bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Assessment of Surface Markers on Cancer Cells Using Immuno-Magnetic Separation and Multi-frequency Impedance Cytometry for Targeted Therapy
Authors: Lin Zhongtian , Lin Siang-Yo , Xie Pengfei , Lin Chen-Yong , Rather Gulam M. , Bertino Joseph R. , Javanmard Mehdi 
Published: February 2020

AbstractThe rapid qualitative assessment of surface markers on cancer cells can allow for point-of-care prediction of patient response to various cancer drugs. Preclinical studies targeting cells with an antibody to “activated” matriptase conjugated to a potent toxin show promise as a selective treatment for a variety of solid tumors. In this paper, we implemented a novel technique for electrical detection of proteins on surfaces of cancer cells using multi-frequency microfluidic impedance cytometry. The biosensor, consists of two gold microelectrodes on a glass substrate embedded in a PDMS microfluidic channel, is used in conjugation with immuno-magnetic separation of cancer cells, and is capable of differentiating between bare magnetic beads, cancer cells and bead-cell aggregates based on their various impedance and frequency responses. We demonstrated proof-of-concept based on detection of “activated” matriptase proteins on the surface of cultured Mantle cells.
Modeling the allosteric modulation on a G-Protein Coupled Receptor: the case of M2 muscarinic Acetylcholine Receptor in complex with LY211960
Authors: Maggi L. , Carloni P. , Rossetti G. 
Published: February 2020

AbstractAllosteric modulation is involved in a plethora of diverse protein functions, which are fundamental for cells’ life. This phenomenon can be thought as communication between two topographically distinct site of a protein structure. How this communication occurs is still matter of debate. Many different descriptions have been presented so far. Here we consider a specific case where any significant conformational change is involved upon allosteric modulator binding and the phenomenon is depicted as a vibrational energy diffusion process between distant protein regions. We applied this model, by employing computational tools, to the human muscarinic receptor M2, a transmembrane protein G-protein coupled receptor known to undergo allosteric modulation whose recently X-ray structure has been recently resolved both with and without the presence of a particular allosteric modulator. Our calculations, performed on these two receptor structures, suggest that for this case the allosteric modulator modifies the energy current between functionally relevant regions of the protein; this allows to identify the main residues responsible for this modulation. These results contribute to shed light on the molecular basis of allosteric modulation and may help design new allosteric ligands.
Study on antibiotic susceptibility of Salmonella typhimurium L forms to the third and forth generation cephalosporins
Authors: Yang Cuiping , Li Huihui , Zhang Tao , Chu Yifan , Zuo Junli , Chen Dengyu 
Published: February 2020

AbstractSalmonella typhimurium is a pathogenic gram-negative bacterium, which is found primarily in the intestinal lumen. It often causes diarrhea in infants and young children and leads to food poisoning. Drug resistance of Salmonella typhimurium presented serious complications in clinical patients. In this study, we investigated the antibiotic susceptibility of Salmonella typhimurium standard strain L forms to the third and forth generation cephalosporins, in order to control and eliminate Salmonella typhimurium L forms in infection treatment. Salmonella typhimurium L forms were induced by β-lactam antibiotic cefazolin in the culture medium of bacterial L forms. The antibiotic susceptibility of Salmonella typhimurium L forms was analyzed by K-B drug susceptibility testing. The change trend of drug susceptibility and resistance of Salmonella typhimurium L forms was obtained in accordance with USA clinical and laboratory standards institute (CLSI) evaluation data and statistical analysis. Drug resistance of Salmonella typhimurium L forms showed little increasing trend compared with their parent bacteria. The L form inhibition zone was smaller than in the parent bacteria. However, the drug susceptibility of L forms of Salmonella typhimurium to the third and forth generation cephalosporins remained sensitive.The antibiotic susceptibility of Salmonella typhimurium L forms to the third and forth generation cephalosporins remains sensitive, and the combined use of multi-antibiotics is a convenient and effective method to reduce Salmonella typhimurium L forms occurrence.
c-di-GMP-related phenotypes are modulated by the interaction between a diguanylate cyclase and a polar hub protein
Authors: Nicastro Gianlucca G. , Kaihami Gilberto H. , Pulschen André A. , Hernandez-Montelongo Jacobo , Boechat Ana Laura , de Oliveira Pereira Thays , Rosa Caio Gomes Tavares , Stefanello Eliezer , Colepicolo Pio , Bordi Christophe , Baldini Regina L. 
Published: February 2020

