bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic RNA-based logic computation in mammalian cells
Authors: Matsuura Satoshi , Ono Hiroki , Kawasaki Shunsuke , Kuang Yi , Fujita Yoshihiko , Saito Hirohide 
Published: November 2018

AbstractSynthetic biological circuits are designed to regulate gene expressions to control cell function. To date, these circuits often use DNA-delivery methods, which may lead to random genomic integration. To lower this risk, an all RNA system, in which the circuit and delivery method are constituted of RNA components, is preferred. However, the construction of complexed circuits using RNA-delivered devices in living cells has remained a challenge. Here we show synthetic mRNA-delivered circuits with RNA-binding proteins for logic computation in mammalian cells. We create a set of logic circuits (AND, OR, NAND, NOR, and XOR gates) using microRNA (miRNA)- and protein-responsive mRNAs as decision-making controllers that are used to express transgenes in response to intracellular inputs. Importantly, we demonstrate that an apoptosis-regulatory AND gate that senses two miRNAs can selectively eliminate target cells. Thus, our synthetic RNA circuits with logic operation could provide a powerful tool for future therapeutic applications.
Sumoylation of RORγt regulates TH17 differentiation and thymocyte development
Authors: He Zhiheng , Zhang Jing , Huang Zhaofeng , Du Qian , Li Ning , Zhang Qiang , Chen Yuan , Sun Zuoming 
Published: November 2018

AbstractRORγt controls the differentiation of TH17 cells, which are mediators of autoimmune conditions such as experimental autoimmune encephalomyelitis (EAE). RORγt also regulates thymocyte development and lymph node genesis. Here we show that the function of RORγt is regulated by its sumoylation. Loss of Sumo3, but not Sumo1, dampens TH17 differentiation and delays the progression of thymic CD8+ immature single-positive cells (ISPs). RORγt is SUMO3-modified by E3 ligase PIAS4 at lysine 31 (K31), and the mutation of K31 to arginine in mice prevents RORγt sumoylation, leading to impaired TH17 differentiation, resistance to TH17-mediated EAE, accumulation of thymic ISPs, and a lack of Peyer’s patches. Mechanistically, sumoylation of RORγt-K31 recruits histone acetyltransferase KAT2A, which stabilizes the binding of SRC1 to enhance RORγt transcription factor activity. This study thus demonstrates that sumoylation is a critical mechanism for regulating RORγt function, and reveals new drug targets for preventing TH17-mediated autoimmunity.
Cell metabolism regulates integrin mechanosensing via an SLC3A2-dependent sphingolipid biosynthesis pathway
Authors: Boulter Etienne , Estrach Soline , Tissot Floriane S. , Hennrich Marco L. , Tosello Lionel , Cailleteau Laurence , de la Ballina Laura R. , Pisano Sabrina , Gavin Anne-Claude , Féral Chloé C. 
Published: November 2018

AbstractMechanical and metabolic cues independently contribute to the regulation of cell and tissue homeostasis. However, how they cross-regulate each other during this process remains largely unknown. Here, we show that cellular metabolism can regulate integrin rigidity-sensing via the sphingolipid metabolic pathway controlled by the amino acid transporter and integrin coreceptor CD98hc (SLC3A2). Genetic invalidation of CD98hc in dermal cells and tissue impairs rigidity sensing and mechanical signaling downstream of integrins, including RhoA activation, resulting in aberrant tissue mechanical homeostasis. Unexpectedly, we found that this regulation does not occur directly through regulation of integrins by CD98hc but indirectly, via the regulation of sphingolipid synthesis and the delta-4-desaturase DES2. Loss of CD98hc decreases sphingolipid availability preventing proper membrane recruitment, shuttling and activation of upstream regulators of RhoA including Src kinases and GEF-H1. Altogether, our results unravel a novel cross-talk regulation between integrin mechanosensing and cellular metabolism which may constitute an important new regulatory framework contributing to mechanical homeostasis.
Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase
Authors: Kim Sunghwan , Kim Chang Min , Son Young-Jin , Choi Jae Young , Siegenthaler Rahel K. , Lee Younho , Jang Tae-Ho , Song Jaeyoung , Kang Hara , Kaiser Chris A. , Park Hyun Ho 
Published: November 2018

