Ula-Ula man's island

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

Image: (A) The electron density map; (B) the difference Fourier map.

Boutet, S., Lomb, L., Williams, G.J., Barends, T.R.M., Aquila, A., Doak, R.B., Weierstall, U., DePonte, D.P., Steinbrener, J., Shoeman, R.L. & (2012). High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography, Science, 337 (6092) 364. DOI: 10.1126/science.1217737

High-Resolution Maps of Science⁽¹⁾, via rangle

(1) Bollen J, Van de Sompel H, Hagberg A, Bettencourt L, Chute R, et al. (2009) Clickstream Data Yields High-Resolution Maps of Science. PLoS ONE 4(3): e4803. doi:10.1371/journal.pone.0004803

A framework for human microbiome

The Human Microbiome Project Consortium (HMPC) two interesting papers about the human microbiome.
First of all it

has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community.⁽¹⁾

The constructed catalogue is

the largest and most comprehensive reference set of human microbiome data associated with healthy adult individuals. ⁽¹⁾

The HMPC has also analized the micro-diversity in our bodies, producing the first map of our microbiota… but the story isn’to closed:

Many details remain for further work to fill in, building on this reference study. How do early colonization and lifelong change vary among body habitats? Do epidemiological patterns of transmission of beneficial or harmless microbes mirror patterns of transmission of pathogens? Which co-occurrences among microbes reflect shared response to the environment, as opposed to competitive or mutualistic interactions? How large a role does host immunity or genetics play in shaping patterns of diversity, and how do the patterns observed in this North American population compare to those around the world? Future studies building on the gene and organism catalogues established by the Human Microbiome Project, including increasingly detailed investigations of metatranscriptomes and metaproteomes, will help to unravel these open questions and allow us to more fully understand the links between the human microbiome, health and disease.⁽²⁾

In the image (via Matthew Herper for Forbes): Principal coordinates plot showing variation among samples demonstrates that primary clustering is by body area, with the oral, gastrointestinal, skin and urogenital habitats separate; the nares habitat bridges oral and skin habitats.⁽²⁾

(1) The Human Microbiome Project Consortium (2012). A framework for human microbiome research Nature, 486 (7402), 215-221 DOI: 10.1038/nature11209
(2) The Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome Nature, 486 (7402), 207-214 DOI: 10.1038/nature11234

Evolutionary outcomes caused by differences in community composition.

Cartoon examples of how community complexity can lead to unexpected ecological and evolutionary outcomes in populations. The illustrations are taken from a subset of idealized simulations that are depicted as animations in Movies 1–6. The panels on the left (A,C,E) represent initial conditions at the beginning of a simulation, and the panels on the right (B,D,F) show populations and communities after evolution has reached an equilibrium. In these examples, different consumer species (purple, green, and yellow) move in the environment consuming renewable resources (green circles and red squares; orange diamonds represent excrement). If they consume enough resources they reproduce, and if they do not they die. In all cases, species start as generalist consumers, represented here as non-specialized mouth parts capable of consuming any resource. Species can subsequently evolve to specialize on a resource by changing mouth shape to correspond to resource shape, which increases resource capture efficiency and reproduction. In reality, these examples apply to any case where a trait influences consumer efficiency, whether it involves morphological (e.g., beak morphology), physiological (e.g., metabolic rate), or behavioral (hunting method) change. (A) and (B) represent the evolution of specialization in a one species community. A single generalist species feeds on a common resource and evolves more efficient resource consumption (Movie 1). (C) and (D) represent the evolution of character displacement in a two-species community whereby two generalist consumer species initially compete for two limited resources. Competition causes each species to specialize on different resources and thus avoid extinction (Movie 3). (E) and (F) represent coexistence of three species that evolve to specialize on one of the two limited resources (green circles and red squares) or on the waste products produced by other species (orange diamonds) (Movie 6), as observed by Lawrence et al.⁽¹⁾

(1) Turcotte, M., Corrin, M., & Johnson, M. (2012). Adaptive Evolution in Ecological Communities PLoS Biology, 10 (5) DOI: 10.1371/journal.pbio.1001332

A Supernova Cocoon Breakthrough

Observations with NASA’s Chandra X-ray Observatory have provided the first X-ray evidence of a supernova shock wave breaking through a cocoon of gas surrounding the star that exploded. This discovery may help astronomers understand why some supernovas are much more powerful than others.
On Nov. 3, 2010, a supernova was discovered in the galaxy UGC 5189A, located about 160 million light years away. Using data from the All Sky Automated Survey telescope in Hawaii taken earlier, astronomers determined this supernova exploded in early October 2010 (in Earth’s time-frame).
This composite image of UGC 5189A shows X-ray data from Chandra in purple and optical data from Hubble Space Telescope in red, green and blue. SN 2010jl is the very bright X-ray source near the top of the galaxy.
A team of researchers used Chandra to observe this supernova in December 2010 and again in October 2011. The supernova was one of the most luminous that has ever been detected in X-rays.
The results of these observations were published in a paper that appeared in the May 1, 2012 issue of The Astrophysical Journal Letters⁽¹⁾.

Credits: X-ray: NASA/CXC/Royal Military College of Canada/P.Chandra et al); Optical: NASA/STScI

(1) Chandra, P., Chevalier, R., Irwin, C., Chugai, N., Fransson, C., & Soderberg, A. (2012). STRONG EVOLUTION OF X-RAY ABSORPTION IN THE TYPE IIn SUPERNOVA SN 2010jl The Astrophysical Journal, 750 (1) DOI: 10.1088/2041-8205/750/1/L2

The Map of Life is an interactive resource for global biodiversity analysis that it’s launched today.
On Nature Virginia Gewin writes:

On first glance, Map of Life may seem just one more in the dozens of biodiversity databases online, but it has a novel capability — a web-mapping tool that integrates disparate data types, from single-occurrence records in museum collections to expert-derived ranges found in field guides.

In the image⁽¹⁾ there is a schematic diagram about the project:

Schematic diagram showing how producers and consumers of species distribution information interact with the envisioned infrastructure, currently under implementation as ‘Map of Life’. The planned web platform facilitates the uploading of species distribution information from many different organizations and sources, including data on habitat preferences, point occurrences and expert range maps. The infrastructure stores these data and provides a workbench for integrating them for one or many species. The data compiled, resulting summary information such as binary and probabilistic occurrence maps, and products from analysis tools can be provided to individual consumers, or served via Application Programming Interfaces (APIs) to other services or institutions such as Encyclopedia of Life (EOL), GEO Biodiversity Observation Network (GEO BON), initiatives connected to the Convention on Biodiversity (CBD) or the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES).⁽²⁾

If you can try the site, there is a search box where insert the key to search:

You can select the species:

Select the layer that you want:

And visualize the results on the map:

Enjoy with this new scientific project!

(1) Integrating biodiversity distribution knowledge: toward a global map of life (presentation in pdf)
(2) Jetz, W., McPherson, J., & Guralnick, R. (2012). Integrating biodiversity distribution knowledge: toward a global map of life Trends in Ecology & Evolution, 27 (3), 151-159 DOI: 10.1016/j.tree.2011.09.007