You'd Prefer An Argonaute

Great Adaptations

Posted in Evolution, Science Journalism, YPAA Journal Club by YPAA on November 10, 2012

great-adaptations

An article that I wrote, Great Adaptations, has just been published in the September/October issue of Natural History Magazine. It’s about the research of Dianne Newman, Lars Dietrich, and their colleagues. Read it to learn about how bacteria and us are really just two peas in a pod, evolutionarily speaking.

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Oh No Journal Club 10/13/11

Posted in YPAA Journal Club by YPAA on October 13, 2011

Holy smokes–four back-to-back papers on candy RNAs in today’s Cell?!

(1) Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

Yvonne Tay, Lev Kats, Leonardo Salmena, Dror Weiss, Shen Mynn Tan, Ugo Ala, Florian Karreth, Laura Poliseno, Paolo Provero, Ferdinando Di Cunto, Judy Lieberman, Isidore Rigoutsos, Pier Paolo Pandolfi

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(2) A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

Marcella Cesana, Davide Cacchiarelli, Ivano Legnini, Tiziana Santini, Olga Sthandier, Mauro Chinappi, Anna Tramontano, Irene Bozzoni

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(3) An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, Andrea Califano

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(4) In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

Florian A. Karreth, Yvonne Tay, Daniele Perna, Ugo Ala, Shen Mynn Tan, Alistair G. Rust, Gina DeNicola, Kaitlyn A. Webster, Dror Weiss, Pedro A. Perez-Mancera, Michael Krauthammer, Ruth Halaban, Paolo Provero, David J. Adams, David A. Tuveson, Pier Paolo Pandolfi

Hey essay—what’s up wit your ceRNA?

Posted in YPAA Journal Club by YPAA on August 1, 2011

My feelings for this “Leading Edge Essay” have simmered for a few days now, and I still think it’s the worst piece of work I’ve encountered in the field of regulatory RNAs during my four years of training.

First of all, Cell, why did you publish this?

To the authors: why did you invent a generic new class of biomolecule, the ceRNA, with essentially only the weak support from a research paper of your own? My colleagues and I thought that paper had noticeably significant flaws.

To the community: you may consider the ceRNA idea—as abstract as it is—an intriguing one, but here it is expressed so poorly, with such insistent language, and peppered with simplistic statements, that it sounds completely ridiculous.

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A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, and Pier Paolo Pandolfi

Cell (2011)
doi:10.1016/j.cell.2011.07.014

If your last name begins with two letter “A”s, you should get into high energy physics

Posted in YPAA Journal Club by YPAA on April 19, 2011

Observation of a centrality-dependent dijet asymmetry in lead-lead collisions at sqrt[S(NN)] =2.76 TeV with the ATLAS detector at the LHC.

