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https://www.readbyqxmd.com/read/28637351/tuning-surface-chemistry-of-polyetheretherketone-by-gold-coating-and-plasma-treatment
#1
Zdeňka Novotná, Silvie Rimpelová, Petr Juřík, Martin Veselý, Zdeňka Kolská, Tomáš Hubáček, Jakub Borovec, Václav Švorčík
Polyetheretherketone (PEEK) has good chemical and biomechanical properties that are excellent for biomedical applications. However, PEEK exhibits hydrophobic and other surface characteristics which cause limited cell adhesion. We have investigated the potential of Ar plasma treatment for the formation of a nanostructured PEEK surface in order to enhance cell adhesion. The specific aim of this study was to reveal the effect of the interface of plasma-treated and gold-coated PEEK matrices on adhesion and spreading of mouse embryonic fibroblasts...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28637337/matrix-completion-with-side-information-and-its-applications-in-predicting-the-antigenicity-of-influenza-viruses
#2
Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang
Motivation: Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition (HI) table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637320/biological-functions-based-on-protein-interplays
#3
Jiarui Wu
No abstract text is available yet for this article.
June 1, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28637316/incorporating-comparative-genomics-into-the-design-test-learn-cycle-of-microbial-strain-engineering
#4
Maria Sardi, Audrey P Gasch
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals, and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling, and regulatory rewiring have proven to significantly advance industrial strain engineering...
June 16, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#5
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637286/structure-seq2-sensitive-and-accurate-genome-wide-profiling-of-rna-structure-in-vivo
#6
Laura E Ritchey, Zhao Su, Yin Tang, David C Tack, Sarah M Assmann, Philip C Bevilacqua
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage...
June 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637276/repetitive-element-transcripts-are-elevated-in-the-brain-of-c9orf72-als-ftld-patients
#7
Mercedes Prudencio, Patrick K Gonzales, Casey N Cook, Tania F Gendron, Lillian M Daughrity, Yuping Song, Mark T W Ebbert, Marka van Blitterswijk, Yong-Jie Zhang, Karen Jansen-West, Matthew C Baker, Michael DeTure, Rosa Rademakers, Kevin B Boylan, Dennis W Dickson, Leonard Petrucelli, Christopher D Link
Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analyzed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls...
June 16, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28637261/further-simulations-and-analyses-demonstrate-open-problems-of-phylostratigraphy
#8
Bryan A Moyers, Jianzhi Zhang
Phylostratigraphy, originally designed for gene age estimation by BLAST-based protein homology searches of sequenced genomes, has been widely used for studying patterns and inferring mechanisms of gene origination and evolution. We previously showed by computer simulation that phylostratigraphy underestimates gene age for a non-negligible fraction of genes and that the underestimation is severer for genes with certain properties such as fast evolution and short protein sequences. Consequently, many previously reported age distributions of gene properties may have been methodological artifacts rather than biological realities...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28637221/digital-direct-detection-of-micrornas-using-single-molecule-arrays
#9
Limor Cohen, Mark R Hartman, Aaron Amardey-Wellington, David R Walt
MicroRNAs (miRNAs) are involved in many biological pathways, and detecting miRNAs accurately is critical for diagnosing a variety of diseases including cancer. However, most current methods for miRNA detection require lengthy sample preparation and amplification steps that can bias the results. In addition, lack of specificity and reproducibility give rise to various challenges in detection of circulating miRNAs in biological samples. In this work, we applied the Single Molecule Array (Simoa) technique to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637164/biological-nutrient-removal-and-molecular-biological-characteristics-in-an-anaerobic-multistage-anaerobic-oxic-a-mao-process-to-treat-municipal-wastewater
#10
Xiao Huang, Wenyi Dong, Hongjie Wang, Shilong Jiang
This study aimed to present an anaerobic-multistage anaerobic/oxic (A-MAO) process to treat municipal wastewater. The average COD, NH4(+)-N, TN, and TP removal efficiency were 91.81%, 96.26%, 83.73% and 94.49%, respectively. Temperature plunge and C/N decrease have a certain impact on the modified process. Characteristics of microbial community, function microorganism, and correlation of microbial community with environmental variables in five compartments were carried out by Illumina Miseq high-throughput sequencing...
