Monday, August 29, 2005


Plant derived antibiotic resistance gene

In an upcoming Nature Biotechnology issue, Mentewab Ayalew and C. Neal Stewart, Jr. from the Univeristy of Tennessee will report on the use of an ABC transporter gene from Arabidopsis to confer Kanamycin resistance in tobacco. Kanamycin resistance is used as a selectable marker in plant transformation. Usually, a resistance gene is linked to the gene of interest. Plants that are then shown to be resistant to an antibiotic, the selectable marker, will also contain the gene of interest. Usually, this antibiotic resistance gene has come from bacteria, which raises concerns that the gene could be horizontally transfered to native bacteria or other plants. Because this new gene is an ABC transporter normally found in plants, this concern is muted. A copy of the paper can be found here.


Chlorogen eyes possible expansion

Chlorogen announced friday a collaboration with Missouri State Univeristy that could lead to the building of a manufacturing plant on their campus. Chlorogen would receive tax incentives in return for purchasing equipment to fill new lab space and manufacturing equipment that will be leased back to them. As released earlier, Chlorogen is also close to closing on another $6 million in venture capital funding.


Common Sense for the Biochemist, pt 7

Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet, because you're being had. Michael Crichton (1942 - ), Caltech Michelin Lecture, January 17, 2003

Friday, August 26, 2005


Common Sense for Symposiums

I just learned that my old school, WKU will be holding the first ever symposium dedicated to Bluegrass Music. The deadline to register has already passed but I may try and make it. Talks such as "Smokin’ Grass without Prejudice: Kentucky’s Bluegrass Connection to Nashville’s MusikMafia" to be given by David Pruett will sure be a change from the presentations I've been sitting in on. And on the subject of meetings and symposiums, I ran across a very humorous article (count this as the weekend funny) at Respectful Insolence catagorizing the creatures that attend surgical meetings.


I am still alive

Thanks to all of you out there for visiting, it seems like I am getting more and more unique visitors everyday. Sorry I haven't posted in a while, but I've been really busy lately. I promise I should be back up to full steam in a day or two.

Tuesday, August 16, 2005


New York times article regarding Ventria

This is the second of two stories found on This New York Times article in today's edition does a good job covering the ongoing move of Ventria from Sacramento, CA to Marysville, MO. If nothing else, the NY Times article has a good picture of a rice being grown in a field for those of you who have never seen it. I was wondering if rice could be grown in northern Missouri, I guess I was not the only one.


Chlorogen firms up its chloroplast expression platform

This is the first of two stories today taken from Chlorogen today firmed up its expression platform utilizing expression of recombinant proteins in the plant chloroplast. In this story found on, the company stated that it has acquired a license to CTT (Chloroplast transformation technology) patents held by Rutgers university. Not much to this story, but it looks like I could do a little research to find out how these patents match up with what Chlorogen already has. From the sounds of the press release, it looks like this will prevent Chlorogen from having to dance around some potential patent issues with CTT and will probably give them some more room to develop their technology. Clearing up patent issues without the use of vultures - I mean - lawyers is always a good thing in my book. Chlorogen is also in the middle of raising about $6 million in capital which should be closing in October. Looks like it may be a busy winter for these guys.