AbstractOsm1 and Frd1 are soluble fumarate reductases from yeast that are critical for allowing survival under anaerobic conditions. Although they maintain redox balance during anaerobiosis, the underlying mechanism is not understood. Here, we report the crystal structure of a eukaryotic soluble fumarate reductase, which is unique among soluble fumarate reductases as it lacks a heme domain. Structural and enzymatic analyses indicate that Osm1 has a specific binding pocket for flavin molecules, including FAD, FMN, and riboflavin, catalyzing their oxidation while reducing fumarate to succinate. Moreover, ER-resident Osm1 can transfer electrons from the Ero1 FAD cofactor to fumarate either by free FAD or by a direct interaction, allowing de novo disulfide bond formation in the absence of oxygen. We conclude that soluble eukaryotic fumarate reductases can maintain an oxidizing environment under anaerobic conditions, either by oxidizing cellular flavin cofactors or by a direct interaction with flavoenzymes such as Ero1.
Wnt/β-catenin signaling regulates VE-cadherin-mediated anastomosis of brain capillaries by counteracting S1pr1 signaling
Authors: Hübner Kathleen , Cabochette Pauline , Diéguez-Hurtado Rodrigo , Wiesner Cora , Wakayama Yuki , Grassme Kathrin S. , Hubert Marvin , Guenther Stefan , Belting Heinz-Georg , Affolter Markus , Adams Ralf H. , Vanhollebeke Benoit , Herzog Wiebke 
Published: November 2018

AbstractCanonical Wnt signaling is crucial for vascularization of the central nervous system and blood-brain barrier (BBB) formation. BBB formation and modulation are not only important for development, but also relevant for vascular and neurodegenerative diseases. However, there is little understanding of how Wnt signaling contributes to brain angiogenesis and BBB formation. Here we show, using high resolution in vivo imaging and temporal and spatial manipulation of Wnt signaling, different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling, premature Sphingosine-1-phosphate receptor (S1pr) signaling reduces VE-cadherin and Esama at cell-cell junctions. We suggest that Wnt signaling suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis, whereas later S1pr signaling regulates BBB maturation and VE-cadherin stabilization. Our data provides a link between brain angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis.
Flow of cerebrospinal fluid is driven by arterial pulsations and is reduced in hypertension
Authors: Mestre Humberto , Tithof Jeffrey , Du Ting , Song Wei , Peng Weiguo , Sweeney Amanda M. , Olveda Genaro , Thomas John H. , Nedergaard Maiken , Kelley Douglas H. 
Published: November 2018

AbstractFlow of cerebrospinal fluid (CSF) through perivascular spaces (PVSs) in the brain is important for clearance of metabolic waste. Arterial pulsations are thought to drive flow, but this has never been quantitatively shown. We used particle tracking to quantify CSF flow velocities in PVSs of live mice. CSF flow is pulsatile and driven primarily by the cardiac cycle. The speed of the arterial wall matches that of the CSF, suggesting arterial wall motion is the principal driving mechanism, via a process known as perivascular pumping. Increasing blood pressure leaves the artery diameter unchanged but changes the pulsations of the arterial wall, increasing backflow and thereby reducing net flow in the PVS. Perfusion-fixation alters the normal flow direction and causes a 10-fold reduction in PVS size. We conclude that particle tracking velocimetry enables the study of CSF flow in unprecedented detail and that studying the PVS in vivo avoids fixation artifacts.
Two-dimensional tessellation by molecular tiles constructed from halogen–halogen and halogen–metal networks
Authors: Cheng Fang , Wu Xue-Jun , Hu Zhixin , Lu Xuefeng , Ding Zijing , Shao Yan , Xu Hai , Ji Wei , Wu Jishan , Loh Kian Ping 
Published: November 2018

AbstractMolecular tessellations are often discovered serendipitously, and the mechanisms by which specific molecules can be tiled seamlessly to form periodic tessellation remain unclear. Fabrication of molecular tessellation with higher symmetry compared with traditional Bravais lattices promises potential applications as photonic crystals. Here, we demonstrate that highly complex tessellation can be constructed on Au(111) from a single molecular building block, hexakis(4-iodophenyl)benzene (HPBI). HPBI gives rise to two self-assembly phases on Au(111) that possess the same geometric symmetry but different packing densities, on account of the presence of halogen-bonded and halogen–metal coordinated networks. Sub-domains of these phases with self-similarity serve as tiles in the periodic tessellations to express polygons consisting of parallelograms and two types of triangles. Our work highlights the important principle of constructing multiple phases with self-similarity from a single building block, which may constitute a new route to construct complex tessellations.
Effective connectivity of the anterior hippocampus predicts recollection confidence during natural memory retrieval
Authors: Ren Yudan , Nguyen Vinh T. , Sonkusare Saurabh , Lv Jinglei , Pang Tianji , Guo Lei , Eickhoff Simon B. , Breakspear Michael , Guo Christine C. 
Published: November 2018

