The new basic biology

by Cushing Memorial Library and Archives, Texas A&M
I’ve collected my data, now what do I do with it?:
[Via Bench Marks]

4-dimensional live cell imaging has gone from being a rare technique used only by cutting-edge laboratories to a mainstream method in use everywhere. While more and more labs are becoming comfortable with the equipment and protocols needed to collect imaging data, performing detailed analyses is often problematic. The application of computational image processing is still far from routine. Researchers need to determine which measurements are necessary and sufficient to characterize a system and they need to find the appropriate tools to extract these data. In Computational Image Analysis of Cellular Dynamics: A Case Study Based on Particle Tracking, Gaudenz Danuser and Khuloud Jaqaman introduce the basic concepts that make the application of computational image processing to live cell imaging data successful. As one of the featured articles in December’s issue of Cold Spring Harbor Protocols, it is freely accessible for subscribers and non-subscribers alike.

The article is adapted from the new edition of Live Cell Imaging: A Laboratory Manual, now available from CSHL Press.

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My first year as a biochemistry graduate student, one of the classes simply dealt with the analytical technologies we would be using. Things like NMR, UV spectroscopy, circular dichroism, fluorescence and X-ray crystallography. They would help us understand the properties of isolated biological molecules

This paper gives a great view of some of the new analytical approaches that examine entire living cells, not just isolated molecules. Now it looks like students will also have to get some firm understanding of image analysis. There will be some really interesting results from these sorts of technologies. The conclusions provide insights into the promise and the problems:

Computational image analysis is a complex yet increasingly central component of live cell imaging experiments. Much has to be done to make these techniques useful for cell biological investigation. First, algorithms must be transparent, not necessarily at the level of the code but in terms of their sensitivity to changing image quality and the effect that control parameters have on the output. Second, the design of imaging experiments must be tightly coupled to the design of the analysis software. All too often, images are taken without careful consideration of the subsequent analysis and are forwarded to the computer scientist to retrieve information from the images. To avoid these problems, communication must be initiated early on, and experiments must be designed with the appreciation that data acquisition and analysis are equivalent components. Third, software development and application require careful controls, as is customary for molecular cell biology experiments. This article provides a brief introduction to the ideas useful for implementing such controls. Hopefully, the cell biological literature will include a more extensive discussion of the measures taken to substantiate the validity of results from image analysis. On the other hand, manual image analysis should no longer be an option. As discussed in this article, manual analyses fall short in consistency and completeness, two essential criteria underlying the validity of a scientific model derived from image data.

While the results can be amazing, there needs to be close collaboration between the different researchers involved. Because very few people will have all the expertise necessary for success. This tight coupling of researchers with vastly different backgrounds and focus (i.e. cell biology and bioinformatics) is a relative new aspect of modern biological research.

There may be slowing of this coupling in some labs but the successful results by those that can accomplish this type of collaboration will rapidly overtake those who take a slower course. As I mentioned below, large collaborations may be a big part of the published record as we move forward.

Technorati Tags: Science, Social media

Not a word I understand but it must be important

Observation of B^0 → χ_(c0)K^(*0) and evidence for B^+ → χ_(c0)K^(*+):
[Via CaltechAUTHORS: No conditions]

