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  • May 8, 2017
  • 05:45 PM
  • 199 views

Let those who never smelled bad cast the first stone

by Aurametrix team in Aurametrix Blog

Analysis of our metabolism is crucial to comprehending the responses of our genes and microbes to the stresses of daily life, and to elucidating the causes and consequences of health and disease. And measurement of urinary metabolites - small molecules produced from foods, drinks, drugs, environmental contaminants, bodily waste products and bacterial by-products - is key to the analysis. We applied this approach to an elusive condition that has always evaded diagnosis: s........ Read more »

Bouatra, S., Aziat, F., Mandal, R., Guo, A., Wilson, M., Knox, C., Bjorndahl, T., Krishnamurthy, R., Saleem, F., Liu, P.... (2013) The Human Urine Metabolome. PLoS ONE, 8(9). DOI: 10.1371/journal.pone.0073076  

Irene S. Gabashvili. (2017) Raw Data from Clinical Trial NCT02692495. Mendeley Data. info:/DOI: 10.17632/8bk6h6bmkr.1

  • February 24, 2017
  • 06:18 PM
  • 364 views

Symbiote Separation: Coral Bleaching and Climate Change

by Melissa Chernick in Science Storiented

It’s been a while since I’ve broken down some studies for you, so I took on a big one.I’m sure you’ve heard of coral bleaching. What is it? Why does it happen? Why does it matter? To start off, you need to know a little bit more about the individuals that make up a head (fan, whip, etc.): the polyp. Coral polyps look like tiny plants but are actually tiny animals (less than ½ an inch in diameter). They produce calcium carbonate to create a protective shell or skeleton that, when thousan........ Read more »

  • May 24, 2016
  • 10:02 AM
  • 867 views

Should Biologists be Guided by Beauty?

by Jalees Rehman in The Next Regeneration

One key characteristic of a beautiful scientific theory is the simplicity of the underlying concepts. According to Weinberg, Einstein's theory of gravitation is described in fourteen equations whereas Newton's theory can be expressed in three. Despite the appearance of greater complexity in Einstein's theory, Weinberg finds it more beautiful than Newton's theory because the Einsteinian approach rests on one elegant central principle – the equivalence of gravitation and ........ Read more »

Dietrich, M., Ankeny, R., & Chen, P. (2014) Publication Trends in Model Organism Research. Genetics, 198(3), 787-794. DOI: 10.1534/genetics.114.169714  

Weinberg, Steven. (1992) Dreams of a Final Theory . Vintage Books. info:/

  • February 8, 2016
  • 09:30 AM
  • 560 views

Pathway Commons and paxtoolsr: An Introduction

by cannin in Lunean

Pathway Commons is an aggregation of public pathway databases and provides infrastructure for querying this rich dataset. Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC. paxtoolsr is a package that builds on the strengths of Pathway Commons and its native BioPAX format to Read More ...The post Pathway Commons and paxtoolsr: An Introduction appeared first on Lunean. ... Read more »

Luna A, Babur Ö, Aksoy BA, Demir E, & Sander C. (2015) PaxtoolsR: Pathway Analysis in R Using Pathway Commons. Bioinformatics (Oxford, England). PMID: 26685306  

  • January 10, 2016
  • 07:00 AM
  • 895 views

Endosperm: the pivot of the sexual conflict in flowering plants

by Piter Boll in Earthling Nature

by Piter Kehoma Boll The theory of sexual selection, based on the idea that there are conflict of interests between males and females, is quite recognized, but almost entirely focused on animals, especially dioecious animals, i.e., animals in which males … Continue reading →... Read more »

Maruyama, D., Hamamura, Y., Takeuchi, H., Susaki, D., Nishimaki, M., Kurihara, D., Kasahara, R., & Higashiyama, T. (2013) Independent Control by Each Female Gamete Prevents the Attraction of Multiple Pollen Tubes. Developmental Cell, 25(3), 317-323. DOI: 10.1016/j.devcel.2013.03.013  

Schärer, L., Janicke, T., & Ramm, S. (2015) Sexual Conflict in Hermaphrodites. Cold Spring Harbor Perspectives in Biology, 7(1). DOI: 10.1101/cshperspect.a017673  