Abstractc-di-GMP is a major player in the switch between biofilm and motile lifestyles. Several bacteria exhibit a large number of c-di-GMP metabolizing proteins, thus a fine-tuning of this nucleotide levels may occur. It is hypothesized that some c-di-GMP metabolizing proteins would provide the global c-di-GMP levels inside the cell whereas others would maintain a localized pool, with the resulting c-di-GMP acting at the vicinity of its production. Although attractive, this hypothesis has yet to be demonstrated in Pseudomonas aeruginosa. We found that the diguanylate cyclase DgcP interacts with the cytosolic region of FimV, a polar peptidoglycan-binding protein involved in type IV pilus assembly. Moreover, DgcP is located at the cell poles in wild type cells but scattered in the cytoplasm of cells lacking FimV. Overexpression of dgcP leads to the classical phenotypes of high c-di-GMP levels (increased biofilm and impaired motilities) in the wild-type strain, but not in a ΔfimV background. Therefore, our findings suggest that DgcP activity is regulated by FimV. The polar localization of DgcP might contribute to a local c-di-GMP pool that can be sensed by other proteins at the cell pole, bringing to light a specialized function for a specific diguanylate cyclase.
Genome-wide analysis of WRKY transcription factors in Aquilaria sinensis (Lour.) Gilg
Authors: Xu Yan-Hong , Sun Pei-Wen , Tang Xiao-Lin , Gao Zhi-Hui , Zhang Zheng , Wei Jian-He 
Published: February 2020

AbstractThe WRKY proteins are a superfamily of transcription factor that regulate diverse developmental and physiological processes in plants. Completion of the whole-genome sequencing of Aquilaria sinensis allowed us to perform a genome-wide investigation for WRKY proteins. Here, we predicted 70 WRKY genes from the A. sinensis genome and undertaken a comprehensive bioinformatic analysis. Due to their diverse structural features, the 70 AsWRKY genes are classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II, except two belong to none of them. Distinct expression profiles of AsWRKYs with RNA sequencing data revealed their diverse expression patterns among different tissues and in the process of whole-tree-inducing agarwood formation. Based on the expression characteristics, we predict some AsWRKYs are pseudogenes, and some may be involved in the biosynthesis of agarwood sesquiterpenes as activators or repressors. Among the tested genes treated with MeJA and H2O2, most of them are induced by H2O2, but downregulated by MeJA, implying the complexity of their involvement in signal transduction regulation. Our results not only provide a basic platform for functional identification of WRKYs in A. sinensis but important clues for further analysis their regulation role in agarwood formation.
Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms
Authors: Shirouzu Takashi , Matsuoka Shunsuke , Doi Hideyuki , Nagata Nobuaki , Ushio Masayuki , Hosaka Kentaro 
Published: February 2020

AbstractAmong terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis
Authors: Liu Zhang-Wei , Zhao Nan , Su Yin-Na , Chen Shan-Shan , He Xin-Jian 
Published: February 2020

AbstractInvolvement of long non-coding RNAs (lncRNAs) in the regulation of gene expression in cis has been well studied in eukaryotes but relatively little is known whether and how lncRNAs affect gene expression in tans. In Arabidopsis thaliana, COLDAIR, a previously reported lncRNA, is produced from the first intron of FLOWERING LOCUS C (FLC), which encodes a repressor of flowering time. Our results indicated that the exogenously overexpressed COLDAIR enhances the expression of FLC in trans, resulting in a late-flowering phenotype. In 35S-COLDAIR lines, the enhanced expression of FLC is correlated with the down-regulation of the repressive histone mark H3K27me3 and with the up-regulation of the active histone mark H3K4me3 at the FLC chromatin. Furthermore, we demonstrated that overexpression of intronic lncRNAs from several other H3K27me3-enriched MADS-box genes also activates the expression of their host genes. This study suggests that the involvement of overexpressed intronic lncRNAs in gene activation may be conserved in H3K27me3-enriched genes in eukaryotes.
An investigation of the long-range and local structure of sub-stoichiometric zirconium carbide sintered at different temperatures
Authors: Rana Dhan-sham B. K. , Solvas Eugenio Zapatas , Lee William E. , Farnan Ian 
Published: February 2020

