Archive for August, 2012

Memorial Service for Simon Chan

August 24, 2012 Leave a comment

For those who would like to say goodbye to Simon in person:

Simon’s Viewing
When: Wed 29th August, 3-6pm
Where: Wiscombe Funeral Home
116 D Street Davis CA 95616
phone #: 530 758 5500

Simon’s Memorial Service
When: Thurs 30th August, from 3pm
Where: Alpha Gamma Rho Hall, Buehler Alumni Center
Mrak Hall Drive and Old Davis Rd, on UC Davis campus
* Please wear your most ‘Simon’ shirt and cool sneakers if the mood takes you *

The Chan family wishes that in lieu of flowers, donations to be made to

Also, on both events you will be able to leave a personal note in the memorial book that is currently at the office of the Department of Plant Biology (1002 Life Sciences).

Remembrance book for Simon Chan

August 23, 2012 1 comment

For those people who would like to write a piece (notes/messages/stories/etc) to Simon’s parents and sister, there is a remembrance book in the office of the Department of Plant Biology in 1002 Life Sciences.


A memorial service in Davis is being planned. Once more information becomes available, it will be posted.

Simon Chan (1974-2012)

August 22, 2012 166 comments

It is with great regret that I (Daniël Melters, one of his graduate students) bring to you the death of Simon Chan.

More information will follow soon, other than he passed away in the presence of his beautiful and great family.

Simon’s bag as he brought is with him to the hospital. His work ethic never left, neither did his mental capacity.

Simon will be greatly missed.

Quick update: Regarding his condition. Simon had primary sclerosing cholangitis or PSC. A autoimmune disorder that he shared with olympic medalist Chris Klug. In contrast to Chris Klug, Simon was initially misdiagnosed. The correct treatment worked for the time being, but he needed a new liver either way, as that is the only realistic treatment available for PSC. As worst case scenarios happen, he was diagnosed with sepsis and after that with fungal pneumonia. At the end with combination of all that his body had to endure was too much and he died on August 22,2012 at the age of 38.

If you would like, please give your condolences to his parents and his sister and his family by responding to this blog entry. We will pass this on.

The In Memory by the Department of Plant Biology with many many comments as well:

Simon’s lab webpage:

Simon’s famous restaurant blog (read Jim Leff’s comment below):


One of his many academic accomplishments:

Here is a talk by Simon Chan on the use of PacBio sequencing to study centromeres:


Memories of Simon Chan by Keith Bradnam:

Tribute for Simon on the Paul Knoepfler lab blog:

An obituary by UC Davis for Simon Chan:

Obituary in the Sacramento Bee:

UC Davis Designated Emphasis Biotechnology facebook:

UC Davis facebook:


Here is Simon’s bio on the HHMI website:

Central Valley Business Times article on Simon:

Daily Democrat article on Simon:

On Jonathan Eisen’s blog: Simon presenting a poster to Bill Gates:

News article from New Zealand on Simon’s death:

New Zealand Herald:

Radio New Zealand News:

Manufactured “Nanomaterials” can affect soybean growth and commensal microorganisms

August 21, 2012 Leave a comment

Researchers from Patricia Holden‘s lab at UC Santa Barbara decided to take a look at soybeans grown to maturity in soil contaminated with two common “manufactured nanomaterials” zinc oxide  or cesium oxide, additives commonly found in make up and diesel fuel respectively. The results from growing soybeans in this contaminated soils were disturbing. Plants grown in the presence of zinc oxide show widespread distribution through edible plant tissues, this has implications for bioaccumulation and toxicity (the effects of zinc oxide buildup are detrimental in animal models but largely untested in humans). Also unnerving is how cesium oxide reduced plant yields, most like because it entered the roots and interfered with nitrogen fixing bacteria present in root nodules.

While the results of this study are indeed pretty scary, the distribution and concentration of these synthetic nanomaterial byproducts is hard to predict. High concentrations of both zinc oxide and cesium oxide could indeed be detrimental to crop production and human health, but chances are most soils have very low levels of these compounds. Certain places where waste waters accumulate, or where there is alot of diesel traffic could certainly see elevated levels of these compounds. Regulation and detection of these compounds may well be important for the health and future of humanity, but don’t freak out yet. Buying produce locally from growers you know and trust should help to alleviate any fears you may have after learning about these nanomaterials. Further work definitely needs to be done.


Published in PNAS

Soybean susceptibility to manufactured nanomaterials with evidence for food quality and soil fertility interruption

Priester, J.H. et al. 2012

Based on previously published hydroponic plant, planktonic bacterial, and soil microbial community research, manufactured nanomaterial (MNM) environmental buildup could profoundly alter soil-based food crop quality and yield. However, thus far, no single study has at once examined the full implications, as no studies have involved growing plants to full maturity in MNM-contaminated field soil. We have done so for soybean, a major global commodity crop, using farm soil amended with two high-production metal oxide MNMs (nano-CeO2 and -ZnO). The results provide a clear, but unfortunate, view of what could arise over the long term: (i) for nano-ZnO, component metal was taken up and distributed throughout edible plant tissues; (ii) for nano-CeO2, plant growth and yield diminished, but also (iii) nitrogen fixation—a major ecosystem service of leguminous crops—was shut down at high nano-CeO2 concentration. Juxtaposed against widespread land application of wastewater treatment biosolids to food crops, these findings forewarn of agriculturally associated human and environmental risks from the accelerating use of MNMs.

