Scripps Research Institute appoints leadership duo

Nature 525, 7570 (2015). http://www.nature.com/doifinder/10.1038/nature.2015.18391

Author: Erika Check Hayden

Pair will focus on resolving financial issues after controversial failed merger.

by Michael A. Cerullo

by Thembi Mdluli, Gregery T. Buzzard, Ann E. Rundell

This model-based design of experiments (MBDOE) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study. The ideal global solution for this experiment design problem is generally computationally intractable because of parametric uncertainties in the mathematical model of the biological system. Others have addressed this issue by limiting the solution to a local estimate of the model parameters. Here we present an approach that is independent of the local parameter constraint. This approach is made computationally efficient and tractable by the use of: (1) sparse grid interpolation that approximates the biological system dynamics, (2) representative parameters that uniformly represent the data-consistent dynamical space, and (3) probability weights of the represented experimentally distinguishable dynamics. Our approach identifies data-consistent representative parameters using sparse grid interpolants, constructs the optimal input sequence from a greedy search, and defines the associated optimal measurements using a scenario tree. We explore the optimality of this MBDOE algorithm using a 3-dimensional Hes1 model and a 19-dimensional T-cell receptor model. The 19-dimensional T-cell model also demonstrates the MBDOE algorithm’s scalability to higher dimensions. In both cases, the dynamical uncertainty region that bounds the trajectories of the target system states were reduced by as much as 86% and 99% respectively after completing the designed experiments in silico. Our results suggest that for resolving dynamical uncertainty, the ability to design an input sequence paired with its associated measurements is particularly important when limited by the number of measurements.

by Marcos Economides, Zeb Kurth-Nelson, Annika Lübbert, Marc Guitart-Masip, Raymond J. Dolan

Model-based and model-free reinforcement learning (RL) have been suggested as algorithmic realizations of goal-directed and habitual action strategies. Model-based RL is more flexible than model-free but requires sophisticated calculations using a learnt model of the world. This has led model-based RL to be identified with slow, deliberative processing, and model-free RL with fast, automatic processing. In support of this distinction, it has recently been shown that model-based reasoning is impaired by placing subjects under cognitive load—a hallmark of non-automaticity. Here, using the same task, we show that cognitive load does not impair model-based reasoning if subjects receive prior training on the task. This finding is replicated across two studies and a variety of analysis methods. Thus, task familiarity permits use of model-based reasoning in parallel with other cognitive demands. The ability to deploy model-based reasoning in an automatic, parallelizable fashion has widespread theoretical implications, particularly for the learning and execution of complex behaviors. It also suggests a range of important failure modes in psychiatric disorders.

by Thomas K. Karikari

Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

by Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, Jay D. Keasling

Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.

by Jasmine Foo, Lin L Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor

The traditional view of cancer as a genetic disease that can successfully be treated with drugs targeting mutant onco-proteins has motivated whole-genome sequencing efforts in many human cancer types. However, only a subset of mutations found within the genomic landscape of cancer is likely to provide a fitness advantage to the cell. Distinguishing such “driver” mutations from innocuous “passenger” events is critical for prioritizing the validation of candidate mutations in disease-relevant models. We design a novel statistical index, called the Hitchhiking Index, which reflects the probability that any observed candidate gene is a passenger alteration, given the frequency of alterations in a cross-sectional cancer sample set, and apply it to a mutational data set in colorectal cancer. Our methodology is based upon a population dynamics model of mutation accumulation and selection in colorectal tissue prior to cancer initiation as well as during tumorigenesis. This methodology can be used to aid in the prioritization of candidate mutations for functional validation and contributes to the process of drug discovery.

Canadian election spotlights scientists' frustrations

Nature 525, 7570 (2015). http://www.nature.com/doifinder/10.1038/nature.2015.18381

Author: Nicola Jones

Prime Minister Stephen Harper's government has cut funding and limited researchers' influence over policy.

