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  • December 18, 2014
  • 02:35 PM
  • 15 views

Gene fragments linked to brain development and autism

by Gabriel in Lunatic Laboratories

While the anti-vaccine movement enjoys the simple (and very wrong) answer to the cause of autism, there are people who want the actual truth. This drive had lead to a slew of causes (and risk factors) for autism in recent times. Now scientists have found that very small segments of genes called “microexons” influence how proteins interact with each other in the nervous system. In turn, this opens up a new line of research into the cause of autism.... Read more »

Irimia, M., Weatheritt, R., Ellis, J., Parikshak, N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D.... (2014) A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains. Cell, 159(7), 1511-1523. DOI: 10.1016/j.cell.2014.11.035  

  • December 18, 2014
  • 09:36 AM
  • 16 views

What’s the Answer? (FANTOM5 promoter atlas)

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 »

Forrest Alistair R. R., Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, & Robin Andersson. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493), 462-470. DOI: http://dx.doi.org/10.1038/nature13182  

Severin Jessica, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, Nicolas Bertin, & Alistair R R Forrest. (2014) Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nature Biotechnology, 32(3), 217-219. DOI: http://dx.doi.org/10.1038/nbt.2840  

  • December 18, 2014
  • 05:08 AM
  • 21 views

Autistic traits in adults with epilepsy

by Paul Whiteley in Questioning Answers

"Increased autistic characteristics found in adults with epilepsy without an ASD [autism spectrum disorder] diagnosis suggest that epilepsy syndromes may incorporate behavioral aspects of autism in the absence of some of its core cognitive features."Contrariwise, if you think we're alive you ought to speak to us.That was the intriguing finding reported by Sally Ann Wakeford and colleagues [1] who examined test performance on the Autism Spectrum Quotient (AQ) and "systemizing ........ Read more »

Wakeford S, Hinvest N, Ring H, & Brosnan M. (2014) Autistic characteristics in adults with epilepsy. Epilepsy , 203-207. PMID: 25461216  

  • December 17, 2014
  • 02:54 PM
  • 30 views

Epigenetic changes and autism

by Gabriel in Lunatic Laboratories

Despite what you may think, the supposed “explosion” of children diagnosed with autism can directly attributed to better diagnosing techniques and — more importantly — the change of definition to make Autism spectrum disorders more broad. Thankfully more causes of autism have been found, none of them remotely related to vaccines and now scientists have found that chemical modifications to DNA’s packaging—known as epigenetic changes—can activate or repress genes involved in autism s........ Read more »

Gao, Z., Lee, P., Stafford, J., von Schimmelmann, M., Schaefer, A., & Reinberg, D. (2014) An AUTS2–Polycomb complex activates gene expression in the CNS. Nature, 516(7531), 349-354. DOI: 10.1038/nature13921  

Ntziachristos, P., Tsirigos, A., Welstead, G., Trimarchi, T., Bakogianni, S., Xu, L., Loizou, E., Holmfeldt, L., Strikoudis, A., King, B.... (2014) Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia. Nature, 514(7523), 513-517. DOI: 10.1038/nature13605  

  • December 17, 2014
  • 09:38 AM
  • 39 views

Video Tip of the Week: yEd Graph Editor for visualizing pathways and networks

by Mary in OpenHelix

This week’s video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week’s tool is the final piece that you need to know about if you want to create the kind of […]... Read more »

  • December 17, 2014
  • 08:00 AM
  • 41 views

Christmas Greenery - Friend Or Foe?

by Mark Lasbury in As Many Exceptions As Rules

Your Christmas tree can kill you, but it can also save your life. The same holds true for mistletoe, ivy, and holly. Each is toxic, but each has uses in medicine. The least toxic Christmas plant is the most often thought of as poisonous – poinsettias really aren’t that bad, kids would have to eat 500 leaves to bring on the nastiest effects.... Read more »

  • December 17, 2014
  • 07:11 AM
  • 34 views

Humpback Whales Sing For Their Supper

by beredim in Strange Animals

Humpback whales (Megaptera novaeangliae) are known to employ group foraging techniques, however details on how individuals coordinate with each other still remain a mystery.

