CHIMERAS

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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
164 posts

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  • December 7, 2014
  • 11:23 AM
  • 99 views

Synthetic gene circuits with a memory!

by EE Giorgi in CHIMERAS

Imagine having a USB port in the body that we could use to insert a "flash drive" and transfer genetic data, therapies, or monitoring devices. The flash drive would have to be some kind of removable biological entity that has no problem getting in and out of the body. If you think about it, bacteria are the perfect candidates to be such devices. So, what if bacteria could be used as storage for genetic memory? This is not so far-fetched if you think that recent studies have shown for example tha........ Read more »

Ausländer D, Ausländer S, Charpin-El Hamri G, Sedlmayer F, Müller M, Frey O, Hierlemann A, Stelling J, & Fussenegger M. (2014) A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Molecular cell, 55(3), 397-408. PMID: 25018017  

  • November 8, 2014
  • 10:59 AM
  • 141 views

Are we really evolving into super-humans?

by EE Giorgi in CHIMERAS

© EEGI came across an article on the Popular Science website, which, turns out, is the excerpt of a new book on evolution by Science Guy Bill Nye. From the reviews I gather that Bill Nye is an excellent writer and, being also an entertainer, he knows how to not only expose well but also infuse some good humor to what he says. That's all fantastic. But while the article starts off with some rigor, his conclusion had me roll my eyes. Because, even though he does include some speculations th........ Read more »

Salih NA, Hussain AA, Almugtaba IA, Elzein AM, Elhassan IM, Khalil EA, Ishag HB, Mohammed HS, Kwiatkowski D, & Ibrahim ME. (2010) Loss of balancing selection in the betaS globin locus. BMC medical genetics, 21. PMID: 20128890  

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  

Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, & Pritchard JK. (2009) The role of geography in human adaptation. PLoS genetics, 5(6). PMID: 19503611  

  • November 2, 2014
  • 09:47 AM
  • 164 views

The heritability of fears

by EE Giorgi in CHIMERAS

Cyborg © EEGAs many of you know, one of my favorite topics here on the blog is epigenetic inheritance, i.e. the mechanisms that regulate changes in gene expression that can be passed from one generation to the next. Epigenetics has revolutionized the way we look at genetic inheritance: Darwin had taught us that the only way the environment can shape the genome of a species is through natural selection. While this is certainly still true, today we also know that:1) Most of the mutations we see i........ Read more »

  • October 26, 2014
  • 11:00 AM
  • 194 views

Ebola could mutate as rapidly as the flu

by EE Giorgi in CHIMERAS

© Science MagazineThe largest genomic data collected on the Ebola virus to date has been recently published in Science [1], giving unique insights on the origin and spread of the greatest Ebola outbreak so far. The Ebola virus was first discovered in 1976, when it caused 318 cases: until now, it was the largest outbreak. "The current outbreak started in February 2014 in Guinea, West Africa, and spread into Liberia in March, Sierra Leone in May, and Nigeria in late July. It is the largest known ........ Read more »

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G.... (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science (New York, N.Y.), 345(6202), 1369-72. PMID: 25214632  

  • October 19, 2014
  • 11:00 AM
  • 178 views

Ten years into the making, the HIV-1 mosaic vaccine finally goes into human trial

by EE Giorgi in CHIMERAS

© Bette Korber et al. I hope you will all forgive me if this week I'm gushing over my amazing mentor Bette Korber, as last week she shared some awesome news on Facebook:"A landmark in my life happened yesterday, a major step in a long story. A decade ago I had an idea for making an HIV vaccine that had the potential to work globally. After a struggle (in my first 2 failed proposals, reviewers declared what I proposed was impossible), I got an internal grant from Los Alamos to develop the idea (........ Read more »

Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD.... (2007) Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nature medicine, 13(1), 100-6. PMID: 17187074  

Nkolola JP, Bricault CA, Cheung A, Shields J, Perry J, Kovacs JM, Giorgi E, van Winsen M, Apetri A, Brinkman-van der Linden EC.... (2014) Characterization and immunogenicity of a novel mosaic M HIV-1 gp140 trimer. Journal of virology, 88(17), 9538-52. PMID: 24965452  

Barouch DH, Stephenson KE, Borducchi EN, Smith K, Stanley K, McNally AG, Liu J, Abbink P, Maxfield LF, Seaman MS.... (2013) Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys. Cell, 155(3), 531-9. PMID: 24243013  

Barouch DH, O'Brien KL, Simmons NL, King SL, Abbink P, Maxfield LF, Sun YH, La Porte A, Riggs AM, Lynch DM.... (2010) Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nature medicine, 16(3), 319-23. PMID: 20173752  

