130 posts · 83,180 views
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
130 posts
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- May 16, 2013
- 07:34 PM
- 39 views
Angelina no longer has them. Does that mean I should get rid of them too?
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 »
Hall, J., Lee, M., Newman, B., Morrow, J., Anderson, L., Huey, B., & King, M. (1990) Linkage of early-onset familial breast cancer to chromosome 17q21. Science, 250(4988), 1684-1689. DOI: 10.1126/science.2270482
Bernstein, L. (2008) Identifying population-based approaches to lower breast cancer risk. Oncogene. DOI: 10.1038/onc.2009.348
- May 5, 2013
- 11:44 AM
- 49 views
Pumping fuel from bacteria
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
- May 1, 2013
- 09:24 AM
- 51 views
Fill the tank, please. With bacteria!
I apologize if you've already heard about this, but the paper is really cool and I couldn't resist discussing it here.Escherichia coli, or E. coli for brevity, is a bacterium normally associated with "bad" things like food poisoning. Even though most strains are actually harmless, even the CDC has a page dedicated to E. coli outbreaks. Since it's part of our gut flora, the lower intestines in particular, it's usually not a good sign when E. coli is found in places like restaurants and cafeterias........ Read more »
Howard, T., Middelhaufe, S., Moore, K., Edner, C., Kolak, D., Taylor, G., Parker, D., Lee, R., Smirnoff, N., Aves, S.... (2013) Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1215966110
Schirmer, A., Rude, M., Li, X., Popova, E., & del Cardayre, S. (2010) Microbial Biosynthesis of Alkanes. Science, 329(5991), 559-562. DOI: 10.1126/science.1187936
- April 26, 2013
- 03:46 PM
- 76 views
North Korea and the USA can indeed unite: in the battle against TB.
Tuberculosis (TB) is an infectious disease caused by a bacterium. It spreads through cough or sneeze from subjects with an active infection. While in most cases the disease is asymptomatic, a minority of latent infections does become active (i.e. the subject develops symptoms), and when it does, if left untreated, the disease can be deadly. According to the CDC one third of the world's population are infected with TB, and while in the US the incidence of the disease has been declining over time,........ Read more »
Stone, R. (2013) Public Enemy Number One. Science, 340(6131), 422-425. DOI: 10.1126/science.340.6131.422
- April 18, 2013
- 07:36 PM
- 99 views
Can we functionally cure HIV?
Last March, Dr. Deborah Persaud, from the John's Hopkins Children Center, presented a stunning finding at the conference CROI, receiving great resonance across several newscasts: Persaud reported the first case of infant functionally cured of HIV. You can watch Persaud's presentation by downloading the podcast here, it's the seventh talk of the session "Is there hope for HIV eradication?"Up until this finding, the only living person cured from HIV was the Berlin Patient, who was cured after rece........ Read more »
Persaud, D., Palumbo, P., Ziemniak, C., Hughes, M., Alvero, C., Luzuriaga, K., Yogev, R., Capparelli, E., & Chadwick, E. (2012) Dynamics of the resting CD4 T-cell latent HIV reservoir in infants initiating HAART less than 6 months of age. AIDS, 26(12), 1483-1490. DOI: 10.1097/QAD.0b013e3283553638
Sáez-Cirión, A., Bacchus, C., Hocqueloux, L., Avettand-Fenoel, V., Girault, I., Lecuroux, C., Potard, V., Versmisse, P., Melard, A., Prazuck, T.... (2013) Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study. PLoS Pathogens, 9(3). DOI: 10.1371/journal.ppat.1003211
- February 14, 2013
- 07:20 PM
- 192 views
Antiviral drugs to fight the flu: yes or no?
