Mol. Biol. Cell Table of Contents for 1 July 2009; Vol. 20, No. 13

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A new issue of Molecular Biology of the Cell is available online:

1 July 2009; Vol. 20, No. 13

The below Table of Contents is available online at: http://www.molbiolcell.org/content/vol20/issue13/?etoc

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Articles

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Dynein-Driven Mitotic Spindle Positioning Restricted to Anaphase by She1p Inhibition of Dynactin Recruitment

Jeffrey B. Woodruff, David G. Drubin, and Georjana Barnes

Clustering of Syndecan-4 and Integrin β1 by Laminin 3 Chain–derived Peptide Promotes Keratinocyte Migration

Eri Araki, Yutaka Momota, Takeshi Togo, Miki Tanioka, Kentaro Hozumi, Motoyoshi Nomizu, Yoshiki Miyachi, and Atsushi Utani

Analysis of Dom34 and Its Function in No-Go Decay

Dario O. Passos, Meenakshi K. Doma, Christopher J. Shoemaker, Denise Muhlrad, Rachel Green, Jonathan Weissman, Julie Hollien, and Roy Parker

Integrin-linked Kinase Interactions with ELMO2 Modulate Cell Polarity

Ernest Ho, Tames Irvine, Gregory J.A. Vilk, Gilles Lajoie, Kodi S. Ravichandran, Sudhir J.A. D'Souza, and Lina Dagnino

IC97 Is a Novel Intermediate Chain of I1 Dynein That Interacts with Tubulin and Regulates Interdoublet Sliding

Maureen Wirschell, Chun Yang, Pinfen Yang, Laura Fox, Haru-aki Yanagisawa, Ritsu Kamiya, George B. Witman, Mary E. Porter, and Winfield S. Sale

IC138 Defines a Subdomain at the Base of the I1 Dynein That Regulates Microtubule Sliding and Flagellar Motility

Raqual Bower, Kristyn VanderWaal, Eileen O'Toole, Laura Fox, Catherine Perrone, Joshua Mueller, Maureen Wirschell, R. Kamiya, Winfield S. Sale, and Mary E. Porter

Rec8 Guides Canonical Spo11 Distribution along Yeast Meiotic Chromosomes

Kazuto Kugou, Tomoyuki Fukuda, Shintaro Yamada, Masaru Ito, Hiroyuki Sasanuma, Saori Mori, Yuki Katou, Takehiko Itoh, Kouji Matsumoto, Takehiko Shibata, Katsuhiko Shirahige, and Kunihiro Ohta

PUMA Promotes Bax Translocation by Both Directly Interacting with Bax and by Competitive Binding to Bcl-X_L during UV-induced Apoptosis

Yingjie Zhang, Da Xing, and Lei Liu

The Cytoplasmic Tail of GM3 Synthase Defines Its Subcellular Localization, Stability, and In Vivo Activity

Satoshi Uemura, Sayaka Yoshida, Fumi Shishido, and Jin-ichi Inokuchi

The Signaling Mucins Msb2 and Hkr1 Differentially Regulate the Filamentation Mitogen-activated Protein Kinase Pathway and Contribute to a Multimodal Response

Andrew Pitoniak, Barbara Birkaya, Heather M. Dionne, Nadia Vadaie, and Paul J. Cullen

Zyxin Mediates Actin Fiber Reorganization in Epithelial–Mesenchymal Transition and Contributes to Endocardial Morphogenesis

Masaki Mori, Hironori Nakagami, Nobutaka Koibuchi, Koichi Miura, Yoichi Takami, Hiroshi Koriyama, Hiroki Hayashi, Hisataka Sabe, Naoki Mochizuki, Ryuichi Morishita, and Yasufumi Kaneda

Revisiting the Role of Cystic Fibrosis Transmembrane Conductance Regulator and Counterion Permeability in the pH Regulation of Endocytic Organelles

Herve Barriere, Miklos Bagdany, Florian Bossard, Tsukasa Okiyoneda, Gabriella Wojewodka, Dieter Gruenert, Danuta Radzioch, and Gergely L. Lukacs

Cortical F-Actin, the Exocytic Mode, and Neuropeptide Release in Mouse Chromaffin Cells Is Regulated by Myristoylated Alanine-rich C-Kinase Substrate and Myosin II

Bryan W. Doreian, Tiberiu G. Fulop, Robert L. Meklemburg, and Corey B. Smith

Epidermal Growth Factor–induced Contraction Regulates Paxillin Phosphorylation to Temporally Separate Traction Generation from De-adhesion

Ian C. Schneider, Cristen K. Hays, and Clare M. Waterman

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July 2009 Volume 89 Number 7, pp 728 - 840

