20 posts · 31,035 views
The Scientific Activist is your source for news and commentary on science, politics, and the exciting areas where these dynamic fields clash. Recognizing science as a path toward understanding nature, distinct from corporate and other applications, The Scientific Activist opens up a new dialogue on the proper role of science in an ever changing society.
Nick Anthis
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- April 7, 2010
- 09:23 AM
- 1,274 views
Anaerobic Animals Discovered on Sea Floor
by Nick Anthis in The Scientific Activist
This is pretty neat: scientists have apparently discovered the first example of truly anaerobic animal life (i.e. an animal that can survive in the absence of oxygen). This isn't some sort of fuzzy critter, though; instead, these are tiny (less than 1 mm in length) animals that were found on the floor of the Mediterranean Sea. Significantly, these animals lack mitochondria, the sub-cellular organelles where oxygen is employed to produce ATP in aerobic (oxygen-dependent) life.
You can check out ........ Read more »
Danovaro, R., Dell'Anno, A., Pusceddu, A., Gambi, C., Heiner, I., & Kristensen, R. (2010) The first metazoa living in permanently anoxic conditions. BMC Biology, 8(1), 30. DOI: 10.1186/1741-7007-8-30
Levin, L. (2010) Anaerobic Metazoans: No longer an oxymoron. BMC Biology, 8(1), 31. DOI: 10.1186/1741-7007-8-31
Mentel, M., & Martin, W. (2010) Anaerobic animals from an ancient, anoxic ecological niche. BMC Biology, 8(1), 32. DOI: 10.1186/1741-7007-8-32
- February 21, 2010
- 07:08 PM
- 1,405 views
More on the M2 Channel Structure Controversy
by Nick Anthis in The Scientific Activist
Last year, I wrote about a scientific controversy over the structure of the influenza M2 proton channel, particularly over the protein's binding site for adamantane type anti-flu drugs. The Schnell/Chou model, based on solution NMR, had the drug binding to the outside of the channel, within the membrane (at a 4:1 drug:protein ratio). On the other hand, the Stouffer/DeGrado model had the drug binding inside the channel (1:1 ratio), based on X-ray crystallography studies.
A new study was recently........ Read more »
Cady, S., Schmidt-Rohr, K., Wang, J., Soto, C., DeGrado, W., & Hong, M. (2010) Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature, 463(7281), 689-692. DOI: 10.1038/nature08722
- November 12, 2009
- 07:39 AM
- 1,447 views
On Mimicking Phosphotyrosine
by Nick Anthis in The Scientific Activist
When doing science, there's generally one totally optimal way of performing an experiment. But, there may also be several other less optimal means of gathering similar data, and one of those may be much more feasible than the totally optimal method. As a scientist, you have to determine whether this other method is sufficient, or whether it's necessary to expend the extra effort and/or resources on the more difficult method. Sometimes it's totally fine to take the simpler approach (and this will........ Read more »
Anthis, N., Haling, J., Oxley, C., Memo, M., Wegener, K., Lim, C., Ginsberg, M., & Campbell, I. (2009) integrin tyrosine phosphorylation is a conserved mechanism for regulating talin-induced integrin activation. Journal of Biological Chemistry. DOI: 10.1074/jbc.M109.061275
- October 20, 2009
- 08:39 AM
- 1,399 views
Two New Papers on Integrin Activation
by Nick Anthis in The Scientific Activist
Just as I was in the process of finishing my doctorate in August, I found out that my first first-author paper had been accepted for publication by The EMBO Journal. This was good news, because we were reporting some pretty fundamental findings in a relatively saturated field, and one of our competitors had managed to successfully stall the acceptance of this paper since March. Up until that point, witnessing this happen firsthand had been a somewhat frustrating and disillusioning experience for........ Read more »
Anthis NJ, Wegener KL, Ye F, Kim C, Goult BT, Lowe ED, Vakonakis I, Bate N, Critchley DR, Ginsberg MH.... (2009) The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. The EMBO journal. PMID: 19798053
Goult BT, Bouaouina M, Harburger DS, Bate N, Patel B, Anthis NJ, Campbell ID, Calderwood DA, Barsukov IL, Roberts GC.... (2009) The Structure of the N-Terminus of Kindlin-1: A Domain Important for alphaIIbbeta3 Integrin Activation. Journal of molecular biology. PMID: 19804783
- October 20, 2009
- 12:46 AM
- 1,557 views
