disclaimer

It has been a couple of weeks since the ECFG meeting in Edinburgh, but there were a few things I wanted to share from my visit.

I presented some interesting data on strain distribution at the 5th International Aspergillus Meeting	I got to run a fair bit, including one memorable run up the Salsbury Crags to Arthurs Seat	I learned that not everyone shares the same ideas.
Some of those people had a nice drum circle going outside McEwan Hall during our Sunday Plenary sessions	Not everybody seemed to understand and appreciate genetic engineering	There was also the sentiment that blood need not be exchanged for oil.
Moreover, people seemed to appreciate places where blood was favored over oil.	And of course, the Scot Nationalism was in evidence.	Finally, there was an opportunity to broaden one's horizons beyond just Fungal Genetics.

This all made Edinburgh a nice place to visit. The weather was what one would expect for April in Scotland but we never got completely rained out. The science was good, even if we had to squeeze in for the poster sessions. I tried Haggis a number of times. The vegetarian Haggis was also quite nice. We also had some nice beer. Not being a Scotch drinker, I did not go in for the Whiskey tasting.
I enjoyed visiting with some people including Mikael Andersen of DTU, Scott Baker of PNNL, Daren Brown of the USDA, Geoff Turner of Sheffield, Susanna Braus-Stromeyer from Georg August University, Jon Palmer of Wisconsin, as well as the whole crew from Rhodes College in Memphis and many others.

Several people promised to send strains. You know who you are. Remember: when you deposit materials at the FGSC you are not enabling competitors, but rather people who can build upon your contribution and make it more meaningful.

One last note, I was talking to my twin brother and mentioned the famous quote from Issac Newton, who said that in making our contributions to scientific progress, "we stand upon the shoulders of giants." In his uniquely insightful way, my brother added, "and midgets too."  This reminded me that all progress, no matter how incremental, is important in moving science forward.

4/1/08

I have just returned from the Neurospora 2008 meeting at Asilomar and was profoundly impressed with how far the community has come in just two years. The quality of research, both in terms of the depth and the breadth, shows the impact that high quality research materials can do in a field of dedicated people. Another important thing I noticed was the large number of young people coming into the system. This can only bode well.

 

Happy April Fools Day!

3/112/08

A recent and startling trend has reached the FGSC!

The FGSC follows all relevant and applicable shipping guidelines. Examples include the IATA guidelines for air transit. We buy specialized mailers for some applications, but for other applications we just keep the packaging that comes with supplies. We do try to avoid anything such as corn starch packing pellets that could be 'nutritive' to the organisms that we ship. We recently noticed that bubble wrap has undergone a sea-change in its construction such that it can no longer be popped. It is constructed as interconnected rows either in a traditional configuration (Fig 1.), or in a completely new one (Fig 2).
Figure 1. Innocent looking, yet still evil. While this bubble-wrap LOOKS like the old favorite, it contains an array of connected cells such that if one cell is breached, one row deflates. For example, see the third row from the left. If one squeezes one cell, the other connected cells absorb the pressure change and no the cell does not pop.	Figure 2. A new paradigm in packing. Having abandoned any vestige of traditional sealed cell bubble wrap, this new format is both effective and resilient, yet the interconnected cells prevent popping by transferring pressure from one cell to the connected adjacent cells.
To combat the buildup of inevitable frustration associated with no longer being able to pop bubble wrap, we are providing the version below. Have fun.
Virtual Bubblewrap © www.virtual-bubblewrap.com virtual-bubblewrap-distv1.1

2/27/08

In order to keep tabs on the status of the FGSC lab, Matt Kinney carried out a series of open-plate test plates. He left plates containing either Vogels minimal medium or Complete medium (Tryptone, Yeast extract and glucose) open for one hour on the bench in the main room and the transfer room. These were incubated at room temperature for two nights and then moved to the 37C incubator for one week. On the plates left in the main room there was ONE colony. On the plates left in the transfer room there were NO colonies. Nice to know that we run a clean lab (although in a recent transformation experiment with Aspergillus nidulans, we succeeded in transforming it into something that looked like Streptomyces).