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RESEARCH ARTICLES
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Reactive oxygen species modulate growth of cerebral aneurysms: a study using the free
radical scavenger edaravone and p47phox-/- mice
Tomohiro Aoki, Masaki Nishimura, Hiroharu Kataoka, Ryota Ishibashi, Kazuhiko Nozaki and Nobuo Hashimoto
Abstract: http://links.ealert.nature.com/ctt?kn=63&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Macrophages of multiple sclerosis patients display deficient SHP-1 expression and
enhanced inflammatory phenotype
George P Christophi, Michael Panos, Chad A Hudson, Rebecca L Christophi, Ross C Gruber,
Akos T Mersich, Scott D Blystone, Burk Jubelt and Paul T Massa
Abstract: http://links.ealert.nature.com/ctt?kn=27&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Functional evaluation of pallid mice with genetic emphysema
Mitsuteru Yoshida, Shoji Sakiyama, Koichiro Kenzaki, Hiroaki Toba, Kou Uyama,
Masatsugu Takehisa, Kazuya Kondo and Akira Tangoku
Abstract: http://links.ealert.nature.com/ctt?kn=83&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Vesicle-mediated secretion of human eosinophil granule-derived major basic protein
Rossana C N Melo, Lisa A Spencer, Sandra A C Perez, Josiane S Neves, Staci P Bafford,
Ellen S Morgan, Ann M Dvorak and Peter F Weller
Abstract: http://links.ealert.nature.com/ctt?kn=50&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Transgenic mitochondrial superoxide dismutase and mitochondrially targeted catalase
prevent antiretroviral-induced oxidative stress and cardiomyopathy
James J Kohler, Ioan Cucoranu, Earl Fields, Elgin Green, Stanley He, Amy Hoying, Rodney Russ,
Allison Abuin, David Johnson, Seyed H Hosseini, C Michael Raper and William Lewis
Abstract: http://links.ealert.nature.com/ctt?kn=42&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Epigenetic silencing of TTF-1/NKX2-1 through DNA hypermethylation and histone
H3 modulation in thyroid carcinomas
Tetsuo Kondo, Tadao Nakazawa, Defu Ma, Dongfeng Niu, Kunio Mochizuki, Tomonori Kawasaki,
Nobuki Nakamura, Tetsu Yamane, Makio Kobayashi and Ryohei Katoh
Abstract: http://links.ealert.nature.com/ctt?kn=57&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Poor vessel formation in embryos from knock-in mice expressing ALK5 with L45 loop
mutation defective in Smad activation
Fumiko Itoh, Susumu Itoh, Rita L C Carvalho, Tomomi Adachi, Masatsugu Ema,
Marie-Jose Goumans, Jonas Larsson, Stefan Karlsson, Satoru Takahashi, Christine L Mummery,
Peter ten Dijke and Mitsuyasu Kato
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Genistein induces adipogenesis but inhibits leptin induction in human synovial fibroblasts
Biserka Relic, Mustapha Zeddou, Aline Desoroux, Yves Beguin, Dominique de Seny and Michel G Malaise
Abstract: http://links.ealert.nature.com/ctt?kn=2&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Alteration of the PKC-mediated signaling pathway for smooth muscle contraction in
obstruction-induced hypertrophy of the urinary bladder
Shaohua Chang, Joseph A Hypolite, Sunish Mohanan, Stephen A Zderic, Alan J Wein and Samuel Chacko
Abstract: http://links.ealert.nature.com/ctt?kn=70&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0
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Urinary trypsin inhibitor protects against liver injury and coagulation pathway dysregulation
induced by lipopolysaccharide/D-galactosamine in mice
Hirohisa Takano, Ken-ichiro Inoue, Akinori Shimada, Hiroyuki Sato, Rie Yanagisawa and Toshikazu Yoshikawa
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CORRIGENDUM
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Indistinguishable genomic profiles and shared prognostic markers in undifferentiated pleomorphic
sarcoma and leiomyosarcoma: different sides of a single coin?
Ana Carneiro, Princy Francis, Par-Ola Bendahl, Josefin Fernebro, Mans Akerman, Christopher Fletcher,
Anders Rydholm, Ake Borg and Mef Nilbert
http://links.ealert.nature.com/ctt?kn=6&m=33476499&r=MTc2Mjk0MzQ4MgS2&b=2&j=NTIzMjEwNzcS1&mt=1&rt=0

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July 2009 Volume 6 Number 7

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----------------------
EDITORIAL
----------------------
The most important news at ASCO 2009
Vincent T. DeVita, Jr
p371 | doi:10.1038/nrclinonc.2009.93
http://links.ealert.nature.com/ctt?kn=76&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

