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The musings and ravings of a computational biologist about science, computers, music and, you know, stuff

Iddo Friedberg
98 posts

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September 17, 2009
12:07 PM
2,236 views

What they really found in Niger

by Iddo Friedberg in Byte Size Biology

A big buzz over the discovery of a skeleton of an early Sauropod dinosaur in Niger. The finding looks amazing even to my paleontologically-ignorant eyes. It is beautifully intact and well-ordered, as opposed to the mixed jumble of bone fragments that are usually found. It has that lovely aesthetic quality that would cause anyone to [...]... Read more »

Remes, K., Ortega, F., Fierro, I., Joger, U., Kosma, R., Marín Ferrer, J., , ., , ., Ide, O., & Maga, A. (2009) A New Basal Sauropod Dinosaur from the Middle Jurassic of Niger and the Early Evolution of Sauropoda. PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0006924

May 29, 2009
04:55 PM
1,871 views

Skin flick

by Iddo Friedberg in Byte Size Biology

The researchers at the National Human Genome Research Institute in Bethesda, MD USA swabbed ten volunteers from different parts of their skin, and sequenced the 16S ribosmal RNA used for phylogenetic classification. They then looked at composition and the diversity of the bacterial communities in different areas of the skin. There are seven tie-ins for first place in diversity: behind the knee, on the heel, inner elbow, between the fingers, on the forearm, in the navel and the gluteal crease . The least diverse populations were on the back, and behind the ears(!?)... Read more »

Elizabeth A. Grice, Heidi H. Kong, Sean Conlan, Clayton B. Deming, Joie Davis, Alice C. Young, NISC Comparative Sequencing Program, Gerard G. Bouffard, Robert W. Blakesley, Patrick R. Murray.... (2009) Topographical and Temporal Diversity of the Human Skin Microbiome. Science, 324(5931), 1190-1192. DOI: http://www.sciencemag.org/cgi/content/full/324/5931/1190

March 14, 2009
01:59 AM
1,709 views

A very loose and circular association to Pi Day

by Iddo Friedberg in Byte Size Biology

You were probably taught that proteins are linear chains of amino acids that fold into a shape that produces their function. The links connecting the chains are peptide bonds. But there is no real reason why the carboxy terminus (right side) and amino terminus (left side) would not bond themselves. It just has never been observed, or looked for. Well, they do. And some proteins are circular, like a snake biting its own tail.... Read more »

Trabi, M. (2002) Circular proteins — no end in sight. Trends in Biochemical Sciences, 27(3), 132-138. DOI: 10.1016/S0968-0004(02)02057-1

PELEGRINI, P., QUIRINO, B., & FRANCO, O. (2007) Plant cyclotides: An unusual class of defense compounds. Peptides, 28(7), 1475-1481. DOI: 10.1016/j.peptides.2007.04.025

Wang, C., Hu, S., Martin, J., Sjogren, T., Hajdu, J., Bohlin, L., Claeson, P., Goransson, U., Rosengren, K., Tang, J.... (2009) Combined X-ray and NMR analysis of the stability of the cyclotide cystine knot fold that underpins its insecticidal activity and potential use as drug scaffold. Journal of Biological Chemistry. DOI: 10.1074/jbc.M900021200

July 13, 2009
02:14 PM
1,672 views

The workings of a cellular water pore, and something about obesity

by Iddo Friedberg in Byte Size Biology

Maintaining a water balance is essential to life. Cells must regulate their water content carefully and within a very narrow margin. Too much water intake, and the cell bursts like a water balloon; too much water outflow, and it shrivels like a raisin.

