Skip to content

Gender, Race, Sexuality, and the Neuroscience of Healthy Relationships

Monday, October 13, 2014

The thing that ties each of the following links together is a discussion of the need to incorporate equity, affirmation, and continued learning into social, scientific, and political spheres.  And to recognize that the lines between these spaces is a social construct.

This article offers an explanation of how sexism affects both the oppressed and the oppressor.  While they use a binary gender system in their drawings (male vs. female), it  is easy to understand how this could be applied to people in any gender system: http://imgur.com/gallery/n01WW

This article describes the work of Malala Yousafzai and Kailash Satyarthi who were recently awarded the Nobel Peace Prize for their work on expanding women’s and children’s rights in Pakistan and India, respectively.  Their stories highlight how personal identities are political and politics is personal: http://www.nytimes.com/2014/10/11/world/europe/kailash-satyarthi-and-malala-yousafzai-are-awarded-nobel-peace-prize.html?_r=0

This article goes in depth about African American and AfroCarribean identities in the U.S. as part of a larger history of colonization and slavery – how has this history impacted black Americans now and how is this oppression and the struggle for mutual humanization ongoing: http://www.washingtonpost.com/opinions/ferguson-wasnt-black-rage-against-copsit-was-white-rage-against-progress/2014/08/29/3055e3f4-2d75-11e4-bb9b-997ae96fad33_story.html

This article highlights some of the queer and trans* people of color working on gender, race, and sexuality equity in the U.S.  This is especially important given that the U.S. media (news, movies, t.v., radio, etc) predominately rewards and publicizes white, domestic, heterosexual, and cisgender people: http://www.autostraddle.com/22-badass-qtpoc-couples-that-make-our-hearts-flutter-253889/

Lastly, this article shows some really interesting research being done about children’s responsiveness and understanding of human emotions and interactions.  It has incredible implications for understanding the impacts of trauma, domestic violence, and healthy or unhealthy relationships on children as young as 15 months old!  http://www.huffingtonpost.com/2014/10/10/toddlers-angry-behave-study-video_n_5959482.html?ncid=fcbklnkushpmg00000063

 

Best,

Skye

 

Filed in education, fun, history of science, human behaviour, medicine and medical research, science and society | | Comments (1)

Ig Nobel prize 2014

Tuesday, September 23, 2014

Wonderful studies as usual!

http://www.improbable.com/ig/winners/#ig2014

The 2014 Ig Nobel Winners: Banana Peels to Nasal Pork

Filed in Fai's sharing, fun, Ig Nobel prize | | Comments Off on Ig Nobel prize 2014

Autism, The Politics of “Normal”, and Thinking Fast and Slow (the book)

Friday, September 19, 2014

A Cognitive Defense of Stimming (or Why “Quiet Hands” Makes Math Harder)

In the last decade or so, autism spectrum disorders (ASDs) have been in the forefront of the news and research.  Originally, the people thought autism was a psychological disorder and that it was similar to schitzophrenia.  There was a complete lack of understanding about what autism was, how it affected those with it, and how people who were not autistic could relate to people with autism.  People assumed the behaviors of autistic children or adults were just “bad behaviors” that needed to be corrected, often through electroshock therapies, LSD, and other harmful (pain-based) “treatments”.  All of this was administered under the philosphy that “normal” = healthy.

In the 80’s, the genetic and biological basis of behavior started to become a focus in research and health practitioner skills, propelled in part by discoveries about the genetic basis of circadian rhythms.  Behavioral therapy began and the new focus for autistic children was to help the mask the biological basis of their behaviors and confirm to “normal” social behavior so that they could have “normal” lives.  At some point, researchers and parents began to realize that a lot of autistic behaviors were a response to stimulation – over and under stimulation – and research began focusing on the neurobiology and neurogenetics of autism.

