Category: Misc.

My talk for “Publication Mismatches” meeting” “The Bleeting Edge: Blog and Tweet or Perish”

 

Global Engage Plant Genomics Meeting – Bring Your Y Chromosome Because they Don’t Take XX – Calling for a Boycott of this Group

Saw this tweet earlier today

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And something seemed hauntingly familiar about the organization referenced.  Turns out this is not the first time they have had issues with Gender Balance.  So I responded

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Incredibly distasteful and painful to see this. This group “Global Engage” ran a Plant Genomics meeting last year that I posted about becuase the gender ratio was quite bad for the speakers: YAMMGM – yet another mostly male genomics meeting (series): Plant Genomic Congresses by Global Engage

And after seeing this new Tweet I dug around their web site some more and it is really unpleasant.  Look at their Advisory Panel (which is what Female Scientist was pointing to):

24 scientists.  All of them men.  If you know any of them, as I do, I would recommend you contact them and suggest they resign from this apparently gender-biased organization or force them to add some women to their advisory panel.

The speaker list for their next plant genomics meeting is quite skewed too.  I could find 49 men and 5 women.  What a joke.

I call upon everyone in the community to boycott this meeting and any organized by Global Engage in the future.  They have been informed previously of their gender ratio issues and are clearly not doing anything about it.  And in plant genomics there are so many excellent female scientists that this simply has to be a case of some type of bias.

In addition, I would recommend calling on the sponsors to withhold funding from this meeting and others organized by this group.

Sponsors include

Illumina

Life Technologies

Lucigen

Raindance

Takara

Clontech

Nugen

and

Sigma-Aldrich

——–
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.

——–

Sheffrin Lecture – Sendhil Mullainathan – 4/17 5:30 PM “Scarcity: A Talk for People Too Busy to Attend Talks”

From an email I recieved:

The annual Sheffrin Lecture in Public Policy (an annual Division of Social Sciences Event) will take place this Thursday, April 17th, 5:30 pm in the Alumni Center (AGR Room) and will feature Professor Sendhil Mullainathan from Harvard, talking about his recent book, Scarcity (co-authored with Princeton Psychologist Eldar Shafir).

Some more detail is below:

Sheffrin2014.pdf

Special Seminar: Single Cell Genomics – 4/25 at #UCDavis

Sharing …

**Please share this special seminar announcement with others who may be interested

Luke Stewart

Senior Field Application Specialist

Fluidigm Corporation

Noriko Satake, MD

Assistant Professor, UC Davis

Single Cell Genomics – cutting edge microfluidic tools defy the law of averages by enabling resolution at the single cell level

Friday, April 25, 12:10 – 1:00 pm

Education Building, Lecture Hall 1222

4610 X Street, Sacramento 95817

UC Davis Health System campus

Light lunch will be provided for those who

RSVP by April 22 to ocr@ucdavis.edu

Co-hosted by:

BGI@UC Davis, the UCDCCC Genomics Shared Resource and the Department of Pathology & Laboratory Medicine

BGI@UC Davis will be presenting a seminar series to be held once per quarter during the academic year. If you have questions or need additional information, please email bgi-ucdavis@ucdavis.edu.
BGI UC Davis seminar Stewart 4-2014.pdf

And let the microbiology word play begin (re Entamoeba feeding)

New paper out about feeding by the parasitic amoeba Entamoeba histolytica.  Apparently, the work shows that this organism feeds by in essence taking bites out of cells.  (I say apparently because the paper is not open access and I don’t have access to it from where I am writing).

Anyway – there are a lot of news stories about this.  And for some reason (I am not quite sure why) this has inspired headline writers to get out their pun pens and creative thinking caps.  Here are some of the headlines:

And more coming I assume.

Though as far as I can tell none of the stories picked up on a key word play that could have been made.  The lead scientist behind the study is named Petri.   Someone really should have had “dish” in the title …

——–
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.

