Wednesday, December 25, 2013

Happy Holidays and Happy New Year

Happy holidays and happy new year!  Even our lab bacteriophage is in the holiday spirit (enjoy the pictures below).

Thanks for reading Prophage as I got it started this year.  This has been a great year and I look forward to another wonderful year of blogging in 2014.

Our lab phage is ready for its next experiment, as well as the holiday season.

Thursday, December 12, 2013

How You can Learn the Programming Basics in an Hour (Code Week 2013)

This probably would have best been posted a few days ago, but this week is computer science education week, or "code week" (coding just means writing computer programs).  From December 9th to the 15th, over a million people all over the US are promoting computer science for students ranging from elementary school to college, as well as those of us finished with school.  This is not only really cool because it is generating enthusiasm for computer science education, but it is also providing a lot of real educational resources (like online tutorials) for people of all ages to learn how to code (how cool is that?!).  In this post I want to go over some of the cool things about the code week initiative, talk about why it's important, and offer some of my experiences as a biomedical scientist who started computer science work in his graduate thesis lab with little previous computational knowledge.

Many people are intimidated by the prospect of working with computers (programming).  In my experience, one of the biggest things that really turns people off to programming is that they think it is super difficult to learn a computer language and that they can't do it.  I have experienced this multiple times when talking to fellow biomedical researchers who want to start integrating computational biology into their own work.  People are often concerned that they will be unable to learn because they don't have a computational background, and/or they are worried because they don't know where to start or what the learning process will entail.  To this I always respond by telling them that they certainly do not need a computer background to learn programming, and that the basics are surprisingly easier to learn than they think.

Wednesday, December 4, 2013

Recent Publication: The Skin Microbiome in Health and Disease

A couple of days ago, Elizabeth Grice (my research advisor) and I had a review published in this month's issue of Cold Spring Harbor Perspectives in Medicine.  The title of our featured piece is "Microbial Ecology of the Skin in the Era of Metagenomics and Molecular Microbiology", and it is all about the skin microbiome in health and disease.  This is an open source article (meaning you can access it for free), and is worth a read because it offers a nice general summary of the skin microbiome.

Thursday, November 28, 2013

Standing on the Shoulders of Giants: A Brief Overview of Microbiome Studies and Why They are Important


The discovery and characterization of microbial species continues to be a long and painstaking process.  Scientists have spent decades (well... really centuries) carefully studying the distinct properties of different microbes, examining the evolutionary relationships between different microbes, and organizing microbes into taxonomic groups based on various commonalities.  One of the many benefits from this research program, and especially the DNA sequence characterization and organization of microbes, have been the resulting reference database collections which are used in sequence-based microbiome studies.  In recent years there has been a lot of excitement growing aroung the use these DNA sequence reference databases to characterize microbial communities.  While the spotlight has really been on microbial communities as a whole, the importance of individual microbial species discovery and characterization has been somewhat overlooked.

Flowchart illustrating the synergistic relationship between studies focusing on
microbial community characterization and individual microbe characterization.
Studies involving characterization of individual microbes provide references
for microbial community studies, while microbial community studies provide
context for individual microbe characterization studies.  This relationship is
sometimes overlooked.

Saturday, November 16, 2013

How Scientist Soldiers Are Directly Aiding Overseas Military Efforts

Although most people think of scientists as people in lab coats working in University labs and teaching college courses, scientists overall apply their skills to a wide range of jobs and careers.  One of those careers I, and probably most people, don't often associate with scientists is that of a soldier.  Although we don't hear about them much, soldier-scientists are playing important roles in the US military efforts overseas.  Science recently published a relatively brief article about soldier-scientists in Afghanistan, and specifically the experiences of Dr. Alexander Stewart, a glacier morphologist and soldier-scientist of the U.S. Army’s 143rd Infantry Detachment.  Here I am going to just briefly highlight some of the points I found interesting, and bring up some discussion points that I think are worth talking about.  The citation for the article can be found in my works cited, and it is definitely worth a read.