The cell itself is contained in a waterproof membrane. But there are gateways [...]... Read more »

Fischer, G., Kosinska-Eriksson, U., Aponte-Santamaría, C., Palmgren, M., Geijer, C., Hedfalk, K., Hohmann, S., de Groot, B., Neutze, R., & Lindkvist-Petersson, K. (2009) Crystal Structure of a Yeast Aquaporin at 1.15 Å Reveals a Novel Gating Mechanism. PLoS Biology, 7(6). DOI: 10.1371/journal.pbio.1000130

Tajkhorshid, E. (2002) Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning. Science, 296(5567), 525-530. DOI: 10.1126/science.1067778

Frühbeck, G. (2005) Obesity: Aquaporin enters the picture. Nature, 438(7067), 436-437. DOI: 10.1038/438436b

July 8, 2009
10:00 AM
1,652 views

A Romantic, Maybe too Romantic, Scientist

by Iddo Friedberg in Byte Size Biology

In the Hatena story about symbiosis, I posted the following picture drawn by Ernst Haeckel:

Beautiful! In this day and age of imaging, high resolution photography, and molecular graphics, we forget that scientific drawing was a skill as necessary to life scientists as microscopic imaging, or molecular graphics is today. Indeed, biology was very much a [...]... Read more »

Richardson, M., Hanken, J., Gooneratne, M., Pieau, C., Raynaud, A., Selwood, L., & Wright, G. (1997) There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development. Anatomy and Embryology, 196(2), 91-106. DOI: 10.1007/s004290050082

RICHARDSON, M., & KEUCK, G. (2002) Haeckel's ABC of evolution and development. Biological Reviews of the Cambridge Philosophical Society, 77(4), 495-528. DOI: 10.1017/S1464793102005948

Robert J. Richards. (2008) The Tragic Sense of Life. Book. DOI: http://books.google.com/books?id

August 25, 2009
06:45 PM
1,641 views

Freeloading pays off, but only up to a point.

by Iddo Friedberg in Byte Size Biology

Quorum sensing
Social behavior is not exactly the first term that comes to mind with relation to microbes. After all, we assume a certain amount of intelligence and an ability to implement a behavioral pattern in response to peer actions. Humans, yes. Apes, yes. Birds of a feather flock together… so birds, yes. Ants and bees [...]... Read more »

Diggle, S., Griffin, A., Campbell, G., & West, S. (2007) Cooperation and conflict in quorum-sensing bacterial populations. Nature, 450(7168), 411-414. DOI: 10.1038/nature06279

Czárán T, & Hoekstra RF. (2009) Microbial communication, cooperation and cheating: quorum sensing drives the evolution of cooperation in bacteria. PloS one, 4(8). PMID: 19684853

April 9, 2009
08:00 AM
1,621 views

Multitasking Antibody

by Iddo Friedberg in Byte Size Biology

One interesting question this study raises is an evolutionary one. Could we have evolved antibodies that bind two completely different epitopes? When we use antibodies in the lab, we tend to screen against those that are promiscuous: bind more than one epitope. But maybe such antibodies do exist?... Read more »

Bostrom, J., Yu, S., Kan, D., Appleton, B., Lee, C., Billeci, K., Man, W., Peale, F., Ross, S., Wiesmann, C.... (2009) Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site. Science, 323(5921), 1610-1614. DOI: 10.1126/science.1165480

February 23, 2009
12:00 AM
1,608 views

Searching for Life on Earth

by Iddo Friedberg in Byte Size Biology

It is clear that Earth was once all non-life. We can also agree that it is now teeming with life. At some point in its history life has emerged from non-life ingredients, by a process still unknown. But could that process have occurred more than once? There are four possible answers:... Read more »

Felisa Wolfe-Simon, Paul C.W. Davies, & Ariel D. Anbar. (2009) Did nature also choose arsenic?. International Journal of Astrobiology, 1. DOI: 10.1017/S1473550408004394

P.C.W. Davies, & Charles H. Lineweaver. (2005) Finding a Second Sample of Life on Earth. Astrobiology, 5(2), 154-163. DOI: 10.1089/ast.2005.5.154

Paul Davies. (2007) Are aliens among us?. Scientific American, 297(6), 36-43. DOI: 18237098

T. R. Kulp, S. E. Hoeft, M. Asao, M. T. Madigan, J. T. Hollibaugh, J. C. Fisher, J. F. Stolz, C. W. Culbertson, L. G. Miller, & R. S. Oremland. (2008) Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California. Science, 321(5891), 967-970. DOI: 10.1126/science.1160799

