- December 30, 2009
- 06:45 AM
- 1,114 views
2010, the year when 20/10 vision was promised
by Pablo Artal in Optics confidential
The promise of perfect "20/10" vision for everybody appeared to be a real possibility in the early 2000's. 2010 is already here and your doctor cannot offer you yet supervision...... Read more »
Santamaria, Artal, Bescos. (1987) Determination of the point spread function of human eyes using a hybrid optical-digital method. J.Opt.Soc.Am.A., 1109. info:/
- December 29, 2009
- 08:19 PM
- 718 views
Looking Younger…. Looking Less Masculine?
by Wayne Hooke in The Psychology of Beauty
Egan & Cordan (2008) digitally altered the faces of 17-year-old girls (n=10) to look either younger (morphed to appear similar to the prototype of 10-year-old girls – top row) or older (similar to the prototype of 20-year-old women – bottom row). Additionally, some stimuli were altered by adding digital make-up (right column). The authors had [...]... Read more »
Egan, V., & Cordan, G. (2009) Barely legal: Is attraction and estimated age of young female faces disrupted by alcohol use, make up, and the sex of the observer?. British Journal of Psychology, 100(2), 415-427. DOI: 10.1348/000712608X357858
- December 29, 2009
- 06:38 PM
- 887 views
Economists (don’t) prove that money can buy you happiness… And news outlets prove they’re crap.
by Michael Slezak in Good, Bad, and Bogus
... Read more »
- December 29, 2009
- 02:37 PM
- 525 views
Point of View
by Brian Koberlein in Upon Reflection
Figure 1: Tycho's model of the cosmos. The solar system revolves around a fixed Earth, which is all surrounded by the celestial sphere of stars. (Source: Wikipedia) When you look at the night sky it is easy to imagine that...... Read more »
Miller-Jones, J., Jonker, P., Dhawan, V., Brisken, W., Rupen, M., Nelemans, G., & Gallo, E. (2009) THE FIRST ACCURATE PARALLAX DISTANCE TO A BLACK HOLE. The Astrophysical Journal, 706(2). DOI: 10.1088/0004-637X/706/2/L230
- December 29, 2009
- 02:24 PM
- 394 views
Two for the Price of One
by Journal Watch Online in Journal Watch Online
Conserving carbon-rich regions could also benefit biodiversity
... Read more »
Strassburg, B., Kelly, A., Balmford, A., Davies, R., Gibbs, H., Lovett, A., Miles, L., Orme, C., Price, J., Turner, R.... (2009) Global congruence of carbon storage and biodiversity in terrestrial ecosystems. Conservation Letters. DOI: 10.1111/j.1755-263X.2009.00092.x
- December 29, 2009
- 02:03 PM
- 1,196 views
Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution
by Jonathan Eisen in The Tree of Life
Today is a fun day for me. A paper on which I am the senior author is being published in Nature (yes, the Academic Editor in Chief of PLoS Biology is publishing a paper in Nature, more on that below ..). This paper, entitled, "A phylogeny driven genomic encyclopedia of bacteria and archaea" represents a culmination of years of work by many people from multiple institutions. Today in this blog I am going to do my best to tell the story behind the paper - about the people and the process and a little bit about the science.
First, a brief bit about the science in the paper. In this paper, we (mostly people at the Joint Genome Institute, where I have an Adjunct Appointment -- but also people in my lab at UC Davis and at the DSMZ culture collection) did a relatively simple thing - we started with the rRNA tree of life as a guide. Then we identified branches in the bacterial and archaeal portions of this tree where there were no genome sequences available (or in progress) (this was done mostly by Phil Hugenholtz, Dongying Wu and Nikos Kyrpides) Next we searched for representatives of these "unsequenced" branches in the DSMZ culture collection (a collection of bacteria and archaea that can be grown in the lab). And we identified in total some 200 of these. And then the DSMZ (under the direction of Hans-Peter Klenk) grew these organisms and sent the DNA to the Joint Genome Institute. And then JGI turned on their genome sequencing muscle and sequenced the genomes of the organisms in the DNA samples. And finally, we spent a good deal of time then analyzing the data asking a pretty simple question - are there any general benefits that come from this "phylogeny driven" approach to sequencing genomes compared to what one might find with sequencing just any random genome (after all, any genome sequence could have some value)? The paper, describes what we found, which is that there are in fact many benefits that come from sequencing genomes from branches in the tree for which genomes are not available.
