94 posts · 96,442 views
The musings and ravings of a computational biologist about science, computers, music and, you know, stuff
Iddo Friedberg
94 posts
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- January 8, 2012
- 11:22 PM
- 146 views
Gut microbes and diabetes
by Iddo Friedberg in Byte Size Biology
Together with obesity, insulin resistance is the harbringer of metabolic syndrome. Insulin resistance is when the body cannot use insulin effectively. Insulin is needed to help control the amount of sugar in the body. As a result, blood sugar and fat levels rise. Therein lies the path to morbid obesity, diabetes, stroke, and heart problems.
So what’s the connection of metabolic disease to bacteria? Well, for one thing, we know that in obese people the bacterial population in the gu........ Read more »
Caricilli, A., Picardi, P., de Abreu, L., Ueno, M., Prada, P., Ropelle, E., Hirabara, S., Castoldi, �., Vieira, P., Camara, N.... (2011) Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice. PLoS Biology, 9(12). DOI: 10.1371/journal.pbio.1001212
- December 4, 2011
- 01:39 PM
- 246 views
Circumcision, preventing fraud, and icky toilets
by Iddo Friedberg in Byte Size Biology
In no particular order or ranking, recent and not-so-recent articles from PLoS-1. The common thread (if any): I thought they were pretty cool in one way or another.... Read more »
Thomas, A., Tran, B., Cranston, M., Brown, M., Kumar, R., & Tlelai, M. (2011) Voluntary Medical Male Circumcision: A Cross-Sectional Study Comparing Circumcision Self-Report and Physical Examination Findings in Lesotho. PLoS ONE, 6(11). DOI: 10.1371/journal.pone.0027561
Wicherts, J., Bakker, M., & Molenaar, D. (2011) Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results. PLoS ONE, 6(11). DOI: 10.1371/journal.pone.0026828
Flores, G., Bates, S., Knights, D., Lauber, C., Stombaugh, J., Knight, R., & Fierer, N. (2011) Microbial Biogeography of Public Restroom Surfaces. PLoS ONE, 6(11). DOI: 10.1371/journal.pone.0028132
- November 20, 2011
- 08:31 PM
- 325 views
So what's new with humans?
by Iddo Friedberg in Byte Size Biology
Whatever that elusive quality is that distinguishes us from our closest cousins, the chimps and the bonobos, it is to be found in our genome. Since human and some great apes and other primate genomes have been sequenced, the basis for comparing these blueprints exists. Many studies have been done comparing the conservation of genes, copy numbers of genes, intergenic regions, control regions, synteny, splicing and other mechanisms that may explain the differences between us and our 96% cousins. A........ Read more »
Wu, D., Irwin, D., & Zhang, Y. (2011) De Novo Origin of Human Protein-Coding Genes. PLoS Genetics, 7(11). DOI: 10.1371/journal.pgen.1002379
- October 3, 2011
- 05:33 PM
- 338 views
Using phylogenetics to reconstruct a 59 million year old drug
by Iddo Friedberg in Byte Size Biology
It is no secret that we are losing the arms race against bacteria. We are overusing antibiotics in medicine and in agriculture, virtually nurturing today’s and tomorrow’s killers. Australian scientists have now found an unusual source for a new antimicrobial: the kangaroo's pouch. Kangaroos use a wide array of powerful antimicrobial proteins as part of their innate immune system. With the tammar wallaby's genome recently sequenced, scientists have found several such drug candidates, and also........ Read more »
Wang, J., Wong, E., Whitley, J., Li, J., Stringer, J., Short, K., Renfree, M., Belov, K., & Cocks, B. (2011) Ancient Antimicrobial Peptides Kill Antibiotic-Resistant Pathogens: Australian Mammals Provide New Options. PLoS ONE, 6(8). DOI: 10.1371/journal.pone.0024030
- August 26, 2011
- 01:18 PM
- 585 views
Of Mice and Men or: Revisiting the Ortholog Conjecture
by Iddo Friedberg in Byte Size Biology
I have posted quite a few times before about the acquisition of new functions by genes. In many cases a gene is duplicated, and one of the duplicates acquires a new function. This is one basic evolutionary mechanism of acquiring new functions. Sometimes, gene duplication occurs within a species: part of the chromosome may be [...]... Read more »
Nehrt, N., Clark, W., Radivojac, P., & Hahn, M. (2011) Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. PLoS Computational Biology, 7(6). DOI: 10.1371/journal.pcbi.1002073
Gharib, W., & Robinson-Rechavi, M. (2011) When orthologs diverge between human and mouse. Briefings in Bioinformatics. DOI: 10.1093/bib/bbr031
