Archive for the ‘Contributed Articles’ Category

So, you’re thinking about graduate school?

November 4, 2014 Leave a comment

Your interest in this piece might be to get an idea of how my graduate school experience has been at UC Davis. Perhaps you are thinking about attending or applying to grad school, or maybe you just want to compare your experiences in grad school with mine. If you are the former, congratulations on asking a few questions before you make a life-changing decision. If you are the latter, please leave a comment to affirm my experience or contrast my perspective with your own different experiences. I want to share these words for the people who are trying to find out about the graduate experience, what one may expect in this new environment, and how the first year will be like no other.

For me, I had no question in my mind. I was a non-traditional student returning to school for the best education I could get. I joined an undergrad science program at 24 and never turned back. Fully committed, I applied to a few schools in the Bay Area and went to all of my interviews. The choice I made was based on a number of things, but UC Davis was ultimately the best “fit” for me. Simply based on the feeling I got in the town, from the people and with the academic community, I knew there was something about the environment that just made sense. I arrived in the Summer of 2013 and began my first rotation early. Now, I have joined a lab, I am beginning my second year in BMCDB and I am learning more everyday. Experiments, mentors, seminars, and classes are all a part of this new stage in my development, and for the first time in my life, a text book is the least important source of information for my daily progress and learning.

The first year was designated for a core curriculum and finding a lab to join through research rotations. From my experience, I might suggest a few priorities and considerations for anyone in their first year of grad school. Funding, intellectual stimulus, and social competence are three things I was advised to consider before joining a lab. I feel lucky to have received the advice, and so, I share it with you. Above all, you must secure funding. This could be through a scholarship, fellowship or through a lab that is willing to support you for 5 years, but you must know where your support will come from. If you are not secure, you could face some dire challenges by working or teaching the entire time you’re in grad school or worse, you may not find a supporting lab = you’re out of grad school. They say we’re paid to go to school, but that doesn’t mean that anyone can foot the bill. If the University wants you, that’s great! But you have to find a lab that wants you for the following years. That’s both a personal and financial consideration. So, apply to every source of funding you can. Consider it one of your many jobs as you enter the world of scientific research. It also means you may need to limit your rotations to funded labs. Next thing to consider is your intellectual stimulation, and don’t be fooled by what you thought your interests were during undergrad research. Now is not the time to pursuit the same type of research all over again. Not that there’s anything wrong with that, but rotations are fantastic! Now is the time to explore other options and learn about new types of science and research. If you make it this far, you should think about meeting with as many professors as you can for one-on-one meetings to learn about up-to-date research topics and how different labs operate. Don’t make the mistake of weighing your decisions to rotate in a lab based on internet resources or lab home pages. Plus, if you are flexible, you will find that rotating in almost any lab can be incredibly stimulating. Then, you will only have one remaining task: find the best fit. Social competence can mean different things in different environments. Everyone fits in differently. It is important to find a lab where you feel competent to communicate with the professor and everyone else in lab. This also means you can get along with your potential future colleagues.

So many things that I have not mentioned might include keeping up your grades (yes, you still have to earn your grades), maintaining and building connections to people who can write letters of recommendation, devising research proposals, getting familiar with your new environments, managing your income taxes and living expenses, keeping a sliver of work/life balance, etc. This list can be different for everyone. There are a lot of things that may happen to fall into place, but everyone has a different experience and a different knack for getting things done. I wish everyone the best of luck! I’ll recount my 2nd year in 2015 when it has come to an end. From what I hear, I can expect another year of important grades, vigorous preparations for my Qualifying Exams, and some challenging days with variable rates of success in my research progress. I am looking forward to it! If you feel like you’ve had drastically different experiences, please let me know by leaving a comment. The world of undergraduates in STEM fields deserves to hear your opinion – especially if you disagree with me!

A final thought. I once believed that getting a PhD would be 5 years of my life lost, a delay towards starting my real life. In hindsight, I find this idea to be absurd. I do not feel stagnant. I do not feel restrained. I do not feel like I am missing anything or losing any time. I feel like the education and network I have and will continue to develop during this time is something for which there is no substitute. I was fortunate to have a life structure that allowed me to continue my education. However, graduate school is not for everyone for many different reasons other than life structure. Research requires exhaustive patience, meticulous focus, and perseverance through trial and error. Despite inevitable failures one faces during research, your desire to learn must be greater than ever now. I encourage anyone who is still considering grad school to fully commit and pursuit a program that is right for you. You will gain more than you ever could have imagined.