2/21/08

The FGSC is now listed at Straininfo.net. This data repository is providing a curated and cross referenced way to access information about biological resources around the world. In becoming a straininfo.net partner, the FGSC has joined with most major repositories, including the ATCC, CBS, and the DSMZ, among others. 

At the FGSC we are getting ready for the upcoming Neurospora 2008 meeting as well as the European Conference on Fungal Genetics. The 5th International Aspergillus meeting will be held as a satellite to the ECFG.

1/15/08

The World Federation for Culture Collections has sent out this urgent appeal:

Please help, if you can.

12/4/07

Ceres, The Energy Crop Company, has shared the wealth with the FGSC in the form of a surplus Robbins Hydra.
It is a 100 ul system and may need some refurbishing before we are able to use it, but it is a timely donation when the
FGSC is actively developing new technologies in 96 well format.

Thanksgiving is a unique American holiday. However, since I am not a huge football fan, I spent some time this weekend building a fence. It is only 9 ft long (about 3 meters) but it is essential in that we stack firewood and keep our compost behind it. It is all Cedar and will weather to a nice grey color.

I also celebrated 'black Friday' by conducting NO COMMERCE. To some, the Friday after Thanksgiving is the biggest retail day of the year. To others, it is "buy nothing day." Being the father of teenagers, I was quickly reminded of the fact that I did purchase electricity, natural gas, and water.

11/19/07

In the aftermath of the USDA/APS national culture collection workshop, I have learned of additional efforts being conducted in the US Government regarding collections. The Office of Science and Technology has carried out a survey of existing collections, including collections of everything from arctic ice cores to zebrafish genes. The Federal Register description is here.

I am pretty sure that I did not receive such a survey. If I did, I filled it out without giving it a second thought. In general, that is how I tend to deal with such things. Fill them out (as time permits) as soon as I see them. This keeps things from piling up on my desk.
 

11/16/07

I went to the USDA in Greenbelt, Maryland this week. There was a 2 day workshop sponsored by the American Phytopathological Society and the USDA to discuss the future of culture collections in the US.  The workshop focused on developing a new culture collection system in the US that would allow for the maintenance of large numbers of isolates of a variety of plant associated micro-organisms. 

The workshop was pretty much what I expected. There were people there from the USDA ARS and from the National Mycological Collection. There were even people there from National Program 301 which is the program charged with maintaining important genetic resources. While their mission includes microbial germplasm, there has historically been little motivation to fulfill that mission.

My trip took me through Washington DC National Airport where I noticed an acute gender bias. It was around 7 pm on a Wednesday evening and there were about five men to every one woman. Most of the Men appeared to be Road Warriors: they all had laptops and a vaguely exhausted professionalism about them. I had also noticed when riding the Metro in DC that around 5 pm there appeared a strong cultural shift of the ridership. Earlier it was more tourists and a wide variety of locals but at 5 pm there were hoards of wonks, geeks and nerds. The difference is whether they were policy workers (suits), science workers (shirt and tie) or information technology workers (t-shirts and jeans). They ALL had their little ID badges on lanyards, pocket clips or around their necks.

10/30/07

Aric Wiest, the FGSC Asst. Curator, got himself on the American Phytopathological Society Collections and Germplasm Committee. This is a key time to be involved. The APS and the USDA are opening discussions on how to preserve microbial germplasm for future researchers. At present neither the ATCC or the NRRL labs have the breadth of  focus to handle the wide variety of organisms that are found in nature.Meanwhile, the USFCC has not published minutes since 2001. The USFCC has been more closely aligned with the Society for Industrial Microbiology in recent years. Perhaps it is time for more APS members to join the USFCC!