Fitch, W. (1970) Distinguishing Homologous from Analogous Proteins. Systematic Zoology, 19(2), 99. DOI: 10.2307/2412448
- June 22, 2011
- 07:18 AM
- 680 views
Zombie science roundup
by Iddo Friedberg in Byte Size Biology
I am fascinated with zombies. Always have been, but even more so since I took an interest in microbiology. The zombie apocalypse is the best known and best chronicled viral infection which hasn’t happened. But it could happen any day, so stock up on non-perishable food, medical supplies, water purification tablets, chainsaws, machetes, baseball [...]... Read more »
Gal, R., & Libersat, F. (2010) A Wasp Manipulates Neuronal Activity in the Sub-Esophageal Ganglion to Decrease the Drive for Walking in Its Cockroach Prey. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010019
Gal, R., & Libersat, F. (2010) On predatory wasps and zombie cockroaches: Investigations of free will and spontaneous behavior in insects. Communicative , 3(5), 458-461. DOI: 10.4161/cib.3.5.12472
Lisch, D., & Bennetzen, J. (2011) Transposable element origins of epigenetic gene regulation. Current Opinion in Plant Biology, 14(2), 156-161. DOI: 10.1016/j.pbi.2011.01.003
Evans, H., Elliot, S., & Hughes, D. (2011) Hidden Diversity Behind the Zombie-Ant Fungus Ophiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil. PLoS ONE, 6(3). DOI: 10.1371/journal.pone.0017024
- May 19, 2011
- 03:04 PM
- 582 views
Crowdsourcing genomics
by Iddo Friedberg in Byte Size Biology
Genomics data generated by student participants will be used by other researchers to answer medical, ecological, and evolutionary scientific questions. Bacteriophages (viruses that infect bacteria) affect the biopsphere so profoundly, it is almost impossible to imagine. Their sheer biomass is equal to that of 75 million blue whales, and marine bacteriophages kill about half of marine microbes every day. Bacteriophages have a huge host range, mind-boggling number of particles in the biosphere (1........ Read more »
Pope, W., Jacobs-Sera, D., Russell, D., Peebles, C., Al-Atrache, Z., Alcoser, T., Alexander, L., Alfano, M., Alford, S., Amy, N.... (2011) Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution. PLoS ONE, 6(1). DOI: 10.1371/journal.pone.0016329
- March 29, 2011
- 11:48 AM
- 815 views
Ratting out landmines and tuberculosis
by Iddo Friedberg in Byte Size Biology
Thanks to John Stevenson for drawing my attention to this one: Giant African Pouched Rats are trained as detectors; a good solution for low-income countries and communities. HeroRATS, as they are called, come in two "models": landmine detectors and tuberculosis detectors. Rats born in captivity (captured rats are impossible to train) are trained to sniff out landmines in historically war-ravaged zones where many landmines are laying unmapped, and using other detection or disposal tech........ Read more »
Poling, A., Weetjens, B., Cox, C., Mgode, G., Jubitana, M., Kazwala, R., Mfinanga, G., & Huis in 't Veld, D. (2010) Using Giant African Pouched Rats to Detect Tuberculosis in Human Sputum Samples: 2009 Findings. American Journal of Tropical Medicine and Hygiene, 83(6), 1308-1310. DOI: 10.4269/ajtmh.2010.10-0180
Alan Poling, Bart J. Weetjens, Christophe Cox, Negussie W. Beyene, & Andrew Sully. (2010) USING GIANT AFRICAN POUCHED RATS (CRICETOMYS GAMBIANUS) TO DETECT LANDMINES. The Psychological Record, 60(4), 715-728. info:other/http://opensiuc.lib.siu.edu/tpr/vol60/iss4/11/
- March 16, 2011
- 04:22 PM
- 566 views
http://bytesizebio.net/index.php/2011/03/16/why-are-there-no-disease-causing-archaea/
by Iddo Friedberg in Byte Size Biology
Quite a few people think that microbes are evil, disease causing minions of Hell that should be eradicated. Supermarkets are handing out sanitary wipes: wipe the handlebar if you want to live, never mind that 90% of the food in the supermarket is worse for you than anything you may catch off that cart handle. Almost every public space looks like the secret basement level of the CDC, with alcoholic hand sanitizers and posters portraying the horrors of aerosol-borne infections. Microbes are the i........ Read more »
Gill, E., & Brinkman, F. (2011) The proportional lack of archaeal pathogens: Do viruses/phages hold the key?. BioEssays, 33(4), 248-254. DOI: 10.1002/bies.201000091
- March 16, 2011
- 03:48 PM
- 563 views
Why are there no (or almost no) disease-causing Archaea?