——–

CSIS/UCHRI Event: “Authorship Between Literature & Science” 4/15

AUTHORSHIP BETWEEN LITERATURE AND SCIENCE

A workshop of the “The Material Cultures of Knowledge” Multi-campus Research Group, sponsored by UCHRI
(materialcultures.ucr.edu)

When: Tuesday, April 15, 3:00-6:00PM
Where: CSIS/STS Room, SSH 1246 (Map: http://tinyurl.com/1246ssh)

*Please RSVP if you plan to attend: http://tinyurl.com/AuthorshipDavis2014

Speakers will include:

ADRIANA CRACIUN (English, UC Riverside), “ADVENTURERS AND AUTHORS: CULTURES OF ARCTIC EXPLORATION AND INSTITUTIONAL AUTHORSHIP”

IAN DUNCAN (English, UC Berkeley), “AFTER NATURAL MAN: CONJECTURE, HISTORY, SCIENCE, FICTION”

MARIO BIAGIOLI (STS, Law, & History, UC Davis), “WHEN MACHINES WERE TEXTS: AUTHORS V. INVENTORS IN EARLY COPYRIGHT DEBATES”

With Comments From:

STANLEY ROBINSON (Author)

DAVID SIMPSON (English, UCD)

Guest post by Kevin Penn: In Search of Bacteria on Drugs: Secondary Metabolites and Microbial Ecology

Below is a guest post from Kevin Penn, who used to work in my lab …

I am a former Research Associate of Jonathan’s interested in understanding evolution and ecology of microbes in natural environments.  Recently I’ve become interested in learning about the expression of secondary metabolite related genes in natural settings to put the gene’s products into an ecological context, because almost certainly microbes are not making natural products just to benefit humans.   I am currently studying these topics as a post-doc in Janelle Thompson’s lab at MIT. 


When I got to MIT there was a set of paired end Illumina HiSeq data from six time points collected over one day night cycle from the Kranji Reservoir in Singapore, which was experiencing a cyanobacterial Harmful Algal Bloom (cyanoHAB).  Note algal in this case means bacterial, I used to argue that this is taxonomically incorrect but used colloquially I think it works.  These samples are what the paper “Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacteria bloom” is based on.  MIT has a program in Singapore called Center for Environmental Sensing and modeling/Singapore MIT Alliance (CENSAM/SMART) and one of the projects is to learn about microbial populations associated with the drainage and reservoirs over the city/state/country.  The motivation for the study (Penn, et al 2014) is based on two observations.  1) The idea to sample a day night cycle of a harmful algal bloom derived from experiments done for marine Prochlorococcus showing major changes in gene expression in the evenings and morning and more similar profiles at noon and midnight (Zinser, et al 2009). 2) An initial sample collection and analysis for this study did not readily detect genes for the toxin microcystin from drainages around the reservoir catchment (Nshimyimana, et al 2014) indicating the Cyanobacterium was growing in the reservoir (i.e. not being flushed in).  We knew the bloom in the Reservoir was dominated by Microcystis aeruginosa but now we wanted to learn if microcystin toxin genes were expressed in the reservoir and if so were they expressed around the clock.

cyanoHABS

Harmful algal blooms are of concern because they appear to be increasing in frequency on a global scale.  HABs are not only eyesores they also produce toxins that make lakes unusable for drinking water and recreation.  For a good introduction to HABs I suggest reading an excellent book “The algal bowl: overfertilization of the world’s freshwaters and estuaries” by David W. Schindler & John R. Vallentyne.  But I should note there are probably thousands of books written on the subject.  Below you can see what our study site looked like during a bloom with a surface scum visible and during conditions where the water is a bit more clear (post bloom).


Polyketide synthases (PKS) and Non-ribsomal peptide synthetases (NRPS)

The search for expression of microcystin toxin genes is also a part of my larger interest to learn about the expression of PKS and NRPS genes in natural settings.  PKS and NRPS derived molecules represent a large class of natural products famous for being toxins and used as medicine to treat human disease.  Two phyla of bacteria are historically known for their production of these compounds (Actinobacteria and Cyanobacteria).  For example the PKS and NRPS derived microcystin toxin is produced by M. aeruginosa and members of the Phylum Actinobacteria produce the potent antibiotic rifamycin.  The expression and presence of most PKS and NRPS pathways in natural settings is currently not very well understood. 

