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https://www.readbyqxmd.com/read/29454082/a-straightforward-sted-background-corrected-fitting-model-for-unbiased-sted-fcs-analyses
#1
Ruixing Wang, Sophie Brustlein, Sébastien Mailfert, Roxane Fabre, Mathieu Fallet, Siddharth Sivankutty, Hervé Rigneault, Didier Marguet
Combining stimulated emission depletion and fluorescence correlation spectroscopy (STED-FCS) provides a powerful and sensitive tool for studying the molecular dynamics in live cells with high spatio-temporal resolution. STED-FCS gives access to molecular diffusion characteristic at the nanoscale occurring within short period of times. However due to the incomplete suppression of fluorescence in the STED process, the STED-FCS point spread function (PSF) deviates from a Gaussian shape and challenges the analysis of the auto-correlation curves obtained by FCS...
February 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29453916/distinguishing-smilax-glabra-and-smilax-china-rhizomes-by-flow-injection-mass-spectrometry-combined-with-principal-component-analysis
#2
Jian Liang, Meng Zhou, Lin-Yu Li, Ji-Cheng Shu, Yong-Hong Liang, Feng-Qin Li, Li Xiong, Hui-Lian Huang
Flow-injection mass spectrometry (FIMS) coupled with a chemometric method is proposed in this study to profile and distinguish between rhizomes of Smilax glabra (S. glabra) and Smilax china (S. china). The proposed method employed an electrospray-time-of-flight MS. The MS fingerprints were analyzed using principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) with the aid of SIMCA software. Findings showed that the two kinds of samples perfectly fell into their own classes...
March 1, 2018: Acta Pharmaceutica
https://www.readbyqxmd.com/read/29453747/clinical-applications-of-patient-specific-models-the-case-for-a-simple-approach
#3
Jeffrey W Holmes, Joost Lumens
Over the past several decades, increasingly sophisticated models of the heart have provided important insights into cardiac physiology and are increasingly used to predict the impact of diseases and therapies on the heart. In an era of personalized medicine, many envision patient-specific computational models as a powerful tool for personalizing therapy. Yet the complexity of current models poses important challenges, including identifying model parameters and completing calculations quickly enough for routine clinical use...
February 16, 2018: Journal of Cardiovascular Translational Research
https://www.readbyqxmd.com/read/29453636/assessment-of-oximetry-based-statistical-classifiers-as-simplified-screening-tools-in-the-management-of-childhood-obstructive-sleep-apnea
#4
Andrea Crespo, Daniel Álvarez, Leila Kheirandish-Gozal, Gonzalo C Gutiérrez-Tobal, Ana Cerezo-Hernández, David Gozal, Roberto Hornero, Félix Del Campo
PURPOSE: A variety of statistical models based on overnight oximetry has been proposed to simplify the detection of children with suspected obstructive sleep apnea syndrome (OSAS). Despite the usefulness reported, additional thorough comparative analyses are required. This study was aimed at assessing common binary classification models from oximetry for the detection of childhood OSAS. METHODS: Overnight oximetry recordings from 176 children referred for clinical suspicion of OSAS were acquired during in-lab polysomnography...
February 16, 2018: Sleep & Breathing, Schlaf & Atmung
https://www.readbyqxmd.com/read/29453616/laser-induced-plasma-spectroscopy-lips-use-of-a-geological-tool-in-assessing-bone-mineral-content
#5
László Andrássy, Izabella Gomez, Ágnes Horváth, Katalin Gulyás, Zsófia Pethö, Balázs Juhász, Harjit Pal Bhattoa, Zoltan Szekanecz
Bone may be similar to geological formulations in many ways. Therefore, it may be logical to apply laser-based geological techniques in bone research. The mineral and element oxide composition of bioapatite can be estimated by mathematical models. Laser-induced plasma spectrometry (LIPS) has long been used in geology. This method may provide a possibility to determine the composition and concentration of element oxides forming the inorganic part of bones. In this study, we wished to standardize the LIPS technique and use mathematical calculations and models in order to determine CaO distribution and bone homogeneity using bovine shin bone samples...
