Extracting neuronal functional network dynamics via adaptive Granger causality analysis
Alireza Sheikhattar, Sina Miran, Ji Liu, Jonathan B. Fritz, Shihab A. Shamma, Patrick O. Kanold, and Behtash Babadi
Probing functional interactions among the nodes in a network is crucial to understanding how complex systems work. Existing methodologies widely assume static network structures or Gaussian statistics or do not take account of likely sparse interactions. They are therefore not well-suited to neuronal spiking data with rapid task-dependent dynamics, binary statistics, and sparse functional dependencies. We develop an inference framework for extracting functional network dynamics from neuronal data by integrating techniques from adaptive filtering, compressed sensing, point processes, and high-dimensional statistics. We derive efficient estimation algorithms and precise statistical inference procedures. We apply our proposed techniques to experimentally recorded neuronal data to probe the neuronal functional networks underlying attentive behavior. Our techniques provide substantial gains in computation, resolution, and statistical robustness. (See pp. E3869–E3878.)
Transcriptome-wide discovery of coding and noncoding RNA-binding proteins
Rongbing Huang, Mengting Han, Liying Meng, and Xing Chen
RNAs, both mRNAs and noncoding RNAs, usually exert their functions in the form of RNA–protein complexes. Although mRNA-binding proteins have been extensively studied, comprehensive identification of coding and noncoding RNA-binding proteins (RBPs) remains challenging. Herein, we developed a click chemistry-assisted RNA interactome capture (CARIC) strategy, which combines metabolic labeling of RNAs with an alkynyl uridine analog and in vivo RNA-protein photocross-linking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. In HeLa cells, CARIC identified 597 RBPs, including 130 proteins not previously known as RBPs. Since CARIC captures RBPs bound to both mRNAs and noncoding RNAs, the obtained CARIC RBP list provides a valuable resource for studying the posttranscriptional gene regulation network. (See pp. E3879–E3887.)
Facet-specific interaction between methanol and TiO2 probed by sum-frequency vibrational spectroscopy
Deheng Yang, Yadong Li, Xinyi Liu, Yue Cao, Yi Gao, Y. Ron Shen, and Wei-Tao Liu
Facet engineering has become a major strategy for designing crystalline catalysts, yet many fundamental issues, including facet-specific interaction with adsorbates, remain unsolved due to lack of experimental investigation. Using surface-specific sum-frequency vibrational spectroscopy, we have conducted an in-depth study of methanol adsorption on four different facets of TiO2 under ambient conditions. The spectra revealed that for the four facets investigated, dissociation of adsorbed methanol occurs only when surface defects are present. Adsorption kinetics and energetics appeared nearly the same on different facets, but the Fermi resonance coupling strength for CH3 of adsorbed methanol was found to depend sensitively on facets and methanol coverage, and could serve as a gauge for studying facet effects on molecular adsorption and surface reactions. (See pp. E3888–E3894.)
A Mesoproterozoic iron formation
Donald E. Canfield, Shuichang Zhang, Huajian Wang, Xiaomei Wang, Wenzhi Zhao, Jin Su, Christian J. Bjerrum, Emma R. Haxen, and Emma U. Hammarlund
Iron formations (IFs) are common before 1,800 million years ago (Ma) and again at ∼750 Ma, but are remarkably absent for the billion years in between. We report on a 1,400-Ma IF of ∼520 gigatons Fe from the Xiamaling Formation on the North China Craton. Biomarker analyses suggest that anoxygenic phototrophic bacteria were involved in Fe(II) oxidation, and further geochemical analysis shows that IF sediments supported active microbial Fe reduction that rivaled oxic respiration in its efficiency of organic matter oxidation. The Xiamaling Formation IF demonstrates that geochemical conditions occasionally conspired to produce world-class IFs during Earth’s “middle ages,” permitting critical insights into the biogeochemical processes of IF emplacement. (See pp. E3895–E3904.)
Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates
James K. Carrow, Lauren M. Cross, Robert W. Reese, Manish K. Jaiswal, Carl A. Gregory, Roland Kaunas, Irtisha Singh, and Akhilesh K. Gaharwar
We demonstrate the use of next-generation sequencing technology (RNA-seq) to understand the effect of a two-dimensional nanomaterial on human stem cells at the whole-transcriptome level. Our results identify more than 4,000 genes that are significantly affected, and several biophysical and biochemical pathways are triggered by nanoparticle treatment. We expect that this systematic approach to understand widespread changes in gene expression due to nanomaterial exposure is key to develop new bioactive materials for biomedical applications. (See pp. E3905–E3913.)
