bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity
Authors: Winters Ian P. , Chiou Shin-Heng , Paulk Nicole K. , McFarland Christopher D. , Lalgudi Pranav V. , Ma Rosanna K. , Lisowski Leszek , Connolly Andrew J. , Petrov Dmitri A. , Kay Mark A. , Winslow Monte M. 
Published: December 2017

AbstractLarge-scale genomic analyses of human cancers have cataloged somatic point mutations thought to initiate tumor development and sustain cancer growth. However, determining the functional significance of specific alterations remains a major bottleneck in our understanding of the genetic determinants of cancer. Here, we present a platform that integrates multiplexed AAV/Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple genomic alterations in de novo cancers in mice. Using this approach, we introduce a barcoded library of non-synonymous mutations into hotspot codons 12 and 13 of Kras in adult somatic cells to initiate tumors in the lung, pancreas, and muscle. High-throughput sequencing of barcoded Kras
HDR
alleles from bulk lung and pancreas reveals surprising diversity in Kras variant oncogenicity. Rapid, cost-effective, and quantitative approaches to simultaneously investigate the function of precise genomic alterations in vivo will help uncover novel biological and clinically actionable insights into carcinogenesis.
Insights into the structure and assembly of a bacterial cellulose secretion system
Authors: Krasteva Petya Violinova , Bernal-Bayard Joaquin , Travier Laetitia , Martin Fernando Ariel , Kaminski Pierre-Alexandre , Karimova Gouzel , Fronzes Rémi , Ghigo Jean-Marc 
Published: December 2017

AbstractSecreted exopolysaccharides present important determinants for bacterial biofilm formation, survival, and virulence. Cellulose secretion typically requires the concerted action of a c-di-GMP-responsive inner membrane synthase (BcsA), an accessory membrane-anchored protein (BcsB), and several additional Bcs components. Although the BcsAB catalytic duo has been studied in great detail, its interplay with co-expressed subunits remains enigmatic. Here we show that E. coli Bcs proteins partake in a complex protein interaction network. Electron microscopy reveals a stable, megadalton-sized macromolecular assembly, which encompasses most of the inner membrane and cytosolic Bcs components and features a previously unobserved asymmetric architecture. Heterologous reconstitution and mutational analyses point toward a structure–function model, where accessory proteins regulate secretion by affecting both the assembly and stability of the system. Altogether, these results lay the foundation for more comprehensive models of synthase-dependent exopolysaccharide secretion in biofilms and add a sophisticated secretory nanomachine to the diverse bacterial arsenal for virulence and adaptation.
Endocytosis regulates TDP-43 toxicity and turnover
Authors: Liu Guangbo , Coyne Alyssa N. , Pei Fen , Vaughan Spencer , Chaung Matthew , Zarnescu Daniela C. , Buchan J. Ross 
Published: December 2017

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal motor neuron degenerative disease. ALS-affected motor neurons exhibit aberrant localization of a nuclear RNA binding protein, TDP-43, into cytoplasmic aggregates, which contributes to pathology via unclear mechanisms. Here, we demonstrate that TDP-43 turnover and toxicity depend in part upon the endocytosis pathway. TDP-43 inhibits endocytosis, and co-localizes strongly with endocytic proteins, including in ALS patient tissue. Impairing endocytosis increases TDP-43 toxicity, aggregation, and protein levels, whereas enhancing endocytosis reverses these phenotypes. Locomotor dysfunction in a TDP-43 ALS fly model is also exacerbated and suppressed by impairment and enhancement of endocytic function, respectively. Thus, endocytosis dysfunction may be an underlying cause of ALS pathology.
Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors
Authors: Martin-Malpartida Pau , Batet Marta , Kaczmarska Zuzanna , Freier Regina , Gomes Tiago , Aragón Eric , Zou Yilong , Wang Qiong , Xi Qiaoran , Ruiz Lidia , Vea Angela , Márquez José A. , Massagué Joan , Macias Maria J. 
Published: December 2017