Disclaimer: I'm not a medical doctor. I cannot recommend taking or not taking a certain drug. However, I am a human being, I've got kids who do get sick from time to time, and I work on viruses. So when I heard that people were battling the unusually nasty flu this year with antiviral drugs, well, I had to do a bit of research. Antiviral drugs have become increasingly popular after the highly pathogenic avian flu strain emerged. The idea is that in order to be prepared for a possible pandemic, w........ Read more »
Jefferson, T., Jones, M., Doshi, P., & Del Mar, C. (2009) Neuraminidase inhibitors for preventing and treating influenza in healthy adults: systematic review and meta-analysis. BMJ, 339(dec07 2). DOI: 10.1136/bmj.b5106
Kay Wang, Matthew Shun-Shin, Peter Gill, Rafael Perera, Anthony Harnden. (2012) Neuraminidase inhibitors for preventing and treating influenza in children (published trials only). The Cochrane Library. DOI: 10.1002/14651858.CD002744.pub4
Tom Jefferson, Mark A Jones, Peter Doshi, Chris B Del Mar, Carl J Heneghan, Rokuro Hama, Matthew J Thompson. (2012) Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children. The Cochrane Library. DOI: 10.1002/14651858.CD008965.pub3
Urushihara, H., Doi, Y., Arai, M., Matsunaga, T., Fujii, Y., Iino, N., Kawamura, T., & Kawakami, K. (2011) Oseltamivir Prescription and Regulatory Actions Vis-à-Vis Abnormal Behavior Risk in Japan: Drug Utilization Study Using a Nationwide Pharmacy Database. PLoS ONE, 6(12). DOI: 10.1371/journal.pone.0028483
- December 10, 2012
- 09:30 AM
- 167 views
Whole genome harvesting
You think the human genome, with its three billion base pairs and 23 chromosome pairs, is too complex to unravel? Turns out, the wheat genome is six times as big and it's hexaploid, in other words, instead of chromosome pairs it's organized in chromosome sextets! I've recently discussed genetically modified organisms, crops in particular, and while I still can't provide a definite answer on whether they are absolutely good or absolutely bad, one thing struck me as relevant as I was researching t........ Read more »
Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G., D’Amore, R., Allen, A., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D.... (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491(7426), 705-710. DOI: 10.1038/nature11650
Mayer, K., Waugh, R., Langridge, P., Close, T., Wise, R., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbauer, G.... (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature. DOI: 10.1038/nature11543
- December 7, 2012
- 09:30 AM
- 235 views
The simulated brain
His name is Spaun, which stands for Semantic Pointer Architecture Unified Network, and he's a brain -- a simulated, brain. His 2.5 million neurons, organized in subsystems that simulate different brain areas, allow Spaun to perform tasks such as image recognition and recalling sequences, and respond through a motor arm. For example, Spaun can recognize numbers on a screen and write them on a piece of paper. Spaun is the brain child (pun intended!) of authors Eliasmith et al. [1]. It models three........ Read more »
Eliasmith, C., Stewart, T., Choo, X., Bekolay, T., DeWolf, T., Tang, Y., & Rasmussen, D. (2012) A Large-Scale Model of the Functioning Brain. Science, 338(6111), 1202-1205. DOI: 10.1126/science.1225266
- November 19, 2012
- 09:33 AM
- 249 views
Proteins as gene carriers
By now you probably know everything about pluripotent stem cells, right? They are the hot topic in genetics right now, to the point that the fear of being scooped has pushed some people to lie about their results. Pluripotent stem cells are cells that have the ability to divide into a specialized cell and another undifferentiated cell. This of course is greatly useful in repairing damaged organs and/or regenerating tissue, and has great potential in medicine.Lately there has been a lot of buzz o........ Read more »
Lee, J., Sayed, N., Hunter, A., Au, K., Wong, W., Mocarski, E., Pera, R., Yakubov, E., & Cooke, J. (2012) Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming. Cell, 151(3), 547-558. DOI: 10.1016/j.cell.2012.09.034
- October 29, 2012
- 07:26 PM
- 258 views
GMOs love me, GMOs love me not..