Aad G, Abbott B, Abdallah J, Abdelalim AA, Abdesselam A, Abdinov O, Abi B, Abolins M, Abramowicz H, Abreu H, Acerbi E, Acharya BS, Ackers M, Adams DL, Addy TN, Adelman J, Aderholz M, Adomeit S, Adragna P, Adye T, Aefsky S, Aguilar-Saavedra JA, Aharrouche M, Ahlen SP, Ahles F, Ahmad A, Ahsan M, Aielli G, Akdogan T, Akesson TP, Akimoto G, Akimov AV, Alam MS, Alam MA, Albrand S, Aleksa M, Aleksandrov IN, Aleppo M, Alessandria F, Alexa C, Alexander G, Alexandre G, Alexopoulos T, Alhroob M, Aliev M, Alimonti G, Alison J, Aliyev M, Allport PP, Allwood-Spiers SE, Almond J, Aloisio A, Alon R, Alonso A, Alonso J, Alviggi MG, Amako K, Amaral P, Amelung C, Ammosov VV, Amorim A, Amorós G, Amram N, Anastopoulos C, Andeen T, Anders CF, Anderson KJ, Andreazza A, Andrei V, Andrieux ML, Anduaga XS, Angerami A, Anghinolfi F, Anjos N, Annovi A, Antonaki A, Antonelli M, Antonelli S, Antos J, Anulli F, Aoun S, Bella LA, Apolle R, Arabidze G, Aracena I, Arai Y, Arce AT, Archambault JP, Arfaoui S, Arguin JF, Arik E, Arik M, Armbruster AJ, Arms KE, Armstrong SR, Arnaez O, Arnault C, Artamonov A, Artoni G, Arutinov D, Asai S, Silva J, Asfandiyarov R, Ask S, Asman B, Asquith L, Assamagan K, Astbury A, Astvatsatourov A, Atoian G, Aubert B, Auerbach B, Auge E, Augsten K, Aurousseau M, Austin N, Avramidou R, Axen D, Ay C, Azuelos G, Azuma Y, Baak MA, Baccaglioni G, Bacci C, Bach AM, Bachacou H, Bachas K, Bachy G, Backes M, Badescu E, Bagnaia P, Bahinipati S, Bai Y, Bailey DC, Bain T, Baines JT, Baker OK, Baker S, Pedrosa FB, Banas E, Banerjee P, Banerjee S, Banfi D, Bangert A, Bansal V, Bansil HS, Barak L, Baranov SP, Barashkou A, Galtieri AB, Barber T, Barberio EL, Barberis D, Barbero M, Bardin DY, Barillari T, Barisonzi M, Barklow T, Barlow N, Barnett BM, Barnett RM, Baroncelli A, Barr AJ, Barreiro F, da Costa JB, Barrillon P, Bartoldus R, Barton AE, Bartsch D, Bates RL, Batkova L, Batley JR, Battaglia A, Battistin M, Battistoni G, Bauer F, Bawa HS, Beare B, Beau T, Beauchemin PH, Beccherle R, Bechtle P, Beck HP, Beckingham M, Becks KH, Beddall AJ, Beddall A, Bednyakov VA, Bee C, Begel M, Harpaz SB, Behera PK, Beimforde M, Belanger-Champagne C, Bell PJ, Bell WH, Bella G, Bellagamba L, Bellina F, Bellomo G, Bellomo M, Belloni A, Belotskiy K, Beltramello O, Ben Ami S, Benary O, Benchekroun D, Benchouk C, Bendel M, Benedict BH, Benekos N, Benhammou Y, Benjamin DP, Benoit M, Bensinger JR, Benslama K, Bentvelsen S, Berge D, Kuutmann EB, Berger N, Berghaus F, Berglund E, Beringer J, Bernardet K, Bernat P, Bernhard R, Bernius C, Berry T, Bertin A, Bertinelli F, Bertolucci F, Besana MI, Besson N, Bethke S, Bhimji W, Bianchi RM, Bianco M, Biebel O, Biesiada J, Biglietti M, Bilokon H, Bindi M, Bingul A, Bini C, Biscarat C, Bitenc U, Black KM, Blair RE, Blanchard JB, Blanchot G, Blocker C, Blocki J, Blondel A, Blum W, Blumenschein