AbstractSmad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.
A modular synthesis of tetracyclic meroterpenoid antibiotics
Authors: Wildermuth Raphael , Speck Klaus , Haut Franz-Lucas , Mayer Peter , Karge Bianka , Brönstrup Mark , Magauer Thomas 
Published: December 2017

AbstractStachyflin, aureol, smenoqualone, strongylin A, and cyclosmenospongine belong to a family of tetracyclic meroterpenoids, which, by nature of their unique molecular structures and various biological properties, have attracted synthetic and medicinal chemists alike. Despite their obvious biosynthetic relationship, only scattered reports on the synthesis and biological investigation of individual meroterpenoids have appeared so far. Herein, we report a highly modular synthetic strategy that enabled the synthesis of each of these natural products and 15 non-natural derivatives. The route employs an auxiliary-controlled Diels–Alder reaction to enable the enantioselective construction of the decalin subunit, which is connected to variously substituted arenes by either carbonyl addition chemistry or sterically demanding sp2–sp3 cross-coupling reactions. The selective installation of either the cis- or trans-decalin stereochemistry is accomplished by an acid-mediated cyclization/isomerization reaction. Biological profiling reveals that strongylin A and a simplified derivative thereof have potent antibiotic activity against methicillin-resistant Staphylococcus aureus.
Reproducible flaws unveil electrostatic aspects of semiconductor electrochemistry
Authors: Vogel Yan B. , Zhang Long , Darwish Nadim , Gonçales Vinicius R. , Le Brun Anton , Gooding J. Justin , Molina Angela , Wallace Gordon G. , Coote Michelle L. , Gonzalez Joaquin , Ciampi Simone 
Published: December 2017

AbstractPredicting or manipulating charge-transfer at semiconductor interfaces, from molecular electronics to energy conversion, relies on knowledge generated from a kinetic analysis of the electrode process, as provided by cyclic voltammetry. Scientists and engineers encountering non-ideal shapes and positions in voltammograms are inclined to reject these as flaws. Here we show that non-idealities of redox probes confined at silicon electrodes, namely full width at half maximum <90.6 mV and anti-thermodynamic inverted peak positions, can be reproduced and are not flawed data. These are the manifestation of electrostatic interactions between dynamic molecular charges and the semiconductor’s space-charge barrier. We highlight the interplay between dynamic charges and semiconductor by developing a model to decouple effects on barrier from changes to activities of surface-bound molecules. These findings have immediate general implications for a correct kinetic analysis of charge-transfer at semiconductors as well as aiding the study of electrostatics on chemical reactivity.
Peritoneal tissue-resident macrophages are metabolically poised to engage microbes using tissue-niche fuels
Authors: Davies Luke C. , Rice Christopher M. , Palmieri Erika M. , Taylor Philip R. , Kuhns Douglas B. , McVicar Daniel W. 
Published: December 2017

AbstractThe importance of metabolism in macrophage function has been reported, but the in vivo relevance of the in vitro observations is still unclear. Here we show that macrophage metabolites are defined in a specific tissue context, and these metabolites are crucially linked to tissue-resident macrophage functions. We find the peritoneum to be rich in glutamate, a glutaminolysis-fuel that is exploited by peritoneal-resident macrophages to maintain respiratory burst during phagocytosis via enhancing mitochondrial complex-II metabolism. This niche-supported, inducible mitochondrial function is dependent on protein kinase C activity, and is required to fine-tune the cytokine responses that control inflammation. In addition, we find that peritoneal-resident macrophage mitochondria are recruited to phagosomes and produce mitochondrially derived reactive oxygen species, which are necessary for microbial killing. We propose that tissue-resident macrophages are metabolically poised in situ to protect and exploit their tissue-niche by utilising locally available fuels to implement specific metabolic programmes upon microbial sensing.
High efficiency and long-term intracellular activity of an enzymatic nanofactory based on metal-organic frameworks
Authors: Lian Xizhen , Erazo-Oliveras Alfredo , Pellois Jean-Philippe , Zhou Hong-Cai 
Published: December 2017

