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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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  • March 19, 2012
  • 09:25 AM

Different viruses, different replication mechanisms

by EE Giorgi in CHIMERAS

I often talk about HIV because that's my research field. However, HIV is not the only virus for which we currently don't have a vaccine. A recent news post on Scientific American warned that while HIV-related deaths are going down, chronic hepatitis C deaths are on the rise. According to the World Health Organization:"It is estimated that 3-4 million people are infected with HCV each year. Some 130‚Äì170 million people are chronically infected with HCV and at risk of developing liver cirrhos........ Read more »

Ashfaq, U., Javed, T., Rehman, S., Nawaz, Z., & Riazuddin, S. (2011) An overview of HCV molecular biology, replication and immune responses. Virology Journal, 8(1), 161. DOI: 10.1186/1743-422X-8-161  

  • March 15, 2012
  • 09:02 AM

Young or old it doesn't matter: we need them both

by EE Giorgi in CHIMERAS

To honor Brain Awareness Week I thought I'd try and discuss a neuroscience paper this week. It's not my field, so you'll have to be patient with me (and you experts out there are more than welcome to pitch in). I found a really fascinating story in the latest issue of Science [1] on the differences in information processing between "young" and "old" neurons. In order to understand the story, I had to take a couple of steps back and review a few things about the brain. The hippocampus is the part........ Read more »

  • March 12, 2012
  • 09:54 AM

How nucleosomes "protect" our DNA

by EE Giorgi in CHIMERAS

Did you know that not all mutations happen at an equal rate? There are several kinds of mutations: substitutions, insertions, deletions, etc. Insertions and deletions happen when bits of DNA are either inserted or deleted, whereas substitutions happen when the overall length of the DNA locus doesn't change, but a base is substituted for another. As you all know, we have 4 nucleotides (A, C, G, and T), however, not all possible changes are equally likely. The most frequent substitutions are As wi........ Read more »

Chen, X., Chen, Z., Chen, H., Su, Z., Yang, J., Lin, F., Shi, S., & He, X. (2012) Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes. Science, 335(6073), 1235-1238. DOI: 10.1126/science.1217580  

  • March 8, 2012
  • 09:30 AM

How are new viruses made?

by EE Giorgi in CHIMERAS

I'm sure you are all familiar with H1N1, the influenza strain that emerged in 2009 and which contained genetic elements from four different strains: two swine flu strains, one avian flu strain, and one human flu strain.How did this incredible mix-up happen? One thing I've learned in the five years I've spent studying viruses is that these little things are genetic brewing machines (I just made that expression up, please don't quote me!). They can carry genetic material from different organisms,........ Read more »

Greenbaum, B., Li, O., Poon, L., Levine, A., & Rabadan, R. (2012) From the Cover: Viral reassortment as an information exchange between viral segments. Proceedings of the National Academy of Sciences, 109(9), 3341-3346. DOI: 10.1073/pnas.1113300109  

  • March 5, 2012
  • 08:40 AM

It takes all the running you can do to keep in the same place

by EE Giorgi in CHIMERAS

"Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!"~Lewis Carroll, Through the Looking Glass The Red Queen Effect is a genetic effect named after Lewis Carroll's famous quote, "It takes all the running you can do to keep in the same place." As it turns out, Carroll's witty and paradoxical thinking fits viral host evolution: out of the whole viral population, only a few manage to infe........ Read more »

  • March 1, 2012
  • 11:03 AM

MicroRNAs found for the first time in a retrovirus

by EE Giorgi in CHIMERAS

MicroRNAs (miRNAs) are small non-coding RNAs that play a regulatory role in many cellular processes such as immune function, apoptosis and tumorigenesis. MicroRNAs are about 22 nucleotide long (on average) and they typically derive from primary transcripts "snipped" during a process called "endonucleolytic cleavage," which involves a protein that recognizes a double-helix RNA and cleaves the nucleotides in halves for degradation. MicroRNAs are post-transcriptional regulators, meaning they regula........ Read more »

Kincaid, R., Burke, J., & Sullivan, C. (2012) From the Cover: RNA virus microRNA that mimics a B-cell oncomiR. Proceedings of the National Academy of Sciences, 109(8), 3077-3082. DOI: 10.1073/pnas.1116107109  

  • February 27, 2012
  • 09:24 AM

Mendelian puzzles

by EE Giorgi in CHIMERAS

A Mendelian disorder is a disease caused by a single-gene mutation that's usually inherited according to Mendel's laws. Despite being for the most part quite debilitating, they persist in the population, though at a very low prevalence. This is due in part to the effect called heterozygote advantage. Recessive mutations bear no symptoms and are carried on from one generation to the next until an individual with both mutated alleles is born. A Perspective in the latest issue of Science [1] gives ........ Read more »

Chakravarti, A., & Kapoor, A. (2012) Mendelian Puzzles. Science, 335(6071), 930-931. DOI: 10.1126/science.1219301  