How to keep your web-self organized pt. 4

Keep those e-mails coming! The discussion over social bookmarking seems to be a hot topic right now. Solving the world's (and internet's) problems through blogging is the way to go, well, outside of actually doing something about the world's problems. Thanks to Ben Lund the project manager for Connotea for dropping an e-mail regarding the ongoing discussion over social bookmarking - Part 3, Part 2. I post parts of it (in no particular order) and give my response.
I'm the project manager for Connotea at Nature Publishing Group. I'm always looking for feedback (both good and bad) from users and visitors, so I was interested to read your post about Connotea and CiteULike.
Once again, thanks for the e-mail.
I was also puzzled by your comparison of us to Google. The primary aim of Connotea is for it to be a useful service that enables users to organise their own resources -- the idea of finding or discovering new articles is a secondary, albeit very important, one.
With this remark, I was thinking down the road business-wise. I'll probably ruffle a few feathers here, but I think and CiteULike will eventually get bought out by the likes of Google or Yahoo or another big time web player. This discussion started with my review of MyJeeves, which combines a search function with a bookmarking function. I think this would probably be advantageous for both and CiteULike, as it would give them access to virtually unlimited server power and storage space, not to mention virtually unlimited brain power for improvements. I may be mistaken since I don't know the full business plan for Connotea, but I just don't see it being sold off or eventually having the resources that these other two sites potentially may have access to.
We're still in the stage of constant development on Connotea, and have already altered out plans to take account of user feedback and developments on the wider web, so if you have any ideas about how to make it more useful, feel free to let me know. You mentioned a couple of things in your post: * Difficulty of manually adding a bookmark: 'Add a bookmark' is the first option in the toolbox on the right hand side after you log in. Does the toolbox blend in too much in with the background? Any suggestions for how to make it more prominent? Also, the idea is for users to mostly use the bookmarklets, so they can add links as they're reading them. Do we need to make that more prominent too? * General difficulty in navigation: Is there any chance you can give me a couple of examples of what you were trying to do? Then I can look at the navigation we have right now and work out how best to make it more usable. Again, if you have any suggestions, please let me know.
As soon as you log in you are directed to your homepage, you then have to go to "My library" to view your toolbox options. In the other two cases, you have the option to start adding links or references as soon as you log in (OK that is kind of getting nit-picky but it made an impression on me).
I was intrigued that you contrasted Connotea with CiteULike, since the underlying functionality and concepts of the two are virtually identical. It's true that we emphasise different aspects of the services, but in essence both Connotea and CiteULike are about saving and sharing links online.
A science based social bookmarking site is a good idea and I am sure there will be quite a few people out there who will find your site useful. However in the grand scheme of things, you can not forget in these comparisons, which beats both CiteULike and Connotea hands down because of its simplicity. I don't know how to describe it, but has a very clean, user-friendly interface. The CiteULike interface is just as "busy" as Connotea's (more on that comparison further down). Let's talk speed issues. While I have been writing this post, I have been adding links to both and Connotea. Maybe it is because I am "across the pond", but I have been able to add 2-3 links in to every one in Connotea, and this is simply because I have been waiting for pages to load in Connotea. As stated in a previous post, this is not the first time I have had speed issues with a NPG site. CiteULike is loading maybe a little slower than but not by much. To me, its those little things that can give one site an edge over the other. So I have declared the winner to be, however, there's a catch. With CiteULike, I can store my copy of a PDF version of a reference article on their server and attach that to a bookmarked reference. Therefore no matter where I am I can get access not only to a reference, but to my copy of the actual paper. This is the only reason why I would use CiteULike and its a very good reason. Thanks again for your e-mail, and I hope that I have answered some of your questions. Now about those rising journal subsciption costs. . . As a side note: This string of posts has made me realize how important blogging is regarded by the professional world. It is easy to see what has been said in the blogosphere about a particular subject or thing through a simple search on Technorati or Bloglines. I am impressed by the attention that CSFTB has been garnering lately. Note added in proof: Sorry for the format of the quotes. I am working on that issue.

Monday, August 15, 2005


How to keep your web-self organized pt. 3

I just received an e-mail from Richard Cameron from CiteULike regarding a recent post on social bookmarking that reads in part:
Hi Brian, I just noticed your blog post about CiteUlike. I didn't want to post this as a comment to avoid any attempts at blatant self-publicity, but did you know you can actually upload the yours PDFs to CiteULike? I can keep them on the server for you, so you can access them from anywhere regardless of whether you've got your computer at home set up to proxy through your university's network? There no quota at the moment, but there's obviously a limit to the proportion of the world's information I can keep on my servers, so that that may change at some point. However, hard drive space is cheap and I'm keen to keep the content because it means I can ultimately do full-text searches on it.
Thanks Richard for the heads up (and by the way, you deserve some blatant self-publicity just for visiting my site). I definitely missed a huge feature of your site that changed my entire opinion about it. I have tested this feature out and it works great! I have also noticed that you can import your references from BibTex although I haven't tried that feature out. I am currently using EndNote but I am sure there is a way to save my EndNote references as a BibTex file and import them that way. To be honest, I will still probably keep my full PDF library on my hard drive space simply because a good library can be very time consuming and expensive to collect and I don't want it to be managed by anyone else but me. However, this is a great way to keep a small collection of articles to read while you are travelling or away from your home base or have on hand when traveling to conferences to share with your peers. For those of you who are still fastidiously filing away paper copies of interesting articles and keeping an index with index cards, this could be a great way to start experimenting with an electronic library. I haven't been able to test any of the other features of this site, such as tagging documents or searching them since I haven't built my own library yet but I imagine you could develop some pretty neat ways of organizing your documents with with the tag feature. I think the guy(s) at CiteULike are on to something and you should try it out. But don't blame me when you spend a full day reorganizing your references!

