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  • April 17, 2014
  • 09:39 AM
  • 5 views

What’s the Answer? (new Biostars interface)

by Mary in OpenHelix

BioStars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here […]... Read more »

Parnell Laurence D., Lindenbaum Pierre, Shameer Khader, Dall'Olio Giovanni Marco, Swan Daniel C., Jensen Lars Juhl, Cockell Simon J., Pedersen Brent S., Mangan Mary E., & Miller Christopher A. (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216.g002  

  • April 17, 2014
  • 09:26 AM
  • 2 views

April 17, 2014

by Erin Campbell in HighMag Blog

The endoplasmic reticulum and humans have quite a bit in common. Both are dynamic and constantly changing, but both also need something to ground and stabilize them. Maybe I’m reading too much into the beauty of the ER, but the image today is from a paper that only fuels my fascination. The endoplasmic reticulum (ER) is a large, complex membrane-bound organelle that spreads throughout the cell and hosts the synthesis, folding, and sorting of membrane and secretory proteins. This network is ........ Read more »

Joensuu, M., Belevich, I., Ramo, O., Nevzorov, I., Vihinen, H., Puhka, M., Witkos, T., Lowe, M., Vartiainen, M., & Jokitalo, E. (2014) ER sheet persistence is coupled to myosin 1c-regulated dynamic actin filament arrays. Molecular Biology of the Cell, 25(7), 1111-1126. DOI: 10.1091/mbc.E13-12-0712  

  • April 17, 2014
  • 07:49 AM
  • 6 views

Cannabis use and structural changes in the brain

by Robb Hollis in Antisense Science

“One or two spliffs a week could mess up your brain” – Metro, 16 April 2014

Spark your interest? This headline caught the eyes of the Antisense team, so we chased down the original article in the Journal of Neuroscience and took a closer look!

Cannabis is the most commonly used illegal drug in the US, and the ‘casual use’ culture surrounding marijuana is a subject of great debate and controversy, with arguments for drug legalisation making their way into our ........ Read more »

  • April 17, 2014
  • 04:31 AM
  • 7 views

Mitochondrial dysfunction as a neurobiological subtype of autism

by Paul Whiteley in Questioning Answers

The paper by Suzanne Goh and colleagues [1] reporting on "a possible neurobiological subtype of mitochondrial dysfunction in ASD [autism spectrum disorder]" is a worthy addition to the research roll call which has graced this blog down the years. Based on the analysis of brain lactate levels - a potential marker of mitochondrial dysfunction - via the analysis of lactate doublets on brain magnetic resonance spectroscopic imaging (MRSI), authors picked up a significantly higher rate of l........ Read more »

  • April 16, 2014
  • 04:19 PM
  • 17 views

Sex in (floral) advertising

by Brooke LaFlamme in Molecular Love (and other facts of life)

Having a wingman can be helpful, but for many plants it’s absolutely crucial. Flowering plants don’t have smoky bars, speed dating or eHarmony. They have to rely entirely on their tiny wing—well, I guess “men” isn’t really appropriate. But unlike your witty friend who backs you up in the bar, pollinators don’t help plants with their dating life out of friendship alone. They need something in return, and flowers flaunt their assets to advertise the sweet ........ Read more »

  • April 16, 2014
  • 09:37 AM
  • 23 views

Video Tip of the Week: NaviCell for custom interaction maps for systems biology

by Mary in OpenHelix

The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a […]... Read more »

Kuperstein Inna, Cohen David PA, Pook Stuart, Viara Eric, Calzone Laurence, Barillot Emmanuel, & Zinovyev Andrei. (2013) NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Systems Biology, 7(1), 100. DOI: 10.1186/1752-0509-7-100  

Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N., & Kitano H. (2008) CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE, 96(8), 1254-1265. DOI: 10.1109/JPROC.2008.925458  

  • April 16, 2014
  • 08:05 AM
  • 18 views

Using Pain To Stop Pain

by Mark Lasbury in As Many Exceptions As Rules

Chronic pain can involve TRPV1 pathways, yet traditional TRPV1 antagonists cannot be used due to incidence of hyperthermia. New research has identified new routes of administration, new agonists and new allosteric functions that will make TRPV1 a viable target for chronic, acute, and cancer-mediated pains. Alternative mechanisms, such as counter irritants and acupuncture are also gaining in evidence for mechaisms that involve TRPV1 signaling pathways... Read more »