The idea that difference is “abnormal” and that “abnormal” = unhealthy is the basis of a LOT of oppression, violence, and harm caused and maintained in communities and cultures across the world at every time in history.  White colonists believed black, brown, yellow, and red people were lesser than and qualified this with “science”, suggesting that white was normal and non-white was abnormal (and of course this thinking continues to dictate structures and communities in colonized spaces today).  This raises larger questions: Who gets to determine what is normal or healthy?  When does normal = healthy?  How does society use standards of “normal” to force marginalized communities out of power?

In 2005 an organization named Autism Speaks was formed (but non-autistic people) to support research that would find a “cure” for autism spectrum disorders.  The organizations viewpoint then and now is that autism is a devastating health crisis that causes children to be lesser than and results in a poor quality of life.  As an autistic person, I find this not only offensive, but hugely damaging (in too many ways to describe here) to parents with autistic children, to autistic children and adults, and to prospective support systems that could be formed for autistic people.  “Curing” autism is similar to the argument about “curing” queerness.  Should we “fix” queer people so that they are all straight and cisgender, or should we support and embrace diverse experiences and lives for what they bring to the table?

As the recognition of autism and the number of autistic children has grown and continues to grow drastically, it is very important to address these questions.  One of the more visible effects of most autism spectrum disabilities is stimming, a word that is short for “self stimulation”.  Researchers now understand the the neurological systems of autistic people are different than those of most “neurotypical” people, making autistic individuals extra sensitive to some sensation and under-sensitive to others (as defined by neurotypical standards).  For example, many autistic people find that repetitive movements are calming (perhaps movement sensory input channels are chronically under-stimulated), so they may stim by tapping fingers or feet, flapping their hands, rocking, or doing something similar.  There is a big divide currently in the world of working with autistic children – should adults teach children to repress their stims or should they be accepted as supportive of childhood development?

I recently found a wonderfully written article on this topic and it refers to Thinking Fast and Slow.  I need to read this book soon (and maybe post on it later), but in the mean time, enjoy this article!  What are your thoughts on this or the other articles at the end of this one?

~Skye

Filed in education, fun, history of science, human behaviour, science and society | | Comments (2)

Spider Dog – for some humor

Wednesday, September 10, 2014

Since we all need to laugh more than we do:

Best,

Skye  🙂

Filed in fun | | Comments Off on Spider Dog – for some humor

2014-07-20 new articles we read this week

Sunday, July 20, 2014

Nature’s special on “Challenges in irreproducible research”

Human Behaviour/Psychology

  1. Kramer AD, Guillory JE, Hancock JT. Experimental evidence of massive-scale emotional contagion through social networks. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8788-90. doi: 10.1073/pnas.1320040111. Epub 2014 Jun 2. PubMed PMID: 24889601.

Retinal development

  1. Hoon M, Okawa H, Della Santina L, Wong RO. Functional Architecture of the Retina: Development and Disease. Prog Retin Eye Res. 2014 Jun 28. pii: S1350-9462(14)00038-X. doi: 10.1016/j.preteyeres.2014.06.003. [Epub ahead of print] Review. PubMed PMID: 24984227.

Stem cells

  1. Ksander BR, Kolovou PE, Wilson BJ, Saab KR, Guo Q, Ma J, McGuire SP, Gregory MS, Vincent WJ, Perez VL, Cruz-Guilloty F, Kao WW, Call MK, Tucker BA, Zhan Q, Murphy GF, Lathrop KL, Alt C, Mortensen LJ, Lin CP, Zieske JD, Frank MH, Frank NY. ABCB5 is a limbal stem cell gene required for corneal development and repair. Nature. 2014 Jul 17;511(7509):353-7. doi: 10.1038/nature13426. Epub 2014 Jul 2. PubMed PMID: 25030174.
  2. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  3. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  4. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  5. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  6. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.