Sunday, August 14, 2005


1 badger + 1 linux box = The Weekend

So it is time again for a (belated) weekend odd story and this week's pick is Installing linux on a dead badger. Other notable notes: I posted my 100th post this week, the honor went to the Mexican corn invasion. I hosted my 1000th visitor this week - If you were reading from Washington, D.C. using a firefox browser and you came from In The Pipeline at 3:15 this last Thursday, then you are the lucky reader! Posts are still going to be kind of spotty this week. Got a few things going on, more later.


Your quest is over Monty Python, the holy grail has been found?

The holy grail of flowering that is. This article gives a good introduction to "Florigen" and its history. I guess I am supposed to be interested in this subject by default as several researchers in the department I work in have been chasing this molecule all of their lives. Florigen is proposed to be a hormone that tells a flower that it is time to make a flower. Classic experiments have shown that florigen is a signalling compound that can be transmitted through a plant. Florigen is produced in leaves in response to being exposed to a certain time period of light. Leaves that are producing florigen can be grafted onto plants that are not flowering and cause them to flower. Furthermore, once this plant has started to flower, leaves from this plant can be grafted onto another plant and cause it to flower, even though both plants have not "seen" the correct amount of light to stimulate natural flowering. The trouble with all of these experiments is that no one has been able to nail down what that signalling compound is and so this mythical florigen compound has become a "holy grail" of some sorts to the plant biology community. However, a group of Swedish researchers have reported in Science that they have identified the gene responsible for the production of florigen. I'll be honest with you though, I have not had time to read the article so I can not comment on it myself. Plant flowering is a big concern in the PMP industry. Of course, transgenic plants that don't flower don't shed pollen that could contaminate the native flora. Added 8/26/05 - After reading the article, the authors imply that an RNA transcript is the actual signal. These transcripts are being produced in the leaf and then transported to the meristem where they are translated into a protein that promotes the expression of flowering genes. Note added in proof: The link to the Science abstract can only be viewed if you have a subscription. I'll try to work on getting another link for this article.


How to keep your web-self organized pt. 2

Thanks to Matthew Wygant for a few suggestions of other social bookmarks that I should check out from a previous post. Per his suggestion, I did check out Connotea and CiteULike and here are my thoughts: Connotea: Nature Magazine still doesn't have this website stuff down. Granted, in the last year or so they have made their website a little easier to navigate, before that, reading Nature online was atrocious. The site is still a little hard to navigate. The same can be said for Connotea. The user interface is pretty clean, which is a plus, but it is really hard to manually add a bookmark (is the add form even accesible from your login homepage?). Nature's servers are also slow, probably because of them being located 1/3 of the world away (I assume). I did run into some problems with slow loading pages with Connotea also. Of course, has some server slowdowns also. All-in-all, I would say don't even try it, well, try it, but I'll bet you won't like it after you have tried I am willing to bet that at some point, Nature will lose interest in this project (they are magazine publisher, not Google), and this project will eventually wither out. CiteULike Actually, this is a pretty neat little site. However, in order to access a paper from this site, you must have a subscription to the journal that it is located in. OK for me, I just have to work through MSUs network (I can proxy from home too). Personally, if I have a paper that I want to keep as a reference, I get a PDF copy of it on my hard drive. When coupled with a reference manager program like EndNote, you can make yourself a pretty nice little reference library. I don't want to suddenly not have access to a paper simply because the new institution I am at does not have a subscription to that journal. CiteULike is a good idea and may work for some people, but it doesn't help me.

Tuesday, August 09, 2005


Hey you, get back to work

I am beginning to notice a trend when people visit this site. It seems like I get a rush of traffic (what little there is of it) comes early in the morning or right around 5:00 in the afternoon my time. So, for those of you enjoying your first cup of coffee reading the days news on the company's dime - welcome. And for those of you catching up on the days events trying to kill that last 15 minutes before its time to punch out - enjoy the evening!


Stand down men, Science reports the Mexican corn invasion is over

According to Science Magazine News researchers report in an upcoming issue of PNAS data refuting earlier reports of contamination of native maize cultivars with transgenic genes. Researchers reported several years ago in the journal Nature that transgenes had been identified in samples of landrace maize in southern Mexico. However, this research and findings from a Mexican governmental agency could not stand up to further scientific scrutiny. In the new findings, researches were not able to find any evidence of transgenic gene contamination. More coverage of this story at the Pew Initiative on Food and Biotechnology The battle may have been lost, but the transgene-contamination wars have only just begun.