New Interactive 3D Molecular Images in Scientific Articles
by Nick Anthis in The Scientific Activist
Late last week, I received emails from two journals (The Journal of Biological Chemistry (JBC) and PLoS ONE) indicating that they are now incorporating interactive 3D images of molecular structures in their papers. The atomic coordinates of all published biomolecular structures have been available for some time at the Protein Data Bank. However, making sense of something as complex as a protein structure can require quite a bit of analysis. So, scientists go through great pains to represent impo........ Read more »
Kumar, P., Vahedi-Faridi, A., Saenger, W., Merino, E., Lopez de Castro, J., Uchanska-Ziegler, B., & Ziegler, A. (2009) Structural Basis for T Cell Alloreactivity among Three HLA-B14 and HLA-B27 Antigens. Journal of Biological Chemistry, 284(43), 29784-29797. DOI: 10.1074/jbc.M109.038497
Raush, E., Totrov, M., Marsden, B., & Abagyan, R. (2009) A New Method for Publishing Three-Dimensional Content. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007394
- May 1, 2009
- 07:49 AM
- 1,640 views
Why Swine Flu Is Resistant to Adamantane Drugs
by Nick Anthis in The Scientific Activist
On Wednesday, the CDC reported that influenza A H1N1 viruses from 13 patients with confirmed diagnoses of swine flu had been tested for resistance to a variety of antiviral drugs. The good news was that all of the isolates were susceptible to the antiviral drugs oseltamivir (Tamiflu) and zanamivir (Relenza). However, all 13 were resistant to adamantane-based drugs (amantadine and rimantadine). Resistance to adamantane drugs (which were developed first) has actually become quite widespread amo........ Read more »
Schnell, J., & Chou, J. (2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 451(7178), 591-595. DOI: 10.1038/nature06531
Pielak, R., Schnell, J., & Chou, J. (2009) Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0902548106
Stouffer, A., Acharya, R., Salom, D., Levine, A., Di Costanzo, L., Soto, C., Tereshko, V., Nanda, V., Stayrook, S., & DeGrado, W. (2008) Structural basis for the function and inhibition of an influenza virus proton channel. Nature, 451(7178), 596-599. DOI: 10.1038/nature06528
Stouffer, A., Ma, C., Cristian, L., Ohigashi, Y., Lamb, R., Lear, J., Pinto, L., & DeGrado, W. (2008) The Interplay of Functional Tuning, Drug Resistance, and Thermodynamic Stability in the Evolution of the M2 Proton Channel from the Influenza A Virus. Structure, 16(7), 1067-1076. DOI: 10.1016/j.str.2008.04.011
- April 11, 2009
- 02:12 PM
- 1,906 views
Download Counts Predict Future Impact of Scientific Papers
by Nick Anthis in The Scientific Activist
The gold standard for measuring the impact of a scientific paper is counting the number of other papers that cite that paper. However, due to the drawn-out nature of the scientific publication process, there is a lag of at least a year or so after a paper is published before citations to it even begin to appear in the literature, and at least a few years are generally needed to get an accurate measure of how heavily cited an article will actually be. It's reasonable to ask, then, if there exists........ Read more »
Brody, T., Harnad, S., & Carr, L. (2006) Earlier Web usage statistics as predictors of later citation impact. Journal of the American Society for Information Science and Technology, 57(8), 1060-1072. DOI: 10.1002/asi.20373
(none). (2008) Deciphering citation statistics. Nature Neuroscience, 11(6), 619-619. DOI: 10.1038/nn0608-619
Perneger, T. (2004) Relation between online "hit counts" and subsequent citations: prospective study of research papers in the BMJ. BMJ, 329(7465), 546-547. DOI: 10.1136/bmj.329.7465.546
Watson, A. (2009) Comparing citations and downloads for individual articles. Journal of Vision, 9(4), 1-4. DOI: 10.1167/9.4.i
- April 2, 2009
- 07:01 AM
- 1,386 views
THC Gives Cancer Cells the Munchies Too
by Nick Anthis in The Scientific Activist
Through the results of widespread experimentation of the... well... let's say "non-scientific" variety, it's pretty well known that marijuana has the side effect of making the user very hungry. This is one of the many physiological effects of the active ingredient THC (Δ9-tetrahydrocannabinol). More relevantly, however, THC and other cannabinoids are actively being investigated for various useful clinical purposes, including the treatment of cancer through the inhibition of tumor growth.