  • December 2, 2015
  • 08:00 AM
  • 1,046 views

The Best Cure for Insomnia Is To Get A Lot Of Sleep

by Mark Lasbury in As Many Exceptions As Rules

We all need to sleep, but why? Recent studies investigate the requirement of sleep for neural plasticity and learning, so how come bullfrogs never sleep?... Read more »

  • October 8, 2015
  • 12:30 PM
  • 824 views

Neury Thursday: Modeling disrupted sleep in Angelman Syndrome

by Allison in Dormivigilia

This study came out of our group here at Morehouse School of Medicine. It concerns a mouse model of disrupted sleep in Angelman Syndrome. Basically, was it the circadian or homeostatic system that is responsible, or both? It was the homeostatic. ... Read more »

Ehlen, J., Jones, K., Pinckney, L., Gray, C., Burette, S., Weinberg, R., Evans, J., Brager, A., Zylka, M., Paul, K.... (2015) Maternal Ube3a Loss Disrupts Sleep Homeostasis But Leaves Circadian Rhythmicity Largely Intact. Journal of Neuroscience, 35(40), 13587-13598. DOI: 10.1523/JNEUROSCI.2194-15.2015  

  • August 7, 2015
  • 07:38 AM
  • 1,171 views

Seeing With Bionic Eyes!

by Viputheshwar Sitaraman in Draw Science

Pulse trains to percepts: the challenge of creating a perceptually intelligible world with sight recovery technologies.... Read more »

  • July 29, 2015
  • 09:39 AM
  • 683 views

Video Tip of the Week: PathWhiz for Pathways, Part II

by Mary in OpenHelix

This week’s tip is a follow-up to the PathWhiz one featured last week. After I had finished writing that one, the second video in the series became available. It has a lot more detail on how to work with the tool. I’m not going to go into the introduction here again, you can flip back […]... Read more »

Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015) Pathways with PathWhiz. Nucleic Acids Research, 43(W1). DOI: 10.1093/nar/gkv399  

  • July 22, 2015
  • 09:36 AM
  • 643 views

Video Tip of the Week: PathWhiz for graphical appeal and computational readability

by Mary in OpenHelix

“Pathway diagrams are the road maps of biology.” This is how the folks from PathWhiz begin their recent paper. I came across it in the Nucleic Acids Research web server issue which was recently announced. The NAR database issue in January and the mid-year web server issue are perfectly timed items that I can content […]... Read more »

Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015) Pathways with PathWhiz. Nucleic Acids Research, 43(W1). DOI: 10.1093/nar/gkv399  

  • June 19, 2015
  • 06:30 PM
  • 1,302 views

Fibonacci Numbers And Odd Lungs

by Mark Lasbury in As Many Exceptions As Rules

Most people think that because they have a pair of lungs, they must be symmetrical – but they’re far from it. The Fibonacci sequence has a lot to do with structural asymmetries in the lungs. On the other hand, some animals have only one lung, some have three lungs, and some have no lungs at all.... Read more »

Wilkinson M, Kok PJ, Ahmed F, & Gower DJ. (2014) Caecilita Wake . Zootaxa, 383-8. PMID: 24871732  

Bickford, D., Iskandar, D., & Barlian, A. (2008) A lungless frog discovered on Borneo. Current Biology, 18(9). DOI: 10.1016/j.cub.2008.03.010  

Goldberger AL, West BJ, Dresselhaus T, & Bhargava V. (1985) Bronchial asymmetry and Fibonacci scaling. Experientia, 41(12), 1537-8. PMID: 4076397  

  • April 20, 2015
  • 11:39 AM
  • 965 views

The Human Epigenome Roadmap

by Daniel Koboldt in Massgenomics

Aside from the occasional somatic mutation, the genome of every cell in an individual’s body is largely preserved. Yet different types of cells (and tissues, and organs) are incredibly diverse. The majority of that specialization is governed by epigenetic changes — histone modifications, DNA accessibility, and methylation — that influence when and how genes are expressed. […]... Read more »

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J.... (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518(7539), 317-30. PMID: 25693563  

  • March 22, 2015
  • 03:37 PM
  • 728 views

In Search for the Function of Sleep Continues

by Allison in Dormivigilia

Today, I was a guest host on an awesome neuroscience podcast entitled On Your Mind. We discussed these two papers that aim to yet probe for another significant function of sleep... Read more »