LSBC receives $15 million in equity financing, reports 2nd quarter financials

LSBC yesterday reported that they have secured $15 million in equity financing, keeping the doors open for a little while longer. According to the press release, and I think I'm going to have to read the 10-Ks or 8-Ks to really figure out what is going on, Brittany Capital Management Limited will provide the funding in exchange for shares. However, the press release title suggests this is an equity line of credit. Once again, I'm not quite sure what is going on here. Also today, LSBC released their second quarter financial results. The company reported a net loss of about $4.2 million for the quarter.

Sunday, August 07, 2005


I'll take potpourri for $500 Alex

Finally made some time for my blog, got a few things running around in my head so instead of breaking them down into separate posts, I'll give you a potpourri of postings. A nod from the big man: Thanks to Derek Lowe at In the Pipeline for a link on his blogroll. Derek was recently quoted in a Science article covering Drug Discovery. Jeeves is out of a job: In what has turned into an ongoing controversy on this blog, maybe Jeeve's passing the ole resume around wasn't that bad of an idea. In a previous post, I gave good reviews for MyJeeve's as a way to organize and bookmark your webpages of interest. However, after further review, blows it out of the water. I have been working on my list of bookmarks and you can view them here. I cain't speil too gud: Hey Google, I have a new product for your labs - Google Spellcheck. When I am writing e-mails or any other correspondance in my Firefox browser and I am unsure of a spelling for a word, I just type it into the integrated Google search bar (making sure that I have a blank tab open for the search results). If a have misspelled the word, then Google will suggest the correct spelling of the word ("Did you mean . . .") at the top of the search listing. Unfortunately, grammer is another subject. Recent PMP articles that I have ran across, nothing new, just a new spin on old stories. 8/7/05 - STLtoday - Biotech startup gets tangled in SBA rule
4/22/05 - Wired - Cave Pharming Yields Big Crops
More props to Google: Most of this site has been indexed by Google so the Google searchbar in the left-hand column of this site is working very well. Okay that's it, I've got a poster I should be working on.


Mahna Mahna

The posts have been lacking lately I know. Friday and Saturday were pretty busy days for me. Friday I was working on a project that I can hopefully share more details about later. Saturday a neighbor and I cut down a pine tree that had overgrown (literally) its stay beside my house. So, here is a very special audio weekend funny, a collection of Bushisms (click the play button on the icon below). This audio clip of Bushisms was stolen outright from Assassination Press Note Added in Proof: The third track of this compilation contains vulgar language (it's George Carlin, you kind of expect it).

Thursday, August 04, 2005


And equity for all MannKind

MannKind announced today that it had raised $175 million in a private placement of their stock. Of this, $87.5 million came from MannKind's CEO Alfred Mann with the rest coming from institutional investors. That seems like quite a chunk of cash to be coming from a private placement. Although I really don't know much about this company, I would say that this type of investor confidence is a good sign. MannKind currently trades on the NASDAQ National Market, symbol MNKD. MannKind's current leading product in development is an inhalable form of insulin, which is in Phase II clinical trials. What really struck me about this company is that in their latest quarterly reports, Selling General and Administration costs were only ~$4 million while R&D costs were $18 million. These guys are really beefing up the R&D while keeping the admin on bread and water. I know I am probably a little biased but I really like to see the majority of money being spent on product development and not on lawyer's and business developer's salaries. From the little research I have done on Alfred Mann (okay, so there are probably more than a few of you that are scoffing right now and saying "I can't believe you don't know who Alfred Mann is!"), he seems to be really good at starting companies based around solid technology and then selling them off. Looking at his humanitarian efforts, I would say he has sold these companies off at quite a profit.

Wednesday, August 03, 2005


A slow news day

Not much in the way of news, biotech or otherwise today. In the place of news, I will direct you to a webpage dedicated to the Society for Moleculture's Conference on Plant-Made Pharmaceuticals - 2005. The conference occurred in March. Unfortunately, I was not able to attend. However, the site has archived many of the PowerPoint presentations given and access to a free paper on Plant Factories. I just discovered this paper for myself on this site. I will try to get through most of the 168 pages and bring you the good parts. I'm still working on improving the reference entries and I am constantly editing old posts, so make sure and take a good look around the site.