AbstractHuman interactions with the world are influenced by memories of recent events. This effect, often triggered by perceptual cues, occurs naturally and without conscious effort. However, the neuroscience of involuntary memory in a dynamic milieu has received much less attention than the mechanisms of voluntary retrieval with deliberate purpose. Here, we investigate the neural processes driven by naturalistic cues that relate to, and presumably trigger the retrieval of recent experiences. Viewing the continuation of recently viewed clips evokes greater bilateral activation in anterior hippocampus, precuneus and angular gyrus than naïve clips. While these regions manifest reciprocal connectivity, continued viewing specifically modulates the effective connectivity from the anterior hippocampus to the precuneus. The strength of this modulation predicts participants’ confidence in later voluntary recall of news details. Our study reveals network mechanisms of dynamic, involuntary memory retrieval and its relevance to metacognition in a rich context resembling everyday life.
Vimentin deficiency in macrophages induces increased oxidative stress and vascular inflammation but attenuates atherosclerosis in mice
Authors: Håversen Liliana , Sundelin Jeanna Perman , Mardinoglu Adil , Rutberg Mikael , Ståhlman Marcus , Wilhelmsson Ulrika , Hultén Lillemor Mattsson , Pekny Milos , Fogelstrand Per , Bentzon Jacob Fog , Levin Malin , Borén Jan 
Published: November 2018

AbstractThe aim was to clarify the role of vimentin, an intermediate filament protein abundantly expressed in activated macrophages and foam cells, in macrophages during atherogenesis. Global gene expression, lipid uptake, ROS, and inflammation were analyzed in bone-marrow derived macrophages from vimentin-deficient (Vim−/−) and wild-type (Vim+/+) mice. Atherosclerosis was induced in Ldlr−/− mice transplanted with Vim−/− and Vim+/+ bone marrow, and in Vim−/− and Vim+/+ mice injected with a PCSK9 gain-of-function virus. The mice were fed an atherogenic diet for 12–15 weeks. We observed impaired uptake of native LDL but increased uptake of oxLDL in Vim−/− macrophages. FACS analysis revealed increased surface expression of the scavenger receptor CD36 on Vim−/− macrophages. Vim−/− macrophages also displayed increased markers of oxidative stress, activity of the transcription factor NF-κB, secretion of proinflammatory cytokines and GLUT1-mediated glucose uptake. Vim−/− mice displayed decreased atherogenesis despite increased vascular inflammation and increased CD36 expression on macrophages in two mouse models of atherosclerosis. We demonstrate that vimentin has a strong suppressive effect on oxidative stress and that Vim−/− mice display increased vascular inflammation with increased CD36 expression on macrophages despite decreased subendothelial lipid accumulation. Thus, vimentin has a key role in regulating inflammation in macrophages during atherogenesis.
Hydrostatic pressure-generated reactive oxygen species induce osteoarthritic conditions in cartilage pellet cultures
Authors: Rieder Bernhard , Weihs Anna M. , Weidinger Adelheid , Szwarc Dorota , Nürnberger Sylvia , Redl Heinz , Rünzler Dominik , Huber-Gries Carina , Teuschl Andreas H. 
Published: November 2018

AbstractOsteoarthritis (OA) is one of the most common causes of disability and represents a major socio-economic burden. Despite intensive research, the molecular mechanisms responsible for the initiation and progression of OA remain inconclusive. In recent years experimental findings revealed elevated levels of reactive oxygen species (ROS) as a major factor contributing to the onset and progression of OA. Hence, we designed a hydrostatic pressure bioreactor system that is capable of stimulating cartilage cell cultures with elevated ROS levels. Increased ROS levels in the media did not only lead to an inhibition of glycosaminoglycans and collagen II formation but also to a reduction of already formed glycosaminoglycans and collagen II in chondrogenic mesenchymal stem cell pellet cultures. These effects were associated with the elevated activity of matrix metalloproteinases as well as the increased expression of several inflammatory cytokines. ROS activated different signaling pathways including PI3K/Akt and MAPK/ERK which are known to be involved in OA initiation and progression. Utilizing the presented bioreactor system, an OA in vitro model based on the generation of ROS was developed that enables the further investigation of ROS effects on cartilage degradation but can also be used as a versatile tool for anti-oxidative drug testing.
Properties of cell signaling pathways and gene expression systems operating far from steady-state
Authors: Di-Bella Juan Pablo , Colman-Lerner Alejandro , Ventura Alejandra C. 
Published: November 2018