10/17/07

The FGSC Advisory Board meeting has come and gone. I am left with a charge to make more progress in updating the FGSC database and web-site. There are tools out there. At the ICCC11, I met with Peter Dawyndt of StrainInfo.net. They have an interface that searches many sites for strains and compiles the output into a meaningful format.
The ICCC11 was a great success and a tremendous learning opportunity for me. I got to meet people I had previously only known from e-mail including Lynne Sigler of the University of Alberta Microfungus collection and herbarium and David Smith of CABI and also President of the WFCC.

I also learned a bit about the Organization for Economic Co-operation and Development and met the Director of Biotechnology, Iain Gillespie. The OECD has published guidelines for Best Practices in a Biological Resource Center.

I did finally get the traffic data on the FGSC web-site. We are well used. The 6 million hits came from nearly 400,000 unique users. Many pages in the FGSC site are viewed with the top ten pages only accounting for about 5 percent of the hits.

9/14/07

In the last 24 months, the FGSC website has received over 6 MILLION hits. That is the only statistic I can tell you right now.

I am trying to get into our statistics, but the package that is being used, Sawmill, is somewhat balky. I have a login name, and a password, that allow me to get into a web application to view our statistics. The guys in IT can login and run reports, but when I login, it only ever shows me the login page. Sometimes, it gives me a 'you have been logged out because of inactivity' and if I put in the WRONG password, it tells me that.

It knows me, but it wont show me the data. 

I have tried the login on four different computers in both Internet Explorer and Firefox (and in different versions). I have set my browser to accept cookies and to allow pop-ups and still cannot get in. Later today, I will go over to the IT department and run my reports on their computers.

And who among us has not called a company or government office and been told to wait while they 'bring up that screen?'
We have become slaves to our software. If you do not fit into a category, you do not exist. If there is no blank, you cannot enter the data. Different countries have different orders in which they put mailing information yet, as we have done here a the FGSC, we have inflexible formats for our mailing labels based on the most common format. This is why your address may appear mangled.

Its not my fault. Its because of the software.

9/10/07

The production of arrayed sets of Neurospora crassa Knock Out mutants continues here at the FGSC. We have finished through plate 42. So far we have distributed plates to several states in the US as well as labs in Canada, Germany, and several labs in Asia.

What can YOU do with this resource?

In other news, we have recently received strains including the Aspergillus niger strain 513.88 (FGSC A1513) used in the genome sequencing program at DSM. This strain is derived from the industrial workhorse NRRL 3122 by conventional mutagenesis and is the progenitor of current protein production strains. Remarkably, it has fewer secreted carbohydrate active enzymes than  A. nidulans or A. oryzae and similar numbers of gluco and alpha amylase genes. 

We recently upgraded our microscopes here at the FGSC. Since we work on a limited budget, we replaced our old binocular Olympus EH. We got a new Amscope 420a with a 1.3 Mpixel USB camera. It was economical, but arrived defective. Once one pushed in the sliding rod, a piece of the head blocked the left eyepiece. Precision World DID replace the head, but it took a week and I had to pay shipping. Not really how I would have chosen for it to all go.

9/5/07

As promised, here are some photos of the inside of my shoulder.

This image shows the tear in the labrum	This image shows the longhead biceps tendon
This image shows the tear in my rotator cuff	This image shows the stitches used to close the rotator cuff tear	This shows the underside of the acromium and clavicle which were resurfaced to prevent impingement

I have to keep my arm immobilized until early October. Mostly it does not hurt anymore. Certainly it hurts no more than it did before the surgery.

I am very disappointed that I will not be able to run the 4th Kansas City Zoo run, though I will go anyway. Some traditions are important to maintain and going to this with my charming children is one such tradition.

Meanwhile, my house has been "TP'd" two weekends in a row. I guess that the 14 yr old girls in my son's school want him to feel appreciated...

 8/27/07

It has been a while since I last wrote. Have I been too busy? No. It has been a number of things. In reverse chronological order, I have been away from the lab following reconstructive surgery on my badly torn right rotator cuff (pictures to follow). During the recuperation, I became 46 (This, in response to George Carlin's Question of why it is that in English we "turn" an age. He posits that when bad things happen, like when milk spoils, you say that it 'turned' and hence aging is described as 'turning' while when good things happen they "become). Not surprisingly, so did my twin brother. He did not, however, have surgery on his shoulder.

