tirsdag 20. desember 2011

MULTI-AWARD WINNING YOUNG CAST SCIENTIST


This week, Hanne Røberg-Larsen (SFI-CAST) was recently awarded the GE Healthcare Young Scientist award, for her Master thesis entitled “Determination of oxysterols in cancer stem cells using on-line automated filtration and filter-flush solid phase extraction liquid chromatography tandem mass spectrometry”.  In addition to this achievement, Hanne has had a good year; In January, she was awarded the Water Innovation Prize, for her lecture on analysis of oxysterols using “AFFL-SPE-LC”, a technique that she and two other co-inventors (Kristin Svendsen and supervisor Steven Ray Wilson) have applied for a patent together with Inven2. Also, she is second author of a paper that was published this summer, and first author on a paper recently submitted.  Hanne was supervised by Steven Ray Wilson, Elsa Lundanes, Tyge Greibrokk and Stefan Krauss.

Way to go!!!

torsdag 6. oktober 2011

No more clogged columns: AFFL-SPE-LC

Automatic filtration and filter flush for robust online solid-phase extraction liquid chromatography

Kristin O. Svendsen, Hanne R. Larsen, Siri A. Pedersen, Ida Brenna, Elsa Lundanes, Steven R. Wilson

J. Sep. Sci. DOI: 10.1002/jssc.201100553

Abstract

Online solid-phase extraction-liquid chromatography (SPE-LC) with microbore or capillary columns was significantly improved regarding robustness, as an easily installed automatic filtration and filter flushing (AFFL) procedure was added to avoid system clogging. Specifically, an injected sample is passed through a union containing a stainless steel filter prior to SPE trapping. The filter stops any particulate matter from reaching the SPE. When the SPE is subsequently connected to the LC column by column switching, a separate pump backflushes the filter-union, removing the particulate matter off the filter after each injection. This feature greatly reduced backpressure buildup over the entire system.

tirsdag 23. august 2011

Our method for fast, low pressure nano LC-MS

High efficiency, high temperature separations on silica based monolithic columns

Magnus Rogeberg, Steven Ray Wilson, Helle Malerod, Elsa Lundanes, Nobuo Tanaka and Tyge Greibrokk

The effect of temperature on separation using reversed-phase monolithic columns has been investigated using a nano-LC pumping system for gradient separation of tryptic peptides with MS detection. A goal of this study was to find optimal conditions for high-speed separations. The chromatographic performance of the columns was evaluated by peak capacity and peak capacity per time unit. Column lengths ranging from 20 to 100 cm and intermediate gradient times from 10 to 30 minutes were investigated to assess the potential of these columns in a final step separation, e.g. after fractionation or specific sample preparation. Flow rates from 250 to 2000 nL/min and temperatures from 20 to 120 °C were investigated. Temperature had a significant effect on fast separations, and a flow rate of 2000 nL/min and a temperature of 80 °C gave the highest peak capacity per time unit. These settings produced 70% more protein identifications in a biological sample compared to a conventional packed column. Alternatively, an equal amount of protein identifications was obtained with a 40% reduction in run time compared to the conventional packed column. 

torsdag 16. juni 2011

Open access to our latest paper:

A Novel Synthetic Smoothened Antagonist Transiently Inhibits Pancreatic Adenocarcinoma Xenografts in a Mouse Model

Martin F. Strand, Steven R. Wilson, Jennifer L. Dembinski, Daniel D. Holsworth, Alexander Khvat, Ilya Okun, Dirk Petersen, Stefan Krauss

Using Shh-Light II (Shh-L2) and alkaline phosphatase (AP) based screening formats on a “focused diversity” library we identified a novel small molecule inhibitor of the Hh pathway, MS-0022 (2-bromo-N-(4-(8-methylimidazo[1,2-a]pyridin-2-yl)phenyl)benzamide). MS-0022 showed effective Hh signaling pathway inhibition at the level of SMO in the low nM range, and Hh pathway inhibition downstream of Suppressor of fused (SUFU) in the low µM range. MS-0022 reduced growth in the tumor cell lines PANC-1, SUIT-2, PC-3 and FEMX in vitro. MS-0022 treatment led to a transient delay of tumor growth that correlated with a reduction of stromal Gli1 levels in SUIT-2 xenografts in vivo.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019904

 

 

 

 

 

 

onsdag 25. mai 2011

"Likes", "comments" and "pokes" in scientific litterature?

