SysBio Open Journal Club

From November the 4th 2014 we started the SysBio Open Journal Club. As it is common in these kind of activities the idea is to expose a published paper meanwhile the rest of assistants are criticizing. This Journal Club, in addition, has a series of characteristics devoted to scientific development of pre-graduate, PhD students as well as postdocs. Although we created this activity from our group of Systems Biology (SysBio), we believe it is interesting to open it to anyone interested in participate.


  NEXT JOURNAL CLUB



Rules

The main Journal Club characteristics are as follows:

  1. Journal Club activities are in English.
  2. Both, expositions as well as cryticism must proceed under the mutual participants respect.
  3. In each encounter, there will be a speaker who will expose a paper previously agreed with the rest of the assistants.
  4. In each encounter, there will be a chairperson who will assure that all the questions during exposition are constrained to be brief moving the extended ones (involving longer discussions) to the end of the exposition.
  5. The speaker of a Journal Club will be the chairperson of the following one.
  6. The chairperson is in charge of the food and drinks during the Journal Club.
  7. Each exposition will be constrained to 30 min + 15 min of discussions in the end.
  8. Spacetime coordinates: Each Thursday 9:30 hs (may vary) in the Seminars Room at the Institute of Physics of Liquids and Biological Systems (IFLYSIB), CONICET and University of La Plata (UNLP). Calle 59, nro 789 (between streets 10 and 11).
  9. The Journal Club is being performed in weekly basis.

  PREVIOUS JOURNAL CLUBS

17/05/2019 – “Analysis of speed, curvature, planarity and frequency characteristics of heart vector movement to evaluate the electrophysiological substrate associated with ventricular tachycardia”

Larisa G. Tereshchenko, Jonathan W. Waks, Muammar Kabir, Elyar Ghafoori, Alexei Shvilkin, Mark E. Josephson. Computers in Biology and Medicine 65(2015)150–160.

Expositor: Juan Fernández

Chairman: Alberto Ceccarelli

Presentation


21/03/2019 – “Vertex stability and topological transitions in vertex models of foams and epithelia”

Meryl A. Spencer, Zahera Jabeen & David K. Lubensky. Eur J Phys E (2017).

Expositor: Augusto Borges

Chairman: Osvaldo Chara


14/03/2019 – “Scutoids are a geometrical solution to three-dimensional packing of epithelia”

P Gómez-Gálvez, P Vicente-Munuera, A Tagua, C Forja, A M Castro, M Letrán, A Valencia-Expósito, C Grima, M Bermúdez-Gallardo, Ó Serrano-Pérez-Higueras, F Cavodeassi, S Sotillos, M D Martín-Bermudo, A Márquez, J Buceta & L M Escudero. Nature Communications, (2018).

Expositor: Osvaldo Chara

Chairman: Alberto Ceccarelli

Presentation


07/03/2019 – “The surface evolver”

Brakke K. Experimental Mathematics (1992).

Expositor: Alberto Ceccarelli

Chairman: Osvaldo Chara

Presentation


20/11/2018 – “A fluid-to-solid jamming transition underlies vertebrate body axis elongation”

Mongera, Rowghanian, Gustafson, Shelton, Kealhofer, Carn, Serwane, Lucio, Giammona & Campàs. Nature (2018).

Expositor: Emanuel Cura Costa

Chairman: H. Ariel Alvarez


30/10/2018 – “A density-independent rigidity transition in biological tissues”

Dapeng Bi, J. H. Lopez, J. M. Schwarz and M. Lisa Manning. Nature physics (2015).

Expositor: H. Ariel Alvarez

Chairman: Alberto Ceccarelli

Presentation


16/10/2018 – “Simulation of Cell Patterning Triggered by Cell Death and Differential Adhesion in Drosophila Wing”

Tatsuzo Nagai, Hisao Honda and Masahiko Takemura. Biophysical Journal (2018)

Expositor: Alberto Ceccarelli

Chairman: Vanessa Vidal

Presentation


09/10/2018 – “A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule”

K Meyer, O Ostrenko, G Bourantas, H Morales-Navarrete, N Porat-Shliom, F Segovia-Miranda, H Nonaka, A Ghaemi, J Verbavatz, L Brusch, I Sbalzarini, Y Kalaidzidis, R Weigert and M Zerial. Cell Systems (2017).

Expositor: Vanessa Vidal

Chairman: Martín Gil Folgar


18/09/2018 – “A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

Morales-Navarrete H, Segovia-Miranda F, Klukowski P, Meyer K, Nonaka H, Marsico G, Chernykh M, Kalaidzidis A, Zerial M, Kalaidzidis Y. eLife (2015).

