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.