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https://www.readbyqxmd.com/read/28811607/localized-iron-accumulation-precedes-nucleation-and-growth-of-magnetite-crystals-in-magnetotactic-bacteria
#1
Jacques Werckmann, Jefferson Cypriano, Christopher T Lefèvre, Kassiogé Dembelé, Ovidiu Ersen, Dennis A Bazylinski, Ulysses Lins, Marcos Farina
Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles that originate from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here we address the question: can iron transported inside MTB for the production of magnetite crystals be spatially mapped using electron microscopy? Cultured and uncultured MTB from brackish and freshwater lagoons were studied using analytical transmission electron microscopy in an attempt to answer this question...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28809978/phase-separation-dynamics-of-polydisperse-colloids-a-mean-field-lattice-gas-theory
#2
Pablo de Castro, Peter Sollich
New insights into phase separation in colloidal suspensions are provided via a dynamical theory based on the polydisperse lattice-gas model. The model gives a simplified description of polydisperse colloids, incorporating a hard-core repulsion combined with polydispersity in the strength of the attraction between neighbouring particles. Our mean-field equations describe the local concentration evolution for each of an arbitrary number of species, and for an arbitrary overall composition of the system. We focus on the predictions for the dynamics of colloidal gas-liquid phase separation after a quench into the coexistence region...
August 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28808136/eplant-visualizing-and-exploring-multiple-levels-of-data-for-hypothesis-generation-in-plant-biology
#3
Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence Kelley, Michael Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J Provart
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data, and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis data through a zoomable user interface...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28808016/hydrodynamics-of-microbial-filter-feeding
#4
Lasse Tor Nielsen, Seyed Saeed Asadzadeh, Julia Dölger, Jens H Walther, Thomas Kiørboe, Anders Andersen
Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807817/assessment-of-glutathione-glutathione-disulphide-ratio-and-s-glutathionylated-proteins-in-human-blood-solid-tissues-and-cultured-cells
#5
REVIEW
Daniela Giustarini, Graziano Colombo, Maria Lisa Garavaglia, Emanuela Astori, Nicola Marcello Portinaro, Francesco Reggiani, Salvatore Badalamenti, Anna Maria Aloisi, Annalisa Santucci, Ranieri Rossi, Aldo Milzani, Isabella Dalle-Donne
Glutathione (GSH) is the major non-protein thiol in humans and other mammals, which is present in millimolar concentrations within cells, but at much lower concentrations in the blood plasma. GSH and GSH-related enzymes act both to prevent oxidative damage and to detoxify electrophiles. Under oxidative stress, two GSH molecules become linked by a disulphide bridge to form glutathione disulphide (GSSG). Therefore, assessment of the GSH/GSSG ratio may provide an estimation of cellular redox metabolism. Current evidence resulting from studies in human blood, solid tissues, and cultured cells suggests that GSH also plays a prominent role in protein redox regulation via S-glutathionylation, i...
August 11, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28803792/rapid-and-visual-detection-of-leptospira-in-urine-by-ligb-lamp-assay-with-pre-addition-of-dye
#6
Syed Atif Ali, Gurpreet Kaur, Nongthombam Boby, T Sabarinath, Khushal Solanki, Dheeraj Pal, Pallab Chaudhuri
Leptospirosis is considered to be the most widespread zoonotic disease caused by pathogenic species of Leptospira. The present study reports a novel set of primers targeting LigB gene for visual detection of pathogenic Leptospira in urine samples through Loop-mediated isothermal amplification (LAMP). The results were recorded by using Hydroxyl napthol blue (HNB), SYBR GREEN I and calcein. Analytical sensitivity of LAMP was as few as 10 leptospiral organisms in spiked urine samples from cattle and dog. LigB gene based LAMP, termed as LigB-LAMP, was found 10 times more sensitive than conventional PCR...
August 10, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28798928/functional-virtual-flow-cytometry-a-visual-analytic-approach-for-characterizing-single-cell-gene-expression-patterns
#7
Zhi Han, Travis Johnson, Jie Zhang, Xuan Zhang, Kun Huang
We presented a novel workflow for detecting distribution patterns in cell populations based on single-cell transcriptome study. With the fast adoption of single-cell analysis, a challenge to researchers is how to effectively extract gene features to meaningfully separate the cell population. Considering that coexpressed genes are often functionally or structurally related and the number of coexpressed modules is much smaller than the number of genes, our workflow uses gene coexpression modules as features instead of individual genes...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28795295/predictive-value-of-n95-waveforms-of-pattern-electroretinograms-pergs-in-children-with-optic-nerve-hypoplasia-onh
#8
Daphne McCulloch, Pamela Garcia-Filion, Cassandra Fink, Anthony C Fisher, Antonio Eleuteri, Mark S Borchert
PURPOSE: As part of a long-term, prospective study of prenatal and clinical risk factors for optic nerve hypoplasia (ONH) at Children's Hospital Los Angeles, pattern ERGs (PERGs) were evaluated for prognostic value using an automated objective and robust analytical method. METHODS: Participants were 33 children with ophthalmoscopically diagnosed ONH [disc diameter-to-disc macula ratio (DD/DM) less than 0.35 in one or both eyes on fundus photographs]. Using cycloplegia and chloral hydrate sedation in one session before 26 months of age, we recorded PERGs to checkerboard reversal using five check sizes...