  • October 12, 2014
  • 10:55 AM
  • 199 views

Is EV-D68 causing mysterious polio-like symptoms in children?

by EE Giorgi in CHIMERAS

Bubble fun at the Santa Fe Renaissance Fair © EEG One of the twists in my latest book, Gene Cards, is an unknown pathogen threatening the fictional city of Liasis. I confess that when I came up with the idea I was a little nervous. My story is set in the future, and with all the state-of-the-art technology we already have, is it feasible to think that we will still deal with diseases without a known causative agent? The thing is, new viruses and new pathogens arise all the time. Take the f........ Read more »

Zangwill KM, Yeh SH, Wong EJ, Marcy SM, Eriksen E, Huff KR, Lee M, Lewis EM, Black SB, & Ward JI. (2010) Paralytic syndromes in children: epidemiology and relationship to vaccination. Pediatric neurology, 42(3), 206-12. PMID: 20159431  

  • August 17, 2014
  • 11:26 AM
  • 427 views

A mosaic vaccine that could potentially protect from different ebola strains

by EE Giorgi in CHIMERAS

Disclaimer: The mosaic vaccine paper discussed in this article is from my own group and overlaps with some of the research I do. I'm sure you've been following the latest news about the Ebola virus outbreak in Africa."The Ebola outbreak in West Africa is the world's deadliest to date and the World Health Organization has declared an international health emergency as more than 1,000 people have died of the virus in Guinea, Liberia, Sierra Leone and Nigeria this year." [Source: BBC News]The e........ Read more »

Friedrich BM, Trefry JC, Biggins JE, Hensley LE, Honko AN, Smith DR, & Olinger GG. (2012) Potential vaccines and post-exposure treatments for filovirus infections. Viruses, 4(9), 1619-50. PMID: 23170176  

Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD.... (2007) Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nature medicine, 13(1), 100-6. PMID: 17187074  

  • May 21, 2014
  • 09:06 AM
  • 304 views

The Human Knock-out: looking for non-working genes

by EE Giorgi in CHIMERAS

© EEGThe word "knock-out" in biology is used for lab animals like mice, for example, when one of their genes is silenced in order to study the effects of not having that gene. Silencing a gene (or knocking it out, hence the nomenclature "knock-out mouse") means that gene is no longer producing the protein it codes for. This is a condition sought for in situations where you have to test for a drug and hence the first step is to reproduce the genetic condition that caused the disease. Mice are of........ Read more »

MacArthur, D., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J., Montgomery, S.... (2012) A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. Science, 335(6070), 823-828. DOI: 10.1126/science.1215040  

Kaiser, J. (2014) The Hunt for Missing Genes. Science, 344(6185), 687-689. DOI: 10.1126/science.344.6185.687  

  • May 17, 2014
  • 12:59 PM
  • 330 views

Viruses and bacteria could be the missing piece in the missing heritability puzzle

by EE Giorgi in CHIMERAS

© EEGI've discussed the issue of the missing heritability before: in layman words, same mutations shared across people don't lead to the same phenotype. This is particularly true for diseases. Many whole genome studies have looked at possible associations between DNA mutations and diseases, but, alas, the mutations that have been found generally explain only 10% of the cases. This suggests that there's a lot more to who and what we are than genes alone, and that complex interactions between DNA........ Read more »

Cadwell K, Patel KK, Maloney NS, Liu TC, Ng AC, Storer CE, Head RD, Xavier R, Stappenbeck TS, & Virgin HW. (2010) Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell, 141(7), 1135-45. PMID: 20602997  

Edwards, M., Symbor-Nagrabska, A., Dollard, L., Gifford, D., & Fink, G. (2014) Interactions between chromosomal and nonchromosomal elements reveal missing heritability. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1407126111  

  • May 9, 2014
  • 08:59 AM
  • 347 views

Prying minds with mind-blowing optogenetics

by EE Giorgi in CHIMERAS

Did you know there was such a thing as optogenetics? The idea alone completely blows my mind:"Optogenetics uses light to control neurons which have been genetically sensitised to light. It is a neuromodulation technique employed in neuroscience that uses a combination of techniques from optics and genetics to control and monitor the activities of individual neurons in living tissue to precisely measure the effects of those manipulations in real-time. The key reagents used in optogenetics are lig........ Read more »

  • April 26, 2014
  • 01:37 PM
  • 372 views

Forget the "obesity gene": it's the "obesity microbes" that we need to fight.

