bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antagonistic odor interactions in olfactory sensory neurons are widespread in freely breathing mice
Authors: Zak Joseph D. , Reddy Gautam , Vergassola Massimo , Murthy Venkatesh N. 
Published: July 2020

AbstractOdor landscapes contain complex blends of molecules that each activate unique, overlapping populations of olfactory sensory neurons (OSNs). Despite the presence of hundreds of OSN subtypes in many animals, the overlapping nature of odor inputs may lead to saturation of neural responses at the early stages of stimulus encoding. Information loss due to saturation could be mitigated by normalizing mechanisms such as antagonism at the level of receptor-ligand interactions, whose existence and prevalence remains uncertain. By imaging OSN axon terminals in olfactory bulb glomeruli as well as OSN cell bodies within the olfactory epithelium in freely breathing mice, we find widespread antagonistic interactions in binary odor mixtures. In complex mixtures of up to 12 odorants, antagonistic interactions are stronger and more prevalent with increasing mixture complexity. Therefore, antagonism is a common feature of odor mixture encoding in OSNs and helps in normalizing activity to reduce saturation and increase information transfer.
C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression
Authors: Sun Yu , Eshov Aziz , Zhou Jeffrey , Isiktas Atagun U. , Guo Junjie U. 
Published: July 2020

AbstractExpansion of an intronic (GGGGCC)n repeat region within the C9orf72 gene is a main cause of familial amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). A hallmark of c9ALS/FTD is the accumulation of misprocessed RNAs, which are often targets of cellular RNA surveillance. Here, we show that RNA decay mechanisms involving upstream frameshift 1 (UPF1), including nonsense-mediated decay (NMD), are inhibited in c9ALS/FTD brains and in cultured cells expressing either of two arginine-rich dipeptide repeats (R-DPRs), poly(GR) and poly(PR). Mechanistically, although R-DPRs cause the recruitment of UPF1 to stress granules, stress granule formation is independent of NMD inhibition. Instead, NMD inhibition is primarily a result from global translational repression caused by R-DPRs. Overexpression of UPF1, but none of its NMD-deficient mutants, enhanced the survival of neurons treated by R-DPRs, suggesting that R-DPRs cause neurotoxicity in part by inhibiting cellular RNA surveillance.
De novo design of Au36(SR)24 nanoclusters
Authors: Liu Xu , Xu Wen Wu , Huang Xinyu , Wang Endong , Cai Xiao , Zhao Yue , Li Jin , Xiao Min , Zhang Chunfeng , Gao Yi , Ding Weiping , Zhu Yan 
Published: July 2020

AbstractThe discovery of atomically precise nanoclusters is generally unpredictable, and the rational synthesis of nanoclusters guided by the theoretical design is still in its infancy. Here we present a de novo design of Au36(SR)24 nanoclusters, from theoretical prediction to experimental synthesis and characterization of their physicochemical properties. The crystal structure of an Au36(SR)24 nanocluster perfectly matches the simulated structural pattern with Au4 tetrahedral units along a two-dimensional growth. The Au36(SR)24 nanocluster indeed differs from its structural isomer whose kernel is dissected in an Au4 tetrahedral manner along a one-dimensional growth. The structural isomerism in the Au36(SR)24 nanoclusters further induces distinct differences in ultrafast electron dynamics and chirality. This work will not only promote the atomically precise synthesis of nanoclusters enlightened by theoretical science, but also open up exciting opportunities for underpinning the widespread applications of structural isomers with atomic precision.
Heteroatom-bridged molecular belts as containers
Authors: Xie Jialin , Li Xia , Wang Shenghua , Li Anquan , Jiang Long , Zhu Kelong 
Published: July 2020

AbstractHoop-shaped or belt-like molecules have been fascinating not only due to their challenging synthesis, but also unique physical and chemical properties. The incorporation of heteroatoms (N, O, S, etc.) into these belts could alter both molecular structures and electronic properties which will lead to versatile applications, from advanced host-guest systems to functional materials. Despite numerous computational studies, the synthesis and characterization of heteroatom-bridged double-stranded molecular belts remains scarce. Here we report the synthesis, crystal structure, and host-guest chemistry of two novel heteroatom-bridged belt-like macrocycles composed of phenoxathiin. The bowl-shaped belt demonstrates a strong binding affinity (Ka = 3.6 × 109 M‒2) towards fullerene C60 and forms a 2:1 capsule-like complex with the aid of C‒H···S hydrogen bonds. The column-like belt can bind the cyclic guest [2,2]paracyclophane to form a ring-in-ring complex. The modular synthesis, structural specificity, and diverse host-guest chemistry of cyclophenoxathiins markedly expands the known chemistry of molecular belts.
Structural insight into mitochondrial β-barrel outer membrane protein biogenesis
Authors: Diederichs Kathryn A. , Ni Xiaodan , Rollauer Sarah E. , Botos Istvan , Tan Xiaofeng , King Martin S. , Kunji Edmund R. S. , Jiang Jiansen , Buchanan Susan K. 
Published: July 2020

