Beauty in the abstract

July 27, 2009

Currently I am doing a spot of mathematical modelling, with the highly valuable assistance of my brother who is experienced with implementing models in MatLab.

Take a look at this graph, which emerged from his efforts today:

More to come!


Selenite against mesothelioma – mechanism of action explained

July 17, 2009

Our latest paper is now freely available online as a fully formatted pdf from the Journal of Experimental and Clinical Cancer Research. As I have promised, here is a non-technical summary!

What did we study?

This work is about malignant mesothelioma, an unusual type of cancer that is caused by asbestos. It is always deadly, and current treatment extends life expectancy only by a few months. We have been working for some time on a new experimental drug called selenite – a simple, selenium-based compound.

Interestingly, mesothelioma cells come in two kinds – epithelioid and sarcomatoid. If a tumor contains sarcomatoid cells, the patient will be expected to respond worse to therapy and die sooner. We have previously found that selenite is particularly effective against sarcomatoid cells, and that it is able to induce apoptosis, the “suicide program” of the cancer cells.

In this paper, we studied the apoptosis mechanisms in both epithelioid and sarcomatoid cells, to see if there were any differences that could explain why sarcomatoid cells are more sensitive. Also, very little was known about the apoptotic response to selenite in mesothelioma cells, we wanted to see how they compare to other cells.

What did we find?

Selenite caused the activation of a number of apoptosis signaling molecules. There was a difference between sarcomatoid and epithelioid cells in the activation of two proteins in the so-called Bcl-family. Sarcomatoid cells clearly overexpressed a protein called Bax. Perhaps this is part of the reason why they are more sensitive to selenite.

There is a “master regulator” of apoptosis called p53, and we investigated it rather thoroughly. It turned out that the cells amassed lots of p53 in their nuclei after selenite treatment, but it didn’t do anything! Normally, it would regulate the DNA and determine which genes should be read. But after selenite treatment, p53 became inactive and unable to regulate gene expression.

Cells stained for p53. Brown nuclei contain much p53 that is inactive. A and C are controls, B and D are treated with selenite. Sell the full paper for details (figure 2).

Cells stained for p53. Brown nuclei contain much p53 that is inactive. A and C are controls, B and D are treated with selenite. Sell the full paper for details (figure 2).

My greatest surprise was that the apoptosis signaling network was so robust and redundant. It’s really not a well-defined linear cascade of events, but rather an interlaced network of protein interactions which depend on and modulate each other. In this paper, we found that inhibition of some of the major apoptosis-signalling proteins had virtually no effect at all on the events following selenite treatment, even though we could prove that the inhibitors were effective in themselves.

What are the implications for the future?

We hope that selenite will become a useful drug for the treatment of mesothelioma in the future. If so, part of its mechanism of action has now been established.

Check out the full paper, it’s open access!

Nilsonne, G., Olm, E., Szulkin, A., Mundt, F., Stein, A., Kocic, B., Rundlöf, A., Fernandes, A., Björnstedt, M., & Dobra, K. (2009). Phenotype-dependent apoptosis signalling in mesothelioma cells after selenite exposure Journal of Experimental & Clinical Cancer Research, 28 (1) DOI: 10.1186/1756-9966-28-92

Blatant misconduct

July 16, 2009

Publish or perish!

That’s more or less how it works, and how it probably needs to be. But sometimes it has humorous consequences. A retraction was just published in the Journal of Experimental and Clinical Cancer Research. I quote it in full (except the references):

The corresponding author submitted this article [1] to Journal of Experimental and Clinical Cancer Research although this article had been accepted and previously published by Cancer Biotherapy & Radiopharmaceuticals [2]. The article was also received and subsequently accepted and published by Nucleosides, Nucleotides and Nucleic Acids [3]. Since it has been brought to the attention of all authors that duplicate submission and publication have taken place the decision has been made to retract the article published in Journal of Experimental and Clinical Cancer Research. The authors are deeply sorry for any inconvenience this may have caused to the editorial staff and readers.

Amazingly, these people seem to have published the same article three times, but with different titles and wildly different author lists. And they would probably have gotten away with it if somebody hadn’t noticed and started making trouble over it.

Notice that their retraction contains no admission of actually doing anything wrong! They apologise for causing inconvinence by their retraction, but not for the actual multiple publication. Could it be that there are quarters where this sort of behaviour is accepted – or, perhaps, even encouraged?

I have always believed that fabrication and plagiarism are more widespread than reported. My guess is that about 15-20% of scientific papers contain deliberate fabrication or plagiarism, and at least 80% of the rest contain subtle omissions, “dressing up” of data, manipulation of images, changes of outcome criteria, and other dubious practices.

What to do?

I don’t know. Open online lab books might be a solution, although they are hard to reconcile with the need, in some cases, for secrecy. In the mean time, we must continue to doubt everything we read.

Do we need language to understand concepts?

July 14, 2009

AK doesn’t think so.

In another of his lengthy and well-researched posts, he argues that the understanding of more or less abstract concepts occurred in primates before a language based on words. This is based on a recent study of the mirror neurons in rhesus macaques. This research seems to indicate that rhesuses divide other rhesuses into two categories when the mirror neurons are activated: those within such a short distance that interaction is immediately possible, and those further away.

The post also includes an interesting reflection on how visual information is encoded in terms of a set of vectors in multidimensional space, suggesting that the same principle applies as a general form for representation in the brain.