  • February 24, 2015
  • 03:55 PM
  • 795 views

Humans in the Wild.

by Allison in Dormivigilia

My graduate lab did a really neat study brainstormed over libations on Bourbon Street in NOLA, actually. Basically, they took the power grid data from the Pacific Northwest and imported it into a circadian-specific computer program to see seasonal and monthly rhythms of human activity based on the power grid. ... Read more »

  • January 11, 2015
  • 01:00 PM
  • 881 views

A decade's worth of data on alcohol and circadian rhythms

by Allison in Dormivigilia

Across the past decade, the lab where I completed my PhD work and our collaborator have undertaken numerous experiments reflected in over 10 original research publications on how alcohol affects circadian timekeeping. The journey continues. ... Read more »

  • November 5, 2014
  • 10:30 AM
  • 780 views

Neury Thursday: Sleep and the Blood Brain Barrier, with some hesitation

by Allison in Dormivigilia

Researchers found that the permeability of the blood brain barrier is compromised with chronic sleep deprivation. However, the methods section brings these findings into question. Scientists, do your job and make those methods detailed. ... Read more »

He, J., Hsuchou, H., He, Y., Kastin, A., Wang, Y., & Pan, W. (2014) Sleep Restriction Impairs Blood-Brain Barrier Function. Journal of Neuroscience, 34(44), 14697-14706. DOI: 10.1523/JNEUROSCI.2111-14.2014  

  • October 14, 2014
  • 11:30 AM
  • 982 views

Vampire Diaries: Tales of Sleep

by Allison in Dormivigilia

Researchers at UPENN have done gene profiles of blood taken from subjects sensitive or resistant to sleep deprivation. Is the blood gaining some street cred in neuroscience?... Read more »

Arnardottir, E., Nikonova, E., Shockley, K., Podtelezhnikov, A., Anafi, R., Tanis, K., Maislin, G., Stone, D., Renger, J., Winrow, C.... (2014) Blood-Gene Expression Reveals Reduced Circadian Rhythmicity in Individuals Resistant to Sleep Deprivation. SLEEP. DOI: 10.5665/sleep.4064  

  • October 12, 2014
  • 02:45 AM
  • 978 views

How EBOLA Treatment Works

by Viputheshwar Sitaraman in Draw Science

A basic insight into the biology behind the experimental EBOLA treatment. [Infographic]... Read more »

Qiu, X., Wong, G., Audet, J., Bello, A., Fernando, L., Alimonti, J., Fausther-Bovendo, H., Wei, H., Aviles, J., Hiatt, E.... (2014) Reversion of advanced Ebola virus disease in nonhuman primates with ZMapp. Nature, 514(7520), 47-53. DOI: 10.1038/nature13777  

  • October 8, 2014
  • 08:00 AM
  • 1,258 views

A Tale Of Two Tails

by Mark Lasbury in As Many Exceptions As Rules

Recent, and not so recent studies, are showing just how specialized eukaryotic flagella can be. Structures are rigid, except for when they aren’t. Sperm from two species of diatoms have very different sperm tail basal bodies, which might affect how they move and function. On the other hand, rabbits have flagella with at least three different structures. Does each have it’s own function?... Read more »

Prensier, G., Vivier, E., Goldstein, S., & Schrevel, J. (1980) Motile flagellum with a "3 0" ultrastructure. Science, 207(4438), 1493-1494. DOI: 10.1126/science.7189065  

Feistel K, & Blum M. (2006) Three types of cilia including a novel 9 4 axoneme on the notochordal plate of the rabbit embryo. Developmental dynamics : an official publication of the American Association of Anatomists, 235(12), 3348-58. PMID: 17061268  

  • September 24, 2014
  • 06:00 AM
  • 1,340 views

Chase The Good, Evade The Bad

by Mark Lasbury in As Many Exceptions As Rules

New research has found a bacterium that is spherical, yet has flagella all over its surface (peritrichous). This bacterium is also the only magnetotactic organism discovered that has both magnetite and Greigite crystals. Other research is showing that changing fields can turn magnetotactic bacteria on command. With some bacteria able to generate electrical circuits and others being able to open and close circuits on command, can bacterial computers be far away?... Read more »

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