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RESEARCH HIGHLIGHTS
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Genetics: TP53 mutations predict response to cetuximab
p373 | doi:10.1038/nrclinonc.2009.75
http://links.ealert.nature.com/ctt?kn=52&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Mutation status and treatment response
p374 | doi:10.1038/nrclinonc.2009.80
http://links.ealert.nature.com/ctt?kn=88&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Targeted therapies: KRAS wild-type tumors benefit from cetuximab
p374 | doi:10.1038/nrclinonc.2009.81
http://links.ealert.nature.com/ctt?kn=34&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Surgical oncology: Markers of long-term survival in pancreatic cancer
p375 | doi:10.1038/nrclinonc.2009.74
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Maintenance rituximab prolongs PFS
p375 | doi:10.1038/nrclinonc.2009.77
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Screening: Ovarian cancer: feasibility of early detection
p375 | doi:10.1038/nrclinonc.2009.79
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Imaging: FDG-PET/CT: early predictor of treatment response in soft-tissue
sarcoma
p376 | doi:10.1038/nrclinonc.2009.76
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Imaging: FDG-PET accurately detects distant disease
p376 | doi:10.1038/nrclinonc.2009.78
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NEWS AND VIEWS
----------------------
Surgery: Stereotactic radiosurgery alone to treat brain metastases
Laura A. Vallow
p377 | doi:10.1038/nrclinonc.2009.84
Brain metastases are a challenge for the oncologist, with 20-40% of cancer
patients developing intracranial metastases during the course of their
illness. The incidence of brain metastases is increasing as a result of
improvements in systemic therapy and imaging capabilities, and increased
use of screening. Brain metastases pose not only a risk to mortality but
also a risk of neurologic, cognitive and emotional difficulties.
http://links.ealert.nature.com/ctt?kn=85&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Targeted therapies: Cetuximab, chemotherapy and KRAS status in mCRC
Sharlene Gill and Richard M. Goldberg
p379 | doi:10.1038/nrclinonc.2009.83
The first-line treatment for patients with unresectable metastatic
colorectal cancer is chemotherapy in combination with bevacizumab.
Emerging evidence, however, suggests that the addition of cetuximab-an
anti-EGFR monoclonal antibody-to chemotherapy might be beneficial to
patients with wild-type KRAS tumors.
http://links.ealert.nature.com/ctt?kn=25&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Hematology: ASCT in follicular lymphoma
Jennifer R. Brown and Arnold S. Freedman
p380 | doi:10.1038/nrclinonc.2009.87
The use of autologous stem-cell transplantation in the treatment of
follicular lymphoma remains controversial. Results from the GOELAMS trial
show a higher progression-free survival rate in patients treated with
autologous stem-cell transplantation compared to those treated with
chemotherapy.
http://links.ealert.nature.com/ctt?kn=14&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Surgery: Role of lymphadenectomy in the staging of endometrial cancer
Kimberly E. Resnick, David E. Cohn and Jeffrey M. Fowler
p382 | doi:10.1038/nrclinonc.2009.88
Pelvic lymphadenectomy offers no therapeutic benefit to women diagnosed
with early-stage endometrial cancer according to a new study.
Lymphadenectomy can only be recommended as part of a clinical trial in
this disease setting; however, it can offer valuable staging information
in those with advanced disease.
http://links.ealert.nature.com/ctt?kn=50&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Screening: Cervical cancer in rural India
Anthony B. Miller
p384 | doi:10.1038/nrclinonc.2009.85
A study of cervical cancer screening in 52 villages in India has shown
that a single round of human papillomavirus testing was linked to a
significant reduction in the number of deaths from cervical cancer,
compared with other screening methods. This has implications for primary
screening in low-resource settings.
http://links.ealert.nature.com/ctt?kn=72&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Surgery: Apples and oranges: the low and mid versus the upper rectum
Martin Weiser and Leonard Saltz
p385 | doi:10.1038/nrclinonc.2009.86
The role of laparoscopic resection for rectal cancer is currently unclear,
with little supportive evidence from randomized trials. A study by Ng
et al. in a large series of patients with rectal cancer has shown that
laparoscopic resection is safe with good long-term outcomes.
http://links.ealert.nature.com/ctt?kn=68&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

