105 posts · 137,946 views
The musings and ravings of a computational biologist about science, computers, music and, you know, stuff
Iddo Friedberg
105 posts
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- September 17, 2009
- 12:07 PM
- 2,424 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
- 2,386 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 . ........ 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
- July 13, 2009
- 02:14 PM
- 2,251 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
- November 24, 2009
- 05:38 PM
- 2,244 views
Photosynthesis, phages and structures: there’s treasure everywhere!
by Iddo Friedberg in Byte Size Biology
Here’s a really cool work, published this September in Nature.. Why did I choose this work? Well, it’s a major discovery, and it’s all done using bioinformatics, and fairly simple bioinformatics at that. The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and [...]... Read more »
Sharon, I., Alperovitch, A., Rohwer, F., Haynes, M., Glaser, F., Atamna-Ismaeel, N., Pinter, R., Partensky, F., Koonin, E., Wolf, Y.... (2009) Photosystem I gene cassettes are present in marine virus genomes. Nature, 461(7261), 258-262. DOI: 10.1038/nature08284
Lindell, D., Jaffe, J., Johnson, Z., Church, G., & Chisholm, S. (2005) Photosynthesis genes in marine viruses yield proteins during host infection. Nature, 438(7064), 86-89. DOI: 10.1038/nature04111
- March 14, 2009
- 01:59 AM
- 2,168 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
- June 30, 2010
- 07:00 PM
- 1,921 views
This is what it smells like when mice cry
by Iddo Friedberg in Byte Size Biology
A pheromone in the male mouse’s tears causes a sexual response in female mice who smell it. The neural pathway was meticulously mapped in a study published today in Nature. Interestingly, the female mouse actually has to be somewhat in the mood prior to the pheromone secretion for the pheromone to have effect, icing on the [...]... Read more »
Haga, S., Hattori, T., Sato, T., Sato, K., Matsuda, S., Kobayakawa, R., Sakano, H., Yoshihara, Y., Kikusui, T., & Touhara, K. (2010) The male mouse pheromone ESP1 enhances female sexual receptive behaviour through a specific vomeronasal receptor. Nature, 466(7302), 118-122. DOI: 10.1038/nature09142
- February 3, 2009
- 12:00 AM
- 1,920 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 1, 2009
- 05:49 PM
- 1,904 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
- February 15, 2009
- 02:57 PM
- 1,879 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
- October 1, 2009
- 06:50 PM
- 1,861 views
It ain’t necessarily so
by Iddo Friedberg in Byte Size Biology
First, a short glossary.
Homologous genes are descended from a common ancestral gene.
There are two types of homology:
Orthology is homology due to a speciation event. So if there is a gene A’ in humans and A” in mice, and they are obviously similar in sequence, we infer that they homologous. We usually also infer that they [...]... Read more »
Studer, R., & Robinson-Rechavi, M. (2009) How confident can we be that orthologs are similar, but paralogs differ?. Trends in Genetics, 25(5), 210-216. DOI: 10.1016/j.tig.2009.03.004
- May 29, 2010
- 09:20 PM
- 1,860 views
A cure for Ebola?
by Iddo Friedberg in Byte Size Biology
There are few infectious diseases as violent and as lethal as the Ebola Haemorragic Fever. This terrible disease was first described in 1976 at a mission hospital at the Ebola river in Zaire (now the Democratic Republic of Congo). The disease is 80% fatal, the victims die painfully from a literal meltdown of their organs. [...]... Read more »
Prof Thomas W Geisbert Corresponding Amy CH Lee, Marjorie Robbins, Joan B Geisbert, Anna N Honko, Vandana Sood, Joshua C Johnson, Susan de Jong, Iran Tavakoli, Adam Judge, Lisa E Hensley, Ian MacLachlan. (2010) Postexposure protection of non-human primates against a lethal Ebola virus challenge with RNA interference: a proof-of-concept study. The Lancet, 375(9729), 1896-1905. info:/doi:10.1016/S0140-6736(10)60357-1
- July 20, 2009
- 05:57 PM
- 1,848 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, as........ 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
- July 8, 2009
- 10:00 AM
- 1,836 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
- February 23, 2011
- 09:40 AM
- 1,825 views
Giggity
by Iddo Friedberg in Byte Size Biology
The authors and editor knew exactly what they were doing with this one:... Read more »
Chau, R., Hamel, S., & Nellis, W. (2011) Chemical processes in the deep interior of Uranus. Nature Communications, 203. DOI: 10.1038/ncomms1198
- August 25, 2009
- 06:45 PM
- 1,811 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
- June 7, 2010
- 12:52 PM
- 1,804 views
Awesomest Cola & Mentos yet
by Iddo Friedberg in Byte Size Biology
Yeah, yeah, Cola & Mentos videos are getting somewhat tired. Still, this one really goes overboard:
Ha! Now how does the Cola & Mentos reaction work?
Well, first, the Cola & Mentos thing is a physical reaction, more than a chemical one: it happens mainly due to nucleation sites provided by the pitted surface of the Mentos [...]... Read more »
Coffey, T. (2008) Diet Coke and Mentos: What is really behind this physical reaction?. American Journal of Physics, 76(6), 551. DOI: 10.1119/1.2888546
- April 9, 2009
- 08:00 AM
- 1,785 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
- April 19, 2009
- 04:17 PM
- 1,770 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 beyon........ 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
- February 23, 2009
- 12:00 AM
- 1,769 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
- August 9, 2010
- 06:53 PM
- 1,743 views
Goat breath causes aphids to drop to the ground
by Iddo Friedberg in Byte Size Biology
Some headlines just write themselves…
It has been known for some time that an approaching large herbivore causes aphids to abandon ship ...err plant. Makes sense since, after all, there's not much of a point in staying on the particular bit of shrubbery that will be consumed, lock, stalk and barrel by a ravenous forager. However, it was not exactly clear what in the herbivore causes the aphids to drop. Well, it is not the shaking of the twigs, as rustling the plant did not cause a substantial........ Read more »
Moshe Gish, Amots Dafni, & Moshe Inbar. (2010) Mammalian herbivore breath alerts aphids to flee host plant. Current Biology, 20(15). info:/
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