August 9, 2017: Documenta Ophthalmologica. Advances in Ophthalmology
https://www.readbyqxmd.com/read/28789930/commentary-on-an-integrated-metabolic-atlas-of-clear-cell-renal-cell-carcinoma-hakimi-aa-reznik-e-lee-ch-creighton-cj-brannon-ar-luna-a-aksoy-ba-liu-em-shen-r-lee-w-chen-y-stirdivant-sm-russo-p-chen-yb-tickoo-sk-reuter-ve-cheng-eh-sander-c-hsieh-jj-cancer-cell
#9
Byron H Lee
Dysregulated metabolism is a hallmark of cancer, manifested through alterations in metabolites. We performed metabolomic profiling on 138 matched clear cell renal cell carcinoma (ccRCC)/normal tissue pairs and found that ccRCC is characterized by broad shifts in central carbon metabolism, one-carbon metabolism, and antioxidant response. Tumor progression and metastasis were associated with metabolite increases in glutathione and cysteine/methionine metabolism pathways. We develop an analytic pipeline and visualization tool (metabolograms) to bridge the gap between TCGA transcriptomic profiling and our metabolomic data, which enables us to assemble an integrated pathway-level metabolic atlas and to demonstrate discordance between transcriptome and metabolome...
August 5, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28782932/visualization-of-colloidal-nanocrystal-formation-and-electrode-electrolyte-interfaces-in-liquids-using-tem
#10
Zhiyuan Zeng, Wenjing Zheng, Haimei Zheng
Transmission electron microscopy (TEM) has become a powerful analytical tool for addressing unique scientific problems in chemical sciences as well as in materials sciences and other disciplines. There has been a lot of recent interest in the development and applications of liquid phase environmental TEM. In this Account, we review the development and applications of liquid cell TEM for the study of dynamic phenomena at liquid-solid interfaces, focusing on two areas: (1) nucleation, growth, and self-assembly of colloidal nanocrystals and (2) electrode-electrolyte interfaces during charge and discharge processes...
August 7, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28777822/quantifying-gaze-and-mouse-interactions-on-spatial-visual-interfaces-with-a-new-movement-analytics-methodology
#11
Urška Demšar, Arzu Çöltekin
Eye movements provide insights into what people pay attention to, and therefore are commonly included in a variety of human-computer interaction studies. Eye movement recording devices (eye trackers) produce gaze trajectories, that is, sequences of gaze location on the screen. Despite recent technological developments that enabled more affordable hardware, gaze data are still costly and time consuming to collect, therefore some propose using mouse movements instead. These are easy to collect automatically and on a large scale...
2017: PloS One
https://www.readbyqxmd.com/read/28774450/imaging-in-osteoarthritis
#12
REVIEW
Daichi Hayashi, Frank W Roemer, Mohamed Jarraya, Ali Guermazi
With technologic advances and the availability of sophisticated computer software and analytical strategies, imaging plays an increasingly important role in understanding the disease process of osteoarthritis (OA). Radiography has limitations in that it can visualize only limited features of OA, such as osteophytes and joint space narrowing, but remains the most commonly used modality for establishing an imaging-based diagnosis of OA. This article describes the roles and limitations of different imaging modalities and discusses the optimum imaging protocol, imaging diagnostic criteria of OA, differential diagnoses, and what the referring physician needs to know...
September 2017: Radiologic Clinics of North America
https://www.readbyqxmd.com/read/28774016/raman-and-conductivity-analysis-of-graphene-for-biomedical-applications
#13
Chao Qiu, Kevin E Bennet, Tamanna Khan, John D Ciubuc, Felicia S Manciu
In this study, we present a comprehensive investigation of graphene's optical and conductive properties using confocal Raman and a Drude model. A comparative analysis between experimental findings and theoretical predictions of the material's changes and improvements as it transitioned from three-dimensional graphite is also presented and discussed. Besides spectral recording by Raman, which reveals whether there is a single, a few, or multi-layers of graphene, the confocal Raman mapping allows for distinction of such domains and a direct visualization of material inhomogeneity...