Alexander Stewart (Geologist) examining a repaired wall
at the Band-e Sultan Dam in Ghanzi.  Taken from ref [1].
As many of us are probably already aware, the war in Afghanistan has required enormous combat efforts, but has also required a focus on teaching Afghan citizens and helping them rely more on their government and less on the Taliban.  While this has been done in many different ways, one of the approaches has incorporated the expertise of PhD scientists.  The soldier-scientists advise military leaders, as well as aid Afghan citizens in building and farming projects, projects for promoting education, and projects involving climate research.  According to the article (quoting Stewart), this is the first time soldier scientists have been deployed in noncombat missions in a war zone.  

Sunday, October 20, 2013

How 23andMe is Bringing You Genetic Health, Education, and Research

23andMe logo, Source
One company that has been gaining a lot of attention recently is 23andMe.  23andMe (named after the 23 human DNA chromosomes and you) is a genetic testing company that can take a saliva sample that you mail them, perform numerous genetics tests, and give you the results to tell you things about you genetic health (whether you have a higher risk for certain diseases or whether you may pass on disease genes to your children), your ancestry, and your potential responses to drugs.  This is a cool idea for a company because it has important potential implications in education, research, and medicine.

Wednesday, October 16, 2013

Personalization of Medicine and the Science of Scale: A Summary of the 8th Annual ITMAT Symposium

Yesterday was the second and last day of the Institute for Translational Medicine & Therapeutics (ITMAT) 8th Annual International Symposium here at the University of Pennsylvania.  ITMAT is a group that promotes translational research and medical applications around some of the Philadelphia medical campuses.  What is especially cool about this symposium is that it is always an international symposium which features participants from many institutions from all around the world.  The theme of this year's symposium was "Harnessing the Paradox: Personalization and the Science of Scale" and it was all about using huge data sets and high-throughput techniques to improve patient care and our general understanding of medicine.  The three general themes of the meeting that I attended were the general biomedical research landscape, microbiomics, and metabolomics/metabolism (with a focus on cancer).  The fourth, which I missed, was about emerging technologies and concepts in translation.

Friday, October 4, 2013

Standard Error vs Standard Deviation, and Some Other Practical Statistics Stuff You Want to Know


In most professional settings, and especially in the sciences, it is important to know a bit of statistics.  I say that this is particularly true for scientists because our jobs are centered around discovering and describing natural phenomena, and we rely on statistics to help us understand these.  Using inappropriate statistical methods, or interpreting statics incorrectly, can either result in missing interesting trends in data, or in making unjustified conclusions by mistake.  Because this is such an important topic, I want to highlight some major statistical points that all scientists (and professionals in general) should be aware of.  I will try to be brief here, but these topics can get pretty involved so I will also provide directions to more comprehensive literature for further reading in my Works Cited.  My goal here is only to hit some high points of commonly used statistics.

Saturday, September 21, 2013

Prophage is Now Found on "Research Blogging"

Blogging about contemporary research is fun, but I think it is equally fun to read other peoples' blogs.  Now there are lots of science blogging groups out there, but I thought a lot of them have an "exclusive membership" feel where a small, select group of people post blogs about different scientific fields.  These are great, but I found myself wanting more.  I both wanted to find a large, diverse, less exclusive group of bloggers so that I could read about many kinds of science, and also wanted that group to be a community I could become a part of.  After some searching I came across the site "Research Blogging".

Without getting into it too much, this is a site made by research bloggers who wanted the same type of community I was looking for.  This site offers a convenient single location for searching through  diverse groups of research blogs, as well as up-to-date feeds that let you see the community's most recent science blog posts.  In addition, anyone serious about research blogging can join, contribute to the community, and increase the audience that their blog will reach.  Overall I think this is a really cool  site and I am excited to be a part of it through "Prophage".

Saturday, September 14, 2013

Insights into Current Phage Therapeutics: Identification and Safety Evaluation of an Existing Phage Therapy

As I mentioned in a previous post, phage therapy is becoming a more attractive therapeutic avenue to treat bacterial infections, especially in light of increases in antibiotic resistance prevalence. Interest and support for phage therapy continues to increase, but the US & Western Europe are still in the early stages of developing medical phage therapeutics for approved patient use (only a small number of phage preparations are FDA approved for use on food to prevent food poisoning by bacteria; nothing is approved for patients with bacterial infections). While the progress in the US and Western Europe is still in early stages, phage therapy medicines continue to be used in Eastern Europe throughout Russia and nearby countries.