AbstractZrC1−x(sub-stoichiometric zirconium carbide), a group IV transition metal carbide, is being considered for various high temperature applications. Departure from stoichiometry changes the thermo-physical response of the material. Reported thermo-physical properties exhibit, in some cases, a degree of scatter with one likely contributor to this being the uncertainty in the C/Zr ratio of the samples produced. Conventional, methods for assigning C/Zr to samples are determined either by nominal stochiometric ratios or combustion carbon analysis. In this study, a range of stoichiometries of hot-pressed ZrC1−xwere examined by SEM, XRD, Raman spectroscopy and static13C NMR spectroscopy and used as a basis to correct the C/Zr. Graphite, amorphous, and ZrC1−xcarbon signatures are observed in the13C NMR spectra of samples and are determined to vary in intensity with sintering temperature and stoichiometry. In this study a method is outlined to quantify the stoichiometry of ZrC1−xand free carbon phases, providing an improvement over the sole use and reliance of widely adopted bulk carbon combustion analysis. We report significantly lower C/Zr values determined by13C NMR analysis compared with carbon analyser and nominal methods. Furthermore, the location of carbon disassociated from the ZrC1−xstructure is analysed using SEM and Raman spectroscopy.
Giant Endoplasmic Reticulum vesicles (GERVs), a novel model membrane tool
Authors: Grimmer Mona , Bacia Kirsten 
Published: February 2020

AbstractArtificial giant vesicles have proven highly useful as membrane models in a large variety of biophysical and biochemical studies. They feature accessibility for manipulation and detection, but lack the compositional complexity needed to reconstitute complicated cellular processes. For the plasma membrane (PM), this gap was bridged by the establishment of giant PM vesicles (GPMVs). These native membranes have facilitated studies of protein and lipid diffusion, protein interactions, electrophysiology, fluorescence analysis of lateral domain formation and protein and lipid partitioning as well as mechanical membrane properties and remodeling. The endoplasmic reticulum (ER) is key to a plethora of biological processes in any eukaryotic cell. However, its intracellular location and dynamic and intricate tubular morphology makes it experimentally even less accessible than the PM. A model membrane, which will allow the afore-mentioned types of studies on GPMVs to be performed on ER membranes outside the cell, is therefore genuinely needed. Here, we introduce the formation of giant ER vesicles, termed GERVs, as a new tool for biochemistry and biophysics. To obtain GERVs, we have isolated ER membranes from Saccharomyces cerevisiae and fused them by exploiting the atlastin-like fusion protein Sey1p. We demonstrate the production of GERVs and their utility for further studies.
Inhibition of Porphyromonas gulae and periodontal disease in dogs by a combination of clindamycin and interferon alpha
Authors: Nomura Ryota , Inaba Hiroaki , Yasuda Hidemi , Shirai Mitsuyuki , Kato Yukio , Murakami Masaru , Iwashita Naoki , Shirahata So , Yoshida Sho , Matayoshi Saaya , Yasuda Junya , Arai Nobuaki , Asai Fumitoshi , Matsumoto-Nakano Michiyo , Nakano Kazuhiko 
Published: February 2020