November 4, 2016: Materials
https://www.readbyqxmd.com/read/28772828/in-vitro-versus-in-vivo-phase-instability-of-zirconia-toughened-alumina-femoral-heads-a-critical-comparative-assessment
#14
Giuseppe Pezzotti, Saverio Affatato, Alfredo Rondinella, Makiko Yorifuji, Elia Marin, Wenliang Zhu, Bryan McEntire, Sonny B Bal, Kengo Yamamoto
A clear discrepancy between predicted in vitro and actual in vivo surface phase stability of BIOLOX(®)delta zirconia-toughened alumina (ZTA) femoral heads has been demonstrated by several independent research groups. Data from retrievals challenge the validity of the standard method currently utilized in evaluating surface stability and raise a series of important questions: (1) Why do in vitro hydrothermal aging treatments conspicuously fail to model actual results from the in vivo environment? (2) What is the preponderant microscopic phenomenon triggering the accelerated transformation in vivo? (3) Ultimately, what revisions of the current in vitro standard are needed in order to obtain consistent predictions of ZTA transformation kinetics in vivo? Reported in this paper is a new in toto method for visualizing the surface stability of femoral heads...
April 28, 2017: Materials
https://www.readbyqxmd.com/read/28770932/carbon-nano-dots-as-a-fluorescent-and-colorimetric-dual-readout-probe-for-the-detection-of-arginine-and-cu-2-and-its-logic-gate-operation
#15
Wenjing Lu, Yifang Gao, Yuan Jiao, Shaomin Shuang, Chenzhong Li, Chuan Dong
A new visual fluorescent probe based on carbon nano-dots (CNDs) has been facilely synthesized via one step microwave-assisted pyrolysis and utilized for sequential detection of arginine (Arg) and Cu(2+) by fluorescent and colorimetric dual-readout assay. The fluorescence of CNDs can be effectively quenched by Arg, and recovered upon addition of Cu(2+) due to the competitive binding of Arg and Cu(2+) that leads Arg to escape from the surface of CNDs. The probe displayed high sensitivity and selectivity toward Arg and Cu(2+) over other analytes with a low detection limit of 0...
August 3, 2017: Nanoscale
https://www.readbyqxmd.com/read/28764533/visualizing-dispersive-features-in-2d-image-via-minimum-gradient-method
#16
Yu He, Yan Wang, Zhi-Xun Shen
We developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image...
July 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28762245/electrostatics-explains-the-position-dependent-effect-of-g-u-wobble-base-pairs-on-the-affinity-of-rna-kissing-complexes
#17
Josephine Abi-Ghanem, Clémence Rabin, Massimiliano Porrini, Eric Dausse, Jean-Jacques Toulmé, Valérie Gabelica
In the RNA realm, non-Watson Crick base pairs are abundant and affect either the RNA 3D structure and/or its function. Here we investigated the formation of RNA kissing complexes where the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance and UV-melting experiments show that the G*U wobble base pair favors the kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modelling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculation and PBSA calculation of the electrostatic potential surfaces...
July 31, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28758764/meta-analytic-review-of-the-development-of-face-discrimination-in-infancy-face-race-face-gender-infant-age-and-methodology-moderate-face-discrimination
#18
Nicole A Sugden, Alexandra R Marquis
Infants show facility for discriminating between individual faces within hours of birth. Over the first year of life, infants' face discrimination shows continued improvement with familiar face types, such as own-race faces, but not with unfamiliar face types, like other-race faces. The goal of this meta-analytic review is to provide an effect size for infants' face discrimination ability overall, with own-race faces, and with other-race faces within the first year of life, how this differs with age, and how it is influenced by task methodology...
July 31, 2017: Psychological Bulletin
https://www.readbyqxmd.com/read/28758723/critical-comparison-of-fret-sensor-functionality-in-the-cytosol-and-endoplasmic-reticulum-and-implications-for-quantification-of-ions
#19
Kyle P Carter, Margaret C Carpenter, Brett Fiedler, Ralph Jimenez, Amy E Palmer
Genetically encoded sensors based on fluorescence resonance energy transfer (FRET) are powerful tools for quantifying and visualizing analytes in living cells, and when targeted to organelles have the potential to define distribution of analytes in different parts of the cell. However, quantitative estimates of analyte distribution require rigorous and systematic analysis of sensor functionality in different locations. In this work, we establish methods to critically evaluate sensor performance in different organelles and carry out a side-by-side comparison of three different genetically encoded sensor platforms for quantifying cellular zinc ions (Zn(2+))...
August 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28757690/prognostic-preoperative-factors-for-successful-outcome-of-surgery-in-horizontal-strabismus
#20
Namita Kumari, Abadan Khan Amitava, Mohammad Ashraf, Shivani Grover, Ashiya Khan, Prabha Sonwani
CONTEXT: Surgery for horizontal strabismus reportedly has a success rate of 60%-80%. However, which preoperative factors are predictive of this success is not clear. AIMS: To identify prognostic factors those are predictive of successful outcome in horizontal strabismus surgery. SETTINGS AND DESIGN: Observational analytical study using multiple logistic regression (MLR). SUBJECTS AND METHODS: We assessed the medical records of patients who had undergone first-time horizontal muscle strabismus surgery between 2002 and 2013, where complete follow-up data were available for ≥6 weeks, and also, we collected data prospectively on patients operated between January 2014 and September 2015...
May 2017: Oman Journal of Ophthalmology
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