While I was sitting around not moving my arm, I did manage to read a few books. Among them were the first two of Terry Pratchett's diskworld books, the Dark Material trilogy by Phillip Pullman, and the last two Artemis Fowl books by Eoin Colfer.
 

The week of August 12-17 was a banner week at the FGSC. We produced five plates of arrayed mutants. Aric Wiest and Matt Kinney deserve real kudos for this. We did this all without either the Apricot (Left) or Hydra (right). We are in the market for one of these fine machines and are trying to decide between them. If you have any input, please let us know. We would actually be looking at a reconditioned analog Apricot or a reconditioned hydra.

8/8/07

I have just installed Dreamweaver and am learning how to use it. In the past, I have managed the FGSC Web-site by FTP, editing the html code directly in a text editor, then I used Homesite which is a What You See is What You Get editor and when we moved to UMKC, I used Microsoft FrontPage, because it was free.

This blog is the first document I am editing in Dreamweaver. If the entire FGSC web-site goes away, it is because I obviously did something wrong!

Saturday found me running along Big Muddy, also known as the Missouri River. This particular trail was up in Parkville, MO (home to Park University). The Burlington Northern/Santa Fe rail line goes right along the river here and I got a close look at the cargo on one particular train. Along with a lot of empty lumber cars, there were 4 Boeing 737 bodies. They are being shipped from  Wichita, KS to Renton, WA. This was quite a sight and brings home the point that while America may be behind in rail systems we still have the opportunity to catch up with the rest of the world.

Some may have known my blushing bride had a bit of a rough summer and spent a few weeks in the hospital. While the details are best left to the medicos, she is doing better and is home and well on her way to a full recovery.
When neighbors have commented that they want to bring food over, I have replied that I worked my way through college as a cook and that we were ok. When one suggested that I should invite THEM over for a meal, I asked him how he liked Tofu. In the mid-west of the US of A, I might as well have asked him if he liked to eat moldy peanut cakes.......

Michael Hynes wrote to say "The legendary book that Bill Timberlake has been writing in the wilds of New Mexico was published this year.... it is an excellent read as an airport/vacation book. As you might expect the science and sociology of science is so accurate compared to that of author's such as Michael Crichton." 

 Bill wrote the FGSC to say that it is available from Amazon.com

7/3/07

Yet again, I write to say that the FGSC is safe and dry. While areas to our south received over 10 cm of rain, the Kansas City airport just a few Kilometers to the North received only about 1/2 cm. We were just on the 'dry line' and received only about 3-4 cm of rain over several days. FGSC research assistant Matt Kinney had to cut short his weekend at the lake, however, as he wanted to get back before being stranded. Meanwhile, the rain has been good for my grass seed (grass, like fescue and ryegrass, not that other kind of grass).

The FGSC web-site includes descriptions of 'Evolution' and 'Evolutionary genetics' and for that reason,  we are deemed to be IN VIOLATION of the Internet Acceptable Use Policy of the self-appointed Net Authority
Keep your kiddies safe and pure and ignorant of testable and verifiable truths.

6/25/07

One sod cutter and one rototiller later, the lawn has been seeded. I know that seeding a lawn on the first day of summer is probably not the best possible way to make a lawn, but we do what we must. In other news, I spent a significant amount of time yesterday reseating a toilet. It seems that the wax seals do not last forever and somehow having water dripping from the kitchen ceiling was just too disgusting to live with.

6/13/07

The FGSC has broken new ground in accepting deletion mutants of Cryptococcus neoformans. These come from the labs of Jenny Lodge at Saint Louis University and from Hiten Madhani at the University of California, San Francisco. More info will be forthcoming on the FGSC web-page.