----------------------
REVIEWS
----------------------
Molecular targets for treatment of inflammatory breast cancer
Hideko Yamauchi, Massimo Cristofanilli, Seigo Nakamura, Gabriel N.
Hortobagyi and Naoto T. Ueno
Published online: 26 May 2009
p387 | doi:10.1038/nrclinonc.2009.73
The long-term outcome for patients with inflammatory breast cancer is
poor despite advances in combined-modality treatment. Treatments
targeting the vasculolymphatic pathway have shown potential and therapies
targeting cell proliferation pathways are also promising. The authors
of this Review discuss the biology of inflammatory breast cancer and
potential molecular targets.
Abstract: http://links.ealert.nature.com/ctt?kn=29&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=74&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Anticancer strategies involving the vasculature
Victoria L. Heath and Roy Bicknell
Published online: 07 May 2009
p395 | doi:10.1038/nrclinonc.2009.52
Understanding the process of tumor angiogenesis and ways to modify this
is a key point in the fight against cancer. This Review explores the
current status of vascular-disrupting strategies, discusses how
anti-VEGF-based anti-angiogenic therapies can be combined with conventional
chemotherapy and radiotherapy, and highlights potential future targets
for therapeutic intervention.
Abstract: http://links.ealert.nature.com/ctt?kn=38&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=28&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Molecular and cellular mechanisms of CLL: novel therapeutic approaches
Lisa Pleyer, Alexander Egle, Tanja Nicole Hartmann and Richard Greil
Published online: 02 June 2009
p405 | doi:10.1038/nrclinonc.2009.72
The mainstay of therapy of chronic lymphocytic leukemia (CLL) is cytotoxic
chemotherapy; however, CLL is still an incurable disease with resistance
to therapy developing in a majority of patients. This Review summarizes
the progress made in understanding the biological basis of CLL pathogenesis
and other aspects of CLL biology, and describes novel treatment strategies
that have also been exploited in current clinical trials.
Abstract: http://links.ealert.nature.com/ctt?kn=57&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=49&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

Surgical management of pancreatic endocrine tumors
Volker Fendrich, Jens Waldmann, Detlef K. Bartsch and Peter Langer
Published online: 09 June 2009
p419 | doi:10.1038/nrclinonc.2009.82
Pancreatic endocrine tumors (PETs) represent an important subset of
pancreatic neoplasms. Patients with completely resected tumors generally
have a good prognosis, and an aggressive surgical approach in patients
with advanced disease may also prolong survival. The authors of this
Review discuss the current surgical management strategies for treating
PETs, focusing on insulinomas, gastrinomas and nonfunctional PETs.
Abstract: http://links.ealert.nature.com/ctt?kn=62&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=20&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

----------------------
CASE STUDY
----------------------
A stepwise approach to the management of metastatic midgut carcinoid
tumor
Sanjeev Bhattacharyya, Dorothy M. Gujral, Christos Toumpanakis, Gilles
Dreyfus, Brian R. Davidson, Joseph Davar and Martyn E. Caplin
p429 | doi:10.1038/nrclinonc.2009.70
The authors present a case of a 48-year-old man with a history of diarrhea,
flushing and upper abdominal pain who was subsequently diagnosed with
metastatic carcinoid tumor. The authors discuss the importance of a
stepwise approach in a multi-disciplinary team setting to provide
effective patient care.
Abstract: http://links.ealert.nature.com/ctt?kn=22&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=81&m=33476114&r=MTc2NDg2OTc4MQS2&b=2&j=NTIzMTI4NDQS1&mt=1&rt=0

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ScienceDirect Alert: Cell, Vol. 137, Iss. 7, 2009

New Volume/Issue is now available on ScienceDirect

Cell Volume 137, Issue 7,  Pages 1161-1358 (26 June 2009)

Leading Edge

1.

In This Issue Pages 1161, 1163

2.

Developmental Biology Select Pages 1165, 1167

Analysis

3.

Seeing Green in Conference Season Pages 1169-1171 Lila Guterman

Correspondence

4.

Common Ancestry of the CENP-A Chaperones Scm3 and HJURP Pages 1173-1174 Luis Sanchez-Pulido, Alison L. Pidoux, Chris P. Ponting, Robin C. Allshire

Book Review

5.

Glycobiology: Moving into the Mainstream Pages 1175-1176 Raymond A. Dwek

Previews

6.

GABA Keeps Up an Appetite for Life Pages 1177-1179 Marcelo O. Dietrich, Tamas L. Horvath

7.

Ironing Out a Midlife Crisis Pages 1179-1181 Sandra Viviana Vergara, Dennis J. Thiele

8.

The Juxtamembrane Region of EGFR Takes Center Stage Pages 1181-1183 Stevan R. Hubbard

9.

Closing in on Mechanisms of Tissue Morphogenesis Pages 1183-1185 Matteo Rauzi, Thomas Lecuit

10.

Fly Stem Cell Research Gets Infectious Pages 1185-1187 Ryan Conder, Juergen A. Knoblich

Minireview

11.

Plant Asymmetric Cell Division, Vive la Différence! Pages 1189-1192 Frank L.H. Menke, Ben Scheres

Review

12.

CTCF: Master Weaver of the Genome Pages 1194-1211 Jennifer E. Phillips, Victor G. Corces

Articles

13.

Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol Pages 1213-1224 Hyock Joo Kwon, Lina Abi-Mosleh, Michael L. Wang, Johann Deisenhofer, Joseph L. Goldstein, Michael S. Brown, Rodney E. Infante

14.