May 29, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28637048/use-of-light-therapy-by-office-based-physicians
#11
Edda Winkler-Pjrek, Marie Spies, Pia Baldinger-Melich, Lisa Perkmann, Siegfried Kasper, Dietmar Winkler
BACKGROUND: Light therapy (LT) is a non-pharmacological biological treatment that has been used in psychiatry since the 1980s. Previous research has investigated the usage of LT in hospitals. The aim of this study was to examine the pattern of use of LT by office-based physicians. METHODS: A questionnaire was sent by mail to 400 randomly selected doctors in Austria. We made sure that the sample was equally representative of general practitioners (GPs) and psychiatrists, public health service doctors and private doctors, physicians in cities and in the country as well as male and female doctors...
June 22, 2017: Neuropsychobiology
https://www.readbyqxmd.com/read/28637027/phospho-axl-is-widely-expressed-in-glioblastoma-and-associated-with-significant-shorter-overall-survival
#12
Julia Onken, Peter Vajkoczy, Robert Torka, Claudia Hempt, Victor Patsouris, Frank L Heppner, Josefine Radke
Receptor tyrosine kinase AXL (RTK-AXL) is regarded as a suitable target in glioblastoma (GBM) therapy. Since AXL kinase inhibitors are about to get approval for clinical use, patients with a potential benefit from therapy targeting AXL need to be identified. We therefore assessed the expression pattern of Phospho-AXL (P-AXL), the biologically active form of AXL, in 90 patients with newly diagnosed GBM, which was found to be detectable in 67 patients (corresponding to 74%). We identified three main P-AXL expression patterns: i) exclusively in the tumor vasculature (13%), ii) in areas of hypercellularity (35%), or iii) both, in the tumor vasculature and in hypercellular areas of the tumor tissue (52%)...
June 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28637017/diagnostic-and-prognostic-values-of-cerebrospinal-fluid-cyfra-21-1-in-patients-with-leptomeningeal-carcinomatosis
#13
Jae-Won Hyun, Ji Hyun Park, Boo Gil Kang, Eun Young Park, Boram Park, Jungnam Joo, Jong Kuk Kim, Su-Hyun Kim, Jee Hyang Jeong, Hyang Woon Lee, Kee Duk Park, Kyung Gyu Choi, Sang-Hyun Hwang, Ho-Shin Gwak, Ho Jin Kim
OBJECTIVES: To investigate the diagnostic and prognostic values of cerebrospinal fluid (CSF) CYFRA 21-1 in patients with leptomeningeal carcinomatosis (LMC). METHODS: Concentration of CSF CYFRA 21-1 was detected using electro-chemiluminescent immunoassay. The difference in level of CYFRA 21-1 between 61 patients with LMC and 200 patients with other neurological disease was evaluated, and diagnostic performance of CSF CYFRA 21-1 was investigated. In LMC patients treated with ventriculo-lumbar perfusion (VLP) chemotherapy, prognostic performance of CSF CYFRA 21-1 was evaluated...