February 17, 2018: Lasers in Medical Science
https://www.readbyqxmd.com/read/29453537/toxicogenomics-a-new-paradigm-for-nanotoxicity-evaluation
#6
Sourabh Dwivedi, Quaiser Saquib, Bilal Ahmad, Sabiha M Ansari, Ameer Azam, Javed Musarrat
The wider applications of nanoparticles (NPs) has evoked a world-wide concern due to their possible risk of toxicity in humans and other organisms. Aggregation and accumulation of NPs into cell leads to their interaction with biological macromolecules including proteins, nucleic acids and cellular organelles, which eventually induce toxicological effects. Application of toxicogenomics to investigate molecular pathway-based toxicological consequences has opened new vistas in nanotoxicology research. Indeed, genomic approaches appeared as a new paradigm in terms of providing information at molecular levels and have been proven to be as a powerful tool for identification and quantification of global shifts in gene expression...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29453127/generation-of-d1-1-talen-isogenic-control-cell-line-from-dravet-syndrome-patient-ipscs-using-talen-mediated-editing-of-the-scn1a-gene
#7
Yasuyoshi Tanaka, Takefumi Sone, Norimichi Higurashi, Tetsushi Sakuma, Sadafumi Suzuki, Mitsuru Ishikawa, Takashi Yamamoto, Jun Mitsui, Hitomi Tsuji, Hideyuki Okano, Shinichi Hirose
Dravet syndrome (DS) is an infantile epileptic encephalopathy mainly caused by de novo mutations in the SCN1A gene encoding the α1 subunit of the voltage-gated sodium channel Na v 1.1. As an in vitro model of this disease, we previously generated an induced pluripotent stem cell (iPSC) line from a patient with DS carrying a c.4933C>T (p.R1645*) substitution in SCN1A. Here, we describe developing a genome-edited control cell line from this DS iPSC line by substituting the point mutation with the wild-type residue...
February 2, 2018: Stem Cell Research
https://www.readbyqxmd.com/read/29453056/biological-properties-of-beet-soil-borne-mosaic-virus-and-beet-necrotic-yellow-vein-virus-cdna-clones-produced-by-isothermal-in-vitro-recombination-insights-for-reassortant-appearance
#8
Marlene Laufer, Hamza Mohammad, Edgar Maiss, Katja Richert-Pöggeler, Mattia Dall'Ara, Claudio Ratti, David Gilmer, Sebastian Liebe, Mark Varrelmann
Two members of the Benyviridae family and genus Benyvirus, Beet soil-borne mosaic virus (BSBMV) and Beet necrotic yellow vein virus (BNYVV), possess identical genome organization, host range and high sequence similarity; they infect Beta vulgaris with variable symptom expression. In the US, mixed infections are described with limited information about viral interactions. Vectors suitable for agroinoculation of all genome components of both viruses were constructed by isothermal in vitro recombination. All 35S promoter-driven cDNA clones allowed production of recombinant viruses competent for Nicotiana benthamiana and Beta macrocarpa systemic infection and Polymyxa betae transmission and were compared to available BNYVV B-type clone...
February 13, 2018: Virology
https://www.readbyqxmd.com/read/29453008/forensic-image-analysis-cctv-distortion-and-artefacts
#9
REVIEW
Dilan Seckiner, Xanthé Mallett, Claude Roux, Didier Meuwly, Philip Maynard
As a result of the worldwide deployment of surveillance cameras, authorities have gained a powerful tool that captures footage of activities of people in public areas. Surveillance cameras allow continuous monitoring of the area and allow footage to be obtained for later use, if a criminal or other act of interest occurs. Following this, a forensic practitioner, or expert witness can be required to analyse the footage of the Person of Interest. The examination ultimately aims at evaluating the strength of evidence at source and activity levels...