U, Bobbink GJ, Bobrovnikov VB, Bocci A, Bock R, Boddy CR, Boehler M, Boek J, Boelaert N, Böser S, Bogaerts JA, Bogdanchikov A, Bogouch A, Bohm C, Boisvert V, Bold T, Boldea V, Boonekamp M, Boorman G, Booth CN, Booth P, Booth JR, Bordoni S, Borer C, Borisov A, Borissov G, Borjanovic I, Borroni S, Bos K, Boscherini D, Bosman M, Boterenbrood H, Botterill D, Bouchami J, Boudreau J, Bouhova-Thacker EV, Boulahouache C, Bourdarios C, Bousson N, Boveia A, Boyd J, Boyko IR, Bozhko NI, Bozovic-Jelisavcic I, Bracinik J, Braem A, Brambilla E, Branchini P, Brandenburg GW, Brandt A, Brandt G, Brandt O, Bratzler U, Brau B, Brau JE, Braun HM, Brelier B, Bremer J, Brenner R, Bressler S, Breton D, Brett ND, Bright-Thomas PG, Britton D, Brochu FM, Brock I, Brock R, Brodbeck TJ, Brodet E, Broggi F, Bromberg C, Brooijmans G, Brooks WK, Brown G, Brubaker E, de Renstrom PA, Bruncko D, Bruneliere R, Brunet S, Bruni A, Bruni G, Bruschi M, Buanes T, Bucci F, Buchanan J, Buchanan NJ, Buchholz P, Buckingham RM, Buckley AG, Buda SI, Budagov IA, Budick B, Büscher V, Bugge L, Buira-Clark D, Buis EJ, Bulekov O, Bunse M, Buran T, Burckhart H, Burdin S, Burgess T, Burke S, Busato E, Bussey P, Buszello CP, Butin F, Butler B, Butler JM, Buttar CM, Butterworth JM, Buttinger W, Byatt T, Urbán SC, Caccia M, Caforio D, Cakir O, Calafiura P, Calderini G, Calfayan P, Calkins R, Caloba LP, Caloi R, Calvet D, Calvet S, Camard A, Camarri P, Cambiaghi M, Cameron D, Cammin J, Campana S, Campanelli M, Canale V, Canelli F, Canepa A, Cantero J, Capasso L, Garrido MD, Caprini I, Caprini M, Capriotti D, Capua M, Caputo R, Caramarcu C, Cardarelli R, Carli T, Carlino G, Carminati L, Caron B, Caron S, Carpentieri C, Montoya GD, Montero SC, Carter AA, Carter JR, Carvalho J, Casadei D, Casado MP, Cascella M, Caso C, Hernandez AM, Castaneda-Miranda E, Gimenez VC, Castro NF, Cataldi G, Cataneo F, Catinaccio A, Catmore JR, Cattai A, Cattani G, Caughron S, Cavallari A, Cavalleri P, Cavalli D, Cavalli-Sforza M, Cavasinni V, Cazzato A, Ceradini F, Cerna C, Cerqueira AS, Cerri A, Cerrito L, Cerutti F, Cetin SA, Cevenini F, Chafaq A, Chakraborty D, Chan K, Chapleau B, Chapman JD, Chapman JW, Chareyre E, Charlton DG, Chavda V, Cheatham S, Chekanov S, Chekulaev SV, Chelkov GA, Chen H, Chen L, Chen S, Chen T, Chen X, Cheng S, Cheplakov A, Chepurnov VF, El Moursli RC, Tcherniatine V, Cheu E, Cheung SL, Chevalier L, Chevallier F, Chiefari G, Chikovani L, Childers JT, Chilingarov A, Chiodini G, Chizhov MV, Choudalakis G, Chouridou S, Christidi IA, Christov A, Chromek-Burckhart D, Chu ML, Chudoba J, Ciapetti G, Ciftci AK, Ciftci R, Cinca D, Cindro V, Ciobotaru MD, Ciocca C, Ciocio A, Cirilli M, Ciubancan M, Clark A, Clark PJ, Cleland W, Clemens JC, Clement B, Clement C, Clifft RW, Coadou Y, Cobal M, Coccaro A, Cochran J, Coe P, Cogan JG, Coggeshall