July 20, 2009
05:57 PM
1,567 views

Absolut standards: report from the Metagenomics Metadata and Metaanalysis 2009 meeting. Part 1

by Iddo Friedberg in Byte Size Biology

While in genomics we strive to obtain a full picture of an organism’s DNA, in metagenomics we sample the environment for whatever DNA we can get. We are actually merging population biology with genomics. While in population genomics our basic unit of study is an organism, in metagenomics it is a DNA sequence. This presents many challenges: properly sampling the microbial habitat and extracting the DNA, understanding which organisms the DNA in the samples came from, gauging sample depth, assembling the sequences, identifying genes, assigning a biological function to those genes, to name a few. There are many different experimental and computational procedures for doing so, and they should be meticulously documented... Read more »

Kyrpides, N. (2009) Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nature Biotechnology, 27(7), 627-632. DOI: 10.1038/nbt.1552

Kottmann, R., Gray, T., Murphy, S., Kagan, L., Kravitz, S., Lombardot, T., Field, D., Glöckner, F., & , . (2008) A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML). OMICS: A Journal of Integrative Biology, 12(2), 115-121. DOI: 10.1089/omi.2008.0A10

March 10, 2009
12:00 AM
1,550 views

Baby, it's cold outside

by Iddo Friedberg in Byte Size Biology

Anyone who failed to empty their milk carton on time knows that some microbes do eat (and therefore grow) at near-zero temperatures. Nevertheless, we don’t know about cold bacteria, even though as we have seen, most of the real estate on Earth is cold. Also, if we were to find life in the solar system, it would probably be found on the cold moons of Jupiter and Saturn, in the Martian ice caps, or in subsurface Martian ice. The first step to understand how life might exist there is, to understand how it exists in the cold here.

... Read more »

Debora F Rodrigues, Natalia Ivanova, Zhili He, Marianne Huebner, Jizhong Zhou, & James M Tiedje. (2008) Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics, 9(1), 547. DOI: 10.1186/1471-2164-9-547

Raghu Metpally, & Boojala Reddy. (2009) Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins. BMC Genomics, 10(1), 11. DOI: 10.1186/1471-2164-10-11

P. W. Bergholz, C. Bakermans, & J. M. Tiedje. (2009) Psychrobacter arcticus 273-4 Uses Resource Efficiency and Molecular Motion Adaptations for Subzero Temperature Growth. Journal of Bacteriology. DOI: 10.1128/JB.01377-08

Georges Feller, & Charles Gerday. (2003) Psychrophilic enzymes: hot topics in cold adaptation. Nature Reviews Microbiology, 1(3), 200-208. DOI: 10.1038/nrmicro773

February 15, 2009
02:57 PM
1,548 views

Metagenomes as a diagnostic tool?

by Iddo Friedberg in Byte Size Biology

Can we learn about an environment by looking at the bacteria living in it? Can we sequence a metagenome, and then say: ”according to the active genes in this water sample it appears to be too rich in metal ions / sewage products / other pollutants” ? In the foreseeable future could we sequence a [...]... Read more »

T. A. Gianoulis, J. Raes, P. V. Patel, R. Bjornson, J. O. Korbel, I. Letunic, T. Yamada, A. Paccanaro, L. J. Jensen, M. Snyder.... (2009) Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences, 106(5), 1374-1379. DOI: 10.1073/pnas.0808022106

April 19, 2009
04:17 PM
1,546 views

Reading entrails, 21st-century style

by Iddo Friedberg in Byte Size Biology

We are a species obsessed with knowing what the future holds. Our personal future, the future of our kith and kin, our countries, and our planet.