Loss of GABAergic Signaling by AgRP Neurons to the Parabrachial Nucleus Leads to Starvation Pages 1225-1234 Qi Wu, Maureen P. Boyle, Richard D. Palmiter

15.

Abnormal Behavior in a Chromosome- Engineered Mouse Model for Human 15q11-13 Duplication Seen in Autism Pages 1235-1246 Jin Nakatani, Kota Tamada, Fumiyuki Hatanaka, Satoko Ise, Hisashi Ohta, Kiyoshi Inoue, Shozo Tomonaga, Yasuhito Watanabe, Yeun Jun Chung, Ruby Banerjee, Kazuya Iwamoto, Tadafumi Kato, Makoto Okazawa, Kenta Yamauchi, Koichi Tanda, Keizo Takao, Tsuyoshi Miyakawa, Allan Bradley, Toru Takumi

16.

Mitochondrial Dysfunction Leads to Nuclear Genome Instability via an Iron-Sulfur Cluster Defect Pages 1247-1258 Joshua R. Veatch, Michael A. McMurray, Zara W. Nelson, Daniel E. Gottschling

17.

Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer Pages 1259-1271 Sujun Hua, Ralf Kittler, Kevin P. White

18.

A Synthetic Genetic Edge Detection Program Pages 1272-1281 Jeffrey J. Tabor, Howard M. Salis, Zachary Booth Simpson, Aaron A. Chevalier, Anselm Levskaya, Edward M. Marcotte, Christopher A. Voigt, Andrew D. Ellington

19.

X-Ray Structures of the Hexameric Building Block of the HIV Capsid Pages 1282-1292 Owen Pornillos, Barbie K. Ganser-Pornillos, Brian N. Kelly, Yuanzi Hua, Frank G. Whitby, C. David Stout, Wesley I. Sundquist, Christopher P. Hill, Mark Yeager

20.

Mechanism for Activation of the EGF Receptor Catalytic Domain by the Juxtamembrane Segment Pages 1293-1307 Natalia Jura, Nicholas F. Endres, Kate Engel, Sebastian Deindl, Rahul Das, Meindert H. Lamers, David E. Wemmer, Xuewu Zhang, John Kuriyan

21.

Exocytosis of Post-Golgi Vesicles Is Regulated by Components of the Endocytic Machinery Pages 1308-1319 Jyoti K. Jaiswal, Victor M. Rivera, Sanford M. Simon

22.

BASL Controls Asymmetric Cell Division in Arabidopsis Pages 1320-1330 Juan Dong, Cora A. MacAlister, Dominique C. Bergmann

23.

Pulsed Forces Timed by a Ratchet-like Mechanism Drive Directed Tissue Movement during Dorsal Closure Pages 1331-1342 Jerome Solon, Aynur Kaya-Çopur, Julien Colombelli, Damian Brunner

24.

Cytokine/Jak/Stat Signaling Mediates Regeneration and Homeostasis in the Drosophila Midgut Pages 1343-1355 Huaqi Jiang, Parthive H. Patel, Alexander Kohlmaier, Marc O. Grenley, Donald G. McEwen, Bruce A. Edgar

Erratum

25.

Parkinson's Disease Patient-Derived Induced Pluripotent Stem Cells Free of Viral Reprogramming Factors Page 1356 Frank Soldner, Dirk Hockemeyer, Caroline Beard, Qing Gao, George W. Bell, Elizabeth G. Cook, Gunnar Hargus, Alexandra Blak, Oliver Cooper, Maisam Mitalipova, Ole Isacson, Rudolf Jaenisch

SnapShot

26.

SnapShot: F Box Proteins II Pages 1358.e1-1358.e2 Jeffrey R. Skaar, Vincenzo D'Angiolella, Julia K. Pagan, Michele Pagano

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Latest PhD Studentships - 30 June 2009

Welcome to the FindAPhD weekly Newsletter. Listed below are the latest research projects to be advertised on FindAPhD.com.

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Single Molecule Spintronic Junctions

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Development of tunable terahertz quantum cascade lasers using aperiodic photonic lattices

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Measuring and characterising the physical, psychological, social and occupational outcomes post injury

Kingston University
Ethnic networks and the promise of transnationalism: foreign-born labour and human capital development

Kingston University
Developing monitoring and assessment tools to support post-project appraisal (PPA) of river restoration works

Kingston University
Locating Gold in the Senegal-Mali Shear Zone: an integrated approach using regional structural, fluid inclusion, geochemical and geophysical data sets

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Phytoplankton response to climate and sea-level change in a greenhouse ocean: Cretaceous dinoflagellate cysts as proxies ofpalaeoenvironmental change, from subtropics to subarctic

