Wednesday, December 10, 2014

New lab paper: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types [PeerJ]

A new paper out from my lab (with Jenna Lang as the 1st author and in collaboration with Angela Zivcovic from the UC Davis Food For Health Initiative and the Department of Nutrition):  The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types.  The work in the paper focuses on characterizing the abundance and taxonomy of microbes in food from three model diets.



Basically, Angela prepared meals for these three diets

Food was purchased and prepared in a standard American home kitchen by the same individual using typical kitchen cleaning practices including hand washing with non-antibacterial soap between food preparation steps, washing of dishes and cooking instruments with non-antibacterial dish washing detergent, and kitchen clean-up with a combination of anti-bacterial and non-antibacterial cleaning products. Anti-bacterial products had specific anti-bacterial molecules added to them whereas “non-antibacterial” products were simple surfactant-based formulations. The goal was to simulate a typical home kitchen rather than to artificially introduce sterile practices that would be atypical of how the average American prepares their meals at home. All meals were prepared according to specific recipes (from raw ingredient preparation such as washing and chopping, to cooking and mixing).
And then she blended them and we characterzied the microbial communities in the blended samples:

After food preparation, meals were plated on a clean plate, weighed on a digital scale (model 157W; Escali, Minneapolis, MN), and then transferred to a blender (model 5,200; Vita-Mix Corporation, Cleveland, OH) and processed until completely blended (approximately 1–3 min). Prepared, ready to eat foods that were purchased outside the home were simply weighed in their original packaging and then transferred to the blender. 4 mL aliquots of the blended meal composite were extracted from the blender, transported on dry ice and then stored at −80 °C until analysis. The following analyses were completed using these meal composite samples: (1) total aerobic bacterial plate counts, (2) total anaerobic bacterial plate counts, (3) yeast plate counts, (4) fungal plate counts, and (5) 16S rDNA analysis for microbial ecology.
And Jenna Lang coordainted the sequence analysis and then Angela and Jenna (with some help here and there from me) coordianted the analysis of the different microbial data and the writing of the paper.



Figure 5: Biplot of taxa in sample PCoA space.
.
 

Lots of interesting things reported in the paper (read it, I insist).  I note - this is a demonstration project in a way - trying to get the community and others to think about the source pools of microbes that come into our system from our food.  It is by no means comprehensive or conclusive (read the caveats section of the paper).  Congrats to Jenna and Angela for all their hard work. Anyway - the paper is Open Access in PeerJ.  Eat it up.

Saturday, December 06, 2014

Some history of hype regarding the human genome project and genomics

Just taking some notes here - relates to a discussion going on online.  Would love pointers to other references relating to hype and the human genome project (including references that think it was not overhyped).  I note - see some of my previous posts about this issue including: Human genome project oversold? sure but lets not undersell basic science and various Overselling Genomics awards. 

Here are some things I have found:

White House press conference on announcing completetion of the human genome
Genome science will have a real impact on all our lives -- and even more, on the lives of our children. It will revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases. In coming years, doctors increasingly will be able to cure diseases like Alzheimer's, Parkinson's, diabetes and cancer by attacking their genetic roots. In fact, it is now conceivable that our children's children will know the term cancer only as a constellation of stars.
Collins et al. New Goals for the U.S. Human Genome Project: 1998–2003
The Human Genome Project (HGP) is fulfilling its promise as the single most important project in biology and the biomedical sciences— one that will permanently change biology and medicine.
Human Genome -The Biggest Sellout in Human History

The Human Genome Project: Hype meets reality

NOVA: Nature vs. Nurture Revisited
After a decade of hype surrounding the Human Genome Project, punctuated at regular intervals by gaudy headlines proclaiming the discovery of genes for killer diseases and complex traits, this unexpected result led some journalists to a stunning conclusion. The seesaw struggle between our genes (nature) and the environment (nurture) had swung sharply in favor of nurture.

The human genome project, 10 years in: Did they oversell the revolution? in the Globa and Mail by Paul Taylor referring to: "Deflating the Genomic Bubble"

Also see Genomic Medicine: Too Great Expectations? by PP O Rourke

Also Has the Genomic Revolution Failed?

