Biology posts
- February 3, 2012
- 07:11 PM
- 12 views
On Transposable Elements and Regulatory Evolution
by Habib Maroon in Biobabel
Transposable elements (TEs), generally considered molecular parasites on the genome, are increasingly being linked to the evolution of new biological functions. TEs have been shown to be a source of novel genes and exons, the ‘arms race’ between them and … Continue reading →... Read more »
Lynch, V., Leclerc, R., May, G., & Wagner, G. (2011) Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nature Genetics, 43(11), 1154-1159. DOI: 10.1038/ng.917
Schmidt, D., Schwalie, P., Wilson, M., Ballester, B., Gonçalves, A., Kutter, C., Brown, G., Marshall, A., Flicek, P., & Odom, D. (2012) Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages. Cell, 148(1-2), 335-348. DOI: 10.1016/j.cell.2011.11.058
- February 3, 2012
- 06:47 PM
- 7 views
Why Margarita Can Purr, but Can’t Roar
I rolled out of bed later than I intended to this morning. I blame the cats. Our youngest cat, a diminutive calico named Margarita, sprung onto the bed as soon as she heard me start to stir. She immediately started purring — the sound started as a low rumble and rose to a constant vibrato [...]... Read more »
Peters, G. (2002) Purring and similar vocalizations in mammals. Mammal Review, 32(4), 245-271. DOI: 10.1046/j.1365-2907.2002.00113.x
Sissom, D., Rice, D., & Peters, G. (1991) How cats purr. Journal of Zoology, 223(1), 67-78. DOI: 10.1111/j.1469-7998.1991.tb04749.x
Weissengruber, G., Forstenpointner, G., Peters, G., Kubber-Heiss, A., & Fitch, W. (2002) Hyoid apparatus and pharynx in the lion (Panthera leo), jaguar (Panthera onca), tiger (Panthera tigris), cheetah (Acinonyx jubatus) and domestic cat (Felis silvestris f. catus). Journal of Anatomy, 201(3), 195-209. DOI: 10.1046/j.1469-7580.2002.00088.x
- February 3, 2012
- 02:57 PM
- 15 views
Ameloblast from the past
by zacharoo in Lawn Chair Anthropology
I've posted a couple times about the prospects of using high-resolution computed tomography imaging to assess cellular-level processes of growth and development. Today, Paul Tafforeau and colleagues present a synchrotron-based visualization of the adventurous paths that individual enamel-forming cells'(ameloblasts) take to form tooth crowns. I've been focusing more on using these techniques for studying bone growth, but I got the idea of that from previous studies of teeth (see Ma........ Read more »
Macchiarelli, R., Bondioli, L., Debénath, A., Mazurier, A., Tournepiche, J., Birch, W., & Dean, M. (2006) How Neanderthal molar teeth grew. Nature, 444(7120), 748-751. DOI: 10.1038/nature05314
Smith, T., Tafforeau, P., Reid, D., Pouech, J., Lazzari, V., Zermeno, J., Guatelli-Steinberg, D., Olejniczak, A., Hoffman, A., Radovcic, J.... (2010) Dental evidence for ontogenetic differences between modern humans and Neanderthals. Proceedings of the National Academy of Sciences, 107(49), 20923-20928. DOI: 10.1073/pnas.1010906107
Tafforeau, P., Zermeno, J., & Smith, T. (2012) Tracking cellular-level enamel growth and structure in 4D with synchrotron imaging. Journal of Human Evolution. DOI: 10.1016/j.jhevol.2012.01.001
- February 3, 2012
- 12:12 PM
- 23 views
Evolutionary Road: Runoff Breeds Super Salamanders
by Elizabeth Preston in Inkfish
There's no comic-book hero I know of whose origin story begins, "I was lying in a swampy forest when suddenly, some dirty water trickled onto me."* But with roads and traffic crisscrossing their habitat--and runoff leaking into the pools where they breed and grow--salamanders have had to develop their own superpowers to survive.