In the process, AK also manages to discredit Plato’s idea that concepts are classes of things resembling an “ideal” concept that is by definition beyond our grasp. Instead, we construct concepts “bottom-up”, by grouping together objects and ideas that appear to us to have many similarities.

Implicit to AK’s argument is also the notion of a well-developed spatial modularity in the brain, with different areas encoding different concepts. While there is strong evidence for spatial modularity e.g. from split-brain experiments, showing that the two hemispheres can accurately identify and interact with objects independently of each other, it is very likely that at least some concepts are represented only by the concurrent activation of several areas in synchrony.

Monstrous effort to map a transcriptional network

July 8, 2009

ResearchBlogging.orgThe FANTOM consortium report in the latest issue of Nature Genetics that they have measured what happens with the entire, total, gene expression during the specific differentiation of a cell line called THP-1. Not the expression of just the 10 000 most important genes, all of them. At the same time.

Their findings are a heap of data which is probably larger than the whole body of research on medicine and biology up until the early 1900’s. If I try to say what their main finding is, I’d lean towards the interconnectedness of the signaling network. It doesn’t have one single weak spot, where you could knock out a certain gene and profoundly change the network dynamics. Knock-out of some genes had effects on many other parts of the network, but in general the system seems to be robust because of redundancy and interconnectedness. I have drawn similar conclusions in my own latest paper, though my methodology is a pair of binoculars compared to their multinational telescope.

Professor Hayashizaki of the RIKEN Omics Science Center was the general organiser of this study.

Professor Hayashizaki of the RIKEN Omics Science Center was the general organiser of this study.

My main thoughts, however, upon reading this paper were not so much about the actual research, but more about the way it was done.

  1.  With the advent of large-scale initiatives like these, we will perhaps have charted most of the “connectome” of the cell within the next decades. This is the map of the decision-making pathways. The neuroanatomy of the cell, if you wish. It has enormous potential to explain how, exactly, things go wrong in diseases such as cancer.
  2.  Biology is starting to resemble some branches of physics, where research advances through large concerted efforts. The author list of this paper is half a page long, with the authors’ affiliations taking up another half page. There will be less space for the nerdy loner scientists and greater demand for the entrepreneurial, outgoing kind of researcher in the future.
  3.  Seventeen figures and fourteen tables, and the whole methods section, have been relegated to the “supplementary material” that is only available online. Reporting on this kind of science in an 8-page article is like writing a short essay on “World War II”. I’m sure the best parts are in there, but you can’t begin to reenact it based on their descriptions. Lots of the interesting sub-analyses, which I presume must have been performed, will never see daylight. This is exactly the sort of science that benefits from the innovation of the online journal. No page limitations are needed there. Just last week, for example, I noticed that PlosOne had published a paper entitled “New Mid-Cretaceous (Latest Albian) Dinosaurs from Winton, Queensland, Australia”, which is 51 pages long and contains 40 illustrations, mainly of various bones photographed from different angles. Try getting that into a conventional journal!

Full reference:
Suzuki, H., Forrest, A., van Nimwegen, E., Daub, C., Balwierz, P., Irvine, K., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V., Bauer, D., Beckhouse, A., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P., Essack, M., Faulkner, G., Fink, J., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hörnquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., MacPherson, C., Maeda, N., Maher, C., Maqungo, M., Mar, J., Matigian, N., Matsuda, H., Mattick, J., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schönbach, C., Schwartz, A., Semple, C., Sera, M., Severin, J., Shirahige, K., Simons, C., St. Laurent, G., Suzuki, M., Suzuki, T., Sweet, M., Taft, R., Takeda, S., Takenaka, Y., Tan, K., Taylor, M., Teasdale, R., Tegnér, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., & Hayashizaki, Y. (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line Nature Genetics, 41 (5), 553-562 DOI: 10.1038/ng.375

BMC Research Notes – a place to publish the results languishing in my drawer?

July 1, 2009

I have previously addressed the unfortunate bias in the scientific literature that arises from the tendency not to publish results that are negative, or that simply show that a certain direction of scientific exploration is not very promising.

The other day, I learned about the relatively new journal BMC Research Notes. This is an open access online journal with the mission to publish:

scientifically sound research across all fields of biology and medicine, enabling authors to publish updates to previous research, software tools and databases, data sets, small-scale clinical studies, and reports of confirmatory or ‘negative’ results. Additionally the journal welcomes descriptions of incremental improvements to methods as well as short correspondence items and hypotheses.

Here is, at last, a scientific journal that will not shy away from making accessible data that will only be valuable to a small set of researchers. There have been several times when I have run across scientific questions that I know must have been addressed many times before, but the results of which haven’t been published. I also know that if my new question were known to the other scientists, they would probably have published. From this I have learned that it is difficult to predict which findings might become important in the future, and that the best course is to simply make data available.

The key question is not whether BMC Research Notes will come to be regarded as a ”dump journal”. It will, by arrogant investigators who would rather drop a project than publish it in a less prestigious publication. But their attitude is doing the scientific endeavour a great disservice by contributing to the already heavy bias of what gets published.

When you see another researcher’s publication list and it includes only top journals with the occasional Nature or Science paper like icing on the cake, the relevant response is not just “excellent!”, but also “what is this person hiding?”. Where are the great heaps of data that this scientist has generated, but that never made it into one of the top articles? Have they been forever discarded? Is that in anybody’s interest?