AbstractEnhancing or restoring enzymatic function in cells is highly desirable in applications ranging from ex vivo cellular manipulations to enzyme replacement therapies in humans. However, because enzymes degrade in biological milieus, achieving long-term enzymatic activities can be challenging. Herein we report on the in cellulo properties of nanofactories that consist of antioxidative enzymes encapsulated in metal–organic frameworks (MOFs). We demonstrate that, while free enzymes display weak activities for only a short duration, these efficient nanofactories protect human cells from toxic reactive oxygen species for up to a week. Remarkably, these results are obtained in spite of the nanofactories being localized in lysosomes, acidic organelles that contain a variety of proteases. The long-term persistence of the nanofactories is attributed to the chemical stability of MOF in low pH environment and to the protease resistance provided by the protective cage formed by the MOF around the encapsulated enzymes.
Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator
Authors: Carayol Jérôme , Chabert Christian , Di Cara Alessandro , Armenise Claudia , Lefebvre Gregory , Langin Dominique , Viguerie Nathalie , Metairon Sylviane , Saris Wim H. M. , Astrup Arne , Descombes Patrick , Valsesia Armand , Hager Jörg 
Published: December 2017

AbstractThousands of genetic variants have been associated with complex traits through genome-wide association studies. However, the functional variants or mechanistic consequences remain elusive. Intermediate traits such as gene expression or protein levels are good proxies of the metabolic state of an organism. Proteome analysis especially can provide new insights into the molecular mechanisms of complex traits like obesity. The role of genetic variation in determining protein level variation has not been assessed in obesity. To address this, we design a large-scale protein quantitative trait locus (pQTL) analysis based on a set of 1129 proteins from 494 obese subjects before and after a weight loss intervention. This reveals 55 BMI-associatedcis-pQTLs andtrans-pQTLs at baseline and 3trans-pQTLs after the intervention. We provide evidence for distinct genetic mechanisms regulating BMI-associated proteins before and after weight loss. Finally, by functional analysis, we identify and validateFAM46Aas atransregulator for leptin.
Structure of outer membrane protein G in lipid bilayers
Authors: Retel Joren S. , Nieuwkoop Andrew J. , Hiller Matthias , Higman Victoria A. , Barbet-Massin Emeline , Stanek Jan , Andreas Loren B. , Franks W. Trent , van Rossum Barth-Jan , Vinothkumar Kutti R. , Handel Lieselotte , de Palma Gregorio Giuseppe , Bardiaux Benjamin , Pintacuda Guido , Emsley Lyndon , Kühlbrandt Werner , Oschkinat Hartmut 
Published: December 2017

Abstractβ-barrel proteins mediate nutrient uptake in bacteria and serve vital functions in cell signaling and adhesion. For the 14-strand outer membrane protein G of Escherichia coli, opening and closing is pH-dependent. Different roles of the extracellular loops in this process were proposed, and X-ray and solution NMR studies were divergent. Here, we report the structure of outer membrane protein G investigated in bilayers of E. coli lipid extracts by magic-angle-spinning NMR. In total, 1847 inter-residue 1H–1H and 13C–13C distance restraints, 256 torsion angles, but no hydrogen bond restraints are used to calculate the structure. The length of β-strands is found to vary beyond the membrane boundary, with strands 6–8 being the longest and the extracellular loops 3 and 4 well ordered. The site of barrel closure at strands 1 and 14 is more disordered than most remaining strands, with the flexibility decreasing toward loops 3 and 4. Loop 4 presents a well-defined helix.
Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase
Authors: Abplanalp Jeannette , Leutert Mario , Frugier Emilie , Nowak Kathrin , Feurer Roxane , Kato Jiro , Kistemaker Hans V. A. , Filippov Dmitri V. , Moss Joel , Caflisch Amedeo , Hottiger Michael O. 
Published: December 2017

