Sunday, December 27, 2015

Understanding How Silent Phages Can Prevent Detection of Potentially Deadly Food Contaminants

Many bacteria are detected by culturing, or growing them
out on plates of artificial media.
Contamination of food with bacteria is a huge issue that can sometimes cause life-threatening illness. The bacterial culprits can include E. coli, as well as Listeria monocytogenes. L. monocytogenes is a potent bacteria that can very effectively infect its human host. This bacterium is especially problematic for pregnant women whose newborn children can develop meningitis that can lead to complications as severe as death. Because this is a serious infectious agent, there have been a lot of quality control efforts towards detecting this bacterium in food before it is sold. In this week's post, we are going to discuss a relatively recent study that highlights the role of phages in these efforts. The study does this by showing that nutrients used in the tests can activate silent phage infections and prevent bacterial detection.

Sunday, December 13, 2015

"Year of the Phage" in Review: Three Major Advances for Phage Therapy

An artist's interpretation of a phage, as
part of the year of the phage.
Bacteriophages were first described by Frederick Twort in 1915 as agents that destroyed bacteria, leaving small areas of destruction (plaques) on bacterial lawns. It is now one hundred years later and we have made great advances both in our understanding of bacteriophage biology and how to use these viruses as tools to understand basic, general principles of biology including DNA being the hereditary material of life. Because 2015 was one hundred years following the first description of phages, it has been termed the year of the phage by many scientists. Not only does this year bear symbolic importance, but it actually marks some important advances in the field of phage therapy. Because we are nearing the end of the year of the phage, I thought it would be appropriate to briefly go over some of the advances I thought stood out the most.

Sunday, December 6, 2015

Recent Study Sheds New Light on the Roles of Viruses in Weight Gain

We know that drugs cause side effects, and sometimes these side effects include weight gain. This is the case for Risperidone, an antipsychotic drug used to control a variety of illnesses including autism and schizophrenia. As with other cases of weight gain (obesity being the poster child), the gut microbiome has been implicated as a major player. Understanding the role for microbes in weight gain is important because it will provide us with a more complete picture of how this drug affects the body, and may lead to the creation of a better drug without as many side effects. The research group of Bahr et al from the University of Iowa recently published a study that provides an in-depth look into the microbial and metabolic responses associated with Risperidone treatment. Perhaps what is most exciting is that they end with data suggesting viruses are playing a significant role in the weight gain. This is actually a big deal for the field, and I will get into it more below.

Sunday, November 15, 2015

Pathway to a Better Electronic Notebook: A Markdown Experience

Scientists are relying more and more on electronic
lab notebooks.
One of the exciting parts of starting in a new lab is the chance to start establishing some better lab practices. As I wrote a few months ago, I was gaining a lot of traction using Microsoft OneNote as an electronic notebook. I liked it, but after a lot of use, I found it was not meeting my needs for customization, formatting, and most importantly, version control. As I started in the new lab, I decided to drop the ol' OneNote notebook and try out markdown on GitHub, as is used in my new lab. Ultimately I found markdown to be much more functional than OneNote. This week I want to share this experience so that you can try it out too.

Sunday, November 8, 2015

Pathway to the Doctorate: A Brief Reflection on Grad School

Elizabeth and myself celebrating after the defense.
Last week I took some time to talk about our lab's most recent manuscript about the skin virome. This has been an exciting paper and it gained a lot of traction in the press. This week I want to go back and reflect on another exciting event from the last month, which was my PhD thesis defense at Penn. You can think of this as the "PhD graduation".

Saturday, October 31, 2015

New Study Looking at the Viruses Colonizing Your Skin

Illustration of the complex microbial communities of
the skin. This includes viruses!
If you have been keeping up with previous posts, you have noticed that this has been a busy time on my end, and unfortunately blogging has had to take a back seat. I defended my doctoral thesis, earned my PhD, moved to a different University, and started a new position as a postdoctoral research fellow with Pat Schloss. Even though this has resulted in some busy weeks, these have been wonderful events and I am really fortunate to be going through this. Although these events are blog-worthy, I wanted to spend this week discussing one of our recent major publications about the skin virome.

Sunday, September 27, 2015

Program Sharing: My Experience Submitting to CRAN

R is an open source statistical programming environment that we have discussed here on the blog before. This is the statistical software of choice for most scientists because it is freely available, incredibly powerful, and backed up by a strong, enthusiastic community. In addition to being openly available to anyone, it is also open to your programming contributions. Contributions to R are most often made as packages, which are defined as the following:

Sunday, September 20, 2015

Blogger Update: My New Adventure in Michigan

You may have noticed that I have not been around my blog lately. What's been going on? Well like most bloggers from time to time, I got hit over the head with a lot of other projects, and the blog had to take a back seat. Fortunately these projects have been starting to wrap up nicely and I am excited to get back to Prophage.

