UCSC Stem Cell Journal Club

This journal club for the UCSC CIRM training program is open to anyone interested in stem cell research. The program is a roundtable format, so please read the paper beforehand and come prepared to discuss it.

599 Engineering 2
UC Santa Cruz
12:00-1:30 pm
Refreshments served

Sponsors:
UCSC CIRM Training Program in Systems Biology of Stem Cells
California Institute for Quantitative Biosciences (QB3)
Millipore

Upcoming meetings:

December 8, 2009

Presenters: TBA
Paper: TBA
Figure presenters: TBA

Past meetings:

November 17, 2009

Presenters: Andy Nguyen and Camilla Forsberg
Paper: Jaiswal S, Jamieson CH, Pang WW, Park CY, Chao MP, Majeti R, Traver D, van Rooijen N, Weissman IL. CD47 is upregulated on circulating hematopoietic stem cells and leukemia cells to avoid phagocytosis. Cell. 2009 Jul 23;138(2):271-85. Supplemental data.
Figure presenters: Andrew Nguyen (figure 1), David Greenburg (figure 2), Muriel Kmet (figure 3), Daniel Carlin (figure 4), Rebecca Marlow (figure 5),  Neal Sweeney (figure 6), Frank Jacobs (figure 7), Fernando Ugarte (supplemental figures 1-3), Chao Guo (supplemental figures 4-6), Manny Ares (supplemental figures 7-8), Sofie Salama (supplemental figures 9-10)

Jun 1, 2009

Presenter: Debra Hoover, Millipore
Paper: Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008 Jul 3;454(7200):49-55.

May 4, 2009

Presenter: Megan Hall
Paper: Lin SL, Chang DC, Chang-Lin S, Lin CH, Wu DT, Chen DT, Ying SY. Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state. RNA. 2008 Oct;14(10):2115-24.
Figure presenters: Megan Hall (background, figures 1 & 3), Martina Koeva (figure 2), Anne Royou (figure 4), Courtney Onodera (figure 5), Dave Feldheim (figure 6)

Apr 6, 2009

Presenter: David Greenberg
Paper #1: Chambers SM, Fasano CA, Papapetrou EP, Tomishima M, Sadelain M, Studer L. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nature Biotechnology. 2009 Mar;27(3):275-80.

Paper #2: Eiraku M, Watanabe K, Matsuo-Takasaki M, Kawada M, Yonemura S, Matsumura M, Wataya T, Nishiyama A, Muguruma K, Sasai Y. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell. 2008 Nov 6;3(5):519-32.

Mar 9, 2009, 3:30-5:30 pm

Presenter: Martina Koeva
Paper: Liu Y, Elf SE, Miyata Y, Sashida G, Liu Y, Huang G, Di Giandomenico S, Lee JM, Deblasio A, Menendez S, Antipin J, Reva B, Koff A, Nimer SD. p53 Regulates hematopoietic stem cell quiescence. Cell Stem Cell. 2009 Jan 9;4(1):37-48.
Figure presenters: Martina Koeva (background & figure 1), Anne Royou (figure 2), Courtney Onodera (figure 3), Kristel Dorighi (figure 4), Megan Hall (figure 5), Dave Feldheim (figure 6), Dave Greenberg (figure 7)

Feb 9, 2009

Presenter: Kristel Dorighi
Paper: Colmone A, Amorim M, Pontier AL, Wang S, Jablonski E, Sipkins DA. Leukemic cells create bone marrow niches that disrupt the behavior of normal hematopoietic progenitor cells. Science. 19 Dec 2008;322(5909):1861-5.
Figure presenters: Courtney Onodera (figure 1), Anne Royou (figure 2), Megan Hall (figure 3), Martina Koeva (figure 4), Kristel Dorighi (introduction and supplementary figures)