Anyone who has been following this story remembers that I was pounding away on an old path that cut a lawn into three unusable spaces. Well, the path is gone. As much fun as it was to destroy it with just a wrecking bar, I finally had to rent a jackhammer to break it up. I have, however, learned how to build a path that will last for a hundred years. Start off with coarse aggregate concrete maybe 10- 12 cm and make sure that you put in welded-wire-mesh. Then lay the paving stones in about 5 cm of fine mortar. It also helps if you use good quality pavers- 3-4 cm thick. We ended up taking out about 7 cubic yards of rubble! Now, all we have left to do is to re-grade the lawn and seed out the bare places and then to enjoy our new grass patch.

Whats in my MP3 player?  Thom Yorke's The Eraser

Today is a DARK DAY at the FGSC. It is Ms. Sheera Walker's last day. Sheera has been with the FGSC for over 8 years and we have come to depend on her organizational skills, her careful bench work, and her pleasant demeanor. Sheera has taken a position with a clinical testing lab where she will have more opportunity to advance her career (and her salary). Please join me in wishing Sheera all the best in her future endeavors.

In other news, I finally got around to setting up a wikipedia page for the FGSC.

I have just returned from Stanford where I helped prepare materials to be shipped to the FGSC. Among them are silica gel stocks from David Perkins' lab as well as frozen stocks of many strains. The former are well cataloged while the latter are not. The Perkins lab held a wealth of resources beyond the strains, however. We do not have space to house all of the books, unpublished theses and reprints that David Perkins collected over the years. The bound Tatum reprint collection will go to the Editor of the FGN (The FGSC holds a duplicate set of these reprints).

It was interesting to see what has been maintained, both in the Perkins lab and in the adjacent Yanofsky lab. While removing materials from a walk-in -20 freezer, I noticed what appeared to be cosmid pools from the original Volmer pSV50 cosmid library. These are presumably what had been used to clone by sib selection in the late 1980's and early 1990's. There was a lot of old historical material like this including the original wax-paper envelopes David Perkins used to send strains back from his collecting trips.

5/9/07

Thanks to everyone who inquired about our status. The FGSC sits atop a 5 story building, on a hill overlooking Brush Creek in Kansas City, Missouri. We are a couple of miles from the confluence of the Missouri and Kansas Rivers. There was some local flooding, but it all drained away in a few hours.

For those who may have wondered, I did finally sell my handsome 1986 Toyota Landcruiser. I sold it on e-bay and got about 15% more than I was asking locally! I really hated to do it, but even the money I received for it would not have been enough to fix it up.

5/4/07

The internet gives many opportunities to validate what we do. Remember to cite the FGSC.

• Articles from ASM press that cite the FGSC.
• Articles from Nature Press that cite the FGSC
• Articles in Science that cite the FGSC

4/23/07

In anticipation of the FGSC renewal submission this summer, I visited Google Scholar today and found the following interesting numbers.
 

If you do not restrict the search years, you find 1580 hits for 'FGSC'.

Based on the number of orders we receive and how widespread the materials from the FGSC are, this number ought to be higher.
Please remember to cite the FGSC in publications. We do keep track.

4/17/07

Today the USDA Biotechnology Regulatory Services (BRS) issued its Spring 2007 Stakeholder Update where they announced that they are undergoing a major revision of their how they regulate genetically engineered organisms. They say:

"BRS is undertaking a major revision of its guidance on the regulation of GE organisms. The project will update and consolidate all agency guidance related to compliance with APHIS’ biotechnology regulations (7 CFR 340) into a single printed publication, entitled the BRS User’s Guide. In January 2007, the first two chapters of the new BRS User's Guide were posted online. These include a chapter on document preparation guidelines, including how to handle CBI, and guidance for notifications. As BRS completes new guidance chapters they will also be placed online, until all existing guidance is replaced with new guidance. All BRS User’s Guide chapters are available at http://www.aphis.usda.gov/brs/brs_usersguide.html"

The last time the regulations were updated was November 1996. Officially "Developers and researchers may petition APHIS to remove the regulated organism from BRS oversight, " but the petition process is geared entirely toward crop plants.