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Stem Cells Accepted Articles for June 26th

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Copyright © 2009 AlphaMed Press Published on behalf of AlphaMed Press This Publication Alert is being sent to individuals who requested receipt of this information. For additional details, see the bottom of this message. Stem Cells Express (Accepted Articles) The Stem Cell Niche Endothelial Cells Support Survival, Proliferation and Neuronal Differentiation of Transplanted Adult Ischemia-Induced Neural Stem/Progenitor Cells after Cerebral Infarction (p N/A) Nami Nakagomi, Takayuki Nakagomi, Shuji Kubo, Akiko Nakano-Doi, Orie Saino, Masashi Takata, Hiroo Yoshikawa, David M. Stern, Tomohiro Matsuyama, Akihiko Taguchi Accepted Article Online: Jun 25 2009 6:52PM DOI: 10.1002/stem.161 Letter to the Editor Validation of -Actin Used As Endogenous Control for Gene Expression Analysis in Mechanobiology Studies (p N/A) Jun Liu, Ling Zou, Jun Wang, Zhihe Zhao Accepted Article Online: Jun 23 2009 9:33PM DOI: 10.1002/stem.160 Translational and Clinical Research Genetic Basis of Inherited Macular Dystrophies and Implications for Stem Cell Therapy (p N/A) Carla B Mellough, David HW Steel, Majlinda Lako Accepted Article Online: Jun 23 2009 9:33PM DOI: 10.1002/stem.159 Embryonic Stem Cells/Induced Pluripotent Stem Cells Birth of Parthenote Mice Directly from Parthenogenetic Embryonic Stem Cells (p N/A) Zhisheng Chen, Zhong Liu, Junjiu Huang, Tomokazu Amano, Chao Li, Shanbo Cao, Chao Wu, Bodu Liu, Lingjun Zhou, Mark G. Carter, David L. Keefe, Xiangzhong Yang, Lin Liu Accepted Article Online: Jun 19 2009 1:44PM DOI: 10.1002/stem.158 Tissue-Specific Stem Cells Co-transplantation of Placental MSCs Enhances Single and Double Cord Blood Engraftment in NOD/SCID Mice (p N/A) Smita D Hiwase, Pamela G Dyson, L.B. To, Ian Lewis Accepted Article Online: Jun 19 2009 1:45PM DOI: 10.1002/stem.157 This message is sent to subscribers and alert registrants for Stem Cells. To UNSUBSCRIBE from future mailings go to The Stem Cells Express Alert list. If you have any questions or concerns about this message, please contact lwoo@wiley.com. Do not reply directly to this message. Wiley InterScience is a division of:      John Wiley & Sons, Inc.  |  111 River Street  |  Hoboken, NJ 07030      Phone: 800-225-5945  |  Fax: 800-605-2665  |  www.wiley.com

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Nature Methods Contents: July 2009 Volume 6 pp 471-546

NATURE METHODS

July 2009 Volume 6 Number 7, pp 471 - 546

Visit Nature Methods online to browse the journal.

Now available at http://links.ealert.nature.com/ctt?kn=66&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

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=====================================================================

----------------------
EDITORIAL
----------------------
Summer reading: science in fiction p471
Though somewhat rare, there are a few good fiction books to be found
with refreshingly realistic biologists as central characters in
laboratory settings.
doi:10.1038/nmeth0709-471
http://links.ealert.nature.com/ctt?kn=40&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

----------------------
CORRESPONDENCE
----------------------
MoDIL: detecting small indels from clone-end sequencing with mixtures
of distributions pp473 - 474
Seunghak Lee, Fereydoun Hormozdiari, Can Alkan and Michael Brudno
doi:10.1038/nmeth.f.256
http://links.ealert.nature.com/ctt?kn=32&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Limitations and possibilities of small RNA digital gene expression
profiling pp474 - 476
Sam E V Linsen et al.
doi:10.1038/nmeth0709-474
http://links.ealert.nature.com/ctt?kn=137&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

RNAiCut: automated detection of significant genes from functional
genomic screens pp476 - 477
Irene M Kaplow et al.
doi:10.1038/nmeth0709-476
http://links.ealert.nature.com/ctt?kn=82&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Enabling IMAC purification of low abundance recombinant proteins from
E. coli lysates pp477 - 478
Audur Magnusdottir et al.
doi:10.1038/nmeth0709-477
http://links.ealert.nature.com/ctt?kn=75&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

