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2011 in review

January 1, 2012

The stats helper monkeys prepared a 2011 annual report for this blog.

Here’s an excerpt:

A New York City subway train holds 1,200 people. This blog was viewed about 5,800 times in 2011. If it were a NYC subway train, it would take about 5 trips to carry that many people.

Click here to see the complete report.

2011 UGA Conference on Drug Discovery: anti-HIV RNAs, enhanced DNA vaccines, and adenosine ligands

November 3, 2011

The real highlight of the 2011 UGA Conference on Drug Discovery (sponsored by the University of Georgia Center for Drug Discovery) was the food. After all the free soda, scones, biscuits, fried chicken and rice, strawberry shortcake, malt balls, and gummy worms, I feel a little sick to my stomach.

In addition to all the good food, there were some good talks, including “Small RNAs: their biology and therapeutic applications in HIV and cancer” by John Rossi, PhD, “Synthetic DNA vaccines for treatment or prophylaxis of difficult pathogens” by David Weiner, PhD, and “Drug discovery based on G protein-coupled receptors for extracellular nucleosides and nucleotides” by Kenneth Jacobson, PhD. These talks are summarized below.

Small RNAs: their biology and therapeutic applications in HIV and cancer

John Rossi’s group works on RNA-based therapies. For therapy of HIV, they have developed 3 different RNAs:

  1. nucleolar localizing TAR decoy (Michienzi et. al. 2002, 2006)
    This therapeutic small RNA works by binding to Tat, an HIV protein that enhances HIV gene expression, thereby preventing Tat binding to the transactivation response (TAR) element in the HIV-1 LTR, and subsequent transcription from the HIV-1 LTR.
  2. chimeric VA1CCR5 ribozyme (Cagnon et. al. 2000)
    This is a ribozyme that targets CCR5 mRNA, reducing expression of this HIV coreceptor.
  3. anti tat/rev shRNA (Lee et. al. 2002)
    This siRNA targets tat/rev, which regulate HIV gene expression.

These RNAs were delivered to AIDS/lymphoma patients in combination, using a gene therapy approach – a lentiviral vector encoding the RNAs was transduced into patient CD34+ cells, which were then re-introduced to the patient (DiGuisto et. al. 2010). Expression of these RNAs has been observed for up to 2 years in treated individuals, demonstrating the feasibility of this approach (DiGuisto et. al.). This is not the only study suggesting that gene therapy could work as a functional cure for HIV. In a 2009 study, Hutter et. al. were able to cure an HIV patient by transplanting stem cells from a CCR5 delta32 homozygous individual into this patient (Hutter et. al. 2009). Currently, Rossi aims to further optimize delivery of anti-HIV RNAs such that they will better control HIV replication, will only need to be delivered once (at a cost of $100,000), and will possibly replace HAART ($20,000/yr) one day.

This group has also tried aptamers (“in vitro evolved nucleic acids that bind to selected ligands”) as a means of delivering anti-HIV siRNAs. Aptamer-based delivery of anti-HIV siRNAs was tested in RAG-hu mice, was nontoxic, and resulted in decreased HIV replication (Neff et. al. 2011).

Synthetic DNA vaccines for treatment or prophylaxis of difficult pathogens

David Weiner, one of the founding fathers of DNA vaccines, started his talk by discussing the importance of vaccines in general, showing a life expectancy graph from 1200-2000 AD, with a major increase around 1800-1900 as a result of antibiotics and vaccination (Fig. 1, Akbar et. al. 2004).

DNA vaccine work started around 1992 with multiple mouse studies. To quote Weiner (slightly paraphrased), “DNA vaccines have eliminated all mouse diseases. We could start a mouse hospital and set it up next to the roach motel.” Unfortunately, DNA vaccines have not yet done this for human diseases due to an initial lack of immune potency in humans. A data slide from Merck shows that early DNA vaccines were not very potent compared to other vaccine vectors, especially Ad5.