I've been asked to discuss genetically modified foods and I confess I've been procrastinating. Why? Because I don't have an answer on whether or not GMOs are good or bad, and I can't offer one. But, what I can do is offer a few thoughts. Food for thought is usually super-natural, organic, and pesticide-free, so here it goes. :-)1. What are GMOs? Technically, all domesticated plants and animals are "genetically modified" since, rather than letting the species evolve through natural selection, man........ Read more »
Baker, M. (2012) Companies set to fight food-label plan. Nature, 488(7412), 443-443. DOI: 10.1038/488443a
Ronald, P. (2011) Plant Genetics, Sustainable Agriculture and Global Food Security. Genetics, 188(1), 11-20. DOI: 10.1534/genetics.111.128553
- October 22, 2012
- 09:30 AM
- 293 views
Lorenzo's oil got upgraded to stem cell research
Have you seen the 1992 movie Lorenzo's oil? The film portrays the true (and sad!) story of Lorenzo Odone, who, at age 6, was diagnosed with adrenoleukodystrophy, one of the most common forms of leukodystrophies, a family of degenerative diseases that affects the growth of the myelin sheath. Myelin wraps around nerve fibers creating a fatty covering that increases the speed at which impulses propagate. Leukodystrophy is a genetic disorder caused by mutations in the genes that code myelin proteins........ Read more »
Uchida, N., Chen, K., Dohse, M., Hansen, K., Dean, J., Buser, J., Riddle, A., Beardsley, D., Wan, Y., Gong, X.... (2012) Human Neural Stem Cells Induce Functional Myelination in Mice with Severe Dysmyelination. Science Translational Medicine, 4(155), 155-155. DOI: 10.1126/scitranslmed.3004371
Gupta, N., Henry, R., Strober, J., Kang, S., Lim, D., Bucci, M., Caverzasi, E., Gaetano, L., Mandelli, M., Ryan, T.... (2012) Neural Stem Cell Engraftment and Myelination in the Human Brain. Science Translational Medicine, 4(155), 155-155. DOI: 10.1126/scitranslmed.3004373
- October 19, 2012
- 07:45 PM
- 331 views
Why extra fat is bad, even when it's in the "right" spots.
Have you been thinking of going on a diet but haven't found the right motivation yet? How about this one: fat feeds tumor cells and enhances their growth. And another question, for the ladies this time: have you ever wondered how those annoying love handles would look so much better inside a bra? No, I don't mean to put a bra around my waist, rather to move that bit of fat up to my chest . . . Somehow the two things are related. Stay with me and I'll explain.Numerous studies have shown that obes........ Read more »
Zhang, Y., Daquinag, A., Amaya-Manzanares, F., Sirin, O., Tseng, C., & Kolonin, M. (2012) Stromal Progenitor Cells from Endogenous Adipose Tissue Contribute to Pericytes and Adipocytes That Populate the Tumor Microenvironment. Cancer Research, 72(20), 5198-5208. DOI: 10.1158/0008-5472.CAN-12-0294
Yoshimura, K., Sato, K., Aoi, N., Kurita, M., Hirohi, T., & Harii, K. (2007) Cell-Assisted Lipotransfer for Cosmetic Breast Augmentation: Supportive Use of Adipose-Derived Stem/Stromal Cells. Aesthetic Plastic Surgery, 32(1), 48-55. DOI: 10.1007/s00266-007-9019-4
- October 16, 2012
- 11:21 AM
- 275 views
Reprogrammable cells
Can't remember if I already shared the above picture... it's my favorite sunset shot so far, so forgive me if it's a deja vu.The Nobel Prize in medicine this year was awarded to John Gurdon and Shinya Yamanaka for pioneering the reprogramming of cells into an embryonic-like state. Embryonic stem cells are cells that undergo asymmetric division, as they divide into an undifferentiated cell and into a specialized cell. This way, they can grow indefinitely while maintaining their undifferentiated s........ Read more »
Takahashi, K., & Yamanaka, S. (2006) Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell, 126(4), 663-676. DOI: 10.1016/j.cell.2006.07.024
Serwold, T., Hochedlinger, K., Swindle, J., Hedgpeth, J., Jaenisch, R., & Weissman, I. (2010) T-cell receptor-driven lymphomagenesis in mice derived from a reprogrammed T cell. Proceedings of the National Academy of Sciences, 107(44), 18939-18943. DOI: 10.1073/pnas.1013230107
- October 11, 2012
- 09:41 AM
- 325 views
Gene therapy goes... topical
The paper I'm discussing today is so cool, I don't know how I missed it when it came out last July. As the name implies, gene therapy is a technique used to "fix" defective genes either by replacing them with fully functional ones or by silencing them with the use of antisense RNA. Defective genes either fail to produce the proteins they code for, or produce defective proteins, thus causing genetic disorders. A defective gene can be silenced (so that it will no longer produce the defective prote........ Read more »
Dan Zheng, David A. Giljohann, David L. Chen, Matthew D. Massich, Xiao-Qi Wang, Hristo Iordanov, Chad A. Mirkina, & Amy S. Paller. (2012) Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation. PNAS. DOI: 10.1073/pnas.1118425109
- October 4, 2012
- 09:55 AM
- 270 views