I am a big user of Facebook. I use it to keep in touch, comment on stuff I am doing and...Oh come on, you're on FB too. But one thing that is also fun is to comment on what other people are up to. Maybe press "like" when someone has gotten married (congratulations Hanna!). Actually, I have gotten so used to being able to express myself in this blink of a second, that I sometimes wish other parts of my life was like this. For instance, in scientific literature.

When I read a paper and I see something is good, I wish I could press "like". Ok, I know this can sound a bit corny. But what if a doctor reads a report in a medical journal, and this helps her properly diagnose a patient, wouldn't it be a good idea for the doctor to express this opinion, without having to write a paper, and cite the work months later? Not everybody publishes a paper every day either. And lets say a second doctor saw the "like", and say "hmm, if this doctor likes this approach to treatment, maybe this could be worth a closer read to regarding my patient?"

Another thing that is appealing to me, is being able to comment on a paper online. Some journals already do this, like PLoS ONE (stay tuned for a paper by our group in this journal). This gives an opportunity to express one's opinion, although in this forum, the opinion is of course in a more scientific form. But it' s still more informal, and feels more dynamic. It could also potentially give the author the possibility to add quick corrections etc. before a more formal action is taken (i.e. submitting an erratum).
This can also be potentially used to quickly point out obvious wrongdoings by others. This can be especially important if your work, maybe life work, is under attack, without proper investigation or due to a misunderstanding (reviewers aren't perfect!). Submitting a letter to the journal, pointing out an obvious mistake, can take weeks/months, and the delay can potentially hurt your career for a long time! I was recently at a talk where the speaker felt the need to extensively defend his work from the conclusions of a weak paper (where is the "dislike" button?).

On the other hand, if you are the author of many papers, it would be impossible to address all comments made on your work, including unjust ones. But I guess this is the world we are heading towards anyway, as anyone can express their tired minds without revision or rejection, such as in a blog like this one.

I decided not to elaborate on how to poke a scientist.

lørdag 7. mai 2011

Scientific papers are read by non-experts too

Summary: Don't use the internet for self-diagnosis. If you want to learn more about your condition after consultation with a doctor, I suggest you try to find it in proper scientific literature. To authors: Remember that many non-experts read your abstracts, and can potentially lead people dangerously astray.

Have you ever had an itch on your arm, a headache or a weird dream and googled it find out whats going on? Take a look when you google itch + arm: forums, commercials, and pop-ups fill the empty space of the even more empty advice. As a result, you can go crazy self-diagnosing yourself on the internet. For example,  I had a rash some years ago, and I googled rash + lower arms. The stuff that popped up made me fear that I had caught a terrible disease and would soon not be able to leave the house due to my future hideousness. I would definitely not be able to eat pasta. Luckily I talked to a skin doctor who pointed out that all the mosquitoes that were biting me the day before might have had something to do with it. I'm fine now!

Of course, this is just everyday post-90's stuff that nerve-wrecks like me get mixed up in. But how does web-surfing fit in when there is something wrong with you? And how do scientific papers fit in to all this?

If something isn't right, there are fair chances are that your doctor will pick it up. But sometimes you will feel the need to do some research on your own. For instance, my Dad was about to have back surgery, and had found so much relevant information online that he could have a very meaningful discussion with his surgeon, which likely improved the patient-doctor relation and maybe even the quality of the work.

But finding relevant info is not easy (as my itchy googling examplifies). Relevant, scientific info, is often reported in scientific literature, in big medical journals like The Lancet, NEJM, or hundreds of other "smaller" ones. The reason you can trust the quality of such sources are that the work is critically reviewed by experts, and fake reports are seldom and very often caught by the experts who read the journal.

But remember that these papers will most often not fit your (likely common) case; It is seldom that top journals report curing an itch by not scratching, a little cream and just waiting it out. Therefore, this exercise might just add paranoia to your worried, scratchy self. But, like in my Dad's case, having checked some serious sources might keep your doctor on the ball.

However, to some, searching scientific literature have had more damaging consequences than a little edginess before your doctor's appointment. For example, there are a lot of courageous people who are fighting cancer, and will do whatever it takes to get well. I have seen internet forums where fighters of cancer discuss prototype drugs that have been reported in scientific literature, and how they have spent tens of thousands of dollars on self-treatment using prototype drugs. However, it is extremely important to point out that, even though a synthetic or natural compound shows promise in the lab, it is definitely not considered to be safe, at least before an FDA approval. For example, scientific literature describes the Hedgehog inhibitor cyclopamine as a prototype which several drugs are based upon, but can be extremely harmful to use, especially if one is pregnant. There are unfortunately several examples of infants who have been born with severe deformations because of the mother's intake of cyclopamine during pregnancy.