A new study by Susan Parks, assistant professor of biology in the College of Arts and Sciences, in collaboration with a consortium of other researchers examined the importance of specific auditory cues that these whales emit... Read more »

Parks SE, Cusano DA, Stimpert AK, Weinrich MT, Friedlaender AS, & Wiley DN. (2014) Evidence for acoustic communication among bottom foraging humpback whales. Scientific reports, 7508. PMID: 25512188  

  • December 17, 2014
  • 04:29 AM
  • 27 views

Folate receptor autoantibodies and (some) schizophrenia

by Paul Whiteley in Questioning Answers

I am the league's director, Silas Ramsbottom.Upon reading the paper published by Ramaekers and colleagues [1] talking about the use of folinic acid in cases of schizophrenia as a function of the presence of "Auto-antibodies against folate receptor alpha (FRα)", I raised a little smile. Not only because the authors suggested that there may be quite a lot more to see in this area on top of some already interesting discussions about the folate cycle and schizophrenia, but also because of the ........ Read more »

Ramaekers VT, Thöny B, Sequeira JM, Ansseau M, Philippe P, Boemer F, Bours V, & Quadros EV. (2014) Folinic acid treatment for schizophrenia associated with folate receptor autoantibodies. Molecular genetics and metabolism. PMID: 25456743  

  • December 16, 2014
  • 04:29 PM
  • 39 views

Rift Valley Fever Virus and Autophagy: MyD88 and DRAM-1

by thelonevirologist in Virology Tidbits

Upon viral entry and release of the viral genome, viral RNA and DNA can be recognised by Toll-like Receptors (TLR), which once stimulated induce the expression of specific genes such as Interferon that are part of the antiviral response. TLR mediated signalling pathways predominantly signal through interferon regulatory factors (IRF) as well as Nuclear Factor-κB (NF-κB) and AP-1, eliciting the induction of the Interferon type-1 response and the expression of inflammatory cytokines as........ Read more »

Moy, R., Gold, B., Molleston, J., Schad, V., Yanger, K., Salzano, M., Yagi, Y., Fitzgerald, K., Stanger, B., Soldan, S.... (2014) Antiviral Autophagy Restricts Rift Valley Fever Virus Infection and Is Conserved from Flies to Mammals. Immunity, 40(1), 51-65. DOI: 10.1016/j.immuni.2013.10.020  

Shi CS, & Kehrl JH. (2008) MyD88 and Trif target Beclin 1 to trigger autophagy in macrophages. The Journal of biological chemistry, 283(48), 33175-82. PMID: 18772134  

Mah LY, O'Prey J, Baudot AD, Hoekstra A, & Ryan KM. (2012) DRAM-1 encodes multiple isoforms that regulate autophagy. Autophagy, 8(1), 18-28. PMID: 22082963  

Wang RC, Wei Y, An Z, Zou Z, Xiao G, Bhagat G, White M, Reichelt J, & Levine B. (2012) Akt-mediated regulation of autophagy and tumorigenesis through Beclin 1 phosphorylation. Science (New York, N.Y.), 338(6109), 956-9. PMID: 23112296  

Narayanan A, Amaya M, Voss K, Chung M, Benedict A, Sampey G, Kehn-Hall K, Luchini A, Liotta L, Bailey C.... (2014) Reactive oxygen species activate NFκB (p65) and p53 and induce apoptosis in RVFV infected liver cells. Virology, 270-86. PMID: 24418562  

Liang Q, Chang B, Brulois KF, Castro K, Min CK, Rodgers MA, Shi M, Ge J, Feng P, Oh BH.... (2013) Kaposi's sarcoma-associated herpesvirus K7 modulates Rubicon-mediated inhibition of autophagosome maturation. Journal of virology, 87(22), 12499-503. PMID: 24027317  

Mukhopadhyay S, Panda PK, Sinha N, Das DN, & Bhutia SK. (2014) Autophagy and apoptosis: where do they meet?. Apoptosis : an international journal on programmed cell death, 19(4), 555-66. PMID: 24415198  

