[Report] Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation

Coinfection with intestinal parasites leads to altered antiviral immunity in mice. [Also see Perspective by Maizels and Gause] Authors: Lisa C. Osborne, Laurel A. Monticelli, Timothy J. Nice, Tara E. Sutherland, Mark C. Siracusa, Matthew R. Hepworth, Vesselin T. Tomov, Dmytro Kobuley, Sara V. Tran, Kyle Bittinger, Aubrey G. Bailey, Alice L. Laughlin, Jean-Luc Boucher, E. John Wherry, Frederic D. Bushman, Judith E. Allen, Herbert W. Virgin, David Artis

[New Products] New Products

A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.

[Special Issue Research Article] A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide. Authors: , Klaus F. X. Mayer, Jane Rogers, Jaroslav Doležel, Curtis Pozniak, Kellye Eversole, Catherine Feuillet, Bikram Gill, Bernd Friebe, Adam J. Lukaszewski, Pierre Sourdille, Takashi R. Endo, Marie Kubaláková, Jarmila Číhalíková, Zdeňka Dubská, Jan Vrána, Romana Šperková, Hana Šimková, Melanie Febrer, Leah Clissold, Kirsten McLay, Kuldeep Singh, Parveen Chhuneja, Nagendra K. Singh, Jitendra Khurana, Eduard Akhunov, Frédéric Choulet, Adriana Alberti, Valérie Barbe, Patrick Wincker, Hiroyuki Kanamori, Fuminori Kobayashi, Takeshi Itoh, Takashi Matsumoto, Hiroaki Sakai, Tsuyoshi Tanaka, Jianzhong Wu, Yasunari Ogihara, Hirokazu Handa, P. Ron Maclachlan, Andrew Sharpe, Darrin Klassen, David Edwards, Jacqueline Batley, Odd-Arne Olsen, Simen Rød Sandve, Sigbjørn Lien, Burkhard Steuernagel, Brande Wulff, Mario Caccamo, Sarah Ayling, Ricardo H. Ramirez-Gonzalez, Bernardo J. Clavijo, Jonathan Wright, Matthias Pfeifer, Manuel Spannagl, Mihaela M. Martis, Martin Mascher, Jarrod Chapman, Jesse A. Poland, Uwe Scholz, Kerrie Barry, Robbie Waugh, Daniel S. Rokhsar, Gary J. Muehlbauer, Nils Stein, Heidrun Gundlach, Matthias Zytnicki, Véronique Jamilloux, Hadi Quesneville, Thomas Wicker, Primetta Faccioli, Moreno Colaiacovo, Antonio Michele Stanca, Hikmet Budak, Luigi Cattivelli, Natasha Glover, Lise Pingault, Etienne Paux, Sapna Sharma, Rudi Appels, Matthew Bellgard, Brett Chapman, Thomas Nussbaumer, Kai Christian Bader, Hélène Rimbert, Shichen Wang, Ron Knox, Andrzej Kilian, Michael Alaux, Françoise Alfama, Loïc Couderc, Nicolas Guilhot, Claire Viseux, Mikaël Loaec, Beat Keller, Sebastien Praud

[Special Issue Research Article] Genome interplay in the grain transcriptome of hexaploid bread wheat

Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome. Authors: Matthias Pfeifer, Karl G. Kugler, Simen R. Sandve, Bujie Zhan, Heidi Rudi, Torgeir R. Hvidsten, , Klaus F. X. Mayer, Odd-Arne Olsen

[Special Issue Research Article] Ancient hybridizations among the ancestral genomes of bread wheat

The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic. Authors: Thomas Marcussen, Simen R. Sandve, Lise Heier, Manuel Spannagl, Matthias Pfeifer, , Kjetill S. Jakobsen, Brande B. H. Wulff, Burkhard Steuernagel, Klaus F. X. Mayer, Odd-Arne Olsen, Jane Rogers, Jaroslav Doležel, Curtis Pozniak, Kellye Eversole, Catherine Feuillet, Bikram Gill, Bernd Friebe, Adam J. Lukaszewski, Pierre Sourdille, Takashi R. Endo, Marie Kubaláková, Jarmila Číhalíková, Zdeňka Dubská, Jan Vrána, Romana Šperková, Hana Šimková, Melanie Febrer, Leah Clissold, Kirsten McLay, Kuldeep Singh, Parveen Chhuneja, Nagendra K. Singh, Jitendra Khurana, Eduard Akhunov, Frédéric Choulet, Adriana Alberti, Valérie Barbe, Patrick Wincker, Hiroyuki Kanamori, Fuminori Kobayashi, Takeshi Itoh, Takashi Matsumoto, Hiroaki Sakai, Tsuyoshi Tanaka, Jianzhong Wu, Yasunari Ogihara, Hirokazu Handa, P. Ron Maclachlan, Andrew Sharpe, Darrin Klassen, David Edwards, Jacqueline Batley, Sigbjørn Lien, Mario Caccamo, Sarah Ayling, Ricardo H. Ramirez-Gonzalez, Bernardo J. Clavijo, Jonathan Wright, Mihaela M. Martis, Martin Mascher, Jarrod Chapman, Jesse A. Poland, Uwe Scholz, Kerrie Barry, Robbie Waugh, Daniel S. Rokhsar, Gary J. Muehlbauer, Nils Stein, Heidrun Gundlach, Matthias Zytnicki, Véronique Jamilloux, Hadi Quesneville, Thomas Wicker, Primetta Faccioli, Moreno Colaiacovo, Antonio Michele Stanca, Hikmet Budak, Luigi Cattivelli, Natasha Glover, Lise Pingault, Etienne Paux, Sapna Sharma, Rudi Appels, Matthew Bellgard, Brett Chapman, Thomas Nussbaumer, Kai Christian Bader, Hélène Rimbert, Shichen Wang, Ron Knox, Andrzej Kilian, Michael Alaux, Françoise Alfama, Loïc Couderc, Nicolas Guilhot, Claire Viseux, Mikaël Loaec, Beat Keller, Sebastien Praud