And Human genome 10th anniversary. Waiting for the revolution.

Science communication in transition: genomics hype, public engagement, education and commercialization pressures.

The Medical Revolution in Slate.

A Decade Later, Genetic Map Yields Few New Cures in the New York Times.
In announcing on June 26, 2000, that the first draft of the human genome had been achieved, Mr. Clinton said it would “revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.” 
At a news conference, Francis Collins, then the director of the genome agency at the National Institutes of Health, said that genetic diagnosis of diseases would be accomplished in 10 years and that treatments would start to roll out perhaps five years after that.




NNB report: Ten years later, Harvard assesses the genome map where regarding Eric Lander:
At the same time, , he said genomic research has “gone so much faster than I would have imagined.” He cited " an explosion of work that will culminate, I think in the next five years, in a pretty comprehensive list of all the target that lead to different kinds of cancers and give us a kind of roadmap for finding the Achilles heel of cancers for therapeutics and diagnostics."
while at the same time he blamed the press for the hype

From Great 15-Year Project To Decipher Genes Stirs Opposition in the Times June 1990
'Our project is something that we can do now, and it's something that we should do now,'' said Dr. James D. Watson, a Nobel laureate who heads the National Center for Human Genome Research at the National Institutes of Health. ''It's essentially immoral not to get it done as fast as possible.''
  • Note the article has many complaining about the hype in the genome project even then ..

From SCIENTIST AT WORK: Francis S. Collins; Unlocking the Secrets of the Genome
And, Dr. Collins adds, there is nothing more important in science and medicine than the project he heads
Dr. Collins predicts that within 10 years everyone will have the opportunity to find out his or her own genetic risks, to know if cancer or heart attacks or diabetes or Alzheimer's disease, for example, lies in the future. 

From READING THE BOOK OF LIFE: THE DOCTOR'S WORLD; Genomic Chief Has High Hopes, and Great Fears, for Genetic Testing June 2000 in the NY Times

The story goes through some predictions Francis Collins made for the future in a talk.  These included:

  • BY 2010, the genome will help identify people at highest risk of particular diseases, so monitoring efforts can focus on them.
  • In cancer, genetic tests will identify those at highest risk for lung cancer from smoking. Genetic tests for colon cancer will narrow colonoscopy screening to people who need it most. A genetic test for prostate cancer could lead to more precise use of the prostate specific antigen, or P.S.A., test by identifying those men in whom the cancer is most likely to progress fastest. Additional genetic tests would guide treatment of breast and ovarian cancer.
  • Three or four genetic tests will help predict an individual's risk for developing coronary artery disease, thus helping to determine when to start drugs and other measures to reduce need for bypass operations.
  • Tests predicting a high risk for diabetes should help encourage susceptible individuals to exercise and control their weight. Those at higher risk might start taking drugs before they develop symptoms.
  • BY 2020, doctors will rely on individual genetic variations in prescribing new and old drugs and choosing the dose. Pharmaceutical companies will take a second look at some drugs that were never marketed, or were taken off the market, because some people who took them suffered adverse reactions. It will take many years to develop such drugs and tests.
  • Cancer doctors will use drugs that precisely target a tumor's molecular fingerprint. One such gene-based designer drug, Herceptin, is already marketed for treating advanced breast cancer.
  • The genome project holds promise for the mental health field. ''One of the greatest benefits of genomic medicine will be to unravel some biological contributions to major mental illnesses like schizophrenia and manic depressive disease'' and produce new therapies, Dr. Collins said.






Friday, December 05, 2014

Some notes on "Citations for Sale" about King Abdulaziz University offerring me $$ to become an adjunct faculty

There is a news story in the Daily Cal titled "Citations for Sale" by Megan Messerly about King Abdullah University King Abdulaziz University trying to pay researchers who are highly cited to become adjunct professors there to boost their rankings.  This article stemmed from a blog post by Lior Pachter.  I was interviewed by the Daily Cal reporter about this because I had sent Lior some of the communications I had had with people from KAU where they tried to get me to do this.

I am posting here some of the email discussions / threads that I shared with Lior and Megan.

Thread #1.

