UC Berkeley Developmental Biology Journal Club 2011-2012

(Last year's journal club schedule, papers, and paper bank can be found here)

September 9
Jess Lyons
Limiting Ago protein restricts RNAi and microRNA biogenesis during early development
in Xenopus laevis.
Lund et al. Genes Dev. 2011 Jun 1;25(11):1121-31.
September 16
Andrew Glazer
Ectodysplasin and Wnt pathways are required for salivary gland branching morphogenesis.
Häärä et al. Development. 2011 Jul;138(13):2681-91.
September 23
Angela Kaczmarczyk
Cxcl12 evolution--subfunctionalization of a ligand through altered interaction with the
chemokine receptor.
Boldajipour et al. Development. 2011 Jul;138(14):2909-14.
September 30
Caitlin DeJong
Notch destabilises maternal beta-catenin and restricts dorsal-anterior development in Xenopus.
Acosta et al. Development. 2011 Jun;138(12):2567-79.
October 7
Nathan Shih
The regenerative capacity of zebrafish reverses cardiac failure caused by genetic
cardiomyocyte depletion.
Wang et al. Development. 2011 Aug;138(16):3421-30.
October 14
Adam Session
SoxE gene duplication and development of the lamprey branchial skeleton: Insights into development
and evolution of the neural crest.
Lakiza et al. Dev Biol. 2011 Nov 1;359(1):149-61.
October 21
Cameron Exner
Nephronectin regulates atrioventricular canal differentiation via Bmp4-Has2 signaling in zebrafish.
Patra et al. Development. 2011 Oct;138(20):4499-509.
October 28
Adrienne Maxwell
Subcellular spatial regulation of canonical Wnt signalling at the primary cilium.
Lancaster, Schroth, & Gleeson. Nat Cell Biol. 2011 Jun;13(6):700-7.
November 4
Jade Glashauser
Snail2 controls mesodermal BMP/Wnt induction of neural crest.
Shi et al. Development. 2011 Aug;138(15):3135-45.
November 11
John Young
A novel mechanism for the transcriptional regulation of Wnt signaling in development.
Vacik et al. Genes Dev. 2011 Sep 1;25(17):1783-95.
November 18
Isabelle Philipp
Angiogenic morphogenesis driven by dynamic and heterogeneous collective endothelial cell movement.
Arima et al. Development. 2011 Nov;138(21):4763-76.
November 25
no JC--Thanksgiving
December 2
Valérie Hilgers
A regulatory archipelago controls hox genes transcription in digits.
Montavon et al. Cell. 2011 Nov 23;147(5):1132-45.
December 9
Sharon Amacher
Waif1/5T4 Inhibits Wnt/Beta-Catenin Signaling and Activates Noncanonical Wnt Pathways by Modifying LRP6 Subcellular Localization. Kagermeier-Schenk et al. Dev Cell. 2011 Dec 13;21(6):1129-43.
December 16
Tom Gallagher
Complex functions of Mef2 splice variants in the differentiation of endoderm and of a neuronal cell type in a sea anemone. Genikhovich & Technau. Development. 2011 Nov;138(22):4911-9.
January 13
Priscilla Erickson
Sox2 and Mitf cross-regulatory interactions consolidate progenitor and melanocyte lineages in the
cranial neural crest
. Adameyko et al. Development. 2012 Jan;139(2):397-410.
January 20
Nick Ellis
Smad1/Smad5 signaling in limb ectoderm functions redundantly and is required for interdigital
programmed cell death.
Wong, Behringer, & Kwan. Dev Biol. 2012 Jan 3. [Epub ahead of print]
January 27
Sofía Medina-Ruiz
Complement Fragment C3a Controls Mutual Cell Attraction during Collective Cell Migration.
Carmona-Fontaine et al. Dev Cell. 2011 Dec 13;21(6):1026-37.
February 3
Emilia Esposito
Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells.
Takemoto et al. Nature. 2011 Feb 17;470(7334):394-8.
February 10
Richard Harland
Canonical Wnt Signaling Dynamically Controls Multiple Stem Cell Fate Decisions during Vertebrate Body Formation. Martin & Kimelman. Dev Cell. 2012 Jan 17;22(1):223-32.
February 17
Phil Cleves
Bmp signaling regulates a dose-dependent transcriptional program to control facial skeletal
Bonilla-Claudio et al. Development. 2012 Feb;139(4):709-19.
February 24
Darwin Dichmann
Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3.
Liu et al. Cell. 2011 Sep 2;146(5):720-31.
March 2
Craig Miller
Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters.
Tschopp, Christen, and Duboule. Development. 2012 Mar;139(5):929-39.
March 9
Russell Fletcher
Optimality in the development of intestinal crypts.
Itzkovitz et al. Cell. 2012 Feb 3;148(3):608-19.
March 16
Guest Speaker
"Morphogens and morphogenesis in the palate."
Jeremy Green, King's College London
March 23
Hyeyoung Chung
Wnt/beta-catenin signaling directly regulates Foxj1 expression and ciliogenesis in
zebrafish Kupffer's vesicle.
Caron, Xu, & Lin. Development. 2012 Feb;139(3):514-24.
March 30
Blair Gainous
Islet1 regulates establishment of the posterior hindlimb field upstream of the Hand2-Shh morphoregulatory gene network in mouse embryos. Itou et al. Development. 2012 Mar 21. [Epub ahead of print]
April 6
Dave Stafford
Antagonistic interactions of hedgehog, Bmp and retinoic acid signals control zebrafish endocrine
pancreas development.
Tehrani & Lin. Development. 2011 Feb;138(4):631-40.
April 13
Jared Talbot
Jamb and jamc are essential for vertebrate myocyte fusion.
Powell & Wright. PLoS Biol. 2011 Dec;9(12):e1001216.
April 20 Eric Gonzales
Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome
Lindeman et al. Dev Cell. 2011 Dec 13;21(6):993-1004.
April 27 Justin Bosch
Mechanical Control of Morphogenesis by Fat/Dachsous/Four-Jointed Planar Cell Polarity Pathway.
Bosveld et al. Science. 2012 Apr 12. [Epub ahead of print]
May 4 Mounia Lagha
Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube.
Balaskas et al. Cell. 2012 Jan 20;148(1-2):273-84.
May 11 Brock Roberts
Secreted Wingless-interacting molecule (Swim) promotes long-range signaling by maintaining
Wingless solubility.
Mulligan et al. Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):370-7.
May 18 Emma Farley
Coding exons function as tissue-specific enhancers of nearby genes.
Birnbaum et al. Genome Res. 2012 Apr 17. [Epub ahead of print]