Yale researcher Steven Brady recently studied spotted salamanders (Ambystoma maculatum) living in range of street runoff. Amphibians such as salamanders ........ Read more »
Brady, S. (2012) Road to evolution? Local adaptation to road adjacency in an amphibian (Ambystoma maculatum). Scientific Reports. DOI: 10.1038/srep00235
- February 3, 2012
- 10:35 AM
- 19 views
Friday Roundup-Rattlesnake Festivals and New Vipers Discovered
by David Steen in Living Alongside Wildlife
Making Strides in Georgia: In recent weeks, there have been many news stories coming out of Georgia that demonstrate how committed individuals and organizations have been making great strides in reptile conservation.
I have written previously about rattlesnake roundups in the southeastern United States (as have others). These events encourage people to catch rattlesnakes over the course of the ... Read more »
D. B. Means. (2009) EFFECTS OF RATTLESNAKE ROUNDUPS ON THE EASTERN DIAMONDBACK RATTLESNAKE (CROTALUS ADAMANTEUS). Herpetological Conservation and Biology, 132-141. info:/
Brown, D., Farallo, V., Dixon, J., Baccus, J., Simpson, T., & Forstner, M. (2011) Freshwater turtle conservation in Texas: harvest effects and efficacy of the current management regime. The Journal of Wildlife Management, 75(3), 486-494. DOI: 10.1002/jwmg.73
- February 3, 2012
- 10:17 AM
- 17 views
Gene therapy in VHL-null cells using human artificial chromosomes
by Vicki Colledge, Sanjay Thakrar, Galina Shyndriayeva in BHD Research Blog
Last month, our conference summary highlighted some of the work that is taking place in the field of gene therapy. Currently, many advanced gene therapy systems are derived from viruses, such as the adenovirus and lentivirus. However, these viral vectors … Continue reading →... Read more »
Kim JH, Kononenko A, Erliandri I, Kim TA, Nakano M, Iida Y, Barrett JC, Oshimura M, Masumoto H, Earnshaw WC.... (2011) Human artificial chromosome (HAC) vector with a conditional centromere for correction of genetic deficiencies in human cells. Proceedings of the National Academy of Sciences of the United States of America, 108(50), 20048-53. PMID: 22123967
- February 3, 2012
- 08:00 AM
- 29 views
Jumping spiders still have use for muscles
by Zen Faulkes in NeuroDojo
You can’t push on a rope.
This is why you typically need two muscles to get things done. Muscles only shorten; if you flex a joint, you can’t expand your muscles to push that joint back to its original position. You have to pull a different muscle, with different insertion points, to get that limb back to where it was. For instance, you have biceps to flex your forearm, and triceps to extend it.
Spiders have always been something of a puzzle, because many of their limb joints have unpaired........ Read more »
Weihmann T, Gunther M, & Blickhan R. (2012) Hydraulic leg extension is not necessarily the main drive in large spiders. The Journal of Experimental Biology, 215(4), 578-583. DOI: 10.1242/jeb.054585
- February 3, 2012
- 02:05 AM
- 28 views
A gene for trauma
by Suzanne Elvidge in Genome Engineering
Why do some people go through some really traumatic experiences and emerge unscathed, and others end up traumatised? It might be down to coping strategies, but genes might influence it too, according to research from Rutgers University.... Read more »
Martel, G., Hevi, C., Wong, A., Zushida, K., Uchida, S., & Shumyatsky, G. (2012) Murine GRPR and Stathmin Control in Opposite Directions both Cued Fear Extinction and Neural Activities of the Amygdala and Prefrontal Cortex. PLoS ONE, 7(2). DOI: 10.1371/journal.pone.0030942
- February 3, 2012
- 01:36 AM
- 42 views
Recurrent histone alterations in pediatric brain cancer
by Daniel Koboldt in Massgenomics
Brain tumors are a particularly deadly form of cancer, and the leading cause of cancer-related death in children. Two studies published this week in Nature journals applied next-generation sequencing to pediatric brain tumors, revealing a striking pattern of recurrent somatic mutations in H3F3A, a gene encoding the histone prorein H3.3. These are the first unbiased [...]... Read more »
Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tönjes M.... (2012) Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. PMID: 22286061
St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project, Wu G, Broniscer A, McEachron TA, Lu C, Paugh BS, Becksfort J, Qu C, Ding L, Huether R.... (2012) Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nature genetics. PMID: 22286216
- February 2, 2012
- 10:59 AM
- 30 views
Why Does a Blind, Fossorial Mammal Have Iridescent Fur?
by Jim Ryan in Wild Mammals
Golden moles (Chrysochloridae) are members of the mammalian Order Afrosoricida, an African group that also includes then tenrecs of Madagascar. Golden moles and true moles (Talpidae) evolved their fossorial habits independently. ... Scientists working with golden moles noticed that their silky fur often appears slightly iridescent (Figure 1).