Prior to this work it was not clear that bacterial PKS and NRPS pathways are expressed in natural settings.  The products of the microcystin pathways are present in harmful algal blooms (thus the term Harmful). This made Kranji Reservoir a good system to study because we should observe the transcripts for microcystin.  PKS and NRPS genes can be highly repetitive and similar between different pathways so we were not sure we find them with Illumina type sequencing.  Based on my initial tests using a tool called NaPDoS, which I helped developed at Scripps to quickly identify sequence tags from PKS and NRPS gene pathways, it was clear we could see the expression of many different pathways in our data.  This spurred me on to look at the differences in expression over time.  The examination of the time series revealed that there appears to be a rhythm to expression of PKS and NRPS genes and that strikingly, one of the most highly expressed PKS/NRPS gene cluster in M. aeruginosa has not been linked to a molecule.  This is especially interestingly from an ecological perspective, as one of the most highly expressed PKS/NRPS pathways have yet to be associated with a product.

Interplay

One of the cool things about science is that it can be predictive. Within an experiment of photosynthetic bacteria then you would hope that your expression data reflects the idea that photosynthetic life uses light to photosynthesize and that the genes that code for the machines that harness light would be most highly expressed during the day.  We call that,  the the “sanity check,”  and it came out very nicely in our metatranscript data; showing that photosynthesis related genes cycle in the environment and are highly correlated with the day night cycle.  Our observation that the things we expected to be highly expressed were highly expressed gave us confidence that our data may have other patterns that we would not necessarily think to look for.  We started to look at broader categories of function genes for the top four phyla.  From this analysis we noticed that some phyla were enriched for particular genes relative to other phyla, which in turn allowed us to make some ecological predictions in relation to how each group, might be functioning in the bloom community.  For example look at figure 4and 5 in the paper and you can see that Actinobacteria are mostly transporting photosynthetically derived carbohydrates but Bacteroidetes groups are mostly transporting peptides furthermore groups within the proteobacteria are expressing most of the motility and chemotaxis related genes. 

Quantifying natural microbial communities remains a significant challenge and more importantly identifying ecological functions for phenotypes promises to provide microbial evolutionary biologist with crucial data to learn about the evolution of bacteria.  Imagine trying to study the evolution of a hand if you had no idea of the ecological function for the hand.

Problem Solving- paired end reads

One of the important decisions we had to make for us to start the analysis of Illumina data center on the state of paired end sequencing in metatranscriptomics.  Paired end sequencing is a great boon for Illumina sequencing and Illumina sequencing created a huge opportunity for the field of metagenomics.  But paired Illumina reads that do not collapse into one can represent a large portion of an Illumina sequence run despite efforts to create short enough sequences to have overlap and yet make the fragments large enough to make paired end sequences more informative.  Paired ends can complicate issues because they may represent two genes but one operon, or two genes from different operons which is a problem for analysis trying to assign function to reads. The other issue is that in assigning taxonomy to reads by chance alone similar sequences although part of a pair may match different organisms.  MEGAN tries to deal with this by increasing bit scores for sequences that match the same thing.   We made the decision to use paired information to improve the confidence in function assignment in MEGAN if both reads hit the same gene, and treated 1 and 2 reads as separate for counting total reads matching a gene if the read counts were not to be normalized to gene length.  Another aspect of the study focused on calculating expression for genes from the bloom former M. aeruginosa using RPKM which does take into account gene length thus we decided to treat the 1 and 2 reads as technical replicates for calculating RPKMs and averaged the values.

Future

This experiment has given us the first glimpse at expression of toxin genes in a natural setting and provided us with some clues of microbial phylum level interplay. The next experiment to further test our observations includes a greater sampling effort over two day night cycles at a greater frequency and with replicates and sampling at the surface and subsurface.  This work is being done in collaboration with another research group interested in Microcystisand harmful algal blooms at the National University of Singapore led by Prof. Karina Gin. It is known that M. aeruginosa strains migrate up and down in the water column and we want to check to see if some of our cyclic observations relate to the presence of different strains present on the surface throughout the day. A follow up study in progress is to look at the reservoir community during non-bloom conditions and run perturbations to identify the effects of the addition of nitrate, phosphate, and microcystin on the microbial community in hopes to learn if there are expression patterns that show how Microcystisis able to bloom.