AbstractPorphyromonas gulaeis a major periodontal pathogen in dogs, which can be transmitted to their owners. A major virulence factor ofP. gulaeconsists of a 41-kDa filamentous appendage (FimA) on the cell surface, which is classified into three genotypes: A, B, and C. Thus far, inhibition of periodontal disease in dogs remains difficult. The present study assessed the inhibitory effects of a combination of clindamycin and interferon alpha (IFN-α) formulation againstP. gulaeand periodontal disease. Growth ofP. gulaewas significantly inhibited by clindamycin; this inhibition had a greater effect on type CP. gulaethan on type A and B isolates. In contrast, the IFN-α formulation inhibited the expression of IL-1β and COX-2 elicited by type A and B isolates, but not that elicited by type C isolates. Furthermore, periodontal recovery was promoted by the administration of both clindamycin and IFN-α formulation to dogs undergoing periodontal treatment; moreover, this combined treatment reduced the number of FimA genotypes in oral specimens from treated dogs. These results suggest that a combination of clindamycin and IFN-α formulation inhibitP. gulaevirulence and thus may be effective for the prevention of periodontal disease induced byP. gulae.
Effect of bisphenol A on human neutrophils immunophenotype
Authors: Ratajczak-Wrona Wioletta , Rusak Małgorzata , Nowak Karolina , Dabrowska Milena , Radziwon Piotr , Jablonska Ewa 
Published: February 2020

AbstractNeutrophils (PMN) play a key role in eliciting congenital immune response. These cells are equipped with specific receptors that are located on the surface of their cell membrane. These receptors produce various signals which in turn help in the effective functioning of PMN. The activity of these cells may be modified by factors of endo- and exogenous origin, including xenoestrogens such as bisphenol A (BPA). The aim of this study was to evaluate the effect of BPA on the expression of CD11c, CD14, CD15, CD16, CD62L and CD284 compounds on the surface of neutrophils in women and men. The study material included PMN isolated from the whole blood. The cells were incubated in the presence of BPA and/or LPS. Flow cytometry technique was used to evaluate the expression of CD antigens. Studies of these receptors indicate that BPA, at a concentration corresponding to the serum level of this compound in healthy subjects as well as at higher doses, induces changes in the immunophenotype of PMN, which may lead to immunity disorders associated with the dysfunction of these cells. Moreover, the observed effects of xenoestrogen on the expression of CD11c, CD14, CD15, CD16, CD62L and CD284 differentiation markers on these cells are sex-independent.
The effects of electroporation buffer composition on cell viability and electro-transfection efficiency
Authors: Sherba Joseph J. , Hogquist Stephen , Lin Hao , Shan Jerry W. , Shreiber David I. , Zahn Jeffrey D. 
Published: February 2020

AbstractElectroporation is an electro-physical, non-viral approach to perform DNA, RNA, and protein transfections of cells. Upon application of an electric field, the cell membrane is compromised, allowing the delivery of exogenous materials into cells. Cell viability and electro-transfection efficiency (eTE) are dependent on various experimental factors, including pulse waveform, vector concentration, cell type/density, and electroporation buffer properties. In this work, the effects of buffer composition on cell viability and eTE were systematically explored for plasmid DNA encoding green fluorescent protein following electroporation of 3T3 fibroblasts. A HEPES-based buffer was used in conjunction with various salts and sugars to modulate conductivity and osmolality, respectively. Pulse applications were chosen to maintain constant applied electrical energy (J) or total charge flux (C/m2). The energy of the pulse application primarily dictated cell viability, with Mg2+-based buffers expanding the reversible electroporation range. The enhancement of viability with Mg2+-based buffers led to the hypothesis that this enhancement is due to ATPase activation via re-establishing ionic homeostasis. We show preliminary evidence for this mechanism by demonstrating that the enhanced viability is eliminated by introducing lidocaine, an ATPase inhibitor. However, Mg2+ also hinders eTE compared to K+-based buffers. Collectively, the results demonstrate that the rational selection of pulsing conditions and buffer compositions are critical for the design of electroporation protocols to maximize viability and eTE.
Rational design of novel benzisoxazole derivatives with acetylcholinesterase inhibitory and serotoninergic 5-HT4 receptors activities for the treatment of Alzheimer’s disease
Authors: Lalut Julien , Payan Hugo , Davis Audrey , Lecoutey Cédric , Legay Rémi , Sopkova-de Oliveira Santos Jana , Claeysen Sylvie , Dallemagne Patrick , Rochais Christophe 
Published: February 2020