Nanoparticle ‘risk’ to food crops by By Jonathan Ball of BBC News

Whilst many of their effects have been well documented, some of their mechanisms of action are not fully understood. Concern has arisen that widespread long-term nanoparticle use may “trickle down” into the environment, sparking unforeseen effects on plant or animal, or even human, health.


They grew soybeans in a greenhouse in the presence of increasing amounts of the nanoparticles, monitoring the plants’ growth. In addition, the accumulation of the nanoparticles in different parts of the plant was also scrutinised.

The plants grown in the presence of zinc oxide nanoparticles actually grew slightly better than control plants grown in the absence of nanoparticles. However, zinc built up in the edible parts of the plants, which included the leaves and the beans.

Zinc oxide nanoparticles have been shown to be toxic to mammalian cells grown in the laboratory, but effects in humans remain to be examined fully.

Soybean growth was significantly stunted when the plants were cultivated in the presence of high levels of cerium oxide nanoparticles.

The cerium was able to enter the plants’ roots. Soybeans are members of a group of plants called legumes. The roots of these plants host bacteria that turn atmospheric nitrogen into a form that the plant can use for growth – so-called nitrogen fixation.

The cerium nanoparticles seemed to completely inhibit the bacteria’s ability to fix nitrogen.

Commenting on the wider toxicity of nanoparticles, Prof Vicki Stone from the Heriot-Watt University, Scotland, said: “Nanomaterials are equally hazardous or conversely equally safe. Effects seem to depend upon their physical and chemical characteristics – this is what scientists are aiming at better understanding, so that in future they can predict toxicity or safety based on these characteristics.”

DNA: the ultimate storage device

August 17, 2012 Leave a comment

Harvard researchers George Church, Yuan Gao and Sriram Kosuri have figured out how to encode massive amounts of  binary data  as DNA sequences with “barcodes” so they can be sequenced and easily assembled. This new method allows them to store up to 700 terabytes (that is 700 trillion bytes) of data in a single gram of DNA, pretty incredible stuff!

Abstract from Next-Generation Digital Information Storage in DNA

Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. Here, we develop a strategy to encode arbitrary digital information in DNA, write a 5.27-megabit book using DNA microchips, and read the book using next-generation DNA sequencing.

Excerpt from Harvard cracks DNA storage, crams 700 terabytes of data into a single gram  by 

It is only with recent advances in microfluidics and labs-on-a-chip that synthesizing and sequencing DNA has become an everyday task, though. While it took years for the original Human Genome Project to analyze a single human genome (some 3 billion DNA base pairs), modern lab equipment with microfluidic chips can do it in hours. Now this isn’t to say that Church and Kosuri’s DNA storage is fast — but it’s fast enough for very-long-term archival.

Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored.

Excerpt from Writing the Book in DNA by R. ALAN LEO

About four grams of DNA theoretically could store the digital data humankind creates in one year.
Although other projects have encoded data in the DNA of living bacteria, the Church team used commercial DNA microchips to create standalone DNA. “We purposefully avoided living cells,” Church said. “In an organism, your message is a tiny fraction of the whole cell, so there’s a lot of wasted space. But more importantly, almost as soon as a DNA goes into a cell, if that DNA doesn’t earn its keep, if it isn’t evolutionarily advantageous, the cell will start mutating it, and eventually the cell will completely delete it.”
In another departure, the team rejected so-called “shotgun sequencing,” which reassembles long DNA sequences by identifying overlaps in short strands. Instead, they took their cue from information technology, and encoded the book in 96-bit data blocks, each with a 19-bit address to guide reassembly. Including jpeg images and HTML formatting, the code for the book required 54,898 of these data blocks, each a unique DNA sequence. “We wanted to illustrate how the modern world is really full of zeroes and ones, not As through Zs alone,” Kosuri said.

A invite to a “conference” – scam aimed at academics

August 16, 2012 Leave a comment

Below you can read the email one of our BMCDB students received recently; an invite to give a speech at a “renowned conference” to which 100+ other leading scientist have agreed to come. But why would a graduate student be asked to give a speech at a “conference”, besides wanting your money.

A simple google search by Damian Guerra led to various blogs already mentioning this ‘new’ scam (read here and here). Except this scam is directly aimed at academics. A profession not known for their high paying jobs.