Here is one thread of emails in which KAU tried to get me to become an Adjunct Professor.  I have pulled out the text of the emails and removed the senders ID just in case this would get him in trouble.

Received this email 3/6/14
Dear Prof Jonathan, 
How are you? I hope every thing is going well. I hope to share work with you and initiate a collaboration between you and me in biology department, Kind Abdulaziz university . My research focuses on (redacted detail). I hope that you would agree . 
Redacted Name,Ph.D
Assistant Professor, Faculty of Sciences, King Abdulaziz University, Jeddah, KSA.
My response:
What kind of collaboration are you imagining?
His response:
Hi Prof Jonathan, 
Let me to explain that the king abdulaziz university initiated a project which is called Highly Cited Professor ( HiCi). This project can provide a contract between you and our university and from this contract you can get 7000 US$ as a monthly salary .So  this project will allow you to generate two research proposal between you and a research stuff here in order to make an excellent publications in high quality journals as you always do. 
I hope that I was clear. I' m looking forward to hear from you. Finally, I think that a very good chance to learn from you. 
 Another email from him:
Dear prof Jonathan, 
I' d like to tell that Prof Inder Verma will come tomorrow to our university  as a highly cited professor and he also signed a contract with us. At March 28 Prof Paul Hebert will come to our university and we actually generated two projects with Prof Paul. I hope you trust me and you call Prof  Inder and  Paul to be sure. 
From me:
I trust you - just am very busy so not sure if this is right for me
Sent from my iPhone
From him:
You will come to our university for just two visits annually and each visit will take only  one week. Take you time to think. Bye
Another email from him
Seat Dr Jonathan, 
What is your decision?

Monday, November 24, 2014

A night with Matt Groening and the importance of faeces, feces and faces

So - I participated in a fundraiser for Emily Levine's "The Edge of Chaos" film a week ago. And one of the key guests was Matt Groening. Not only did I get to hang out with him and discuss fecal transplants with him (really) but I had a front row seat to Matt discussing the history of how he came up with the general outline of the Simpson's characters.



And in addition to this being just awesome to witness, one part of it struck me. See the video below and in particular the part that struck me was the beginning:

  Groening
basically said that only a few simple changes in faces can be recognized by people very easily. This reminds me of Jenna Lang's talk at the Lake Arrowhead meeting this year where she discussed using facial drawings as a form of visualizing microbiome data.

 

So - since I discussed fecal transplants with Matt and since he gave a good description of facial characteristics being easy to identify, I think we should definitely (1) try and get him to include microbiomes on the Simpsons and (2) for our work we should use Simpsons characters as model faces for different microbiomes ...

Oh and I also showed Groening some of the pics of my kids reading his "Hell" books:





So - basically it was a night of feces, faeces and faces.  Seems ideal.

Sunday, November 23, 2014

Whole issues of Genome Biology/Genome Medicine on "Genomics of Infectious Disease"

Wow this has really got some nice papers: BioMed Central | Article collections | Genomics of infectious diseases special issue.  I note - this goes well as a follow up to the series I co-coordinated in PLOS a few years back: Genomics of Emerging Infectious Disease - PLOS Collections

From their site:
Infectious diseases are major contributors to global morbidity and mortality, and have a devastating impact on public health. The World Health Organization estimates that 1 in 3 deaths worldwide are due to an infectious disease, with a disproportionate number occurring in developing regions. 
While the completion of the first genome sequence of a pathogen, Haemophilus influenzae, in 1995 took decades of work, in recent years, high-throughput technologies have revolutionized the study of pathogens. Whole-genome sequences are now achievable within days and available for multiple pathogens, including those that cause neglected tropical diseases, which has advanced our understanding of the biology and evolution of pathogens. Crucially, such research has enabled important advances in the clinical management of infectious diseases, and continues to guide public health interventions worldwide. 
In this cross-journal special issue, guest edited by George Weinstock (The Jackson Laboratory for Genomic Medicine, USA) and Sharon Peacock (University of Cambridge, UK), Genome Biology and Genome Medicine take stock of where we are now, with a collection of primary research and commissioned articles that discuss different aspects of the genomics of infectious diseases in human populations, including the progress made towards their eradication, and the remaining challenges in terms of both fundamental science and clinical management.
I have copied the list from their site (I am pretty sure this is OK since these are #OpenAccess journals but not 100% sure):

