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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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  • May 28, 2012
  • 12:54 PM
  • 1,542 views

Bacteria, biodiversity, and allergies.

by EE Giorgi in CHIMERAS

You may not have heard of gammaproteobacteria, but I'm sure the names salmonella, escherichia coli, pests and cholera do ring a bell. They are all caused by bacteria that belong to the gammaproteobacteria family. Hanski et al. took small skin samples from 118 Finnish adolescents and found a variety of bacteria, the most represented being Actinobacteria, Bacilli, Clostridia, Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria."Ew," you're probably thinking. Well. . . think again. On ........ Read more »

Hanski, I., von Hertzen, L., Fyhrquist, N., Koskinen, K., Torppa, K., Laatikainen, T., Karisola, P., Auvinen, P., Paulin, L., Makela, M.... (2012) Environmental biodiversity, human microbiota, and allergy are interrelated. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1205624109  

  • May 25, 2012
  • 09:13 AM
  • 1,054 views

DNA vaccines: a work in progress

by EE Giorgi in CHIMERAS

You are all familiar with the idea behind vaccines: an attenuated form of the pathogen stimulates the immune system to produce T-cells and antibodies specific to that particular antigen. These immune responses then become part of our T- and B-memory cells, cells that have previously encountered a certain antigen and have already specialized to recognize it. The challenge behind a vaccine is to use a form of antigen that's weak enough so not to cause the actual disease, but strong enough so to pr........ Read more »

Ferraro, B., Morrow, M., Hutnick, N., Shin, T., Lucke, C., & Weiner, D. (2011) Clinical Applications of DNA Vaccines: Current Progress. Clinical Infectious Diseases, 53(3), 296-302. DOI: 10.1093/cid/cir334  

  • May 23, 2012
  • 09:00 AM
  • 817 views

Hail to the Bonobos!

by EE Giorgi in CHIMERAS

Is human nature prone to violence or is cooperation the dominant trait? The latest issue of Science magazine is dedicated to "Human Conflict" and touches a variety of topics, from racism to terrorism, addressing the question: are we good or evil? Is our true nature aggressive and violent, but tamed by social constraints, or is it the other way around, and we are in fact neutrally inclined towards empathy and cooperation, while violence and aggression are the exceptions?Concepts like "survival o........ Read more »

de Waal, F. (2012) The Antiquity of Empathy. Science, 336(6083), 874-876. DOI: 10.1126/science.1220999  

  • May 20, 2012
  • 12:10 PM
  • 827 views

Juggling languages and sounds

by EE Giorgi in CHIMERAS

Growing up my dominant language was Italian. However, thanks to my dad's sabbaticals, on more than one occasions we lived in English-speaking countries for long periods of time. My brain would reset to Italian as soon as we returned, but I never forgot English, and it was definitely easier to transition again when, as an adult, I moved to the US. However, to this day, I have yet to get rid of that feeling of inadequateness that sticks to me in many situations, whether here or back in Italy. You ........ Read more »

  • May 16, 2012
  • 08:01 AM
  • 1,006 views

Jumping genes and epigenetics

by EE Giorgi in CHIMERAS

Speciation is the evolutionary process by which new species emerge. This can happen through several mechanisms, for example, a population can become geographically split and no longer interbreed. The two subgroups will then slowly form new species just by random drift alone. In general any change that forces a split in interbreeding will have a similar effect, as for example a strong selective sweep, or chromosomal rearrangements. Each chromosome is made of a molecule of double-stranded DNA. If........ Read more »

Rebollo, R., Horard, B., Hubert, B., & Vieira, C. (2010) Jumping genes and epigenetics: Towards new species. Gene, 454(1-2), 1-7. DOI: 10.1016/j.gene.2010.01.003  