Tradeoffs between immune function and childhood growth among Amazonian forager-horticulturalists
Samuel S. Urlacher, Peter T. Ellison, Lawrence S. Sugiyama, Herman Pontzer, Geeta Eick, Melissa A. Liebert, Tara J. Cepon-Robins, Theresa E. Gildner, and J. Josh Snodgrass
The energetic impact of immune function on human growth remains unclear. Using data from Amazonian forager-horticulturalists, we show that diverse, low-level immune activity predicts reduced childhood growth over periods of competing energy use ranging from 1 wk to 20 mo. We also demonstrate that modest body fat stores (i.e., energy reserves) protect children from the particularly detrimental impact of acute inflammation on growth. These findings provide evidence for considerable energetic tradeoffs between immune function and growth among humans, highlighting the energy constraint of childhood and the characteristic ability of our species to respond sensitively to dynamic environmental conditions. We outline the possible role of immune-related tradeoffs in driving patterns of human growth faltering, developmental metabolic plasticity, and life history evolution. (See pp. E3914–E3921.)
Complete biosynthesis of noscapine and halogenated alkaloids in yeast
Yanran Li, Sijin Li, Kate Thodey, Isis Trenchard, Aaron Cravens, and Christina D. Smolke
We demonstrate yeast’s capacity for biosynthesis of complex plant natural products by reconstructing a de novo noscapine biosynthetic pathway and optimizing noscapine production toward scalable manufacturing. Engineered strain contains 25 heterologous plant, bacteria, and mammalian genes and 6 mutant or overexpressed yeast genes. The noscapine biosynthetic pathway incorporates seven endomembrane-localized plant enzymes, highlighting yeast’s ability to functionally express and properly localize large numbers of heterologous enzymes into the endoplasm reticulum. Noscapine titers were improved by 18,000-fold (to low mg/L levels) via a combination of enzyme engineering, pathway and strain engineering, and fermentation optimization. We demonstrated that microbial fermentation can be used to produce halogenated alkaloid derivatives, which can ultimately serve as potential drug leads, through feeding amino acid derivatives to strains. (See pp. E3922–E3931.)
Crystal structure and mechanism of human carboxypeptidase O: Insights into its specific activity for acidic residues
Maria C. Garcia-Guerrero, Javier Garcia-Pardo, Esther Berenguer, Roberto Fernandez-Alvarez, Gifty B. Barfi, Peter J. Lyons, Francesc X. Aviles, Robert Huber, Julia Lorenzo, and David Reverter
Carboxypeptidase O (CPO) is a membrane-anchored brush-border enzyme associated with the small intestinal phase of protein digestion with distinctive specificity toward acidic C-terminal (C-t) amino acids. The combined activity of human CPO (hCPO) and pancreatic carboxypeptidases enables the C-t proteolysis of the great majority of amino acids present in dietary proteins. Here we disclose mechanism and structures of hCPO, both ligand-free and -bound with a natural peptidic inhibitor ascribing the exquisite specificity toward C-t acidic residues to a single amino acid, Arg275, in the substrate-binding pocket. Mutations of this residue to Asp and Ala suffices to reverse the specificity to C-t basic and hydrophobic residues, respectively, and faithfully mirror the specificity variants (hCPB, hCPA1, hCPA2) in enzyme kinetic assays. (See pp. E3932–E3939.)
Conformational sampling of membranes by Akt controls its activation and inactivation
Iva Lučić, Manoj K. Rathinaswamy, Linda Truebestein, David J. Hamelin, John E. Burke, and Thomas A. Leonard
Akt is a paradigmatic lipid-activated kinase, which is frequently hyperactivated in human cancer. In the absence of PI(3,4,5)P3 or PI(3,4)P2, Akt is maintained in an inactive conformation by an inhibitory interaction between its membrane-binding PH domain and its kinase domain. Here, we describe the conformational changes associated with its binding to PI(3,4,5)P3, leading to disruption of the inhibitory PH–kinase interface, and its consequent activation by protein kinases. Intriguingly, we find that reversal of those conformational changes promotes its inactivation by protein phosphatases. The activation of Akt is thereby restricted to discrete membrane locations, and it is rapidly inactivated upon dissociation. We propose a model in which activation, substrate phosphorylation, and inactivation of Akt are tightly coupled to the membrane. (See pp. E3940–E3949.)
Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds
Lucky Ahmed, Yuetian Zhang, Eric Block, Michael Buehl, Michael J. Corr, Rodrigo A. Cormanich, Sivaji Gundala, Hiroaki Matsunami, David O’Hagan, Mehmet Ozbil, Yi Pan, Sivakumar Sekharan, Nicholas Ten, Mingan Wang, Mingyan Yang, Qingzhi Zhang, Ruina Zhang, Victor S. Batista, and Hanyi Zhuang
While natural musk has been used for 2,000 years in perfumery, and in traditional medicine for its cardioprotective effects, its mode of activating odorant receptors (ORs) is unknown. ORs, G protein-coupled receptors (GPCRs), which constitute 40% of all pharmacophore receptors, are also expressed in nonolfactory tissues. Understanding the activation of ORs at the molecular level is challenging due to lack of crystallographic models. By combining site-directed mutagenesis with computational studies of human musk ORs involving 35 chiral and achiral muscone analogues, we propose structural models, including binding site prediction and responsible amino acid residues identification. Our studies of musk-responsive ORs should assist the study of the pharmacological effects of musks involving non-OR GPCRs. (See pp. E3950–E3958.)
Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation
Haidai Hu, Ákos Nemecz, Catherine Van Renterghem, Zaineb Fourati, Ludovic Sauguet, Pierre-Jean Corringer, and Marc Delarue
Pentameric ligand-gated ion channels (pLGICs) mediate fast signal transduction in animal nerve cells through neurotransmitters. Mutation of some of these receptors in the brain causes severe nervous system diseases. The high sequence diversity of prokaryotic receptors makes them unique model systems to understand evolutionary conservation in gating and sensitivity to allosteric modulators. We present the 2.3 Å X-ray structure of a pLGIC (sTeLIC) from a gammaproteobacteria that is activated at alkaline pH. The structure at pH 8.0 displays an unusually open pore. It is unchanged, but less flexible, in the presence of a positive allosteric modulator that binds in a cavity where benzodiazepines are found in Erwinia chrysanthemi pLGIC. This cavity is also present (and druggable) in the 5HT3-receptor. (See pp. E3959–E3968.)
Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy
Sasikumar Rajoo, Pascal Vallotton, Evgeny Onischenko, and Karsten Weis
The nuclear pore complex (NPC) is one of the largest protein assemblies in eukaryotes comprising over 500 nucleoporin subunits. The NPC is essential for the transport of biomolecules across the nuclear envelope; however, due to its enormous size, it has been a challenge to characterize its molecular architecture. Herein, we have developed a widely applicable imaging pipeline to determine the absolute nucleoporin abundances in native yeast NPCs. This reveals that the NPC composition dramatically differs between yeast and humans despite overall conservation of individual subunits. We also applied our imaging pipeline to examine yeast mutants revealing remarkable compositional plasticity of NPCs. Our stoichiometry analyses provide an important resource for the generation of high-resolution structure models of the NPC. (See pp. E3969–E3977.)
In vivo CRISPR screening unveils histone demethylase UTX as an important epigenetic regulator in lung tumorigenesis
Qibiao Wu, Yahui Tian, Jian Zhang, Xinyuan Tong, Hsinyi Huang, Shuai Li, Hong Zhao, Ying Tang, Chongze Yuan, Kun Wang, Zhaoyuan Fang, Lei Gao, Xin Hu, Fuming Li, Zhen Qin, Shun Yao, Ting Chen, Haiquan Chen, Gong Zhang, Wanting Liu, Yihua Sun, Luonan Chen, Kwok-Kin Wong, Kai Ge, Liang Chen, and Hongbin Ji
Tumor suppressor genes (TSGs) play important roles in lung cancer initiation, progression, and even metastasis. Here, we take advantage of the clustered regularly interspaced short palindromic repeats/Cas9-mediated screening in vivo technique to identify multiple tumor suppressor genes contributing to lung cancer malignant progression. Using genetically engineered mouse models, we further confirm the tumor-suppressive role of epigenetic regulator UTX and provide therapeutic implications for UTX-deficient lung tumors. Thus, our work provides a systematic screening of TSGs in vivo and demonstrates UTX functions as the important epigenetic regulator in lung tumorigenesis. (See pp. E3978–E3986.)