Editorial   Open Access
Ripudaman K Bains Genome Biology 2014, 15:529 (22 November 2014)
Review   Subscription
Lucy M Li, Nicholas C Grassly, Christophe Fraser Genome Biology 2014, 15:541 (22 November 2014)
Research   Open Access
Hayley M Bennett, Hoi Ping Mok, Effrossyni Gkrania-Klotsas, Eleanor J Stanley, Isheng J Tsai,
Nagui M Antoun, Avril Coghlan, Bhavana Harsha, Alessandra Traini, Diogo M Ribeiro, 
Sascha Steinbass, Sebastian B Lucas, Kieren S.J Allinson, Stephen J Price, Thomas S Santarius, 
Andrew J Carmichael, Peter L Chiodini, Nancy Holroyd,
Andrew F Dean, Matthew Berriman Genome Biology 2014, 15:510 (21 November 2014)
Research highlight   Subscription
Patrick Tang, Jennifer L Gardy Genome Medicine 2014, 6:104 (20 November 2014)
Software   Open Access
Darren Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers,
Judith Berman Genome Medicine 2014, 6:100 (20 November 2014)
Comment   Subscription
Jeffrey S McLean, Roger S Lasken Genome Medicine 2014, 6:108 (20 November 2014)
Software   Open Access
Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope,
Takehiro Tomita, Justin Zobel, Kathryn E Holt 
Genome Medicine 2014, 6:90 (20 November 2014)
Research   Open Access
Mihail R Halachev, Jacqueline Chan, Chrystala I Constantinidou, Nicola Cumley, Craig Bradley,
Matthew Smith-Banks, Beryl Oppenheim, Mark J Pallen Genome Medicine 2014, 6:70 (20 November 2014)
Editorial   Open Access
George M Weinstock, Sharon J Peacock Genome Biology 2014, 15:528 (19 November 2014)
Software   Open Access
Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M Phillippy Genome Biology 2014, 15:524 (19 November 2014)
Method   Open Access
Lewis Z Hong, Shuzhen Hong, Han Teng Wong, Pauline PK Aw, Cheng Yan, Andreas Wilm,
Paola F de Sessions, Seng Gee Lim, Niranjan Nagarajan, Martin L Hibberd, Stephen R Quake,
William F Burkholder Genome Biology 2014, 15:517 (19 November 2014)
Editorial   Open Access
Sharon J Peacock, George M Weinstock Genome Medicine 2014, 6:103 (19 November 2014)
Opinion   Free
Gail Geller, Rachel Dvoskin, Chloe L Thio, Priya Duggal, Michelle H Lewis, Theodore C Bailey,
Andrea Sutherland, Daniel A Salmon, Jeffrey P Kahn Genome Medicine 2014, 6:106 (18 November 2014)
Review   Subscription
Yonatan H Grad, Marc Lipsitch Genome Biology 2014, 15:538 (18 November 2014)
Method   Open Access
Christian B Matranga, Kristian G Andersen, Sarah Winnicki, Michele Busby, Adrianne D Gladden,
Ryan Tewhey, Matthew Stremlau, Aaron Berlin, Stephen K Gire, Eleina England, Lina M Moses, T
arjei S Mikkelsen, Ikponmwosa Odia, Philomena E Ehiane, Onikepe Folarin, Augustine Goba,
S.Humarr Khan, Donald S Grant, Anna Honko, Lisa Hensley, Christian Happi, Robert F Garry,
Christine M Malboeuf, Bruce W Birren, Andreas Gnirke, Joshua Z Levin, Pardis C Sabeti

