"Former California Supreme Court Associate Justice Cruz Reynoso, chair of the task force investigating the pepper-spray incident on November 18, 2011, said today the task force is working toward public release of findings and recommendations on Tuesday, March 6, at a time and location on the UC Davis campus to be determined.
Additional information will be provided as soon as it is available."
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Figure 1 from 10.1007/s00253-011-3819-9. Sediment cross section
exposing the characteristic Y-shaped burrow dug by S. velum.
Positioning itself at the triple junction of the Y, the bivalve alternates
between actively pumping oxygenated water from the upper arms of
the burrow through the mantle cavity and across the gills and
accessing reduced sulfur compounds diffusing up from the anoxic
zones below and pumped through a ventral incurrent opening in the
mantle. Scale bar equals 2.5 cm
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| Figure 1. Number of OTUs as a function of fractional sequence difference (OTU cut-off) for the 16S rRNA marker gene (A) and the rpoB marker gene (B). |
Vos, M., Quince, C., Pijl, A., de Hollander, M., & Kowalchuk, G. (2012). A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity PLoS ONE, 7 (2) DOI: 10.1371/journal.pone.0030600
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| From here. Maximum-parsimony tree of the 89 CC398 isolates (including ST398SO385) based on 4,238 total SNPs, including 1,102 parsimony-informative SNPs with a CI of 0.9591. Clades and groups of importance are labeled in a hierarchical fashion to facilitate description in the text. The tree was rooted with clade I based on an iterative selection process that identified this group as the most ancestral (see Materials and Methods). COO, country of origin; AT, Austria; BE, Belgium; CA, Canada; CH, Switzerland; CN, China; DE, Germany; DK, Denmark; ES, Spain; FI, Finland; FR, France; GF, French Guiana; HU, Hungary; IT, Italy; NL, The Netherlands; PE, Peru; PL, Poland; PT, Portugal; SI, Slovenia; US, United States; P, pig; H, human; R, horse; T, turkey; B, bovine; MET, methicillin susceptibility; R, resistant; S, susceptible. |
"A prize is offered to the individual or team that can provide a very large, phylogenetically-organized set(s) of scientific names suitable for ingestion into the Encyclopedia of Life as an alternate browsing hierarchy.
- Names must be provided in Darwin Core Archive1 format.
- Extinct organisms may be treated but are not required.
- Ranks are not required for names but may be included.
- Internal nodes need not all have formal Linnaean names but require a label which can be arbitrary. Leaf nodes also need not have formal names but ideally most will overlap with current EOL species pages.
- For the purpose of this contest, metrics and source of node support, branch lengths, vernaculars, and synonyms are not required. These may be included; not all are currently displayable on EOL.
- Trees must be rooted. Multiple, overlapping hierarchies may be submitted as a set (e.g. to handle reticulation)
Among other factors, the total number of uniquely named nodes, node/leaf ratios and tree height may be used to compare entries so contestants should consider how they wish to trade off strict consensus versus other methods of reflecting the state of phylogenetic knowledge.Problems to solve include 1) how to assign labels to unnamed nodes, 2) how to fill in gaps so that the set of taxa included is as comprehensive as possible, even if trees are not fully resolved or all taxa have not been analyzed, 3) how to handle competing hypotheses, 4) how to update the hierarchy at least annually.The winning submission must be available to EOL and others under an acceptable CC license if it is under copyright. The tree need not be previously published in peer-reviewed form.Questions about the challenge may be asked in the Phylogenetic Tree Challenge community on EOL."
Development of our "Global Warming Curriculum for K-12 Classrooms" project. Principals and teachers are heavily biased toward the alarmist perspective. To counter this we are considering launching an effort to develop alternative materials for K-12 classrooms. We are pursuing a proposal from Dr. David Wojick to produce a global warming curriculum for K-12 schools. Dr. Wojick is a consultant with the Office of Scientific and Technical Information at the U.S. Department of Energy in the area of information and communication science. His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain- two key points that are effective at dissuading teachers from teaching science. We tentatively plan to pay Dr. Wojick $100,000 for 20 modules in 2012, with funding pledged by the Anonymous Donor.Let me repeat one part:
His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain - two key points that are effective at dissuading teachers from teaching science.
Yes, there are 120 papers that come up in Pubmed Central w/ a search for "Valentine's Day"shar.es/fSi8b
— Jonathan Eisen (@phylogenomics) February 14, 2012
@phylogenomics @David_Dobbs uplifting. among results, "sweet nothings?", "parasuicide","diabetes bingo" + "HIV epidemics". #loveisintheair
— Kaitlin Thaney (@kaythaney) February 14, 2012
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| Figure 3. Circovirus-like NI sequence coverage and phylogeny. |
The inappropriateness of the analogy was clear by the end of paragraph 2. For the rest: TL;DR
For those of us not as hip as Alex, TL DR means “too long, didn’t read.” I won’t comment on the inappropriateness of the semicolon in his Urban Dictionaryesque construction. The post is about 850 words, by the way
MICROORGANISM microscopic plants and animals.They exist in soil for the purpose of breaking down organic matter into basic mineral elements.They include bacteria, fungi, actinomycetes, algae, protozoa, yeast, germs, ground pearls, and nematodes.Gonna have to get them to work on this ...
@phylogenomics you should add in the Official Sci Scout page too: scq.ubc.ca/sciencescouts/ Explains the backstory
— Karyn Traphagen (@kTraphagen) February 12, 2012
Dear Colleague,
On behalf of the Conference Organizing Committee, I would like to inform you of the:
FOURTH INTERNATIONAL CONFERENCE ON SCIENCE IN SOCIETY
University of California, Berkeley, USA
17 - 19 November 2012
http://science-society.com/conference-2012/
This conference addresses the social impacts, values, pedagogies, politics and economics of science. It is an inclusive forum that welcomes a breadth of perspectives on science from practitioners, teachers and researchers representing a wide range of academic disciplines.
A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. It was a collaboration between Kathy Collins, multiple Tetrahymena researchers, the Eisen lab, and the UC Davis Genome Center Bioinformatics core (Joseph Fass and Dawei Lin). The paper is in G3, an open access journal from the Genetics Society.  |
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The Pique software package processes ChIP-seq coverage data to predict protein-binding sites. Strand-specific coverage data are output as tracks for the Gaggle Genome Browser, and putative-binding sites (peaks) are output as ‘bookmark files’. (A) Screenshot of data browsing in the Gaggle Genome Browser. Green box outlines the navigation window for clicking through bookmarks of predicted binding sites. Details of each site can be displayed (inset). The Gaggle toolbar (shown with black arrow) can be used to broadcast selected data to other ‘geese’ in the gaggle package, programs such as R, cytoscape, BLAST or KEGG. (B) Schematic overview of bioinformatics workflow.
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Wilbanks, E., Larsen, D., Neches, R., Yao, A., Wu, C., Kjolby, R., & Facciotti, M. (2012). A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq Nucleic Acids Research DOI: 10.1093/nar/gks063
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| Figure 1. Phylogenetic tree of 1,254 cyanobacterial species. |
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| Figure 4. Phylogenetic tree of a cyanobacterial subset. |
