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- March 29, 2013
- 07:20 PM
- 144 views
The power of single-cell genomics: the mysterious SR1 bacteria have a unique genetic code
by Iddo Friedberg in Byte Size Biology
SR1 bacteria are not exactly a household name, even among microbiologists. They were first discovered in contaminated aquifers, and since then they were found to be also in animal and insect guts, as well as in human mouths. They are even suspected of being a cause of periodontal disease. I should probably say here that SR1 is a whole phylum of bacteria, and not a single genus or species. The reason that they are not that well known is that their discovery was fairly recent.
Also, no one ha........ Read more »
Campbell, J., O'Donoghue, P., Campbell, A., Schwientek, P., Sczyrba, A., Woyke, T., Soll, D., & Podar, M. (2013) UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1303090110
- March 2, 2013
- 11:09 PM
- 204 views
The Black Queen Hypothesis
by Iddo Friedberg in Byte Size Biology
The Red Queen hypothesis is well-accepted in evolutionary biology. Organisms evolve and adapt not to gain an evolutionary advantage, but simply to not fall behind competing organisms that evolve and adapt. Hence, everyone has to “run as fast as they can” (evolve) to “stay in the same place” (reproduce). It’s a nice hypothesis, and has been shown to be fairly descriptive when dealing with close competitors, such as host-parasite or predator-prey relationships.
Wh........ Read more »
Morris, J., Lenski, R., & Zinser, E. (2012) The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss. mBio, 3(2). DOI: 10.1128/mBio.00036-12
- February 6, 2013
- 12:59 PM
- 241 views
Life Stands on the shoulders of Giants (Viruses)
by Iddo Friedberg in Byte Size Biology
Viruses are… well… not really life. Or so says common wisdom. They have some elements of life: a genome, the ability to reproduce, and being subject to evolution by natural selection. But they cannot reproduce independently: they need to hijack the reproductive machinery of an actual living cell to do that. They do not have a metabolism: they are basically syringes with DNA or RNA, equipped with basic sensors that help them lock onto cells and use them to reproduce, usually destr........ Read more »
Nasir, A., Kim, K., & Caetano-Anolles, G. (2012) Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evolutionary Biology, 12(1), 156. DOI: 10.1186/1471-2148-12-156
- October 13, 2012
- 11:30 AM
- 501 views
DNA half life, and my dream of an Allosaurus Army
by Iddo Friedberg in Byte Size Biology
...but for some reason, Spielberg thought that the T. rex was cooler than the Allosaurus, and featured it as the terror-du-jour in Jurassic Park. (Jurassic? Allosaurus lived during the Jurassic. Rexie lived in the late Cretaceous, some 90 million years later). The lack of credibility of his choice is apparent, as ol’ rexie was cast alongside large Velociraptors. The real Velociraptor was the size of a goose, and with feathers & all probably looked a bit like one, albeit with teeth and a ........ Read more »
Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MT, Willerslev E.... (2012) The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings. Biological sciences / The Royal Society. PMID: 23055061
- August 13, 2012
- 08:50 PM
- 270 views
ZomBee Watch, a new citizen-scientist project
by Iddo Friedberg in Byte Size Biology
See the little fly riding the bee’s back? That’s the female Apocephalus borealis, laying its eggs in the bee. A. borealis’s larva hatch within the bee, causing it to leave the hive at night and be attracted to lights. The bee dies, while the larva leave it and pupate around it. New flies then emerge, which will infect more bees.... Read more »
Andrew Core, Charles Runckel, Jonathan Ivers, Christopher Quock, Travis Siapno, Seraphina DeNault, Brian Brown, Joseph DeRisi, Christopher D. Smith, & John Hafernik. (2012) A New Threat to Honey Bees, the Parasitic Phorid Fly Apocephalus borealis. PLoS ONE. info:/10.1371/journal.pone.0029639
- June 19, 2012
- 11:29 AM
- 390 views
The Evolution of Music
by Iddo Friedberg in Byte Size Biology
A collaboration between a group in Imperial College and Media Interaction group in Japan yielded a really cool website: darwintunes.org. The idea is to apply Darwinian-like selection to music. Starting form a garble, after several generations producing something that is actually melodic and listen-able. Or a Katy Perry tune. Whatever. The selective force being the appeal of the tune to the listener. ... Read more »
Robert M. MacCallum, Matthias Mauchb, Austin Burta, & Armand M. Leroia. (2012) (2012-06-18) Evolution of music by public choice. . Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1203182109
- June 14, 2012
- 02:51 PM
- 300 views
Annotating proteins in the uncanny valley
by Iddo Friedberg in Byte Size Biology
Every day, software appears to do more things that we thought were exclusively in the human realm. Like beating a grandmaster in chess, or carrying out a conversation. I say “appears” because there is obviously no self-aware intelligence involved, as this rather bizarre conversation between Cleverbots demonstrates. For humans, playing chess and carrying out a conversation are products of a self-aware intelligence, which gives rise to symbolic representation of information which ca........ Read more »
Škunca, N., Altenhoff, A., & Dessimoz, C. (2012) Quality of Computationally Inferred Gene Ontology Annotations. PLoS Computational Biology, 8(5). DOI: 10.1371/journal.pcbi.1002533
- May 4, 2012
- 02:03 PM
- 390 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
- 342 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,........ 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
- 532 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
- 487 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
- 608 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
- 690 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
- 698 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
- 674 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
- 1,396 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
- 1,415 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
- 1,054 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
- 1,653 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
- 1,034 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
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