Eisen Lab Blog

Is this a new form of #OpenAccess Spam – spammy blog comments pointing to Bentham

Well, this is very very weird and not sure what to make of it.  In the last week the filter that Google runs for Blogger Comments has picked up a slew of highly spammy comments coming from one account.  And all of the comments include a link to Bentham Science publishers – one of the annoying Spammy new publishers. See some of them below (note I have removed the links to Bentham but trust me, this went to a Bentham site).  Anyone else getting Spam comments pointing to Bentham?  

Jesica Mack has left a new comment on your post “Science SPAMMER of the month: OMICS publishing gro…“:

For me it has been a surge of meeting welcomes, for the most part in China, having nothing to do with my examination: bentham science publishers.
—–
Jesica Mack has left a new comment on your post “I am highly skeptical of the CHORUS system propose…“:

I don’t see anything in this that seems particularly useful.Please click: bentham science publishers
——-
Jesica Mack has left a new comment on your post “Wow – Google Scholar “Updates” a big step forward …“:

Snap. I likewise found this advancement a couple of days prior and discovered one recommended paper of immediate pertinence.Please click:bentham science publishers

——
Jesica Mack has left a new comment on your post “ADVANCE Journal Club: Developing Graduate Students…“:

This is very interesting I appreciate this effort.Please click:bentham science publishers

—–
Jesica Mack has left a new comment on your post “UCDavis IT and GMail think this “Open Journal of G…“:

What’s particularly annoying about all these SPAM journals is that they are training filters to ignore legitimate journal activity.Please Click:bentham science publishers




——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Microbial genomics job opening at Bayer CropScience

Bioinformatics position.pdf

Bayer Crop Science is looking for a Microbiologist …

Microbiologist.pdf

Eisen Lab (Science) Art Show

This past week the lab did something a bit different for lab meeting: we talked about and shared our science (and not-so-science related) art. All possible art mediums were encouraged for submission (baking, poetry, music, paintings, photographs, etc). The following slides contain the submitted art work shared at our lab meeting.

 

The following are descriptions of each artist’s work:

Alex Alexiev: These photographs of unidentified fungi were taken at Muir Woods National Monument in the Bay Area of California. The forest is constituted by redwoods, ferns, and small waterfalls. The high humidity creates a great habitat for various awesome fungi and molds to flourish.

Marisano James: The poem was written by Marisano when he was 19 years old and only recently mailed to him by a friend. The photographs he submitted included two dragon flies in the middle of a mating ritual, an intricately painted mailbox, a photograph of the UC Davis graduation, a dragonfly close-up and a silk moth emerging from its cocoon.

Katie Dahlhausen: These are pictures of mushroom spores taken on a scanning electron microscope that Katie built herself!

Madison Dunitz: These are images of a microbe an undergraduate student in the lab, Andrew Stump, is characterizing.

Ruth Lee: Ruth painted the two acrylic paintings and made the collage during her senior year of high school. The snow leopard was painted for a friend who had red-green color blindness. She wanted to give him something that looked the same to him as it would for everyone else. It was the first painting she ever did. The landscape painting was also a done for a friend and was the production of just her mind (no photo reference was used!). Her friend’s favorite movie was Disney’s Pocahontas, and this is her rendition of the waterfall scene. The prompt for the collage was how she thought the world should be changed and back then, Ruth thought that the best way to change the world would be to educate future generations about adopting an active approach towards the issues of today.

Hannah Holland-Moritz: Hannah enjoys amateur photography and is interested in the intersection of science photography and art. The majority of these photographs were taken on various hikes in Northern California. The microscope photo was from one of the first microbiology experiments she ever performed. It’s a biofilm stained for polysaccharides and bacterial DNA.

Cassie Ettinger: For my submission, I included a poster I made for our Seagrass Microbiome Project which I made using Adobe InDesign. I made all of the graphics included on the poster in Adobe Photoshop from scratch. I also enjoy amateur photography and included some photographs of flowers and birds that I have taken in the past. My last submission includes some photographs I took of trenches dug at an archaeological dig I took part in at Boltby Scar in the United Kingdom.
 
Chris Beitel: This is a photo Chris took of an object and then distorted to obscure what the object was. The purpose being that people would look at something they usually found familiar, but not recognize what the familiar object was.
 
Dongying Wu: Dongying talked to us about a Persian miniature painting that he made using Adobe Illustrator CS6. The last three slides provide references and background information for the story he was trying to represent and the archeological evidence that he used for inspiration.

