Wednesday, March 6, 2013

Grainy Westerns and Fuzzy Logic: A Review of Shi, et al 2011

A review of Shi et al. Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis. Science (2011) vol. 333 (6049) pp. 1630-2
PMCID: PMC3502614

This study was recently published in the prestigious journal Science attempted to explain the mode of action for an important antibiotic, Pyrazinamide, used in treating tuberculosis. Due both to the high profile of this work, and the conclusion they draw regarding trans-translation, I will provide below a review of this article.

The interested reader should be aware of one important fact when approaching this article: there are different versions of it, depending on how you access it. The open access version at Pubmed is outdated; a more recent version (with updated Figure 3) is available from the journal Science itself. 

Manuscript Highlights:
  1. Demonstrates binding of ribosomal protein S1 to POA (active form of Pyrazinamide drug)
  2. Suggests mechanism of action for POA: binding to S1 inhibits trans-translation.
  3. Quality of trans-translation related data (western blots) make the conclusion drawn by the authors questionable.
  4. Alternative explanations to trans-translation rescue of stalled ribosomes in their in vitro system are not ruled out, undermining the conclusions drawn.


In this study, Shi and colleagues sought to identify the target and antibiotic mechanism of the anti-tuberculosis drug Pyrazinamide. This drug is important in treatment of tuberculosis, particularly in clearing persister cells through combination with other compounds. In order to accomplish this task, the authors used affinity chromatography to capture M. tuberculosis proteins that are capable of interacting with the drug. Through this approach, ribosomal protein S1 is identified as the primary target.

Using ribosomal protein S1 (RpsA) as a lead, the authors attempt to explain the mode of action for PZA. Binding studies using isothermal titration demonstrate more conclusively that PZA is capable of binding RpsA Furthermore, a PZA resistant strain with mutant RpsA genes that cannot bind the drug is identified. Finally, the authors use an in vitro translation system to assess the effect of PZA on translation and trans-translation. The conclusion drawn from these studies is that PZA specifically inhibits trans-translation, but only in the context of M. tuberculosis ribosomes.

Tuesday, March 5, 2013

Perspectives on Scientific Publishing

I'd like to kick off this blog by highlighting a sentiment made by several others: the model of academic publishing is broken. It is a business model in which publishing companies receive content, copyright, editing services, and peer review services from (mostly) government paid researchers on a volunteer basis. These same companies take the content and place it behind a paywall, selling the work back to universities through subscriptions, and denying the taxpayer which funds most of these transactions (namely, the research, the researchers, and the university) any access to the results. At least, this is the often repeated compliant about the publishing industry.

There have been efforts to change from some. Digital publishers have arisen with different business models, such as open access publishing. In this model, the copyright is not always forfeited by the authors of the manuscript, and the publisher derives profit not from subscriptions but rather through fees assessed by the authors themselves. This model is logical, since there is usually great incentive for the authors to publish, enough for them to devote precious grant dollars or other funds towards these fees. After all, publishing articles in peer reviewed journals is important for maintaining funding from government agencies.

Most of these new models claim represent some improvement over traditional publishing, although each is unique. These include PeerJ, Frontiers, and PLoS One. You can read more about PeerJ in a insightful post at Likewise, the Chronicle of Higher Education ProfHacker blog has an interesting interview with the founder of Frontiers.

You can read more about the issue and make up your own mind. I think that publishing companies should adapt to new technologies, but that their business model or presence is not necessarily a problem in research. The editing and peer review services offered by these companies is important for scientific research; as technology improves, these services should be augmented in ways that more fully engage the readership of academic journals as well as the authors. In particular, I would like to see an effort to promote scientific communication from graduate students, who usually are responsible for executing the experiments and gathering the data that supports a manuscript.

By more actively engaging graduate students, and making them aware of the role of communication in the scientific community as well as their own careers, publishing companies will not only be empowering an important segment of this community but fostering good relationships with future lead researchers.

Introducing Another Bacteria Blog

Welcome to "Just me and Eubacteria", a blog about Microbiology, Molecular Biology, and related fields. 

Within the confines of these pages, I hope to share interesting facts and stories about bacteria and the people who study them with a general audience. Also featured here will be commentary on molecular biology research in bacteria, as well as some of my own observations. Although I will endeavor to make each post accessible to the widest possible audience, the jargon heavy and highly specialized nature of contemporary research complicates this task.

I can write about some of these topics with at least a modicum of authority, as I have spent the last six years studying E. coli as a graduate student in the laboratory of Dr. Wali Karzai. During this time, I have worked on various aspects of the trans-translation ribosome rescue system. Unfortunately, the secretive and competitive nature of research prohibits me from discussing the details of my unpublished work. Eventually I hope to share the details of the more interesting projects, after they have been accepted in a peer reviewed journal. Thankfully, at least some of my work, opinions, observations, and perspectives are free from such restrictions.

This blog stems from my long standing interest in synthetic biology and bacterial gene expression. I believe that increasing our understanding of how bacteria do what they do allows us to better realize the potential benefits that come from engineering them to accomplish a specific task. Alongside recent developments in the fields of synthetic biology, I will also share my interests in the study of infectious bacteria. While synthetic biology holds great promise for the future, the study and treatment of bacterial infections (especially antibiotic resistant ones) is a very serious and immediate concern.

Of course, for a topic so broad and important, there are many other interesting blogs and websites available. Some of the notable examples include the excellent website Microbe World, the ASM blog Small Things Considered, and fellow blogspot users Of Bacteria and Men and Twisted Bacteria. Rather than simply parroting these great sources, I hope to provide my own insights on the field. In addition, you can look forward to plenty of reflections on graduate education and the way science is conducted. During my fledging career as a scientist, I have witnessed many interesting projects and results, as well as a great deal of stupid ideas, cheap papers, and bad science! Most of this seems to be hidden from the public; many other sources seem intent on only celebrating science. While scientific research is a wonderful endeavor, I will attempt to present it in a more honest light.

Finally, I should note that this blog is technically an offshoot of an earlier project of mine, Science on the Squares. This blog, currently on hiatus (undergoing renovations soon returning) had a dual focus on Chess and Science. I am an avid chess player, and I found it appropriate to blog about Science alongside my favorite hobby, sometimes evening drawing analogies between these two intellectual pursuits. Because of the dual audience, I have written some great introductory articles to molecular biology for Science on the Squares. These include a introduction to the central dogma, an explanation on how data in this field is collected and (should be) analyzed, and comments about Occam's Razor. If you feel you need a refresher on any of these topics, I strongly encourage you check out those pages.

If you'd like to learn more about me, you can also check out my personal website.