Expositor: Martín Gil Folgar

Chairman: Osvaldo Chara


11/09/2018 – “Robust cell tracking in epithelial tissues through identification of maximum common subgraphs”

Kursawe J, Bardenet R, Zartman JJ, Baker RE, Fletcher AG. J R Soc Interface (2016).

Expositor: Osvaldo Chara

Chairman: Augusto Borges


04/09/2018 – “Entropy-driven spatial organization of highly confinedpolymers: Lessons for the bacterial chromosome”

Suckjoon Jun and Bela Mulde. PNAS (2006).

Expositor: Augusto Borges

Chairman: Emanuel Cura Costa


28/08/2018 – “Contraction and elongation: Mechanics underlying cell boundary deformations in epithelial tissue”

Yusuke Hara. Develop. Growth Differ. (2017).

Expositor: Emanuel Cura Costa

Chairman: Vanessa Vidal


13/08/2018 – “Systemic cell cycle activation is induced following complex tissue injury in axolotl”

Kimberly Johnson, Joel Bateman, Tia DiTommaso, Alan Y. Wong, Jessica L. Whited.
Developmental Biology (2018).

Expositor: Vanessa Vidal

Chairman: H. Ariel Alvarez


09/08/2018 – “Shape Transformations of Epithelial Shells”

KMahim Misra, Basile Audoly, Ioannis G. Kevrekidis and Stanislav Y. Shvartsman.

Biophysical Journal (2016).

Expositor: H. Ariel Alvarez

Chairman: Alberto Ceccarelli

Presentation


28/06/2018 and 05/07/2018 – “Feedback, Lineages and Self-Organizing Morphogenesis.”

Kunche S, Yan H, Calof AL, Lowengrub JS & Lander AD. PLoS Comput Biol. (2016).

Expositor: Alberto Ceccarelli

Chairman: Vanessa Vidal

Presentation (first part)

Presentation (second part)


07/06/2018 – “Feedback between tissue packing and neurogenesis in the zebrafish neural tube”.

Tom W. Hiscock, Joel B. Miesfeld, Kishore R. Mosaliganti, Brian A. Link and Sean G. Megason. Development(2018).

Expositor: Vanessa Vidal

Chairman: Osvaldo Chara

Presentation


31/05/2018 – “Positional information specifies the site of organ regeneration and not tissue maintenance in planarians”.

Eric M. Hill and Christian P. Petersen. eLife (2018)

Expositor: Osvaldo Chara

Chairman: Emanuel Cura Costa

Presentation


10/05/2018 – “Scattering of long water waves in a canal with rapidly varying cross-section in the presence of a current“. 

Semyon Churilov, Andrei Ermakov, Germain Rousseaux, and Yury Stepanyants. Phys. Rev. Fluids 2, 094805 – Published 22 September 2017

Expositor: Alberto Ceccarelli

Chairman: Augusto Borges

Presentation


03/05/2018 – “Live cell-lineage tracing and machine learning reveal patterns of organ regeneration”

Oriol Viader-Llargués, Valerio Lupperger, Laura Pola-Morell, Carsten Marr, Hernán López-Schier. eLife, vol. 7 (2018) p. e30823.

Expositor: Augusto Borges

Chairman: Ariel Alvarez

Presentation


12/04/2018 – “Elastic force restricts growth of the murine utricle”.

Gnedeva K, Jacobo A, Salvi JD, Petelski AA & Hudspeth AJ. 2017. eLife. 6: e25681.

Expositor: Ariel Alvarez

Chairman: Osvaldo Chara

Presentation


24/11/2017 – “Lineage tracing of genome-edited alleles reveals high fidelity axolotl limb regeneration”.Flowers GP, Sanor LD, Crews CM.

elife. 2017 Sep 16;6. pii: e25726. doi: 10.7554/eLife.25726.

Expositor: Vanessa Vidal

Chairman: Ariel Alvarez

Presentation


03/11/2017 – “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation”. S. F. Gabriel Krens, Jim H. Veldhuis, Vanessa Barone, Daniel Čapek, Jean-Léon Maître, G. Wayne Brodland and Carl-Philipp Heisenberg.

Development (2017) 144, 1798-1806 doi:10.1242/dev.144964

Expositor: Osvaldo Chara.

Chairman: Vanessa Vidal.

Presentation


27/10/2017 – “Recruitment of cells into the Drosophila wing primordium by a feed-forward circuit of vestigial autoregulation”Myriam Zecca, Gary Struhl

Development 2007 134: 3001-3010; doi: 10.1242/dev.006411

Expositor: Vanessa Vidal

Chairman: Ariel Alvarez

Presentation


13/10/2017 – “Emergent cellular self-organization and mechanosensation
initiate follicle pattern in the avian skin”
Shyer AE, Rodrigues AR, Schroeder GG, Kassianidou E, Kumar S & Harland RM.

