Posts tagged ‘molecular biology’

Neuroscience

  1. Robie AA, Hirokawa J, Edwards AW, Umayam LA, Lee A, Phillips ML, Card GM, Korff W, Rubin GM, Simpson JH, Reiser MB, Branson K. Mapping the Neural Substrates of Behavior. Cell. 2017 Jul 13;170(2):393-406.e28. doi: 10.1016/j.cell.2017.06.032. PubMed PMID: 28709004.
  2. Smith K. How to map the circuits that define us. Nature. 2017 Aug 9;548(7666):150-152. doi: 10.1038/548150a. PubMed PMID: 28796220.

Evolution

  1. Sousa AMM, Meyer KA, Santpere G, Gulden FO, Sestan N. Evolution of the Human Nervous System Function, Structure, and Development. Cell. 2017 Jul 13;170(2):226-247. doi: 10.1016/j.cell.2017.06.036. Review. PubMed PMID: 28708995.

Genetics

  1. New concerns raised over value of genome-wide disease studies

Cell biology

  1. Biology of single cells shines a light on collaboration. Nature. 2017 Jul 5;547(7661):5. doi: 10.1038/547005a. PubMed PMID: 28682351.

Genomics

  1. Nagano T, Lubling Y, Várnai C, Dudley C, Leung W, Baran Y, Mendelson Cohen N, Wingett S, Fraser P, Tanay A. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature. 2017 Jul 5;547(7661):61-67. doi: 10.1038/nature23001. PubMed PMID: 28682332.

Molecular Biology

  1. Lin YL, Pasero P. Transcription-Replication Conflicts: Orientation Matters. Cell. 2017 Aug 10;170(4):603-604. doi: 10.1016/j.cell.2017.07.040. PubMed PMID: 28802036.

Genome editing

  1. Ma H, Marti-Gutierrez N, Park SW, Wu J, Lee Y, Suzuki K, Koski A, Ji D, Hayama T, Ahmed R, Darby H, Van Dyken C, Li Y, Kang E, Park AR, Kim D, Kim ST, Gong J, Gu Y, Xu X, Battaglia D, Krieg SA, Lee DM, Wu DH, Wolf DP, Heitner SB, Belmonte JCI, Amato P, Kim JS, Kaul S, Mitalipov S. Correction of a pathogenic gene mutation in human embryos. Nature. 2017 Aug 2. doi: 10.1038/nature23305. [Epub ahead of print] PubMed PMID: 28783728.

Genome editing

  1. Scheufele DA, Xenos MA, Howell EL, Rose KM, Brossard D, Hardy BW. U.S. attitudes on human genome editing. Science. 2017 Aug 11;357(6351):553-554. doi: 10.1126/science.aan3708. PubMed PMID: 28798120.
  2. Amitai G, Sorek R. Intracellular signaling in CRISPR-Cas defense. Science. 2017 Aug 11;357(6351):550-551. doi: 10.1126/science.aao2210. PubMed PMID: 28798118.
  3. Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V. A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science. 2017 Aug 11;357(6351):605-609. doi: 10.1126/science.aao0100. Epub 2017 Jun 29. PubMed PMID: 28663439.

Eye

  1. Madl T. Patchy proteins form a perfect lens. Science. 2017 Aug 11;357(6351):546-547. doi: 10.1126/science.aao1456. PubMed PMID: 28798115.
  2. Cai J, Townsend JP, Dodson TC, Heiney PA, Sweeney AM. Eye patches: Protein assembly of index-gradient squid lenses. Science. 2017 Aug 11;357(6351):564-569. doi: 10.1126/science.aal2674. PubMed PMID: 28798124.

Funding

  1. Levitt M, Levitt JM. Future of fundamental discovery in US biomedical research. Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6498-6503. doi: 10.1073/pnas.1609996114. Epub 2017 Jun 5. PubMed PMID: 28584129; PubMed Central PMCID: PMC5488913.