Humans have always been trying to predict their personal future. Palms, stars, cards, dreams, knuckle-bones, coffee grounds, tea leaves, bird flight patterns, crystal balls and animal entrails have all been used (and many are still in use) for predicting the future. As we consider ourselves (industrialized nations) to have matured somewhat beyond this pish-posh, we have adopted so-called scientific methods for predicting future events. Even palmistry sounds better when advertised by Professor Mirza!... Read more »

Brenner, S. (2007) Common sense for our genomes. Nature, 449(7164), 783-784. DOI: 10.1038/449783a

Hardy, J., & Singleton, A. (2009) Genomewide Association Studies and Human Disease. New England Journal of Medicine. DOI: 10.1056/NEJMra0808700

Goldstein, D. (2009) Common Genetic Variation and Human Traits. New England Journal of Medicine. DOI: 10.1056/NEJMp0806284

Hirschhorn, J. (2009) Genomewide Association Studies -- Illuminating Biologic Pathways. New England Journal of Medicine. DOI: 10.1056/NEJMp0808934

Kraft, P., & Hunter, D. (2009) Genetic Risk Prediction -- Are We There Yet?. New England Journal of Medicine. DOI: 10.1056/NEJMp0810107

Nicholas Wade. (2009) Genes Show Limited Value in Predicting Diseases. New York Times. DOI: http://www.nytimes.com/2009/04/16/health/research/16gene.html?_r

March 20, 2009
12:43 AM
1,529 views

Killer fungi and zombie ants

by Iddo Friedberg in Byte Size Biology

Once infected, the ant's behavior is hijacked to act as a delivery system for the fungus, which is finding a good location to die and infect more ants.... Read more »

Pontoppidan, M., Himaman, W., Hywel-Jones, N., Boomsma, J., & Hughes, D. (2009) Graveyards on the Move: The Spatio-Temporal Distribution of Dead Ophiocordyceps-Infected Ants. PLoS ONE, 4(3). DOI: 10.1371/journal.pone.0004835

February 3, 2009
12:00 AM
1,528 views

Enzyme promiscuity

by Iddo Friedberg in Byte Size Biology

In a very elegant work published this week in Chembiochem, Eduardo Jucenda and his colleagues have captured a snapshot of the evolution of enzyme promiscuity, with the old function maintained, the new one evolving, and without gene duplication necessary.... Read more »

Israel Sánchez-Moreno, Laura Iturrate, Rocio Martín-Hoyos, María Luisa Jimeno, Montaña Mena, Agatha Bastida, & Eduardo García-Junceda. (2009) From Kinase to Cyclase: An Unusual Example of Catalytic Promiscuity Modulated by Metal Switching. ChemBioChem, 10(2), 225-229. DOI: 10.1002/cbic.200800573

O KHERSONSKY, C ROODVELDT, & D TAWFIK. (2006) Enzyme promiscuity: evolutionary and mechanistic aspects. Current Opinion in Chemical Biology, 10(5), 498-508. DOI: 10.1016/j.cbpa.2006.08.011

June 17, 2009
12:24 AM
1,507 views

Yeah, yeah, the flu virus

by Iddo Friedberg in Byte Size Biology

Since the Swine Influenza Media and Blogging Pandemic has died for now, I think I can finally write about ‘flu myself. A quick aside: until I was about 15, I thought that the word Influenza came from the Arabic “Inf-Il-enza” meaning “goat’s nose”, which it is a bit runny, like a dog’s, or like [...]... Read more »

Allen, J., Gardner, S., Vitalis, E., & Slezak, T. (2009) Conserved amino acid markers from past influenza pandemic strains. BMC Microbiology, 9(1), 77. DOI: 10.1186/1471-2180-9-77

January 30, 2009
12:00 AM
1,506 views

My own post genomic moment

by Iddo Friedberg in Byte Size Biology

Maybe I am slow on the uptake, but I never quite liked the term “post genomic”, and I used it very sparingly. (Yes, I do have that term in one of my better cited papers, smack in the first sentence of the abstract, but I never liked that). Perhaps because of all the associated abuse and hype that vacated the term from any core meaning it may have originally held; or perhaps it was because I saw genomics as an ongoing endeavor that will be embedded in life science for a long time to come, with no obvious “post” planned. I even view metagenomics — hailed by many as a completely new and exciting field — as an extension to genomics, with no clear boundary separating the two disciplines. So for me, a bioinformatician, genomics started somewhere around the mid 1990s when whole genome sequences started coming out, it is ongoing, and will continue, no “post-” in site.... Read more »

Andrew S Warren, & Joao C Setubal. (2009) The Genome Reverse Compiler: an explorative annotation tool. BMC Bioinformatics, 10(1), 35. DOI: 10.1186/1471-2105-10-35