Adam Contreras

2nd Year Graduate Student

BMCDB Graduate Group, UC Davis

Chiu Lab, Department of Entomology

Fairy wands and hypothesis slides; reflections on teaching MCB220L

August 7, 2012 Leave a comment

By Dan Starr

The past three years I had the opportunity to teach the incoming BMCDB students in the rotation course. I was lucky to have great partners in this endeavor, Ted Powers for the first year, and Jodi Nunnari the past two years. The following are some of the highlights from my experience.

Far and away the best thing about teaching this course is the way I got to know the whole class, and watch them as they work hard to constantly improve their skills! I now know the students of these three classes better than any faculty member in BMCDB, and I can say with confidence, we have an awesome group of students!

We made some significant changes to the curriculum of MCB220L. I think the most important change was the requirement of writing an NSF-style grant proposal at the end of each rotation. This not only teaches the students how to write grants, but more importantly, gets them to think about the big picture before joining a lab. I feel this exercise was very successful. Especially to Amy, Nadia, and Alex, who turned their assignments into NSF fellowships—congrats you three! For all the other students, I think the assignment made you better scientists.

The second addition to the curriculum was the chalk talk. This is an important means of scientific communication that was completely new to the students. I hope that with the experience (and stress) of the chalk talks, now any of my students can give you a 5-10 minute version of their research at a chalkboard in a chance encounter in the hallway.

There were of course humorous moments to teaching the class—Ralph’s “pointer” comes immediately to mind. The other occurred at the MCB NIH training grant retreat at Fallen Leaf Lake when all the then second years cornered me after my talk. I still can’t believe I forgot the hypothesis slide!

In all, teaching MCB220L was one of the most rewarding things I have done as a professor! Watching my former students give a talk or hearing about them get a grant fills me with pride. We have an awesome group of students! I’m sure Bob, Elva, and Enoch will continue the high quality experiences of the class. Have fun!

Take A Moment To Remember This Memorial Day Weekend

May 25, 2012 Leave a comment

A note from V&E’s resident veteran, Luke Bohanan


Before we set off in our different directions to enjoy (or work through) this Memorial day weekend, I would like to take a moment of you time, to get on my soap box.
Yesterday I went with a few of my Student Veterans club members to the Memorial Union to lay flowers at the Aggie veterans memorial tucked away in the corner next to the fireplace in the Griffin lounge in the MU.  There, a stainless steel plaque lists the names of 134 UC Davis Graduates that were killed in combat from World War I through 2006, accompanied by a book encased in glass that talks about each service member.  I had never realized that the MU, the Memorial Union, was originally dedicated to these heroes, and I realized how easy it is to forget what memorial day is all about.  For me, the break is always bitter sweet.  Every year since 2003 I have lost at least one of the original 400 some odd soldiers that I crossed the boarder with in Iraq, many of whom I worked closely with, and all of whom I have called my brother.
So, if you have time this weekend, or later on, I invite you to go down to the MU Griffin lounge and take a moment to think about those who sacrificed so much to stand up when the call came out.  Also, if you are at a party, bbq, camping trip, or stuck behind your computer, take a moment, and take a moment and have a drink for all the great men and women who fought so hard and are no longer here to drink with us.
Here is a link to the article about the re-dedication of the wall, if you are interested.

Thank you, and have fun this weekend.

BMCDB Editorial: UC Davis’s Own LEED Platinum Sustainable Winery

May 21, 2012 Leave a comment

By Gordon Walker

With much thanks to Dr. Roger Boulton of UCD V&E

UC Davis is an innovative and amazing University that excels in many areas. From our roots as a Land Grant Agricultural school to our myriad of nationally ranked departments, graduate groups, and professional schools; no facility stands out as much, or is as representative of the true Davis spirit than the Pilot Winery, Brewery and Food Processing facility at the Robert Mondavi Institute on the south side of campus. The building is the culmination and crowning jewel of the RMI, which was made possible by an incredibly generous donation from the late great Robert G. Mondavi. Since starting at Davis I have had the chance to watch the building go from a construction site, to a fully operational research facility that is not only revolutionizing the science of food, wine, and beer but also pushing the boundaries of sustainable architecture and agriculture. This building has been LEED Platinum certified, meaning that it meets and exceeds the requirements of the US Green Building Council to be a “green building”. What is so amazing is that this is not just a “green” building but also a functional research facility capable of super sustainable food and beverage production. This building can serve as a model not only for wineries of the future, but also as a starting point for any structure or complex.