Heterochromatin protects retinal pigment epithelium cells from oxidative damage by silencing p53 target genes
Lili Gong, Fangyuan Liu, Zhen Xiong, Ruili Qi, Zhongwen Luo, Xiaodong Gong, Qian Nie, Qian Sun, Yun-Fei Liu, Wenjie Qing, Ling Wang, Lan Zhang, Xiangcheng Tang, Shan Huang, Gen Li, Hong Ouyang, Mengqing Xiang, Quan Dong Nguyen, Yizhi Liu, and David Wan-Cheng Li
Oxidative stress-induced damage to retinal pigmented epithelial (RPE) cells is critically implicated in the pathogenesis of age-related macular degeneration (AMD), a leading cause of blindness in the elderly. Here we report that oxidative stress-induced heterochromatin formation is essential to promote RPE survival. Mechanistically, oxidative damage-induced formation of heterochromatin occurs at the 53 target promoters of apoptosis genes and is regulated by p53 sumoylation. Our study demonstrates mechanistic links among chromatin conformation, p53 sumoylation, and RPE cell death. We propose that targeting heterochromatin provides a novel strategy for AMD treatment. (See pp. E3987–E3995.)
TMEM59 potentiates Wnt signaling by promoting signalosome formation
Jan P. Gerlach, Ingrid Jordens, Daniele V. F. Tauriello, Ineke van ‘t Land-Kuper, Jeroen M. Bugter, Ivar Noordstra, Johanneke van der Kooij, Teck Y. Low, Felipe X. Pimentel-Muiños, Despina Xanthakis, Nicola Fenderico, Catherine Rabouille, Albert J. R. Heck, David A. Egan, and Madelon M. Maurice
Wnt/β-catenin signaling is crucial for adult homeostasis and stem cell maintenance, and its dysregulation is strongly associated to cancer. Upon Wnt binding, Wnt receptors assemble into large complexes called signalosomes that provide a platform for interactions with downstream effector proteins. The assembly and regulation of these signalosomes remains largely elusive. Here, we use internally tagged Wnt ligands as a tool to isolate and analyze the composition and regulation of endogenous Wnt receptor complexes. We identify a positive regulator of Wnt signaling that facilitates signalosome formation by promoting intramembrane receptor interactions. Our results reveal that the assembly of multiprotein Wnt signalosomes proceeds along well-ordered steps and involves regulated intramembrane interactions. (See pp. E3996–E4005.)
Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia
Constanza de la Fuente, María C. Ávila-Arcos, Jacqueline Galimany, Meredith L. Carpenter, Julian R. Homburger, Alejandro Blanco, Paloma Contreras, Diana Cruz Dávalos, Omar Reyes, Manuel San Roman, Andrés Moreno-Estrada, Paula F. Campos, Celeste Eng, Scott Huntsman, Esteban G. Burchard, Anna-Sapfo Malaspinas, Carlos D. Bustamante, Eske Willerslev, Elena Llop, Ricardo A. Verdugo, and Mauricio Moraga
Recent genomic studies of ancient and modern humans from the Americas have given a comprehensive view of the peopling of the continent. However, regional characterization of ancient and modern individuals is lacking, being key to unveiling fine-scale differences within the continent. We present genome-wide analyses of ancient and modern individuals from South America from Western Patagonia. We found a strong affinity between modern and ancient individuals from the region, providing evidence of continuity in the region for the last ∼1,000 years and regional genetic structure within Southern South America. In particular, the analysis of these ancient genomes helps address questions related to the maritime tradition in the region and its diversification posterior to the split from terrestrial hunter-gatherers. (See pp. E4006–E4012.)
Roles of the CSE1L-mediated nuclear import pathway in epigenetic silencing
Qiang Dong, Xiang Li, Cheng-Zhi Wang, Shaohua Xu, Gang Yuan, Wei Shao, Baodong Liu, Yong Zheng, Hailin Wang, Xiaoguang Lei, Zhuqiang Zhang, and Bing Zhu
Regulators essential for facilitating gene silencing are interesting targets of epigenetic studies. Our work describes a regulator, CSE1L, that is essential for the silencing of many endogenous methylated genes. Depletion of CSE1L reactivates these genes without causing DNA demethylation. Interestingly, such reactivation is not due to a direct chromatin role of CSE1L. Instead, it depends on the role of CSE1L in importin-mediated protein nuclear transportation, which is confirmed by similar effects observed in cells depleted of other players in the same protein transportation pathway. Intriguingly, importin-mediated protein nuclear transportation preferentially facilitates gene silencing with specificity for a subset of genes, suggesting that the cargo specificity of protein nuclear import systems may impact the selectivity of gene regulation. (See pp. E4013–E4022.)