My Background

The exact story behind the paper will be better understood if it is supplemented with a brief background about my introduction to Genomics and microbial ecology which mainly occurred after starting work as a Research Associate for Jonathan.  Looking back “many years ago” I had just finished up an undergrad degree at UCSB in Aquatic biology and I was looking for a job as a scientist when I met Jonathan.  It was really my first meetings with Jonathan that have set my way forward in research.  I wanted to learn about how things evolve and the ecological functions of traits and Jonathan wanted to understand how all life evolved which meant he was studying the genomes of microbes.  In our first meeting we discussed how genomics and methods associated with genomics namely 16S rRNA gene community studies were going to allow us to learn all about microbial ecosystems and even allow us to do insitu ecological studies of microbes (the term metagenomics was not widely known or used at this time).   As TIGR slowly evolved into JCVI, I began my move to grad school to work in Paul Jensen’s lab at Scripps Institute of Oceanography who had recently sequenced the genome of a couple species of marine actinomycetes.  In grad school I spent a lot of time learning about natural products and the genomes of famous group of organism called Actinomycetes, which make about 80% of the antibiotics we take today.  By the time I finished grad school I had become acutely interested in learning about the expression of natural products related genes in a natural setting.

Conclusion

Our latest paper published in ISME reflects a combination of my exposure to some very different fields of scientific research, from studying genomics and community diversity at The Institute for Genomic Research (TIGR) to my PhD work in natural products research at Scripps and now my studies on community gene expression dynamics in Harmful Algal blooms at MIT.  I have been researching the ideas about insitu microbial ecology that Jonathan discussed with me those many years ago and continue to expand our knowledge about what microbes are doing in natural setting in this paper.  

Of course I did not do this paper in a vacuum at MIT. Prof. Janelle Thompson organized the data collection, co-wrote the paper and taught me a lot about the appropriate statistics we needed to use to analyze our data and interpret the results.  Graduate students Tim Helbig and Sonia Timberlake helped me get going on the computer clusters here at MIT. One of my favorite parts of moving institutions is learning the in and outs of new computer clusters.  I have been funded as a postdoctoral associate at MIT and subsequently by the NSF post-doctoral fellowship intersection of math and biology during this research. Singapore CENSAM/SMART has supported our travels to Singapore along with sequencing costs.
——–
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.

——–

4/10 1 PM: John Wingfield “Vision for Biology at the National Science Foundation”

University of California, Davis College of Biological Sciences

Special Seminar

Dr. John Wingfield

Assistant Director for the Biological Sciences National Science Foundation USA

“Vision for Biology at the National Science Foundation”

Thursday, April 10, 2014 1:10 PM
1022 Life Sciences
John Wingfield seminar.pdf

Workshop by @hollybik Using Social Media to Promote Your Research April 10th

Using Social Media
to Promote Your Research

Thursday, April 10, 2014
1:00-3:00pm
Memorial Union, Garrison Room

Many view social media as either a fun distraction, a waste of time – or both! But social media tools can be a tremendous resource for academics seeking to share their research, find new collaborations, and ultimately advance their careers.

Attend this workshop to learn how to:

· Use social media to share and promote your research

· Identify appropriate audiences and avoid pitfalls

· Choose the right platforms to help you achieve your goals

Please pre-register using this online form: http://bit.ly/1ajX6Pc (Pre-registration will help to guide the format of the workshop and the type of social media tools covered)

Workshop Leader: Holly Bik, Ph.D., Holly Bik is a postdoctoral scholar in marine genomics, working in Jonathan Eisen’s lab at the University of California Davis. Dr. Bik is extensively involved in the use and promotion of social media in academic settings. She has several social media sites dedicated to the dissemination of science including: Dr. Holly Bik | Deep Sea News; @hollybik – Twitter; Holly’s personal Homepage; Holly Bik – Google Profile

Sponsored by

Good reading on the history of the terms/concepts of prokaryote & eukaryote

Preparing for some lectures at UC Davis for Biodiversity and The Tree of Life course and came across this: The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology by Jan Sapp which I had not really scrutinized before.  It is quite good and has lots of information on the history of microbiology and the twisted history of the prokaryote – eukaryote distinction.  Veryvery interesting stuff.  And freely available in Pubmed Central. Thank you thank you thank you Pubmed Central and the American Society for Microbiology.

——–
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.

——–