AbstractADP-ribosylation is a posttranslational modification that exists in monomeric and polymeric forms. Whereas the writers (e.g. ARTD1/PARP1) and erasers (e.g. PARG, ARH3) of poly-ADP-ribosylation (PARylation) are relatively well described, the enzymes involved in mono-ADP-ribosylation (MARylation) have been less well investigated. While erasers for the MARylation of glutamate/aspartate and arginine have been identified, the respective enzymes with specificity for serine were missing. Here we report that, in vitro, ARH3 specifically binds and demodifies proteins and peptides that are MARylated. Molecular modeling and site-directed mutagenesis of ARH3 revealed that numerous residues are critical for both the mono- and the poly-ADP-ribosylhydrolase activity of ARH3. Notably, a mass spectrometric approach showed that ARH3-deficient mouse embryonic fibroblasts are characterized by a specific increase in serine-ADP-ribosylation in vivo under untreated conditions as well as following hydrogen peroxide stress. Together, our results establish ARH3 as a serine mono-ADP-ribosylhydrolase and as an important regulator of the basal and stress-induced ADP-ribosylome.
H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1
Authors: Jurkowska Renata Z. , Qin Su , Kungulovski Goran , Tempel Wolfram , Liu Yanli , Bashtrykov Pavel , Stiefelmaier Judith , Jurkowski Tomasz P. , Kudithipudi Srikanth , Weirich Sara , Tamas Raluca , Wu Hong , Dombrovski Ludmila , Loppnau Peter , Reinhardt Richard , Min Jinrong , Jeltsch Albert 
Published: December 2017

AbstractSETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.
Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria
Authors: Bernheim Aude , Calvo-Villamañán Alicia , Basier Clovis , Cui Lun , Rocha Eduardo P. C. , Touchon Marie , Bikard David 
Published: December 2017

AbstractType II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. We report that non-homologous end-joining (NHEJ) and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions using the NHEJ pathway from Bacillus subtilis and the type II-A CRISPR-Cas systems from Streptococcus thermophilus and Streptococcus pyogenes. Our results suggest that the NHEJ system has no effect on CRISPR immunity. On the other hand, we provide evidence for the inhibition of NHEJ repair by the Csn2 protein. Our findings give insights on the complex interactions between CRISPR-Cas systems and repair mechanisms in bacteria, contributing to explain the scattered distribution of CRISPR-Cas systems in bacterial genome.
Efficacy and safety of stereotactic radiosurgery for pulmonary metastases from osteosarcoma: Experience in 73 patients
Authors: Yu Wenxi , Liu Zimei , Tang Lina , Lin Feng , Yao Yang , Shen Zan 
Published: December 2017

AbstractOsteosarcoma pulmonary metastases are typically treated with resection and/or chemotherapy. We hypothesize that stereotactic radiosurgery (SRS) can be an alternative to surgery that can achieve high rates of local control with limited toxicity. From January 2005 to December 2013, 73 patients who developed pulmonary metastasis during period of adjuvant chemotherapy or follow-up were analyzed. 33 patients were treated by stereotactic radiosurgery using the body gamma-knife system. A total dose of 50 Gy was delivered at 5 Gy/fraction to the 50% isodose line covering the planning target volume, whereas a total dose of 70 Gy was delivered at 7 Gy/fraction to the gross target volume. The other 40 patients were treated by surgical resection. Four-year progression-free survival rate, four-year survival rate, median time of PRPFS (post-relapse progress-free survival) and PROS (post-relapse overall survival) in SRS group were parallel to that in surgical group. Patients tolerated gamma knife radiosurgery well. Our study demonstrates that SRS is well-tolerated with excellent local control and less complications. SRS should be considered as a potential option in patients with pulmonary metastases from osteosarcoma, especially in those who are medically inoperable, refuse surgery.
Escherichia coli outer membrane vesicles can contribute to sepsis induced cardiac dysfunction
Authors: Svennerholm Kristina , Park Kyong-Su , Wikström Johannes , Lässer Cecilia , Crescitelli Rossella , Shelke Ganesh V. , Jang Su Chul , Suzuki Shintaro , Bandeira Elga , Olofsson Charlotta S. , Lötvall Jan 
Published: December 2017