...A Grant’s golden mole (Eremitalpa granti) showing it’s silky fur and leathery nose patch.
...Iridescence is common among insect and ........ Read more »
Snyder, H., Maia, R., D'Alba, L., Shultz, A., Rowe, K., Rowe, K., & Shawkey, M. (2012) Iridescent colour production in hairs of blind golden moles (Chrysochloridae). Biology Letters. DOI: 10.1098/rsbl.2011.1168
- February 2, 2012
- 09:17 AM
- 44 views
You can't trust your receptors: Smell
by TheCellularScale in The Cellular Scale
Food smells better when you're hungry, right? This is a common phenomenon that everyone I've ever talked to on the subject has experienced. For a long time, I assumed that the entire process underlying this phenomenon is in the brain proper, and not in the olfactory epithelium (that is, the smell receptors themselves). However, a study on the adorable (and totally weird) salamander known as the 'Axolotl' suggests that the brain proper can actually modulate how sensitive thos........ Read more »
Mousley A, Polese G, Marks NJ, & Eisthen HL. (2006) Terminal nerve-derived neuropeptide y modulates physiological responses in the olfactory epithelium of hungry axolotls (Ambystoma mexicanum). The Journal of neuroscience : the official journal of the Society for Neuroscience, 26(29), 7707-17. PMID: 16855098
- February 2, 2012
- 08:44 AM
- 39 views
The missing heritability: the humble opinion of a mathematician
Tomorrow, February 3, is Eric Lander's birthday, the director of the Broad Institute (the well-known MIT/Harvard genomic research center), and the first author of the historic 2001 Nature paper that marked the completion of the Human Genome Project [1]. I heard him once speak at USC and without ever getting technical he managed to engage the whole audience and share his passion for genetics. As you know, I've been honoring famous geneticists by discussing one of their papers on their birthday an........ Read more »
Lander, E., Linton, L., Birren, B., Nusbaum, C., Zody, M., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W.... (2001) Initial sequencing and analysis of the human genome. Nature, 409(6822), 860-921. DOI: 10.1038/35057062
Zuk, O., Hechter, E., Sunyaev, S., & Lander, E. (2012) The mystery of missing heritability: Genetic interactions create phantom heritability. Proceedings of the National Academy of Sciences, 109(4), 1193-1198. DOI: 10.1073/pnas.1119675109
- February 2, 2012
- 07:09 AM
- 39 views
Design Performs a Key Role in Spider Webs, Scientists Say
by Jaime Menchén in United Academics
The strength of spider webs is not only based on silk’s properties, but also on the quality of their design, as researchers from the Massachusetts Institute of Technology and the Politecnico di Torino have found out.... Read more »
Cranford, S., Tarakanova, A., Pugno, N., & Buehler, M. (2012) Nonlinear material behaviour of spider silk yields robust webs. Nature, 482(7383), 72-76. DOI: 10.1038/nature10739
- February 2, 2012
- 07:00 AM
- 51 views
February 2, 2012
by Erin Campbell in HighMag Blog
When a cell makes it all the way to cytokinesis, it has already achieved greatness. DNA replication and mitosis are Big Deals, but a cell exits mitosis only to find itself in front of that final all-uphill mile of the New York City Marathon (even as a kid watching it, I thought that was so cruel). There is a lot of regulation and reorganizing that happens for a cell to correctly complete cell division and physically split into two cells, and a recent paper sorts out how membrane trafficking pr........ Read more »
Chesneau, L., Dambournet, D., Machicoane, M., Kouranti, I., Fukuda, M., Goud, B., & Echard, A. (2012) An ARF6/Rab35 GTPase Cascade for Endocytic Recycling and Successful Cytokinesis. Current Biology. DOI: 10.1016/j.cub.2011.11.058
- February 1, 2012
- 10:01 PM
- 26 views
Crystallography in a cell
by Michael Clarkson in Conformational Flux