Microgen is a major Russian pharmaceutical company that
produces many different phage therapies.  Source
Phage therapies are approved for human therapeutic use in Eastern European countries, including Russia.  The major pharmaceutical company that produces general phage therapies is Microgen.  Although these common phage therapies have been used for decades in Russia (before Russia, the et al did exactly this, and recently reported their findings in the journal 'Virology' (reference [1]).
former Soviet Union), their composition, safety, and efficacy have not been scientifically evaluated [1].  If we are to move forward in our endeavors toward using phages
therapeutically, we must address this lack of knowledge by evaluating the composition, efficacy, and safety of phage cocktails which have long been used in Russia.

Monday, September 9, 2013

Quickly Combining Fasta Identification and Sequence Lines

When analyzing high-throughput DNA sequencing results, I sometimes want to select sequences with certain names from my fasta file (fasta is a standard sequencing file format).  There are a lot of ways to accomplish this, but here I want to outline one I found fast and easy.

The standard fasta files will always begin looking like the following:

Saturday, August 31, 2013

Phage Therapy: A Brief Primer on the History and Current Outlook

As I discussed in a previous post, bacteriophages can play crucial roles in promoting bacterial pathogenesis by acting as reservoirs for antibiotic resistance genes, and by promoting the transfer of those genes across bacterial populations.  Interestingly, while phages can promote bacterial pathogenesis, they can also be used in "phage therapy", meaning they are used as therapeutic agents to treat bacterial infections.  While this idea may sound like a novel approach for treating bacterial infections, the use of phages to treat bacterial infections is quite old.

Felix d'Herelle (seated) at a bacteriophage research center.
Picture Source: Reference [6]
Bacteriophages were first described by Frederick Twort in 1915 [1], and again independently discovered by Felix d'Herelle in 1917 [2].  Early on, scientists (especially d'Herelle) recognized the potential of phages as therapeutic agents against bacterial infections, and while the interest continued in Eastern Europe (where even today, phage therapy centers treat patients), it was largely abandoned in the Americas and Western Europe.  This abandonment occurred in light of Alexander Fleming's discovery of Penicillin and the promise of the new antibiotic drug type.  With the recent rise in the threat of antibiotic resistant bacteria, and the increasingly apparent limitations of antibiotics in certain infectious scenarios (i.e. antibiotics are often unable to penetrate bacterial biofilms), phage therapeutics have gained a renewed interest as important antibiotic alternatives.

Sunday, August 18, 2013

Graphing with R and Adobe Illustrator

R is a great resource for making graphs, but it is still limited in its ability to fine-tune and format figures.  Adobe Illustrator complements R by providing an incredible amount of tools for figure formatting and fine-tuning.  Using these programs together is a great way to make quality graphs, so I want to make some notes on using R graphs in Illustrator (CS6).
First the graphs need to be generated in R.  I have been using {ggplot2} to generate my graphs, although the R {graphics} package works too.  Once a graph is made in R, it needs to be saved as a pdf and opened in Illustrator.

Sunday, August 11, 2013

R Reference Sheet

Recently I have been spending a lot of time learning about the statistical environment R.  R is command line based and is worth learning because it is more powerful than programs like Excel, and ultimately it saves a lot of time (especially when you will have to perform repetitive tasks or if you will have to redo the analysis again with updated data).  I am still new at R, but I have been learning a lot and I want to share that with others who are learning.

First of all, you can download R by clicking the 'download, packages' CRAN link on the left of the homepage.  Just follow the directions.  In addition to using R, there is a nice program for writing R scripts called R Studio, which has more features in a nice GUI.  It kind of reminds me of the way SAS is set up, and it is worth a try for sure.

Tuesday, July 16, 2013

Insight Into the National Science Foundation Graduate Research Fellowship Program (NSF GRFP) and the National Defense Science and Engineering Graduate (NDSEG) Fellowship Program

When I started graduate school a couple of summers ago, I was thinking a lot about how I was going to start off on the right foot and be a successful grad student (like most grad students do).  One aspect that I knew was important was attempting to secure my own funding.  I knew it was important, but I did not know the best way to go about it.  I had information for student specific training grants, but I was not able to apply for those until I was done with my lab rotations.  Instead of waiting to be done with my rotations, I wanted to get active right away, but I did not know how.  Luckily a friend told me about two big national fellowships that I might be interested in.  These fellowships were the National Science Foundation Graduate Research Fellowship Program (NSF GRFP) and the National Defense Science and Engineering Graduate (NDSEG) Fellowship.

