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https://www.readbyqxmd.com/read/29350029/a-microwell-array-method-for-rapid-generation-of-uniform-agarose-droplets-and-beads-for-single-molecule-analysis
#1
Xingrui Li, Dongfeng Zhang, Huimin Zhang, Zhichao Guan, Yanling Song, Ruochen Liu, Zhi Zhu, Chaoyong James Yang
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with pre-selectable diameters ranging from 20 µm to 100 µm can be produced with relative standard deviations less than 3...
January 19, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29347591/reconstruction-of-three-dimensional-porous-media-using-generative-adversarial-neural-networks
#2
Lukas Mosser, Olivier Dubrule, Martin J Blunt
To evaluate the variability of multiphase flow properties of porous media at the pore scale, it is necessary to acquire a number of representative samples of the void-solid structure. While modern x-ray computer tomography has made it possible to extract three-dimensional images of the pore space, assessment of the variability in the inherent material properties is often experimentally not feasible. We present a method to reconstruct the solid-void structure of porous media by applying a generative neural network that allows an implicit description of the probability distribution represented by three-dimensional image data sets...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347557/constant-pressure-nested-sampling-with-atomistic-dynamics
#3
Robert J N Baldock, Noam Bernstein, K Michael Salerno, Lívia B Pártay, Gábor Csányi
The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are inefficient for condensed systems with general interactions where single-particle moves cannot be evaluated faster than the energy of the whole system. Here we enhance the method by using all-particle moves: either Galilean Monte Carlo or the total enthalpy Hamiltonian Monte Carlo algorithm, introduced in this paper...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347093/self-assembly-of-rigid-magnetic-rods-consisting-of-single-dipolar-beads-in-two-dimensions
#4
Jorge L C Domingos, François M Peeters, W P Ferreira
Molecular dynamics simulations are used to investigate the structural properties of a two-dimensional ensemble of magnetic rods, which are modeled as aligned single dipolar beads. The obtained self-assembled configurations can be characterized as (1) clusters, (2) percolated, and (3) ordered structures, and their structural properties are investigated in detail. By increasing the aspect ratio of the magnetic rods, we show that the percolation transition is suppressed due to the reduced mobility of the rods in two dimensions...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29343722/multiplex-glycan-bead-array-for-high-throughput-and-high-content-analyses-of-glycan-binding-proteins
#5
Sharad Purohit, Tiehai Li, Wanyi Guan, Xuezheng Song, Jing Song, Yanna Tian, Lei Li, Ashok Sharma, Boying Dun, David Mysona, Sharad Ghamande, Bunja Rungruang, Richard D Cummings, Peng George Wang, Jin-Xiong She
Glycan-binding proteins (GBPs) play critical roles in diverse cellular functions such as cell adhesion, signal transduction and immune response. Studies of the interaction between GBPs and glycans have been hampered by the availability of high throughput and high-content technologies. Here we report multiplex glycan bead array (MGBA) that allows simultaneous analyses of 384 samples and up to 500 glycans in a single assay. The specificity, sensitivity and reproducibility of MGBA are evaluated using 39 plant lectins, 13 recombinant anti-glycan antibodies, and mammalian GBPs...
January 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29338194/sequential-and-selective-detection-of-two-molecules-with-a-single-solid-contact-chronopotentiometric-ion-selective-electrode
#6
Jiawang Ding, Nana Yu, Xuedong Wang, Wei Qin
A polymeric membrane ion-selective electrode (ISE) is typically designed for determination of one specific ion using conventional method. In this work, we demonstrate a simple, versatile and sensitive platform for simultaneous detection of two molecules with a single ISE. Under a series of periodic galvanostatic polarization, a solid-contact ISE without ion exchanger properties under zero-current conditions has been successfully used for simultaneous detection of two opposite charged ions with high sensitivity, good selectivity and fast reversibility...
January 17, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29335424/functionalisation-of-detonation-nanodiamond-for-monodispersed-soluble-dna-nanodiamond-conjugates-using-mixed-silane-bead-assisted-sonication-disintegration
#7
Robert Edgington, Katelyn M Spillane, George Papageorgiou, William Wray, Hitoshi Ishiwata, Mariana Labarca, Sergio Leal-Ortiz, Gordon Reid, Martin Webb, John Foord, Nicholas Melosh, Andreas T Schaefer
Nanodiamonds have many attractive properties that make them suitable for a range of biological applications, but their practical use has been limited because nanodiamond conjugates tend to aggregate in solution during or after functionalisation. Here we demonstrate the production of DNA-detonation nanodiamond (DNA-DND) conjugates with high dispersion and solubility using an ultrasonic, mixed-silanization chemistry protocol based on the in situ Bead-Assisted Sonication Disintegration (BASD) silanization method...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334370/scaffolds-that-mimic-antigen-presenting-cells-enable-ex-vivo-expansion-of-primary-t-cells
#8
Alexander S Cheung, David K Y Zhang, Sandeep T Koshy, David J Mooney
Therapeutic ex vivo T-cell expansion is limited by low rates and T-cell products of limited functionality. Here we describe a system that mimics natural antigen-presenting cells (APCs) and consists of a fluid lipid bilayer supported by mesoporous silica micro-rods. The lipid bilayer presents membrane-bound cues for T-cell receptor stimulation and costimulation, while the micro-rods enable sustained release of soluble paracrine cues. Using anti-CD3, anti-CD28, and interleukin-2, we show that the APC-mimetic scaffolds (APC-ms) promote two- to tenfold greater polyclonal expansion of primary mouse and human T cells compared with commercial expansion beads (Dynabeads)...