Eye disease treatment

  1. Jepson LH, Hottowy P, Weiner GA, Dabrowski W, Litke AM, Chichilnisky EJ. High-fidelity reproduction of spatiotemporal visual signals for retinal prosthesis. Neuron. 2014 Jul 2;83(1):87-92. doi: 10.1016/j.neuron.2014.04.044. Epub 2014 Jun 5. PubMed PMID: 24910077.
    • Trenholm S, Roska B. Cell-type-specific electric stimulation for vision restoration. Neuron. 2014 Jul 2;83(1):1-2. doi: 10.1016/j.neuron.2014.06.012. PubMed PMID: 24991948.

Funding

  1. Resnick A. Systemic addiction to research funding. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2634. doi: 10.1073/pnas.1407369111. Epub 2014 Jun 11. PubMed PMID: 24920596.
  2. Alberts B, Kirschner MW, Tilghman S, Varmus H. Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5773-7. doi: 10.1073/pnas.1404402111. Epub 2014 Apr 14. PubMed PMID: 24733905; PubMed Central PMCID: PMC4000813.

Research Career

  1. Smaglik P. Employment: PhD overdrive. Nature. 2014 Jul 10;511(7508):255-6. PubMed PMID: 25013890.

Systems Biology

  1. Bruggner RV, Bodenmiller B, Dill DL, Tibshirani RJ, Nolan GP. Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2770-7. doi: 10.1073/pnas.1408792111. Epub 2014 Jun 16. PubMed PMID: 24979804.

Genomics/ Sequencing

  1. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA-sequencing. Genome Biol. 2014 Jun 30;15(6):R86. [Epub ahead of print] PubMed PMID: 24981968.
  2. Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9869-74. doi: 10.1073/pnas.1400447111. Epub 2014 Jun
    24. PubMed PMID: 24961374.

Genome editing

  1. Sheridan C. First CRISPR-Cas patent opens race to stake out intellectual property. Nat Biotechnol. 2014 Jul 8;32(7):599-601. doi: 10.1038/nbt0714-599. PubMed PMID: 25004207.
  2. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014 Jul;32(7):670-6. doi: 10.1038/nbt.2889. Epub 2014 Apr 20. PubMed PMID: 24752079.
  3. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.
  4. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  5. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  6. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  7. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  8. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.
  9. Güell M, Yang L, Church G. Genome Editing Assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics. 2014 Jul 1. pii: btu427. [Epub ahead of print] PubMed PMID: 24990609.
  10. Spies M. Fulfilling the dream of a perfect genome editing tool. Proc Natl Acad Sci U S A. 2014 Jul 2. pii: 201408985. [Epub ahead of print] PubMed PMID: 24989506.
Filed in Fai's sharing, journal watch | Tagged , , , , , , , , , , , , , , | Comments Off on 2014-07-20 new articles we read this week

2014-07-05 New articles we read this week

Saturday, July 5, 2014

Systems biology

  1. Levo M, Segal E. In pursuit of design principles of regulatory sequences. Nat Rev Genet. 2014 Jul;15(7):453-68. doi: 10.1038/nrg3684. Epub 2014 Jun 10. PubMed PMID: 24913666.
  2. Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20;344(6190):1396-401. doi: 10.1126/science.1254257. Epub 2014 Jun 12. PubMed PMID: 24925914.

Stem cells

  1. Cattaneo E, Corbellini G. Stem cells: taking a stand against pseudoscience. Nature. 2014 Jun 19;509(7505):333-5. PubMed PMID: 24955466.
  2. Bertolotti E, Neri A, Camparini M, Macaluso C, Marigo V. Stem cells as source for retinal pigment epithelium transplantation. Prog Retin Eye Res. 2014 Jun 13. pii: S1350-9462(14)00037-8. doi: 10.1016/j.preteyeres.2014.06.002. [Epub ahead of print] Review. PubMed PMID: 24933042.
  3. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5?32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201407473. [Epub ahead of print] PubMed PMID: 24927590.
  4. Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9253-8. doi: 10.1073/pnas.1323941111. Epub 2014 Jun 9. PubMed PMID: 24927536.