Environmental Sequencing workshops at #ESA2014

As part of RCN EukHiTS, I’m leading two sessions at the Ecological Society of America 2014 Annual Meeting next month (taking place in Sacramento, August 10-15, 2014) – a Sunday workshop including QIIME and metagenomics tutorials, and a special session (most likely panel discussion) on Monday. I encourage anyone who is interested to register for these events:

Workshops #9884: “Environmental sequencing approaches and computational tools for ecologists” 
Sunday, August 10, 2014
8:00 AM – 5:00 PM

Description: This workshop will bring together an interdisciplinary pool of researchers to discuss current approaches, challenges, and future directions for environmental sequencing studies (-omic studies of bacteria, archaea and microbial eukaryotes). The workshop program will introduce ecologists to common data types and scientific workflows currently employed for the analysis of high-throughput sequencing data (e.g. Illumina/454). Participants will be given overview presentations and hands-on demonstrations for a number of different approaches, including rRNA marker gene analysis, shotgun metagenomics, and metatranscriptomics. This workshop will introduce participants to computational biology tools and software pipelines which can be harnessed for DNA/RNA-based “ecometagenomic” studies. In addition, we aim to solicit feedback from workshop participants, fostering discussions on how to establish better links between traditional ecological research and new, high-throughput sequencing approaches.

Special Sessions #9883: “Ecometagenomics”
Monday, August 11, 2014
10:15 AM – 11:30 AM

Description: The goal of this session is to catalyze cross-disciplinary discussions between the ecology and environmental sequencing communities.  High-throughput sequencing technologies now offer tremendous opportunities to make major inroads into our understanding of global biodiversity and biogeographic patterns. However, in order to make the most of emerging high-throughput sequencing approaches, we must move towards a “systems ecology” mindset, drawing expertise from diverse disciplines. For microbial eukaryotic taxa in particular, we can now conduct en mass biodiversity assessment using traditional loci (rRNA genes) at a fraction of the time and cost required for traditional (morphological) approaches. In addition, as databases of genes with functional descriptions expand, metagenomic approaches become useful for elucidating ecosystem function. Despite this promise, current bottlenecks and roadblocks lie in the development of useful distributed tools, links between molecules and morphology/ecology, and common data standards to allow global comparisons across individual studies. This session will begin with an overview of environmental sequencing approaches, introducing participants to the methods, data types and current advantages and limitations of DNA/RNA-based studies. The session is intended to be highly interactive, including brief talks, moderated discussion points, and solicitation of questions and feedback from audience members. This session would stimulate critical discussion related to the 2014 meeting theme of “Its all ecology.” DNA/RNA-based studies represent an emerging ecological discipline, and as such, it is imperative that the growing community of microbial ecologists begins to build strong links to the traditional ecological research that forms the center point of the ESA meetings.

Another ESA session linked to RCN EukHiTS is oral session OOS10: Ecological Genomics as an Emerging Field: Opportunities for Non-model Organisms (organized by Melis Akman, UC Davis)

Paper of interest: Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

For those interested in microbiomes it is definitely worth looking at this paper: BMC Genomics | Abstract | Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

Simple summary – they have sets of identical twins where one twin has Crohn’s and the other does not.  They looked for somatic mutations that could like the ones with Crohn’s and did not find any.  Sure – a negative result.  Could be anything.  But the next obvious thing to do (which they report they are already doing) is to look at the microbioata in these people.  Alas, they probably do not have data from before these people got Crohn’s, but still, this could be interesting …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open (anyone can join with a Mendeley account), and I’m trying to keep them regularly updated with new articles (Mendeley members can also add articles, which I strongly encourage!):

  • Eukaryotic HTP Studies – Publications relevant to high-throughput environmental sequencing approaches focused on microbial eukaryotes. Articles will include any type of -Omic methods (marker gene amplicons, metagenomics, metatranscriptomics, etc.), eukaryote-focused tools/pipelines, and review/opinion pieces.
  • rRNA in Eukaryotes – Literature related to the ribosomal repeat array in eukaryotic genomes – variation in rRNA gene copy number, intragenomic polymorphisms, concerted evolution, transposable elements and their evolutionary and ecological implications.
  • Environmental PCRs – primer sets and bias – Literature related to primer set usage and bias across all taxonomic groups (bacteria, archaea, fungi and microbial eukaryotes) – includes primer sets and methods focused on 16S, 18S, ITS, other rRNA, COI, and other marker genes used for environmental sequencing.
  • eDNA in aquatic ecosystems – This group focuses on environmental DNA (eDNA) applications in aquatic ecosystems, include use of eDNA in bioassessment and environmental monitoring. Literature collection covers methods, analytical tools, and empirical studies (both basic and applied science).

