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A mathematician by training, I discovered genetics in 2006 and never turned back. This blog was born to share all the fascinating things I learn about genes and DNA through my current research on viral genetics and HIV.

EE Giorgi
188 posts

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  • February 21, 2014
  • 06:19 PM

Converging genes reveal how plagues have shaped our genome

by EE Giorgi in CHIMERAS

Evolution is shaped by numerous factors. Selection is one of such factors, but, contrary to popular belief, it is not the only force acting on genomes. I cringe when I hear the expression "this gene has been selected for" because most of our alleles (we all have the same genes, but each gene can have different alleles across different ethnic groups/populations) haven't been selected at all. Things change even without any selection pressure from the environment, a phenomenon known as random drift........ Read more »

Hafid Laayounia,1, Marije Oostingb,c,1, Pierre Luisia, Mihai Ioanab,d, Santos Alonsoe, Isis Ricaño-Poncef, Gosia Trynkaf,2, Alexandra Zhernakovaf, Theo S. Plantingab, Shih-Chin Chengb, Jos W. M. van der Meerb, Radu Poppg, Ajit Soodh, B. K. Thelmai, Cisca. (2014) Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors. PNAS. DOI: 10.1073/pnas.1317723111  

  • February 16, 2014
  • 09:45 AM

This season's flu helps inform next season's vaccine

by EE Giorgi in CHIMERAS

Last year I described the arm's race happening between virus and immune system during an HIV infection: as the immune system starts mounting its defense against the virus, the virus mutates trying to evade the attack. This is what pushes the virus to constantly evolve new strains, not just in HIV, but also in the flu virus, which evolves a new strain roughly every year. The HIV virus evolves within the same host to evade the host's immune response. On the other hand, the flu virus evolves more s........ Read more »

  • February 9, 2014
  • 09:52 AM

Gene therapy for the heart

by EE Giorgi in CHIMERAS

My post today is about state-of-the-art gene therapy that delivers genes straight to heart, where the genes activate proteins critical in restoring cardiac tissue in people affected by heart failure. The technique, developed at the Cardiovascular Research Center at Icahn School of Medicine at Mount Sinai, is undergoing clinical trial.Cardiovascular disease is the leading cause of death worldwide. Heart failure--a condition by which the heart weakens and no longer pumps blood efficiently througho........ Read more »

  • February 2, 2014
  • 10:52 AM

Computer generated viruses

by EE Giorgi in CHIMERAS

By "computer generated viruses" I don't mean bits of code that can harm your desktop. I mean actual viruses, objects that have the ability to infect and replicate, but were created in silico, by a computer algorithm. I know this is a concept that has the anti-vaxxers enraged, but in HIV it has become quite common to generate vaccine candidates through computer algorithms. Today I want to address two questions: why and how. Candidate vaccines are made from virus isolates: you take a real virus, m........ Read more »

Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B, Hahn BH, Bhattacharya T.... (2002) Diversity considerations in HIV-1 vaccine selection. Science (New York, N.Y.), 296(5577), 2354-60. PMID: 12089434  

Santra S, Korber BT, Muldoon M, Barouch DH, Nabel GJ, Gao F, Hahn BH, Haynes BF, & Letvin NL. (2008) A centralized gene-based HIV-1 vaccine elicits broad cross-clade cellular immune responses in rhesus monkeys. Proceedings of the National Academy of Sciences of the United States of America, 105(30), 10489-94. PMID: 18650391  

  • January 13, 2014
  • 07:44 PM

Mitochondria to the rescue

by EE Giorgi in CHIMERAS

Yes, I confess I'm quite fascinated by mitochondria. Not only their well functioning seems to be correlated to lifespan, like I discussed last time, but it's also implicated in cancer. Briefly, last post taught us that mitochondria provide energy to the cell by producing ATP through four different oxidative complexes. However, mitochondria's oxidative activity wanes with age. Researchers found one pathway in particular that is activated in low-fat diets and high-exercise regimens, which can reve........ Read more »

Gomes AP, Price NL, Ling AJ, Moslehi JJ, Montgomery MK, Rajman L, White JP, Teodoro JS, Wrann CD, Hubbard BP.... (2013) Declining NAD( ) Induces a Pseudohypoxic State Disrupting Nuclear-Mitochondrial Communication during Aging. Cell, 155(7), 1624-38. PMID: 24360282  

  • January 3, 2014
  • 08:05 PM

The secret to a long life? Active mitochondria!

