bluuebunny/crossref_metadata_2025_split huggingface dataset:
Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens
Authors: Kumar Ashish , Kaur Harmeet , Jain Abha , Nair Deepak T. , Salunke Dinakar M. 
Published: January 2018

AbstractSequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.
Alteration in yield and oil quality traits of winter rapeseed by lodging at different planting density and nitrogen rates
Authors: Khan Shahbaz , Anwar Sumera , Kuai Jie , Noman Ali , Shahid Muhammad , Din Mairaj , Ali Ahmed , Zhou Guangsheng 
Published: January 2018

AbstractLodging is a factor that negatively affects yield, seed quality, and harvest ability in winter rapeseed (Brassica napus L.). In this study, we quantified the lodging-induced yield losses, changes in fatty acid composition, and oil quality in rapeseed under different nitrogen application rates and planting densities. Field experiments were conducted in 2014–2017 for studying the effect of manually-induced lodging angles (0°, 30°, 60°, and 90°), 10, 20 and 30 d post-flowering at different densities and nitrogen application rates. The fertilization/planting density combination N270D45 produced the maximum observed yield and seed quality. Timing and angle of lodging had significant effects on yield. Lodging at 90° induced at 10 d post-flowering caused the maximum reduction in yield, biomass, and silique photosynthesis. Seed yield losses were higher at high N application rates, the maximum being at N360D45. Lodging decreased seed oil content and altered its fatty acid composition by increasing stearic and palmitic acid content, while decreasing linoleic and linolenic acid content, and deteriorating oil quality by increasing erucic acid and glucosinolate content. Therefore, lodging-induced yield loss and reduction in oil content might be reduced by selecting optimum N level and planting density.
Development of a PET radioligand for potassium channels to image CNS demyelination
Authors: Brugarolas Pedro , Sánchez-Rodríguez Jorge E. , Tsai Hsiu-Ming , Basuli Falguni , Cheng Shih-Hsun , Zhang Xiang , Caprariello Andrew V. , Lacroix Jerome J. , Freifelder Richard , Murali Dhanabalan , DeJesus Onofre , Miller Robert H. , Swenson Rolf E. , Chen Chin-Tu , Herscovitch Peter , Reich Daniel S. , Bezanilla Francisco , Popko Brian 
Published: January 2018

AbstractCentral nervous system (CNS) demyelination represents the pathological hallmark of multiple sclerosis (MS) and contributes to other neurological conditions. Quantitative and specific imaging of demyelination would thus provide critical clinical insight. Here, we investigated the possibility of targeting axonal potassium channels to image demyelination by positron emission tomography (PET). These channels, which normally reside beneath the myelin sheath, become exposed upon demyelination and are the target of the MS drug, 4-aminopyridine (4-AP). We demonstrate using autoradiography that 4-AP has higher binding in non-myelinated and demyelinated versus well-myelinated CNS regions, and describe a fluorine-containing derivative, 3-F-4-AP, that has similar pharmacological properties and can be labeled with 18F for PET imaging. Additionally, we demonstrate that [18F]3-F-4-AP can be used to detect demyelination in rodents by PET. Further evaluation in Rhesus macaques shows higher binding in non-myelinated versus myelinated areas and excellent properties for brain imaging. Together, these data indicate that [18F]3-F-4-AP may be a valuable PET tracer for detecting CNS demyelination noninvasively.
RGS7 is recurrently mutated in melanoma and promotes migration and invasion of human cancer cells
Authors: Qutob Nouar , Masuho Ikuo , Alon Michal , Emmanuel Rafi , Cohen Isadora , Di Pizio Antonella , Madore Jason , Elkahloun Abdel , Ziv Tamar , Levy Ronen , Gartner Jared J. , Hill Victoria K. , Lin Jimmy C. , Hevroni Yael , Greenberg Polina , Brodezki Alexandra , Rosenberg Steven A. , Kosloff Mickey , Hayward Nicholas K. , Admon Arie , Niv Masha Y. , Scolyer Richard A. , Martemyanov Kirill A. , Samuels Yardena 
Published: January 2018