J, Cogneras E, Cojocaru CD, Colas J, Cole B, Colijn AP, Collard C, Collins NJ, Collins-Tooth C, Collot J, Colon G, Coluccia R, Comune G, Muiño PC, Coniavitis E, Conidi MC, Consonni M, Constantinescu S, Conta C, Conventi F, Cook J, Cooke M, Cooper BD, Cooper-Sarkar AM, Cooper-Smith NJ, Copic K, Cornelissen T, Corradi M, Correard S, Corriveau F, Cortes-Gonzalez A, Cortiana G, Costa G, Costa MJ, Costanzo D, Costin T, Côté D, Torres RC, Courneyea L, Cowan G, Cowden C, Cox BE, Cranmer K, Cristinziani M, Crosetti G, Crupi R, Crépé-Renaudin S, Almenar CC, Donszelmann TC, Cuneo S, Curatolo M, Curtis CJ, Cwetanski P, Czirr H, Czyczula Z, D’Auria S, D’Onofrio M, D’Orazio A, Mello Ada R, Da Silva PV, Da Via C, Dabrowski W, Dahlhoff A, Dai T, Dallapiccola C, Dallison SJ, Dam M, Dameri M, Damiani DS, Danielsson HO, Dankers R, Dannheim D, Dao V, Darbo G, Darlea GL, Daum C, Dauvergne JP, Davey W, Davidek T, Davidson N, Davidson R, Davies M, Davison AR, Dawe E, Dawson I, Dawson JW, Daya RK, De K, de Asmundis R, De Castro S, De Cecco S, de Graat J, De Groot N, de Jong P, De La Cruz-Burelo E, De La Taille C, De Lotto B, De Mora L, De Nooij L, Branco Mde O, De Pedis D, de Saintignon P, De Salvo A, De Sanctis U, De Santo A, De Regie JB, Dean S, Debbe R, Dedes G, Dedovich DV, Degenhardt J, Dehchar M, Deile M, Del Papa C, Del Peso J, Del Prete T, Dell’Acqua A, Dell’Asta L, Della Pietra M, Della Volpe D, Delmastro M, Delpierre P, Delruelle N, Delsart PA, Deluca C, Demers S, Demichev M, Demirkoz B, Deng J, Denisov SP, Dennis C, Derendarz D, Derkaoui JE, Derue F, Dervan P, Desch K, Devetak E, Deviveiros PO, Dewhurst A, DeWilde B, Dhaliwal S, Dhullipudi R, Di Ciaccio A, Di Ciaccio L, Di Girolamo A, Di Girolamo B, Di Luise S, Di Mattia A, Di Nardo R, Di Simone A, Di Sipio R, Diaz MA, Diblen F, Diehl EB, Dietl H, Dietrich J, Dietzsch TA, Diglio S, Yagci KD, Dingfelder J, Dionisi C, Dita P, Dita S, Dittus F, Djama F, Djilkibaev R, Djobava T, do Vale MA, Wemans Ado V, Doan TK, Dobbs M, Dobinson R, Dobos D, Dobson E, Dobson M, Dodd J, Dogan OB, Doglioni C, Doherty T, Doi Y, Dolejsi J, Dolenc I, Dolezal Z, Dolgoshein BA, Dohmae T, Donadelli M, Donega M, Donini J, Dopke J, Doria A, Dos Anjos A, Dosil M, Dotti A, Dova MT, Dowell JD, Doxiadis AD, Doyle AT, Drasal Z, Drees J, Dressnandt N, Drevermann H, Driouichi C, Dris M, Drohan JG, Dubbert J, Dubbs T, Dube S, Duchovni E, Duckeck G, Dudarev A, Dudziak F, Dührssen M, Duerdoth IP, Duflot L, Dufour MA, Dunford M, Yildiz HD, Duxfield R, Dwuznik M, Dydak F, Dzahini D, Düren M, Ebke J, Eckert S, Eckweiler S, Edmonds K, Edwards CA, Efthymiopoulos I, Ehrenfeld W, Ehrich T, Eifert T, Eigen G, Einsweiler K, Eisenhandler E, Ekelof T, El Kacimi M, Ellert M, Elles S, Ellinghaus F, Ellis K, Ellis N, Elmsheuser J, Elsing M, Ely R, Emeliyanov D, Engelmann R, Engl A, Epp B, Eppig A, Erdmann