These fellowships are ideal for new graduate students because they can apply during their lab rotations (the fellowships are specifically for new graduate students).  I was fortunate to hear about these fellowships shortly after I started grad school, and was additionally very fortunate to be awarded the NDSEG fellowship.  Because I know many students don't know about these fellowships, I want to spread the word and offer whatever insight I can think of.  The following are some points I think are useful to think about when preparing the applications, and especially when writing the personal statements.

Friday, July 5, 2013

Phage Communities Respond to Antibiotics and May Spread Resistance

Antibiotics have been, and continue to be, a cornerstone of modern medicine.  Unfortunately, their widespread use has not come without cost.  The use of antibiotics has continued to result in an increased prevalence of antibiotic resistant bacteria, a problem that was even recognized by Alexander Fleming following his discovery of Penicillin [1, 2].  Presently we do have some understanding of how antibiotic resistance is propagated throughout bacterial populations, such as through mutations that prevent antibiotic efficacy, and through antibiotic driven selection for antibiotic resistant bacteria.  In addition to these mechanisms for the propagation of antibiotic resistance, there are also less well characterized means through which antibiotic resistance is spread through bacterial populations.  One of these mechanisms is through bacteriophages, which have been shown to mediate transfer of bacterial genes, especially when their hosts are stressed by antibiotics (this often occurs when prophages are induced in response to antibiotics, a process that results gene transduction).

Saturday, June 15, 2013

HHMI Med Into Grad Research Symposium 2013

As part of my PhD training, I am also earning a certificate in medical science through our University of Pennsylvania Med into Grad (MIG) Program, which is funded by the Howard Hughes Medical Institute (HHMI).  This program is all about promoting a greater understanding of medicine in graduate education through additional classes, clinic shadowing experiences, and other opportunities.

The HHMI has funded multiple MIG programs at Universities across the country, and each year we get together with other nearby MIG program schools for a two-day symposium.  The symposium is a time for us to meet other graduate students with similar interests, learn about how other MIG programs are working, discuss our science with each other, and have some fun.  This year we met at Yale, along with students from Harvard, Columbia, and the Sloan Kettering Cancer Center.  The theme for this year’s meeting was ‘Personal Genomics & Personalized Medicine’, which allowed for some really cool presentations about topics that are an important future direction in medicine.

Friday, May 24, 2013

Our Phage Immune System: Phages Providing Mucosal Immunity

Mucosal surfaces, including those found at the intestines, mouth, nasal passages, and airways, are directly exposed to the external environment and are particularly susceptible to pathogenic bacteria.  Human mucosal surfaces maintain numerous defense mechanisms, both by secreting antimicrobial and immune-stimulating molecules, as well as by maintaining a beneficial commensal microbial community that aids in the prevention of infection [1].  Interestingly, Barr et al recently reported a model (the bacteriophage adherence to mucus [BAM] model) for how phages may also play an important role in mucosal immunity [2].  This is important because it outlines a medically relevant, previously unrecognized tripartite symbiosis between humans (and other metazoans), bacteria, and phages, whereby phages will control bacterial populations to preserve human mucosal health, which is in turn beneficial for both commensal bacteria and phages.  This report also provides us with a new understanding of how phages may interact with their environment, how phages can affect human immunity, and how we might use phages for therapeutic interventions at mucosal surfaces. 

The BAM model proposed by Barr et al (see figure to left) suggests that phages persist longer in mucous environments, compared to other environments, because they have Ig-like domains (immunoglobulin-like domains that bind certain motifs, similar to how antibodies bind to certain motifs) which bind to mucin glycoproteins.  The increased phage persistence results in higher concentrations of phages at the mucus layer, thereby providing a greater chance that phages will infect and destroy a bacterial pathogen that enters the mucus.  The group supports their model by performing a variety of experiments that use T4 bacteriophage, E. coli, and mucus secreting human cells.