More on the details of the science below. But first, I want to note that this paper was truly an amazing team effort, with all sorts of people from the JGI in particular, going above and beyond the call of duty to make sure it happened and worked well. And the Department of Energy has been truly phenomenal in my opinion in supporting this project which in the end is not explicitly about "energy" per se but is really about providing a reference set of genomes that should improve the value of all microbial genome data.
Anyway, now for the story behind the story. And be prepared, because this is a bit long. But I think it is important to place this work in a bigger context both in terms of my background as well as some of the background of other people in the project. If you can't wait for more on the GEBA project then perhaps you should go to some of these links:
Videos of talks I have given on the project:
"Genomic Encyclopedia of Bacteria and Archaea (GEBA)"- Jonathan ...
Recent talk I gave at the Sackler NAS "Microbes and Health" meeting
Podcast of interview of me for ASM's Meet the scientist
Stories about GEBA
Nature News from 11.17.2009
Stories about our paper
Nature News
GenomeWeb "GEBA Researchers Publish Results from Dozens of Bacterial, Archaeal Genomes"
Ars Technica article "Presenting a genomic encyclopedia of bacteria (and archaea" by John Timmer
Iddo Friedberg blogged about it
The OpenHelix Blog on it
Leonardo Martins blogs about it here and helps translate a Spanish story about the project
R&D magazine has a post based on the press releases here
NY Times story by Carl Zimmer here.
FriendFeed Discussions here (includes a thread about Nature using a Creative Commons license)
And I will post more links as they come up. Below what I try to provide is some of the story behind the story:
My personal interest in applied uses of phylogenetics stage 1: undergraduate preparation at Harvard
As this paper is primarily about an applied use of phylogenetics (in selecting genomes for sequencing), I thought it would be worth going into some of how I personally became a bit obsessed with applied uses of phylogenetics. For me, my obsession began as an undergraduate at Harvard where I got exposed to the value of phylogeny as a tool from many many angles including but not limited to:
Freshman year taking a course taught by Stephen Jay Gould where Wayne and David Maddison were Teaching Assistant's and where they were demoing their new phylogenetics software called MacClade
Sophomore year taking a conservation biology class with Eric Fajer and Scott Melvin where I was exposed to the concept of "phylogenetic diversty" as a tool in assessing conservation plans
Junior year working in the lab of Fakhri Bazzaz with people like David Ackerly and Peter Wayne who made use of phylogeny as a key tool in their research projects
Senior year and the year after graduating where I worked in the lab of Colleen Cavanaugh using rRNA based phylogenetic analysis to characterize uncultured chemosynthetic symbionts. I note it was in Colleen's lab that I also became obsessed you could say with microbes and why they rock.
My personal interest in applied uses of phylogenetics stage 2: graduate school at Stanford
All of this and more gave me a strong passion for phylogeny as a tool. And so when I went to graduate school at Stanford (originally to work with Ward Watt on butterflies, but then I switched to working in Phil Hanawalt's lab on the "Evolution of DNA repair genes, proteins and processes"). And while in that lab I become pretty much obsessed with three things, all related to phylogeny.
First, I was interested in whether the rRNA tree of life, which I had used in my studies in Colleen Cavanaugh's lab (and in my first paper in J. Bacteriology, which, thanks to ASM, is now in Pubmed Central and free at ASM's site too), was robust or, as some critics argued, was not that useful. This was a critical question since the best way to study the phylogeny of microbes at the time, and also the best way to study uncultured microbes, was to leverage the ability to clone rRNA genes by PCR and then to build evolutionary trees of those rRNA genes. As part of my graduate work, I did a study where I compared the phylogenetic trees of rRNA to trees of another gene from the same speci... 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
- December 29, 2009
- 11:38 AM
- 1,370 views
SNP Discovery in NGS Data, Atlas-SNP2, and VarScan
by Daniel Koboldt in Massgenomics
A paper in this month’s Genome Research sheds light on predictors of sequencing error in next-generation sequencing. Using data from both 454 and Illumina platforms, Shen et al applied logistic regression models to identify sequence- and platform-related factors that contribute to substitution (SNP) errors.