........ Read more »
Salazar, M., Carracedo, A., Salanueva, I., Hernández-Tiedra, S., Lorente, M., Egia, A., Vázquez, P., Blázquez, C., Torres, S., García, S.... (2009) Cannabinoid action induces autophagy-mediated cell death through stimulation of ER stress in human glioma cells. Journal of Clinical Investigation. DOI: 10.1172/JCI37948
- March 23, 2009
- 04:48 PM
- 1,764 views
Fine-Tuning Cell Adhesiveness
by Nick Anthis in The Scientific Activist
Cells in higher organisms exist in a dynamic environment, requiring the ability to alternately grasp and disengage from the three-dimensional web of their surroundings. One family of proteins in particular, the integrins, plays a key role in this process by acting as the hands of the cell. Spanning the cell membrane, they link the extracellular matrix to the cell's internal cytoskeleton. Integrins are especially interesting, though, because the cell uses them to uniquely pass signals in both ........ Read more »
Goult, B., Bate, N., Anthis, N., Wegener, K., Gingras, A., Patel, B., Barsukov, I., Campbell, I., Roberts, G., & Critchley, D. (2009) The structure of an interdomain complex which regulates talin activity. Journal of Biological Chemistry. DOI: 10.1074/jbc.M900078200
- September 24, 2008
- 08:36 PM
- 1,825 views
Feedback on "Advancing Science Through Conversations"
by Nick Anthis in The Scientific Activist
Since our paper on the role of blogs in academia was published earlier this week, we've received quite a bit of feedback from the across blogosphere. Befittingly, the authors of the paper have contributed to this, as Tara gave her thoughts on her blog, I gave mine on my blog (Shelley has been busy traveling for interviews, so she hasn't had a chance to weigh in yet), and we published a list of acknowledgments. (I'd also like to thank our respective universities' press offices for their outreach........ Read more »
Shelley A. Batts, Nicholas J. Anthis, & Tara C. Smith. (2008) Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy. PLoS Biology, 6(9). DOI: 10.1371/journal.pbio.0060240
- September 22, 2008
- 09:47 PM
- 976 views
Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy
by Nick Anthis in The Scientific Activist
Just over a year ago, I joined fellow science bloggers Shelley Batts (Of Two Minds) and Tara Smith (Aetiology) in setting out to catalogue the accomplishments--and pitfalls--of the scientific blogosphere and to explain why people should pay attention. In a sense, we wanted to say "We are the science bloggers; hear us roar!" And, in order to make our case, we drew from the collective experience of our fellow science bloggers, far and wide, asking how blogging had affected their work, their care........ Read more »
Shelley A. Batts, Nicholas J. Anthis, & Tara C. Smith. (2008) Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy. PLoS Biology, 6(9). DOI: 10.1371/journal.pbio.0060240
J WILKINS. (2008) The roles, reasons and restrictions of science blogs. Trends in Ecology , 23(8), 411-413. DOI: 10.1016/j.tree.2008.05.004
L Bonetta. (2007) Scientists Enter the Blogosphere. Cell, 129(3), 443-445. DOI: 10.1016/j.cell.2007.04.032
A. Ashlin and R.J. Ladle. (2006) Environmental Science Adrift in the Blogosphere. Science, 312(5771), 201-201. DOI: 10.1126/science.1124197
- July 31, 2008
- 09:01 AM
- 1,646 views
Water on Mars, Part 2
by Nick Anthis in The Scientific Activist
Below is the second part of my interview with planetary geologist Bethany Ehlmann. In the first part, she discussed two of her recent papers on Martian geology (see citations below). In this segment, she discusses water on Mars more generally.