by EE Giorgi in CHIMERAS

Antelope Canyo ©EEGThis is going to be gross. So, if you're eating, finish up your snack first. Ready?Let's do the following experiment: take two twins, one chubby, the other lean. Why one is chubby and the other is lean is a question we'll leave for another time. For the time being, all we do is take fecal samples from both, extract the microbiota (the bacteria living in feces) and transplant them in mice.You'd been warned it was kinda gross.The reason for such an experiment is that large inte........ Read more »

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR.... (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (New York, N.Y.), 341(6150), 1241214. PMID: 24009397  

  • April 20, 2014
  • 09:31 AM
  • 476 views

Was Lamarck right after all? A look at epigenetic inheritance

by EE Giorgi in CHIMERAS

Myths © EEGFrom the Wikipedia definition of epigenetics: "In biology, and specifically genetics, epigenetics is the study of heritable changes in gene activity that are not caused by changes in the DNA sequence."Wait a minute... how can we inherit anything that's not encoded in the DNA? All the information we inherit from our parents is coded in the DNA ... Right?That's correct. However, there's something very important that goes hand in hand with the information contained in the genes: how and........ Read more »

  • April 10, 2014
  • 09:54 AM
  • 408 views

Aluminum adjuvants in vaccines: are they safe?

by EE Giorgi in CHIMERAS

Multnomah Falls, © EEGDisclaimer: I work on HIV vaccine design and I'm quite proud of it. I know that for three million HIV-positive kids in Africa, a vaccine is the only hope they have to grow into adulthood. So, when people tell me that vaccines are bad I cringe. Infant mortality rates have dropped since vaccinations have been introduced. We live longer, healthier lives thanks to vaccines. Diseases like polio can paralyze and kill, yet they are no longer a concern for children in the western ........ Read more »

  • March 30, 2014
  • 11:26 AM
  • 366 views

What do one trillion different scents smell like?

by EE Giorgi in CHIMERAS

I've been really happy with the comments on my upcoming detective thriller CHIMERAS. The book will be released in two weeks, but I've already heard back from some early readers (and yes, I'm still offering free ARC's, see details here), and many have praised Track's sensitivity to smells. Apparently, it's a trait many relate to and yet you don't find so often in fiction. Most of our memories are stored as images. So, even when we write, we tend to over-emphasize visual descriptions and forget al........ Read more »

Bushdid C, Magnasco MO, Vosshall LB, & Keller A. (2014) Humans can discriminate more than 1 trillion olfactory stimuli. Science (New York, N.Y.), 343(6177), 1370-2. PMID: 24653035  

Vanderhaeghen P, Schurmans S, Vassart G, & Parmentier M. (1993) Olfactory receptors are displayed on dog mature sperm cells. The Journal of cell biology, 123(6 Pt 1), 1441-52. PMID: 8253843  

  • March 21, 2014
  • 09:46 AM
  • 451 views

I carry my son's DNA: a look at microchimerism and its effects

by EE Giorgi in CHIMERAS

To celebrate the upcoming release of my detective thriller CHIMERAS, the next few Research Blogging posts will be dedicated to the different forms of chimerism. I'm sure you are all familiar with dispermic chimeras, which occur when two fertilized eggs fuse together shortly after conception. The result is one individual with two sets of genetically distinct cells. Have you ever heard of microchimerism, though?"Microchimerism refers to a small number of cells (or DNA) harbored by one individual t........ Read more »

Gammill HS, & Nelson JL. (2010) Naturally acquired microchimerism. The International journal of developmental biology, 54(2-3), 531-43. PMID: 19924635  

  • March 9, 2014
  • 11:42 AM
  • 522 views

Pregnancy and breast cancer risk: why age counts

by EE Giorgi in CHIMERAS

That an early pregnancy is protective against breast cancer is something I've known for ten years now. I remember one of my professors, back when I started studying genetics, saying: "Having a baby at 16 may ruin your life but it sure protects you from breast cancer." Today we know a lot more about the cellular and genetic mechanisms that a first pregnancy triggers in the body. And yet how these mechanisms turn out to be protective against breast cancer is still a mystery. "The ovarian hormones,........ Read more »

Medina D. (2005) Mammary developmental fate and breast cancer risk. Endocrine-related cancer, 12(3), 483-95. PMID: 16172188  

Meier-Abt F, & Bentires-Alj M. (2014) How pregnancy at early age protects against breast cancer. Trends in molecular medicine, 20(3), 143-153. PMID: 24355762  

  • February 21, 2014
  • 06:19 PM
  • 378 views

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
  • 342 views

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
  • 562 views

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
  • 421 views

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  

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