Andreev YA, Kozlov SA, Korolkova YV, Dyachenko IA, Bondarenko DA, Skobtsov DI, Murashev AN, Kotova PD, Rogachevskaja OA, Kabanova NV.... (2013) Polypeptide modulators of TRPV1 produce analgesia without hyperthermia. Marine drugs, 11(12), 5100-15. PMID: 24351908  

Lee MG, Huh BK, Choi SS, Lee DK, Lim BG, & Lee M. (2012) The effect of epidural resiniferatoxin in the neuropathic pain rat model. Pain physician, 15(4), 287-96. PMID: 22828682  

Kelly S, Chapman RJ, Woodhams S, Sagar DR, Turner J, Burston JJ, Bullock C, Paton K, Huang J, Wong A.... (2013) Increased function of pronociceptive TRPV1 at the level of the joint in a rat model of osteoarthritis pain. Annals of the rheumatic diseases. PMID: 24152419  

  • April 16, 2014
  • 06:16 AM
  • 21 views

Tiger sharks: Each to their own diving depth

by Aileen Cudmore in Natural Reactions

Despite some broad similarities, the diving behaviour of tiger sharks appears to vary greatly amongst individuals.... Read more »

  • April 16, 2014
  • 01:54 AM
  • 24 views

Joined by HDAC (inhibitors)

by Paul Whiteley in Questioning Answers

I'm treading quite carefully with this post which came about following my [non-expert] reading of the paper abstract from Anand Venkatraman and colleagues [1] on a potential downside to the use of HDAC (histone deacetylase) inhibitors for treating spinocerebellar ataxia type 1 (SCA1), a progressive disease affecting movement and other knock-on functions. This follows other work suggesting that certain HDAC inhibitors might offer some important new lines of investigation when it co........ Read more »

  • April 15, 2014
  • 09:32 PM
  • 32 views

Stone Soup Eyes

by Reed College Dev Neuro in the Node

Another installment from the Developmental Neurobiology Students at Reed College. Hope you enjoy! It’s not often that you get to recount the classic tale of Stone Soup when thinking about developmental biology, but that’s exactly what we did when discussing an almost classic 2011 Nature paper from Yoshiki Sasai’s group. In the story, a grumpy […]... Read more »

Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K., Adachi, T., & Sasai, Y. (2011) Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature, 472(7341), 51-56. DOI: 10.1038/nature09941  

Nakano, T., Ando, S., Takata, N., Kawada, M., Muguruma, K., Sekiguchi, K., Saito, K., Yonemura, S., Eiraku, M., & Sasai, Y. (2012) Self-Formation of Optic Cups and Storable Stratified Neural Retina from Human ESCs. Cell Stem Cell, 10(6), 771-785. DOI: 10.1016/j.stem.2012.05.009  

  • April 15, 2014
  • 10:00 AM
  • 17 views

The perfect marriage of crystallography and mass spectrometry: PI3K

by Clay Clark in Biochem Blogs

  Sorry for the cheesy title, but I’m getting married in a couple of weeks and it is all I can think about (oh, and science of course).  I have to admit that I chose a GREAT paper this time!: “Molecular determinants of PI3Kγ-mediated activation downstream of G-protein–coupled receptors” which was published last year in […]... Read more »

Vadas O., Dbouk H. A., Shymanets A., Perisic O., Burke J. E., Abi Saab W. F., Khalil B. D., Harteneck C., Bresnick A. R., & Nurnberg B. (2013) Molecular determinants of PI3K -mediated activation downstream of G-protein-coupled receptors (GPCRs). Proceedings of the National Academy of Sciences, 110(47), 18862-18867. DOI: 10.1073/pnas.1304801110  

  • April 15, 2014
  • 04:37 AM
  • 45 views

A Brief History Of Lions

by Gunnar de Winter in United Academics

New DNA study reveals lion history and could guide conservation efforts.... Read more »

  • April 14, 2014
  • 04:02 PM
  • 38 views

Mosquito sperm need to smell to swim

by Brooke LaFlamme in Molecular Love (and other facts of life)

You’ve probably had someone tell you, at some point in your life, that the sense of smell is the sense most tightly linked to memory. Now, scientists have found that at least for mosquitoes, the sense of smell is also linked to the ability of their sperm to swim. The research was published in February in the journal Proceedings of the National Academy of Sciences.