Distinct MHC class I-like interacting invariant T cell lineage at the forefront of mycobacterial immunity uncovered in Xenopus
Eva-Stina Edholm, Maureen Banach, Kun Hyoe Rhoo, Martin S. Pavelka Jr., and Jacques Robert
Contrasting with the dominance of conventional adaptive T cells in adult frogs, Xenopus tadpoles prominently rely on innate-like T (iT) cells expressing invariant TCRα rearrangements to combat pathogens. Here, we use three complementary loss-of-function approaches combining RNA interference with transgenesis or CRISPR/Cas9 genome editing to unveil an ancestral antimycobacterial immune surveillance system represented by MHC-like interacting innate-like T cells. Notably, this MHC-like (XNC4)/iVα45T cell system is critical for host defense against mycobacteria and distinctive from the key antiviral MHC-like XNC10-restricted iVα6T cells previously identified. These findings imply diversification and specialization of an ancestral innate-like T cell recognition system that is evolutionarily convergent to that of mammals. (See pp. E4023–E4031.)
Programmed self-assembly of peptide–major histocompatibility complex for antigen-specific immune modulation
Chih-Ping Mao, Shiwen Peng, Andrew Yang, Liangmei He, Ya-Chea Tsai, Chien-Fu Hung, and T.-C. Wu
T cells play a critical role in the control of diseases, ranging from infection to cancer. However, the activation of antigen-specific T cells against low-affinity antigens, such as tumor self-antigens, remains a challenge. Here, we report a technology for amplifying antigen-specific lymphocyte responses based on orchestrating coordinated signaling events at the level of peptide–major histocompatibility complex (pMHC)–TCR interactions. We engineered a soluble chimeric protein composed of annexin V (ANXA5) linked to pMHC. ANXA5 behaves as an anchor that facilitates stable, repeated cognate pMHC–TCR contacts and TCR cross-linking via programmed self-assembly. pMHC/ANXA5 fusion augments lymphocyte responses by several orders of magnitude and overcomes low-affinity pMHC–TCR interactions. (See pp. E4032–E4040.)
Macrophages impede CD8 T cells from reaching tumor cells and limit the efficacy of anti–PD-1 treatment
Elisa Peranzoni, Jean Lemoine, Lene Vimeux, Vincent Feuillet, Sarah Barrin, Chahrazade Kantari-Mimoun, Nadège Bercovici, Marion Guérin, Jérôme Biton, Hanane Ouakrim, Fabienne Régnier, Audrey Lupo, Marco Alifano, Diane Damotte, and Emmanuel Donnadieu
Cancer immunotherapy is a promising therapeutic intervention. However, complete and durable responses are seen in only a fraction of cancer patients. A key factor that limits therapeutic success is the lack of T cells in tumor cell regions, a profile termed “immune-excluded.” Here, we provide evidence that tumor-associated macrophages (TAMs) are an important determinant of the establishment of a T cell-excluded tumor phenotype. In human and murine tumors, we found that CD8 T cells poorly migrate and invade tumor nests due to long-lasting interactions with TAMs. The depletion of TAMs restores T cell migration and infiltration into tumor islets and improves the efficacy of anti–PD-1 immunotherapy. This study highlights the rationale of combining approaches targeting TAM and immune checkpoint proteins. (See pp. E4041–E4050.)
Genome-wide CRISPR screen identifies FAM49B as a key regulator of actin dynamics and T cell activation
Wanjing Shang, Yong Jiang, Michael Boettcher, Kang Ding, Marianne Mollenauer, Zhongyi Liu, Xiaofeng Wen, Chang Liu, Piliang Hao, Suwen Zhao, Michael T. McManus, Lai Wei, Arthur Weiss, and Haopeng Wang
Recent success of T cell-based cancer immunotherapies highlights the importance of further understanding molecular mechanisms in the regulation of T cell responsiveness. Here, we performed a genome-wide CRISPR screen to identify genes that regulate T cell activation upon anti-T cell receptor (TCR) stimulation. Our screen confirmed many of the known regulators in proximal T cell signaling. Moreover, we identified a previously uncharacterized gene named FAM49B, which acts as a negative regulator in T cell activation. Our study suggests that genome-wide CRISPR screening is a powerful means to identify key regulators of TCR signaling. The same strategy could be applied to CD28-mediated costimulatory signaling or PD-1–mediated coinhibitory signaling. The unbiased approach presented here may allow us to identify new therapeutic targets for cancer immunotherapy. (See pp. E4051–E4060.)