Maybe Jeeve's job is not in jeopardy

Maybe Jeeve's shouldn't be looking for a new job. I have recently tried out MyJeeves, Ask Jeeves answer to Google's personal search. This site (after creating an account) allows you to store webpages found during searches in folders. You can also tag these sites and later search for sites by their tags. MyJeeves also allows you to save images from their image search engine. There is also apparently a toolbar that you can add to your browser that lets you save any website to your MyJeeves account. All-in-all, it is a pretty neat way to organize your bookmarks and searches on the web, as opposed to your computer. I have not tried out yet, but I have heard that is a pretty neat way to manage your bookmarks on the web also.

Tuesday, August 02, 2005


Welcome new martian readers!

I would like to welcome all the new extraterrestrial readers to this blog! I have just arranged via to have my blog feed broadcast throughout the universe. Are these guys really broadcasting my feed to all the E.T.s out there or is this just a ploy to get my e-mail address on some spam list? Oh well, I guess its worth the extra spam if it means a few extra readers. I just hope they don't start asking for CSFTB in martian, it would probably be pretty hard to find a martian language keyboard.


Reference entries - more information than you would care to know!

Some of you have started to notice a new addition to the content on this site: Reference Entries. Basically, there is a separate entry that contains all the information that I have collected pertaining to a certain subject, for instance, a company involved in PMP production. When a company is mentioned in one of my new entries, it will be linked to its reference entry where you can find more information about that company. These entries will include links to articles about or from the company, patent lists, and various information that I have may have not mentioned about anywhere else in this blog. A list of the reference entries that I have so far compiled can be found at the bottom of the left hand column of this page. These are a work in progress so check back often.


LSBC transfers to NASDAQ smallcap

A day after being granted an orphan designation for LAL, LSBC has announced that their stock listing will be transfered to the NASDAQ smallcap market. Their stock was not able to meet minimal stockholder equity levels to remain on the national market. Not big news, but still notable.


A bit of common sense for the Biochemist pt. 6

Air Force Lt. Gen. Henry A. Obering III, director of the Missile Defense Agency, summed up the progress of 93 billion dollars worth of research into a national missile defense shield with this comment:
"We have a better than zero chance of successfully intercepting, I believe, an inbound warhead," Obering said. "That confidence will improve over time."
I wonder if that data is statistically significant . . .

Monday, August 01, 2005


Mo. legislators and Chlorogen push to change SBIR rules

If you are an avid reader of this blog (and there may be about 5 of you out there now, a 500% gain from a month or so ago), then you will remember the topic of the SBIR changing their rules regarding eligibility for their grants. If a company was more than 50% backed by venture capital, then they would not be eligible for these grants. Here is a link to a San Diego Tribune article that reviews the whole story. This rule change apparently has had effects in the PMP world as outlined in this St. Louis Business Journal article. Legislative representatives from Missouri and David Duncan, CEO of Chlorogen traveled to Washington to lobby on behalf of "Save America's Biotechnology Innovative Research Act of 2005". A bill that would reverse these rules. Duncan goes on to say that their company has had to cut some programs due to these changes. In my opinion, there probably are some venture capital-back companies out there that abuse the SBIR system. However, I think many small biotech companies are going to be hurt if the current rules stay in place. A possible resolution would be to suggest that companies with a certain amount (not a certain percentage) of capital invested by venture capitalists should be excluded. Of course a million dollars goes a lot farther in some other industries than biotech so once again, a biotech company would have an arguement that are at an unfair disadvantage when compared to other industries. On a side note, there were no weekend posts here as I had the opportunity to travel back home to Kentucky this weekend. Got to see lots of friends and family and catch up on all the latest gossip.


LSBC gets orphan status for LAL

Large Scale Biology announced today that the FDA had approved an orphan drug designation for a lysosomal acid lipase product that it was developing. This drug is being exclusively licensed to LSBC through a collaboration with researchers at the Cincinatti Children's Hospital. What does this mean? If this drug makes it through the FDA approval process, then LSBC would have seven years to exclusively market their drug for treatment of the disease that is targeted for. Orphan drugs are designed for treatment of diseases that affect less than 200,000 people in the U.S. This designation gives LSBC a little more leverage when negotiating with potential development and marketing partners for this drug. This is not the first orphan drug designation that LSBC has received. Their alpha-galactosidase treatment for Fabray's disease has also received the same designation. However, no developments regarding the progress of that product has been released recently.

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