105 posts · 138,076 views
The musings and ravings of a computational biologist about science, computers, music and, you know, stuff
I recently received an email from a graduate student in Philosophy regarding protein function. Not sure if that person wants his name advertised, so I will keep it to myself.
I am a fan of your blog, and interested in the philosophy of biology. One particularly interesting question is what makes something have a function; when [...]... Read more »
Khersonsky O, Roodveldt C, & Tawfik DS. (2006) Enzyme promiscuity: evolutionary and mechanistic aspects. Current opinion in chemical biology, 10(5), 498-508. PMID: 16939713
Jeffery, C. (2003) Moonlighting proteins: old proteins learning new tricks. Trends in Genetics, 19(8), 415-417. DOI: 10.1016/S0168-9525(03)00167-7
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
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
In case you have been vacationing in a parallel universe in the past two days, you should have heard about the new synthetic bacterium created at the J Craig Venter Institute. In a nutshell, the scientific team synthesized an artificial chromosome of the bacterium Mycoplasma mycoides and transferred it to another bacterium, Mycoplasma capricolum. The [...]... Read more »
Gibson, D., Glass, J., Lartigue, C., Noskov, V., Chuang, R., Algire, M., Benders, G., Montague, M., Ma, L., Moodie, M.... (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. DOI: 10.1126/science.1190719
Big party at Science journal today, with the publication of a comprehensive draft Neanderthal genome. (Free access, nice going Science). Actually, it is a partially assembled draft of 60% of the total genome, but 60% of the genome from a human that was last seen on Earth 28,000 years ago is quite an achievement. The [...]... Read more »
No, not the flesh-blood-and-feathers penguin, but rather Tux, the beloved mascot of the Linux operating system. Compared with Escherichia coli, the model organism of choice for microbiologists.
We refer to DNA as “the book of life”; some geeks refer to it as the “operating system of life”. Just like in a computer’s operating system, DNA contains [...]... Read more »
Yan, K., Fang, G., Bhardwaj, N., Alexander, R., & Gerstein, M. (2010) Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0914771107
Nature is colorful. And the family of pigments that is mostly responsible for these colors are carotenoids. Carotenoids make the apples red, the lemons yellow, the pumpkins oranges and, yes carrots, (from which their name is derived), orange.
Carotenoids also make flamingos and salmon pink, and color the puffin’s bill orange. But those animals cannot produce [...]... Read more »
Moran, N., & Jarvik, T. (2010) Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids. Science, 328(5978), 624-627. DOI: 10.1126/science.1187113
Obesity is one symptom of several, which together constitute what is now termed metabolic syndrome. Morbid obesity is also associated with a host of other symptoms including high blood sugar, high blood lipids, insulin resistance and liver disorders. The root causes of which are traced back to excessive food consumption, reduced physical activity and in some cases, genetic predisposition.
I have written before on the connection found between gut microbe populations and metabolic syndrome.... Read more »
Vijay-Kumar, M., Aitken, J., Carvalho, F., Cullender, T., Mwangi, S., Srinivasan, S., Sitaraman, S., Knight, R., Ley, R., & Gewirtz, A. (2010) Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science, 328(5975), 228-231. DOI: 10.1126/science.1179721
It seems like there is no institution that is more criticized in science than that of the peer-review system — an no one that is less mutable. While published paper evaluation metrics are being revised (such as the recently introduced PLoS article level metrics, or the Australian National Health and Medical Research Council abandonment of [...]... Read more »
Friedberg, E. (2010) Peer review of scientific papers—A never-ending conumdrum. DNA Repair. DOI: 10.1016/j.dnarep.2010.03.003
“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2
“What-ever” – Me
In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic sequencing data [...]... Read more »
There are more microbial cells in our body than our own. Those microbes are not just passive hitchhikers or conversely, malicious agents of disease. They affect our well-being and health in a much broader spectrum than simply “bad” or “passive”. Among other things our gut microbes play an important role in digestion, have been linked [...]... Read more »
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T.... (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59-65. DOI: 10.1038/nature08821
As part of the process of manufacturing a new car, the designers will take the blueprints to the factory floor. There they will set up an experimental assembly line, tinkering with the manufacturing process of the prototype until it is ready for mass-production. Can we do the same with the machinery of life – the assembly [...]... Read more »
Neumann, H., Wang, K., Davis, L., Garcia-Alai, M., & Chin, J. (2010) Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature. DOI: 10.1038/nature08817
Seriously, this is what I first thought when I saw the cover of this week’s Nature, and the associated drawings in the press. The dude’s haircut seems like it was even bad in the ’80s… 2080 BCE that is, which is when his body is dated. Approximately.