Zebrafish

  1. Adatto I, Krug L, Zon LI. The Red Light District and Its Effects on Zebrafish Reproduction. Zebrafish. 2016 Mar 15. [Epub ahead of print] PubMed PMID: 26978703.
  2. Brocal I, White RJ, Dooley CM, Carruthers SN, Clark R, Hall A, Busch-Nentwich EM, Stemple DL, Kettleborough RN. Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish. BMC Genomics. 2016 Mar 24;17(1):259. doi: 10.1186/s12864-016-2563-z. PubMed PMID: 27009152.
  3. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise Editing of the Zebrafish Genome Made Simple and Efficient. Dev Cell. 2016 Mar 21;36(6):654-67. doi: 10.1016/j.devcel.2016.02.015. PubMed PMID: 27003937.
  4. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6. doi: 10.1093/nar/gkv998. Epub 2015 Oct 4. PubMed PMID: 26438539; PubMed Central PMCID: PMC4702947.

Retina

  1. Mullally M, Albrecht C, Horton M, Laboissonniere LA, Goetz JJ, Chowdhury R, Manning A, Wester AK, Bose Q, Trimarchi JM. Expression Profiling of Developing Zebrafish Retinal Cells. Zebrafish. 2016 Mar 16. [Epub ahead of print] PubMed PMID: 26982811.

Disease

  1. Roy DS, Arons A, Mitchell TI, Pignatelli M, Ryan TJ, Tonegawa S. Memory retrieval by activating engram cells in mouse models of early Alzheimer’s disease. Nature. 2016 Mar 16. doi: 10.1038/nature17172. [Epub ahead of print] PubMed PMID: 26982728.

Molecular Biology

  1. Louder RK, He Y, López-Blanco JR, Fang J, Chacón P, Nogales E. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature. 2016 Mar 23. doi: 10.1038/nature17394. [Epub ahead of print] PubMed PMID: 27007846.

Cell Biology

  1. Norris DP, Jackson PK. Cell biology: Calcium contradictions in cilia. Nature. 2016 Mar 23. doi: 10.1038/nature17313. [Epub ahead of print] PubMed PMID: 27007852.

Systems Biology

  1. Hashimoto M, Nozoe T, Nakaoka H, Okura R, Akiyoshi S, Kaneko K, Kussell E, Wakamoto Y. Noise-driven growth rate gain in clonal cellular populations. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201519412. [Epub ahead of print] PubMed PMID: 26951676.
  2. Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, Barenholz U, Goldenfeld M, Shlomi T, Milo R. Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201514240. [Epub ahead of print] PubMed PMID: 26951675.

Genome editing

  1. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise Editing of the Zebrafish Genome Made Simple and Efficient. Dev Cell. 2016 Mar 21;36(6):654-67. doi: 10.1016/j.devcel.2016.02.015. PubMed PMID: 27003937.
  2. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6. doi: 10.1093/nar/gkv998. Epub 2015 Oct 4. PubMed PMID: 26438539; PubMed Central PMCID: PMC4702947.


				

Genomics

  1. Bintu L, Yong J, Antebi YE, McCue K, Kazuki Y, Uno N, Oshimura M, Elowitz MB. Dynamics of epigenetic regulation at the single-cell level. Science. 2016 Feb 12;351(6274):720-4. doi: 10.1126/science.aab2956. PubMed PMID: 26912859.
    • Commentary: Keung AJ, Khalil AS. MOLECULAR BIOLOGY. A unifying model of epigenetic regulation. Science. 2016 Feb 12;351(6274):661-2. doi: 10.1126/science.aaf1647. PubMed PMID: 26912843.
  2. Cahan P. Enabling direct fate conversion with network biology. Nat Genet. 2016 Feb 24;48(3):226-7. doi: 10.1038/ng.3516. PubMed PMID: 26906680.
  3. Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J. A predictive computational framework for direct reprogramming between human cell types. Nat Genet. 2016 Jan 18. doi: 10.1038/ng.3487. [Epub ahead of print] PubMed PMID: 26780608.
  4. Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA. Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. Nat Genet. 2016 Jan 25. doi: 10.1038/ng.3493. [Epub ahead of print] PubMed PMID: 26808112.
  5. Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx BW, Jansen R, de Geus EJ, Boomsma DI, Wright FA, Sullivan PF, Nikkola E, Alvarez M, Civelek M, Lusis AJ, Lehtimäki T, Raitoharju E, Kähönen M, Seppälä I, Raitakari OT, Kuusisto J, Laakso M, Price AL, Pajukanta P, Pasaniuc B. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet. 2016 Feb 8. doi: 10.1038/ng.3506. [Epub ahead of print] PubMed PMID: 26854917.