AbstractAnalysis of 501 melanoma exomes revealed RGS7, which encodes a GTPase-accelerating protein (GAP), to be a tumor-suppressor gene. RGS7 was mutated in 11% of melanomas and was found to harbor three recurrent mutations (p.R44C, p.E383K and p.R416Q). Structural modeling of the most common recurrent mutation of the three (p.R44C) predicted that it destabilizes the protein due to the loss of an H-bond and salt bridge network between the mutated position and the serine and aspartic acid residues at positions 58 as 61, respectively. We experimentally confirmed this prediction showing that the p.R44C mutant protein is indeed destabilized. We further show RGS7 p.R44C has weaker catalytic activity for its substrate Gαo, thus providing a dual mechanism for its loss of function. Both of these effects are expected to contribute to loss of function of RGS7 resulting in increased anchorage-independent growth, migration and invasion of melanoma cells. By mutating position 56 in the R44C mutant from valine to cysteine, thereby enabling the formation of a disulfide bridge between the two mutated positions, we slightly increased the catalytic activity and reinstated protein stability, leading to the rescue of RGS7′s function as a tumor suppressor. Our findings identify RGS7 as a novel melanoma driver and point to the clinical relevance of using strategies to stabilize the protein and, thereby, restore its function.
Development of versatile non-homologous end joining-based knock-in module for genome editing
Authors: Sawatsubashi Shun , Joko Yudai , Fukumoto Seiji , Matsumoto Toshio , Sugano Shigeo S. 
Published: January 2018

AbstractCRISPR/Cas9-based genome editing has dramatically accelerated genome engineering. An important aspect of genome engineering is efficient knock-in technology. For improved knock-in efficiency, the non-homologous end joining (NHEJ) repair pathway has been used over the homology-dependent repair pathway, but there remains a need to reduce the complexity of the preparation of donor vectors. We developed the versatile NHEJ-based knock-in module for genome editing (VIKING). Using the consensus sequence of the time-honored pUC vector to cut donor vectors, any vector with a pUC backbone could be used as the donor vector without customization. Conditions required to minimize random integration rates of the donor vector were also investigated. We attempted to isolate null lines of the VDR gene in human HaCaT keratinocytes using knock-in/knock-out with a selection marker cassette, and found 75% of clones isolated were successfully knocked-in. Although HaCaT cells have hypotetraploid genome composition, the results suggest multiple clones have VDR null phenotypes. VIKING modules enabled highly efficient knock-in of any vectors harboring pUC vectors. Users now can insert various existing vectors into an arbitrary locus in the genome. VIKING will contribute to low-cost genome engineering.
Novel endogenous simian retroviral integrations in Vero cells: implications for quality control of a human vaccine cell substrate
Authors: Sakuma Chisato , Sekizuka Tsuyoshi , Kuroda Makoto , Kasai Fumio , Saito Kyoko , Ikeda Masaki , Yamaji Toshiyuki , Osada Naoki , Hanada Kentaro 
Published: January 2018

AbstractAfrican green monkey (AGM)-derived Vero cells have been utilized to produce various human vaccines. The Vero cell genome harbors a variety of simian endogenous type D retrovirus (SERV) sequences. In this study, a transcriptome analysis showed that DNA hypomethylation released the epigenetic repression of SERVs in Vero cells. Moreover, comparative genomic analysis of three Vero cell sublines and an AGM reference revealed that the genomes of the sublines have ~80 SERV integrations. Among them, ~60 integrations are present within all three cell sublines and absent from the reference sequence. At least several of these integrations consist of complete SERV proviruses. These results strongly suggest that SERVs integrated in the genome of Vero cells did not retrotranspose after the establishment of the cell lineage as far as cells were maintained under standard culture and passage conditions, providing a scientific basis for controlling the quality of pharmaceutical cell substrates and their derived biologics.
Induction of ferroptosis and mitochondrial dysfunction by oxidative stress in PC12 cells
Authors: Wu Chuanhong , Zhao Wenwen , Yu Jie , Li Shaojing , Lin Ligen , Chen Xiuping 
Published: January 2018

