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Byte Size Biology
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- May 4, 2012
- 02:03 PM
- 128 views
The Inside Poop
by Iddo Friedberg in Byte Size Biology
It’s pretty much common knowledge that mother’s milk is the healthiest food for infants, and that it bestows health benefits upon mother and baby that formula feeding cannot match. The unique combination of lipids, sugars, proteins and antibodies is not even close to being rivaled by baby formula manufacturers. With few exceptions, such as when there is a concern that the mother is contagious and may infect the baby, breastmilk is the recommended diet for infants.... Read more »
Schwartz, S., Friedberg, I., Ivanov, I., Davidson, L., Goldsby, J., Dahl, D., Herman, D., Wang, M., Donovan, S., & Chapkin, R. (2012) A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biology, 13(4). DOI: 10.1186/gb-2012-13-4-r32
- April 27, 2012
- 04:46 PM
- 74 views
It’s a smORF world, after all?
by Iddo Friedberg in Byte Size Biology
But throwing away the baby with the bathwater is not a good solution, since short peptides are known to be responsible for many of life’s activities: mating pheromones, small compound transporters, hormones, neurotransmitters and regulation of other proteins’ activities, to name a few. Many of these short peptides are the result of the cleavage of larger proteins, which means that the ORFs encoding for them are originally longer than 300bp. But some may actually have their own ORFs, coding only for them. How can we find those small ORFs or smORFs out? How many of them are there? Is the number of smORFs large enough to make it worth re-annotating genomes?... Read more »
Ladoukakis, E., Pereira, V., Magny, E., Eyre-Walker, A., & Couso, J. (2011) Hundreds of putatively functional small open reading frames in Drosophila. Genome Biology, 12(11). DOI: 10.1186/gb-2011-12-11-r118
- March 8, 2012
- 06:13 PM
- 247 views
The Origin of Gender Symbols
by Iddo Friedberg in Byte Size Biology
A quick post for International Women’s Day: how did the gender symbols originate in biology? What do ♀ and ♂ actually stand for?
The answer starts in antiquity, when planets and gods were almost synonymous. Religious rites (at least in Europe) were also associated with the working of metals. Thus, each heavenly body was associated with a metal, a god and provided with a proper symbol, thus... Read more »
William T. Stearn. (1962) The Origin of the Male and Female Symbols of Biology. Taxon, 11(4), 109-113. info:other/
- February 11, 2012
- 03:16 PM
- 213 views
Life is short
by Iddo Friedberg in Byte Size Biology
Continuing with rather philosophical musings about life, Ed Trifonov has recently suggested a new approach to defining life: let’s just vote on the definition.
So how does that work? And why should it work in the first place?... Read more »
Trifonov EN. (2011) Vocabulary of definitions of life suggests a definition. Journal of biomolecular structure , 29(2), 259-66. PMID: 21875147
- January 8, 2012
- 11:22 PM
- 320 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 gut is different, and the different population of bacteria may lead to a vicious cycle contributing to obesity.... 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
- 440 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
- 463 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. As expected, no one factor can explain why bonobos are peaceful and sexual, chimps are aggressive and patriarchal, and humans worry about taxes and blog.... 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
- 480 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 reconstructed an ancestral bacteria-killing protein, deemed to be 59-million years old. So maybe the answer to the increase in bacterial resistance to antibiotics lies in Kanga’s pouch. After all, she was very protective of Roo.... 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
- 880 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
- 923 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
- 761 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 (1030) and, above all, the genetic diversity is unmatched by all other life combined. Participating students will see how their data may be used by other researchers in the SEA network — truly collaborative, crowdsourced science. Here are the genomic sequences of SEA-sequenced bacteriophages already in GenBank.... 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
- 1,103 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 techniques are too expensive. Their light weight is insufficient to trip the mines. Their veterinary requirements are less than those of dogs, and they are not dependent upon a single handler.... 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
- 717 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 invisible enemy: you can’t see them, but they are deadly. You can sure kill them with copious amounts of ethanol.
Actually, only a minority of microbes are pathogens. Some eukaryotes are parasitic and disease causing. There is Athlete’s foot (caused by a fungus) amoebal dysentery and other unpleasant experiences. But most are not. Also, most bacteria that live in us or on us are symbiotic and like us for our throwaway proteins, carbohydrates, nice 36.6C temperature, high humidity (armpit or mouth) and other goodies. Yes, some are pathogenic, and some do seem like evil little minions of the Devil. Those have ingenious mechanism which infect, wreak havoc, sometimes kill, and move on. But for every plague bacillus or burger bug out there, there are millions of other kinds of bacteria that really don’t do much, good or bad.... 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
- 706 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
- 1,232 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
- 1,087 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 urination becomes difficult and painful. In women, if left untreated, gonorrhea can lead to pelvic inflammatory disease, a painful condition that can cause sterility or ectopic pregnancy.... 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
- 1,203 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
- 696 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 growers.
One thing I learned form the Cocoa paper: Cocoa may be a recent descendant of the common eudicot ancestor, and becuase of that and because it is easily manipulated, it can bee a good model for tree fruit crops.
It does not, however, boost immunity:... 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
- 787 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 have occurred in the first place. Playing the media game to draw attention to science is good and welcome, and scientists should probably verse themselves a lot more in the skill of properly communicating their findings to the general public. However, to build expectations so high, that once the actual findings are revealed,the pre-embargo expectation (Life on Titan!) has led to an undeserved disappointment ( Arsenate-based life on Earth… yawn…), where actually, arsenate-based life is really cool!
... 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
- 756 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
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