by EE Giorgi in CHIMERAS

For quite a while now we've known that if we want to live a long, healthy life, we must exercise regularly and be good about what we eat. Recent studies have added another piece to the equation: maintain mitochondrial function. Mitochondria are organelles found in every cell of our body. They hold a very important function: they provide energy to the cell. Most cellular processes take place using energy stored in a molecule called adenosine triphosphate, or ATP, and most of a cell's supply of AT........ Read more »

Lanza IR, & Nair KS. (2010) Mitochondrial function as a determinant of life span. Pflugers Archiv : European journal of physiology, 459(2), 277-89. PMID: 19756719  

Gomes AP, Price NL, Ling AJ, Moslehi JJ, Montgomery MK, Rajman L, White JP, Teodoro JS, Wrann CD, Hubbard BP.... (2013) Declining NAD( ) Induces a Pseudohypoxic State Disrupting Nuclear-Mitochondrial Communication during Aging. Cell, 155(7), 1624-38. PMID: 24360282  

  • December 14, 2013
  • 11:46 AM

ASD and inflammation: more than just a correlation

by EE Giorgi in CHIMERAS

There has been a lot of speculation, lately, about vaccines possibly being harmful and, in particular, causing autism. You know I work on HIV vaccine design, so there's no need to say where I stand on the need of vaccinations. No link has been found between the incidence of autism and vaccination. Of course, medicine is not an exact science. Outliers will always exist. The U.S. seem to be a special case, as the vaccination schedule in this country requires a high number of vaccine doses, yet the........ Read more »

Hsiao EY, McBride SW, Chow J, Mazmanian SK, & Patterson PH. (2012) Modeling an autism risk factor in mice leads to permanent immune dysregulation. Proceedings of the National Academy of Sciences of the United States of America, 109(31), 12776-81. PMID: 22802640  

  • December 8, 2013
  • 11:25 AM

Autism: not one disease but a spectrum of disorders; not one gene but a network of gene coexpressions.

by EE Giorgi in CHIMERAS

"Autism spectrum disorder (ASD) is a lifelong developmental condition that affects about 1 in 110 individuals, with onset before the age of three years. It is characterized by abnormalities in communication, impaired social function, repetitive behaviors and restricted interests [1]."ASD is more common among males than females, with a 4:1 male to female ratio. Numerous studies in the literature have shown evidence for a strong genetic component of autism, with a risk up to 25 times higher among ........ Read more »

Neelroop N. Parikshak, Rui Luo, Alice Zhang, Hyejung Won, Jennifer K. Lowe, Vijayendran Chandran, Steve Horvath, Daniel H. Geschwind. (2013) Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism. Cell. DOI: 10.1016/j.cell.2013.10.031  

A. Jeremy Willsey, Stephan J. Sanders, Mingfeng Li, Shan Dong, Andrew T. Tebbenkamp, Rebecca A. Muhle, Steven K. Reilly, Leon Lin, Sofia Fertuzinhos, Jeremy A. Miller, Michael T. Murtha, Candace Bichsel, Wei Niu, Justin Cotney, A. Gulhan Ercan-Sencicek, J. (2013) Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism. Cell. DOI: 10.1016/j.cell.2013.10.020  

  • November 3, 2013
  • 10:31 AM

A new viral vector raises hopes for an HIV vaccine

by EE Giorgi in CHIMERAS

Because I work on HIV vaccine research, I often talk about vaccines and HIV vaccine design in particular. So far, there have been several phase I HIV vaccine trials, but very few have made it into phase III. One such case was the STEP trial, which was abruptly halted in 2007 after preliminary results showed that not only the vaccine was not protecting people from getting the virus, but the rate of HIV infections was actually higher in the vaccinated subjects compared to the subjects that receive........ Read more »

Nilu Goonetilleke, Andrew J. McMichael. (2013) Antigen Processing Takes a New Direction. Science. DOI: 10.1126/science.1239649  

Scott G. Hansen, Jonah B. Sacha, Colette M. Hughes, Julia C. Ford, Benjamin J. Burwitz, Isabel Scholz, Roxanne M. Gilbride, Matthew S. Lewis, Awbrey N. Gilliam, Abigail B. Ventura, Daniel Malouli, Guangwu Xu, Rebecca Richards, Nathan Whizin, Jason S. Reed. (2013) Cytomegalovirus Vectors Violate CD8 T Cell Epitope Recognition Paradigms. Science. DOI: 10.1126/science.1237874  

