Hilbert curve or Hilbert space-filling curve is a continuous fractal space-filling curve that densely fills higher-dimensional space without crossing itself. It was first described by the German mathematician David Hilbert in 1891. In a recent article Aiden et al. describe a new method called as Hi-C for reconstructing the three-dimensional architecture of the human genome which not only reveals folding principles of the human genome but also resembles a polymer analog of Hilbert's curve at th........ Read more »
Lieberman-Aiden, E., van Berkum, N., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B., Sabo, P., Dorschner, M.... (2009) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science, 326(5950), 289-293. DOI: 10.1126/science.1181369
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Cooley, H., Wielgus, R., Koehler, G., Robinson, H., & Maletzke, B. (2009) Does hunting regulate cougar populations? A test of the compensatory mortality hypothesis. Ecology, 90(10), 2913-2921. DOI: 10.1890/08-1805.1
Most of data sharing policies share some common principles such as protecting the cumulative data outputs, recognizing data as a public good and data sharing as strong value chains of innovation for subsequent scientific exploitation. A improved data access and sharing not only helps to maximize the research potential but it also reinforces open scientific research which encourages diversity of analysis and opinion. In a latest article published in October 9 issue of journal Science, Dawn Fiel........ Read more »
I would never select Treponema pallidum as my experimental model if I had to study gene regulation in a spirochete. The main problem is that no one has figured out how to grow T. pallidum in any type of culture medium. T. pallidum can be propagated only by growing the spirochete in the testes of rabbits. Consequently, investigators have not even begun to develop the genetic tools (e.g., gene knock outs, shuttle plasmids) necessary to unravel the regulatory mechanisms that control T. pallidum ........ Read more »
Giacani, L., Godornes, C., Puray-Chavez, M., Guerra-Giraldez, C., Tompa, M., Lukehart, S.A., & Centurion-Lara, A. (2009) TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum ssp. pallidum . Molecular Microbiology, 72(5), 1087-1099. DOI: 10.1111/j.1365-2958.2009.06712.x
Radolf, J.D., & Desrosiers, D.C. (2009) Treponema pallidum, the stealth pathogen, changes, but how? . Molecular Microbiology, 72(5), 1081-1086. DOI: 10.1111/j.1365-2958.2009.06711.x
The new Science has an extremely impressive paper tackling the problem of orphan enzymes. Due primarily to Watson-Crick basepairing, our ability to sequence nucleic acids has shot far past our ability to characterize the proteins they may encode. If I want to measure an RNA's expression, I can generate an assay almost overnight by designing specific real-time PCR (aka RT-PCR aka TaqMan) probes. If I want to analyze any specific protein's expression, it generally involves a lot of teeth gnashi........ Read more »
Ana Beloqui, María-Eugenia Guazzaroni, Florencio Pazos, José M. Vieites, Marta Godoy, Olga V. Golyshina,, Tatyana N. Chernikova, Agnes Waliczek, Rafael Silva-Rocha, Yamal Al-ramahi.... (2009) Reactome array: Forging a link between metabolome and genome. Science, 326(5950), 252-257. info:/10.1126/science.1174094
Autophagy seems to be the topic of the week, and here's another example of research demonstrating enhanced longevity in laboratory animals through increased autophagy: Here, we report that administration of spermidine, a natural polyamine whose intracellular concentration declines during human ageing, markedly extended the lifespan of yeast, flies and worms, and human immune cells. In addition, spermidine administration potently inhibited oxidative stress in ageing mice [and] led to significant ........ Read more »
Eisenberg, T., Knauer, H., Schauer, A., Büttner, S., Ruckenstuhl, C., Carmona-Gutierrez, D., Ring, J., Schroeder, S., Magnes, C., Antonacci, L.... (2009) Induction of autophagy by spermidine promotes longevity. Nature Cell Biology. DOI: 10.1038/ncb1975
Boyish good looks - the next generation of sexy?I couldn't help but notice that a new study has come out about the behavioral effects of hormonal contraception. It's all over the science news sites. With titles ranging from the conservative "Pill May Change Attraction" to the bolder "Taking the pill for past 40 years 'has put women off masculine men'"and "The pill 'gives women a taste for boyish men like Zac Efron'," this new publication has swept the media outlets by storm. This idea that birth........ Read more »
Alexandra Alvergne, & Virpi Lummaa. (2009) Does the contraceptive pill alter mate choice in humans?. Trends in Ecology and Evolution. info:/10.1016/j.tree.2009.08.003