AbstractNeurodegenerative diseases (NDD) are typically associated with neuron loss in nervous system areas. Interventions with related death mechanisms may ameliorate NDD progression. Oxidative stress plays an important role in NDD cell death routines. However, tert-butylhydroperoxide (t-BHP), a widely used oxidative stress stimulus, induces neural cell death through a mechanism that remains elusive. In our study, the ferroptosis marker events occurred after co-treatment with 100 μM t-BHP for 1 h, all of which were reversed in the presence of the ferroptosis inhibitor ferrostatin-1 (Fer-1) and the iron chelator deferoxamine, implying the occurrence of ferroptosis. Moreover, mitochondrial dysfunction accompanied by a decreased in membrane potential and ATP production, increased mitochondrial ROS generation. Furthermore, this mitochondrial dysfunction could be reversed by Fer-1. In addition, JNK1/2 and ERK1/2 were activated upstream of the ferroptosis and mitochondrial dysfunction. In summary, these data suggest that ferroptosis, coupled with mitochondrial dysfunction, was involved in t-BHP-induced PC12 death. JNK1/2 and ERK1/2 played important roles in t-BHP-induced cell death. Overall, this study might provide clues to the oxidative stress-based strategies for cell protection in NDD.
Titania (TiO2) nanoparticles enhance the performance of growth-promoting rhizobacteria
Authors: Timmusk Salme , Seisenbaeva Gulaim , Behers Lawrence 
Published: January 2018

AbstractA novel use of nanotitania (TNs) as agents in the nanointerface interaction between plants and colonization of growth promoting rhizobacteria (PGPR) is presented. The effectiveness of PGPRs is related to the effectiveness of the technology used for their formulation. TNs produced by the Captigel patented SolGel approach, characterized by the transmission and scanning electron microscopy were used for formulation of the harsh environment PGPR strains. Changes in the biomass of wheat seedlings and in the density of single and double inoculants with and without TNs were monitored during two weeks of stress induced by drought salt and by the pathogen Fusarium culmorum. We show that double inoculants with TNs can attach stably to plant roots. Regression analysis indicates that there is a positive interaction between seedling biomass and TN-treated second inoculant colonization. We conclude that TN treatment provides an effectual platform for PGPR rational application via design of root microbial community. Our studies illustrate the importance of considering natural soil nanoparticles for PGPR application and thereby may explain the generally observed inconsistent behavior of PGPRs in the field. These new advancements importantly contribute towards solving food security issues in changing climates. The model systems established here provide a basis for new PGPR nanomaterials research.
Multiscale and luminescent, hollow microspheres for gas phase thermometry
Authors: Bischoff Lothar , Stephan Michael , Birkel Christina S. , Litterscheid Christian F. , Dreizler Andreas , Albert Barbara 
Published: January 2018

AbstractRecently developed laser-based measurement techniques are used to image the temperatures and velocities in gas flows. They require new phosphor materials with an unprecedented combination of properties. A novel synthesis procedure is described here; it results in hierarchically structured, hollow microspheres of Eu3+-doped Y2O3, with unusual particle sizes and very good characteristics compared to full particles. Solution-based precipitation on polymer microballoons produces very stable and luminescent, ceramic materials of extremely low density. As a result of the – compared to established template-directed syntheses – reduced mass of polymer that is lost upon calcination, micron-sized particles are obtained with mesoporous walls, low defect concentrations, and nanoscale wall thicknesses. They can be produced with larger diameters (~25 µm) compared to known hollow spheres and exhibit an optimized flow behavior. Their temperature sensing properties and excellent fluidic follow-up behavior are shown by determining emission intensity ratios in a specially designed heating chamber. Emission spectroscopy and imaging, electron microscopy and X-ray diffraction results are presented for aerosolizable Y2O3 with an optimized dopant concentration (8%). Challenges in the field of thermofluids can be addressed by combined application of thermometry and particle image velocimetry with such hollow microparticles.
Three-Dimensional Speckle Light Self-Healing-Based Imaging System
Authors: Pires Danilo G. , Sonsin Artur F. , Jesus-Silva Alcenísio J. , Fonseca Eduardo J. S. 
Published: January 2018