  • October 5, 2013
  • 01:07 PM

Sex Is Always Well Worth Its Two-Fold Cost

by EE Giorgi in CHIMERAS

Title borrowed from Feigel et al. [1].Sex is costly. In an asexual population, all individuals bear offsprings, resulting in a higher growth rate than in a sexual population (two-fold cost of sex). Finding a partner is risky, costly in terms of energy and resources, and it results in sexual selection which may not always favor survival. Finally, in sexual populations each individual passes only 50% of its genetic make-up to their offsprings and, furthermore, genetic recombination could break-up ........ Read more »

  • October 1, 2013
  • 07:15 AM

Ms. Stick Insect

by EE Giorgi in CHIMERAS

Image credit:  You're looking at a stick insect, a critter I was quite used to growing up as my dad, an evolutionary biologist, used to grow them at home. I know, most households have cats, dogs, guinea pigs and rabbits; ours had cats, dogs, toads, fruit flies, and stick insects. :-)Children have a tendency to personify everything, animals in particular, so imagine my shock when my dad told me that stick insects are all... ladies. Yup. It's Ms. Stick Insect. And the reason why ........ Read more »

  • September 23, 2013
  • 09:24 AM

Vaccines: what is the meaning of phase I, II and III?

by EE Giorgi in CHIMERAS

I'm often asked, "How long will it take to finally have an HIV vaccine? Are we close? What about this study that published good results on an HIV vaccine?" Right now, the HIV community is generally optimistic that we will indeed have an HIV vaccine within the next decade. This is based on the relatively recent discovery of new broadly neutralizing antibodies and the mildly positive results obtained by one of the five major efficacy trials, the RV144 Thai trial, which found a 31% reduction in HIV........ Read more »

Lawrence Corey, Gary J. Nabel, Carl Dieffenbach, Peter Gilbert, Barton F. Haynes, Margaret Johnston, James Kublin, H. Clifford Lane, Giuseppe Pantaleo, Louis J. Picker and Anthony S. Fauci. (2011) HIV-1 Vaccines and Adaptive Trial Designs. Sci Transl Med. DOI: 10.1126/scitranslmed.3001863  

  • September 15, 2013
  • 11:19 AM

Bacteria to the rescue!

by EE Giorgi in CHIMERAS

Last month I talked about a cancer killing virus. Well, guess what comes next? A cancer killing bacterium, of course! :-) Our hero is once again, the one and only E. coli, a bacteria that normally resides in our guts and that is much beloved by experimentalists because it's cheap and easy to grow. In 2011, a group from Nanyang Technological University, in Singapore, genetically modified a strain of E. coli so it would sense and kill the human pathogen Pseudomonas aeruginosa[1], a bacterium re........ Read more »

Nazanin Saeidi, Choon Kit Wong, Tat-Ming Lo, Hung Xuan Nguyen, Hua Ling, Susanna Su Jan Leong, Chueh Loo Poh . (2011) Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Molecular Systems Biology. DOI: 10.1038/msb.2011.55  

Hsuan-Chen Wu, Chen-Yu Tsao, David N Quan, Yi Cheng, Matthew D Servinsky, Karen K Carter, Kathleen J Jee, Jessica L Terrell, Amin Zargar, Gary W Rubloff, Gregory F Payne, James J Valdes . (2013) Autonomous bacterial localization and gene expression based on nearby cell receptor density. Molecular Systems Biology. DOI: 10.1038/msb.2012.71  

  • September 8, 2013
  • 10:22 AM

The HPV vaccine: a few things you should know

by EE Giorgi in CHIMERAS

If you are a young woman under 25 years of age, or if you have a teenager at home, chances are, your doctor told you about the HPV vaccine. HPV, or Human Papillomavirus is a DNA virus that infects keratinocytes, cells found in the epidermis and in mucous membranes. Though in some cases the virus causes painful warts, HPV infections are often asymptomatic. So why bother screening an asymptomatic virus? Because while the majority of the infected people clear the virus within 1-2 years, in less tha........ Read more »

Helen Trottier, Salaheddin Mahmud, José Carlos M Prado3, Joao S Sobrinho, Maria C Costa, Thomas E Rohan, Luisa L Villa and Eduardo L Franco. (2008) Type-Specific Duration of Human Papillomavirus Infection: Implications for Human Papillomavirus Screening and Vaccination. Infectious Diseases. DOI: 10.1086/587698  

Schiffman M, Castle PE, Jeronimo J, Rodriguez AC, & Wacholder S. (2007) Human papillomavirus and cervical cancer. Lancet, 370(9590), 890-907. PMID: 17826171  