I say an initial lack of immune potency, because Weiner has continued working to optimize the immune potency of DNA vaccines in humans. His enhanced DNA vaccines have done the following:

  1. increased the amount of antigen produced per cell
  2. increased the number of cells transfected in vivo
  3. increased the response to antigens delivered by use of IL-12 as an adjuvant

Now, data from a more recent trial shows that enhanced DNA vaccines are able to perform better than Ad5.

For a review of DNA vaccines, see Kutzler and Weiner (2008). DNA Vaccines: Ready for Prime Time? Nature Reviews Genetics Vol.9:1-13.

Drug discovery based on G protein-coupled receptors for extracellular nucleosides and nucleotides

Adenosine is a neuromodulator. As such, adenosine receptor agonists and antagonists are desired for treating various diseases, especially inflammatory conditions (see Jacobson et. al. for a review). Interestingly, adenosine A3 receptor (A3AR) is highly expressed on inflammatory cells (e.g. PBMN cells), and A3AR agonists are in clinical trials for several inflammatory diseases, including rheumatoid arthritis, psoriasis, and Crohn’s disease.

Jacobson went into structure-based drug discovery at length as it relates to adenosine receptors. However, this portion of the talk was over my head.


Michienzi, A. (2002). A nucleolar TAR decoy inhibitor of HIV-1 replication Proceedings of the National Academy of Sciences, 99 (22), 14047-14052 DOI: 10.1073/pnas.212229599

Michienzi A, De Angelis FG, Bozzoni I, & Rossi JJ (2006). A nucleolar localizing Rev binding element inhibits HIV replication. AIDS research and therapy, 3 PMID: 16712721

Cagnon L, & Rossi JJ (2000). Downregulation of the CCR5 beta-chemokine receptor and inhibition of HIV-1 infection by stable VA1-ribozyme chimeric transcripts. Antisense & nucleic acid drug development, 10 (4), 251-61 PMID: 10984119

Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra P, & Rossi J (2002). Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature biotechnology, 20 (5), 500-5 PMID: 11981565

DiGiusto, D., Krishnan, A., Li, L., Li, H., Li, S., Rao, A., Mi, S., Yam, P., Stinson, S., Kalos, M., Alvarnas, J., Lacey, S., Yee, J., Li, M., Couture, L., Hsu, D., Forman, S., Rossi, J., & Zaia, J. (2010). RNA-Based Gene Therapy for HIV with Lentiviral Vector-Modified CD34+ Cells in Patients Undergoing Transplantation for AIDS-Related Lymphoma Science Translational Medicine, 2 (36), 36-36 DOI: 10.1126/scitranslmed.3000931

Hütter G, Nowak D, Mossner M, Ganepola S, Müssig A, Allers K, Schneider T, Hofmann J, Kücherer C, Blau O, Blau IW, Hofmann WK, & Thiel E (2009). Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. The New England journal of medicine, 360 (7), 692-8 PMID: 19213682

Neff CP, Zhou J, Remling L, Kuruvilla J, Zhang J, Li H, Smith DD, Swiderski P, Rossi JJ, & Akkina R (2011). An aptamer-siRNA chimera suppresses HIV-1 viral loads and protects from helper CD4(+) T cell decline in humanized mice. Science translational medicine, 3 (66) PMID: 21248316

Akbar AN, Beverley PC, & Salmon M (2004). Will telomere erosion lead to a loss of T-cell memory? Nature reviews. Immunology, 4 (9), 737-43 PMID: 15343372

Kutzler MA, & Weiner DB (2008). DNA vaccines: ready for prime time? Nature reviews. Genetics, 9 (10), 776-88 PMID: 18781156

Jacobson, K., & Gao, Z. (2006). Adenosine receptors as therapeutic targets Nature Reviews Drug Discovery, 5 (3), 247-264 DOI: 10.1038/nrd1983

Antiviral Immunity – a gift from viruses?