We will start promptly at 9AM in 547 LSA. This is because there is another meeting at 10. Please be on time.

Out of respect to the presenters, members are expected to attend journal club regularly.

Each member presents 1-2 times per year.

The week that you present, you should send the organizer the link to the paper you've chosen--ideally on Tuesday, by Wednesday at the latest, so that people have time to look at it before we meet. The goal here is to have the group ready to contribute to a good discussion.

The week after you present, you are asked to bring snacks for the group.

If you come across a paper that you'd like to see presented at journal club, you can send me the citation for our Paper Bank, a list of papers to which upcoming presenters can refer for suggestions.

Paper/Presentation guidelines:

1. Since the majority of participants are from vertebrate labs, Developmental Biology Journal Club focuses on vertebrate developmental biology. However, papers from invertebrate systems and/or that yield evolutionary insights are more than welcome, provided they fall within guideline #2. Historically we have presented papers that use Drosophila, C. elegans and other non-vertebrate systems to provide new mechanistic insight into signaling pathways.

2. We ask that papers be chosen based on one of several parameters: mechanistic insight, new technologies and tools, or if not one of those, a paper that has an interesting insight with broad application to the participants. We would like to stick to papers that really get at the mechanisms and signaling patterns driving developmental biology. If you find a paper you'd really like to present but consists simply of expression patterns, we ask that you also present a related mechanism paper to accompany it.

3. Presenters should briefly state why the paper or question being asked is important or applicable to the group. Is it groundbreaking work? Does it provide a new insight into how a signaling pathway works? Why is it important that we read this paper? ("I needed to pick a paper to present" is not a good reason.)

4. Your presentation should include some brief background that is relevant to the paper, such as a summary of what is known about the process/tissue being discussed, of the signaling pathway being studied, or of the line of research from which this paper is derived.


The Msx1 Homeoprotein Recruits Polycomb to the Nuclear Periphery during Development.
Wang et al. Dev Cell. 2011 Sep 13;21(3):575-88.

Two additional midline barriers function with midline lefty1 expression to maintain asymmetric Nodal signaling during left-right axis specification in zebrafish.
Lenhart et al. Development. 2011 Oct;138(20):4405-10.

Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish.
Zhu et al. Development. 2011 Oct;138(20):4555-64.

The dynamic architecture of Hox gene clusters.
Noordermeer et al. Science. 2011 Oct 14;334(6053):222-5.

Protein Kinase A acts at the basal body of the primary cilium to prevent Gli2 activation and ventralization of the mouse neural tube.
Tuson, He, & Anderson. Development. 2011 Nov;138(22):4921-30.

Novel functions of Noggin proteins: inhibition of Activin/Nodal and Wnt signaling.
Bayramov et al. Development. 2011 Dec;138(24):5345-56.

Phosphorylation of Mad controls competition between wingless and BMP signaling.
Eivers et al. Sci Signal. 2011 Oct 11;4(194):ra68.

Canonical BMP7 activity is required for the generation of discrete neuronal populations in the dorsal spinal cord.
Le Dréau et al. Development. 2012 Jan;139(2):259-68.

Synchronous and symmetric migration of Drosophila caudal visceral mesoderm cells requires dual input by two FGF ligands.
Kadam, Ghosh, & Stathopoulos. Development. 2012 Feb;139(4):699-708.

Pitx1 is necessary for normal initiation of hindlimb outgrowth through regulation of Tbx4 expression and shapes hindlimb morphologies via targeted growth control.
Duboc & Logan. Development. 2011 Dec;138(24):5301-9.

Sequential signaling crosstalk regulates endomesoderm segregation in sea urchin embryos.
Sethi et al. Science. 2012 Feb 3;335(6068):590-3.

Protein kinase A acts at the basal body of the primary cilium to prevent Gli2 activation and ventralization of the mouse neural tube.
Tuson & Anderson. Development. 2011 Nov;138(22):4921-30.

Turning gene function ON and OFF using sense and antisense photo-morpholinos in zebrafish.
Tallafuss et al. Development. 2012 May; 139:1691-99.

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer.
Sudou et al. Development. 2012 May; 139: 1651-61.

GLI3 Constrains Digit Number by Controlling Both Progenitor Proliferation and BMP-Dependent Exit to Chondrogenesis.
Lopez-Rios et al. Dev Cell. 2012 Mar 28. [Epub ahead of print].

Please send all comments, questions, and Paper Bank submissions to Jess Lyons. Thanks!