on by Kelly Grooms

dificult_cloningPlasmid DNA preparation is one of the fundamental techniques of molecular biology research. It goes without saying that you want to maximize your plasmid DNA yield as much as possible. Below are a few tips to help you get the most out of every Plasmid prep.

Increase Your Culture Volume

Most plasmid prep systems can process a range of volumes. For example, the PureYield™ Miniprep System can process 600μl to 3 ml of culture. Note: Exceeding the recommended culture volume can result in decreased yields because the increased biomass can lead to insufficient lysis and lysate clearing problems.

Use Optimized Culture Conditions

Media: We recommend growing cells in 1X Luria-Bertani (LB) medium. The use of rich medium, such as 2X YT, CircleGROW®, Terrific broth, or LB-Miller medium, which contains more NaCl, can significantly increase yields, provided that the biomass is within the acceptable range.

Culture incubation times: Low-density bacterial cultures yield relatively low amounts of DNA. Overgrown cultures produce suboptimal yields and excessive chromosomal DNA contamination. Do not use cultures grown longer than 18–20 hours. Continue reading “Getting the Most DNA from Your Plasmid Prep”

Designer Bacteria Detect Cancer

Posted on by Isobel Maciver

Every day scientists apply creative ideas to solve real-world problems. Every so often a paper comes up that highlights the creativity and elegance of this process in a powerful way. The paper “Programmable probiotics for detection of cancer in urine”, published May 27 in Science Translational Medicine, provides one great example of the application of scientific creativity to develop potential new ways for early detection of cancer.

The paper describes use of an engineered strain of E.coli to detect liver tumors in mice. The authors (Danino et al) developed a potential diagnostic assay that uses a simple oral delivery method and provides a readout from urine, all of which is made possible by some seriously complex and elegant science. Continue reading “Designer Bacteria Detect Cancer”

Your Health has a Season

Posted on by Kari Kenefick
Photo of pasque flowers
Pasque flowers in a northern hemisphere garden in spring.

As the seasons change so does the general state of health for many of us. The further from the equator we live, the more pronounced these effects are. For instance, did you know that blood pressure elevation for many people increases with the distance they live from the equator, an effect most pronounced during the low sunlight season (winter in the northern hemisphere)?

A report published online in Nature Communications May 12, shows evidence of changes in cellular physiology with the seasons. Todd et al. published a study entitled: “Widespread seasonal gene expression reveals annual differences in human immunity and physiology”, where they note,

“Here we find more than 4,000 protein-coding mRNAs in white blood cells and adipose tissue to have seasonal expression profiles, with inverted patterns observed between Europe and Oceania.”

Let’s Take a Look at the Research

Todd et al. looked at ethnically and geographically distinct populations, including subjects from Australia, The Gambia (Africa), Germany, the UK and Iceland. Individuals from the various studies were infants, adults with type 1 diabetes and asthmatics in the range of 18-83 years of age. The authors analyzed RNA from peripheral blood mononuclear cells and subcutaneous adipose tissue biopsies, as well as examining peripheral blood cell counts and circulating levels of proinflammatory cytokines. Continue reading “Your Health has a Season”

Animal or Plant? FISH Labeling Reveals Horizontal Transfer of Algae Gene into Sea Slug Chromosome

Posted on by Kelly Grooms

There are times when I ask myself why I chose a career in science. This happens on what I call “grass is greener” days. On these days I dream of other careers—like National Geographic reporter or Caribbean tour guide–which all sound way more exciting than scientist. Admittedly these alternative careers are not ones that many people have the privilege of attaining, but sometimes reality gets to take a vacation. Fortunately, science is a fast-moving, always-changing field. As much as I might occasionally dream of exotic jobs in far away locations, science always pulls me back in with something new and unexpected. Because as much as we’d like to think we know, the truth is there is so much more that we don’t.

Image from: Pelletreau KN, Weber APM, Weber KL, Rumpho ME (2014) Lipid Accumulation during the Establishment of Kleptoplasty in Elysia chlorotica. PLoS ONE 9(5): e97477. doi:10.1371/journal.pone.0097477
The sea slug Elysia chlorotica. Image from: Pelletreau K.N., et al. (2014)  PLoS ONE 9: e97477.

A case in point—sea slugs. These unfortunately named, exotic looking creatures have some surprising secrets.

Continue reading “Animal or Plant? FISH Labeling Reveals Horizontal Transfer of Algae Gene into Sea Slug Chromosome”

Could This be the Next Generation Ebola Virus Vaccine?

Posted on by Sara Klink

Ebola virus has received a lot of press in the last year due to the extended epidemic outbreak in Africa. Ebola is part of the family of Filioviruses (filamentous virus) and causes hemorrhagic fever that leads to internal bleeding and loss of bodily fluids. As the epidemic in Africa has illustrated so starkly, once the virus infects a large enough population, the human suffering it causes is devastating to individuals and communities. Because no treatment other than palliative fluid support is available to those infected by Ebola virus, virologists have focused attention on potential therapeutics and vaccines. The vaccine strategies now in clinical trials are based on a single Ebola virus glycoprotein, GP, and involve a DNA-based vaccine or innoculation with an Ebola protein expressed from a viral vector. How effective and safe this approach may be for protection from Ebola virus infection is currently under investigation.