Development

  1. Aggarwal V, Dickinson RB, Lele TP. Concentration Sensing by the Moving Nucleus in Cell Fate Determination: A Computational Analysis. PLoS One. 2016 Feb 12;11(2):e0149213. doi: 10.1371/journal.pone.0149213. eCollection 2016. PubMed PMID: 26872214.
  2. Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J. A predictive computational framework for direct reprogramming between human cell types. Nat Genet. 2016 Jan 18. doi: 10.1038/ng.3487. [Epub ahead of print] PubMed PMID: 26780608.

Molecular Biology

  1. Burgers PM, Gordenin D, Kunkel TA. Who Is Leading the Replication Fork, Pol ε or Pol δ? Mol Cell. 2016 Feb 18;61(4):492-3. doi: 10.1016/j.molcel.2016.01.017. PubMed PMID: 26895421.
  2. Johnson RE, Klassen R, Prakash L, Prakash S. Response to Burgers et al. Mol Cell. 2016 Feb 18;61(4):494-5. doi: 10.1016/j.molcel.2016.01.018. PubMed PMID: 26895422.

Funding

  1.  Vachelard J, Gambarra-Soares T, Augustini G, Riul P, Maracaja-Coutinho V. A Guide to Scientific Crowdfunding. PLoS Biol. 2016 Feb 17;14(2):e1002373. doi: 10.1371/journal.pbio.1002373. eCollection 2016 Feb. PubMed PMID: 26886064.

Genome editing

  1. Tai DJ, Ragavendran A, Manavalan P, Stortchevoi A, Seabra CM, Erdin S, Collins RL, Blumenthal I, Chen X, Shen Y, Sahin M, Zhang C, Lee C, Gusella JF, Talkowski ME. Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. Nat Neurosci. 2016 Feb 1. doi: 10.1038/nn.4235. [Epub ahead of print] PubMed PMID: 26829649.

Behaviour

  1. Scott CA, Marsden AN, Slusarski DC. Automated, high-throughput, in vivo analysis of visual function using the zebrafish. Dev Dyn. 2016 Feb 18. doi: 10.1002/dvdy.24398. [Epub ahead of print] PubMed PMID: 26890697.

Stem cells

  1. Fatehullah A, Tan SH, Barker N. Organoids as an in vitro model of human development and disease. Nat Cell Biol. 2016 Feb 25;18(3):246-54. doi: 10.1038/ncb3312. Review. PubMed PMID: 26911908.
  2. Wang Y, Gao S. Human Naive Embryonic Stem Cells: How Full Is the Glass? Cell Stem Cell. 2016 Mar 3;18(3):301-3. doi: 10.1016/j.stem.2016.02.012. PubMed PMID: 26942847.
  3. Pastor WA, Chen D, Liu W, Kim R, Sahakyan A, Lukianchikov A, Plath K, Jacobsen SE, Clark AT. Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell Stem Cell. 2016 Mar 3;18(3):323-9. doi: 10.1016/j.stem.2016.01.019. Epub 2016 Feb 4. PubMed PMID: 26853856; PubMed Central PMCID: PMC4779431.
  4. Passier R, Orlova V, Mummery C. Complex Tissue and Disease Modeling using hiPSCs. Cell Stem Cell. 2016 Mar 3;18(3):309-21. doi: 10.1016/j.stem.2016.02.011. Review. PubMed PMID: 26942851.
  5. Orlova V, Mummery C. SnapShot: Key Advances in hiPSC Disease Modeling. Cell Stem Cell. 2016 Mar 3;18(3):422. doi: 10.1016/j.stem.2016.02.013. PubMed PMID: 26942854.
  6. Nat Rev Mol Cell Biol; Focus on: Pluripotent Stem cells

Medicine

  1. Peplow M. Synthetic biology’s first malaria drug meets market resistance. Nature. 2016 Feb 25;530(7591):389-90. doi: 10.1038/530390a. PubMed PMID: 26911755.

Genome editing

  1. Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, Wiedenheft B, Ke A. Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature. 2016 Feb 10. doi: 10.1038/nature16995. [Epub ahead of print] PubMed PMID: 26863189.

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.