The results, I think, offer new insight into the challenge of accurate [...]... Read more »
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA.... (2009) A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome research. PMID: 20019143
- December 29, 2009
- 10:41 AM
- 564 views
Interpreting Dreams
by Daniel Hawes in Ingenious Monkey | 20-two-5
Many people hold Freudian notions of their dreams as meaningful messages. Indeed, the idea that dreams communicate messages from the subconscious, or even from a higher power, is deeply entrenched in our culture through religion, art and literature. This post takes a look at a recent study of how laypeople make sense of their dreams, and how dreams affect the decisions we make during the day...... Read more »
Morewedge, C., & Norton, M. (2009) When dreaming is believing: The (motivated) interpretation of dreams. Journal of Personality and Social Psychology, 96(2), 249-264. DOI: 10.1037/a0013264
- December 29, 2009
- 08:30 AM
- 1,018 views
Finding patterns in wildlife attacks on domestic livestock
by Rob Goldstein in Conservation Maven
... Read more »
Karlsson, J., & Johansson, O. (2009) Predictability of repeated carnivore attacks on livestock favours reactive use of mitigation measures. Journal of Applied Ecology. DOI: 10.1111/j.1365-2664.2009.01747.x
- December 29, 2009
- 04:43 AM
- 623 views
Right-handers sit to the right of the movie screen to optimise neural processing of the film
by Christian Jarrett in BPS Research Digest
Although our bodies appear largely symmetrical on the outside, the way our brains are organised and wired is rather more lop-sided. This is obvious to us in relation to handedness, whereby the brain is better at controlling one hand than the other. The idea that, for many of us, the left-hemisphere is dominant for language is also widely known. However, functional asymmetry between the brain hemispheres also affects our behaviour in more subtle ways that are still being explored. The latest example of this comes from Japan where Matia Okubo has shown that right-handers have a preference for sitting to the right of the cinema screen, but only when they are motivated to watch the film. The finding is consistent with the idea that in right-handers, the right-hemisphere is dominant for processing visual and emotional input. By sitting to the right of the screen, the film is predominantly processed by the right-hemisphere and the suggestion is that, without realising it, right-handers are choosing to sit in an optimal position for their brain to digest the movie.Okubo presented 200 students with a grid showing the seats available in a cinema (a central area was shown as occupied). In the first experiment, all the students were told that the film was enjoyed by friends and critics, with half also told that the story was sad and depressing and to imagine that they'd rather avoid seeing it. For students who only heard the recommendation, the right-handers were far more likely to choose a seat to the right of the screen (74 per cent did so), whereas the left-handers and mixed-handers showed no such bias. For the students who were put off the film, none showed a preference for the right-hand seats, regardless of their handedness. This suggests that we only choose an optimal seat for our brain organisation when we're motivated to watch the film. A second experiment was nearly identical, but this time half the students were told the film was excellent and depressing, whereas the other students were simply told they wouldn't enjoy it. Again, when they were motivated to watch the film, even a depressing one, the right-handers showed a bias for seats to the right of the screen. 'People tend to adopt the most effective manner in which their hemispheric functions can be utilised,' Okubo said, adding that: 'It is tempting to think that some other undiscovered behavioural asymmetries can also be discovered through this approach'.This new research comes after a past study showed that adults with a more artistic, less analytic thinking style (associated with the right hemisphere) were more likely to sit on the right-hand side of the classroom; and another that showed people are more likely to exhibit the left side of their face (controlled by the right hemisphere) when asked to express emotion in a family photo, but to show their right profile when asked to pose as a scientist. _________________________________Okubo, M. (2010). Right movies on the right seat: Laterality and seat choice. Applied Cognitive Psychology, 24 (1), 90-99 DOI: 10.1002/acp.1556[Related Digest item here]
... Read more »
Okubo, M. (2010) Right movies on the right seat: Laterality and seat choice. Applied Cognitive Psychology, 24(1), 90-99. DOI: 10.1002/acp.1556