Bethany Ehlmann Nick Anthis: Would it be possible to briefly take our readers through the history of the discovery of water (or traces of past water) on Mars? I know that this is an important area, but it seems like there's so much work on it comi........ Read more »
Bethany Ehlmann, John F Mustard, Caleb I Fassett, Samuel C Schon, James W Head III, David J Des Marais, John A Grant, & Scott L Murchie. (2008) Clay minerals in delta deposits and organic preservation potential on Mars. Nature Geoscience, 1(6), 355-358. DOI: 10.1038/ngeo207
John Mustard, S L Murchie, S M Pelkey, B L Ehlmann, R E Milliken, J A Grant, J-P Bibring, F Poulet, J Bishop, E Noe Dobrea.... (2008) Hydrated silicate minerals on Mars observed by the Mars Reconnaissance Orbiter CRISM instrument. Nature, 454(7202), 305-309. DOI: 10.1038/nature07097
- July 30, 2008
- 08:39 AM
- 1,889 views
Water on Mars, Part 1
by Nick Anthis in The Scientific Activist
Planetary geology is a fascinating area--particularly when it pertains to the search for extraterrestrial life. I wrote about it once during my brief stint as a student science writer, but it's not an area that I've really covered on my blog. However, a former colleague of mine from Oxford, Bethany Ehlmann, was recently involved with a couple of papers on geological formations left by ancient Martian water, so I thought that this would be a perfect opportunity. Ehlmann is currently ........ Read more »
Bethany Ehlmann, John F Mustard, Caleb I Fassett, Samuel C Schon, James W Head III, David J Des Marais, John A Grant, & Scott L Murchie. (2008) Clay minerals in delta deposits and organic preservation potential on Mars. Nature Geoscience, 1(6), 355-358. DOI: 10.1038/ngeo207
John Mustard, S L Murchie, S M Pelkey, B L Ehlmann, R E Milliken, J A Grant, J-P Bibring, F Poulet, J Bishop, E Noe Dobrea.... (2008) Hydrated silicate minerals on Mars observed by the Mars Reconnaissance Orbiter CRISM instrument. Nature, 454(7202), 305-309. DOI: 10.1038/nature07097
- April 17, 2008
- 09:04 AM
- 1,447 views
Why Are Veins Blue?
by Nick Anthis in The Scientific Activist
When someone asks the question "why are veins blue?" a likely response is that they're blue because the blood in veins is deoxygenated. While it's true that venous blood vessels carry a lower concentration of oxygen than their arterial counterparts, this isn't the reason for their blue appearance in your skin. Still, when someone invariably responds to the veins-are-blue-because-they're-deoxygenated argument with the observation that "I've never seen blu........ Read more »
Alwin Kienle, Lothar Lilge, I. Vitkin, Michael Patterson, Brian Wilson, Raimund Hibst, & Rudolf Steiner. (1996) Why do veins appear blue? A new look at an old question. Applied Optics, 35(7), 1151-1160. http://www.imt.liu.se/edu/courses/TBMT36/pdf/blue.pdf
- February 11, 2008
- 10:02 PM
- 2,152 views
An Integrin Is Identified as a Co-Receptor for HIV
by Nick Anthis in The Scientific Activist
The New York Times reported yesterday that "scientists find new receptor for HIV," referring to a paper published online in Nature Immunology on Sunday by Arthos et al. This is basically correct, although it would be more accurate to call the new receptor a co-receptor, since the infection of a cell with HIV still depends on the primary receptor, CD4, in combination with either CCR5 or CXCR4. The newly-identified co-receptor, just like the other HIV receptors, is a protein located on........ Read more »
James Arthos, Claudia Cicala, Elena Martinelli, Katilyn Macleod, Donald Van Ryk, Danlan Wei, Zhen Xiao, Timothy Veenstra, Thomas Conrad, Richard Lempicki.... (2008) HIV-1 envelope protein binds to and signals through integrin α4β7, the gut mucosal homing receptor for peripheral T cells. Nature Immunology. DOI: 10.1038/ni1566
- February 5, 2008
- 08:02 AM
- 1,135 views
On Drugs, Circumcision, and John McCain
by Nick Anthis in The Scientific Activist
A few interesting items have recently come up in the news and in the scientific literature about various methods for preventing the transmission of HIV.
First up is a study (1) published in PLoS Medicine this week that demonstrated the effectiveness of a combination of antiretroviral drugs in preventing viral transmission in a monkey model of HIV. The researchers demonstrated that taking the antiretroviral drug emtricitabine (FTC) orally could reduce the chance that a macaque would become infe........ Read more »
J García-Lerma, Ron A Otten, Shoukat H Qari, Eddie Jackson, Mian-er Cong, Silvina Masciotra, Wei Luo, Caryn Kim, Debra R Adams, Michael Monsour.... (2008) Prevention of Rectal SHIV Transmission in Macaques by Daily or Intermittent Prophylaxis with Emtricitabine and Tenofovir . PLoS Medicine, 5(2). DOI: 10.1371/journal.pmed.0050028
Paul Denton, Jacob D Estes, Zhifeng Sun, Florence A Othieno, Bangdong L Wei, Anja K Wege, Daniel A Powell, Deborah Payne, Ashley T Haase, & J Victor Garcia. (2008) Antiretroviral Pre-exposure Prophylaxis Prevents Vaginal Transmission of HIV-1 in Humanized BLT Mice. PLoS Medicine, 5(1). DOI: 10.1371/journal.pmed.0050016
- January 24, 2008
- 05:06 PM
- 1,562 views
Embryonic Stem Cell Debate Over; Thousands of Researchers Now Jobless
by Nick Anthis in The Scientific Activist
That could easily have been the shared title of a pair of articles in today's New York Times discussing the science and political implications of two very significant stem cell papers published online yesterday. The biggest offender was Sheryl Stolberg:
It has been more than six years since President Bush, in the first major televised address of his presidency, drew a stark moral line against the destruction of human embryos in medical research.