Science. 357(6353):811-815. doi: 10.1126/science.aai7868 (2017)

Expositor: Ariel Alvarez

Chairman: Osvaldo Chara

Presentation


29/09/2017 – “Cell lineages and the logic of proliferative control”.  

Lander AD, Gokoffski KK, Wan FY, Nie Q, Calof AL. PLoS Biol. 7(1):e15 (2009).

Expositor: Osvaldo Chara

Chairman: Emanuel Cura Costa

Presentation


8/09/2017 – “Scaling morphogen gradients during tissue growth by a cell division rule”. Inna Averbukh, Danny Ben-Zvi, Siddhartha Mishra & Naama Barkai. Development (2009).

Expositor: Alberto Ceccarelli

Chairman: Vanessa Vidal

Presentation


16/03/2017 – Increased Cell Bond Tension Governs Cell Sorting at the Drosophila Anteroposterior Compartment Boundary. Landsberg, Farhadifar, Ranft, Umetsu, Widmann, Bittig, Said, Jülicher, Dahmann. Current Biology (2009).

Expositor: Alberto Ceccarelli

Chairman: Emanuel Cura Costa

Presentation


23/08/2016 – Reaction and diffusion on growing domains: Scenarios for robust pattern formation. E.J. Crampin, E.A. Gaffney, P.K. Maini. Bulletin of Mathematical Biology (1999).

Expositor: Augusto Borges

Chairman: H. Ariel Alvarez


19/08/2016 – A Vertex Model of Drosophila Ventral Furrow Formation. Philipp Spahn and Rolf Reuter. PLOS ONE (2013) .

Expositor: H. Ariel Alvarez

Chairman: Emanuel Cura Costa

Presentation


30/06/2016 – Morphogen rules: design principles of gradient-mediated embryo patterning. James Briscoe y Stephen Small. Development (2015) .

Expositor: Emanuel Cura Costa

Chairman: Alberto Ceccarell



2/05/2016 – Nonequilibrium Glassy Dynamics of Self-Propelled Hard Disks.
Ludovic Berthier.  Phys. Rev. Lett. (2014).

Expositor: Alberto Ceccarelli

Chairman: Augusto Borges

Presentation


12/05/2016 – The influence of gene expression time delays on Gierer-Meinhardt pattern formation systems. Seirin Lee S, Gaffney EA, Monk NA. Bull Math Biol. (2010).

Expositor: Augusto Borges

Chairman: Emanuel Cura Costa


05/05/2016 – The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis.  A. F. M. Marée, V. A. Grieneisen y P. Hogeweg.  Book Chapter in “Single-Cell-Based Models in Biology and Medicine” (2007).

Expositor: Emanuel Cura Costa

Chairman: Ariel Alvarez

Presentation


28/04/2016 – “Computer simulation of wound closure in epithelial tissues: Cell–basal-lamina adhesion. Phil.Mag.B – 2001” & “A dynamic cell model for the formation of epithelial tissues. Phys.Rev.E – 2009”
Tatsuzo Nagai and Hisao Honda.

Expositor: Ariel Alvarez

Chairman: Alberto Ceccarelli

Presentation


18/04/2016 – How Long Does It Take to Establish a Morphogen Gradient?
 
Alexander M. Berezhkovskii, Christine Sample y Stanislav Y. Shvartsman. Biophysical Journal (2010).

Expositor: Alberto Ceccarelli

Chairman: Augusto Borges

Presentation


11/04/2016 – Mechanical instabilities of biological tubes.
  
Edouard Hannezo, Jacques Prost, Jean-Francois Joanny. Physical Review Letters (2012).

Expositor: Augusto Borges

Chairman: Emanuel Cura Costa

Presentation


4/04/2016 – Cell-pattern disordering during convergent extension in Drosophila
 
Jennifer A Zallen and Richard Zallen. Journal Physics (2004).

Expositor: Emanuel Cura Costa

Chairman: Alberto Ceccarelli

Presentation


21/03/2016 – How Long Does It Take to Establish a Morphogen Gradient?
 
Alexander M. Berezhkovskii, Christine Sample y Stanislav Y. Shvartsman. Biophysical Journal (2010).

Expositor: Alberto Ceccarelli

Chairman: Emanuel Cura Costa

Presentation


14/03/2016 – Cdks, cyclins and CKIs: roles beyond cell cycle regulation.
  Shuhui Lim and Philipp Kaldis.
Development 140, 3079-3093 (2013).