AbstractSepsis induced cardiac dysfunction (SIC) is a severe complication to sepsis which significantly worsens patient outcomes. It is known that bacteria have the capacity to release outer membrane vesicles (OMVs), which are nano-sized bilayered vesicles composed of lipids and proteins, that can induce a fatal inflammatory response. The aim of this study was to determine whether OMVs from a uropathogenicEscherichia colistrain can induce cardiac dysfunction, and to elucidate any mechanisms involved. OMVs induced irregular Ca2+oscillations with a decreased frequency in cardiomyocytes through recordings of intracellular Ca2+dynamics. Mice were intraperitoneally injected with bacteria-free OMVs, which resulted in increased concentration of pro-inflammatory cytokine levels in blood. Cytokines were increased in heart lysates, and OMVs could be detected in the heart after OMVs injection. Troponin T was significantly increased in blood, and echocardiography showed increased heart wall thickness as well as increased heart rate. This study shows thatE. coliOMVs induce cardiac injuryin vitroandin vivo, in the absence of bacteria, and may be a causative microbial signal in SIC. The role of OMVs in clinical disease warrant further studies, as bacterial OMVs in addition to live bacteria may be good therapeutic targets to control sepsis.
Dynamic regulation of TREK1 gating by Polycystin 2 via a Filamin A-mediated cytoskeletal Mechanism
Authors: Li Fraine Steven , Patel Amanda , Duprat Fabrice , Sharif-Naeini Reza 
Published: December 2017

AbstractMechanosensing is essential for several physiological functions including touch and pain sensations, osmoregulation, and controlling the myogenic tone of resistance arteries. Understanding how mechanosensitive ion channels (MSCs) are gated can provide important information regarding these processes. We have previously demonstrated that during pathological conditions such as polycystic kidney disease, polycystin 2 (TRPP2) inhibits the activity of potassium-selective MSCs through a filamin A-mediated cytoskeletal effect, and renders tubular epithelial cells susceptible to apoptosis. However, the nature of this cytoskeletal inhibition remains poorly understood. In this study we use a combination of electrophysiology, structured illumination microscopy, and fluorescence recovery after photobleaching (FRAP) to examine the dynamic nature of the TRPP2-mediated cytoskeletal inhibition of the potassium-selective MSC TREK1. Our data indicate that this inhibition of MSC activity occurs through an accelerated cytoskeletal inhibition, and ultimately decreases the open probability of the TREK1 channel. These results shed light on a novel mode of regulation of MSCs gating, which may be at play in several physiological functions.
Oral immunotherapy combined with omalizumab for high–risk cow’s milk allergy: a randomized controlled trial
Authors: Takahashi Masaya , Soejima Kazuhiko , Taniuchi Shoichiro , Hatano Yasuko , Yamanouchi Sohsaku , Ishikawa Hideki , Irahara Makoto , Sasaki Youhei , Kido Hiroshi , Kaneko Kazunari 
Published: December 2017

AbstractWe evaluated the efficacy and safety of oral immunotherapy (OIT) combined with 24 weeks of omalizumab (OMB) at inducing desensitization in children with cow’s milk allergy (CM) compared with an untreated group. The present study was a prospective randomized controlled trial. Sixteen patients (age, 6–14 years) with high IgE levels to CM were enrolled in the present study. Patients were randomized 1:1 to receive OMB-OIT group or untreated group. The primary outcome was the induction of desensitization at 8 weeks after OMB was discontinued in OMB-OIT treated group and at 32 weeks after study entry. None of the 6 children in the untreated group developed desensitization to CM while all of the 10 children in the OIT-OMB treated group achieved desensitization (P < 0.001). A significantly decreased wheal diameter in response to a skin prick test using CM was found in the OMB-OIT treated group (P < 0.05). These data suggest that OIT combined with OMB using microwave heated CM may help to induce desensitization for children with high-risk CM allergy. This prospective randomized controlled trial was intended for 50 participants but was prematurely discontinued due to overwhelming superiority of OMB combined with microwave heated OIT over CM avoidance.