Since then, he has steadfastly maintained ........ Read more »
K TAKAHASHI, K TANABE, M OHNUKI, M NARITA, T ICHISAKA, K TOMODA, & S YAMANAKA. (2007) Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors. Cell, 131(5), 861-872. DOI: 10.1016/j.cell.2007.11.019
J Yu, M Vodyanik, K Smuga-Otto, J Antosiewicz-Bourget, J Frane, S Tian, J Nie, G Jonsdottir, V Ruotti, R Stewart.... (2007) Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. Science, 318(5858), 1917-1920. DOI: 10.1126/science.1151526
- January 24, 2008
- 05:06 PM
- 1,038 views
Stem Cells from Down Under
by Nick Anthis in The Scientific Activist
Two weeks ago, on November 15th, researchers reported in the Journal of Translational Medicine (see citation below) that they had successfully isolated and characterized stem cells from menstrual blood. The researchers, Meng et al., were able to differentiate these cells--called Endometrial Regenerative Cells (ERCs)--into nine distinct cell types, and the stem cells displayed other encouraging characteristics (including rapid proliferation, unique expression of an embryonic stem cell marker, an........ Read more »
Xiaolong Meng, Thomas Ichim, Jie Zhong, Andrea Rogers, Zhenglian Yin, James Jackson, Hao Wang, Wei Ge, Vladimir Bogin, Kyle Chan.... (2007) Endometrial regenerative cells: A novel stem cell population. Journal of Translational Medicine, 5(1), 57. DOI: 10.1186/1479-5876-5-57
- January 24, 2008
- 05:06 PM
- 1,252 views
Best Headline Ever: "Creature from Hell Promises Salvation"
by Nick Anthis in The Scientific Activist
From today's (well, technically, tomorrow's) New Zealand Herald:
Creature from hell promises salvation
by Errol Kiong
Scientists have discovered a methane-eating bacterium at Hell's Gate in Rotorua which may offer hope for global warming.
Researchers at GNS Science hope their discovery of the bacterium could one day be used to cut down methane gas emissions from landfills and geothermal power stations.
The bug is part of a group of methane-eating micro-organisms known as metha........ Read more »
Peter Dunfield, Anton Yuryev, Pavel Senin, Angela V Smirnova, Matthew B Stott, Shaobin Hou, Binh Ly, Jimmy H Saw, Zhemin Zhou, Yan Ren.... (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature, 450(7171), 879-882. DOI: 10.1038/nature06411
Arjan Pol, Klaas Heijmans, Harry Harhangi, Dario Tedesco, Mike Jetten, & Huub Op den Camp. (2007) Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature, 450(7171), 874-878. DOI: 10.1038/nature06222
- January 24, 2008
- 05:06 PM
- 2,335 views
Integrin Phosphorylation as an Off Switch for Integrin Activation
by Nick Anthis in The Scientific Activist
An individual cell inside the human body is in a dynamic environment: it not only has to anchor itself to its surroundings but also be able to communicate with them and respond as appropriate. One group of proteins--the integrins--play a central role in all of these tasks. The integrins are large (about 200,000 Da) membrane-spanning proteins, and each integrin consists of two subunits (alpha and beta). The vast majority of the integrin is located on the exterior of the cell, where it anchors........ Read more »
C Oxley, N J Anthis, E D Lowe, I Vakonakis, I D Campbell, & K L Wegener. (2007) An integrin phosphorylation switch: the effect of beta3 integrin tail phosphorylation on DOK1 and talin binding. Journal of Biological Chemistry. DOI: 10.1074/jbc.M709435200
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