Female mosquitoes use their sense of smell to find people (so they can suck their blood) and suitable sites to lay their eg........ Read more »

Pitts RJ, Liu C, Zhou X, Malpartida JC, & Zwiebel LJ. (2014) Odorant receptor-mediated sperm activation in disease vector mosquitoes. Proceedings of the National Academy of Sciences of the United States of America, 111(7), 2566-71. PMID: 24550284  

  • April 14, 2014
  • 06:04 AM
  • 56 views

Interview with Beddington Medal winner William Razzell

by the Node in the Node

Each year, the British Society for Developmental Biology (BSDB) awards the Beddington Medal to the best PhD thesis in developmental biology. This year’s award went to William Razzell, who completed his PhD in Paul Martin’s lab at the University of Bristol. At the BSDB Spring Meeting last month, Will presented his thesis studies of wound […]... Read more »

  • April 14, 2014
  • 03:58 AM
  • 54 views

Neurology of inflammatory bowel diseases

by Paul Whiteley in Questioning Answers

The paper by Ben-Or and colleagues [1] talking about a neurologic profile present in a small participant cohort of children and adolescents diagnosed with an inflammatory bowel disease (IBD) caught my eye recently. Their findings reporting that over two-thirds of their paediatric participant group diagnosed with IBD also "exhibited neurologic manifestations" provides some compelling preliminary evidence for further investigation in this area.Outside of reports of headache and dizziness, the pres........ Read more »

  • April 12, 2014
  • 11:54 PM
  • 66 views

Early brain development and heat shock proteins

by in Neuroscientifically Challenged

The brain development of a fetus is really an amazing thing. The first sign of an incipient nervous system emerges during the third week of development; it is simply a thickened layer of tissue called the neural plate. After about 5 more days, the neural plate has formed an indentation called the neural groove, and the sides of the neural groove have curled up and begun to fuse together (see pic to the right). This will form the neural tube, which will eventually become the brain and spinal cord........ Read more »

  • April 12, 2014
  • 04:58 PM
  • 59 views

Summer and winter Blackcaps and evolution

by Africa Gomez in BugBlog

During April, Blackcaps return to thickets and woodland, where the male's beautiful song joins the resident birds. These Blackcaps have just arrived from their winter quarters in Spain and North and coastal West Africa. We tend to think of migration behaviour as something fixed, but recent research shows that many birds have recently changed their migration routes. One of these is the Blackcap.In the last 50 years or so, a small contingent of Blackcaps have started to winter in the UK. About 30%........ Read more »

  • April 12, 2014
  • 01:38 PM
  • 66 views

Polycystic Ovary Syndrome: Causes, Symptoms, and Home Remedies

by Imtiaz Ibne Alam in Medical-Reference - A Pioneer in Medical Blogging

Polycystic ovary syndrome (PCOS) is one of the most common causes of woman's infertility. It is a problem results from an imbalance of female sex hormones. It may cause irregular menstruation, difficulties in getting pregnant, and cysts in the ovaries. If it's not treated, overtime it can lead to diabetes and several other troubling health conditions.... Read more »

Pau CT, Keefe CC, & Welt CK. (2013) Cigarette smoking, nicotine levels and increased risk for metabolic syndrome in women with polycystic ovary syndrome. Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology, 29(6), 551-5. PMID: 23656383  

  • April 11, 2014
  • 06:25 PM
  • 70 views

Dad's obesity and risk of offspring autism

by Paul Whiteley in Questioning Answers

In this post I'm talking about the paper by Pål Surén and colleagues [1] and their suggestion that "paternal obesity is an independent risk factor for ASDs [autism spectrum disorders] in children". I do so not with the intent of stigmatising parents and specifically parents with weight issues, which tend to be present for many more reasons than just food and exercise (see here), but merely to highlight how parental physical health may show some relationship to offspring cog........ Read more »

Suren, P., Gunnes, N., Roth, C., Bresnahan, M., Hornig, M., Hirtz, D., Lie, K., Lipkin, W., Magnus, P., Reichborn-Kjennerud, T.... (2014) Parental Obesity and Risk of Autism Spectrum Disorder. PEDIATRICS. DOI: 10.1542/peds.2013-3664  

  • April 11, 2014
  • 12:46 PM
  • 87 views

Variant Annotation in Coding Regions

by Daniel Koboldt in Massgenomics

The analysis of NGS data comes with many challenges — data management, read alignment, variant calling, etc. — that the bioinformatics community has tackled with some success. Today I want to discuss another critical component of analysis that remains an unsolved problem: annotation of genetic variants. This process, in which we try to predict the […]... Read more »

Davis J McCarthy, Peter Humburg, Alexander Kanapin, Manuel A Rivas, Kyle Gaulton, The WGS500 Consortium, Jean-Baptiste Cazier and Peter Donnelly. (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Medicine, 6(26). info:/doi:10.1186/gm543

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