PARP-1 protects against colorectal tumor induction, but promotes inflammation-driven colorectal tumor progression
Bastian Dörsam, Nina Seiwert, Sebastian Foersch, Svenja Stroh, Georg Nagel, Diana Begaliew, Erika Diehl, Alexander Kraus, Maureen McKeague, Vera Minneker, Vassilis Roukos, Sonja Reißig, Ari Waisman, Markus Moehler, Anna Stier, Aswin Mangerich, Françoise Dantzer, Bernd Kaina, and Jörg Fahrer
Poly(ADP-ribose) polymerase-1 (PARP-1) is a DNA repair protein and part of the genome maintenance network. On the other hand, PARP-1 is involved in pathophysiological processes such as inflammation. Chronic inflammation has emerged as a key event in carcinogenesis, including the formation of colorectal cancer (CRC). Our data reveal that PARP-1 is abundantly expressed in human CRC, correlating with disease progression. Using transgenic mouse models, we show that PARP-1 fosters inflammation-driven colorectal tumor growth and stimulates the IL6-STAT3-cyclin D1 axis in tumors. In turn, PARP-1 protects against alkylation-triggered colorectal tumor induction dependent on the repair protein O6-methylguanine-DNA methyltransferase (MGMT). These findings unveil the opposing functions of PARP-1 in CRC initiation and CRC progression and its link to MGMT. (See pp. E4061–E4070.)
Human hydroxymethylbilane synthase: Molecular dynamics of the pyrrole chain elongation identifies step-specific residues that cause AIP
Navneet Bung, Arijit Roy, Brenden Chen, Dibyajyoti Das, Meenakshi Pradhan, Makiko Yasuda, Maria I. New, Robert J. Desnick, and Gopalakrishnan Bulusu
Human hydroxymethylbilane synthase (hHMBS) is a monomeric enzyme that catalyzes the stepwise head-to-tail condensation of four porphobilinogen (PBG) molecules to form the linear tetrapyrrole 1-hydroxymethylbilane (HMB). Mutations in the hHMBS gene cause autosomal-dominant acute intermittent porphyria (AIP). Although crystal structures of hHMBS have been reported, the specific active-site residues and the molecular mechanism of the stepwise PBG chain elongation are unknown. Here, by using molecular-dynamics simulations, the mechanisms and active-site residues for the HMB stepwise synthesis and HMB exit were determined. Mutagenesis of key active-site residues and in vitro expression studies identified the molecular basis of mutations causing AIP. (See pp. E4071–E4080.)
Harmonics added to a flickering light can upset the balance between ON and OFF pathways to produce illusory colors
Andrew T. Rider, G. Bruce Henning, Rhea T. Eskew Jr., and Andrew Stockman
By varying the temporal waveforms of complex flickering stimuli, we can produce alterations in their mean color that can be predicted by a physiologically based model of visual processing. The model highlights the perceptual effects of a well-known feature of most visual pathways, namely the early separation of visual signals into increments and decrements. The role of this separation in improving the efficiency and sensitivity of the visual system has been discussed before, but its effect on perception has been neglected. The application of a model incorporating half-wave rectification offers an exciting psychophysical method for investigating the inner workings of the human visual system. (See pp. E4081–E4090.)
Ultradian rhythmicity of plasma cortisol is necessary for normal emotional and cognitive responses in man
K. Kalafatakis, G. M. Russell, C. J. Harmer, M. R. Munafo, N. Marchant, A. Wilson, J. C. Brooks, C. Durant, J. Thakrar, P. Murphy, N. J. Thai, and S. L. Lightman
The hypothalamic-pituitary-adrenal axis is a critical neurohormonal network regulating homeostasis and coordinating stress responses. Here we demonstrate that an oscillating pattern of plasma cortisol is important for maintenance of healthy brain responses as measured by functional neuroimaging and behavioral testing. Our data highlight the crucial role of glucocorticoid rhythmicity in (i) modulating sleep behavior and working memory performance, and (ii) regulating the human brain’s responses under emotional stimulation. Current optimal cortisol replacement therapies for patients with primary or secondary adrenal insufficiently are associated with poor psychological status, and these results suggest that closer attention to aspects of chronotherapy will benefit these patients and may also have major implications for improved glucocorticoid dynamics in stress and psychiatric disease. (See pp. E4091–E4100.)