Background: Stimulation of phospholipase Cβ (PLCβ) by the activated α-subunit of G q (Gα q ) constitutes a major signaling pathway for cellular regulation, and structural studies have recently revealed the molecular interactions between PLCβ and Gα q . Yet, most of the PLCβ-interacting residues identified on Gα q are not unique to members of the Gα q family. Molecular modeling predicts that the core PLCβ-interacting residues located on the switch regions of Gα q are similarly positioned in Gα z which does not stimulate PLCβ. Using wild-type and constitutively active chimeras constructed between Gα z and Gα 14 , a member of the Gα q family, we examined if the PLCβ-interacting residues identified in Gα q are indeed essential. Results: Four chimeras with the core PLCβ-interacting residues composed of Gα z sequences were capable of binding PLCβ2 and stimulating the formation of inositol trisphosphate. Surprisingly, all chimeras with a Gα z N-terminal half failed to functionally associate with PLCβ2, despite the fact that many of them contained the core PLCβ-interacting residues from Gα 14 . Further analyses revealed that the non-PLCβ2 interacting chimeras were capable of interacting with other effector molecules such as adenylyl cyclase and tetratricopeptide repeat 1, indicating that they could adopt a GTP-bound active conformation. Conclusion: Collectively, our study suggests that the previously identified PLCβ-interacting residues are insufficient to ensure productive interaction of Gα 14 with PLCβ, while an intact N-terminal half of Gα 14 is apparently required for PLCβ interaction.

Background: The c-Jun N-terminal kinases (JNKs), members of the mitogen-activated protein kinase (MAPK) family, engage in diverse cellular responses to signals produced under normal development and stress conditions. In Drosophila, only one JNK member is present, whereas ten isoforms from three JNK genes (JNK1, 2, and 3) are present in mammalian cells. To date, several mammalian JNK structures have been determined, however, there has been no report of any insect JNK structure. Results: We report the first structure of JNK from Drosophila melanogaster (DJNK). The crystal structure of the unphosphorylated form of DJNK complexed with adenylyl imidodiphosphate (AMP-PNP) has been solved at 1.79 Å resolution. The fold and topology of DJNK are similar to those of mammalian JNK isoforms, demonstrating their evolutionarily conserved structures and functions. Structural comparisons of DJNK and the closely related mammalian JNKs also allow identification of putative catalytic residues, substrate-binding sites and conformational alterations upon docking interaction with Drosophila scaffold proteins. Conclusions: The DJNK structure reveals common features with those of the mammalian JNK isoforms, thereby allowing the mapping of putative catalytic and substrate binding sites. Additionally, structural changes upon peptide binding could be predicted based on the comparison with the closely-related JNK3 structure in complex with pepJIP1. This is the first structure of insect JNK reported to date, and will provide a platform for future mutational studies in Drosophila to ascertain the functional role of insect JNK.

Abstract

Antibodies are indispensable tools in biochemical research and play an expanding role as therapeutics. While hybridoma technology is the dominant method for antibody production, phage display is an emerging technology. Here, we developed and employed a high-throughput pipeline that enables selection of antibodies against hundreds of antigens in parallel. Binding selections using a phage-displayed synthetic antigen-binding fragment (Fab) library against 110 human SH3 domains yielded hundreds of Fabs targeting 58 antigens. Affinity assays demonstrated that representative Fabs bind tightly and specifically to their targets. Furthermore, we developed an efficient affinity maturation strategy adaptable to high-throughput, which increased affinity dramatically but did not compromise specificity. Finally, we tested Fabs in common cell biology applications and confirmed recognition of the full-length antigen in immunoprecipitation, immunoblotting and immunofluorescence assays. In summary, we have established a rapid and robust high-throughput methodology that can be applied to generate highly functional and renewable antibodies targeting protein domains on a proteome-wide scale.

Immunology: Caspase target drives pyroptosis

Nature 526, 7575 (2015). doi:10.1038/nature15632

Authors: Petr Broz

Inflammatory caspase proteins help to control pathogen replication by triggering pyroptotic cell death. It now emerges that cleavage of the caspase substrate gasdermin D is sufficient to induce pyroptosis. See Articles p.660 & p.666

Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death

Nature 526, 7575 (2015). doi:10.1038/nature15514

Authors: Jianjin Shi, Yue Zhao, Kun Wang, Xuyan Shi, Yue Wang, Huanwei Huang, Yinghua Zhuang, Tao Cai, Fengchao Wang & Feng Shao

Inflammatory caspases (caspase-1, -4, -5 and -11) are critical for innate defences. Caspase-1 is activated by ligands of various canonical inflammasomes, and caspase-4, -5 and -11 directly recognize bacterial lipopolysaccharide, both of which trigger pyroptosis. Despite the crucial role in immunity and endotoxic shock, the

