PLOS Data Policy from March 1, 2014 PLOS journals require authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception1.
(…) the publications from these countries [Italy, Spain, Norway] with international collaborators contribute significantly to the average impact of their scientific production.
- Raj Kumar Pan, Kimmo Kaski, Santo Fortunato
In their natural environment, microbes organize into communities held together by an extracellular matrix composed of polysaccharides and proteins. We developed an in vivo labeling strategy to allow the extracellular matrix of developing biofilms to be visualized with conventional and superresolution light microscopy. Vibrio cholerae biofilms displayed three distinct levels of spatial organization: cells, clusters of cells, and collections of clusters. Multiresolution imaging of living V. cholerae biofilms revealed the complementary architectural roles of the four essential matrix constituents: RbmA provided cell-cell adhesion; Bap1 allowed the developing biofilm to adhere to surfaces; and heterogeneous mixtures of Vibrio polysaccharide, RbmC, and Bap1 formed dynamic, flexible, and ordered envelopes that encased the cell clusters.
Berk, V., Fong, J.C.N., Dempsey, G.T., Develioglu, O.N., Zhuang, X., Liphardt, J., Yildiz, F.H. & Chu, S. (2012). Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms, Science, 337 (6091) 239. DOI: 10.1126/science.1222981
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
The self-assembly(1, 2)and the evolution(3)of a molecular nanowheel
Or, in other words, the creation of life-like cells from metal: Leroy Cronin and his team have try to demonstrate that life could be born also from metal atoms.
There is every possibility that there are life forms out there which aren’t based on carbon, On Mercury, the materials are all different. There might be a creature made of inorganic elements.
(Tadashi Sugawara, University of Tokyo)
(1) Haralampos N. Miras, Geoffrey J. T. Cooper, De-Liang Long, Hartmut Bögge, Achim Müller, Carsten Streb, Leroy Cronin (2010). Unveiling the Transient Template in the Self-Assembly of a Molecular Oxide Nanowheel Science, 327 (5961), 72-74 DOI: 10.1126/science.1181735
(2) Johannes Thiel, Pedro I. Molina, Mark D. Symes, Leroy Cronin (2012). Insights into the Self-Assembly Mechanism of the Modular Polyoxometalate “Keggin-Net” Family of Framework Materials and Their Electronic Properties Crystal growth and design, 12 (2), 902-908 DOI: 10.1021/cg201342z
(3) Haralampos N. Miras, Craig J. Richmond, De-Liang Long, Leroy Cronin (2012). Solution-Phase Monitoring of the Structural Evolution of a Molybdenum Blue Nanoring Jouornal of the American Chemical Society, 134 (852), 3816-3824 DOI: 10.1021/ja210206z
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
Drawings of the elements of CMS detector, in the style of Leonardo da Vinci
The pictures are used for the covers of the official CMS Technical Design Reports
The study of the fundamental theory of the strong interaction - Quantum Chromodynamics (QCD) - in extreme conditions of temperature, density and parton momentum fraction (low-x) has attracted an increasing experimental and theoretical interest during the last 20 years. Indeed, QCD is not only a quantum ﬁeld theory with an extremely rich dynamical content - such as asymptotic freedom, infrared slavery, (approximate) chiral symmetry, non-trivial vacuum topology, strong CP violation problem, UA(1) axial-vector anomaly, colour superconductivity, … - but also the only sector of the Standard Model (SM) whose full collective behaviour - phase diagram, phase transitions, thermalisation of fundamental ﬁelds - is accessible to scrutiny in the laboratory. The study of the many-body dynamics of high-density QCD covers a vast range of fundamental physics problems.(1)
(1) ., d’Enterria, D., Ballintijn, M., Bedjidian, M., Hofman, D., Kodolova, O., Loizides, C., Lokthin, I., Lourenço, C., Mironov, C., Petrushanko, S., Roland, C., Roland, G., Sikler, F., & Veres (editors), G. (2007). CMS Physics Technical Design Report: Addendum on High Density QCD with Heavy Ions Journal of Physics G: Nuclear and Particle Physics, 34 (11), 2307-2455 DOI: 10.1088/0954-3899/34/11/008 (pdf)
(thanks to Peppe Liberti)
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