Genome Biology 2014, 15:519 (18 November 2014)
Research   Open Access
Yanjiao Zhou, Martin J Holland, Pateh Makalo, Hassan Joof, Chrissy h Roberts, David Maybe,
Robin L Bailey, Matthew J Burton, George M Weinstock, Sarah E Burr Genome Medicine 2014, 6:99 (15 November 2014)
Research   Open Access
James W Wynne, Brian J Shiell, Glenn A Marsh, Victoria Boyd, Jennifer A Harper, Kate Heesom,
Paul Monaghan, Peng Zhou, Jean Payne, Reuben Klein, Shawn Todd, Lawrence Mok, Diane Green,
John Bingham, Mary Tachedjian, Michelle L Baker, David Matthews, Lin-Fa Wang Genome Biology 2014, 15:532 (15 November 2014)
Method   Open Access
Maha R Farhat, B Shapiro, Samuel K Sheppard, Caroline Colijn, Megan Murray Genome Medicine 2014, 6:101 (15 November 2014)
Review   Subscription
Paolo Gabrieli, Andrea Smidler, Flaminia Catteruccia Genome Biology 2014, 15:535 (15 November 2014)
Research   Open Access
Jonathan D Herman, Daniel P Rice, Ulf Ribacke, Jacob Silterra, Amy A Deik, Eli Moss,
Kate M Broadbent, Daniel E Neafsey, Michael M Desai, Clary B Clish, Ralph Mazitschek,
Dyann F Wirth Genome Biology 2014, 15:511 (14 November 2014)
Research highlight   Subscription
Anastasia Koch, Robert Wilkinson Genome Biology 2014, 15:520 (13 November 2014)
Research highlight   Subscription
Chase L Beisel, Ahmed A Gomaa, Rodolphe Barrangou Genome Biology 2014, 15:516 (8 November 2014)
Research   Open Access Highly Accessed
Vegard Eldholm, Gunnstein Norheim, Bent von der Lippe, Wibeke Kinander, Ulf R Dahle,
Dominique A Caugant, Turid Mannsåker, Anne Mengshoel, Anne Dyrhol-Riise, Francois Balloux Genome Biology 2014, 15:490 (7 November 2014)
Opinion   Open Access
Digby F Warner, Valerie Mizrahi Genome Biology 2014, 15:514 (7 November 2014)
Comment   Open Access Highly Accessed
Onikepe A Folarin, Anise N Happi, Christian T Happi Genome Biology 2014, 15:515 (7 November 2014)
Research highlight   Subscription
Eric J Vallender Genome Biology 2014, 15:507 (7 November 2014)
Research   Open Access
Adam J Ericsen, Gabriel J Starrett, Justin M Greene, Michael Lauck, Muthuswamy Raveendran,
 David Deiros, Mariel S Mohns, Nicolas Vince, Brian T Cain, Ngoc H Pham, Jason T Weinfurter,
Adam L Bailey, Melisa L Budde, Roger W Wiseman, Richard Gibbs, Donna Muzny, T
homas C Friedrich, Jeffrey Rogers, David H O’Connor Genome Biology 2014, 15:478 (7 November 2014)
Research   Open Access
Laura Gomez Valero, Christophe Rusniok, Monica Rolando, Mario Neou, Delphine Dervins-Ravault,
Jasmin Demirtas, Zoe Rouy, Robert J Moore, Honglei Chen, Nicola K Petty, Sophie Jarraud,
Jerome Etienne, Michael Steinert, Klaus Heuner, Simonetta Gribaldo, Claudine Médigue,
Gernot Glöckner, Elizabeth L Hartland, Carmen Buchrieser Genome Biology 2014, 15:505 (3 November 2014)
Research   Open Access
Frank Hanses, Christelle Roux, Paul M Dunman, Bernd Salzberger, Jean C Lee Genome Medicine 2014, 6:93 (3 November 2014)
Research   Open Access Highly Accessed
Paul McAdam, Charles vander broek, Diane Lindsay, Melissa Ward, Mary Hanson, Michael Gillies,
Mike Watson, Joanne Stevens, Giles Edwards, Ross Fitzgerald Genome Biology 2014, 15:504 (3 November 2014)
Research   Open Access Highly Accessed
Tige R Rustad, Kyle J Minch, Shuyi Ma, Jessica K Winkler, Samuel Hobbes, Mark J Hickey,
William Brabant, Serdar Turkarslan, Nathan D Price, Nitin S Baliga, David R Sherman Genome Biology 2014, 15:502 (3 November 2014)