  • February 23, 2012
  • 11:52 PM

Modifying gene expression through riboswitches

by EE Giorgi in CHIMERAS

Messenger RNA (mRNA), the RNA transcribed from a DNA template in order to make proteins, contains elements able to sense and bind to specific targeting molecules (metabolites or metal ions). In bacteria, fungi and plants, these binding mechanisms are used to control gene expression, and therefore act as genetic "switches", which is why these RNA elements are called "riboswitches". They are often found at the 5' end of the mRNA, in the untranslated region (the stretch that precedes the start codo........ Read more »

  • February 21, 2012
  • 08:15 AM

Is cancer contagious? Sometimes. But it may not be bad thing.

by EE Giorgi in CHIMERAS

About 15% of all cancers worldwide are caused by infectious pathogens such as viruses, bacteria, or parasites [1]. Viruses that are capable of inducing cancer are called oncoviruses -- HPV is an example. The pathogen is transmitted from a donor to a recipient, starts the infection, and the infection eventually causes the cancer. But did you know there existed such a thing as a transmissible cancer? In this case, it's not the pathogen, but the cancer cell line itself that gets transmitted from on........ Read more »

Welsh, J. (2011) Contagious Cancer. The Oncologist, 16(1), 1-4. DOI: 10.1634/theoncologist.2010-0301  

Rebbeck, C., Leroi, A., & Burt, A. (2011) Mitochondrial Capture by a Transmissible Cancer. Science, 331(6015), 303-303. DOI: 10.1126/science.1197696  

  • February 17, 2012
  • 04:17 PM

Avian influenza, ferrets, and bioterrorism: fear versus science

by EE Giorgi in CHIMERAS

I learned about this last week, when Science published a short article on how the National Science Advisory Board for Biosecurity had recommended two research groups NOT to publish details on how avian influenza strains were modified in order to make them transmissible through aerosol in ferrets. You can read that story here.The first thing that struck me was: is this censorship? Because for as long as I've been a scientist I've known that the great bulk of scientific progress is made through th........ Read more »

Palese, P., & Wang, T. (2012) H5N1 influenza viruses: Facts, not fear. Proceedings of the National Academy of Sciences, 109(7), 2211-2213. DOI: 10.1073/pnas.1121297109  

  • February 16, 2012
  • 08:56 AM

Large intergenic noncoding RNAs affect gene expression

by EE Giorgi in CHIMERAS

I learned this amazing fact from a talk I went to last week: currently, somewhere between 70% and 90% of DNA is estimated to be transcribed into RNA but not translated into proteins. So, the question is: if it's not making proteins, what's all this non-coding RNA doing?In mammalians in particular, more than a thousand large (over 5 kb) intergenic noncoding RNAs (lincRNA) have been identified [1] and, by looking at expression patterns, researchers were able to see that they are involved in many d........ Read more »

Guttman, M., Amit, I., Garber, M., French, C., Lin, M., Feldser, D., Huarte, M., Zuk, O., Carey, B., Cassady, J.... (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223-227. DOI: 10.1038/nature07672  

Khalil, A., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B., van Oudenaarden, A.... (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences, 106(28), 11667-11672. DOI: 10.1073/pnas.0904715106  

  • February 13, 2012
  • 08:05 AM

The "not-so-universal" genetic code, its origin and its evolution

by EE Giorgi in CHIMERAS

From [1]:"Until relatively recently, the [genetic] code was thought to be invariable, frozen, in all organisms, because of the way in which any change would produce widespread alteration in the amino acid sequences of proteins. The universality of the genetic code was first challenged in 1979, when mammalian mitochondria were found to use a code that deviated somewhat from the universal."A brief refresher: proteins are chains of amino acids. They are made from messenger RNA by assigning each tri........ Read more »

Ohama T, Inagaki Y, Bessho Y, & Osawa S. (2008) Evolving genetic code. Proceedings of the Japan Academy. Series B, Physical and biological sciences, 84(2), 58-74. PMID: 18941287  

  • February 10, 2012
  • 08:09 AM

Migrating genes

by EE Giorgi in CHIMERAS

I've been talking quite a lot about mitochondria lately. The fact that these organelles contain their own DNA (called mtDNA) and were the result of a horizontal gene transfer during evolution is simply fascinating. And I know many of you agree, as proved by the wonderful questions my last post on mitochondria sparked (thank you Hollis and Marleen!)Plastids, plant organelles that are responsible for photosynthesis, also have a circular, double-stranded DNA molecule (called ptDNA). Like mitochondr........ Read more »

  • February 8, 2012
  • 07:40 PM

You're being watched. That's okay, though, we do it for your own benefit. Or so we'd like you to think...

by EE Giorgi in CHIMERAS

Starting March 1st Google's much anticipated new privacy policy will take place. Of course, how much it will or will not affect your life depends upon your own personal choices. It strikes me, though, how much the Internet has become a place like those Italian marketplaces I used to love growing up: lots to see, stands full of goodies, lots of people, lots of entertaining distractions, yet if you don't keep a constant eye on your wallet next thing you know it'll be gone.What can you lose on the ........ Read more »