[Special Issue Research Article] Structural and functional partitioning of bread wheat chromosome 3B

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits. Authors: Frédéric Choulet, Adriana Alberti, Sébastien Theil, Natasha Glover, Valérie Barbe, Josquin Daron, Lise Pingault, Pierre Sourdille, Arnaud Couloux, Etienne Paux, Philippe Leroy, Sophie Mangenot, Nicolas Guilhot, Jacques Le Gouis, Francois Balfourier, Michael Alaux, Véronique Jamilloux, Julie Poulain, Céline Durand, Arnaud Bellec, Christine Gaspin, Jan Safar, Jaroslav Dolezel, Jane Rogers, Klaas Vandepoele, Jean-Marc Aury, Klaus Mayer, Hélène Berges, Hadi Quesneville, Patrick Wincker, Catherine Feuillet

[Editorial] Science advocacy, defined

When one thinks of advocacy, the first—usually cynical—idea that comes to mind is generously compensated lobbyists walking the halls of legislature and advocating on behalf of their clients over expensive dinners. While this image may make for great television drama, it is an incomplete picture, especially as regards science advocacy. Author: Joanne Padrón Carney

[In Depth] A radical change in peer review

A pilot project to ease pressure on NSF's vaunted peer-review system required grant applicants to review seven competing proposals. Author: Jeffrey Mervis

[Feature] The elusive heart fix

After years of hope and hype, researchers still don't agree whether cell infusions rejuvenate the human heart. Author: Jennifer Couzin-Frankel

[Feature] Top heart lab comes under fire

A high-profile heart research lab is in the spotlight while under investigation by Harvard Medical School. Author: Kelly Servick

[Perspective] Mind the midzone

Is the separation of chromosomes during cell division monitored by a checkpoint? [Also see Report by Afonso et al.] Authors: Michael A. Hadders, Susanne M.A. Lens

[Perspective] Charge transfer goes the distance

Electronic relaxation following x-ray excitation illuminates steps in molecular dissociation. [Also see Report by Erk et al.] Author: Stephen T. Pratt

[Perspective] Quantum systems under control

Optical trapping enables the building of quantum matter one atom at a time. [Also see Report by Kaufman et al.] Authors: Jeff Thompson, Mikhail D. Lukin

[Policy Forum] NIH Roadmap/Common Fund at 10 years

A mechanism for funding biomedical research at NIH that transcends Institute and Center boundaries is bearing fruit Authors: Francis S. Collins, Elizabeth L. Wilder, Elias Zerhouni

[Letter] Partnering with Cuba: Weather extremes

Authors: Juan Carlos Antuña Marrero, M. Meghan Miller, Glen Mattioli, Karl Feaux, Richard Anthes, John Braun, Guoquan Wang, Alan Robock

This Week in Science

How the worm changes its tastes | Bosons of a feather flit together | Reprogrammed heart cells set the pace | Improved perovskite photovoltaic performance | Circulating between different cycles | How to optimize global food production | Evolving from an enzyme and into a regulator | Taking a check on chromosome spacing | Turning cells into garbage collectors | The making of bodies part by part | Iodine blooms as an oxidation catalyst | Tightly tracking charge migration | Extending the range of planar optics | Fault-tolerant quantum computing | A more simple route to metrology standards | Spinning up ocean circulation discretely | How dynein makes the right moves

Editors' Choice

Putting the genetic breaks on breeding | Packaging DNA for a better nucleus | Looking for signs of ozone recovery | A copper oxide's electronic structure | Tick tock, synchronizing biological clocks | Measuring sea ice through thick and thin | Macrophages help food move through

[Review] Organogenesis in a dish: Modeling development and disease using organoid technologies

Classical experiments performed half a century ago demonstrated the immense self-organizing capacity of vertebrate cells. Even after complete dissociation, cells can reaggregate and reconstruct the original architecture of an organ. More recently, this outstanding feature was used to rebuild organ parts or even complete organs from tissue or embryonic stem cells. Such stem cell–derived three-dimensional cultures are called organoids. Because organoids can be grown from human stem cells and from patient-derived induced pluripotent stem cells, they have the potential to model human development and disease. Furthermore, they have potential for drug testing and even future organ replacement strategies. Here, we summarize this rapidly evolving field and outline the potential of organoid technology for future biomedical research. Authors: Madeline A. Lancaster, Juergen A. Knoblich

[Report] Imaging charge transfer in iodomethane upon x-ray photoabsorption

A free-electron laser enables precise tracking of electron movement between segments of a dissociating molecule. [Also see Perspective by Pratt] Authors: Benjamin Erk, Rebecca Boll, Sebastian Trippel, Denis Anielski, Lutz Foucar, Benedikt Rudek, Sascha W. Epp, Ryan Coffee, Sebastian Carron, Sebastian Schorb, Ken R. Ferguson, Michele Swiggers, John D. Bozek, Marc Simon, Tatiana Marchenko, Jochen Küpper, Ilme Schlichting, Joachim Ullrich, Christoph Bostedt, Daniel Rolles, Artem Rudenko