October 27, 2011

Anyone who’s ever taken an evolutionary biology class has probably heard the famous Dobzhansky quote, “Nothing in Biology Makes Sense Except in the Light of Evolution”. It’s actually the title of an essay he wrote promoting evolution by natural selection as the only way to make sense of both the unity and the diversity of life.

Many years ago, discovering this quote as a graduate student simultaneously studying virology and evolutionary biology, I wondered how viruses fit in to evolutionary theory. At the time, I was particularly curious about when the first viruses originated, and if they could have come before the first cells. I ended up assembling my thoughts on this subject into a scholarly paper, a requirement for my non-thesis masters degree.

Since then, more has been published on the subject of virus-host evolution. This includes the paper which inspired this post, “Viral Ancestors of Antiviral Systems”, published in Viruses this month. In this review article, Luis Villarreal of UC Irvine argues that early antiviral defenses may have been provided by viruses.

Why would a virus want to improve host defenses against itself? Since a virus depends upon its host, it is desirable for a host to protect itself well enough to survive viral infection without completely eliminating virus. Since viruses evolve a lot faster than their hosts – up to a million times faster – they could easily kill the host if that was their goal. But once the host dies, the virus dies with it. So in the light of evolution, or rather in the light of avoiding extinction, it makes sense for a virus to do what it takes to keep its host alive.

Now the question is: What can a virus do to help keep its host alive? Villarreal suggests several possible mechanisms, including the following:

  • Horizontal transfer of restriction-modification sets from phage to bacteria.
  • Expression of siRNA from LTR regions of endogenous retroviruses and transposons in eukaryotes.
  • Viral reprogramming of cells for participation in adaptive immunity.

The mechanisms presented here are merely attempts to make sense of various host-virus interactions, and are yet to be proven. However, they present interesting possibilities to explore.


Villarreal, L. (2011). Viral Ancestors of Antiviral Systems Viruses, 3 (10), 1933-1958 DOI: 10.3390/v3101933

What do we have to do to prove that a vaccine is safe?

September 11, 2011

photo from Brian Deer’s website:

This week was the fall kick-off of Emory’s Vaccine Dinner Club (VDC). The topic of discussion was scientific misconduct. Back in 1998 Andrew Wakefield published a paper in the Lancet, in which he reported autism in 9 out of 12 children referred to a clinic in London after receiving the MMR vaccine.

In 2004, Brian Deer, a reporter for the Sunday Times, was asked to investigate the study. During his investigation, he unveiled several startling facts about Andrew Wakefield and his “science”:

  • Wakefield was secretly paid by a lawyer, hoping to file a class action law suit against the drug companies that manufactured the MMR shot, to create evidence that the MMR shot was unsafe.
  • Wakefield was planning several business ventures meant to profit from the resulting MMR scare, including a “safer” single measles vaccine.
  • The children in Wakefield’s study were pre-selected by anti-vaccine campaign groups, most of the children’s parents were clients/contacts of the lawyer that was secretly paying Wakefield to prove the vaccine unsafe, and none of the children lived in London.
  • Wakefield misreported medical information about the children in his study.

Scandal! How come I never heard about this in the news? Individuals at the BMJ were equally confused and bothered by this. The VDC speaker was Fiona Godlee, editor-in-chief of the British Medical Journal (BMJ). She said there was some debate over at the BMJ as to whether results of investigative journalism belonged in the BMJ. However, in the end, Brian Deer’s work was subjected to peer review, and published in the BMJ as a series of three articles in the January 8, 2011 issue.

The MMR crises resulted in a drop in MMR vaccinations in the UK, and some children died of measles. Because the Wakefield study resulted in a disastrous lack of public confidence in vaccines, the questions were raised:

  • What do we have to do to prove that a vaccine is safe?
  • How many patients are needed to prove that a vaccine is safe? 100? 1000? 1,000,000?
  • Should vaccines be made mandatory for children in the UK as they are mandatory in the US?