Limb regeneration: a lesson from salamanders
As much as we would love to enlist limb regeneration among modern science's best accomplishments, so far it is still very much confined to science fiction. That doesn't mean it won't happen, though. Key to limb regeneration is cellular reprogramming that allows differentiated cells to return to a germline-like (undifferentiated) state. Genes involved in embryonic development need to be reactivated in order to restart the same process that created the limb during the growth of the embryo. The ver........ Read more »
Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, & Tony Hunter. (2012) Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Developmental Biology. DOI: 10.1016/j.ydbio.2012.07.021
- October 1, 2012
- 09:30 AM
- 250 views
The sleep conundrum
How many hours of night sleep do you get? Are you ever surprised at how many more/less hours other people sleep? Well, if you are, you might find comfort knowing that the variation in number of sleep hours across species is huge and, so far, very much an evolutionary mystery. Common thought is that sleep provides us with a much necessary "recharging" and common that it has an evolutionary advantage. However, it takes time away from foraging/preying and mating, and makes individuals more vulnerab........ Read more »
John A. Lesku, Niels C. Rattenborg, Mihai Valcu, Alexei L. Vyssotski, Sylvia Kuhn, Franz Kuemmeth, Wolfgang Heidrich, & Bart Kempenaers. (2012) Adaptive Sleep Loss in Polygynous Pectoral Sandpipers. Science. DOI: 10.1126/science.1220939
- September 27, 2012
- 09:13 AM
- 265 views
Healthy habits are easier when you stop thinking about it
Raising health awareness has done little so far in actually improving global health. Humans seem to be stubbornly attached to certain behaviors, even when fully aware that such behaviors pose a health risk. Currently, the four most prevalent noncommunicable diseases are diabetes, cardiovascular disease, lung disease, and cancer. The risk of death from any of the four can be significantly lowered by changing basic behaviors such as lowering the consumption of calories, alcohol and tobacco, while ........ Read more »
Theresa M. Marteau, Gareth J. Hollands, & Paul C. Fletcher. (2012) Changing Human Behavior to Prevent Disease: The Importance of Targeting Automatic Processes. Science. info:/
- September 24, 2012
- 09:48 AM
- 239 views
ENCODE sheds light on non-coding variants
Back when I started studying human genetics, we were still doing single-gene associations. Namely, we would type a bunch of variants in a single gene and then do a case-control association study to see which, if any, of those variants marked an increase in disease risk. That's how breast cancer markers such as BRCA1 and BRCA2 have been found.When the Human Genome Project was completed in 2003, scientists started looking for disease risk alleles across the whole genome. The findings were puzzling........ Read more »
Matthew T. Maurano, Richard Humbert, Eric Rynes, Robert E. Thurman, Eric Haugen, Hao Wang, Alex P. Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody.... (2012) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. DOI: 10.1126/science.1222794
- September 20, 2012
- 09:53 AM
- 236 views
The encyclopedia of DNA - Part III
The ENCODE project effectively marked the transition from genomics to functional genomics. The goal of the Human Genome Project was to type the entire human genome. Once that was achieved people realized they had just scraped the tip of the iceberg. Today, the goal of functional genomics is go one step beyond DNA sequences, and understand the dynamics of gene expression, transcription, translation and all the complex pathways that lead from DNA to the making of proteins. In order to do this, the........ Read more »
Robert E. Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T. Maurano, Eric Haugen, Nathan C. Sheffield, & Andrew B. Stergachis, et al. (2012) The accessible chromatin landscape of the human genome. Nature. DOI: 10.1038/nature11232
- September 17, 2012
- 09:30 AM
- 278 views
The enciclopedia of DNA - Part II
Last week I started discussing the exciting news about the six ENCODE papers published in the Nature September 6 issue. If you haven't already, I highly recommend reading the review ENCODE explained [1], which has a nice summary of the papers and an excellent perspective on what these results mean. One paragraph in particular is worth quoting:"The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA’s transcription in........ Read more »
Joseph R. Ecker,, Wendy A. Bickmore,, Inês Barroso,, Jonathan K. Pritchard,, Yoav Gilad, & . (2012) Genomics: ENCODE explained. Nature. DOI: 10.1038/489052a
Sarah Djebali,, Carrie A. Davis,, Angelika Merkel,, Alex Dobin,, Timo Lassmann,, Ali Mortazavi,, Andrea Tanzer,, Julien Lagarde,, Wei Lin,, Felix Schlesinger,.... (2012) Landscape of transcription in human cells. Nature. DOI: 10.1038/nature11233
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