So what have I been up to? Well the biggest update is that I will be defending my thesis in the very near future (October 2), which is essentially the graduation event for PhD candidates in biomedical research. Shortly after I defend, I will be moving to Ann Arbor to conduct research as a post doctoral fellow in the Pat Schloss lab at the University of Michigan. While it will be tough to leave Penn and my current lab, I am excited for the amazing people and research at Michigan. I will be continuing to focus on microbiome research in my new position.

Sunday, August 2, 2015

New Blog Release: Epigenator

You have a hardcoded genetic code, but external factors can
affect how those genes are expressed! <SOURCE>
With my graduation on the horizon (PhD), and the work involved in figuring out the next step, it's been a busy but exciting time. Because things have been so hectic, we I really wanted to keep the topic light this week. To that end, I wanted to take this opportunity to introduce you to a really cool new blog, called Epigenator, that was recently setup by my colleague (and awesome sister-in-law) Ashley Bauer.

Monday, July 27, 2015

Coding Responsibly Part III: Testing Your Code

Keep practicing, and code responsibly! :)
Earlier this week I was reading about code testing and control, and I thought this topic would also be a great addition to the 'Coding Responsibly' series here on Prophage. Because many other people have written about the topic, I am going to offer some of my own perspectives and experiences to the discussion. The goal here is for us to simply become better programmers.

Sunday, July 19, 2015

Advances in Antibiotic Alternatives for Better Health: Promising Research for "Weeding" Bacterial Communities

Antibiotic treatment can be like weeding a garden with
pesticides that kill everything. Scientists are working on
more targeted approaches, like pulling individual weeds.
The discovery and production of antibiotics, which was certainly one of the most significant medical breakthroughs of the twentieth century, has not been without its shortcomings. One shortcoming that has gained recent attention is the lack of bacterial specificity. Antibiotics are often used to prevent or treat specific bacterial infections, but they often target a range of bacteria, many of which are actually beneficial to human health.

The broad destruction of bacteria within a human ecosystem can open the niche up to other harmful bacteria, and can cause long lasting effects due to altered bacterial recolonization. This is a similar effect to covering your entire garden with harsh herbicides to kill the weeds. You will certainly kill the weeds, but you will also destroy the beneficial flowers and vegetables. Because the resulting garden bed is an open patch of dirt, other plants will start to recolonize, including other weeds, leaving the garden very different from how it started. This is why other approaches are generally used in gardening.

Sunday, July 12, 2015

The Hidden Microbial World On Your Cash And What It Means For Your Health

We all know cash can be super dirty! <SOURCE>
We have all thought and talked about how dirty money is. Those notes are transferred all over the world, touched by thousands of people, and find themselves in every sort of hygienic situation. But how dirty is money really? What kinds of microbes (bacteria, viruses, etc) are sitting on your cash, and can they make you sick? To provide us with some insight into these questions, Jalali S et al recently reported a study in which they used high throughput sequencing techniques to look at the money microbiome and its potential for causing disease. The goal of this post is going to be briefly discussing the main points of the paper, and what they mean for us in general. This work was published in the open access journal PLOS ONE, so you can go ahead and check it out for yourself for free.

Sunday, July 5, 2015

Tips for Quick and Easy File Transfer

And we're back! As I mentioned on my Twitter (below), I took a brief hiatus through June to focus on other projects. It was a great month, marked by gaining permission to begin writing my thesis and set the date for my defense/graduation. I am very excited to complete my graduate training and move on to the next stage in my career. But enough about me. My goal for this post is to talk a little about computer file transfer.

Sunday, May 24, 2015

Five Reasons Why Scientists and Non-Scientists Should be on Twitter

Twitter has certainly remained one of the social media giants, along with Facebook, Instagram, etc. But unlike Facebook and the other social media sites, I have found Twitter to be a great place to improve my science. I know, I know, I'm that guy now who thinks Twitter is just sooOOoo cool. But there is actually a lot of good that comes out of this website, and I want to dedicate this post to discussing why I think you should be on Twitter, especially if you are a scientist.

Sunday, May 17, 2015

A Look Into The Viruses That Control Your Stomach Bacterial Infections (Including Probiotics)

Microscopy image of Enterococcus. <SOURCE>
Biofilms continue to be hugely significant problems when treating bacterial infections. Biofilms are groups of bacteria that stick together and to a surface while surrounding themselves in a thick extracellular matrix. You can think of this as the collective bacteria sticking to a surface like a slimy ball of goo. These are very serious infections because the bacteria adhere very tightly to the surface (which could be your bone, a catheter, or your wounded tissue), and antibiotics often have a difficult time penetrating the thick mucous matrix. This means the bacteria are particularly hard to kill.

Sunday, May 10, 2015

Helping Your Skin Get Healthier Every Year: The SID 2015 Meeting

Logo for the SID. <SOURCE>
This past week I attended the annual meeting of the Society for Investigative Dermatology (SID). The SID is the premier organization for promoting dermatological research, and they meet ever year to discuss recent advances in all sciences related to the skin. Since I was lucky enough to attend the meeting this year, I wanted to share my experience with you, the reader. I will talk about my impressions of the conference, but I am going to refrain from discussing the research presented because the focus was on unpublished research and this was a closed meeting.