  • May 11, 2012
  • 08:20 AM
  • 1,896 views

Flat tori in 3D

by EE Giorgi in CHIMERAS

It's been a while since I've read a pure math paper, but when I saw the picture I knew I had to pick this one up. For the pure mathematicians out there: I haven't done pure math since my grad years, so feel free to pitch in and correct me if I misunderstood any of the following! "Torus" is mathematics for donut. Take a very flexible square -- imagine it's made of rubber -- roll it, then glue together the circles at the two ends. Congratulations. You've made a torus. Now suppose you live on the........ Read more »

Borrelli, V., Jabrane, S., Lazarus, F., & Thibert, B. (2012) From the Cover: Flat tori in three-dimensional space and convex integration. Proceedings of the National Academy of Sciences, 109(19), 7218-7223. DOI: 10.1073/pnas.1118478109  

  • May 10, 2012
  • 09:44 AM
  • 1,292 views

Hijacking dendritic cells

by EE Giorgi in CHIMERAS

Dendritic cells are antigen-presenting cells: their main function is to patrol in search for "foreign objects" (the antigens). When it finds an antigen, the dendritic cells "chops it up" (by either phagocytosis or endocytosis), and presents the fragments on its surface. It then migrates to the lymph nodes, which are rich in T-cells. The antigen fragments it carries on its surface are like red flags: once a T-cell recognizes a specific fragment, it gets "activated" and new T-cells with the same a........ Read more »

Izquierdo-Useros, N., Naranjo-Gómez, M., Erkizia, I., Puertas, M., Borràs, F., Blanco, J., & Martinez-Picado, J. (2010) HIV and Mature Dendritic Cells: Trojan Exosomes Riding the Trojan Horse?. PLoS Pathogens, 6(3). DOI: 10.1371/journal.ppat.1000740  

Izquierdo-Useros, N., Lorizate, M., Contreras, F., Rodriguez-Plata, M., Glass, B., Erkizia, I., Prado, J., Casas, J., Fabriàs, G., Kräusslich, H.... (2012) Sialyllactose in Viral Membrane Gangliosides Is a Novel Molecular Recognition Pattern for Mature Dendritic Cell Capture of HIV-1. PLoS Biology, 10(4). DOI: 10.1371/journal.pbio.1001315  

  • May 3, 2012
  • 09:18 AM
  • 1,068 views

The viruses inside us

by EE Giorgi in CHIMERAS

One of my first and still most popular posts was on endogenous retroviruses, or ERV: these are viral sequences that got integrated in the host DNA and became part of the noncoding genome. With time, Mother Nature found a way to reuse these viral proteins, for example in the placenta, as I was explaining in the earlier post, and some of those proteins became expressed. I was at a conference last week, and one of the talks discussed the evolution of these endogenous viral elements (EVEs) and how t........ Read more »

  • April 30, 2012
  • 08:30 AM
  • 1,107 views

Fixing mitochindrial mutations with targeted mitochondrial RNA import

by EE Giorgi in CHIMERAS

If you've been reading the blog for a while now, you've heard this many times: not all mutations are deleterious, but the ones that are can increase the risk of certain cancers and diseases. Numerous genetic defects have been attributed to mutations, and mutation in the mtDNA, the mitochondrial DNA, are no exceptions: "Specific mutations in mtDNA have been implicated in muscular and neuronal disease and in the decline of organ function with aging. Despite a significant need, there are currently ........ Read more »

Wang, G., Shimada, E., Zhang, J., Hong, J., Smith, G., Teitell, M., & Koehler, C. (2012) Correcting human mitochondrial mutations with targeted RNA import. Proceedings of the National Academy of Sciences, 109(13), 4840-4845. DOI: 10.1073/pnas.1116792109  

  • April 26, 2012
  • 07:11 AM
  • 679 views

Towards a new era of synthetic genetics

by EE Giorgi in CHIMERAS

NOTE: this is a short post since this particular study has already been extensively discussed all over the scientific blogosphere, see for example this post. Here I just want to give a very general overview for those who may have not yet heard about this. I think my writer friends in particular will be extremely intrigued by this news.In life as we know it, the storage and propagation of genetic information relies on two molecules: RNA and DNA. Both are made of building blocks called nucleotides........ Read more »