A study claims that it's possible to immunize against cocaine: Cocaine Vaccine for the Treatment of Cocaine Dependence in Methadone-Maintained Patients. But does it work? And will it be useful?The idea of an anti-drug vaccine is not new; as DrugMonkey explains in his post on this paper, monkeys were being given experimental anti-morphine vaccines as long ago as the 1970s. This one has been under development for years, but this is the first randomized controlled trial to investigate whether it he........ Read more »
Martell BA, Orson FM, Poling J, Mitchell E, Rossen RD, Gardner T, & Kosten TR. (2009) Cocaine vaccine for the treatment of cocaine dependence in methadone-maintained patients: a randomized, double-blind, placebo-controlled efficacy trial. Archives of general psychiatry, 66(10), 1116-23. PMID: 19805702
Shortly after I developed sore throat, cough, and congestion last week, a package of 'Cold - Eeze' materialized on my kitchen counter. The writing on the package of zinc-laden lozenges promised to 'shorten your cold', and noted that they were 'clinically proven to reduce the duration of the common cold'. Do zinc lozenges have any effect on the common cold?... Read more »
Geist FC, Bateman JA, & Hayden FG. (1987) In vitro activity of zinc salts against human rhinoviruses. Antimicrobial agents and chemotherapy, 31(4), 622-4. PMID: 3038000
Krenn, B., Gaudernak, E., Holzer, B., Lanke, K., Van Kuppeveld, F., & Seipelt, J. (2008) Antiviral Activity of the Zinc Ionophores Pyrithione and Hinokitiol against Picornavirus Infections. Journal of Virology, 83(1), 58-64. DOI: 10.1128/JVI.01543-08
Roxas M, & Jurenka J. (2007) Colds and influenza: a review of diagnosis and conventional, botanical, and nutritional considerations. Alternative medicine review : a journal of clinical therapeutic, 12(1), 25-48. PMID: 17397266
Photo by Phillip ‘Scooter’ Trosclair.
Birds are often touted as the monogamists of the animal kingdom, with most bird species mating with the same individual and displaying biparental care, sometimes for many years. Their cousins, the reptiles, are no match for their faithfulness: most reptiles show no mate fidelity, let alone parental care.
But a new [...]
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LANCE, S., TUBERVILLE, T., DUECK, L., HOLZ-SCHIETINGER, C., TROSCLAIR, P., ELSEY, R., & GLENN, T. (2009) Multiyear multiple paternity and mate fidelity in the American alligator, . Molecular Ecology. DOI: 10.1111/j.1365-294X.2009.04373.x
Our weekly compilation of science news for the week of October 4, 2009.... Read more »
Brusatte, S., Carr, T., Erickson, G., Bever, G., & Norell, M. (2009) A long-snouted, multihorned tyrannosaurid from the Late Cretaceous of Mongolia. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0906911106
Parks, J., Guo, H., Momany, C., Liang, L., Miller, S., Summers, A., & Smith, J. (2009) Mechanism of Hg−C Protonolysis in the Organomercurial Lyase MerB. Journal of the American Chemical Society, 131(37), 13278-13285. DOI: 10.1021/ja9016123
Researchers look at 29-years of data in Texas and find that coastal birds have declined as development has risen...read more... Read more »
Foster, C., Amos, A., & Fuiman, L. (2009) Trends in Abundance of Coastal Birds and Human Activity on a Texas Barrier Island Over Three Decades. Estuaries and Coasts. DOI: 10.1007/s12237-009-9224-2
Today's Nature contains a great paper which is one more step forward for cancer genomics. Using Illumina sequencing a group in British Columbia sequenced both the genome and transcriptome of a metastatic lobular (estrogen receptor positive) breast cancer. Furthermore, they searched a sample of the original tumor for mutations found in the genome+transcriptome screen in order to identify those that may have been present early vs. those which were acquired later.From the combined genome sequence........ Read more »
Sohrab P. Shah, Ryan D. Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh, Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Guliany, Janine Senz.... (2009) Mutational evolution in a lobular breast tumor profiled at single nucleotide resolution. Nature, 809-813. info:/10.1038/nature08489
Most denizens of the interwebs (at least of this corner of the interwebs) will have heard the announcement that the 2009 Nobel Prize in Physiology or Medicine will be given to Elizabeth Blackburn, Carol Greider and Jack Szostak for their work on telomeres – the structures found at the ends of human chromosomes. You may [...]... Read more »
A new investigation of the sedimentology and ichnology of the Early Jurassic Moyeni tracksite in Lesotho, southern Africa has yielded new insights into the behavior and locomotor dynamics of early dinosaurs. Read the rest of this post... | Read the comments on this post...... Read more »
Wilson, J., Marsicano, C., & Smith, R. (2009) Dynamic Locomotor Capabilities Revealed by Early Dinosaur Trackmakers from Southern Africa. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007331
4. Nuclear DNA: Forays into 3 billion base pairs
4.1 Before Vi-80
The Vindija-80 (Vi-80) specimen is an important find for geneticists: it yielded a minimally contaminated sample and provided those first steps into Neanderthal genomics.