The winery features 152 mobile modular fermenters with the capability to do real time wireless monitoring of sugar levels, allowing students to actually track and manage their fermentations through their smart phones. These 152 fermenters are also linked to a ventilation system that works to sequester and trap carbon dioxide as calcium carbonate, this system greatly reduces cooling costs in the winery and provides a value added product.   The brewery features a state of the art Clean In Place (CIP) system that allows the entire brewing process to be done “in line” without any chance for contamination. The brewery also features a state of the art computerized brewery management system which allows students to mimmic commercial conditions but in small scale productions. The food processing facility is a large modular set of machines with capabilities to process a wide variety of crops such as tomatoes, peaches, almonds and other California staples. There is even a soon to be opened dairy processing facility that will serve to find practical solutions to problems faced by industry. While I could go on and on about all of the cool features of the Pilot facility, and the soon to be built Jess Jackson Sustainability Building, I will let Dr. Roger Boulton espouse some of the concepts and features that make this project so special.

Watch Dr. Boulton’s incredible power point presentation of the capabilities of the Winery and Jess Jackson Sustainability Building

Dr. Boulton’s Power Point Presentation

Long quote on the importance of the UC Winery Dr. Boulton

First LEED Platinum Winery, one of the highest (the highest?) point 
scores with 60 out of 69. One of 16 buildings at this level in 2011. It 
is energy and water positive as a building, probably the only LEED 
Platinum building to be so. It has gone beyond the LEED points for 
on-site water and energy, so a friend called it "Platinum plus"

The 152 research fermentors make the largest research facility in the 
world and with its wireless density and temperature sensors, the largest 
wireless network in the fermentation world. These fermentors has several 
innovative design features, from carbon capture, water-only heating and 
cooling for temperature control, mobile and suitable for both red and 
white wine fermentations.

The Jess Jackson Sustainable Winery Building is in the detailed design 
stage, and will be completed in Feb 2013. It is a passive utility 
building that will house the membrane systems for the filtration of all 
rainwater and cleaning solutions. It will house the carbon dioxide 
sequestration columns that will make calcium carbonate, the passive 
solar hot water, and the solar powered ice maker for the chilled water. 
It will make hydrogen electrolyticaly from solar power and store it for 
a hydrogen fuel cell for night time energy. These systems will be 
leadership commercial systems that will make the Winery self-sustainable 
in water and energy from on-site sources. This building will have 
insulations values between 60 to 80, compared to 20 in most houses. It 
will be among the most thermally-insulated (and therefore 
energy-efficient) buildings in the world, cooled only by night-time air. 
While the summer air temperatures might reach 100 to 105 in Davis, the 
building will not go above 82 F inside.

The rainwater capture from the three buildings of the Robert Mondavi 
Institute will be held in 6 x 40K gal tanks, like the 4 that are at the 
south side of the Winery complex. It will be filtered into RO water over 
a 6 month period. This will require about 1 or 2 KW for 180 days but is 
a preferred alternative to a filtration that is completed in a week, at 
26 times the KW requirement and sits idle for 51 weeks. The entire 
winery has been planned so that it can operate on storage rather than 
on-demand systems for all water and energy.

The cleaning solutions will be simple inorganic buffers, dilute KOH and 
KHSO4, at pH around 11 and 2.5 respectively. No pathogens grow in either 
solution and hydrogen peroxide is a sterilant at both pHs. These 
solutions can be re-filtered through a nanofilter for 90% recovery of 
both water and salts. After 10 cycles this will require only 1/5th the 
usual water and chemistry. The solutions will be pH 7 when mixed and can 
be used in irrigation without any clay destruction, a problem with 
sodium salts. There will be no phosphate for algal blooms in streams, no 
nitrate for soil nitrification, no organic to contribute to BOD 
(biological oxygen demand) or COD (chemical oxygen demand) requiring 
waste water treatment. The 10% retentate stream which has most of the 
juice or wine organics will go to the biodigestor on campus to become 

All of these facilities have been privately-funded at a time of 
recession and financial problems at the State level and budget cuts at 
UC. It is a stunning example of what is possible without any government 
support and speaks to the wide array of personal support that we are 
fortunate to have.