Pinheiro, V., Taylor, A., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J., Wengel, J., Peak-Chew, S., McLaughlin, S.... (2012) Synthetic Genetic Polymers Capable of Heredity and Evolution. Science, 336(6079), 341-344. DOI: 10.1126/science.1217622  

Joyce, G. (2012) Toward an Alternative Biology. Science, 336(6079), 307-308. DOI: 10.1126/science.1221724  

  • April 22, 2012
  • 10:07 AM
  • 1,122 views

Canalization and epigenetic landscapes: if horses and rhinoceroses share the same ancestor, why don't we have rhinohorses?

by EE Giorgi in CHIMERAS

A concept that has always puzzled me is: how do new species arise? Of course, you're thinking, mutations accumulate, until you produce a brand new organism. But if that's the case, why don't we see human-monkey hybrids, or rhinohorses, or . . . you get the picture. What puzzles me is where do the intermediate steps between two closely related species go? There are so many mutations that make one species diverge from another, yet you don't see one organism for each new mutations that arises. You ........ Read more »

Flatt T. (2005) The evolutionary genetics of canalization. The Quarterly review of biology, 80(3), 287-316. PMID: 16250465  

  • April 19, 2012
  • 10:43 AM
  • 996 views

Four decades of computational genomics.

by EE Giorgi in CHIMERAS

"Every genome is the result of a mostly shared, but partly unique, 3.8-billion-year evolutionary journey from the origin of life. Diversity is created mostly by copy errors during replication."The above is taken from a review in the latest issue of Science [1] that summarizes the progress made in the field of computational genomics since the first sequences obtained back in the mid-seventies. I highly recommend reading the review. Here, I'd like to highlight a few relevant points.Zerbino, Paten,........ Read more »

Zerbino, D., Paten, B., & Haussler, D. (2012) Integrating Genomes. Science, 336(6078), 179-182. DOI: 10.1126/science.1216830  

  • April 16, 2012
  • 08:57 AM
  • 1,087 views

The molecular evolution of the senses

by EE Giorgi in CHIMERAS

Last week we learned that vertebrates react to smells and tastes using G-protein-coupled receptors (GPCRs), a family of proteins that "sense" molecules outside the cell surface and, depending on the molecule, activate a series of cascade events inside the cell which triggers the appropriate cellular response. This is how we distinguish good flavors from bad flavors and similarly with smells.We also learned that tastes are not always shared across species. In fact, the genes that encode GPCRs hav........ Read more »

  • April 12, 2012
  • 09:11 AM
  • 969 views

Cats (and other carnivores) don't have a sweet tooth, they have a sweet pseudogene

by EE Giorgi in CHIMERAS

Cats are insensitive to sweet foods. Like all vertebrates, they react to smells and tastes using G-protein-coupled receptors (GPCRs), a family of proteins that "sense" molecules outside the cell surface. Depending on the molecule, GPCRs activate a series of cascade events inside the cell that triggers the appropriate cellular response. There are five distinct flavors: sweet, salty, bitter, sour, and umami. We have different GPCRs for each different taste, and each group is encoded by a family of........ Read more »

Jiang, P., Josue, J., Li, X., Glaser, D., Li, W., Brand, J., Margolskee, R., Reed, D., & Beauchamp, G. (2012) From the Cover: Major taste loss in carnivorous mammals. Proceedings of the National Academy of Sciences, 109(13), 4956-4961. DOI: 10.1073/pnas.1118360109  

  • April 11, 2012
  • 07:50 PM
  • 763 views

Avian flu papers will be published!

by EE Giorgi in CHIMERAS

Apologies if you've heard about this already, I was away last week and I'm slowly catching up. The members of the National Science Advisory Board for Biosecurity (NSABB) finally gave the green light for the two papers on the avian flu virus to be published in full in Science and Nature respectively. I originally discussed the issue in this post, and you can read about the update here. Basically, the two papers independently showed that an artificially mutated strain of H5N1 (the so-called avian ........ Read more »