  • February 6, 2012
  • 08:22 AM

The first tree of life

by EE Giorgi in CHIMERAS

I came to learn the meaning of the word phylogenetics in 2006, when I started working on HIV. With a highly variable virus like HIV, it is convenient to be able to reconstruct its molecular evolution through a graph called phylogenetic tree. It gives researchers a visual sense of the genetic diversity found in the sample of viral sequences and infer what the infecting strain (the "patriarch", so to speak) might have looked like. These trees are not specific to virology. In fact, they are used in........ Read more »

  • February 2, 2012
  • 08:44 AM

The missing heritability: the humble opinion of a mathematician

by EE Giorgi in CHIMERAS

Tomorrow, February 3, is Eric Lander's birthday, the director of the Broad Institute (the well-known MIT/Harvard genomic research center), and the first author of the historic 2001 Nature paper that marked the completion of the Human Genome Project [1]. I heard him once speak at USC and without ever getting technical he managed to engage the whole audience and share his passion for genetics. As you know, I've been honoring famous geneticists by discussing one of their papers on their birthday an........ Read more »

Lander, E., Linton, L., Birren, B., Nusbaum, C., Zody, M., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W.... (2001) Initial sequencing and analysis of the human genome. Nature, 409(6822), 860-921. DOI: 10.1038/35057062  

Zuk, O., Hechter, E., Sunyaev, S., & Lander, E. (2012) The mystery of missing heritability: Genetic interactions create phantom heritability. Proceedings of the National Academy of Sciences, 109(4), 1193-1198. DOI: 10.1073/pnas.1119675109  

  • January 30, 2012
  • 08:11 AM

The wondrous mitochondrion and its proteome

by EE Giorgi in CHIMERAS

The sequencing of human mitochondrial DNA, a circular DNA molecule contained in mitochondria, was completed in 1981, and, since then, roughly 150 mutations have been found that are associated with maternally inherited diseases (if you don't remember why mtDNA is inherited from the mother and not the father, check out this earlier post of mine). Despite this, the majority of human mitochondrial syndromes are actually caused by defects in the nuclear genome. This is sort of obvious if you think ab........ Read more »

Calvo, S., & Mootha, V. (2010) The Mitochondrial Proteome and Human Disease. Annual Review of Genomics and Human Genetics, 11(1), 25-44. DOI: 10.1146/annurev-genom-082509-141720  

  • January 27, 2012
  • 09:06 AM

Have you been blogging lately?

by EE Giorgi in CHIMERAS

I have to admit I'm obsessed with social networking. I have a love-hate relationship with the whole thing. Until last year I would've sworn I'd never jump the "networking" fence. My thoughts: "There's enough background noise already on the Internet." And: "I've got nothing interesting today."Whether my posts are background noise or not, I'll leave it to you guys to decide, but I'm myself appalled by the fact that I've been blogging since last July and recently surpassed the threshold of 100 post........ Read more »

Cha, M., Pérez, J., & Haddadi, H. (2011) The spread of media content through blogs. Social Network Analysis and Mining. DOI: 10.1007/s13278-011-0040-x  

  • January 25, 2012
  • 07:02 AM

Surfing the wave of genetics: the man who invented genetic landscapes

by EE Giorgi in CHIMERAS

  Today is the 90th birthday of the one and only Luigi Luca Cavalli-Sforza, professor emeritus at Stanford University and a pillar of population genetics. Oh, and in case you couldn't tell by the name, he's Italian, too. Not that I'm biased, mind you.Cavalli-Sforza is best known for his book The History and Geography of Human Genes, in which he reconstructs the history of human migrations by mapping the distribution of gene alleles and correlating gene frequencies in populations with the ge........ Read more »

Chiaroni, J., Underhill, P., & Cavalli-Sforza, L. (2009) Y chromosome diversity, human expansion, drift, and cultural evolution. Proceedings of the National Academy of Sciences, 106(48), 20174-20179. DOI: 10.1073/pnas.0910803106  

  • January 22, 2012
  • 09:57 AM

Mapping HIV-human protein to protein interaction reveals new targets for better drug design

by EE Giorgi in CHIMERAS

HIV has a small genome (roughly 9,000 bases) and it survives by using the host's proteins and DNA. Understanding how these proteins come in contact and interact with one another is crucial in order to unravel the mechanisms by which HIV hijacks the cellular machinery and proliferates. A comprehensive work [1] by a group of researchers at UCSF lead by Nevan Krogan looked at two human cell lines in particular and identified 497 HIV-human protein-protein interactions between 16 HIV proteins and 435........ Read more »

Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J., McGovern, K., Clarke, S., Shales, M., Mercenne, G., Pache, L., Li, K.... (2011) Global landscape of HIV–human protein complexes. Nature. DOI: 10.1038/nature10719  

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