Liang C, Oh BH, & Jung JU. (2014) Novel functions of viral anti-apoptotic factors. Nature reviews. Microbiology. PMID: 25363821  

  • December 16, 2014
  • 02:37 PM
  • 40 views

Methamphetamine use and the onset of parkinson’s

by Gabriel in Lunatic Laboratories

We’ve all seen the PSA’s trying to show the effects of meth use and in particular, what it does to your teeth. Typically, when it comes to drug use, people will not look at the long term side effects from their addiction instead thinking in the short term. This is unfortunate because as it turns out, methamphetamine users are three times more at risk for getting Parkinson’s disease than non-illicit drug users with even worse news for women, new research shows.... Read more »

  • December 16, 2014
  • 08:00 AM
  • 54 views

Giving, Getting, and Grey Matter

by Mark E. Lasbury in The 'Scope

It’s time to search out Christmas gifts! Let brain research guide you in your giving. We now know why women are often better at picking out gifts, and we know that you expect people to like your homemade gifts more than you should. We have learned that we give gifts to make ourselves feel good, and that too many gifts can screw your kids up for life. But most importantly, it actually is the thought that counts! Merry Christmas.... Read more »

Moll, J., Krueger, F., Zahn, R., Pardini, M., de Oliveira-Souza, R., & Grafman, J. (2006) Human fronto-mesolimbic networks guide decisions about charitable donation. Proceedings of the National Academy of Sciences, 103(42), 15623-15628. DOI: 10.1073/pnas.0604475103  

  • December 16, 2014
  • 04:41 AM
  • 59 views

Thioredoxin... a new 'diagnosis indicator' for autism?

by Paul Whiteley in Questioning Answers

My name's Buttercup. You've met Baron von Shush."Our study demonstrated that serum TRX [thioredoxin] levels were associated with ASD [autism spectrum disorder], and elevated levels could be considered as a novel, independent diagnosis indicator of ASD." So was the conclusion reported by Qing-biao Zhang and colleagues [1] looking at serum levels of TRX in 80 children diagnosed with an ASD compared against "100 sex and age matched typically developing children".I'll freely admi........ Read more »

Zhang QB, Gao SJ, & Zhao HX. (2014) Thioredoxin: A novel, independent diagnosis marker in children with autism. International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience. PMID: 25433158  

  • December 15, 2014
  • 03:07 PM
  • 68 views

Finding the neurons that deal with distraction

by Gabriel in Lunatic Laboratories

What’s that over there!? The next time you are around people, count how many people are on their phone? Distractions invade every aspect of our lives. Status updates, text messages, email notifications all threaten to steal our attention away from the moment. While we fight the urge to check the phone, our brains are making constant judgment calls about where to focus attention. The brain must continually filter important information from irrelevant interference.... Read more »

Ahrens, S., Jaramillo, S., Yu, K., Ghosh, S., Hwang, G., Paik, R., Lai, C., He, M., Huang, Z., & Li, B. (2014) ErbB4 regulation of a thalamic reticular nucleus circuit for sensory selection. Nature Neuroscience. DOI: 10.1038/nn.3897  

  • December 15, 2014
  • 07:00 AM
  • 63 views

The Paradoxical Shrinking Frog

by beredim in Strange Animals



Pseudis paradoxa in a pond
Credit: Mauricio Rivera Correa

Kingdom: Animalia
Phylum: Chordata
Class: Amphibia
Order: Anura
Family: Hylidae
Genus: Pseudis
Species: Pseudis paradoxa
Common Name(s): Paradoxical frog or Shrinking frog
Conservation Status: Least Concern (Not Threatened)

Looks like a pretty much regular frog, doesn't it? Well.. it's not! Meet P. paradoxa, a frog that grows down ... Read more »

  • December 15, 2014
  • 04:45 AM
  • 59 views

Rates of medical illnesses in bipolar disorder

by Paul Whiteley in Questioning Answers

I've mentioned a few times on this blog that a diagnosis of autism or autism spectrum disorder (ASD) is by no means protective against any other diagnosis being received, be it based on a somatic illness or condition, or something more behaviourally defined.Reading through the paper by Liz Forty and colleagues [1] (open-access) it appears that a similar scenario might also pertain to other behaviourally-defined conditions as per the example of bipolar disorder (BD) and their conclusion: "Bi........ Read more »