J, Ereditato A, Eriksson D, Ernst J, Ernst M, Ernwein J, Errede D, Errede S, Ertel E, Escalier M, Escobar C, Curull XE, Esposito B, Etienne F, Etienvre AI, Etzion E, Evangelakou D, Evans H, Fabbri L, Fabre C, Facius K, Fakhrutdinov RM, Falciano S, Falou AC, Fang Y, Fanti M, Farbin A, Farilla A, Farley J, Farooque T, Farrington SM, Farthouat P, Fasching D, Fassnacht P, Fassouliotis D, Fatholahzadeh B, Favareto A, Fayard L, Fazio S, Febbraro R, Federic P, Fedin OL, Fedorko I, Fedorko W, Fehling-Kaschek M, Feligioni L, Fellmann D, Felzmann CU, Feng C, Feng EJ, Fenyuk AB, Ferencei J, Ferguson D, Ferland J, Fernandes B, Fernando W, Ferrag S, Ferrando J, Ferrara V, Ferrari A, Ferrari P, Ferrari R, Ferrer A, Ferrer ML, Ferrere D, Ferretti C, Parodi AF, Fiascaris M, Fiedler F, Filipčič A, Filippas A, Filthaut F, Fincke-Keeler M, Fiolhais MC, Fiorini L, Firan A, Fischer G, Fischer P, Fisher MJ, Fisher SM, Flammer J, Flechl M, Fleck I, Fleckner J, Fleischmann P, Fleischmann S, Flick T, Castillo LR, Flowerdew MJ, Föhlisch F, Fokitis M, Martin TF, Forbush DA, Formica A, Forti A, Fortin D, Foster JM, Fournier D, Foussat A, Fowler AJ, Fowler K, Fox H, Francavilla P, Franchino S, Francis D, Frank T, Franklin M, Franz S, Fraternali M, Fratina S, French ST, Froeschl R, Froidevaux D, Frost JA, Fukunaga C, Torregrosa EF, Fuster J, Gabaldon C, Gabizon O, Gadfort T, Gadomski S, Gagliardi G, Gagnon P, Galea C, Gallas EJ, Gallas MV, Gallo V, Gallop BJ, Gallus P, Galyaev E, Gan KK, Gao YS, Gapienko VA, Gaponenko A, Garberson F, Garcia-Sciveres M, García C, Navarro JE, Gardner RW, Garelli N, Garitaonandia H, Garonne V, Garvey J, Gatti C, Gaudio G, Gaumer O, Gaur B, Gauthier L, Gavrilenko IL, Gay C, Gaycken G, Gayde JC, Gazis EN, Ge P, Gee CN, Geich-Gimbel Ch, Gellerstedt K, Gemme C, Genest MH, Gentile S, Georgatos F, George S, Gerlach P, Gershon A, Geweniger C, Ghazlane H, Ghez P, Ghodbane N, Giacobbe B, Giagu S, Giakoumopoulou V, Giangiobbe V, Gianotti F, Gibbard B, Gibson A, Gibson SM, Gieraltowski GF, Gilbert LM, Gilchriese M, Gildemeister O, Gilewsky V, Gillberg D, Gillman AR, Gingrich DM, Ginzburg J, Giokaris N, Giordano R, Giorgi FM, Giovannini P, Giraud PF, Giugni D, Giusti P, Gjelsten BK, Gladilin LK, Glasman C, Glatzer J, Glazov A, Glitza KW, Glonti GL, Godfrey J, Godlewski J, Goebel M, Göpfert T, Goeringer C, Gössling C, Göttfert T, Goldfarb S, Goldin D, Golling T, Gollub NP, Golovnia SN, Gomes A, Fajardo LS, Gonçalo R, Gonella L, Gong C, Gonidec A, Gonzalez S, de la Hoz SG, Silva ML, Gonzalez-Sevilla S, Goodson JJ, Goossens L, Gorbounov PA, Gordon HA, Gorelov I, Gorfine G, Gorini B, Gorini E, Gorišek A, Gornicki E, Gorokhov SA, Gorski BT, Goryachev VN, Gosdzik B, Gosselink M, Gostkin MI, Gouanère M, Eschrich IG, Gouighri M, Goujdami D, Goulette MP, Goussiou AG, Goy C, Grabowska-Bold I, Grabski V, Grafström