Jan 12, 2009

Presenter: Anne Royou
Paper: Cheng J, Türkel N, Hemati N, Fuller MT, Hunt AJ, Yamashita YM. Centrosome misorientation reduces stem cell division during ageing. Nature. 2008 Dec 4;456(7222):599-604.
Figure presenters: Anne Royou (introduction and figure 1), Courtney Onodera (figure 2), Martina Koeva (figure 3), Kristel Dorighi (figure 4), Megan Hall (figure 5), David Feldheim (figure 6)

Dec 1, 2008

Presenter: David Feldheim
Paper: Zhou Q, Brown J, Kanarek A, Rajagopal J, Melton DA. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature. 2008 Oct 2;455(7213):627-32.
Figure presenters: David Feldheim (figure 1), Courtney Onodera (figure 2), Martina Koeva (figure 3), Kristel Dorighi (figure 4), Megan Hall (figure 5)

Nov 3, 2008

Presenter: Megan Hall
Paper: Zheng H, Ying H, Yan H, Kimmelman AC, Hiller DJ, Chen AJ, Perry SR, Tonon G, Chu GC, Ding Z, Stommel JM, Dunn KL, Wiedemeyer R, You MJ, Brennan C, Wang YA, Ligon KL, Wong WH, Chin L, DePinho RA. p53 and Pten control neural and glioma stem/progenitor cell renewal and differentiation. Nature. 2008 Oct 23;455(7216):1129-33. Supplementary information
Figure presenters: Anne Royou (figure 1), Kristel Dorighi (figure 2), Martina Koeva (figure 3), Courtney Onodera (figure 4), Megan Hall (supplement)

Oct 6, 2008

Presenter: Courtney Onodera
Paper: Dejosez M, Krumenacker JS, Zitur LJ, Passeri M, Chu LF, Songyang Z, Thomson JA, Zwaka TP. Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. Cell. 2008 Jun 27;133(7):1162-74. Erratum in: Cell. 2008 Aug 22;134(4):692.
Figure presenters: Anne Royou (figure 1), Martin Hudson (figure 2), Martina Koeva (figure 3), Megan Hall (figure 4), Courtney Onodera (figures 5&7), Kristel Dorighi (figure 6)

June 2, 2008

Presenter: Martina Koeva
Paper: Wong DJ, Lui H, Ridky TW, Cassarino D, Segal E, Chang HY. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell. 10 April 2008; 2(4):333-44.
Figure presenters: Courtney Onodera (figure 1), Anne Royou (figure 2), Kristel Dorighi (figure 3), Megan Hall (figure 4), Martin Hudson (figure 5), Jake Kirkland School (figure 6)

May 5, 2008

Presenter: Kristel Dorighi
Paper: Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel CG, Zavolan M, Svoboda P, Filipowicz W. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol. 2 Mar 2008;15(3):259-67.
Figure presenters: Martina Koeva (figure 1), Courtney Onodera (figure 2), Megan Hall (figure 3), Dave F (figure 4), Martin Hudson (figure 5), Kristel Dorighi (figure 6)

April 7, 2008

Presenter: Courtney Onodera
Paper: Stadtfeld M, Maherali N, Breault DT, Hochedlinger K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell. 6 March 2008; 2:230-40.
Figure presenters: Courtney Onodera (figures 1&7), Megan Hall (figure 2), Martina Koeva (figure 3), Martin Hudson (figure 4), Kristel Dorighi (figure 5), Anne Royou (figure 6)

March 10, 2008

Presenter: Martin Hudson
Paper #1: Andäng M et al. Histone H2AX-dependent GABAA receptor regulation of stem cell proliferation. Nature. 24 January 2008; 451:460-4.
Figure presenters: Martin Hudson (intro and figure 1a-e), Martina Koeva (figure 1 f-j), Jake Kirkland School (figure 2 a-f), Courtney Onodera (figure 2 g-j), Anne Royou (figure 3 a-i), Dave Greenberg ( figure 3 j-o), Armen Shamamian (figure 4 a-d), Megan Hall (figure 4 e-j)