Saturday, May 18, 2013

Having Phages do the Dirty Work: Indirect Killing of Bacterial Competitors Through Phage Induction

Microbial communities are elegantly complex, with all members competing, cooperating, or simply co-existing with all other members.  These interactions are especially evident between bacteria and bacteriophages.  In many cases, bacteriophages interact with bacterial populations by destroying bacteria through predation [1], by mediating gene transfer through transduction [2], or by controlling gene expression of their bacterial hosts [3].  Some phages integrate into bacterial chromosomes (prophages), which can confer benefits by preventing further phage infection or modulating gene expression, but this can also make the bacteria host susceptible to death by phage induction (process by which DNA damage stimulates excision of the phage genome from the bacterial chromosome, which is followed by phage assembly and release while destroying the bacteria).  Some bacteria have developed methods to obtain competitive advantages over prophage containing competitors (lysogenic bacteria) by killing them through stimulation of phage induction, such as those reported by Selva et al [4].

In their report, Selva et al studied the competitive interactions between Streptococcus pneumonia (a bacterial pathogen targeted by pneumococcal vaccine) and Staphylococcus aureus (an opportunistic pathogen).  In their study, they report how relatively low levels of hydrogen peroxide are produced by S. pneumonia with the intent of stimulating DNA damage in their S. aureus competitors, thereby promoting phage induction and consequent destruction of the lysogenic bacteria.  This is thought to be a particularly effective strategy because S. aureus bacteria commonly maintain prophages.

In their study, the researchers first showed that lysogenic strains of S. aureus are killed when exposed to levels of hydrogen peroxide often found in S. pneumonia cultures.  The non-lysogenic bacteria were not affected by the treatment of hydrogen peroxide, thereby supporting the selective lethality of hydrogen peroxide in lysogenic bacteria.  Not only did the group show that lysogenic S. aureus is more susceptible to hydrogen peroxide lethality, but they also showed that phages are produced is greater quantities when the cultures are treated with hydrogen peroxide.  S. pneumonia was resistant to the induction effects whether it was lysogenic or not, and co-culture with S. pneumonia and S. aureus resulted in phage induction and destruction of the lysogenic S. aureus strains. The authors made the point that S. aureus produces an effective catalase that protects it from hydrogen peroxide toxicity, suggesting it should be resistant to the effects of hydrogen peroxide.  Interestingly, while catalase protects non-lysogenic S. aureus from destruction by hydrogen peroxide, it was significantly less able to protect lysogenic S. aureus from death.  The authors speculate that this occurs because significantly more hydrogen peroxide is required to kill a bacterium, compared to that required to stimulate the SOS response.  I think this also further emphasizes the potential competitive disadvantage of harboring prophages, because they can make their host susceptible to antimicrobial insults that they would otherwise be resistant to.  This overall effect of prophages on antimicrobial susceptibility was also shown to occur upon antibiotic treatment, in which lysogenic bacteria were more susceptible to prophage inducing antibiotics, compared to non-lysogenic bacteria.

Saturday, May 11, 2013

A Future with Crowd Funded Science

I really enjoy TED talks, as I’m sure many do, because I love seeing the new and amazing things people are doing.  TED (technology, entertainment, and design) talks are talks, usually about 15-20 minutes long and given by amazing and earth moving people, recorded at international TED conferences.   A couple of months ago I watched a talk given by the musician Amanda Palmer, which was entitled “The art of asking”.  She talked about her early days as a street performer and how, as she performed, she was asking for money from those passing by.  As she told this story, she emphasized the connection and relationship that that experience made between her (the performer) and the listener.  Amanda then went on to talk about how she continues to promote that connection in her current music career.  She explained how people should not be made to pay for music, but rather should be allowed to pay for the music, thereby allowing us, the listeners, to directly support our favorite artists in a way that promotes the relationship between artist and fan.  As I listened to this, I could not help but think that this mentality would be useful in the sciences.

As of now most scientific research is supported by companies, government and private granting agencies, and other types of granting groups.  Wouldn’t it be cool if, in addition to those agencies, there were another granting source that promoted a more direct relationship between scientists and those in the general public who enjoy the science performed?  What if the public was able to read about different research projects, learn about what scientists are interested in doing, and directly support their favorites, thereby fostering a direct link between the scientists and those that support their ideas?  What if people were allowed to directly support the projects they believe in, instead of giving money to agencies who make the choice?  This would be a unique and beneficial way for science to progress, and it turns out there already businesses that have started to help make this happen.