Neuroscience

  1. Rose N. The human brain project: social and ethical challenges. Neuron. 2014 Jun 18;82(6):1212-5. doi: 10.1016/j.neuron.2014.06.001. PubMed PMID: 24945767.
  2. Cohen MA, Konkle T, Rhee JY, Nakayama K, Alvarez GA. Processing multiple visual objects is limited by overlap in neural channels. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8955-60. doi: 10.1073/pnas.1317860111. Epub 2014 Jun 2. PubMed PMID: 24889618.
  3. Prevedel R, Yoon YG, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, Vaziri A. Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nat Methods. 2014 Jul;11(7):727-30. doi: 10.1038/nmeth.2964. Epub 2014 May 18. PubMed PMID: 24836920.

Neurobehaviour

  1. Pérez-Escudero A, Vicente-Page J, Hinz RC, Arganda S, de Polavieja GG. idTracker: tracking individuals in a group by automatic identification of unmarked animals. Nat Methods. 2014 Jul;11(7):743-8. doi: 10.1038/nmeth.2994. Epub 2014 Jun 1. PubMed PMID: 24880877.

Psychology

  1. Jung K, Shavitt S, Viswanathan M, Hilbe JM. Female hurricanes are deadlier than male hurricanes. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8782-7. doi: 10.1073/pnas.1402786111. Epub 2014 Jun 2. PubMed PMID: 24889620.

Retinal Development

  1. Laranjeiro R, Whitmore D. Transcription factors involved in retinogenesis are co-opted by the circadian clock following photoreceptor differentiation. Development. 2014 Jun 12. pii: dev.104380. [Epub ahead of print] PubMed PMID: 24924194.

Eye diseases

  1. Huber-Reggi SP, Mueller KP, Straumann D, Huang MY, Neuhauss SC. Individual Larvae of the Zebrafish Mutant belladonna Display Multiple Infantile Nystagmus-Like Waveforms that Are Influenced by Viewing Conditions. Invest Ophthalmol Vis Sci. 2014 May 27;55(6):3971-8. doi: 10.1167/iovs.13-13576. PubMed PMID: 24867578.

Zebrafish

  1. Law SH, Sargent TD. The Serine-Threonine Protein Kinase PAK4 Is Dispensable in Zebrafish: Identification of a Morpholino-Generated Pseudophenotype. PLoS One. 2014 Jun 19;9(6):e100268. doi: 10.1371/journal.pone.0100268. eCollection 2014. PubMed PMID: 24945275.

Genome editing/medicine

  1. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5?32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201407473. [Epub ahead of print] PubMed PMID: 24927590.
  2. Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9253-8. doi: 10.1073/pnas.1323941111. Epub 2014 Jun 9. PubMed PMID: 24927536.
  3. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. CRISPR
    transcriptional repression devices and layered circuits in mammalian cells. Nat
    Methods. 2014 Jul;11(7):723-6. doi: 10.1038/nmeth.2969. Epub 2014 May 5. PubMed
    PMID: 24797424.
  4. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK. Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells. Mol Cell. 2014 May 22;54(4):698-710. doi: 10.1016/j.molcel.2014.04.022. Epub 2014 May 15. PubMed PMID: 24837679.

Drug Discovery

  1. Wang YN, Hou YY, Sun MZ, Zhang CY, Bai G, Zhao X, Feng XZ. Behavioural screening of zebrafish using neuroactive traditional Chinese medicine prescriptions and biological targets. Sci Rep. 2014 Jun 16;4:5311. doi: 10.1038/srep05311. PubMed PMID: 24931174; PubMed Central PMCID: PMC4058885.

Science Career

  1. Casadevall A, Fang FC. Causes for the persistence of impact factor mania. MBio. 2014 Mar 18;5(2):e00064-14. doi: 10.1128/mBio.00064-14. PubMed PMID: 24643863; PubMed Central PMCID: PMC3967521.