P, Grah C, Grahn KJ, Grancagnolo F, Grancagnolo S, Grassi V, Gratchev V, Grau N, Gray HM, Gray JA, Graziani E, Grebenyuk OG, Greenfield D, Greenshaw T, Greenwood ZD, Gregor IM, Grenier P, Griesmayer E, Griffiths J, Grigalashvili N, Grillo AA, Grimm K, Grinstein S, Gris PL, Grishkevich YV, Grivaz JF, Grognuz J, Groh M, Gross E, Grosse-Knetter J, Groth-Jensen J, Gruwe M, Grybel K, Guarino VJ, Guicheney C, Guida A, Guillemin T, Guindon S, Guler H, Gunther J, Guo B, Guo J, Gupta A, Gusakov Y, Gushchin VN, Gutierrez A, Gutierrez P, Guttman N, Gutzwiller O, Guyot C, Gwenlan C, Gwilliam CB, Haas A, Haas S, Haber C, Hackenburg R, Hadavand HK, Hadley DR, Haefner P, Hahn F, Haider S, Hajduk Z, Hakobyan H, Haller J, Hamacher K, Hamilton A, Hamilton S, Han H, Han L, Hanagaki K, Hance M, Handel C, Hanke P, Hansen CJ, Hansen JR, Hansen JB, Hansen JD, Hansen PH, Hansson P, Hara K, Hare GA, Harenberg T, Harper D, Harrington RD, Harris OM, Harrison K, Hart JC, Hartert J, Hartjes F, Haruyama T, Harvey A, Hasegawa S, Hasegawa Y, Hassani S, Hatch M, Hauff D, Haug S, Hauschild M, Hauser R, Havranek M, Hawes BM, Hawkes CM, Hawkings RJ, Hawkins D, Hayakawa T, Hayden D, Hayward HS, Haywood SJ, Hazen E, He M, Head SJ, Hedberg V, Heelan L, Heim S, Heinemann B, Heisterkamp S, Helary L, Heldmann M, Heller M, Hellman S, Helsens C, Henderson RC, Henke M, Henrichs A, Correia AM, Henrot-Versille S, Henry-Couannier F, Hensel C, Henss T, Jiménez YH, Herrberg R, Hershenhorn AD, Herten G, Hertenberger R, Hervas L, Hessey NP, Hidvegi A, Higón-Rodriguez E, Hill D, Hill JC, Hill N, Hiller KH, Hillert S, Hillier SJ, Hinchliffe I, Hines E, Hirose M, Hirsch F, Hirschbuehl D, Hobbs J, Hod N, Hodgkinson MC, Hodgson P, Hoecker A, Hoeferkamp MR, Hoffman J, Hoffmann D, Hohlfeld M, Holder M, Holmes A, Holmgren SO, Holy T, Holzbauer JL, Homer RJ, Homma Y, Horazdovsky T, Horn C, Horner S, Horton K, Hostachy JY, Hott T, Hou S, Houlden MA, Hoummada A, Howarth J, Howell DF, Hristova I, Hrivnac J, Hruska I, Hryn’ova T, Hsu PJ, Hsu SC, Huang GS, Hubacek Z, Hubaut F, Huegging F, Huffman TB, Hughes EW, Hughes G, Hughes-Jones RE, Huhtinen M, Hurst P, Hurwitz M, Husemann U, Huseynov N, Huston J, Huth J, Iacobucci G, Iakovidis G, Ibbotson M, Ibragimov I, Ichimiya R, Iconomidou-Fayard L, Idarraga J, Idzik M, Iengo P, Igonkina O, Ikegami Y, Ikeno M, Ilchenko Y, Iliadis D, Imbault D, Imhaeuser M, Imori M, Ince T, Inigo-Golfin J, Ioannou P, Iodice M, Ionescu G, Quiles AI, Ishii K, Ishikawa A, Ishino M, Ishmukhametov R, Isobe T, Issever C, Istin S, Itoh Y, Ivashin AV, Iwanski W, Iwasaki H, Izen JM, Izzo V, Jackson B, Jackson JN, Jackson P, 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Ziolkowski M, Zitoun R, Zivković L, Zmouchko VV, Zobernig G, Zoccoli A, Zolnierowski Y, Zsenei A, zur Nedden M, Zutshi V, Zwalinski L; ATLAS Collaboration.