by Iddo Friedberg in Byte Size Biology
Some microbes are evil minions of Hell (but not all) Quite a few people think that microbes are evil, disease causing minions of Hell that should be eradicated. Supermarkets are handing out sanitary wipes: wipe the handlebar if you want to live, never mind that 90% of the food in the supermarket is worse for [...]... Read more »
Gill, E., & Brinkman, F. (2011) The proportional lack of archaeal pathogens: Do viruses/phages hold the key?. BioEssays, 33(4), 248-254. DOI: 10.1002/bies.201000091
- February 23, 2011
- 09:40 AM
- 938 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
- February 15, 2011
- 01:09 PM
- 861 views
Humans draw the LINE at Gonorrhea. Not that it helps.
by Iddo Friedberg in Byte Size Biology
The day after Valentine’s Day. Ah! What better day in the year can we find to discuss gonorrhea? In the US alone 700,000 people are infected each year, and 5 million are infected worldwide. In most infected men gonorrhea causes urethral discharge and pain while urinating. The reason is that Neisseria gonhorrea have little hair-like structures called fimbriae. This makes them very sticky and they stick to the urethra’s walls. Then you get inflammation, urethritis and urinatio........ Read more »
Mark T. Anderson, & H. Steven Seifert. (2011) Opportunity and Means: Horizontal Gene Transfer from the Human Host to a Bacterial Pathogen. mBio, 1-4. info:/10.1128/mBio.00005-11
- February 1, 2011
- 08:44 PM
- 930 views
The Oxygen Rush: late January, all of February and a Day in November
by Iddo Friedberg in Byte Size Biology
I have just returned from British Columbia in Canada. I have to admit that their license plate motto is quite accurate: BC is incredibly beautiful. Another thing that struck me is the provincial flag of BC: the Union Jack at the top (OK, it is British Columbia), there are white and blue horizontal stripes, and [...]... Read more »
David, L., & Alm, E. (2010) Rapid evolutionary innovation during an Archaean genetic expansion. Nature, 469(7328), 93-96. DOI: 10.1038/nature09649
- December 27, 2010
- 04:03 PM
- 545 views
Strawberries, Chocolate and Open Access Genomics
by Iddo Friedberg in Byte Size Biology
Nature Genetics seems to have taken a page from the Food Network Magazine by timing two publications to the annual obsession with festive foods among many, NG readership included. I am talking about the genomes of the Strawberry and of the Cocoa plants. Both are important crops, both are components of luxurious eating. Both papers are comprehensive reports, which give no immediate new insights into the biology of either plant but whose data can be hopefully used later to the advantage of crop........ Read more »
Argout, X., Salse, J., Aury, J., Guiltinan, M., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S.... (2010) The genome of Theobroma cacao. Nature Genetics. DOI: 10.1038/ng.736
Shulaev, V., Sargent, D., Crowhurst, R., Mockler, T., Folkerts, O., Delcher, A., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S.... (2010) The genome of woodland strawberry (Fragaria vesca). Nature Genetics. DOI: 10.1038/ng.740
- December 7, 2010
- 10:53 AM
- 689 views
Extraordinary claims attract extraordinary blogging
by Iddo Friedberg in Byte Size Biology
Since its publication, the paper about bacteria using arsenic instead of phosphorous has been criticized by several different sources. First for the media pre-publication stoking, which lead many journalists to speculate about microbes from Titan while the paper was still embargoed (titanic microbes?), when ultimately it was revealed that we are dealing with earthlings, although with a rather unusual biochemistry. This let-down was only enabled by a rather unfortunate build-up which should not ........ Read more »
Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.). PMID: 21127214
- December 2, 2010
- 10:49 PM
- 620 views
A new life form? Not so fast
by Iddo Friedberg in Byte Size Biology
So everybody is excited about the new GFAJ-1 bacterium that Felisa Wolfe-Simon and her colleagues have discovered. A common buzzphrase diffusing through the media and blogosphere is “NASA discovers a new life form“. (Or, better yet alien life.) Big press conference, and I just finished going through the article that Wolfe-Simon and colleagues have published in Science. Great work. But is this really a new life form?... Read more »
Felisa Wolfe-Simon, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E. Hoeft, Jennifer Pett-Ridge, John F. Stolz, Samuel M. Webb, Peter K. Weber, Paul C. W. Davies.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. info:/10.1126/science.119725
- November 20, 2010
- 09:50 PM
- 653 views
Warm blooded turtles?