Development

  1. Nicolas M, Hassan BA. Amyloid precursor protein and neural development. Development. 2014 Jul;141(13):2543-8. doi: 10.1242/dev.108712. PubMed PMID: 24961795.
  2. Deneris ES, Hobert O. Maintenance of postmitotic neuronal cell identity. Nat Neurosci. 2014 Jul;17(7):899-907. doi: 10.1038/nn.3731. Epub 2014 Jun 15. PubMed PMID: 24929660.

Methods

  1. Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer DV, Herr AE. Single-cell western blotting. Nat Methods. 2014 Jul;11(7):749-55. doi: 10.1038/nmeth.2992. Epub 2014  Jun 1. PubMed PMID: 24880876.
Filed in Fai's sharing, journal watch | Tagged , , , , , , , , , , , , , , , , | Comments Off on 2014-07-05 New articles we read this week

Uri Alon: Why truly innovative science demands a leap into the unknown

Sunday, June 22, 2014

Just saw this from a friend’s share. It is a great TED talk by Uri Alon on his experience on doing innovative science.

 

His work has inspired many including myself. Here are a few seminal papers by his groups.

  1. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science. 2002 Oct 25;298(5594):824-7. PubMed PMID: 12399590.
  2. Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 2002 May;31(1):64-8. Epub 2002 Apr 22. PubMed PMID: 11967538.
  3. Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet. 2007 Jun;8(6):450-61. Review. PubMed PMID: 17510665.

 

Filed in Fai's sharing | Tagged , , , , | Comments Off on Uri Alon: Why truly innovative science demands a leap into the unknown

2014-06-21 new articles we read this week

Saturday, June 21, 2014

Stem cells/ regenerative medicine

  1. Zhong X, Gutierrez C, Xue T, Hampton C, Vergara MN, Cao LH, Peters A, Park TS, Zambidis ET, Meyer JS, Gamm DM, Yau KW, Canto-Soler MV. Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs. Nat Commun. 2014 Jun 10;5:4047. doi: 10.1038/ncomms5047. PubMed PMID: 24915161.
  2. Reichman S, Terray A, Slembrouck A, Nanteau C, Orieux G, Habeler W, Nandrot EF, Sahel JA, Monville C, Goureau O. From confluent human iPS cells to self-forming neural retina and retinal pigmented epithelium. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8518-23. doi: 10.1073/pnas.1324212111. Epub 2014 May 27. PubMed PMID: 24912154.
  3. Chong JJ, Yang X, Don CW, Minami E, Liu YW, Weyers JJ, Mahoney WM, Van Biber B, Cook SM, Palpant NJ, Gantz JA, Fugate JA, Muskheli V, Gough GM, Vogel KW, Astley CA, Hotchkiss CE, Baldessari A, Pabon L, Reinecke H, Gill EA, Nelson V, Kiem HP, Laflamme MA, Murry CE. Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts. Nature. 2014 Jun 12;510(7504):273-7. doi: 10.1038/nature13233. Epub 2014 Apr 30. PubMed PMID: 24776797.
  4. Normile D, Vogel G. Cell biology. STAP cells succumb to pressure. Science. 2014 Jun 13;344(6189):1215-6. doi: 10.1126/science.344.6189.1215. PubMed PMID: 24925996.

Eye diseases

  1. Agbaga MP, Tam BM, Wong JS, Yang LL, Anderson RE, Moritz OL. Mutant ELOVL4 That Causes Autosomal Dominant Stargardt-3 Macular Dystrophy Is Misrouted to Rod Outer Segment Disks. Invest Ophthalmol Vis Sci. 2014 May 15;55(6):3669-3680. doi: 10.1167/iovs.13-13099. PubMed PMID: 24833735.

Oxidative stress

  1. Moussavi Nik SH, Croft K, Mori TA, Lardelli M. The comparison of methods for measuring oxidative stress in zebrafish brains. Zebrafish. 2014 Jun;11(3):248-54. doi: 10.1089/zeb.2013.0958. Epub 2014 May 5. PubMed PMID: 24798242.