AbstractRecently new methodologies for imaging have been achieved making use of multiple light scattering. Here we present the self-healing effect using a speckled light field. We present an experiment that constitutes a useful application for a three-dimensional light sheet-based imaging system through an inhomogeneous medium. Each layer can be imaged independently of the others. The axial resolution basically depends on the coherence length, which can be sub-wavelength and controllable. This allows for a simple and direct technique for imaging through scattering layers with axial resolution improvement. Our results may find applications not only in bio-microscopy systems but also in data transmission.
Transcriptional inaccuracy threshold attenuates differences in RNA-dependent DNA synthesis fidelity between retroviral reverse transcriptases
Authors: Sebastián-Martín Alba , Barrioluengo Verónica , Menéndez-Arias Luis 
Published: January 2018

AbstractIn M13mp2 lacZα forward mutation assays measuring intrinsic fidelity of DNA-dependent DNA synthesis, wild-type human immunodeficiency virus type 1 (HIV-1) RTs of group M/subtype B previously showed >10-fold higher error rates than murine leukaemia virus (MLV) and avian myeloblastosis virus (AMV) RTs. An adapted version of the assay was used to obtain error rates of RNA-dependent DNA synthesis for several RTs, including wild-type HIV-1BH10, HIV-1ESP49, AMV and MLV RTs, and the high-fidelity mutants of HIV-1ESP49 RT K65R and K65R/V75I. Our results showed that there were less than two-fold differences in fidelity between the studied RTs with error rates ranging within 2.5 × 10−5 and 3.5 × 10−5. These results were consistent with the existence of a transcriptional inaccuracy threshold, generated by the RNA polymerase while synthesizing the RNA template used in the assay. A modest but consistent reduction of the inaccuracy threshold was achieved by lowering the pH and Mg2+ concentration of the transcription reaction. Despite assay limitations, we conclude that HIV-1BH10 and HIV-1ESP49 RTs are less accurate when copying DNA templates than RNA templates. Analysis of the RNA-dependent mutational spectra revealed a higher tendency to introduce large deletions at the initiation of reverse transcription by all HIV-1 RTs except the double-mutant K65R/V75I.
Transcriptome analysis reveals carbohydrate-mediated liver immune responses in Epinephelus akaara
Authors: Yang Yunxia , Han Tao , Xiao Jia , Li Xinyu , Wang Jiteng 
Published: January 2018

AbstractAs the cheapest energy source, carbohydrates are used in fish feeds to improve physical quality and reduce catabolism of proteins and lipids. The liver is the primary organ for metabolism and is also an important site of immune regulation. Here, we investigated the effect of different dietary carbohydrate levels on growth and health by evaluating the liver transcriptome of Epinephelus akaara. In this study, E. akaara juveniles were fed diets containing few (0% corn starch), moderate (18% corn starch), and high (30% corn starch) levels of dietary carbohydrate. After an 8-week feeding trial, E. akaara fed 30% dietary carbohydrates exhibited poor growth performance compared with those fed 0% and 18% dietary carbohydrates (P > 0.05). Genes related to the immune system, including IL8, TLR9, CXCR4, CCL4, and NFκB inhibitor alpha, were over-expressed in E. akaara fed the highest level of carbohydrate (30%). This general over-expression could indicate activation of inflammatory processes in the liver. The liver transcriptome data of E. akaara reported here indicate that high carbohydrate level of diet can lead to poor growth and inflammatory immune response in E. akaara.
Replication of biocompatible, nanotopographic surfaces
Authors: Sun Xiaoyu , Hourwitz Matt J. , Baker Eleni M. , Schmidt B. U. Sebastian , Losert Wolfgang , Fourkas John T. 
Published: January 2018