AbstractA rigidification strategy was applied to the preclinical candidate donecopride, an acetylcholinesterase inhibitor possessing 5-HT4R agonist activity. Inspired by promising bioactive benzisoxazole compounds, we have conducted a pharmacomodulation study to generate a novel series of multitarget directed ligands. The chemical synthesis of the ligand was optimized and compounds were evaluated in vitro against each target and in cellulo. Structure-activity relationship was supported by docking analysis in human acetylcholinesterase binding site. Among the synthesized compounds, we have identified a novel hybrid 32a (3-[2-[1-(cyclohexylmethyl)-4-piperidyl]ethyl]-4-methoxy-1,2-benzoxazole) able to display nanomolar acetylcholinesterase inhibitory effects and nanomolar Ki for 5-HT4R.
Protective Effect of Statins on Pulmonary Hypertension in Chronic Obstructive Pulmonary Disease Patients: A Nationwide Retrospective, Matched Cohort Study
Authors: Wu Wen-Ting , Chen Chung-Yu 
Published: February 2020

AbstractIn Taiwan, patients with pulmonary hypertension (PH) related to chronic obstructive pulmonary disease (COPD) are most common PH population (group 3). However, efficacy of medical treatments and optimal prevention methods in this group remain uncertain. Statins such as indirect RhoA/Rho-kinase inhibitors influence one of key signalling pathways that promote PH onset. In this study, we explored protective effects of statins against PH in COPD patients using database from Taiwan National Health Insurance programme from 2002 to 2017. The main outcome was the risk of PH. The Cox proportional-hazards model and the Fine and Gray model were used to adjust covariate and competing risks to estimate the subdistribution hazard ratios (sHRs). 553,617 newly diagnosed COPD patients were stratified by statin users (n = 41,168) and statin nonusers (n = 512,449). After 1:1 propensity score matching of statin users (n = 41,163), and 41,163 statin nonusers were included for outcome analysis. Statin users had a 22% lower risk of PH than nonusers (sHR: 0.78, 95% confidence interval: 0.65–0.94). During subgroup analysis, taking higher daily doses and for a longer duration displayed a more significantly reduced risk of PH (both P for trend <0.001). Statins may have a protective effect against PH that is dose- and time-dependent.
Electrophysiological and behavioural response of Philaenus spumarius to essential oils and aromatic plants
Authors: Ganassi Sonia , Cascone Pasquale , Domenico Carmela Di , Pistillo Marco , Formisano Giorgio , Giorgini Massimo , Grazioso Pasqualina , Germinara Giacinto S. , Cristofaro Antonio De , Guerrieri Emilio 
Published: February 2020

AbstractThe meadow spittlebug, Philaenus spumarius, is a highly polyphagous widespread species, playing a major role in the transmission of the bacterium Xylella fastidiosa subspecies pauca, the agent of the “Olive Quick Decline Syndrome”. Essential oils (EOs) are an important source of bio-active volatile compounds that could interfere with basic metabolic, biochemical, physiological, and behavioural functions of insects. Here, we report the electrophysiological and behavioural responses of adult P. spumarius towards some EOs and related plants. Electroantennographic tests demonstrated that the peripheral olfactory system of P. spumarius females and males perceives volatile organic compounds present in the EOs of Pelargonium graveolens, Cymbopogon nardus and Lavandula officinalis in a dose-dependent manner. In behavioral bioassays, evaluating the adult responses towards EOs and related plants, both at close (Y-tube) and long range (wind tunnel), males and females responded differently to the same odorant. Using EOs, a clear attraction was noted only for males towards lavender EO. Conversely, plants elicited responses that varied upon the plant species, testing device and adult sex. Both lavender and geranium repelled females at any distance range. On the contrary, males were attracted by geranium and repelled by citronella. Finally, at close distance, lavender and citronella were repellent for females and males, respectively. Our results contribute to the development of innovative tools and approaches, alternative to the use of synthetic pesticides, for the sustainable control of P. spumarius aiming to contrasting the expansion of X. fastidiosa.