AbstractIn mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex from Myceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates.
Pancreatic circulating tumor cell profiling identifies LIN28B as a metastasis driver and drug target
Authors: Franses Joseph W. , Philipp Julia , Missios Pavlos , Bhan Irun , Liu Ann , Yashaswini Chittampalli , Tai Eric , Zhu Huili , Ligorio Matteo , Nicholson Benjamin , Tassoni Elizabeth M. , Desai Niyati , Kulkarni Anupriya S. , Szabolcs Annamaria , Hong Theodore S. , Liss Andrew S. , Fernandez-del Castillo Carlos , Ryan David P. , Maheswaran Shyamala , Haber Daniel A. , Daley George Q. , Ting David T. 
Published: July 2020

AbstractPancreatic ductal adenocarcinoma (PDAC) lethality is due to metastatic dissemination. Characterization of rare, heterogeneous circulating tumor cells (CTCs) can provide insight into metastasis and guide development of novel therapies. Using the CTC-iChip to purify CTCs from PDAC patients for RNA-seq characterization, we identify three major correlated gene sets, with stemness genes LIN28B/KLF4, WNT5A, and LGALS3 enriched in each correlated gene set; only LIN28B CTC expression was prognostic. CRISPR knockout of LIN28B—an oncofetal RNA-binding protein exerting diverse effects via negative regulation of let-7 miRNAs and other RNA targets—in cell and animal models confers a less aggressive/metastatic phenotype. This correlates with de-repression of let-7 miRNAs and is mimicked by silencing of downstream let-7 target HMGA2 or chemical inhibition of LIN28B/let-7 binding. Molecular characterization of CTCs provides a unique opportunity to correlated gene set metastatic profiles, identify drivers of dissemination, and develop therapies targeting the “seeds” of metastasis.
Germline de novo mutation rates on exons versus introns in humans
Authors: Rodriguez-Galindo Miguel , Casillas Sònia , Weghorn Donate , Barbadilla Antonio 
Published: July 2020

AbstractA main assumption of molecular population genetics is that genomic mutation rate does not depend on sequence function. Challenging this assumption, a recent study has found a reduction in the mutation rate in exons compared to introns in somatic cells, ascribed to an enhanced exonic mismatch repair system activity. If this reduction happens also in the germline, it can compromise studies of population genomics, including the detection of selection when using introns as proxies for neutrality. Here we compile and analyze published germline de novo mutation data to test if the exonic mutation rate is also reduced in germ cells. After controlling for sampling bias in datasets with diseased probands and extended nucleotide context dependency, we find no reduction in the mutation rate in exons compared to introns in the germline. Therefore, there is no evidence that enhanced exonic mismatch repair activity determines the mutation rate in germline cells.
Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes
Authors: Mochida Keisuke , Yamasaki Akinori , Matoba Kazuaki , Kirisako Hiromi , Noda Nobuo N. , Nakatogawa Hitoshi 
Published: July 2020

AbstractThe endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.
Diverse interactions and ecosystem engineering can stabilize community assembly
Authors: Yeakel Justin D. , Pires Mathias M. , de Aguiar Marcus A. M. , O’Donnell James L. , Guimarães Paulo R. , Gravel Dominique , Gross Thilo 
Published: July 2020

AbstractThe complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact directly with each other and indirectly through environmental effects, however to our knowledge the role of these ecosystem engineers has not been considered in ecological network models. Here we explore the dynamics of ecosystem assembly, where species colonization and extinction depends on the constraints imposed by trophic, service, and engineering dependencies. We show that our assembly model reproduces many key features of ecological systems, such as the role of generalists during assembly, realistic maximum trophic levels, and increased nestedness with mutualistic interactions. We find that ecosystem engineering has large and nonlinear effects on extinction rates. While small numbers of engineers reduce stability by increasing primary extinctions, larger numbers of engineers increase stability by reducing primary extinctions and extinction cascade magnitude. Our results suggest that ecological engineers may enhance community diversity while increasing persistence by facilitating colonization and limiting competitive exclusion.
A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids
Authors: Pyne Michael E. , Kevvai Kaspar , Grewal Parbir S. , Narcross Lauren , Choi Brian , Bourgeois Leanne , Dueber John E. , Martin Vincent J. J. 
Published: July 2020