Sunday, May 3, 2015

Recent Advances: Phage Therapy for Antibiotic Resistant Staph Infections

MRSA is an antibiotic resistant form of
Staphylococcus aureus, and a big problem
for hospitals. <SOURCE>


Most of us have experienced, know someone who experienced, or have at least heard of Staph infections. As their name implies, these infections are caused by Staph (short for the bacterial genus Staphylococcus), occur on the skin, are often acquired in hospitals, and are an increasing problem as the bacteria become increasingly antibiotic resistant. One of the most famous of these bacteria is Methicillin Resistant Staphylococcus aureus (MRSA), which is resistant to many of the antibiotics normally used to treat Staph infections. As antibiotic resistance continues to be a problem, researchers and clinicians are looking to new antibiotics, as well as antibiotic alternatives. One of these alternatives is phage therapy.

Sunday, April 26, 2015

Learning R: A Tutorial for Beginners

TryR is another great place to start learning R.
About a month ago, I put together an R tutorial for my departmental colleagues and classmates here at the University of Pennsylvania. In addition to getting my colleagues started with R, I also wanted to make the information available to anyone else who wants to learn. The tutorial was based entirely on a live demonstration and working through some examples, so there are no slides. All of the materials can be found on Github here.

The tutorial package can be downloaded as compressed source code according to the README file. This includes the R script that you can run and work through, as well as an R notebook file that includes the R output so you can see what examples of result output. Finally it includes an example dataset as a comma separated value (csv) file, which I use to illustrate how to import data into R.

Sunday, April 19, 2015

Defining Microbiome Engineering and Our Realistic Expectations

Microbes, including bacteria, viruses, and fungi, are all around
us. <Source>
Most of us are aware of the impacts the human-associated microbial communities (the human microbiome) have on our health. These communities consist of the bacteria, fungi, viruses, and other microbes that live on and in our bodies. As I have mentioned in previous posts, the field of human microbial ecology has really taken off in the past decade, primarily as a result of next generation sequencing that has powered our scientific abilities to discover a more robust human microbiome than previously appreciated.

Sunday, April 12, 2015

Updates on Fecal Microbiome Transplants, Microbiome Study Reproducibility, and Basic Research (IHMC2015)

Paul Wilmes, one of our Luxembourg hosts, presenting
the congress opening remarks.
A couple of weeks ago I had the amazing opportunity to attend the International Human Microbiome Congress (IHMC2015) in Luxembourg. This congress got together the leading microbiome researchers from around the world to share and discuss their science. I met a lot of awesome microbiome researchers, saw a lot of the most recent microbiome research, and even had the opportunity to represent the Grice lab by talking about my research.

Sunday, April 5, 2015

The Scientist’s Obligation to Public Communication

Get out there and share your science! Source
I recently had the opportunity to attend a talk given by the popular and insightful Vincent Racaniello. For those of you who don’t know, Vincent is a virologist who made significant advances in Polio research, but has since taken on science communication and outreach later in his career. He is the host of the popular podcasts TWIM, TWIVTWIP, and Urban Agriculture. On a more personal note, Vincent has been one of my role models in my endeavors in science outreach and communication, including this blog.

Saturday, February 28, 2015

Coding Responsibly Part II: Keeping a Notebook

Myth Buster Adam Savage on lab notebooks. <Source>
In my last post I started writing about the next step a coding student can take after learning the basics. This next step is of course learning not just to code, but to code responsibly. Last time I talked about using version control to keep track of code changes as you work through a project. For this next post, I want to take the conversation further by discussing lab notebooks for coding projects. I am going to go over a good program to use for electronic notebook keeping (Microsoft OneNote), and will review some tips to make the process a little smoother. As always, I'll end with some information for further reading.

Sunday, January 25, 2015

Coding Responsibly Part I: Version Control

GitHub is a great version control resource. Source
As a result of the growing number of resources allowing everyone to learn how to code, as well as numerous other awesome educational efforts, programming is steadily growing in popularity and accessibility. In previous posts, I have offered some resources I found helpful for learning to code, and have even started offering some workshops for my colleagues here at the University of Pennsylvania (find slides here). But what is the next step after getting the basics down? The answer is to make sure you don't just code, but that you learn to code responsibly.

Wednesday, January 7, 2015

A Recent Review of How Today's Clinicians Are Treating Fractures


Open fractures are bone fractures in which the bone breaks through the skin, leaving it exposed to the external environment (see figure below for example). As you can imagine, this exposure leaves the fracture particularly vulnerable to infection and other related complications, including an inability of the bone to heal properly. When treating these wounds, the orthopedic treatment teams (surgeons, nurses, and others) attempt to prevent infection using wound classification, prophylactic antibiotics, irrigation, and other methods. Despite these efforts, infections and related complications still plague fracture patients. In a recent publication, my collaborators and I outlined the current paradigms in open fracture treatment, the infectious challenges facing those treatments, and the future of patient care.