April 11, 2009
08:00 PM
1,506 views

Ribosomal paleontology

by Iddo Friedberg in Byte Size Biology

In the latter epoch of those 1.5 billion-odd years between non-life and life in early Earth, our ancestral molecular replicators were quite probably RNA, not DNA. There are many arguments for this RNA world hypothesis: RNA can store information in its sequence, and self -duplicate; it can also catalyze reactions as a rybozyme. So technically, [...]... Read more »

Kaberdina, A., Szaflarski, W., Nierhaus, K., & Moll, I. (2009) An Unexpected Type of Ribosomes Induced by Kasugamycin: A Look into Ancestral Times of Protein Synthesis?. Molecular Cell, 33(2), 227-236. DOI: 10.1016/j.molcel.2008.12.014

May 1, 2009
12:05 PM
1,480 views

Size matters. Life is Live.

by Iddo Friedberg in Byte Size Biology

So here we have a virus, with 911 protein coding genes -- more than some bacteria -- a nucleus, genome duplication, tRNA, proofreading mechanisms and best of all, this virus has its own virus. Makes you wonder where being a virus stops and where life starts...... Read more »

La Scola, B., Desnues, C., Pagnier, I., Robert, C., Barrassi, L., Fournous, G., Merchat, M., Suzan-Monti, M., Forterre, P., Koonin, E.... (2008) The virophage as a unique parasite of the giant mimivirus. Nature, 455(7209), 100-104. DOI: 10.1038/nature07218

Xiao, C., Kuznetsov, Y., Sun, S., Hafenstein, S., Kostyuchenko, V., Chipman, P., Suzan-Monti, M., Raoult, D., McPherson, A., & Rossmann, M. (2009) Structural Studies of the Giant Mimivirus. PLoS Biology, 7(4). DOI: 10.1371/journal.pbio.1000092

Zauberman, N., Mutsafi, Y., Halevy, D., Shimoni, E., Klein, E., Xiao, C., Sun, S., & Minsky, A. (2008) Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba polyphaga mimivirus. PLoS Biology, 6(5). DOI: 10.1371/journal.pbio.0060114

J.-M.Claverie, C. Abergel, H. Ogata. (2009) Mimivirus. Current Topics in Microbiology and Immunology, 89-121. DOI: 10.1007/978-3-540-68618-7_3

Raoult, D. (2004) The 1.2-Megabase Genome Sequence of Mimivirus. Science, 306(5700), 1344-1350. DOI: 10.1126/science.1101485

Didier Raoult. (2005) The Journey from Rikettsia to Mimivirus. ASM News, 278-285. DOI: www.asm.org/ASM/files/ccLibraryFiles/FILENAME/000000001583/znw00605000278.pdf

June 1, 2009
05:49 PM
1,470 views

Skin Flick 2: Statistic Boogaloo

by Iddo Friedberg in Byte Size Biology

Reports on the first metagenomic survey of skin bacteria (see my previous post) did not go unnoticed by the popular media. Reports appear in US News & world Report, LA Times, Times of India, National Geographic, and Scientific American. All these articles have one thing in common: they are wrong. Yes, even Scientific American.... Read more »

Stephanie Pappas. (2009) Your Body Is a Wonderland .. of Bacteria. ScienceNOW. DOI: http://sciencenow.sciencemag.org/cgi/content/full/sciencenow;2009/528/1

Katherine Harmon. (2009) Genetic survey finds healthy human skin is crawling with bacteria. Scientific American . DOI: http://www.scientificamerican.com/blog/60-second-science/post.cfm?id

Elizabeth A. Grice, Heidi H. Kong, Sean Conlan, Clayton B. Deming, Joie Davis, Alice C. Young, NISC Comparative Sequencing Program, Gerard G. Bouffard, Robert W. Blakesley, Patrick R. Murray.... (2009) Topographical and Temporal Diversity of the Human Skin Microbiome. Science, 324(5931), 1190-1192. DOI: http://www.sciencemag.org/cgi/content/full/324/5931/1190

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