Before internet, the reading of scientific material by non-experts was not a "problem", because they did not have access to the papers or the paper's abstract. But now that everyone has this access to a certain degree, I believe it would often be wise to include a sentence or two in the abstract, describing to the non-expert reader what the practical relevance of the study is, and eventually a guidance/warning regarding the use and interpretation of the information. For example, the description of a rare study of itching should emphasize the rarity. A description of a pathway inhibitor such as cyclopamine (which is relatively easy to get a hold of) could state that the compound is dangerous to humans in its present form.

Of course, a lot of scientist's would say, "give me a break", but guess what? People read your work.

tirsdag 8. mars 2011

Quantitative Proteomics: Berndt Thiede's group

Thanks to the group for teaching me their isobaric labelling technique for quantitative proteomics this week. Will be great to use it for our cancer stem cell research as it is quick and relatively cheap.  It will also be nice to check out their software package, IsobariQ.

onsdag 2. mars 2011

Interview on Norwegian radio on doping analysis

Here is a link to an interview with me this morning on Norwegian radio on doping analysis.

In addition I would like to recommend Prof. Peter Hemmersbach's paper "History of Mass Spectrometry at the Olymic Games".

søndag 13. februar 2011

Waters company Innovation prize

Congrats to Hanne Røberg Larsen for her award-winning presentation at the Hafjell mass spectrometry meeting!
The subject was a novel liquid chromatography column switching system that she uses for analysis of Hedgehog active oxysterols. She took home 150, 000 NOK (about 25,000 American Dollars) in Waters equipment.
We are currently typing up manuscripts describing the instrumentation and application.
Co-authors from our group are Kristin Opsal, Steven Ray Wilson, Siri Altern Pedersen, Ida Brenna.


I am currently working on a scheme to clone these excellent researchers.



tirsdag 1. februar 2011

HILIC and temperature: explanation of inverse Van´t Hoff plots

Hydrophilic Interaction Chromatography (HILIC) of nucleoside triphosphates with temperature as a separation parameter
Elin Johnsen, Steven Ray Wilson, Ingvild Odsbu, Andreas Krapp, Helle Malerod, Kirsten Skarstad and Elsa Lundanes
Journal of Chromatography A, (ahead of print):
doi:10.1016/j.chroma.2011.01.066

Eight deoxynucleoside triphosphates (dNTPs) and nucleoside triphosphates (NTPs): ATP, CTP, GTP, UTP, dATP, dCTP, dGTP and dTTP, were separated with two 15 cm ZIC-pHILIC columns coupled in series, using LC-UV instrumentation. The polymer-based ZIC-pHILIC column gave significantly better separations and peak shape than a silica-based ZIC-HILIC column. Better separations were obtained with isocratic elution as compared to gradient elution. The temperature markedly affected the selectivity and could be used to fine tune separation. The analysis time was also affected by temperature, as lower temperatures surprisingly reduced the retention of the nucleotides. dNTP/NTP standards could be separated in 35 minutes with a flow rate of 200 μL/minute. In Escherichia coli cell culture samples dNTP/NTPs could be selectively separated in 70 minutes using a flow rate of 100 μL/minute.

mandag 3. januar 2011

Cancer Research; 71(1); 197–205. 2010

Novel Synthetic Antagonists of Canonical Wnt Signaling Inhibit Colorectal Cancer Cell Growth 

Jo Waaler, Ondrej Machon, Jens Peter von Kries, Steven Ray Wilson, Elsa Lundenes, Doris Wedlich, Dietmar Gradl, Jan Erik Paulsen, Olga Machonova, Jennifer L. Dembinski, Huyen Dinh, Stefan Krauss

Canonical Wnt signaling is deregulated in several types of human cancer where it plays a central role in tumor cell growth and progression. Here we report the identification of 2 new small molecules that specifically inhibit canonical Wnt pathway at the level of the destruction complex. Specificity was verified in various cellular reporter systems, a Xenopus double-axis formation assay and a gene expression profile analysis. In human colorectal cancer (CRC) cells, the new compounds JW67 and JW74 rapidly reduced active β-catenin with a subsequent downregulation of Wnt target genes, including AXIN2, SP5, and NKD1. Notably, AXIN2 protein levels were strongly increased after compound exposure. Long-term treatment with JW74 inhibited the growth of tumor cells in both a mouse xenograft model of CRC and in ApcMin mice (multiple intestinal neoplasia, Min). Our findings rationalize further preclinical and clinical evaluation of these new compounds as novel modalities for cancer treatment.

http://cancerres.aacrjournals.org/content/71/1/197.abstract