Paper #2: Cavallaro M et al. Impaired generation of mature neurons by neural stem cells from hypomorphic Sox2 mutants. Development. 2008; 135:541-57.
Figure presenters: Martin Hudson (figures 1&2), Martina Koeva (figures 3&4), Anne Royou (figures 5&6), Dave Greenberg (figures 7&8), Megan Hall (figure 9), Courtney Onodera (figures 10&11), Jake Kirkland School (figure 12)

February 11, 2008

Presenter: Megan Hall
Paper: Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 30 November 2007; 131:861-72.
Figure presenters: Megan Hall (intro and figure 1), Courtney Onodera (figure 2) Martina Koeva (figure 3), Kristel Dorighi (figures 4 & 5), Anne Royou (figure 6 & suppl movie S1), Martin Hudson (figure 7 & suppl figures 3A & B)
Additional paper for brief discussion: Yu J et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 21 December 2007; 318(5858):1917-20.

January 14, 2008

Presenter: Anne Royou
Paper: McDermott KM, Zhang J, Holst CR, Kozakiewicz BK, Singla V, Tlsty TD. p16INK4a prevents centrosome dysfunction and genomic instability in primary cells. PLoS Biology. 14 Februay 2006; 4(3): e51.
Figure presenters: Anne Royou (intro and figure 1), Kristel Dorighi (figure 2) Martina Koeva (figures 3, 8a&b), Courtney Onodera (figures 4,8c&d), Sofie Salama (figure 5), Dave F or Anne (figure 6), Sol Katzman or Kristel (figure 7)

December 3, 2007—123 Sinsheimer Labs

Presenter: Martina Koeva
Paper: Czechowicz A, Kraft D, Weissman IL, Bhattacharya D. Efficient transplantation via antibody-based clearance of hematopoietic stem cell niches. Science. 2007 November 23;318(5854):1296-9.
Figure presenters: Anne Royou (figure 1), Courtney Onodera (figure 2), Kristel Dorighi (figure 3), Megan Hall (figure 4)

November 5, 2007—533 Engineering 2

Presenter: Kristel Dorighi
Paper: Jude CD, Climer L, Xu D, Artinger E, Fisher JK, Ernst P. Unique and independent roles of MLL in adult hematopoietic stem cells and progenitors. Cell Stem Cell. 2007 Sept 13;1(3):324-37.
Figure presenters: Megan Hall (figure 1), Martina Koeva (figures 2 and 3), Courtney Onodera (figure 4), Anne Royou (figure 5), Hema Vayadanathan (figure 6), Kristel Dorighi (figure 7)

October 1, 2007—123 Sinsheimer Labs

Presenter: Courtney Onodera
Paper:Seandel M, James D, Shmelkov SV, Falciatori I, Kim J, Chavala S, Scherr DS, Zhang F, Torres R, Gale NW, Yancopoulos GD, Murphy A, Valenzuela DM, Hobbs RM, Pandolfi PP, Rafii S. Generation of functional multipotent adult stem cells from GPR125+ germline progenitors. Nature. 2007 Sep 20;449(7160):346-50.
Figure presenters: Dave F (figure 1), Kristel Dorighi (figure 2), Martina Koeva (figure 3), Megan Hall (figure 4, supp figure 1)

June 18, 2007

Presenter: Will McKenna
Paper:Maherali N, Sridharan R, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R, Plath K, Hochedliner K. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell. 2007 Jun 7; 1:55-70.
Figure presenters: Will McKenna (figure 1), Martina Koeva (figure 2), Courtney Onodera (figure 3), Martina Koeva (figure 4), Hema Vayadanathan (figure 5), Dave F (figure 6), Anne Royou (figure 7), group (figure 8)

May 14, 2007

Presenter: Anne Royou (2 papers)
Paper #1: Yamashita YM, Mahowald AP, Perlin JR, Fuller MT. Asymmetric inheritance of mother versus daughter centrosome in stem cell division. Science. 2007 Jan 26; 315(5811):518-21.
Figure presenters: Hema Vayadanathan (figure 1), Dave F (figure 2), Roland Nagel (figure 3), Will McKenna (figure 4), Anne Royou (supp figure 1)

