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Table of Contents: December 2018

The ability to induce defenses in response to pathogen attack is a critical feature of immunity in any organism. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key players in this process and have evolved to perceive the occurrence of non-self activities or foreign molecules. In plants, coevolution with a variety of pests and pathogens has resulted in repertoires of several hundred diverse NLRs in single individuals and many more in populations as a whole. The mechanism by which defense signaling is triggered by these NLRs is poorly understood. Here, Wróblewski et al. show that upon pathogen perception, NLRs use their N-terminal domains to transactivate other receptors. Plant NLRs oligomerize upon activation, similar to the vertebrate NLRs; however, consistent with their large number in plants, their complexes are highly heteromeric. Also, in contrast to metazoan NLRs, their N-termini, rather than their centrally located nucleotide-binding (NB) domains, mediate initial partner selection. The authors propose that a highly redundant network of NLR interactions provides resilience to perturbation by pathogens. The image shows an Arabidopsis thaliana plant infected with Tobacco Rattle Virus (TRV) harboring a sequence encoding Green Fluorescent Protein. The glowing patterns on the leaves mark tissue infected with the virus. The study used TRV both as a model pathogen and as a vector to deliver NLR fragments to plant cells.

Image Credit: Tadeusz Wróblewski

Essay

Analysis validation has been neglected in the Age of Reproducibility

Kathleen E. Lotterhos, Jason H. Moore, Ann E. Stapleton

Community Page

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder

Research Articles

Widespread winners and narrow-ranged losers: Land use homogenizes biodiversity in local assemblages worldwide

Tim Newbold, Lawrence N. Hudson, Sara Contu, Samantha L. L. Hill, Jan Beck, Yunhui Liu, Carsten Meyer, Helen R. P. Phillips, Jörn P. W. Scharlemann, Andy Purvis

Gut microbiota diversity across ethnicities in the United States

Andrew W. Brooks, Sambhawa Priya, Ran Blekhman, Seth R. Bordenstein

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

Stephanie Lauer, Grace Avecilla, Pieter Spealman, Gunjan Sethia, Nathan Brandt, Sasha F. Levy, David Gresham

Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration

Catherine D. Robinson, Helena S. Klein, Kyleah D. Murphy, Raghuveer Parthasarathy, Karen Guillemin, Brendan J. M. Bohannan

Sex-specific dominance reversal of genetic variation for fitness

Karl Grieshop, Göran Arnqvist

Parental neural responsivity to infants’ visual attention: How mature brains influence immature brains during social interaction

Sam V. Wass, Valdas Noreika, Stanimira Georgieva, Kaili Clackson, Laura Brightman, Rebecca Nutbrown, Lorena Santamaria Covarrubias, Vicky Leong

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver

Adrija Kalvisa, Majken S. Siersbæk, Stine M. Præstholm, Line J. L. Christensen, Ronni Nielsen, Oliver Stohr, Sabine Vettorazzi, Jan Tuckermann, Morris White, Susanne Mandrup, Lars Grøntved

Podoplanin+ tumor lymphatics are rate limiting for breast cancer metastasis

Yang Chen, Doruk Keskin, Hikaru Sugimoto, Keizo Kanasaki, Patricia E. Phillips, Lauren Bizarro, Arlene Sharpe, Valerie S. LeBleu, Raghu Kalluri

An opposing function of paralogs in balancing developmental synapse maturation

Plinio D. Favaro, Xiaojie Huang, Leon Hosang, Sophia Stodieck, Lei Cui, Yu-zhang Liu, Karl-Alexander Engelhardt, Frank Schmitz, Yan Dong, Siegrid Löwel, Oliver M. Schlüter

Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae

Elizabeth K. Brauer, George V. Popescu, Dharmendra K. Singh, Mauricio Calviño, Kamala Gupta, Bhaskar Gupta, Suma Chakravarthy, Sorina C. Popescu

Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity

Tadeusz Wróblewski, Laurentiu Spiridon, Eliza Cristina Martin, Andrei-Jose Petrescu, Keri Cavanaugh, Maria José Truco, Huaqin Xu, Dariusz Gozdowski, Krzysztof Pawłowski, Richard W. Michelmore, Frank L.W. Takken

CD71+VISTA+ erythroid cells promote the development and function of regulatory T cells through TGF-β

Shima Shahbaz, Najmeh Bozorgmehr, Petya Koleva, Afshin Namdar, Juan Jovel, Roy A. Fava, Shokrollah Elahi

Non-proteolytic ubiquitin modification of PPARγ by Smurf1 protects the liver from steatosis

Kun Zhu, Yi Tang, Xuan Xu, Hien Dang, Liu-Ya Tang, Xiang Wang, Xin Wei Wang, Ying E. Zhang

MEKK3 coordinates with FBW7 to regulate WDR62 stability and neurogenesis

Dan Xu, Minghui Yao, Yaqing Wang, Ling Yuan, Joerg D. Hoeck, Jingwen Yu, Liang Liu, Yvonne Y. C. Yeap, Weiya Zhang, Feng Zhang, Yinghang Feng, Tiantian Ma, Yujie Wang, Dominic C. H. Ng, Xiaoyin Niu, Bing Su, Axel Behrens, Zhiheng Xu

Lrrk promotes tau neurotoxicity through dysregulation of actin and mitochondrial dynamics

Farah H. Bardai, Dalila G. Ordonez, Rachel M. Bailey, Matthew Hamm, Jada Lewis, Mel B. Feany

Catalytic mechanism of the tyrosinase reaction toward the Tyr98 residue in the caddie protein

Yasuyuki Matoba, Shogo Kihara, Naohiko Bando, Hironari Yoshitsu, Miyuki Sakaguchi, Kure’e Kayama, Sachiko Yanagisawa, Takashi Ogura, Masanori Sugiyama

Short Reports

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

Eirini M. Kallimasioti-Pazi, Keerthi Thelakkad Chathoth, Gillian C. Taylor, Alison Meynert, Tracy Ballinger, Martijn J. E. Kelder, Sébastien Lalevée, Ildem Sanli, Robert Feil, Andrew J. Wood

Methods and Resources

Direct visualization of single-molecule membrane protein interactions in living cells

Do-Hyeon Kim, Soyeon Park, Dong-Kyun Kim, Min Gyu Jeong, Jungeun Noh, Yonghoon Kwon, Kai Zhou, Nam Ki Lee, Sung Ho Ryu

Methods & Resources

A high-throughput and open-source platform for embryo phenomics

Oliver Tills, John I. Spicer, Andrew Grimmer, Simone Marini, Vun Wen Jie, Ellen Tully, Simon D. Rundle