Read and enjoy:

From: mandy5 <>
Date: Wed, Aug 15, 2012 at 11:17 PM
Subject: Invitation for Speaker at 10th Annual Congress of International Drug Discovery Science and Technology


Dear Dr.  xxxx x. xxxx,

BIT Life Sciences is proud to present the 10th Anniversary for the Congress of International Drug Discovery Science & Technology (IDDST) with the theme “Celebrations of Drug Innovators and Discoverers in Our Decade” will be held during November 8-10, 2012, Nanjing, China. The IDDST 2012 plans to unite 1000+ life sciences, pharmaceutical, clinical, healthcare, managerial professionals and governmental decision makers from 50+ countries. The grand conference provides the perfect meeting place to exchange information and discuss breaking scientific discovery toward enabling technologies that are driving bio/pharmaceutical innovations, the drug discovery & development process.
On behalf of the organizing committee, we’re pleased to welcome you to propose a speech on your recent discovery about Ubiquitin on the Move: The ubiquitin modification pathway plays diverse roles in the regulation of E… at the Session 2-9: Ubiquitin Drug Discovery under the Chapter 2: Drug Discovery Target Validation of the congress by submitting your speech title and CV to us. Meanwhile, we hope you can share your stimulating data, valuable scientific information and influential experiences with other industrial leaders, professionals and research pioneers. You are encouraged to network and explore partnering opportunities.

As a branded Conference of BIT Congress, “Your Think Tank”, IDDST continues to expand with magnificent scientific and social programs to maximize your network in a free communication meeting environment.
Activities of IDDST 2012

l  Keynote Forum – Presentations from Nobel Prize Laureate and Senior Leaders of Renowned Company

l  Parallel Forum – 200+ Sessions and Symposiums provide 1000+ speech opportunities for experts from all of the world

l  Welcome Banquet – All the participants enjoy the formal buffet dinner with wonderful performance show

l  Project Matching Activity – Develop effective platform for Docking Project by free booths supply

l  Keymakers Summit – Special Forum for Enterprisers to discuss hot issues face to face

l  Exhibition and Poster Zone
So far, more than 100 well-known speakers confirmed their participation, please check the partial list below. For more information PS: http://www.iddst.comThe Congress of International Drug Discovery Science & Technology (IDDST) is initiated for filling the gap between Eastern and West World for drug discovery professionals of free information exchange. In the past decade, IDDST has attracted more than 5,000 enthusiastic speakers to communicate on the R & D advances in different therapeutic fields, which have generated great impact on the Chinese Bio/pharmaceutical development, enhanced Research and Development outsourcing, helped regional liaison of big pharma seeking partnership and searching talents, created a lot of opportunities for face-to-face network for multilateral collaboration by sharing both scientific and technological breakthroughs and speed up the process of many challenging drug discovery projects.

Dr. Chris Senanayake, Vice President, Department of Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., USA
Dr. Dan Marquess, Vice President, Theravance Inc, USA
Dr. Manuel C. Peitsch, Vice President, Philip Morris Products S.A., Switzerland
Dr. Michael MarkVice President, Cardio Metabolic Diseases Research, Boehringer Ingelheim, Germany
Dr. Michael Hennig, Vice Director & Head, Discovery Technologies, F. Hoffmann-La Roche Ltd., Switzerland
Dr. Andreas Marzinzik, Director, Exploratory Medicinal Chemistry, Novartis Institutes for BioMedical Research, Switzerland
Dr. Frederic F. Lehmann, Director, Head of Early Clinical Development WW, Cancer Immunotherapeutics, GlaxoSmithKline Biologicals, Belgium
Dr. Jeffrey A. Bacha, President & CEO, DelMar Pharmaceuticals, USA
Dr. Lieven Meerpoel, Senior Director, Head of MedChem Oncology,Medicinal Chemistry Scientifc Affairs, Johnson & Johnson Pharmaceutical Research & Development, Belgium
Dr. Stephen Doxsey, Professor, Program in Molecular Medicine, University of Massachusetts Medical Center, USA
Dr. W. Gibson Wood, Professor, Director of Graduate Studies, Department of Pharmacology, University of Minnesota School of Medicine, USA
Dr. Lucy Lee, Associate Director, Clinical Pharmacologist, Translational Medicine Clinical Pharmacology, Daiichi-Sankyo Pharma Development, USA
Meanwhile, we have a rare opportunity for participants, Biomedical High-level Overseas Professionals Exchange and Project Matchmaking Fair will be held in Nov. 9th, 2012 during our conference. We would like to offer limited booths for free to IDDST participants on a first come first served basis. Hope you do not let this chance slip from your fingers. For more details, please check the introduction online:
Nanjing, one of the six ancient cities of China, enjoys a worldwide reputation for its history and culture. We look forward to seeing you in Nanjing for a stimulating and enjoyable conference.
Kindest regards,

Ms. Catherine Wang
Program Coordinator
Organizing Committee of IDDST-2012
East Area, F11, Building 1,
Dalian Ascendas IT Park,
1 Hui Xian Yuan,
Dalian Hi-tech Industrial Zone,
LN 116025, China
Tel: 0086-411-84799609-801
Fax: 0086-411-84799629
If it is not of interest to you, please disregard and we apologize for any inconvenience this may have caused. To prevent further emails, go to <>

Who’s cool? You’re cool!

August 15, 2012 Leave a comment

The Sierra Club has named UC Davis as the coolest school, despite the ongoing heatwave!


Check it out here!

Categories: Uncategorized