Monday, May 6, 2013

Penn Genomics Retreat 2013

Today I attended the Institute for Biomedical Informatics Genomics and Computational Biology (GCB) Graduate Group 2013 Annual Retreat, through the University of Pennsylvania, here at the beautiful College of Physicians of Philadelphia (also home of the Mutter Museum).  I tried to take a picture of the beautiful auditorium but I don’t think my camera did it justice.  The retreat highlighted talks from past and present members of GCB, as well as some great guests.  Overall it was a great symposium with many interesting presentations, posters, and discussions.

One of the highlights for me was the keynote speaker Michael Snyder, PhD, from Stanford.  The main point I took away from his presentation was that there is currently a huge potential for incorporating omics technology into medicine.  He promoted the idea of integrative Personal Omics Profiling (iPOP), which is the integration of multiple high-throughput analysis techniques with other clinical approaches to provide a better treatment approach for patients.  The omics technologies included in iPOP are the whole genome (collection of personal genome DNA sequences), the transcriptome (collection of your mRNA sequences, which shows what genes are expressed), the proteome (collection of proteins present, which shows what proteins are being produced from the expressed genes), the metabolome (collection of the metabolites), and probably the microbiome in the future (collection of the microbes associated with the body).

Saturday, May 4, 2013

The Bacteriophage as a Vaccine Platform?

Vaccines are a cornerstone of modern public health, and have been successfully used to control diseases such as Polio and Measles, and have also led to the successful eradication of smallpox.  Despite this success, many current vaccines still have room for improvement, and other modern diseases require vaccine development.  To address this need for further development in the vaccine field, Tao et al, from Venigalla Rao's Laboratory, reported an incredibly interesting bacteriophage T4 based technology that allows for concurrent delivery of desired DNA and proteins to mammalian cells [1].  By allowing for concurrent delivery of DNA and proteins, something other technologies do not currently offer, this phage T4 technology could provide novel approaches for vaccination.

Picture of bacteriophage T4 from Dr. Rao's lab website.
Bacteriophage T4 is a well-studied virus that infects the E. coli bacterium, and does not infect humans or other eukaryotes.  During its infectious life cycle, T4 leads production of phage heads (protein capsids) that are filled with phage genomic DNA.  After assembly of viruses, the bacterium is lysed and the new phages go on to infect new bacteria.  Tao et al took advantage of this process by generating phages that, upon genomic DNA insertion into the head, become unstable and release the genomic DNA back out of the head, leaving the empty head intact.  The group then used a DNA packaging motor to fill the empty head with their DNA of interest, with a capacity of up to ~170kb (a substantial increase over another common vector, Adenovirus, which has a capacity of 28kb).  In addition to the incorporation of DNA into the phage head, proteins of interest could be added to decorate the head surface.  The phage particles were collected and, when exposed to mammalian cells, delivered both DNA and protein.

Wednesday, April 24, 2013

Five Helpful Resources

Over the past couple of years I have found some really great websites and online resources to help me keep up with scientific literature, as well as to help me progress through my own research.  In the hopes that these might help you out as well, I want to go through some of the online resources I have found helpful.  If you have other online resources you find helpful, please let me know in the comments section.  I would love to hear about them.

Sunday, April 21, 2013

Hello World

Hello and welcome to “Prophage”.  I am currently a biomedical science PhD student at the University of Pennsylvania, and I will be using this blog as an opportunity to bring some thoughts, ideas, and hopefully discussions to the worldwide community.  Thanks for reading.

I would like to thank Dr. Brendan Hodkinson, PhD for turning me on to the blogging scene.  Be sure to check out his blog here.

Additionally, as some quick blog name background (thanks to Wikipedia):
A prophage is a phage (viral) genome inserted and integrated into the circular bacterial DNA chromosome or existing as an extrachromosomal plasmid. This is a latent form of a bacteriophage, in which the viral genes are present in the bacterium without causing disruption of the bacterial cell.