Previously, attempts at retrieving ancient nuclear DNA sequences proved to be a notoriously difficult process, plagued with problems of degradation, contamination and [...]... Read more »
Green, R., Krause, J., Ptak, S., Briggs, A., Ronan, M., Simons, J., Du, L., Egholm, M., Rothberg, J., Paunovic, M.... (2006) Analysis of one million base pairs of Neanderthal DNA. Nature, 444(7117), 330-336. DOI: 10.1038/nature05336
Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z.... (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (New York, N.Y.), 325(5938), 318-21. PMID: 19608918
Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin JJ, Hänni C, Fortea J, de la Rasilla M.... (2007) The derived FOXP2 variant of modern humans was shared with Neandertals. Current biology : CB, 17(21), 1908-12. PMID: 17949978
Lalueza-Fox C, Römpler H, Caramelli D, Stäubert C, Catalano G, Hughes D, Rohland N, Pilli E, Longo L, Condemi S.... (2007) A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science (New York, N.Y.), 318(5855), 1453-5. PMID: 17962522
It can be argued that one of the most influential articles ever published in the Journal of Applied Physiology is the Analysis of tissue and arterial blood temperatures in the resting human forearm by Harry H. Pennes, which appeared in Volume 1, No. 2, published in August, 1948. Thus begins Prof. Wissler, his 1998 revisit [...]... Read more »
PENNES HH. (1948) Analysis of tissue and arterial blood temperatures in the resting human forearm. Journal of applied physiology, 1(2), 93-122. PMID: 18887578
Decline in hiking and backpacking could hurt conservation donations
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Zaradic, P., Pergams, O., & Kareiva, P. (2009) The Impact of Nature Experience on Willingness to Support Conservation. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007367
At almost any spot on the globe, there are species present that are not native to that locale, having been transported by human activities. Whether and how exotic species impact communities is a multifaceted problem that requires understanding the multitude of direct and indirect species interactions that occur. In a paper published in the Proceedings of the Royal Society, B, Montserrat Vila and colleagues asked if exotic plants where integrated into plant-pollinator networks, and whether this i........ Read more »
Vila, M., Bartomeus, I., Dietzsch, A., Petanidou, T., Steffan-Dewenter, I., Stout, J., & Tscheulin, T. (2009) Invasive plant integration into native plant-pollinator networks across Europe. Proceedings of the Royal Society B: Biological Sciences, 276(1674), 3887-3893. DOI: 10.1098/rspb.2009.1076
How did Komodo dragons evolve to be the world's biggest lizards?
The story goes that cartographers would write, “Here be dragons,” on the places of the map where they had no information. This would only be true in a few areas of the world, namely a few islands in the south Pacific, where Komodo dragons live.
As I talked about in an earlier post, weird things happen to the size of species on islands. Big species get small. Small species get big.
And if there’s one ........ Read more »
Hocknull, S., Piper, P., van den Bergh, G., Due, R., Morwood, M., & Kurniawan, I. (2009) Dragon's Paradise Lost: Palaeobiogeography, Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae). PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0007241
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