Cohen, J., & Malakoff, D. (2012) On Second Thought, Flu Papers Get Go-Ahead. Science, 336(6077), 19-20. DOI: 10.1126/science.336.6077.19  

  • April 9, 2012
  • 08:23 PM
  • 1,017 views

The emergence of new bacterial lineages

by EE Giorgi in CHIMERAS

Bacterial speciation is somehow a mystery given that bacteria reproduce asexually, in other words, they don't have the benefit of genetic cross-overs to ensure enough genetic diversity in the new generations. So how do they achieve enough genetic diversification to ensure new speciation? Horizontal gene transfer is one way, and since it is not restricted to exchanges within species, it does achieve highly divergent traits. Bacteria can exchange genes (often in the form of plasmids, circular bits........ Read more »

B. Jesse Shapiro1, Jonathan Friedman1, Otto X. Cordero, Sarah P. Preheim, Sonia C. Timberlake, Gitta Szabó, Martin F. Polz, & Eric J. Alm1,. (2012) Population Genomics of Early Events in the Ecological Differentiation of Bacteria. Science , 336(6077). DOI: 10.1126/science.1218198  

  • April 5, 2012
  • 10:39 AM
  • 874 views

Renato Dulbecco, February 22, 1914 – February 19, 2012

by EE Giorgi in CHIMERAS

Last February 19 Nobel laureate Renato Dulbecco died at age 97. Dulbecco discovered how viruses integrate their genomes into host cells, something I've often talked about when describing the HIV life cycle. Dulbecco was mostly interested in oncoviruses, (viruses that have the potential to trigger tumors) and, in particular, the molecular mechanisms through which this could happen. He studied a virus called SV40, or simian virus 40, a polyomavirus that infects both monkeys and humans. He was also........ Read more »

  • March 29, 2012
  • 08:37 AM
  • 907 views

Mutagenesis-Mediated Virus Extinction

by EE Giorgi in CHIMERAS

One of the peculiarities of RNA viruses is their high mutation rate, which makes pathogens like HIV or Hepatitis C so elusive when it comes to vaccine design. A high mutation rate ensures that the virus can rapidly adapt to escape not only the host's immune response, but also antiretroviral treatments. Take HIV, for example: once inside the body, HIV evolves into numerous quasispecies -- new viral strains genetically distinct from the initial founder strain (the one that started the infection)......... Read more »

  • March 26, 2012
  • 08:50 AM
  • 1,304 views

Is epigenetics new? Not to a "smart" influenza virus!

by EE Giorgi in CHIMERAS

I was browsing the latest papers on Science when I read:"By mimicking epigenetic regulation in human cells, one flu strain suppresses the expression of antiviral genes [1]."Wow. Epigenetics and viruses? I had to read that paper!I've discussed many times how gene expression in cells can be altered through epigenetic changes. The figure below, also taken from [1], shows one of the most common mechanisms by which cells alter gene expression: inside the nucleus, DNA is wound around proteins called h........ Read more »

Marazzi, I., Ho, J., Kim, J., Manicassamy, B., Dewell, S., Albrecht, R., Seibert, C., Schaefer, U., Jeffrey, K., Prinjha, R.... (2012) Suppression of the antiviral response by an influenza histone mimic. Nature, 483(7390), 428-433. DOI: 10.1038/nature10892  

  • March 22, 2012
  • 08:32 AM
  • 1,250 views

Genome, epigenome, mutations, epimutations... rethinking inheritance

by EE Giorgi in CHIMERAS

I just learned a new word: epimutation. Genetic mutations occur in the DNA, while epimutations describe the transcriptional silencing of a gene that is normally active. What's intriguing about epimutations is that even though they do not change the DNA, these changes can be transmitted from one cell to its daughter cells, a process called epigenetic somatic inheritance. There's another level of inheritance, which happens when such epigenetic changes are passed on from one generation of individua........ Read more »

Migicovsky, Z., & Kovalchuk, I. (2011) Epigenetic Memory in Mammals. Frontiers in Genetics. DOI: 10.3389/fgene.2011.00028  

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