----------------------
RESEARCH HIGHLIGHTS
----------------------
A question of culture p481
Two groups report culture conditions for long-term in vitro growth of
intestinal tissue from the mouse.
Natalie de Souza
doi:10.1038/nmeth0709-481
http://links.ealert.nature.com/ctt?kn=57&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Fluorescent proteins: into the infrared pp482 - 483
An engineered infrared fluorescent protein is the first member of a
new class of genetically encodable probes, with special advantages
over visible-wavelength fluorescent proteins for in vivo imaging.
Allison Doerr
doi:10.1038/nmeth0709-482a
http://links.ealert.nature.com/ctt?kn=135&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Going with the skewed flow pp482 - 483
Computational and experimental biologists teamed up to develop a
new software tool to analyze the rich data generated by new
and powerful flow cytometers.
Wayne Peng
doi:10.1038/nmeth0709-482b
http://links.ealert.nature.com/ctt?kn=71&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

News in brief p483
doi:10.1038/nmeth0709-483
http://links.ealert.nature.com/ctt?kn=116&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Grafting as a potent molecular tool p484
Grafting two transgenic plants triggers lateral gene transfer at the
graft site but does not elicit long-distance transport of DNA into
the scion or root of the graft.
Nicole Rusk
doi:10.1038/nmeth0709-484
http://links.ealert.nature.com/ctt?kn=15&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Fluorescent false neurotransmitters p486
A fluorescent probe designed to incorporate a fluorophore into the
structure of a neurotransmitter finds activity-dependent
heterogeneity in dopamine release at individual synapses.
Daniel Evanko
doi:10.1038/nmeth0709-486
http://links.ealert.nature.com/ctt?kn=113&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Will planets reveal the light of their life? p487
Optical signatures from organic chemicals may help scientists detect
traces of life on other planets.
Michael Eisenstein
doi:10.1038/nmeth0709-487
http://links.ealert.nature.com/ctt?kn=56&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

----------------------
NEWS AND VIEWS
----------------------
Finding multiple needles in one immune haystack pp489 - 490
An approach using multiple fluorochrome combinations allows the
simultaneous detection of many T-cell populations within a single
blood sample.
Katherine Kedzierska, John Stambas and Peter C Doherty
doi:10.1038/nmeth0709-489
http://links.ealert.nature.com/ctt?kn=94&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Downhill protein folding under pressure pp490 - 491
Sub-microsecond, downhill-reaction protein folding can be
investigated by a method to generate large and fast pressure
drops. The approach is complementary to nanosecond
temperature-jump methods and could provide new insights
into the biophysics of protein folding.
Victor Munoz
doi:10.1038/nmeth0709-490
http://links.ealert.nature.com/ctt?kn=156&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

----------------------
BRIEF COMMUNICATIONS
----------------------
Agouti C57BL/6N embryonic stem cells for mouse genetic
resources pp493 - 495
Mouse embryonic stem cell lines from the C57BL/6 strain are reported.
The lines are highly germline competent, suitable for high-throughput
genetic manipulation and will enable the generation of large knockout
mouse resources.
Stephen J Pettitt et al.
doi:10.1038/nmeth.1342
Abstract: http://links.ealert.nature.com/ctt?kn=119&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=38&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Simultaneous detection of many T-cell specificities using
combinatorial tetramer staining pp497 - 499
Combinations of fluorescently labeled peptide-major
histocompatability (pMHC) tetramers are used to simultaneously
detect T cells with multiple antigen specificities from human blood
samples. Also in this issue, Hadrup et al. present a very similar
combinatorial encoding approach.
Evan W Newell, Lawrence O Klein, Wong Yu and Mark M Davis
doi:10.1038/nmeth.1344
Abstract: http://links.ealert.nature.com/ctt?kn=81&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=125&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Protein interaction platforms: visualization of interacting proteins
in yeast pp500 - 502
The protein interaction platform or PIP assay uses a viral
scaffolding protein fused to a bait and a fluorescent reporter
rotein fused to putative prey as the basis for a simple visual
screen for protein-protein interactions in yeast.
Alexa M Schmitz et al.
doi:10.1038/nmeth.1337
Abstract: http://links.ealert.nature.com/ctt?kn=54&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=31&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Quantitative analysis of gene expression in a single cell by
qPCR pp503 - 506
There have been many attempts to measure gene expression in single
cells but counting several different mRNAs in the same cell has been
a challenge. A reusable single-cell cDNA library immobilized on beads
allows quantitative measurement of multiple mRNAs in a single cell
with a large dynamic range and small experimental error.
Kiyomi Taniguchi, Tomoharu Kajiyama and Hideki Kambara
doi:10.1038/nmeth.1338
Abstract: http://links.ealert.nature.com/ctt?kn=112&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=26&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Filter-based hybridization capture of subgenomes enables resequencing
and copy-number detection pp507 - 510
Concatenated PCR products serve as subgenomic traps in this targeted
genome capture technique; subsequent high-throughput sequencing
allows the detection of nucleotide and structural variations in the
captured genomic regions.
Daniel S Herman et al.
doi:10.1038/nmeth.1343
Abstract: http://links.ealert.nature.com/ctt?kn=122&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=42&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