June 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636987/combination-of-calr-and-pdia3-is-a-potential-prognostic-biomarker-for-non-small-cell-lung-cancer
#14
Ke Wang, Hao Li, Ruo Chen, Yang Zhang, Xiu-Xuan Sun, Wan Huang, Huijie Bian, Zhi-Nan Chen
Proteomic-based approaches for biomarker discovery are promising strategies used in cancer research. In this study, we performed quantitative proteomic analysis on 16 paired samples of non-small cell lung cancer (NSCLC) and adjacent non-tumor lung tissues using label-free quantitative proteomics and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS) to identify differentially expressed proteins. A total of 91 proteins were differentially expressed in NSCLC compared with adjacent non-tumor lung tissues among 4047 identified proteins (fold change > 1...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636950/structural-evidence-of-quercetin-multi-target-bioactivity-a-reverse-virtual-screening-strategy
#15
Diego Carvalho, Margot Paulino, Fabio Polticelli, Florencia Arredondo, Robert J Williams, Juan A Abin-Carriquiry
The ubiquitous flavonoid quercetin is broadly recognized for showing diverse biological and health-promoting effects, such as anti-cancer, anti-inflammatory and cytoprotective activities. The therapeutic potential of quercetin and similar compounds for preventing such diverse oxidative stress-related pathologies has been generally attributed to their direct antioxidant properties. Nevertheless, accumulated evidence indicates that quercetin is also able to interact with multiple cellular targets influencing the activity of diverse signaling pathways...
June 18, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28636948/pten%C3%AE-modulates-camkii-signaling-and-controls-contextual-fear-memory-and-spatial-learning
#16
Pan Wang, Fan Mei, Jiapan Hu, Minglu Zhu, Hailong Qi, Xi Chen, Ruiqi Li, Michael A McNutt, Yuxin Yin
PTEN (phosphatase and tensin homology deleted on chromosome 10) has multiple functions, and recent studies have shown that the PTEN family has isoforms. The roles of these PTEN family members in biologic activities warrant specific evaluation. Here, we show that PTENα maintains CaMKII in a state that is competent to induce long-term potentiation (LTP) with resultant regulation of contextual fear memory and spatial learning. PTENα binds to CaMKII with its distinctive N terminus and resets CaMKII to an activatable state by dephosphorylating it at sites T305/306...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636946/ptbp2-controls-an-alternative-splicing-network-required-for-cell-communication-during-spermatogenesis
#17
Molly M Hannigan, Leah L Zagore, Donny D Licatalosi
Alternative splicing has essential roles in development. Remarkably, spermatogenic cells express more alternatively spliced RNAs compared to most whole tissues; however, regulation of these RNAs remains unclear. Here, we characterize the alternative splicing landscape during spermatogenesis and reveal an essential function for the RNA-binding protein Ptbp2 in this highly regulated developmental program. We found that Ptbp2 controls a network of genes involved in cell adhesion, migration, and polarity, suggesting that splicing regulation by Ptbp2 is critical for germ cell communication with Sertoli cells (multifunctional somatic cells necessary for spermatogenesis)...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636920/nanog-fluctuations-in-embryonic-stem-cells-highlight-the-problem-of-measurement-in-cell-biology
#18
Rosanna C G Smith, Patrick S Stumpf, Sonya J Ridden, Aaron Sim, Sarah Filippi, Heather A Harrington, Ben D MacArthur
A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, pluripotency. However, because temporal changes in intracellular protein abundances cannot be measured directly in live cells, fluctuations are typically assessed using genetically engineered reporter cell lines that produce a fluorescent signal as a proxy for protein expression...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#19
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636874/next-generation-matrix-metalloproteinase-inhibitors-novel-strategies-bring-new-prospects
#20
REVIEW
Maxim Levin, Yael Udi, Inna Solomonov, Irit Sagi
Enzymatic proteolysis of cell surface proteins and extracellular matrix (ECM) is critical for tissue homeostasis and cell signaling. These proteolytic activities are mediated predominantly by a family of proteases termed matrix metalloproteinases (MMPs). The growing evidence in recent years that ECM and non-ECM bioactive molecules (e.g., growth factors, cytokines, chemokines, on top of matrikines and matricryptins) have versatile functions redefines our view on the roles matrix remodeling enzymes play in many physiological and pathological processes, and underscores the notion that ECM proteolytic reaction mechanisms represent master switches in the regulation of critical biological processes and govern cell behavior...
June 18, 2017: Biochimica et Biophysica Acta
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