In previous posts on this blog I’ve discussed efforts to perform NMR inside of living cells. These experiments, performed in bacteria, are primarily intended to establish whether dilute-solution experiments veridically reproduce biomolecular structures as they appear in live organisms. Now it seems that crystallography is starting to get in on the act. This week in [...]... Read more »
Koopmann, R., Cupelli, K., Redecke, L., Nass, K., DePonte, D., White, T., Stellato, F., Rehders, D., Liang, M., Andreasson, J.... (2012) In vivo protein crystallization opens new routes in structural biology. Nature Methods. DOI: 10.1038/nmeth.1859
- February 1, 2012
- 08:54 PM
- 29 views
Adipose tissue & Immunity: The basics 1
by Lucas Tafur in Lucas Tafur
The relationship between the adipose tissue and innate immunity.... Read more »
Schäffler A, & Schölmerich J. (2010) Innate immunity and adipose tissue biology. Trends in immunology, 31(6), 228-35. PMID: 20434953
Pond CM. (2005) Adipose tissue and the immune system. Prostaglandins, leukotrienes, and essential fatty acids, 73(1), 17-30. PMID: 15946832
- February 1, 2012
- 04:42 PM
- 11 views
How an African Elephant Comes Together
Before my love of dinosaurs kicked in, I adored elephants. My four-year-old self spent hours on the couch watching elephant documentaries, pith helmet firmly affixed to my head and my faithful companion Koba at my side. (A black, plush elephant bigger than I was, Koba was filled with a cheap stuffing I was allergic to. [...]... Read more »
Hautier, L., Stansfield, F., Allen, W., & Asher, R. (2012) Skeletal development in the African elephant and ossification timing in placental mammals. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2011.2481
- February 1, 2012
- 09:30 AM
- 35 views
Video Tip of the Week: SNPeffect 4.0
One of the most frequent questions we hear when we do workshops is: how to I find out if this SNP has an effect on my favorite protein? Well, that’s assuming it is a coding SNP. Of course, promoter SNPs and splicing SNPs and other features would be great to assess as well. Right now, though, the most mature tools are those that look at the effects of variation on the coding of the amino acids in proteins.... Read more »
De Baets, G., Van Durme, J., Reumers, J., Maurer-Stroh, S., Vanhee, P., Dopazo, J., Schymkowitz, J., & Rousseau, F. (2011) SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr996
- February 1, 2012
- 09:04 AM
- 39 views
The Benefits of Sand Bedding for Cattle (and Humans)
by Sara Klink in Promega Connections
For many people, cows are a clean, docile animal viewed at state or local fairs or seen wandering around pastures on a drive through the countryside. However, managing a herd of dairy animals is no small task. Farmers desire healthy animals that consistently give milk every day. For cows in housed primarily in barns, the quality of the bedding used in the stall is important. Not only should bedding be comfortable but also clean, a task made difficult by cows that have no concern about where they........ Read more »
Westphal, A., Williams, M.L., Baysal-Gurel, F., LeJeune, J.T., & McSpadden Gardener, B.B. (2011) General suppression of Escherichia coli O157:H7 in sand-based dairy livestock bedding. Applied and Environmental Microbiology, 77(6), 2113-21. PMID: 21257815
- February 1, 2012
- 05:20 AM
- 56 views
Are Ecologists too Credulous?
by Mike Fowler in Theoretically Speaking
Do we follow rigorous scientific protocol when reporting our work to our peers? Or do we fall into the sort of traps that the scientific method is supposed to help us avoid? Would Karl Popper be proud of, or pissed off at us?
An interesting study has just been published by Barto & Rillig (2012) in Oikos, analysing the writing and citing habits of ecologists, using a meta-analysis of meta-analyses (a mega-analysis? a meta2-analysis?). They look for evidence of a range of biases present in the ........ Read more »
Barto, E., & Rillig, M. (2012) Dissemination biases in ecology: effect sizes matter more than quality. Oikos, 121(2), 228-235. DOI: 10.1111/j.1600-0706.2011.19401.x
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