Aubert, B. and Bona, M. and Karyotakis, Y. and Lees, J. P. and Poireau, V. and Prencipe, E. and Prudent, X. and Tisserand, V. and Garra-Tico, J. and Grauges, E. and Lopez, L. and Palano, A. and Pappagallo, M. and Eigen, G. and Stugu, B. and Sun, L. and Abrams, G. S. and Battaglia, M. and Brown, D. N. and Cahn, R. N. and Jacobsen, R. G. and Kerth, L. T. and Kolomensky, Yu. G. and Lynch, G. and Osipenkov, I. L. and Ronan, M. T. and Tackmann, K. and Tanabe, T. and Hawkes, C. M. and Soni, N. and Watson, A. T. and Koch, H. and Schroeder, T. and Walker, D. and Asgeirsson, D. J. and Fulsom, B. G. and Hearty, C. and Mattison, T. S. and McKenna, J. A. and Barrett, M. and Khan, A. and Blinov, V. E. and Bukin, A. D. and Buzykaev, A. R. and Druzhinin, V. P. and Golubev, V. B. and Onuchin, A. P. and Serednyakov, S. I. and Skovpen, Yu. I. and Solodov, E. P. and Todyshev, K. Yu. and Bondioli, M. and Curry, S. and Eschrich, I. and Kirkby, D. and Lankford, A. J. and Lund, P. and Mandelkern, M. and Martin, E. C. and Stoker, D. P. and Abachi, S. and Buchanan, C. and Gary, J. W. and Liu, F. and Long, O. and Shen, B. C. and Vitug, G. M. and Yasin, Z. and Zhang, L. and Sharma, V. and Campagnari, C. and Hong, T. M. and Kovalskyi, D. and Mazur, M. A. and Richman, J. D. and Beck, T. W. and Eisner, A. M. and Flacco, C. J. and Heusch, C. A. and Kroseberg, J. and Lockman, W. S. and Martinez, A. J. and Schalk, T. and Schumm, B. A. and Seiden, A. and Wilson, M. G. and Winstrom, L. O. and Cheng, C. H. and Doll, D. A. and Echenard, B. and Fang, F. and Hitlin, D. G. and Narsky, I. and Piatenko, T. and Porter, F. C. and Andreassen, R. and Mancinelli, G. and Meadows, B. T. and Mishra, K. and Sokoloff, M. D. and Bloom, P. C. and Ford, W. T. and Gaz, A. and Hirschauer, J. F. and Nagel, M. and Nauenberg, U. and Smith, J. G. and Ulmer, K. A. and Wagner, S. R. and Ayad, R. and Soffer, A. and Toki, W. H. and Wilson, R. J. and Altenburg, D. 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B. and Nicholson, H. and De-Nardo, G. and Lista, L. and Monorchio, D. and Onorato, G. and Sciacca, C. and Raven, G. and Snoek, H. L. and Jessop, C. P. and Knoepfel, K. J. and LoSecco, J. M. and Wang, W. F. and Benelli, G. and Corwin, L. A. and Honscheid, K. and Kagan, H. and Kass, R. and Morris, J. P. and Rahimi, A. M. and Regensburger, J. J. and Sekula, S. J. and Wong, Q. K. and Blount, N. L. and Brau, J. and Frey, R. and Igonkina, O. and Kolb, J. A. and Lu, M. and Rahmat, R. and Sinev, N. B. and Strom, D. and Strube, J. and Torrence, E. and Castelli, G. and Gagliardi, N. and Margoni, M. and Morandin, M. and Posocco, M. and Rotondo, M. and Simonetto, F. and Stroili, R. and Voci, C. and del-Amo-Sanchez, P. and Ben-Haim, E. and Briand, H. and Calderini, G. and Chauveau, J. and David, P. and Del-Buono, L. and Hamon, O. and Leruste, Ph. and Ocariz, J. and Perez, A. and Prendki, J. and Sitt, S. and Gladney, L. and Biasini, M. and Covarelli, R. and Manoni, E. and Angelini, C. and Batignani, G. and Bettarini, S. and Carpinelli, M. and Cervelli, A. and Forti, F. and Giorgi, M. A. and Lusiani, A. and Marchiori, G. and Morganti, M. and Neri, N. and Paoloni, E. and Rizzo, G. and Walsh, J. J. and Lopes-Pegna, D. and Lu, C. and Olsen, J. and Smith, A. J. S. and Telnov, A. V. and Anulli, F. and Baracchini, E. and Cavoto, G. and del-Re, D. and Di-Marco, E. and Faccini, R. and Ferrarotto, F. and Ferroni, F. and Gaspero, M. and Jackson, P. D. and Li-Gioi, L. and Mazzoni, M. A. and Morganti, S. and Piredda, G. and Polci, F. and Renga, F. and Voena, C. and Ebert, M. and Hartmann, T. and Schröder, H. and Waldi, R. and Adye, T. and Franek, B. and Olaiya, E. O. and Wilson, F. F. and Emery, S. and Escalier, M. and Esteve, L. and Ganzhur, S. F. and Hamel-de-Monchenault, G. and Kozanecki, W. and Vasseur, G. and Yèche, Ch. and Zito, M. and Chen, X. R. and Liu, H. and Park, W. and Purohit, M. V. and White, R. M. and WIlson, J. R. and Allen, M. T. and Aston, D. and Bartoldus, R. and Bechtle, P. and Benitez, J. F. and Cenci, R. and Coleman, J. P. and Convery, M. R. and Dingfelder, J. C. and Dorfan, J. and Dubois-Felsmann, G. P. and Dunwoodie, W. and Field, R. C. and Gabareen, A. M. and Gowdy, S. J. and Graham, M. T. and Grenier, P. and Hast, C. and Innes, W. R. and Kaminski, J. and Kelsey, M. H. and Kim, H. and Kim, P. and Kocian, M. L. and Leith, D. W. G. S. and Li, S. and Lindquist, B. and Luitz, S. and Luth, V. and Lynch, H. L. and MacFarlane, D. B. and Marsiske, H. and Messner, R. and Muller, D. R. and Neal, H. and Nelson, S. and O’Grady, C. P. and Ofte, I. and Perazzo, A. and Perl, M. and Ratcliff, B. N. and Roodman, A. and Salnikov, A. A. and Schindler, R. H. and Schwiening, J. and Snyder, A. and Su, D. and Sullivan, M. K. and Suzuki, K. and Swain, S. K. and Thompson, J. M. and Va’vra, J. and Wagner, A. P. and Weaver, M. and West, C. A. and Wisniewski, W. J. and Wittgen, M. and Wright, D. H. and Wulsin, H. W. and Yarritu, A. K. and Yi, K. and Young, C. C. and Ziegler, V. and Burchat, P. R. and Edwards, A. J. and Majewski, S. A. and Miyashita, T. S. and Petersen, B. A. and Wilden, L. and Ahmed, S. and Alam, M. S. and Ernst, J. A. and Pan, B. and Saeed, M. A. and Zain, S. B. and Spanier, S. M. and Wogsland, B. J. and Eckmann, R. and Ritchie, J. L. and Ruland, A. M. and Schilling, C. J. and Schwitters, R. F. and Drummond, B. W. and Izen, J. M. and Lou, X. C. and Bianchi, F. and Gamba, D. and Pelliccioni, M. and Bomben, M. and Bosisio, L. and Cartaro, C. and Della-Ricca, G. and Lanceri, L. and Vitale, L. and Azzolini, V. and Lopez-March, N. and Martinez-Vidal, F. and Milanes, D. A. and Oyanguren, A. and Albert, J. and Banerjee, Sw. and Bhuyan, B. and Choi, H. H. F. and Hamano, K. and Kowalewski, R. and Lewczuk, M. J. and Nugent, I. M. and Roney, J. M. and Sobie, R. J. and Gershon, T. J. and Harrison, P. F. and Ilic, J. and Latham, T. E. and Mohanty, G. B. and Band, H. R. and Chen, X. and Dasu, S. and Flood, K. T. and Pan, Y. and Pierini, M. and Prepost, R. and Vuosalo, C. O. and Wu, S. L. (2008) Observation of B^0 → χ_(c0)K^(*0) and evidence for B^+ → χ_(c0)K^(*+). Physical Review D, 78 (9). Art. No. 091101. ISSN 0556-2821 http://resolver.caltech.edu/CaltechAUTHORS:20091208-114007039