Paper #2: Rebollo E, Sampaio P, Januschke J, Llamazares S, Varmark H, González C. Functionally unequal centrosomes drive spindle orientation in asymmetrically dividing drosophila neural stem cells. Developmental Cell. 2007 March; 12:467-74.
Figure presenters: Courtney Onodera (figure 1), Martina Koeva (figure 2), Stephanie McClymont (figure 3), Armen Shamamian (figure 4), Anne Royou (supp figures 1 and 2)

April 23, 2007

Presenter: Roland Nagel
Paper: Diamandis P, Wildenhain J, Clarke ID, Sacher AG, Graham J, Bellows DS, Ling EK, Ward RJ, Jamieson LG, Tyers M, Dirks PB. Chemical genetics reveals a complex functional ground state of neural stem cells. Nat Chem Biol. 2007 Apr 8; [Epub ahead of print].
Figure presenters: Hema Vayadanathan, Martina Koeva, Roland Nagel (figure 1, supp figure 1, supp figure2, supp figure3)
Will McKenna, Courtney Onodera, Karen Artiles (figure 2, supp table 1, supp table 2)
Stephanie McClymont, Samir Patel, Gayatri Pal (figure 3 , supp table 3, supp table 4)
David F, Armen Shamamian (figure 4, supplemental methods)
Supplements: http://www.nature.com/nchembio/journal/v3/n5/suppinfo/nchembio873_S1.html

March 26, 2007

Presenter: Will McKenna
Papers:
Simon A, Frisén J. From stem cell to progenitor and back again. Cell, 9 March 2007; 128(5):825-826.

Nakagawa T, Nabeshima Y, Yoshida S. Functional identification of the actual and potential stem cell compartments in mouse spermatogenesis. Developmental Cell. February 2007; 12(2):195-206.
Figure presenters: 1. Anne Royou; 2. Stephanie McClymont; 3. David F; 4. Will McKenna; 5. Martina Koeva; 6. Hema Vayadanathan; 7. Roland Nagel

February 26, 2007

Presenters: Martina Koeva and Courtney Onodera
Paper: Regulation of apoptosis and differentiation by p53 in human embryonic stem cells. J Biol Chem. 2007 Feb 23;282(8):5842-52. Epub 2006 Dec 19.

January 29, 2007

Presenter: Hema Vaidyanathan
Paper: De Coppi P, Bartsch G Jr, Siddiqui MM, Xu T, Santos CC, Perin L, Mostoslavsky G, Serre AC, Snyder EY, Yoo JJ, Furth ME, Soker S, Atala A. Isolation of amniotic stem cell lines with potential for therapy. Nat Biotechnol. 2007 Jan;25(1):100-6. Epub 2007 Jan 7.

December 1, 2006

Presenters: Hema Vaidyanathan and Will McKenna
Topic: Biology and therapeutic uses of neural stem cells
Papers: Androutsellis-Theotokis A et al. Notch signalling regulates stem cell numbers in vitro and in vivo. Nature. 2006 Aug 17;442(7104):823-6.

Roy NS et al. Functional engraftment of human ES cell–derived dopaminergic neurons enriched by coculture with telomerase-immortalized midbrain astrocytes. Nature Medicine. 2006 12:1259-68.

November 3, 2006

Presenters: Martina Koeva and Courtney Onodera
Topics: Stem cell division is regulated by the microRNA pathway: http://www.nature.com/nature/journal/v435/n7044/full/nature03816.html

A microRNA polycistron as a potential human oncogene: http://www.nature.com/nature/journal/v435/n7043/full/nature03552.html

October 20, 2006

Presenters: Kristel Dorighi and Stephanie McClymont
Topic: Epigenetics of stem cells
Papers: http://www.nature.com/nature/journal/v441/n7091/abs/nature04733.html
http://www.nature.com/nature/journal/v423/n6937/abs/nature01587.html