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
158 posts

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  • August 17, 2014
  • 11:26 AM
  • 140 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
  • 190 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
  • 228 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
  • 214 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
  • 279 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
  • 339 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
  • 307 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
  • 241 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
  • 336 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
  • 364 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
  • 284 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
  • 260 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
  • 422 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
  • 311 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  

  • January 13, 2014
  • 07:44 PM
  • 382 views

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
  • 432 views

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
  • 452 views

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
  • 458 views

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
  • 390 views

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
  • 393 views

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 »

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