Expositor: Emanuel Cura Costa

Chairman: Osvaldo Chara

Presentation


16/06/2015 – Cellular Pressure and Volume Regulation and Implications for Cell Mechanics.  H. Jiang & S. X. Sun. Biophysical Journal, Volume 105,  pp 609–619 | 2013.

Expositor: Osvaldo Chara

Chairman: Alberto Ceccarelli

Presentation


14/10/2015 – Multiple SysBio Open Journal Club

Dynamic Interpretation of Hedgehog Signaling in the Drosophila Wing Disc. Nahmad M & Stathopoulos A. PLoS Biol 7(9): e1000202 | 2009. 

Expositor: H. Ariel Alvarez

Presentation

A clonal analysis of neural progenitors during axolotl spinal cord regeneration reveals evidence for both spatially restricted and multipotent progenitors. McHedlishvili L, Epperlein HH, Telzerow A & Tanaka EM. Development. 134(11): 2083-93 | 2007. 

Expositor: Emanuel Cura Costa

Presentation

Kinetics of morphogen gradient formation. 
Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T. Jülicher F & González-Gaitán M. Science. 315: 521-524 | 2007.

Expositor: Lisandro Milocco

Presentation

Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase.  Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C & Cozzarelli NR. PNAS.
102(49): 17618–17623 | 2005.

Expositor: Augusto Borges

Presentation

Dynamic changes in the osmotic water permeability. Moshelion M, Moran N & Chaumont F. Plant Physiol. 135: 2301–2317 | 2004.

 Expositor: Alberto Ceccarelli

Presentation


16/06/2015 – Cellular Pressure and Volume Regulation and Implications for Cell Mechanics.  H. Jiang & S. X. Sun. Biophysical Journal, Volume 105,  pp 609–619 | 2013.

Expositor: Osvaldo Chara

Chairman: Alberto Ceccarelli

Presentation


2/06/2015 –  A General Model for the Dynamics of the Cell Volume.  Julio A. Hernández. Bulletin of Mathematical Biology, Volume 69, Issue 5, pp 1631-1648 | 2007.

Expositor: Alberto Ceccarelli

Chairman: Augusto Borges

Presentation


12/05/2015 – SpoIIIE mechanism of directional translocation involves target search coupled to sequence-dependent motor stimulation. Diego I. Cattoni, Osvaldo Chara, Cédric Godefroy, Emmanuel Margeat, Sonia Pierre-Emmanuel Milhiet & Marcelo Nöllman. EMBO reports VOL 14 | NO 5 | 2013.

Expositor: Agusto Borges

Chairman: Emanuel Cura Costa

Presentation


28/04/2015 – Early Embryonic Vascular Patterning by Matrix-Mediated Paracrine Signalling: A Mathematical Model Study.  Alvaro Köhn-Luque, Walter de Back, Jörn Starruß, Andrea Mattiotti, Andreas Deutsch, José María Pérez-Pomares, Miguel A. Herrero. PLoS ONE 6(9): e24175 | 2011.

Expositor: Emanuel Cura Costa

Chairman: H. Ariel Alvarez

Presentation


14/04/2015 – The Influence of Cell Mechanics, Cell-Cell Interactions, and Proliferation on Epithelial Packing. R. Farhadifar, J-C. Roper, B. Aigouy, S. Eaton and F. Julicher, Current Biology 17, 2095–2104 | 2007.

Expositor: H. Ariel Alvarez

Chairman: Osvaldo Chara

Presentation


25/11/2014 – Comparing methods for modelling spreading cell fronts. Deborah C. Markham, Matthew J. Simpson, Philip K. Maini, Eamonn A. Gaffney, Ruth E. Baker. Journal of Theoretical Biology 353, 95–103 | 2014.

Expositor: Augusto Borges

Chairman: Emanuel Cura Costa

Presentation


18/11/2014 – Structural basis of cellular dNTP regulation by SAMHD1. X. Ji, C. Tang, Q. Zhao, W. Wang, and Y. Xiong. PNAS  111 (41) E4305-E4314 | 2014.

Expositor: Emanuel Cura Costa

Chairman: H. Ariel Alvarez

Presentation


4/11/2014 – Measurements and modeling of water transport and osmoregulation in a single kidney cell using optical tweezers and videomicroscopy. A. D. Lúcio, R. A. S. Santos, and O. N. Mesquita. Phys. Rev. E 68, 041906 | 2003.

Expositor: H. Ariel Alvarez

Chairman: Osvaldo Chara

Presentation

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