AbstractThe ability of cells to sense and respond to nanotopography is being implicated as a key element in many physiological processes such as cell differentiation, immune response, and wound healing, as well as in pathologies such as cancer metastasis. To understand how nanotopography affects cellular behaviors, new techniques are required for the mass production of biocompatible, rigid nanotopographic surfaces. Here we introduce a method for the rapid and reproducible production of biocompatible, rigid, acrylic nanotopographic surfaces, and for the functionalization of the surfaces with adhesion-promoting molecules for cell experiments. The replica surfaces exhibit high optical transparency, which is advantageous for high-resolution, live-cell imaging. As a representative application, we demonstrate that epithelial cells form focal adhesions on surfaces composed of nanoscale ridges and grooves, and that the focal adhesions prefer to localize on the nanoridges. We further demonstrate that both F-actin and microtubules align along the nanoridges, but only F-actin aligns along the nanogrooves. The mass production of nanotopographic surfaces opens the door to the investigation of the effect of physical cues on the spatial distribution and the dynamics of intracellular proteins, and to the study of the mechanism of mechanosensing in processes such as cell migration, phagocytosis, division, and differentiation.
Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats
Authors: Khan Tariq Jamal , Ahmed Youssri M. , Zamzami Mazin A. , Mohamed Saleh A. , Khan Imran , Baothman Othman A. S. , Mehanna Mohamed G. , Yasir Muhammad 
Published: January 2018

AbstractThe aim of the present study was to investigate alterations in gut microbiota associated with hypercholesterolemia and treatment with atorvastatin, a commonly prescribed cholesterol-lowering drug. In this study, seven experimental groups of rats were developed based on diets [high-fat diet (HFD) and normal chow diet (NCD)] and various doses of atorvastatin in HFD and NCD groups. 16S rRNA amplicon sequencing was used to analyze the gut microbiota. Atorvastatin significantly reduced the cholesterol level in treated rats. Bacterial diversity was decreased in the drug-treated NCD group compared to the NCD control, but atorvastatin-treated HFD groups showed a relative increase in biodiversity compared to HFD control group. Atorvastatin promoted the relative abundance of Proteobacteria and reduced the abundance of Firmicutes in drug-treated HFD groups. Among the dominant taxa in the drug-treated HFD groups, Oscillospira, Parabacteroides, Ruminococcus, unclassified CF231, YRC22 (Paraprevotellaceae), and SMB53 (Clostridiaceae) showed reversion in population distribution toward NCD group relative to HFD group. Drug-treated HFD and NCD groups both showed an increased relative abundance of Helicobacter. Overall, bacterial community composition was altered, and diversity of gut microbiota increased with atorvastatin treatment in HFD group. Reversion in relative abundance of specific dominant taxa was observed with drug treatment to HFD rats.
Magnetic and structural properties of glass-coated Heusler-type microwires exhibiting martensitic transformation
Authors: Zhukov A. , Ipatov M. , del Val J. J. , Zhukova V. , Chernenko V. A. 
Published: January 2018

AbstractWe have studied magnetic and structural properties of the Heusler-type Ni-Mn-Ga glass-coated microwires prepared by Tailor-Ulitovsky technique. As-prepared sample presents magnetoresistance effect and considerable dependence of magnetization curves (particularly magnetization values) on magnetic field attributed to the magnetic and atomic disorder. Annealing strongly affects the temperature dependence of magnetization and Curie temperature of microwires. After annealing of the microwires at 973 K, the Curie temperature was enhanced to about 280 K which is beneficial for the magnetic solid state refrigeration. The observed hysteretic anomalies on the temperature dependences of resistance and magnetization in the as-prepared and annealed samples are produced by the martensitic transformation. The magnetoresistance and magnetocaloric effects have been investigated to illustrate a potential technological capability of studied microwires.