Any thoughts?


Deer, B. (2011). How the case against the MMR vaccine was fixed BMJ, 342 (jan05 1) DOI: 10.1136/bmj.c5347

Deer, B. (2011). How the vaccine crisis was meant to make money BMJ, 342 (jan11 4) DOI: 10.1136/bmj.c5258

Deer, B. (2011). The Lancet’s two days to bury bad news BMJ, 342 (jan18 2) DOI: 10.1136/bmj.c7001

When Ebola kills and when it doesn’t

August 31, 2011

The beginning of fall semester means several things for me:

(1) There are no spaces on the bottom level of the parking garage, and now I have to park on the roof.

(2) Crowded halls

(3) Special seminars

It is the third item which is the subject of this post. Today I heard Manisha Gupta from the CDC speak about her work with Ebola virus. There are multiple Ebola virus species, and most are fatal in the majority of infected persons. However, Bundibugyo ebolavirus infection has a much lower fatality rate, especially when compared to Zaire ebolavirus. Gupta compared virus replication and immune responses in Bundibugyo and Zaire ebolavirus infections to determine the basis for the difference in fatality rates between these two species. Conclusions drawn from this study, referenced below, are presented in the boxed list to the left.


Gupta, M., Goldsmith, C., Metcalfe, M., Spipopoulou, C., & Rollin, P. (2010). Reduced virus replication, proinflammatory cytokine production, and delayed macrophage cell death in human PBMCs infected with the newly discovered Bundibugyo ebolavirus relative to Zaire ebolavirus Virology, 402 (1), 203-208 DOI: 10.1016/j.virol.2010.03.024

What’s so special about lambda interferon?

August 29, 2011

The grad students picked a good viral immunology article for immunology journal club this week: “Lambda Interferon Renders Epithelial Cells of the Respiratory and Gastrointestinal Tracts Resistant to Viral Infections” by Mordstein et al.

Type III interferons, or lambda interferons, are the new kids on the block when it comes to antiviral immunity. A role for type I interferons in antiviral immunity was discovered in 1957 (by Isaacs and Lindenmann), while type III interferons were not discovered until 2003. Then IFN- l was described as functioning similar to type I interferons in antiviral immunity.

Type III interferons are induced along with type I interferons during viral infection. Type I interferons bind to the universally-expressed IFNAR on neighboring cells, thereby promoting an antiviral state in neighboring uninfected cells that hinders viral spread. By contrast, type III interferons bind to the IL-28 receptor, which is expressed mainly on epithelial cells. To quote our grad students, “IFN-l targets lung epithelial cells, where [pneumotropic] viruses preferentially replicate, and provides protection”. FYI: Pneumotropic viruses are viruses that replicate in the lungs. It is this targeting that makes interferon-l special.

Using mice in which the IFNA and IL-28 receptors were both knocked out, Mordstein et al. showed that the action of lambda interferons, in addition to type I interferons, makes a big difference in control of viruses infecting the respiratory tract. When IL-28 and IFNA receptors were both knocked out in mice, these mice didn’t control influenza A/B replication as well, and were much less likely to survive infection, than when only IFNAR was knocked out. Similarly, respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and SARS CoV replication were not as well controlled in the double-knockout mice compared to the IFNAR single-knockout mice. The protective effects of interferon-l appear to be specific to viruses that infect epithelial cells of the respiratory tract, as opposed to viruses which enter via the respiratory tract, but do not infect epithelial cells there, moving on to other organs via the bloodstream. For example, Lassa fever virus, forced to infect via the respiratory tract, was not hindered by interferon-l in this study.