In vivo fluorescence imaging with high-resolution
microlenses pp511 - 512
A combination of gradient refractive index lenses with plano-convex
lenses produces high-resolution microlenses with image quality
similar to a conventional high quality microscope objective. The
microlenses are capable of imaging dendritic spines on hippocampal
neurons in live mice.
Robert P J Barretto, Bernhard Messerschmidt and Mark J Schnitzer
doi:10.1038/nmeth.1339
Abstract: http://links.ealert.nature.com/ctt?kn=91&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=23&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

'Injecting' yeast pp513 - 514
Using a topographically patterned substrate for immobilization of
single yeast cells and a piezo-impact micromanipulator to transiently
disrupt the cell wall, molecules can be physically introduced into
yeast.
Daniel Riveline and Paul Nurse
doi:10.1038/nmeth.1335
Abstract: http://links.ealert.nature.com/ctt?kn=131&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=47&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

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ARTICLES
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Reaching the protein folding speed limit with large, sub-microsecond
pressure jumps pp515 - 519
Although fast temperature jump methods to study protein folding
dynamics have long been applied, pressure has been a neglected
thermodynamic parameter. A method to generate rapid and large
drops in pressure is complementary to fast temperature jump
methods and could be useful for direct comparisons to molecular
dynamics simulations.
Charles Dumont, Tryggvi Emilsson and Martin Gruebele
doi:10.1038/nmeth.1336
Abstract: http://links.ealert.nature.com/ctt?kn=11&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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Parallel detection of antigen-specific T-cell responses by
multidimensional encoding of MHC multimers pp520 - 526
Using combinations of fluorescently labeled peptide-major
histocompatability complex (pMHC) tetramers, T-cell populations
with multiple antigen specificities can be monitored in parallel
from small samples of human blood. Also in this issue, Newell et al.
present a very similar combinatorial encoding method for
this purpose.
Sine Reker Hadrup et al.
doi:10.1038/nmeth.1345
Abstract: http://links.ealert.nature.com/ctt?kn=28&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=145&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Doxycycline-dependent photoactivated gene expression in eukaryotic
systems pp527 - 531
Activation of caged doxycycline or cyanodoxycycline by biologically
innocuous doses of UV light allows for precise temporal and spatial
control of transgene expression in hippocampal slices, mouse embryos
and Xenopus laevis tadpoles.
Sidney B Cambridge et al.
doi:10.1038/nmeth.1340
Abstract: http://links.ealert.nature.com/ctt?kn=157&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=123&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Mapping the structure and conformational movements of proteins with
transition metal ion FRET pp532 - 537
Fluorescence resonance energy transfer (FRET) between a
small-molecule fluorophore donor and a transition metal ion
acceptor, a method called 'transition metal ion FRET,' works
over shorter distances than the classical FRET approach and
can thus be used to monitor very small conformational changes
in proteins.
Justin W Taraska et al.
doi:10.1038/nmeth.1341
Abstract: http://links.ealert.nature.com/ctt?kn=155&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
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TECHNOLOGY FEATURE
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Genomics: catch me if you can pp539 - 544
Next-generation sequencing has made decoding entire genomes
cheaper and faster. But what about those researchers who only
want to sequence a small section of a genome or focus on a
couple thousand specific exons? A wave of new technologies
has recently emerged that should help these scientists target their
sequencing efforts to sequences of interest.
Nathan Blow
doi:10.1038/nmeth0709-539
http://links.ealert.nature.com/ctt?kn=128&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

----------------------
CORRIGENDUM
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Corrigendum: A HUPO test sample study reveals common problems
in mass spectrometry-based proteomics p546
doi:10.1038/nmeth0709-546a
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ERRATUM
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Erratum: Transposon-mediated genome manipulation in vertebrates p546
doi:10.1038/nmeth0709-546b
http://links.ealert.nature.com/ctt?kn=120&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

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APPLICATION NOTES
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Analysis of 5' transcript heterogeneity by high-throughput
sequencing of cDNA
Pietro D Spanu and Ken Doyle
Abstract: http://links.ealert.nature.com/ctt?kn=117&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=17&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

CYP2C9 and VKORC1 genotyping reagents from Idaho Technology: rapid
turn-around, accurate results
Jason McKinney, Ranae Lems and Cameron Gundry
Abstract: http://links.ealert.nature.com/ctt?kn=79&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=152&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

Fluidigm Dynamic Arrays provide a platform for single-cell
gene expression analysis
Martin Pieprzyk and Howard High
Abstract: http://links.ealert.nature.com/ctt?kn=148&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=95&m=33474681&r=MTc2NjExMzUwMAS2&b=2&j=NTIyNzg4MDUS1&mt=1&rt=0

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