February 6, 2018: Forensic Science International
https://www.readbyqxmd.com/read/29452171/evolution-of-model-specific-relative-growth-rate-its-genesis-and-performance-over-fisher-s-growth-rates
#10
Arijit Pal, Amiya Ranjan Bhowmick, Farhana Yeasmin, Sabyasachi Bhattacharya
Growth curve models play an instrumental role to quantify the growth of biological processes and have immense practical applications across disciplines. In the modelling approach, the absolute growth rate and relative growth rate (RGR) are two most commonly used measures of growth rates. RGR is empirically estimated by Fisher (1921) assuming exponential growth between two consecutive time points and remains invariant under any choice of the underlying growth model. In this article, we propose a new measure of RGR, called modified RGR, which is sensitive to the choice of underlying growth law...
February 13, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29451855/in-vivo-labeling-by-cd73-marks-multipotent-stromal-cells-and-highlights-endothelial-heterogeneity-in-the-bone-marrow-niche
#11
Martin Breitbach, Kenichi Kimura, Tiago C Luis, Christopher J Fuegemann, Petter S Woll, Michael Hesse, Raffaella Facchini, Sarah Rieck, Katarzyna Jobin, Julia Reinhardt, Osamu Ohneda, Daniela Wenzel, Caroline Geisen, Christian Kurts, Wolfgang Kastenmüller, Michael Hölzel, Sten E W Jacobsen, Bernd K Fleischmann
Despite much work studying ex vivo multipotent stromal cells (MSCs), the identity and characteristics of MSCs in vivo are not well defined. Here, we generated a CD73-EGFP reporter mouse to address these questions and found EGFP + MSCs in various organs. In vivo, EGFP + mesenchymal cells were observed in fetal and adult bones at proliferative ossification sites, while in solid organs EGFP + cells exhibited a perivascular distribution pattern. EGFP + cells from the bone compartment could be clonally expanded ex vivo from single cells and displayed trilineage differentiation potential...
February 1, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29451771/structural-transformation-of-wireframe-dna-origami-via-dna-polymerase-assisted-gap-filling
#12
Nayan P Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L Schmidt
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions...
February 16, 2018: ACS Nano
https://www.readbyqxmd.com/read/29451433/populations-of-phytophthora-rubi-show-little-differentiation-and-high-rates-of-migration-among-states-in-the-western-united-states
#13
Javier F Tabima, Michael D Coffey, Inga Zasada, Niklaus J Grünwald
Population genetics is a powerful tool to understand patterns and evolutionary processes that are involved in plant pathogen emergence and adaptation to agricultural ecosystems. We are interested in studying the population dynamics of Phytophthora rubi, the causal agent of Phytophthora root rot in raspberry. P. rubi is found in the western U.S., where the majority of the fresh and processed raspberries are produced. We used genotyping-by-sequencing to characterize genetic diversity in populations of P. rubi sampled in the U...
February 16, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29451371/young-s-modulus-and-load-complexity-modeling-their-effects-on-proximal-femur-strain
#14
Adam D Sylvester, Patricia A Kramer
Finite element analysis (FEA) is a powerful tool for evaluating questions of functional morphology, but the application of FEA to extant or extinct creatures is a non-trivial task. Three categories of input data are needed to appropriately implement FEA: geometry, material properties, and boundary conditions. Geometric data are relatively easily obtained from imaging techniques, but often material properties and boundary conditions must be estimated. Here we conduct sensitivity analyses of the effect of the choice of Young's Modulus for elements representing trabecular bone and muscle loading complexity on the proximal femur using a finite element mesh of a modern human femur...
February 16, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/29450999/%C3%AE-functionalization-of-2-vinylpyridines-via-a-chiral-phosphine-catalyzed-enantioselective-cross-rauhut-currier-reaction
#15
Cong Qin, Yonghai Liu, Yang Yu, Yiwei Fu, Hao Li, Wei Wang
Herein, 2-vinylpyridines as a new type of electron-poor system for the asymmetric cross Rauhut-Currier reaction are reported. 2-Vinylpyridines are chemo- and enantioselectively activated by a newly designed chiral phosphine catalyst. The new reaction provides a powerful synthetic tool for accessing structurally diverse, highly valued chiral pyridine building blocks in good yields and with high enantioselectivities. Preliminary mechanistic studies reveal that two NH protons in the catalyst are critical for the synergistic activation of the substrates and governing the stereoselectivity of this reaction...