  • August 22, 2013
  • 09:14 AM

Cancer-killing viruses

by EE Giorgi in CHIMERAS

We learned last time that cancer cells are cells whose DNA has been damaged beyond repair. Somatic mutations have accumulated to the point that the cell regulatory mechanisms no longer function, causing uncontrolled growth and proliferation. Despite being anomalous, cancer cells are still part of what the immune system recognizes as "self", which makes finding a cure for cancer such a hurdle. Therapy, when available, is often invasive and debilitating because the only way to make sure that all c........ Read more »

Christian Goetz, Elena Dobrikova, Mayya Shveygert, Mikhail Dobrikov . (2011) Oncolytic poliovirus against malignant glioma. Future Virology. DOI: 10.2217/fvl.11.76  

  • August 18, 2013
  • 08:12 PM

Is there such thing as over-editing?

by EE Giorgi in CHIMERAS

 A while ago I wrote a post based on JS Mattick's work [1] on RNA editing, the introduction of changes in RNA molecules after they have been translated from a gene. This kind of editing confers a certain adaptability to the protein without changing the gene that codes for it. Bacteria and viruses, for example, undergo extensive RNA editing in order to constantly re-adapt to the host's immune response. In eukaryotes RNA editing is rarer, but it still happens and is involved in many epigeneti........ Read more »

Ludmil B. Alexandrov, Serena Nik-Zainal, David C. Wedge, Samuel A. J. R. Aparicio, Sam Behjati, Andrew V. Biankin, Graham R. Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale, Sandrine Boyault, Birgit Burkhardt, Adam P. Butler, Carl. (2013) Signatures of mutational processes in human cancer. Nature. DOI: 10.1038/nature12477  

  • June 8, 2013
  • 09:03 AM

The virus-antibody arms race

by EE Giorgi in CHIMERAS

One of the new concepts I learned when I started working on HIV was the most recent common ancestor, or MRCA. When you look at the genetic make-up of a population, you will find a certain amount of variety but also a much greater amount of overlap, i.e. stretches of DNA that are identical throughout the population. Using phylogenetics, one can look at these patterns of shared vs. mutated stretches, and reconstruct the genetic ancestor of the population. For example, you've probably heard of Mito........ Read more »

Liao, H., Lynch, R., Zhou, T., Gao, F., Alam, S., Boyd, S., Fire, A., Roskin, K., Schramm, C., Zhang, Z.... (2013) Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature, 496(7446), 469-476. DOI: 10.1038/nature12053  

  • May 23, 2013
  • 09:21 AM

Should you worry about vitamin D deficiency? Maybe. Or maybe not.

by EE Giorgi in CHIMERAS

Since my last blog post, where I shared my thoughts on BRCA1, BRCA2, and preventive mastectomies, I've been asked what else can a woman do to reduce her risk of breast cancer. I've heard a big deal about vitamin D, so I did a bit of research on the matter. As a disclaimer, I should tell you up front that, though many correlations between vitamin D deficiency and cancer risk have been found, just as many have been refuted or found inconclusive. You can read more about it on the wikipedia page.Wha........ Read more »

  • May 16, 2013
  • 07:34 PM

Angelina no longer has them. Does that mean I should get rid of them too?

by EE Giorgi in CHIMERAS

We love them and yet we hate them. They get censored, augmented, reduced, replaced, covered, exposed. They get grilled, occasionally, but those are not the ones I'm talking about. We want to see them and yet we pretend we don't. We criticize them and yet we forget what they are made for, the most beautiful thing of all: nourish a new life.Yes, I'm talking about breasts. Angelina Jolie's breasts have been extensively discussed this week, more now that they are reportedly gone than when they were ........ Read more »

  • May 5, 2013
  • 11:44 AM

Pumping fuel from bacteria

by EE Giorgi in CHIMERAS

In my last post I discussed a bioengineered E. coli strain capable of producing an engine compatible biofuel. I hailed the finding as more efficient than ordinary biofuels because this technique has less environmental impact than biofuels from crops, for example, or cellulose, which instead use great amounts of water and forest land. I did some more reading on the topic and found out that, surprise surprise, there are some costs in harvesting biofuels from bacteria as well, so my discussion was ........ Read more »

Dunlop, M., Dossani, Z., Szmidt, H., Chu, H., Lee, T., Keasling, J., Hadi, M., & Mukhopadhyay, A. (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Molecular Systems Biology. DOI: 10.1038/msb.2011.21  

Doshi, R., Nguyen, T., & Chang, G. (2013) Transporter-mediated biofuel secretion. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1301358110  

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