Caspase-11 cleaves gasdermin D for non-canonical inflammasome signalling

Nature 526, 7575 (2015). doi:10.1038/nature15541

Authors: Nobuhiko Kayagaki, Irma B. Stowe, Bettina L. Lee, Karen O’Rourke, Keith Anderson, Søren Warming, Trinna Cuellar, Benjamin Haley, Merone Roose-Girma, Qui T. Phung, Peter S. Liu, Jennie R. Lill, Hong Li, Jiansheng Wu, Sarah Kummerfeld, Juan Zhang, Wyne P. Lee, Scott J. Snipas, Guy S. Salvesen, Lucy X. Morris, Linda Fitzgerald, Yafei Zhang, Edward M. Bertram, Christopher C. Goodnow & Vishva M. Dixit

Intracellular lipopolysaccharide from Gram-negative bacteria including Escherichia coli, Salmonella typhimurium, Shigella flexneri, and Burkholderia thailandensis activates mouse caspase-11, causing pyroptotic cell death, interleukin-1β processing, and lethal septic shock. How caspase-11 executes these downstream signalling events is largely unknown. Here we show

Single cell activity reveals direct electron transfer in methanotrophic consortia

Nature 526, 7574 (2015). doi:10.1038/nature15512

Authors: Shawn E. McGlynn, Grayson L. Chadwick, Christopher P. Kempes & Victoria J. Orphan

Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling

Erratum: Evidence for human transmission of amyloid-β pathology and cerebral amyloid angiopathy

Nature 526, 7574 (2015). doi:10.1038/nature15704

Authors: Zane Jaunmuktane, Simon Mead, Matthew Ellis, Jonathan D. F. Wadsworth, Andrew J. Nicoll, Joanna Kenny, Francesca Launchbury, Jacqueline Linehan, Angela Richard-Loendt, A. Sarah Walker, Peter Rudge, John Collinge & Sebastian Brandner

Nature525, 247–250 (2015); doi:10.1038/nature15369In this Letter, an administrative error led to the publication of an incorrect version of the Competing Financial Interests (CFI) statement. Although the published CFI statement did reference the authors’ affiliation with D-Gen,

Corrigendum: Selective killing of cancer cells by a small molecule targeting the stress response to ROS

Nature 526, 7574 (2015). doi:10.1038/nature15370

Authors: Lakshmi Raj, Takao Ide, Aditi U. Gurkar, Michael Foley, Monica Schenone, Xiaoyu Li, Nicola J. Tolliday, Todd R. Golub, Steven A. Carr, Alykhan F. Shamji, Andrew M. Stern, Anna Mandinova, Stuart L. Schreiber & Sam W. Lee

Nature475, 231–234 (2011); doi:10.1038/nature10167corrigendum Nature481, 534 (2012); doi:10.1038/nature10789In this Letter, we presented findings from experiments using the EJ bladder xenograft cancer model, in which some tumours on some of

Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. Here we first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. We then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated.

Cardiac biology: A protein for healing infarcted hearts

Nature 525, 7570 (2015). doi:10.1038/nature15217

Authors: Gordana Vunjak-Novakovic

Human heart tissue has minimal ability to regenerate following injury. But the protein Fstl1, which is normally expressed in the heart's epicardial region, has now been shown to induce regeneration following heart attack. See Article p.479

Epicardial FSTL1 reconstitution regenerates the adult mammalian heart

Nature 525, 7570 (2015). doi:10.1038/nature15372

Authors: Ke Wei, Vahid Serpooshan, Cecilia Hurtado, Marta Diez-Cuñado, Mingming Zhao, Sonomi Maruyama, Wenhong Zhu, Giovanni Fajardo, Michela Noseda, Kazuto Nakamura, Xueying Tian, Qiaozhen Liu, Andrew Wang, Yuka Matsuura, Paul Bushway, Wenqing Cai, Alex Savchenko, Morteza Mahmoudi, Michael D. Schneider, Maurice J. B. van den Hoff, Manish J. Butte, Phillip C. Yang, Kenneth Walsh, Bin Zhou, Daniel Bernstein, Mark Mercola & Pilar Ruiz-Lozano

The elucidation of factors that activate the regeneration of the adult mammalian heart is of major scientific and therapeutic importance. Here we found that epicardial cells contain a potent cardiogenic activity identified as follistatin-like 1 (Fstl1). Epicardial Fstl1 declines following myocardial infarction and is replaced