AbstractThe tetrahydroisoquinoline (THIQ) moiety is a privileged substructure of many bioactive natural products and semi-synthetic analogs. Plants manufacture more than 3,000 THIQ alkaloids, including the opioids morphine and codeine. While microbial species have been engineered to synthesize a few compounds from the benzylisoquinoline alkaloid (BIA) family of THIQs, low product titers impede industrial viability and limit access to the full chemical space. Here we report a yeast THIQ platform by increasing production of the central BIA intermediate (S)-reticuline to 4.6 g L−1, a 57,000-fold improvement over our first-generation strain. We show that gains in BIA output coincide with the formation of several substituted THIQs derived from amino acid catabolism. We use these insights to repurpose the Ehrlich pathway and synthesize an array of THIQ structures. This work provides a blueprint for building diverse alkaloid scaffolds and enables the targeted overproduction of thousands of THIQ products, including natural and semi-synthetic opioids.
Manipulating interstitial carbon atoms in the nickel octahedral site for highly efficient hydrogenation of alkyne
Authors: Niu Yiming , Huang Xing , Wang Yongzhao , Xu Ming , Chen Junnan , Xu Shuliang , Willinger Marc-Georg , Zhang Wei , Wei Min , Zhang Bingsen 
Published: July 2020

AbstractLight elements in the interstitial site of transition metals have strong influence on heterogeneous catalysis via either expression of surface structures or even direct participation into reaction. Interstitial atoms are generally metastable with a strong environmental dependence, setting up giant challenges in controlling of heterogeneous catalysis. Herein, we show that the desired carbon atoms can be manipulated within nickel (Ni) lattice for improving the selectivity in acetylene hydrogenation reaction. The radius of octahedral space of Ni is expanded from 0.517 to 0.524 Å via formation of Ni3Zn, affording the dissociated carbon atoms to readily dissolve and diffuse at mild temperatures. Such incorporated carbon atoms coordinate with the surrounding Ni atoms for generation of Ni3ZnC0.7 and thereof inhibit the formation of subsurface hydrogen structures. Thus, the selectivity and stability are dramatically improved, as it enables suppressing the pathway of ethylene hydrogenation and restraining the accumulation of carbonaceous species on surface.
Upgrading ketone synthesis direct from carboxylic acids and organohalides
Authors: Ruzi Rehanguli , Liu Kai , Zhu Chengjian , Xie Jin 
Published: July 2020

AbstractThe ketone functional group has a unique reactivity in organic chemistry and is associated with a number of useful reactions. Catalytic methods for ketone synthesis are continually being developed. Here, we report a photoredox, nickel and phosphoranyl radical synergistic cross-electrophile coupling of commercially available chemicals, aromatic acids and aryl/alkyl bromides. This allows for concise synthesis of highly functionalized ketones directly, without the preparation of activated carbonyl intermediates or organometallic compounds, and thus complements the conventional Weinreb ketone synthesis. Use of the appropriate photocatalyst, ligand amount and solvents can match the reaction rate required by any simple catalytic cycle. The practicality and synthetic robustness of the reaction are illustrated by the facile synthesis of complex ketones from readily available feedstock chemicals.
The microscopic origin of DMI in magnetic bilayers and prediction of giant DMI in new bilayers
Authors: Jadaun Priyamvada , Register Leonard F. , Banerjee Sanjay K. 
Published: July 2020

AbstractSkyrmions are widely regarded as promising candidates for emergent spintronic devices. Dzyaloshinskii–Moriya interaction (DMI) is often critical to the generation and manipulation of skyrmions. However, there is a fundamental lack of understanding of the origin of DMI or the mechanism by which DMI generates skyrmions in magnetic bilayers. Very little is known of the material parameters that determine the value of DMI. This knowledge is vital for rational design of skyrmion materials and further development of skyrmion technology. To address this important problem, we investigate DMI in magnetic bilayers using first principles. We present a new theoretical model that explains the microscopic origin of DMI in magnetic bilayers. We demonstrate that DMI depends on two parameters, interfacial hybridization and orbital contributions of the heavy metal. Using these parameters, we explain the trend of DMI observed. We also report four new materials systems with giant DMI and new designs for magnetic multilayers that are expected to outperform the best materials known so far. Our results present a notably new understanding of DMI, uncover highly promising materials and put forth pathways for the controlled generation of skyrmions.
MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding
Authors: Arranz Vanessa , Pearman William S. , Aguirre J. David , Liggins Libby 
Published: July 2020