- December 29, 2009
- 04:30 AM
- 430 views
Protected areas lead to long term transformation of marine ecosystems
by Rob Goldstein in Conservation Maven
Results from a new study in Australia affirm the ability of "no take" marine protected areas to aid the recovery of overfished ecosystems. Researchers found that the reefs within three marine protected areas off eastern Tasmania transformed over time into communities not otherwise seen in the regional seascape, and these changes intensified for at least 16 years.... Read more »
Edgar, G., Barrett, N., & Stuart-Smith, R. (2009) Exploited reefs protected from fishing transform over decades into conservation features otherwise absent from seascapes. Ecological Applications, 19(8), 1967-1974. DOI: 10.1890/09-0610.1
- December 29, 2009
- 01:43 AM
- 1,250 views
More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia"
by Jonathan Eisen in The Tree of Life
Additional discussion of recent paper... 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
- December 28, 2009
- 05:42 PM
- 568 views
Antipodean Pharmaceuticals and their Mitochondrially Targeted Antioxidant
by Reason in Fight Aging!
You might recall the work of Skulachev's research group in producing an ingested antioxidant compound that targets the mitochondria and extends life span in mice. Similarly, mice genetically engineered to produce more naturally-occurring antioxidants in their mitochondria also live longer. By way of comparison, all other forms of antioxidant examined to date generally do nothing for life span, and may even harm your health and longevity. The plausible explanation for the effects of mitochondrially targeted antioxidants rests on the mitochondrial free radical theory of aging. In short, your mitochondria are powerplants, thousands of them in each cell of your body. They convert food into the chemicals used to power cellular processes, but emit damaging free radicals as a byproduct. Some fraction of aging is caused by the chain of events that occur as mitochondria progressively damage themselves with their own emissions. Thus anything that can soak up these free radicals at the source, before they cause any harm, should lower the rate at which biochemical damage occurs, and extend life span. Now let me direct your attention to Antipodean Pharmaceuticals, a New Zealand based research group working to develop an antioxidant targeted to mitochondria. Their compound, called MitoQ, appears similar...... Read more »
Rodriguez-Cuenca S, Cochemé HM, Logan A, Abakumova I, Prime TA, Rose C, Vidal-Puig A, Smith AC, Rubinsztein DC, Fearnley IM.... (2009) Consequences of long-term oral administration of the mitochondria-targeted antioxidant MitoQ to wild-type mice. Free radical biology . PMID: 19854266_id
- December 28, 2009
- 04:09 PM
- 944 views
Reinfection with 2009 influenza H1N1
by Vincent Racaniello in virology blog
In healthy individuals, the first encounter with a virus leads to a primary antibody response. When an infection occurs with the same or a similar virus, a rapid antibody response occurs that is called the secondary antibody response. Antibodies are critical for preventing many viral infections, including influenza. But reinfection may occur if we encounter the same [...]... Read more »
Perez CM, Ferres M, & Labarca JA. (2010) Pandemic (H1N1) 2009 Reinfection, Chile. Emerging infectious diseases, 16(1), 156-7. PMID: 20031070
- December 28, 2009
- 02:18 PM
- 377 views
Closer (and Closer) to Nature
by Journal Watch Online in Journal Watch Online
Housing is encroaching on U.S. protected areas
... Read more »
Radeloff, V., Stewart, S., Hawbaker, T., Gimmi, U., Pidgeon, A., Flather, C., Hammer, R., & Helmers, D. (2009) Housing growth in and near United States protected areas limits their conservation value. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0911131107
- December 28, 2009
- 01:52 PM
- 1,049 views
Shield Pennywort - Hydrocotyle
by Johnny in Ecographica
Shield pennywort represents but one of about a hundred different species that belong to the Genus Hydrocotyle, a.k.a the ‘water pennyworts.’ Though often found listed as members of the Apiaceae Family, the Hydrocotyle group is now included in the ‘Ivy Family’ (Araliaceae). The genus as whole enjoys a worldwide distribution; however, the Facultative Wet H. verticillata is native to the Americas where can be found occupying floodplains, swamps, ditches, and just about anywhere with moist soils.... Read more »
CHANDLER, G., & PLUNKETT, G. (2004) Evolution in Apiales: nuclear and chloroplast markers together in (almost) perfect harmony. Botanical Journal of the Linnean Society, 144(2), 123-147. DOI: 10.1111/j.1095-8339.2003.00247.x
- December 28, 2009
- 11:03 AM
- 703 views
Plant-ant relationships: plants on top?