February 16, 2018: Organic Letters
https://www.readbyqxmd.com/read/29449966/raman-spectroscopic-imaging-for-quantification-of-depth-dependent-and-local-heterogeneities-in-native-and-engineered-cartilage
#16
M B Albro, M S Bergholt, J P St-Pierre, A Vinals Guitart, H M Zlotnick, E G Evita, M M Stevens
Articular cartilage possesses a remarkable, mechanically-robust extracellular matrix (ECM) that is organized and distributed throughout the tissue to resist physiologic strains and provide low friction during articulation. The ability to characterize the make-up and distribution of the cartilage ECM is critical to both understand the process by which articular cartilage undergoes disease-related degeneration and to develop novel tissue repair strategies to restore tissue functionality. However, the ability to quantitatively measure the spatial distribution of cartilage ECM constituents throughout the tissue has remained a major challenge...
2018: NPJ Regenerative Medicine
https://www.readbyqxmd.com/read/29449881/a-copper-controlled-rna-interference-system-for-reversible-silencing-of-target-genes-in-trichoderma-reesei
#17
Lei Wang, Fanglin Zheng, Weixin Zhang, Yaohua Zhong, Guanjun Chen, Xiangfeng Meng, Weifeng Liu
Background: Trichoderma reesei is a primary lignocellulosic enzyme producer in industry. However, the mechanisms underlying cellulase synthesis as well as other physiological processes are insufficiently understood partly due to the sophisticated process for its genetic manipulation. Target gene knockdown by RNA interference (RNAi) is a powerful tool for genetic research and biotechnology in eukaryotes including filamentous fungi. Previously reported RNAi system in T. reesei was either uncontrollable or only applicable in certain nutrition state...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29449872/citizen-crowds-and-experts-observer-variability-in-image-based-plant-phenotyping
#18
M Valerio Giuffrida, Feng Chen, Hanno Scharr, Sotirios A Tsaftaris
Background: Image-based plant phenotyping has become a powerful tool in unravelling genotype-environment interactions. The utilization of image analysis and machine learning have become paramount in extracting data stemming from phenotyping experiments. Yet we rely on observer (a human expert) input to perform the phenotyping process. We assume such input to be a 'gold-standard' and use it to evaluate software and algorithms and to train learning-based algorithms. However, we should consider whether any variability among experienced and non-experienced (including plain citizens) observers exists...
2018: Plant Methods
https://www.readbyqxmd.com/read/29449377/haploid-embryonic-stem-cells-can-be-enriched-and-maintained-by-simple-filtration
#19
Chao Qu, Meng Yan, Suming Yang, Lingbo Wang, Qi Yin, Yuan Liu, Yeguang Chen, Jinsong Li
Haploid mammalian embryonic stem cells (haESCs) serve as a powerful tool for genetic analyses at both cellular and organismal levels. However, spontaneous diploidization of haESCs limits their use in these analyses. Addition of small molecules to culture medium to control the cell cycle can slow down diploidization, but cell-sorting methods such as FACS are still required to enrich haploid cells for long-term maintenance in vitro. Here, acting on our observation that haploid and diploidized cells differ in diameter, we developed a simplified filtration method to enrich haploid cells from cultured haESCs...
February 15, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29448938/comparative-genomic-analysis-of-ten-clinical-streptococcus-pneumoniae-collected-from-a-malaysian-hospital-reveal-31-new-unique-drug-resistant-snps-using-whole-genome-sequencing
#20
Hassan Mahmood Jindal, Babu Ramanathan, Cheng Foh Le, Ranganath Gudimella, Rozaimi Razali, Rishya Manikam, Shamala Devi Sekaran
BACKGROUND: Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. METHODS: In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics...
February 15, 2018: Journal of Biomedical Science
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