Based on the history of effective vaccines, Marzi et al. was interested in testing a whole-virus vaccine for Ebola (EBOV). A whole-virus-based vaccine like smallpox or measles uses an attenuated or inactivated virus. The advantage of this method is that all the proteins as well as the nucleic acid are available for immunological reaction, offering broader-based protection than a single protein. In the recently published Science report from Marzi et al., a replication-incompetent Ebola virus was used as the basis for a whole-virus vaccine that was tested for its efficacy in nonhuman primates.

Continue reading “Could This be the Next Generation Ebola Virus Vaccine?”

Culturing the Unculturable Bacteria

Posted on by Isobel Maciver
Culturing bacteria is't always this easy.
Culturing bacteria is’t always this easy.

It is estimated that all the bacterial species so far described represent only a tiny fraction of the total. The rest remain unknown to science because they are “unculturable” in standard (or known) laboratory media. Given that many antibiotics were first isolated from environmental bacteria, it seems likely that these as yet unknown organisms could also be a rich source of potential new drug candidates. The desperate need for new strategies to combat multi-drug resistant infections gives impetus to studies investigating how we can culture some of these “unculturable” bacteria and uncover their potential as a source of much-needed new treatments. 

Continue reading “Culturing the Unculturable Bacteria”

Tracking the Beginning of a Pathogenic Bacterial Infection

Posted on by Sara Klink

Yersinia pestis by U.S. Center for Disease Control [Public domain], via Wikimedia Commons.
Understanding the course of a pathogenic infection involves not only understanding what ultimately kills the host or how the bacterium or virus enters the body but also how it establishes itself in the host organism. What is the receptor that allows a virus to enter the cell? Which cells does a bacterium first target or how does it evade an immune response? While other studies of bacteria like Yersina pestis have looked at imaging the bacterial burden in model mice, questions remain about how this bacterium gets from the skin after an infected flea bites to the draining lymph nodes, where the bacteria replicate and enter the bloodstream and infection becomes fatal. A recent PLOS Pathogens article examined how the nonmotile Y. pestis disseminated itself starting from a tiny innoculation mimicking a flea bite on a mouse ear and following pathogen interaction with the host from skin to lymph node. Continue reading “Tracking the Beginning of a Pathogenic Bacterial Infection”

Death in the Stars: A Virus Decimates Sea Star Populations Along the Pacific Coast

Posted on by Kelly Grooms

Starfish BlueA killer is lurking in the waters off the pacific coast. Silent and lethal, it leaves its decimated victims in tidal pools. They first began to appear in the early summer of 2013. Limp and curled, missing some or all of their limbs, the bodies were little more than globs of slimy tissue.  They were hardly recognizable as what they once were—Sea Stars. Continue reading “Death in the Stars: A Virus Decimates Sea Star Populations Along the Pacific Coast”

Differentiating but not Mature Adipocytes Provide a Defense Against S. aureus Infection

Posted on by Kari Kenefick

http://upload.wikimedia.org/wikipedia/commons/6/65/Blausen_0012_AdiposeTissue.png
Cross-section of skin and adipose tissue enlargement. Used courtesy of Wikimedia Commons, Blausen.

A basic tenet of immunology is that antibodies produced by B cells are very important and specific immunoprotective agents, released in response to infection.

However, antibodies do not supply immediate protection. The invading organism needs to get into the host, meet up with T cells and then B cells, in order for antibody production to occur. If the host has seen this particular pathogen previously, the antibody response occurs somewhat more quickly, but we’re still talking about days. If the invading organism is a bacterium, it can multiply and double in numbers in just hours. Thus an infection could potentially gain a foothold in a body prior to an antibody response.

Fortunately we have a more rapid, first line of defense to invading pathogens, a cellular response. In the case of a puncture or skin wound, epithelial cells, mast cells and leukocytes are activated quickly in response to pathogens. Neutrophils and monocytes also aid the cellular response.

Now a recently published report demonstrates that fat cells also play a part in the cellular response to invading bacteria. R. Gallo et al. published a study on Jan. 2 in Science, providing more in depth information on the role of adipocytes in the host response to the bacterium Staphylococcus aureus (S. aureus). Continue reading “Differentiating but not Mature Adipocytes Provide a Defense Against S. aureus Infection”

Christensenellaceae—A Natural Way to Stay Thin?

Posted on by Isobel Maciver

microbiome studies show how bacterial colonists influence healthA study published in the Nov 6 issue of Cell outlined results suggesting that an obscure family of bacteria colonizing the human gut may be inherited and may also have a direct influence on body weight. The paper is the first to identify such an association and to link a particular microbial colonist with lower BMI. Continue reading “Christensenellaceae—A Natural Way to Stay Thin?”