A large group of researchers were involved in analyzing [...]... Read more »
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R.... (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, 463(7282), 757-762. DOI: 10.1038/nature08835
Gilbert MT, Kivisild T, Grønnow B, Andersen PK, Metspalu E, Reidla M, Tamm E, Axelsson E, Götherström A, Campos PF.... (2008) Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science (New York, N.Y.), 320(5884), 1787-9. PMID: 18511654
Pharmaceutical companies are always on the lookout for secondary drug targets. After all, if you invest billions developing a single drug, you would be more than happy to sell it as a treatment for two, three, or more different ailments. Sildenafil citrate was developed to treat angina and hypertension. During phase I clinical trials, it [...]... Read more »
Durrant, J., Amaro, R., Xie, L., Urbaniak, M., Ferguson, M., Haapalainen, A., Chen, Z., Di Guilmi, A., Wunder, F., Bourne, P.... (2010) A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Computational Biology, 6(1). DOI: 10.1371/journal.pcbi.1000648
Despite our best attempts to remove species from the face of the Earth, there is still quite a bit of life out there and it is still quite diverse. Also, there are still quite a few people who want to document, describe and make the rest of us aware of the magnitude and diversity of [...]... Read more »
Smith VS, Rycroft SD, Harman KT, Scott B, & Roberts D. (2009) Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC bioinformatics. PMID: 19900302
After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone.
GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of today. [...]... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
Sequencing centers keep pumping large amounts of sequence data into the omics-sphere (will I get a New Worst omics Word Award for this?) There is no way we can annotate even a small fraction of those experimentally and indeed most annotations are automatic, done bioinformatically. Typically function is inferred by homology: if the protein sequence [...]... Read more »
Schnoes, A., Brown, S., Dodevski, I., & Babbitt, P. (2009) Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies. PLoS Computational Biology, 5(12). DOI: 10.1371/journal.pcbi.1000605
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
The first bioinformatics meeting I went to was in 1996 at the Nachsholim resort, north of Tel Aviv. I received a fellowship for the duration, and shared a room with the brilliant Golan Yona, then a grad student at the Hebrew University. I was doing biochemistry at the time and knew next to nothing about [...]... Read more »
, . (2009) Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species. Journal of Heredity. DOI: 10.1093/jhered/esp086
Blog Action Day focuses this year on climate change, which, like everything else on this planet, is also a microbial matter. Howzat? Methane (CH4) is a greenhouse gas which has heat retention capability 23 times of that of CO2. Soil methanogens are the chief global producers of methane. There are an estimated 7.5x 109 tons [...]... Read more »
Walter, K., Zimov, S., Chanton, J., Verbyla, D., & Chapin, F. (2006) Methane bubbling from Siberian thaw lakes as a positive feedback to climate warming. Nature, 443(7107), 71-75. DOI: 10.1038/nature05040
Kennedy, M., Mrofka, D., & von der Borch, C. (2008) Snowball Earth termination by destabilization of equatorial permafrost methane clathrate. Nature, 453(7195), 642-645. DOI: 10.1038/nature06961
WAGNER, D., GATTINGER, A., EMBACHER, A., PFEIFFER, E., SCHLOTER, M., & LIPSKI, A. (2007) Methanogenic activity and biomass in Holocene permafrost deposits of the Lena Delta, Siberian Arctic and its implication for the global methane budget. Global Change Biology, 13(5), 1089-1099. DOI: 10.1111/j.1365-2486.2007.01331.x
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