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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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  • October 4, 2011
  • 06:51 AM

Gene therapy makes sense. And antisense, too!

by EE Giorgi in CHIMERAS

Genes code proteins. When a gene carries a defective mutation, it will either stop coding the protein or it will code a defective one. This is, unfortunately, the basis of many genetic diseases. In principle, if we could substitute the defective gene with a healthy one, the problem would be solved. That's what gene therapy boils down to. In fact, there are ways to deliver the genes to the affected cells. For example, you can take a virus that targets the cells where the defective gene is express........ Read more »

Suto, R., Tominaga, K., Mizuguchi, H., Sasaki, E., Higuchi, K., Kim, S., Iwao, H., & Arakawa, T. (2004) Dominant-negative mutant of c-Jun gene transfer: a novel therapeutic strategy for colorectal cancer. Gene Therapy, 11(2), 187-193. DOI: 10.1038/  

Morgan RA, Dudley ME, Wunderlich JR, Hughes MS, Yang JC, Sherry RM, Royal RE, Topalian SL, Kammula US, Restifo NP.... (2006) Cancer regression in patients after transfer of genetically engineered lymphocytes. Science (New York, N.Y.), 314(5796), 126-9. PMID: 16946036  

Zhang Y, Zhu C, & Pardridge WM. (2002) Antisense gene therapy of brain cancer with an artificial virus gene delivery system. Molecular therapy : the journal of the American Society of Gene Therapy, 6(1), 67-72. PMID: 12095305  

  • September 30, 2011
  • 08:02 PM

Deep sequencing and forensic science: how to improve DNA fingerprinting

by EE Giorgi in CHIMERAS

(In case you missed it, this originally appeared last Thursday as a guest blog on the Writer's Forensics Blog.)There are roughly three billion pairs of nucleotides in human DNA, and the vast majority is identical across individuals. When we talk about “genetic fingerprinting,” we really mean, “looking for a needle in a hay stack.” Luckily, for the most part, we all differ at the same loci. Over the years, the techniques used for DNA typing have improved greatly, diminishing both costs an........ Read more »

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z.... (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437(7057), 376-80. PMID: 16056220  

Fordyce SL, Ávila-Arcos MC, Rockenbauer E, Børsting C, Frank-Hansen R, Petersen FT, Willerslev E, Hansen AJ, Morling N, & Gilbert MT. (2011) High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform. BioTechniques, 51(2), 127-33. PMID: 21806557  

  • September 26, 2011
  • 08:36 AM

Overlapping genes, nested genes, and antisense genes: how complex can genomes be?

by EE Giorgi in CHIMERAS

HIV has 10 genes spread throughout roughly 10 thousand nucleotides. The genes Rev and Tat (and Tev, when it’s present), completely overlap with the larger gene Env. When a gene lies within another, we say that the two genes are “nested.” How does the virus know which protein to code if the information is overlapping? The key is the “reading frame.” Remember, a gene is a string of nucleotides (A, G, C, and T), and a protein is a string of amino acids (also denoted with letters), so it r........ Read more »

Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, & Cui H. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature, 451(7175), 202-6. PMID: 18185590  

Guo JH, Cheng HP, Yu L, & Zhao S. (2006) Natural antisense transcripts of Alzheimer's disease associated genes. DNA sequence : the journal of DNA sequencing and mapping, 17(2), 170-3. PMID: 17076261  

Chatterjee A, Johnson CM, Shu CC, Kaznessis YN, Ramkrishna D, Dunny GM, & Hu WS. (2011) Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation. Proceedings of the National Academy of Sciences of the United States of America, 108(23), 9721-6. PMID: 21606359  

  • September 22, 2011
  • 06:23 PM

Can gene therapy eradicate HIV?

by EE Giorgi in CHIMERAS

When I learned about this, my jaw dropped. It almost felt like the old light bulb joke: is it easier to screw in the bulb or to turn the ladder? It turns out, when it comes to HIV, the question is not so ill-posed.HIV infects white cells in our blood called T-cells. It captures a receptor on the cell surface called CCR5, and once it grabs it, it docks with the cell and infects it. T-cells are part of our immune system and they attack the virus as well. Ever since I started working on HIV, the pr........ Read more »

Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, & Berger EA. (1996) CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science (New York, N.Y.), 272(5270), 1955-8. PMID: 8658171  

van Lunzen J, Fehse B, & Hauber J. (2011) Gene therapy strategies: can we eradicate HIV?. Current HIV/AIDS reports, 8(2), 78-84. PMID: 21331536  

  • September 18, 2011
  • 09:33 AM

Is an HIV vaccine finally possible? Unraveling the secrets of broadly neutralizing antibodies

by EE Giorgi in CHIMERAS

Last month I talked about the daunting challenge that HIV has presented for the past thirty years. HIV is so variable that as soon as the immune system builds a defense against it, the virus comes up with a new variant that allows it to escape. The only way to defeat such an elusive enemy is with immune responses able to recognize a broad range of HIV subtypes and variants. Unfortunately, antibodies with these characteristics are produced by a minority of patients and only years into the infecti........ Read more »

Wu, X., Zhou, T., Zhu, J., Zhang, B., Georgiev, I., Wang, C., Chen, X., Longo, N., Louder, M., McKee, K.... (2011) Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing. Science, 333(6049), 1593-1602. DOI: 10.1126/science.1207532  

Scheid, J., Mouquet, H., Ueberheide, B., Diskin, R., Klein, F., Oliveira, T., Pietzsch, J., Fenyo, D., Abadir, A., Velinzon, K.... (2011) Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding. Science, 333(6049), 1633-1637. DOI: 10.1126/science.1207227  

  • September 15, 2011
  • 12:22 PM

All you need is love... and the right alleles

by EE Giorgi in CHIMERAS

It's been called the "love hormone" because studies have shown that it is released during labor and breastfeeding. Children soothed by their mothers produce it, and, apparently, it has a role in easing social interactions. Oxytocin is a hormone secreted by the pituitary gland. It is a neurotransmitter, which basically means that it helps send signals from the brain to the receiving cells.OXTR is the oxytocin gene receptor, in other words, this gene codes the protein that sits on t........ Read more »

Saphire-Bernstein, S., Way, B., Kim, H., Sherman, D., & Taylor, S. (2011) Oxytocin receptor gene (OXTR) is related to psychological resources. Proceedings of the National Academy of Sciences, 108(37), 15118-15122. DOI: 10.1073/pnas.1113137108  

  • September 11, 2011
  • 11:46 AM

How did that pesky virus end up in our DNA?

by EE Giorgi in CHIMERAS

Last time we talked about the different types of genetic and epigenetic chimeras. We learned what a chimeric virus is, and that retroviruses need to get integrated into the host's DNA in order to replicate. They basically inject their RNA into the cell, the RNA gets transformed into DNA, the viral DNA enters the cell's nucleus and once in the the nucleus it's integrated into the cell's DNA.This process has been going on for as long as viruses have existed. And viruses have existed for a long tim........ Read more »

Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, & Spencer TE. (2006) Endogenous retroviruses regulate periimplantation placental growth and differentiation. Proceedings of the National Academy of Sciences of the United States of America, 103(39), 14390-5. PMID: 16980413  

  • November 30, 1999
  • 12:00 AM

More on the viruses inside us: retrotransposons

by EE Giorgi in CHIMERAS

Retrotransposons... Read more »

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