by Iddo Friedberg in Byte Size Biology
If you entered this post to comment the error in the title, then I have one word for you. Gotcha! Yes, “warm blooded” animals are not, really, warm blooded. After all, a lizard in the baking sun has a core temperature higher than most mammals, but it is still called “cold blooded”. So-called cold blooded [...]... Read more »
Bostrom, B., Jones, T., Hastings, M., & Jones, D. (2010) Behaviour and Physiology: The Thermal Strategy of Leatherback Turtles. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0013925
Paladino, F., O'Connor, M., & Spotila, J. (1990) Metabolism of leatherback turtles, gigantothermy, and thermoregulation of dinosaurs. Nature, 344(6269), 858-860. DOI: 10.1038/344858a0
- October 27, 2010
- 04:18 PM
- 898 views
But did you correct your results using a dead salmon?
by Iddo Friedberg in Byte Size Biology
fMRI tests are very popular. Why should they not be? Take someone, stick them in an MRI, show them a picture of their mother-in-law, see which bits of their brain light up (get more blood, hence are more active) and voila! You’re in the New York Times science supplement under the title “Scientists discover brain region responsible for unmitigated rage.” (Any resemblance to any actual mother-in-law, living or dead, is purely coincidental.) fMRI is a great tool for mapping cogni........ Read more »
Craig M. Bennett, Abigail A. Baird, Michael B. Miller, & George L. Wolford. (2010) Neural Correlates of Interspecies Perspective Taking in the Post-Mortem Atlantic Salmon: An Argument For Proper Multiple Comparisons Correction. JSUR, 1(1), 1-5. info:other/http://jsur.org/v1n1p1
- October 26, 2010
- 03:40 PM
- 780 views
Now that's a f***ing big genome!
by Iddo Friedberg in Byte Size Biology
Why are some genomes so big? I mean, seriously. Why would the marbled lungfish with a genome weighing 132.83 picograms (pg) need an estimated 130,000,000,000 bp? It may have to do with that fact that these fish undergo metamorphosis, and the large developmental coding this could entail.
Then there is the genome of Paris japonica, a rare plant whose genome weighs 152.23 pg, making its genome the largest known so far, at a whopping estimated 150,000,000,000 bp. (Humans have a genome size of 3,........ Read more »
Fischer, M., Allen, M., Wilson, W., & Suttle, C. (2010) Giant virus with a remarkable complement of genes infects marine zooplankton. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1007615107
PELLICER, J., FAY, M., & LEITCH, I. (2010) The largest eukaryotic genome of them all?. Botanical Journal of the Linnean Society, 164(1), 10-15. DOI: 10.1111/j.1095-8339.2010.01072.x
- September 30, 2010
- 02:49 PM
- 974 views
Life serves viruses
by Iddo Friedberg in Byte Size Biology
Sometimes I get the feeling that all life on Earth basically serves as a vehicle for viral replication and propagation. Viruses thrive in all three domains, they embed themselves in all creature’s genomes, they may lie dormant in the genome for eons or decimate whole populations in a few years, and they are the most abundant protein & DNA particle on earth. I am certain that their full impact on evolution is overwhelmingly larger than they are given credit for at present.... Read more »
Gilbert, C., & Feschotte, C. (2010) Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. PLoS Biology, 8(9). DOI: 10.1371/journal.pbio.1000495
McDaniel, L., Young, E., Delaney, J., Ruhnau, F., Ritchie, K., & Paul, J. (2010) High Frequency of Horizontal Gene Transfer in the Oceans. Science, 330(6000), 50-50. DOI: 10.1126/science.1192243
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