AbstractLigand-receptor systems, covalent modification cycles, and transcriptional networks are basic units of signaling systems and their steady-state properties are well understood. However, the behavior of such systems before steady-state is poorly characterized. Here, we analyzed the properties of input-output curves for each of these systems as they approach steady-state. In ligand-receptor systems, the EC50 (concentration of the ligand that occupies 50% of the receptors) is higher before the system reaches steady-state. Based on this behavior, we have previously defined PRESS (for pre-equilibrium sensing and signaling), a general “systems level” mechanism cells may use to overcome input saturation. Originally, we showed that, given a step stimulation, PRESS operates when the kinetics of ligand-receptor binding are slower than the downstream signaling steps. Now, we show that, provided the input increases slowly, it is not essential for the ligand binding reaction itself to be slow. In addition, we demonstrate that covalent modification cycles and gene expression systems may also operate in PRESS mode. Thus, nearly all biochemical processes may operate in PRESS mode, suggesting that this mechanism may be ubiquitous in cell signaling systems.
Clinical management and prevention of dental caries in athletes: A four-year randomized controlled clinical trial
Authors: Frese C. , Wohlrab T. , Sheng L. , Kieser M. , Krisam J. , Frese F. , Wolff D. 
Published: November 2018

AbstractThe aims of this four-year randomized controlled clinical trial were to gain insights into management and prevention of dental caries and the effect of stannous fluoride products in athletes. Fifty-four participants were randomized into test and control groups. The test group used special stannous fluoride products. The primary endpoint dental caries was assessed by the ICDAS-II-System and analyzed both by a linear mixed model for repeated measures and a generalized linear mixed model. During the observation period an increase in caries-free surfaces from 64.91 ± 6.42 at baseline to 73.22 ± 4.43 was observed. In surfaces with caries superficialis and caries media, a decrease from 13.94 ± 5.70 and 2.96 ± 2.55 surfaces at baseline to 7.89 ± 3.18 and 0.46 ± 0.78 after 2.5 years was noted, respectively. The analysis showed no effect of stannous fluoride products, but a significant difference for the time of examination (p < 0.0001). In addition, it could be shown that at any time of examination, the odds of developing caries media on a new surface was significantly lower than at baseline (up to 25-times). Due to biannual dental examinations, professional tooth cleaning and restorative treatment the number of caries-free surfaces increased and the odds of a new surface to be afflicted with caries media decreased 25-fold.
Inactivation of NUPR1 promotes cell death by coupling ER-stress responses with necrosis
Authors: Santofimia-Castaño Patricia , Lan Wenjun , Bintz Jennifer , Gayet Odile , Carrier Alice , Lomberk Gwen , Neira José Luis , González Antonio , Urrutia Raul , Soubeyran Philippe , Iovanna Juan 
Published: November 2018

AbstractIt was already described that genetic inhibition of NUPR1 induces tumor growth arrest. In this paper we studied the metabolism changes after NUPR1 downregulation in pancreatic cancer cells, which results in a significant decrease of OXPHOS activity with a concomitant lower ATP production which precedes the necrotic cell death. We demonstrated that NUPR1 downregulation induces a mitochondrial failure with a loss of the mitochondrial membrane potential, a strong increase in ROS production and a concomitant relocalization of mitochondria to the vicinity of the endoplasmic reticulum (ER). In addition, the transcriptomic analysis of NUPR1-deficient cells shows a decrease in the expression of some ER stress response-associated genes. Indeed, in ER stressors-treated cells with thapsigargin, brefeldin A or tunicamycin, a greater increase in necrosis and decrease of ATP content was observed in NUPR1-defficent cells. Finally, in vivo experiments, using acute pancreatitis which induces ER stress as well as NUPR1 activation, we observed that NUPR1 expression protects acinar cells from necrosis in mice. Importantly, we also report that the cell death observed after knocking-down NUPR1 expression is completely reversed by incubation with Necrostatin-1, but not by inhibiting caspase activity with Z-VAD-FMK. Altogether, these data enable us to describe a model in which inactivation of NUPR1 in pancreatic cancer cells results in an ER stress that induces a mitochondrial malfunction, a deficient ATP production and, as consequence, the cell death mediated by a programmed necrosis.
Toenail manganese as a potential biomarker for in utero and early childhood exposure studies
Authors: Cigan Shannon S. , McGovern Patricia M. , Choudhary Kriti , Miller Neely C. , Georgieff Michael , Rao Raghavendra , Stepanov Irina 
Published: November 2018