Dr. Roger Boulton gives a tour and explanation of the UC Davis Winery

Here are some other press articles about the innovations of the UC Davis LEED Platinum Pilot Winery, Brewery and Food Processing Facility

Eau de Whale Barf

April 12, 2012 Leave a comment

Contributed by Alex Gulevich

Imagine preparing for an elegant night out at a ballroom. Everyone in attendance will be wearing their finest evening gown or tailor-made suit, and most likely many of these people will be wearing their favorite perfume or cologne, say three sprays of Chanel No. 5 or a men’s fragrance from Dolce and Gobanna, These stimulating bouquets of aromas arouse our olfactory system, and those wearing the higher end fragrances will stimulate our senses throughout the night, while those wearing the lower end fragrances will go amiss and fail to last. This is because higher end fragrances have an additive within it that prolongs the lifetime of their scent, and this additive is derived from the dyspeptic discharge of a sperm whale, or in a more crude of way saying it, whale barf.

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Ambergris, a French compound word that translates to grey amber, is a smelly viscous black discharge from the sperm whale’s intestinal tract. A sperm whale’s diet consists primarily of the elusive giant squid, where they dive up to 3000 meters to chow down on fresh deep-sea calamari. Although a hearty meal, these giant squids also have giant indigestible beaks. The whale must produce ambergris in its intestine to help aid in its passage as fecal matter. However, if the ambergris mass becomes too large to pass, the whale will regurgitate (experts emphasize this is assumed, no one has actually observed this) the ambergris with beaks and all. This freshly vomited mass is less dense than seawater and floats to the surface where it is weathered by the sun and the salt from the sea itself, turning into a solid waxy grey substance. Its fate is then left to the tides and eventually washes ashore to Pacific, Atlantic and Caribbean coasts. Aimless and profiteering beachcombers then stroll along the coast and manually harvest the weathered ambergris, to be sold at a market value of $10 per gram (gold is $53 per gram) with the average decent sized lump selling for $6000.

Fresh ambergris smells like fresh fecal matter. It’s speculated that Captain Ahab from Herman Melville’s Moby Dick was able to track sperm whales by using his nose and following this foul odor. However, as ambergris matures its loses its displeasing odor and gains sweeter earthy overtones. Once matured, crude ambergris is treated with heat and alcohol to extract the white ambrein crystals that lie within, which is then further oxidized to ambrox, the main additive in higher end fragrances, and ambrinol. The fragrance molecules in perfumes and colognes naturally have high rates of vaporization, thus a short lifetime. However, when ambrox is added with these molecules their aromas persist and have longer lifetimes. This is because the fragrance molecules are lipophilic and have a high affinity for ambrox, which prevents the molecules from entering the vapor phase all at once and disappearing into thin air. This is why ambrox is highly sought after, but is difficult to obtain because of its scarcity and it’s a byproduct of an endangered species, which technically makes it illegal to harvest in the United States. However, Jörg Bohlmann and his research group at the University of British Columbia have found a new way of obtaining ambrox without making a trip to the beach, or the courts.

Diterpenoids serve as chemical defense molecules produced by coniferous trees and protects them against herbivores and pathogens, and one such compound is cis-abienol. This compound is synthesized in the bark of the balsam fir and is commercially valuable because it’s a precursor two steps removed from chemically synthesizing ambrox. Bohlmann’s group recently identified a diterpene synthase gene, cis-abienol synthase (CAS), being actively expressed in the bark tissue of the balsam fir. Since cis-abienol has the highest abundance in bark tissue, looking at gene expression in the bark made most sense. These researchers were able to create a transcriptome of actively transcribed genes and assemble full-length cDNA sequences of candidate CAS genes by comparing sequence homologies of known diterpene synthases. They then took these genes and expressed them in Escherichia coli to test for cis-abienol biosynthesis, and of the four identified candidates, they conclusively found one candidate gene specifically producing cis-abienol from the appropriate precursor molecules, and uncovered the function of a previously unknown enzyme.

By discovering this enzyme, this opens up the possibility of engineering a microorganism, or perhaps a plant crop, to biosynthesize ambrox through metabolic engineering. People may feel more comfortable knowing that they are spraying themselves with ambrox from a plant product rather than sperm whale vomit, but the future discussion here centers around realizing the potential of metabolic engineering to biosynthesize valuable chemicals that are otherwise difficult to obtain. As the list of characterizations of novel enzymes grows, so do the possibilities of how we can design microorganisms or plant crops as living factories to make products with commercial value for human consumption. But despite all this, if anything is to be learned here, it’s that a little sperm whale barf can go a long way, at least with perfumes and colognes.

Read the original manuscript published in the Journal of Biological Chemistry.

Categories: Contributed Articles