January 15, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29328253/measurements-of-milli-newton-surface-tension-forces-with-tilted-fiber-bragg-gratings
#9
Changyu Shen, Chuan Zhong, Dejun Liu, Xiaokang Lian, Jianyao Zheng, Jingjing Wang, Yuliya Semenova, Gerald Farrell, Jacques Albert, John F Donegan
Small lateral forces (lower than 0.1 N) cannot normally be measured with conventional single-mode fiber-based sensors because of the high value of their Young modulus (>70  GPa). Here we demonstrate the measurement of lateral forces in the range from 0.2 to 1.4×10-3  N with a tilted fiber Bragg grating (TFBG) in conventional single-mode fiber pushed against the surface tension (ST) of a bead of water. The measured transmission changes of individual cladding mode resonances of the TFBG corresponding to these force values are of the order of 29 dB...
January 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29322425/production-of-recombinant-killer-immunoglobulin-like-receptors-for-crystallography-and-luminex-based-assays
#10
Phillip Pymm, Julian P Vivian
The killer immunoglobulin-like receptors (KIR) are a highly diverse family of cell-surface receptors that are of importance to the effector function of Natural Killer cells. KIR have been implicated in the detection and clearance of malignantly transformed cells and in the immune-control of viruses including HIV, HCV and CMV. Recently, the mismatching of donor and recipient KIR has been demonstrated to improve success of hematopoietic stem cell transplantation treatments of leukemias. Due to the high degree of diversity amongst the KIR, a number of strategies are required for the production of recombinant protein for medical, biochemical and structural applications...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29320684/label-free-imaging-and-bending-analysis-of-microtubules-by-rocs-microscopy-and-optical-trapping
#11
Matthias D Koch, Alexander Rohrbach
Mechanical manipulation of single cytoskeleton filaments and their monitoring over long times is difficult because of fluorescence bleaching or phototoxic protein degradation. The integration of label-free microscopy techniques, capable of imaging freely diffusing, weak scatterers such as microtubules (MTs) in real-time, and independent of their orientation, with optical trapping and tracking systems, would allow many new applications. Here, we show that rotating-coherent-scattering microscopy (ROCS) in dark-field mode can also provide strong contrast for structures far from the coverslip such as arrangements of isolated MTs and networks...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29317629/3d-single-molecule-super-resolution-microscopy-with-a-tilted-light-sheet
#12
Anna-Karin Gustavsson, Petar N Petrov, Maurice Y Lee, Yoav Shechtman, W E Moerner
Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29313532/a-label-free-versatile-and-low-background-chemiluminescence-aptasensing-strategy-based-on-gold-nanocluster-catalysis-combined-with-the-separation-of-magnetic-beads
#13
Yueyue Yao, Xiuzhong Wang, Wenna Duan, Feng Li
A label-free, versatile and low-background chemiluminescence (CL) sensing strategy based on gold nanocluster catalysis combined with the separation of magnetic beads (MBs) was developed. Kanamycin was selected as the target analyte to exhibit the analytical performance of this platform. Two single-stranded DNA (named DNA1 and DNA2) are ingeniously designed. DNA1, containing an aptamer sequence of the targets, was firstly immobilized on the MBs which were modified with many amino groups by amidation reaction...
January 9, 2018: Analyst
https://www.readbyqxmd.com/read/29313076/poly-a-tail-length-analysis-of-in-vitro-transcribed-mrna-by-lc-ms
#14
Michael Beverly, Caitlin Hagen, Olga Slack
The 3'-polyadenosine (poly A) tail of in vitro transcribed (IVT) mRNA was studied using liquid chromatography coupled to mass spectrometry (LC-MS). Poly A tails were cleaved from the mRNA using ribonuclease T1 followed by isolation with dT magnetic beads. Extracted tails were then analyzed by LC-MS which provided tail length information at single-nucleotide resolution. A 2100-nt mRNA with plasmid-encoded poly A tail lengths of either 27, 64, 100, or 117 nucleotides was used for these studies as enzymatically added poly A tails showed significant length heterogeneity...
