CHIMERAS

Visit Blog Website

188 posts · 214,056 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
188 posts

Sort by: Latest Post, Most Popular

View by: Condensed, Full

  • May 1, 2013
  • 09:24 AM
  • 840 views

Fill the tank, please. With bacteria!

by EE Giorgi in CHIMERAS

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
  • 742 views

North Korea and the USA can indeed unite: in the battle against TB.

by EE Giorgi in CHIMERAS

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
  • 739 views

Can we functionally cure HIV?

by EE Giorgi in CHIMERAS

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 »

  • February 14, 2013
  • 07:20 PM
  • 854 views

Antiviral drugs to fight the flu: yes or no?

by EE Giorgi in CHIMERAS

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 »

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  

  • December 10, 2012
  • 09:30 AM
  • 648 views

Whole genome harvesting

by EE Giorgi in CHIMERAS

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
  • 634 views

The simulated brain

by EE Giorgi in CHIMERAS

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
  • 806 views

Proteins as gene carriers

by EE Giorgi in CHIMERAS

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
  • 1,155 views

GMOs love me, GMOs love me not..

by EE Giorgi in CHIMERAS

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 »

  • October 22, 2012
  • 09:30 AM
  • 904 views

Lorenzo's oil got upgraded to stem cell research

by EE Giorgi in CHIMERAS

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
  • 923 views

Why extra fat is bad, even when it's in the "right" spots.

by EE Giorgi in CHIMERAS

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 »

  • October 16, 2012
  • 11:21 AM
  • 907 views

Reprogrammable cells

by EE Giorgi in CHIMERAS

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 »

  • October 11, 2012
  • 09:41 AM
  • 1,189 views

Gene therapy goes... topical

by EE Giorgi in CHIMERAS

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
  • 800 views

Limb regeneration: a lesson from salamanders

by EE Giorgi in CHIMERAS

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
  • 830 views

The sleep conundrum

by EE Giorgi in CHIMERAS

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
  • 714 views

Healthy habits are easier when you stop thinking about it

by EE Giorgi in CHIMERAS

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
  • 681 views

ENCODE sheds light on non-coding variants

by EE Giorgi in CHIMERAS

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
  • 658 views

The encyclopedia of DNA - Part III

by EE Giorgi in CHIMERAS

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
  • 710 views

The enciclopedia of DNA - Part II

by EE Giorgi in CHIMERAS

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  

  • September 10, 2012
  • 10:14 AM
  • 599 views

The encyclopedia of DNA - Part I

by EE Giorgi in CHIMERAS

The raw numbers of the human genome: three billion base pairs, of which roughly 1% fall into the 20,000 genes in our genome. So, what's all the extra stuff for?Typing the whole human genome, in 2001, was only the beginning. The next step in disentangling the puzzle was to assign biochemical functions to those three billion base pairs. "The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elemen........ Read more »

  • September 3, 2012
  • 06:53 PM
  • 908 views

Transcription factories for gene expression: the hard working units of the nucleus

by EE Giorgi in CHIMERAS

You've probably heard it many times already: if you could stretch out the DNA contained in any one nucleated cell in your body, it would be 2 meters (~6 feet) long. Now imagine packing this 2-meter long molecule into a sphere whose diameter is of the order of a few micrometers, roughly one millionth smaller than a meter. Yes, it's going to be packed in there, yet those genes have to be accessible to the "workers" that come in and perform daily tasks such as gene transcription, replication, and D........ Read more »

join us!

Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.

If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.

Register Now

Research Blogging is powered by SRI Technology.

To learn more, visit http://selfregulationinstitute.org/.