Phys Rev Lett. 2010 Dec 17;105(25):252303. Epub 2010 Dec 13.

AGO AGO Decoy

Posted in Media, YPAA Journal Club by YPAA on April 14, 2011

A nice looking new paper on AGO10 is accompanied by a video on the Cell website.

Broad-ening our understanding of p53 via lincRNA

Posted in Broad, Media, YPAA Journal Club by YPAA on August 6, 2010

In the first real post on You’d Prefer An Argonaute, I poked great fun at the Broad Institute. It’s not so rare that my colleagues and I do this because well, from its inception the Broad, where King Lander reigns, has lavishly branded itself as a future of biological science, where too often hypothesis-less, behemoth experiments that involve lots of sequencing and money and relatively few papers, rule. So, it’s lovely to see work like this from John Rinn’s lab, which got its start in the Broad, killing it!

Channeling LeVar Burton of Reading Rainbow, Rinn, and lead author Maite Huarte, educate us in this video posted to the Cell website. The Broad applied their characteristic sheen in its production, practically revolutionizing these types of videos. (Check out 4:20 near the end–there’s an awesome “Evening News”-style sound effect discharged as the paper’s titile/authors/affiliations are displayed–it’s ringtone worthy.) But in all seriousness, expect much more lincRNA goodness from the Rinn lab in the near future.

Liquid and intellectual refreshment in S. Brenner

Posted in Lab Life, YPAA Journal Club by YPAA on April 4, 2010

Laboratory biological science hasn’t changed much in the last 40 years:

What, the reader may ask, did we do in the 6 years between starting C. elegans genetics and publishing the first article on it? Since the animal has a short life cycle of 3.5 days, it should not have taken all that much time just to complement and map the mutations. Many visitors who came to the MRC Lab in Cambridge thought that we spent far too much time eating, drinking, and talking. Observing us only during normal working hours, you could see their point. If one arrived at the lab at the reasonable hour of 10 am, there was just time to open one’s mail before adjourning to the canteen for morning coffee, usually prolonged by a very interesting discussion on some aspect of science. This did not leave much time before lunch, which naturally was also accompanied by discussion that was terminated only by rushing off to attend an afternoon seminar on the Bohr effect in hemoglobin or the like. That brought one to afternoon tea and after that there was hardly enough time to start anything in the lab before adjourning to the pub for liquid and intellectual refreshment. It was only after dinner that the real work started and the lab then filled up with the owls. Even these bouts of work had to be interrupted, of course, for midnight coffee and more discussions.

Sydney Brenner, from  In the Beginning Was the Worm . . .

Moonlighting microRNA

Posted in YPAA Journal Club by YPAA on March 4, 2010

A very cool looking new paper aims to show that miR-328 can be an enterprising fellow, able to work two jobs in hematopoietic cells.

Below is a beautiful summary from Drs. Anna Eiring and Danilo Perrotti, first and senior authors of the study, respectively, pulled from the Cell website. All talks should be this clear!

Evolution is Awesome

Posted in YPAA Journal Club by YPAA on July 16, 2009

A new article in the August issue of National Geographic gives me another reason to embrace natural selection–um, despite my many fitness shortcomings. The Art of Deception describes some survival trickery employed by various inhabitants of the Panamanian rainforest and elsewhere, and being in National Geographic, there are a bunch of nice pictures with educational captions.

My favorites: Cathedra serrata, the insect with alarmingly large, fake insect eyes–because it’s always good to have a backup plan; and the nematode that, visually speaking, turns your garden variety Cephalotes atratus into a delicious cherry-ant, an irresistible Central American rainforest hors d’oeuvre.

The Art of Deception, National Geographic, pgs. 70-87, August 2009. Words by Natalie Angier, Photographs by Christian Ziegler.

Tasty, delicious microRNAs

Posted in YPAA Journal Club by YPAA on April 10, 2009

Occasionally I enter the search term ‘miRNA’ in PubMed, sort by most recent, and take a gander. This method is becoming an increasingly needle in the haystack-type proposition for finding solid microRNA papers of broad interest, but sometimes I’m looking for just the opposite:

photograph by wYnand! on Flickr

MicroRNA: mechanism of gene regulation and application to livestock

T.G. McDaneld

Journal of Animal Science 87: E21-E28, 2009.

The last two sentences of the abstract set-up the rationale for the review:

“The role of miRNA in developmental decisions that affect animal biology is of significant interest, yet the current literature is limited in livestock models. Therefore, a review of the mechanisms by which miRNA alter gene translation and the current research evaluating miRNA in production livestock is needed.”

What follows is a simple review of microRNA biogenesis and function, and then several paragraphs on the application of this information to production livestock. A couple revelations:

“Evaluation of regulatory factors that affect development and growth of economically important tissues such as skeletal muscle and adipose tissue is of interest, because profit margin is influenced by nutrient partitioning between these tissues.”

“MicroRNA motifs have also been identified near SNP associated with residual feed intake in cattle, suggesting that miRNA have a functional role in regulation of genes that affect feed efficiency (Barendse et al., 2007).”

OK microRNA researchers, the world is hungry, so get to work!