This means that this is an important time to weigh in with your opinion about how genetically engineered plant pathogenic fungi are regulated. Registering as a BRS Stakeholder is a first step towards being better informed about this important issue. Contacting your Senator or Congress Representative is another way to be heard. You can also contact the USDA Biotechnology Regulatory Services directly.

4/10/07

If you work with plant pathogenic fungi in the US and you use genetic engineering you may want to know that interstate traffic in genetically engineered strains may be illegal. What are you to do? Lobby the USDA to change the rules governing the laboratory use of genetically engineered plant pathogenic fungi. Why is this important? If you publish a paper describing your work, you are essentially admitting guilt.

4/5/07

At the recent meeting someone asked me how we dealt with slant cultures with cotton plugs where the cotton has gotten contaminated with conidia. We hold the tube in a flame to heat the mouth then we withdraw the cotton into the flame and after it has burned for a moment, we drop it into freshly diluted 10% Bleach (Sodium Hypochlorite). Then we re-plug the tube with a fresh cotton plug that we pre-sterilize in empty tubes. This way we can simply transfer a plug from the empty tube to the one with the conidiating culture.

BE A TOOL
This is the message from the latest meeting. In the 1980's we used E. coli as a tool to manipulate DNA. Now we use Yeast as a tool to manipulate DNA. So, to succeed as a model system, you need to be a tool.

Now the 24th Fungal Genetics Conference has come and gone. This was a truly great meeting. It has been diverse for many years, but this year the amazing thing was the tremendous depth accompanying the diversity. It is a good time to be in fungal genetics.

We returned to daffodils, blooming pears and the accursed dandelion. I don't like to use herbicides because I do like to have clover and thyme in my lawn. This makes it a bit of a challenge to control the dandelions. I was also digging out garlic chives from the vegetable garden. They can actually be pretty invasive. Later in the season, the problem will be nut-sedge.

Of course, one man's weeds are another man's native plants.

The program for the FGC is at the printers and today I posted it online. It is a 2.5M pdf. Abstracts for posters and plenary talks are also online in html format.  The program for the Aspergillus satellite meeting is also online.  Having these done is a big load off my back.

I alluded to scorpion toxins in my 3/5 posting. Check out Ray St. Leger's poster (#449).  They have expressed a scorpion toxin gene in Metarhizium anisopliae which renders the fungus 22X more virulent against crop destroying caterpillars. That's science in action!

Also of note, G. Adams and M. Taga  independently used flow cytometry to show that strains of Phytophthora infestans varied in DNA content (posters 31 and 588). Many years ago, we used flow cytometry to confirm variation in DNA content of Ustilago hordei sporidia. CHEF gels showed a 30% variablity in DNA content but we never did publish the figure shown on the left. These strains ARE sexually compatible. Maybe Ustilago hordei does not have MSUD. Maybe this technology has other applications in fungi.

3/5/07

Well, I must be having fun, as time sure has flown. Actually, I have been working on the program book for the upcoming Fungal Genetics Conference at Asilomar as well as the program for the Aspergillus meeting to be held just before the Asilomar meeting.

These meetings look to be very interesting and include things as diverse as the origins of virulence, using scorpion toxins to kill plant pests, making strains that are better at industrial production and how fungal genomes can enlighten us. All in all, there should be more than any mere mortal can assimilate. I am reminded of the parable:

	A specialist knows more and more about less and less until eventually he
	knows everything about nothing.

	A generalist know less and less about more and more until eventually he	
	knows nothing about everything.

This is attributed to E.E. Smith, a science fiction author. 

The Fungal Genetics Conference is organized with Plenary sessions in the morning, where Specialists will try to talk like Generalists followed by concurrent sessions in the afternoon where Specialists get to be Specialists.

One high point of the meeting will be the Saturday Night appearance of the Amplified DNA Band!