Pacific Northwest National Lab (PNNL) is looking for some microbial computational / genomics folks

Check out these job ads. PNNL is looking for a few good microbial people.
Postdoc Flyer.pdf
PNNL Assoc Director Microbiology.pdf

Fun times with whooping cough in #DavisCA

Just got this email.  I have removed the specific sender / facility since that does not seem needed for my purposes here.  I have replaced the name of the site with “Our Facility”. Anyway – thought some people would be interested in the things that can happen when too many people in your community do not vaccinate their kids.

From: Office Administration 
Subject: Possible Exposure to Whooping Cough – Pertussis
Date: June 25, 2014 at 12:55:59 PM PDT
To: Office Administration 

Dear Parent or Guardian,
Our Facility was informed this morning that a student who has been attending a class since 6/16/14 has been diagnosed with pertussis (whooping cough). The child is no longer attending the class and is under a medical care.
If you feel you or your child may have been exposed, watch carefully for symptoms in the next 1-2 weeks, and consult a physician if any occur. Here is some pertinent information regarding pertussis (whooping cough):
Pertussis can spread through the air when people cough. It often starts like a common cold which gets worse and worse over 1-2 weeks. People with pertussis have coughing spells that may last several seconds. As they catch their breath at the end of each coughing spell, they may gasp loudly (“whoop”) and vomit or choke.
The vaccine usually protects against pertussis, but sometimes even immunized children can get pertussis. Pertussis is treated with antibiotics. Antibiotics can also prevent the spread of pertussis to others.
Activities that may help stop the spread of pertussis include:
  • The exclusion of all pertussis cases from classes until they have taken the first five days of the antibiotic.
  • The administration of antibiotics for babies, pregnant women and other high risk contacts of pertussis cases as well as consideration of antibiotic administration for other household or close contacts to prevent the further spread of pertussis.
  • The administration of another dose of DTaP vaccine to babies and Tdap for older children who are not up to date on their vaccine series.
Please know that Our Facility is taking every precaution in this matter and let us know if you have any questions or concerns.
Sincerely,

Office Staff
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

“An Evening with the World’s Leading Marine Microbiologists” in San Jose

Just got this and am sharing:

Dear Dr. Eisen,

The Tech museum in San Jose wanted to invite you to a very special event of ours that might be of your interest. On July 30th, 16 exceptional marine microbiologists from all over the country will gather in The Tech for an evening of conversation with our local community.

The Tech would love for you to join us! I attached a more detailed description of the event below. Please don’t hesitate to contact me if you have any questions or concerns. And we would also highly appreciate if you could forward this email to any of your colleagues and students who might be interested in coming.

Thank you so much and look froward to hearing back from you!

Best Regards,

Haven Yang

The Tech Museum of Innovation

201 S. Market St., San Jose, CA 95113 | thetech.org

Exclusive Engagement!
An Evening with the World’s Leading Marine Microbiologists
A Creative Collisions Initiative
Wednesday, July 30, 2014
5:45 p.m.
The Tech Museum of Innovation’s Lower Level
General admission $25 in advance/$35 at the door
Members $15/$25
Students and Seniors $10/$15
Food & Beverage available for sale at event
Buy Tickets

“The oxygen in every second breath we take is produced by microbes in our oceans—they are thought to produce about 50 percent of the oxygen in the earth’s atmosphere. Yet, we know surprisingly little about these tiny organisms.”

—The Gordon and Betty Moore Foundation’s Marine Microbiology Initiative

The Tech welcomes 16 world-renowned scientists for an evening of discussion and discovery.

Please join us to learn more about our diverse ocean ecosystems through robust conversation with some of the most innovative minds of our time, and to connect with bio-focused community groups and individuals. Listen to Professor Kay Bidle of Rutgers University explore “The Invisible World of Marine Microbes: How Earth’s Smallest Living Things Have the Biggest Impact on How Our Ocean Works.”

Mingle with the 16 Investigators of the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative:

Schedule
5:45—6:45 p.m. Mingling over food, drinks and exhibits
6:45—7:30 p.m. Kay Bidle: “The Invisible World of Marine Microbes: How Earth’s Smallest Living Things Have the Biggest Impact on How Our Ocean Works,” followed by 15-minute Q&A
7:30—10 p.m. More mingling over food and drinks

Click here to learn more about the event.