Neddylation mediates ventricular chamber maturation through repression of Hippo signaling
Jianqiu Zou, Wenxia Ma, Jie Li, Rodney Littlejohn, Hongyi Zhou, Il-man Kim, David J. R. Fulton, Weiqin Chen, Neal L. Weintraub, Jiliang Zhou, and Huabo Su
Myocardium thickening at midgestation to late gestation is crucial for the formation of a functionally competent postnatal heart. However, posttranslational mechanisms regulating this process remain unexplored. Here, we uncover a critical role for the ubiquitin-like protein NEDD8 in heart development. By targeting the E1 enzyme that mediates the conjugation of NEDD8 to protein targets, we show that NEDD8 modification is essential for ventricular compaction and heart function. We further identify that the NEDD8 substrate Cullin 7 mediates the degradation of Hippo kinase Mst1, thereby enabling YAP signaling, cardiomyocyte proliferation, and proper heart development. These results reveal a posttranslational regulatory mechanism in ventricular wall maturation and may provide mechanistic insights into the etiology of left ventricular noncompaction cardiomyopathy. (See pp. E4101–E4110.)
Glucagon contributes to liver zonation
Xiping Cheng, Sun Y. Kim, Haruka Okamoto, Yurong Xin, George D. Yancopoulos, Andrew J. Murphy, and Jesper Gromada
The lobules are the functional units of the liver. They consist of 15–25 layers of hepatocytes with specialized metabolic functions and gene expression patterns relative to their position along the lobule, a phenomenon referred to as metabolic zonation. The Wnt/β-catenin pathway regulates hepatocyte function but how the zonation is controlled to meet the metabolic demands of the liver is unclear. Glucagon regulates hepatic function. We now demonstrate that glucagon contributes to liver zonation by interacting and opposing the actions of the Wnt/β-catenin pathway. (See pp. E4111–E4119.)
KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1
Manoj Majee, Santosh Kumar, Praveen Kumar Kathare, Shuiqin Wu, Derek Gingerich, Nihar R. Nayak, Louai Salaita, Randy Dinkins, Kathleen Martin, Michael Goodin, Lynnette M. A. Dirk, Taylor D. Lloyd, Ling Zhu, Joseph Chappell, Arthur G. Hunt, Richard Vierstra, Enamul Huq, and A. Bruce Downie
The completion of seed germination is an irrevocable event for plants, determining, for most plants, the site of the remainder of their life cycle. One environmental cue important to the completion of seed germination is light, which, in Arabidopsis thaliana, can influence a host of transcription factors, including PHYTOCHROME-INTERACTING FACTOR1 (PIF1), a negative regulator of the completion of germination and seedling de-etiolation. The KELCH F-BOX protein COLD TEMPERATURE GERMINATING10 (CTG10) can recognize and bind to PIF1, negatively influencing PIF1 stability, stimulating the completion of germination, and promoting a de-etiolated seedling morphology. PIF1, in turn, can downregulate CTG10 expression, revealing a complex coregulation orchestrated by light presence and quality that dictates whether the seed completes germination. (See pp. E4120–E4129.)
The plant hormone ethylene restricts Arabidopsis growth via the epidermis
Irina Ivanova Vaseva, Enas Qudeimat, Thomas Potuschak, Yunlong Du, Pascal Genschik, Filip Vandenbussche, and Dominique Van Der Straeten
Ethylene is a gaseous hormone that controls plant life throughout development. Being a simple hydrophobic molecule, it can freely enter cells; therefore, the cell type specificity of its action is challenging. By means of tissue-specific expression of two negative regulators of the signaling cascade, we selectively disrupted the ethylene signal in different cell types without affecting its biosynthesis. We demonstrate that ethylene restricts plant growth by dampening the effect of auxins in the outermost cell layer. We further show that this epidermis-specific signaling has an impact on the growth of neighboring cells, suggesting that the master controller of cell expansion resides in the epidermis, where it senses the environment and, subsequently drives growth, of the inner tissues. (See pp. E4130–E4139.)