As the authors mentioned in their introduction, the relative contribution of interferon-l to antiviral immunity was unclear at the time this study was conducted. Although it was known which cells/tissues express IL-28R, indicating where IFN-l might have the greatest effects during infection, an in-depth analysis of its relevance in the context of viral infection had not been done. By studying infection of IFNAR IL-28R double-knockout mice with several different pneumotropic viruses, Mordstein et al. were able to clarify the relative contribution of IFN-l during respiratory viral infection.


Mordstein, M., Neugebauer, E., Ditt, V., Jessen, B., Rieger, T., Falcone, V., Sorgeloos, F., Ehl, S., Mayer, D., Kochs, G., Schwemmle, M., Gunther, S., Drosten, C., Michiels, T., & Staeheli, P. (2010). Lambda Interferon Renders Epithelial Cells of the Respiratory and Gastrointestinal Tracts Resistant to Viral Infections Journal of Virology, 84 (11), 5670-5677 DOI: 10.1128/JVI.00272-10

Donnelly RP, & Kotenko SV (2010). Interferon-lambda: a new addition to an old family. Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research, 30 (8), 555-64 PMID: 20712453

Antiviral Peanut Butter

August 26, 2011

I often look through the search terms that land people on my blog. I’d like to think that people find what they are looking for when they come to my site. However, every now and then I see a search phrase like “antiviral peanut butter”, and know that one person left my blog unsatisfied. And so this post is for you, antiviral peanut butter boy/girl.

When I saw the phrase “antiviral peanut butter” in my search engine terms, I asked myself the question, “Is peanut butter antiviral?” because I honestly didn’t know. When I threw this search phrase into Google, I was sent to Peanut Butter Information on eHow health.

What I found out is that peanut butter contains a substance called resveratrol, which is in fact antiviral. Note: There is more resveratrol in natural peanut butter than in blended peanut butters (1). Resveratrol is also found in grapes and red wine. The resveratrol illustration on the right is from Gupta et al.

Resveratrol appears to inhibit viral infection/replication by regulating inflammatory responses and cellular stress pathways, rather than interacting directly with virus (2). To be more specific, resveratrol (1) inhibits activation of the NF-kB pathway in response to TNF, and (2) increases activation of p53. NK-kB is a “key regulator” of the inflammatory response. By inhibiting its activation, resveratrol acts as an anti-inflammatory (2,3). Since host NF-kB is necessary for efficient replication of several viruses, including Influenza A, HSV-1, and HIV-1; resveratrol is likely inhibiting viral replication when it inhibits NK-kB (2,4). By increasing activation of p53, a cellular protein involved in type I interferon-mediated antiviral responses; resveratrol is also likely increasing antiviral immunity (2).

In summary, evidence suggests that resveratrol found in peanut butter and red wine could possibly act as an immune therapy during viral infection, inhibiting viral replication via NF-kB inhibition, and enhancing type I interferon-mediated antiviral immune responses via p53 activation. So the next time you have the flu, have some peanut butter toast and a glass of red wine with your chicken soup. And please don’t take that last sentence as real medical advice.


(1) Ibern-Gómez M, Roig-Pérez S, Lamuela-Raventós RM, & de la Torre-Boronat MC (2000). Resveratrol and piceid levels in natural and blended peanut butters. Journal of agricultural and food chemistry, 48 (12), 6352-4 PMID: 11312807

(2) Campagna, M., & Rivas, C. (2010). Antiviral activity of resveratrol Biochemical Society Transactions, 38 (1) DOI: 10.1042/BST0380050

(3) Gupta SC, Kim JH, Kannappan R, Reuter S, Dougherty PM, & Aggarwal BB (2011). Role of nuclear factor κB-mediated inflammatory pathways in cancer-related symptoms and their regulation by nutritional agents. Experimental biology and medicine (Maywood, N.J.), 236 (6), 658-71 PMID: 21565893

(4) Nabel, G., & Baltimore, D. (1987). An inducible transcription factor activates expression of human immunodeficiency virus in T cells Nature, 326 (6114), 711-713 DOI: 10.1038/326711a0


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