AbstractElevated in utero and early childhood exposure to manganese may have adverse effects on neurodevelopment. We conducted preliminary analyses to evaluate toenails as a matrix for investigating manganese exposure in infants. Infant and maternal toenail and hair samples were collected from 25 infants (7 months old) and their mothers. A subset of mothers was recruited in the third trimester of pregnancy and some also provided pre-natal toenail, hair, and blood samples, cord blood, and additional post-natal samples. Collected samples were analyzed by inductively coupled plasma mass-spectrometry. Toenail manganese levels in infants ranged from below the limit of detection (LOD) to 2.80 µg/g. Only 1 toenail sample and 4 hair samples contained levels of manganese below LOD. Associations between infant and maternal biomarkers were not statistically significant. Analysis of multiple post-natal toenail samples from a single infant-mother pair showed an increase in the infant’s toenail manganese and a decrease in maternal toenail manganese over the first year of the infant’s life. Overall, our findings suggest that toenails may serve as a valuable biological matrix for measuring manganese exposure in newborns and infants; however, additional studies are needed to determine the impact of the timing of toenail sample collection on its utility in assessing early life exposure and health outcomes.
Systematic Study of Ferromagnetism in CrxSb2−xTe3 Topological Insulator Thin Films using Electrical and Optical Techniques
Authors: Singh Angadjit , Kamboj Varun S. , Liu Jieyi , Llandro Justin , Duffy Liam B. , Senanayak Satyaprasad P. , Beere Harvey E. , Ionescu Adrian , Ritchie David A. , Hesjedal Thorsten , Barnes Crispin H. W. 
Published: November 2018

AbstractFerromagnetic ordering in a topological insulator can break time-reversal symmetry, realizing dissipationless electronic states in the absence of a magnetic field. The control of the magnetic state is of great importance for future device applications. We provide a detailed systematic study of the magnetic state in highly doped CrxSb2−xTe3 thin films using electrical transport, magneto-optic Kerr effect measurements and terahertz time domain spectroscopy, and also report an efficient electric gating of ferromagnetic order using the electrolyte ionic liquid [DEME][TFSI]. Upon increasing the Cr concentration from x = 0.15 to 0.76, the Curie temperature (Tc) was observed to increase by ~5 times to 176 K. In addition, it was possible to modify the magnetic moment by up to 50% with a gate bias variation of just ±3 V, which corresponds to an increase in carrier density by 50%. Further analysis on a sample with x = 0.76 exhibits a clear insulator-metal transition at Tc, indicating the consistency between the electrical and optical measurements. The direct correlation obtained between the carrier density and ferromagnetism - in both electrostatic and chemical doping - using optical and electrical means strongly suggests a carrier-mediated Ruderman-Kittel-Kasuya-Yoshida (RKKY) coupling scenario. Our low-voltage means of manipulating ferromagnetism, and consistency in optical and electrical measurements provides a way to realize exotic quantum states for spintronic and low energy magneto-electronic device applications.
Sequences encoding C2H2 zinc fingers inhibit polyadenylation and mRNA export in human cells
Authors: Russo Joseph , Jalkanen Aimee L. , Heck Adam M. , Schmidt Caleb M. , Wilusz Jeffrey , Wilusz Carol J. 
Published: November 2018

AbstractThe large C2H2-Zinc Finger (C2H2-ZNF) gene family has rapidly expanded in primates through gene duplication. There is consequently considerable sequence homology between family members at both the nucleotide and amino acid level, allowing for coordinated regulation and shared functions. Here we show that multiple C2H2-ZNF mRNAs experience differential polyadenylation resulting in populations with short and long poly(A) tails. Furthermore, a significant proportion of C2H2-ZNF mRNAs are retained in the nucleus. Intriguingly, both short poly(A) tails and nuclear retention can be specified by the repeated elements that encode zinc finger motifs. These Zinc finger Coding Regions (ZCRs) appear to restrict polyadenylation of nascent RNAs and at the same time impede their export. However, the polyadenylation process is not necessary for nuclear retention of ZNF mRNAs. We propose that inefficient polyadenylation and export may allow C2H2-ZNF mRNAs to moonlight as non-coding RNAs or to be stored for later use.