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For a paper to have so many authors, it must something really useful or important. I think I have written papers with fewer characters than in this list of authors.

I wonder how they figured out who is first author. Because most indexing services shut off the author list after 190 or so. Thus being last author really gets no traction as it seldom shows up in any manner. On papers with a large number of authors, first is best.

By the way, here is the abstract:

We present the observation of the decay B^0 → χ_(c0)K^(*0) as well as evidence of B^+ → χ_(c0)K^(*+), with an 8.9 and a 3.6 standard deviation significance, respectively, using a data sample of 454×10^6 Υ(4S) → B[overline B] decays collected with the BABAR detector at the PEP-II B meson factory located at the Stanford Linear Accelerator Center (SLAC). The measured branching fractions are [script B](B^0 → Χ_(c0)K^(*0))=(1.7±0.3±0.2)×10^(-4) and [script B](B^+ → Χ_(c0)K^(*+))=(1.4±0.5±0.2)×10^(-4), where the first quoted errors are statistical and the second are systematic. We obtain a branching fraction upper limit of [script B](B^+ → Χ_(c0)K^(*+))<2.1×10^(-4) at the 90% confidence level.

Sometimes I am glad I’m a biochemist.

Technorati Tags: Science

Let’s make tobacco good for people

by SuperFantastic
Cancer, melanoma genomes: A story we missed
[Via Knight Science Journalism Tracker]

I missed an important story last week, and so did most of the English-language news media on both sides of the Atlantic.

According to a story by Catharine Paddock for Medical News Today, researchers in England have sequenced the genomes of melanoma and small-cell lung cancer.

Thanks to Victor McElheny, former director of the Knight Fellowhips at MIT, for calling my attention to the story, which was based on research published in Nature last week.

“Both papers came largely from the Sanger Institute outside Cambridge, and got big play in London, little so far over here,” Vic wrote in an email. I’d challenge him on that a bit–I didn’t find a whole lot of play in England, either, although he’s right, it got more attention there than here.

This seems to be a very important development in cancer research, and it should have been front-page news. If you don’t agree, consider one interesting implication of the lung-cancer genome. According to Paddock’s story, the researchers found 23,000 mutation in the lung cancer cells. That works out to about one mutation per pack of cigarettes.

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While the idea that smoking is bad really breaks no new frontiers, having a direct insight into the mutations that can be caused in the lung by smoking is really interesting. This gives us a much better idea of just what happens to produce lung cancer. It is astounding just how many mutations smoking produces.

Yep, we have a legal business that can supply a product to a consumer that appears to cause one mutation every twenty times it is used. Those mutations are random in different lung cells but it may only take a relative handful fo create an immortal cell that becomes a killer.

What other product do we allow that has as high a mutation rate? Why in the world is tobacco allowed for sale at all? I’d feel better if someone developed tobacco for use in biofuels? Then everyone in the business could stay happy but no more people would be killed. It would not displace any food crops and provide farmers with good revenue.

Tobacco plant seeds seem to be an interesting possibility. One report states that “compared with other biofuel crops, tobacco is cheaper to grow and produces bigger yields, according to Fogher. For every hectare (2.5 acres) on which it is grown, two tonnes of oil can be extracted from its seeds, about twice as much as rape or soy.”

It looks like the rest of the plant may have some uses in biofuel generation.

[Listening to: He Walked All The Way Home from the album "Midnight Storm" by Blue Highway]