by Thomas Kluyver in Thomas' Plant-Related Blog
Ants disperse the seeds of several ‘ancient woodland species’ in the UK, such as dog’s mercury. These are woodland plants that take a long time to arrive when a new wood forms, so you tend to only find them in old woods. In the tropics, ‘ant plants’ take it even further: they house and sometimes [...]... Read more »
Pfeiffer, M., Huttenlocher, H., & Ayasse, M. (2009) Myrmecochorous plants use chemical mimicry to cheat seed-dispersing ants. Functional Ecology. DOI: 10.1111/j.1365-2435.2009.01661.x
Willmer, P., Nuttman, C., Raine, N., Stone, G., Pattrick, J., Henson, K., Stillman, P., McIlroy, L., Potts, S., & Knudsen, J. (2009) Floral volatiles controlling ant behaviour. Functional Ecology, 23(5), 888-900. DOI: 10.1111/j.1365-2435.2009.01632.x
- December 28, 2009
- 11:00 AM
- 1,749 views
Do bats REALLY eat mosquitoes?
One of the debates a lot of entomologists have is whether bats actually have an impact on mosquito populations. Sure, we hear all the time that bats eat mosquitoes, but there are good reasons to doubt this. I’ve had this discussion with instructors before and there’s really no consensus.
We know bats occasionally eat mosquitoes. They [...]... Read more »
Reiskind MH, & Wund MA. (2009) Experimental assessment of the impacts of northern long-eared bats on ovipositing Culex (Diptera: Culicidae) mosquitoes. Journal of medical entomology, 46(5), 1037-44. PMID: 19769034
- December 28, 2009
- 09:00 AM
- 1,297 views
Not All Mice Are Created Equal When it Comes to Gonorrhea
by Tim Sampson in The Times Microbial
Neisseria gonorrhoeae, the causative agent of the sexually transmitted infection, gonorrhea, is a Gram-negative diplococcus and an obligate human pathogen. An estimated 800,000 cases of gonorrhea occur each year in the United States (1). The most common sites of infection are the cervix and the male urethra, and symptomatic infection is characterized by a purulent exudate composed of numerous polymorphonuclear leukocytes (PMNs) containing intracellular gonococci (3).
The development of whole model systems to study N. gonorrhoeae infection is important, as several different cell types are involved in host response. ... Read more »
Packiam M, Veit SJ, Anderson DJ, Ingalls RR, & Jerse AE. (2010) Mouse strain-dependent differences in susceptibility to Neisseria gonorrhoeae infection and induction of innate immune responses. Infection and immunity, 78(1), 433-40. PMID: 19901062
- December 28, 2009
- 08:15 AM
- 925 views
Guidelines for genetic rescue: Interview with Philip Hedrick and Richard Fredrickson
by Rob Goldstein in Conservation Maven
We recently interviewed, Philip Hedrick and Richard Fredrickson, leaders in the field of conservation genetics. They had just published an article in which they outlined 10 guiding principles for genetic rescue - a practice that has been used to improve the condition of certain highly endangered species.... Read more »
Hedrick, P., & Fredrickson, R. (2009) Genetic rescue guidelines with examples from Mexican wolves and Florida panthers. Conservation Genetics. DOI: 10.1007/s10592-009-9999-5
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