Forty L, Ulanova A, Jones L, Jones I, Gordon-Smith K, Fraser C, Farmer A, McGuffin P, Lewis CM, Hosang GM.... (2014) Comorbid medical illness in bipolar disorder. The British journal of psychiatry : the journal of mental science. PMID: 25359927  

  • December 15, 2014
  • 04:11 AM
  • 64 views

Electrogenic fish – what’s in charge of the charge?

by Kathrin Garschall in genome ecology evolution etc

Electric organs – organs that are capable of creating and discharging electricity – have evolved independently in at least six different lineages of fish (Torpediniformes, Rajiformes, Mormyroidea, Euteleostei, Siluriformes, Gymnotiformes) and play an important role in communication, navigation, defense and … Continue reading →... Read more »

Gallant, J., Traeger, L., Volkening, J., Moffett, H., Chen, P., Novina, C., Phillips, G., Anand, R., Wells, G., Pinch, M.... (2014) Genomic basis for the convergent evolution of electric organs. Science, 344(6191), 1522-1525. DOI: 10.1126/science.1254432  

  • December 15, 2014
  • 02:39 AM
  • 70 views

Transcription caught on camera part 1: Halo transcription factors

by Gal Haimovich in Green Fluorescent Blog

Transcription factors (TFs) have a fundamental role is regulating gene expression. The basic model, based on numerous biochemical analyses, have determined where TFs bind (usually at specific sites at or near promoters), when they bind the DNA (at a resolution … Continue reading →... Read more »

Chen J, Zhang Z, Li L, Chen BC, Revyakin A, Hajj B, Legant W, Dahan M, Lionnet T, Betzig E.... (2014) Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell, 156(6), 1274-85. PMID: 24630727  

  • December 14, 2014
  • 01:28 PM
  • 79 views

Scientists find a drug (currently used) to turn white fat to brown

by Gabriel in Lunatic Laboratories

It seems like we’ve been on a weight loss campaign here at the labs, but there just has been so much new and interesting research on the subject to report on, this is no exception. Researchers have uncovered the mechanism by which white fat cells from humans (an important distinction) gets reprogrammed to become browner.... Read more »

Anne Loft, Isabel Forss, Majken Storm Siersbæk, Søren Fisker Schmidt, Ann-Sofie Bøgh Larsen, Jesper Grud Skat Madsen, Didier F. Pisani, Ronni Nielsen, Mads Malik Aagaard, Angela Mathison.... (2014) Browning of human adipocytes requires KLF11 and reprogramming of PPARγ superenhancers. Genes . info:/10.1101/gad.250829.114

  • December 13, 2014
  • 01:51 PM
  • 84 views

High fat diet leads to brain inflammation and obesity

by Gabriel in Lunatic Laboratories

The stomach strikes again, or so it seems. We’ve already covered how your stomach seemingly controls your brain and your blood-brain barrier, but now it seems that what you eat –not too indirectly related to your stomach– might make you fatter, but not in the way you might be thinking thinking. What you are eating may be causing inflammation in the brain.... Read more »

  • December 13, 2014
  • 09:56 AM
  • 66 views

Gibbon genome and the fast karyotype evolution of small apes

by Sandra Bosshard in genome ecology evolution etc

Gibbons (Hylobatidae) are small arboreal apes that form a key node in primate evolution. One of the most distinctive phenotype is their high genome plasticity involving large-scale chromosomal rearrangements and karyotype changes. The four gibbon genera (Nomascus, Hylobates, Hoolock, Symphalangus) … Continue reading →... Read more »

Carbone, L., Alan Harris, R., Gnerre, S., Veeramah, K., Lorente-Galdos, B., Huddleston, J., Meyer, T., Herrero, J., Roos, C., Aken, B.... (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. DOI: 10.1038/nature13679  

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