AbstractThe use of DNA metabarcoding to characterise the biodiversity of environmental and community samples has exploded in recent years. However, taxonomic inferences from these studies are contingent on the quality and completeness of the sequence reference database used to characterise sample species-composition. In response, studies often develop custom reference databases to improve species assignment. The disadvantage of this approach is that it limits the potential for database re-use, and the transferability of inferences across studies. Here, we present the MARine Eukaryote Species (MARES) reference database for use in marine metabarcoding studies, created using a transparent and reproducible pipeline. MARES includes all COI sequences available in GenBank and BOLD for marine taxa, unified into a single taxonomy. Our pipeline facilitates the curation of sequences, synonymization of taxonomic identifiers used by different repositories, and formatting these data for use in taxonomic assignment tools. Overall, MARES provides a benchmark COI reference database for marine eukaryotes, and a standardised pipeline for (re)producing reference databases enabling integration and fair comparison of marine DNA metabarcoding results.
Local dispersal pathways during the invasion of the cactus moth, Cactoblastis cactorum, within North America and the Caribbean
Authors: Andraca-Gómez Guadalupe , Lombaert Eric , Ordano Mariano , Pérez-Ishiwara Rubén , Boege Karina , Domínguez César A. , Fornoni Juan 
Published: July 2020

AbstractCactoblastis cactorum, a species of moth native to Argentina, feeds on several prickly pear cactus species (Opuntia) and has been successfully used as a biological control of invading Opuntia species in Australia, South Africa and native ruderal Opuntia species in some Caribbean islands. Since its introduction to the Caribbean its spread was uncontrolled, invading successfully Florida, Texas and Louisiana. Despite this long history of invasion, we are still far from understanding the factors determining the patterns of invasion of Cactoblastis in North America. Here, we explored three non-mutually exclusive explanations: a) a stepping stone model of colonization, b) long distance colonization due to hurricanes, and/or c) hitchhiking through previously reported commercial routes. Genetic diversity, genetic structure and the patterns of migration among populations were obtained by analyzing 10 nuclear microsatellite loci. Results revealed the presence of genetic structure among populations of C. cactorum in the invaded region and suggest that both marine commercial trade between the Caribbean islands and continental USA, as well as recurrent transport by hurricanes, explain the observed patterns of colonization. Provided that sanitary regulations avoiding human-mediated dispersal are enforced, hurricanes probably represent the most important agent of dispersal and future invasion to continental areas.
Bubbles determine the amount of alcohol in Mezcal
Authors: Rage G. , Atasi O. , Wilhelmus M. M. , Hernández-Sánchez J. F. , Haut B. , Scheid B. , Legendre D. , Zenit R. 
Published: July 2020

AbstractMezcal is a traditional Mexican spirit, obtained from the distillation of fermented agave juices. Its preparation has been conducted for centuries in an artisanal manner. The method used to determine the correct alcohol content is of particular interest: a stream of the liquor is poured into a small vessel to induce surface bubbles. These bubbles, known as pearls by the Mezcal artisans, remain stable for tenths of seconds only if the alcohol content is close to 50%. For higher or lower alcohol content, the bubbles burst rapidly. The long bubble lifetime is the result of surfactant-induced surface tension changes. However, the precise mechanism and its relation to alcohol content remain unexplained. In this investigation, the extended lifetime of pearls was studied both experimentally and numerically. It was found that changes in surface tension, density, viscosity (resulting from mixing ethanol and water), and the presence of surfactants are all relevant to extend the bubble lifetime. The dimensionless bubble lifetime was found to reach its maximum value when the Bond number was close to unity, corresponding to 2 mm Mezcal bubbles. These findings show that the traditional empirical method does work. Beyond this, the understanding of the process provides physical insight to many other natural and industrial problems for which the stability of surface bubbles is of importance, such as bio-foams, froth floatation, and volcanic flows.
Impact of quantitative pulmonary emphysema score on the rate of pneumothorax and chest tube insertion in CT-guided lung biopsies
Authors: Theilig Dorothea , Petschelt David , Mayerhofer Anna , Hamm Bernd , Gebauer Bernhard , Geisel Dominik 
Published: July 2020

AbstractThe aim of this study was to evaluate the risk of pneumothorax and need for chest tube insertion in CT-guided lung biopsies and identify predictors focusing on pulmonary emphysema determined with quantitative computed tomography. To that end, we retrospectively analysed the incidence of pneumothorax and chest tube insertion in 371 CT-guided lung biopsies with respect to the quantitative emphysema score determined with the density mask technique. Other possible impact factors considered were lesion diameter, length of biopsy pathway within the lung parenchyma, lung lobe, needle size, puncture technique, patient positioning and interventionalist’s level of experience. Quantitative emphysema scores of the lung were significantly higher in patients who developed instant pneumothorax (27%, p < 0.0001), overall pneumothorax (38%, p = 0.001) and had chest tube insertion (9%, p = 0.006) compared to those who did not when analysed with the Mann–Whitney U-test. In logistic regression analysis with inclusion of the other possible impact factors, the quantitative emphysema score remained a statistically significant predictor for all three output parameters. This was confirmed with least absolute shrinkage and selection operator (Lasso) regression analysis. In conclusion, quantitatively determined pulmonary emphysema is a positive predictor of the pneumothorax rate in CT-guided lung biopsy and likelihood of chest tube insertion.