Molecular Biology

  1. Roberts JW. Molecular biology. Molecular basis of transcription pausing. Science. 2014 Jun 13;344(6189):1226-7. doi: 10.1126/science.1255712. PubMed PMID: 24926002.

Systems Biology

  1. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 2014 Jun 11. doi: 10.1038/nature13437. [Epub ahead of print] PubMed PMID: 24919153.

Synthetic Biology/Gene regulatory Network

  1. Attwater J, Holliger P. A synthetic approach to abiogenesis. Nat Methods. 2014 May;11(5):495-8. doi: 10.1038/nmeth.2893. PubMed PMID: 24781322.
  2. Brophy JA, Voigt CA. Principles of genetic circuit design. Nat Methods. 2014 May;11(5):508-20. doi: 10.1038/nmeth.2926. Review. PubMed PMID: 24781324.

Behaviour

  1. Zhou Y, Cattley RT, Cario CL, Bai Q, Burton EA. Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications. Nat Protoc. 2014 Jul;9(7):1533-48. doi: 10.1038/nprot.2014.094. Epub 2014 Jun 5. PubMed PMID: 24901738.

Education

  1. Wieman CE. Large-scale comparison of science teaching methods sends clear message. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8319-20. doi: 10.1073/pnas.1407304111. Epub 2014 May 22. PubMed PMID: 24853505.
  2. Zhou M, Lee J. Assessing what is cultural about Asian Americans’ academic advantage. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8321-2. doi: 10.1073/pnas.1407309111. Epub 2014 May 29. PubMed PMID: 24876277.
  3. Freeman S, Eddy SL, McDonough M, Smith MK, Okoroafor N, Jordt H, Wenderoth MP. Active learning increases student performance in science, engineering, and mathematics. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8410-5. doi: 10.1073/pnas.1319030111. Epub 2014 May 12. PubMed PMID: 24821756.
  4. Hsin A, Xie Y. Explaining Asian Americans’ academic advantage over whites. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8416-21. doi: 10.1073/pnas.1406402111. Epub 2014 May 5. PubMed PMID: 24799702.

Scientific Career

  1. van Dijk D, Manor O, Carey LB. Publication metrics and success on the academic job market. Curr Biol. 2014 Jun 2;24(11):R516-7. doi: 10.1016/j.cub.2014.04.039. PubMed PMID: 24892909.
Filed in Fai's sharing, journal watch | Tagged , , , , , , , , , , , , , , | Comments Off on 2014-06-21 new articles we read this week

The Hum

Saturday, June 21, 2014

Here is a random/interesting article about a sensory phenomenon that occurs across the world.

 

http://mic.com/articles/91091/a-mysterious-sound-is-driving-people-insane-and-nobody-knows-what-s-causing-it?utm_source=policymicFB&utm_medium=main&utm_campaign=social

Filed in fun, science and society | | Comments (1)

Week – 1 in MBL : Genomics Bootcamp

Thursday, June 19, 2014

Saturday, June 14th marked the end of my first week at Woods Hole (I apologize for the late post). It was certainly a genomics bootcamp! In just one week, we learnt to dissect the ventral nerve chords from 3rd instar Drosophila larvae, extracted RNA, did microarrays, analyzed data and came up with hypotheses of what could be happening in our samples. We interacted and worked closely with wonderful TAs and faculty from different universities. This exercise certainly made me appreciate the hard work put in to genomic techniques (especially microarrays, RNAseq) and the enormity of the data obtained.

To celebrate the end of first week, some of us took a ferry to Martha’s Vineyard before charging up for the next section.

“On the Ferry to Martha's Vineyard”

We rented bikes and explored the beautiful island a little bit before settling for a nice picnic on the beach!

America's oldest platform carousel at Martha's Vineyard

Exploring Martha's Vineyard

Thus ended a great first week.
Next post: EPhys !

Filed in education, fun, lab activities | | Comments Off on Week – 1 in MBL : Genomics Bootcamp