January 8, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29312863/human-leukocyte-antigen-typing-and-crossmatch-a-comprehensive-review
#15
REVIEW
Mohammed Mahdi Althaf, Mohsen El Kossi, Jon Kim Jin, Ajay Sharma, Ahmed Mostafa Halawa
Renal transplantation remains the best option for patients suffering from end stage renal disease (ESRD). Given the worldwide shortage of organs and growing population of patients with ESRD, those waitlisted for a transplant is ever expanding. Contemporary crossmatch methods and human leukocyte antigen (HLA) typing play a pivotal role in improving organ allocation and afford better matches to recipients. Understanding crossmatch as well as HLA typing for renal transplantation and applying it in clinical practice is the key step to achieve a successful outcome...
December 24, 2017: World Journal of Transplantation
https://www.readbyqxmd.com/read/29282315/dynamics-and-mechanisms-of-intracellular-calcium-waves-elicited-by-tandem-bubble-induced-jetting-flow
#16
Fenfang Li, Chen Yang, Fang Yuan, Defei Liao, Thomas Li, Farshid Guilak, Pei Zhong
One of the earliest events in cellular mechanotransduction is often an increase in intracellular calcium concentration associated with intracellular calcium waves (ICWs) in various physiologic or pathophysiologic processes. Although cavitation-induced calcium responses are believed to be important for modulating downstream bioeffects such as cell injury and mechanotransduction in ultrasound therapy, the fundamental mechanisms of these responses have not been elucidated. In this study, we investigated mechanistically the ICWs elicited in single HeLa cells by the tandem bubble-induced jetting flow in a microfluidic system...
December 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29277486/development-of-a-high-throughput-bead-based-assay-system-to-measure-hiv-1-specific-immune-signatures-in-clinical-samples
#17
Thomas Liechti, Claus Kadelka, Hanna Ebner, Nikolas Friedrich, Roger D Kouyos, Huldrych F Günthard, Alexandra Trkola
The monitoring and assessment of a broadly neutralizing antibody (bnAb) based HIV-1 vaccine require detailed measurements of HIV-1 binding antibody responses to support the detection of correlates of protection. Here we describe the development of a flexible, high-throughput microsphere based multiplex assay system that allows monitoring complex binding antibody signatures. Studying a panel of 13 HIV-1 antigens in a parallel assessment of different IgG subclasses (IgG1, IgG2 and IgG3) we demonstrate the potential of our strategy...
December 22, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/29272937/structure-spectroscopy-and-dynamics-of-the-phenol-water-2-cluster-at-low-and-high-temperatures
#18
Nagaprasad Reddy Samala, Noam Agmon
Aqueous solutions are complex due to hydrogen bonding (HBing). While gas-phase clusters could provide clues on the solution behavior, most neutral clusters were studied at cryogenic temperatures. Recent results of Shimamori and Fujii provide the first IR spectrum of warm phenol-(H2O)2 clusters. To understand the temperature (T) effect, we have revisited the structure and spectroscopy of phenol-(H2O)2 at all T. While older quantum chemistry work concluded that the cyclic isomers are the most stable, the inclusion of dispersion interactions reveals that they are nearly isoenergetic with isomers forming π-HBs with the phenyl ring...
December 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29260726/role-of-special-cross-links-in-structure-formation-of-bacterial-dna-polymer
#19
Tejal Agarwal, G P Manjunath, Farhat Habib, Pavana Lakshmi Vaddavalli, Apratim Chatterji
Using data from contact maps of the DNA-polymer of Escherichia coli (E. Coli) (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. Via suitable Monte Carlo simulations, we show that the presence of these cross-links leads to a particular organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain...
December 20, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29248150/multimodal-measurements-of-single-molecule-dynamics-using-fluorbt
#20
Ivan E Ivanov, Paul Lebel, Florian C Oberstrass, Charles H Starr, Angelica C Parente, Athena Ierokomos, Zev Bryant
Single-molecule methods provide direct measurements of macromolecular dynamics, but are limited by the number of degrees of freedom that can be followed at one time. High-resolution rotor bead tracking (RBT) measures DNA torque, twist, and extension, and can be used to characterize the structural dynamics of DNA and diverse nucleoprotein complexes. Here, we extend RBT to enable simultaneous monitoring of additional degrees of freedom. Fluorescence-RBT (FluoRBT) combines magnetic tweezers, infrared evanescent scattering, and single-molecule FRET imaging, providing real-time multiparameter measurements of complex molecular processes...
December 13, 2017: Biophysical Journal
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