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https://www.readbyqxmd.com/read/28346890/high-throughput-system-wide-engineering-and-screening-for-microbial-biotechnology
#1
REVIEW
Yannick Vervoort, Alicia Gutiérrez Linares, Miguel Roncoroni, Chengxun Liu, Jan Steensels, Kevin J Verstrepen
Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes...
March 24, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28225099/ultra-high-throughput-detection-1-million-droplets-per-second-of-fluorescent-droplets-using-a-cell-phone-camera-and-time-domain-encoded-optofluidics
#2
Venkata R Yelleswarapu, Heon-Ho Jeong, Sagar Yadavali, David Issadore
Droplet-based assays-in which ultra-sensitive molecular measurements are made by performing millions of parallel experiments in picoliter droplets-have generated enormous enthusiasm due to their single molecule resolution and robustness to reaction conditions. These assays have great untapped potential for point of care diagnostics but are currently confined to laboratory settings due to the instrumentation necessary to serially generate, control, and measure tens of millions of droplets. To address this challenge, we have developed the microdroplet megascale detector (μMD) that can generate and detect the fluorescence of millions of droplets per second (1000× faster than conventional approaches) using only a conventional cell phone camera...
March 14, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28207249/convection-driven-pull-down-assays-in-nanoliter-droplets-using-scaffolded-aptamers
#3
Xiangmeng Qu, Hongbo Zhang, Hong Chen, Ali Aldalbahi, Li Li, Yang Tian, David A Weitz, Hao Pei
One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing the contents of droplets with nano- or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull down. The convective flux allows complete reaction in <5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of the stationary case)...
March 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28199790/an-integrated-microfluidic-processor-for-dna-encoded-combinatorial-library-functional-screening
#4
Andrew B MacConnell, Alexander K Price, Brian M Paegel
DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits...
March 13, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28176860/massively-parallel-digital-high-resolution-melt-for-rapid-and-absolutely-quantitative-sequence-profiling
#5
Daniel Ortiz Velez, Hannah Mack, Julietta Jupe, Sinead Hawker, Ninad Kulkarni, Behnam Hedayatnia, Yang Zhang, Shelley Lawrence, Stephanie I Fraley
In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28139927/continuous-in-flight-synthesis-for-on-demand-delivery-of-ligand-free-colloidal-gold-nanoparticles
#6
Paul Maguire, David Rutherford, Manuel Macias-Montero, Charles Mahony, Colin Kelsey, Mark Tweedie, Fátima Pérez-Martin, Harold McQuaid, Declan Diver, Davide Mariotti
We demonstrate an entirely new method of nanoparticle chemical synthesis based on liquid droplet irradiation with ultralow (<0.1 eV) energy electrons. While nanoparticle formation via high energy radiolysis or transmission electron microscopy-based electron bombardment is well-understood, we have developed a source of electrons with energies close to thermal which leads to a number of important and unique benefits. The charged species, including the growing nanoparticles, are held in an ultrathin surface reaction zone which enables extremely rapid precursor reduction...
March 8, 2017: Nano Letters
https://www.readbyqxmd.com/read/28121417/adhesion-of-microdroplets-on-water-repellent-surfaces-toward-the-prevention-of-surface-fouling-and-pathogen-spreading-by-respiratory-droplets
#7
Jieke Jiang, Hengdi Zhang, Wenqing He, Tianzhong Li, Hualin Li, Peng Liu, Meijin Liu, Zhaoyue Wang, Zuankai Wang, Xi Yao
Biofouling caused by the adhesion of respiratory microdroplets generated in sneezing and coughing plays an important role in the spread of many infectious diseases. Although water-repellent surfaces are widely used for the long-term repellency of aqueous solutions, their repellency to pathogen-containing microdroplets is elusive. In this work, microdroplets from picoliter to nanoliter were successfully generated in a controlled manner to mimic the exhaled microdroplets in sneezing and coughing, which allowed us to evaluate the adhesion of microdroplets on both superhydrophobic and lubricant-infused "slippery" surfaces for the first time...
February 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28034712/evaluation-of-a-digital-dispenser-for-direct-curve-dilutions-in-a-vaccine-potency-assay
#8
Christopher Roselle, Dana Whitehouse, Thy Follmer, Fran Ansbro, Silikhone Bouaraphan, Liming Guan, Sha-Ke Wang, Mary Shank-Retzlaff, Thorsten Verch
Dilutions are a common source of analytical error, both in terms of accuracy and precision, and a common source of analyst mistakes. When serial dilutions are used, errors compound, even when employing laboratory automation. Direct point dilutions instead of serial dilutions can reduce error but is often impractical as they require either large diluent volumes or very small sample volumes when performed with traditional liquid handling equipment. We evaluated preparation of dilution curves using a picoliter digital dispenser, the HP, Inc...
December 27, 2016: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28009866/centrifugal-micro-channel-array-droplet-generation-for-highly-parallel-digital-pcr
#9
Zitian Chen, Peiyu Liao, Fangli Zhang, Mengcheng Jiang, Yusen Zhu, Yanyi Huang
Stable water-in-oil emulsion is essential to digital PCR and many other bioanalytical reactions that employ droplets as microreactors. We developed a novel technology to produce monodisperse emulsion droplets with high efficiency and high throughput using a bench-top centrifuge. Upon centrifugal spinning, the continuous aqueous phase is dispersed into monodisperse droplet jets in air through a micro-channel array (MiCA) and then submerged into oil as a stable emulsion. We performed dPCR reactions with a high dynamic range through the MiCA approach, and demonstrated that this cost-effective method not only eliminates the usage of complex microfluidic devices and control systems, but also greatly suppresses the loss of materials and cross-contamination...
December 22, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27995242/surface-acoustic-wave-enabled-pipette-on-a-chip
#10
Muhsincan Sesen, Citsabehsan Devendran, Sean Malikides, Tuncay Alan, Adrian Neild
Mono-disperse droplet formation in microfluidic devices allows the rapid production of thousands of identical droplets and has enabled a wide range of chemical and biological studies through repeat tests performed at pico-to-nanoliter volume samples. However, it is exactly this efficiency of production which has hindered the ability to carefully control the location and quantity of the distribution of various samples on a chip - the key requirement for replicating micro well plate based high throughput screening in vastly reduced volumetric scales...
December 20, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27993964/plasma-circulating-tumor-dna-in-pancreatic-cancer-patients-is-a-prognostic-marker
#11
Daniel Pietrasz, Nicolas Pécuchet, Fanny Garlan, Audrey Didelot, Olivier Dubreuil, Solène Doat, Francoise Imbert-Bismut, Mehdi Karoui, Jean-Christophe Vaillant, Valérie Taly, Pierre Laurent-Puig, Jean-Baptiste Bachet
PURPOSE: Despite recent therapeutic advances, prognosis of patients with pancreatic adenocarcinoma remains poor. Analyses from tumor tissues present limitations; identification of informative marker from blood might be a promising alternative. The aim of this study was to assess the feasibility and the prognostic value of circulating tumor DNA (ctDNA) in pancreatic adenocarcinoma. EXPERIMENTAL DESIGN: From 2011 to 2015, blood samples were prospectively collected from all consecutive patients with pancreatic adenocarcinoma treated in our center...
January 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27933984/statistical-thermodynamic-model-for-surface-tension-of-organic-and-inorganic-aqueous-mixtures
#12
Hallie C Boyer, Bryan R Bzdek, Jonathan P Reid, Cari S Dutcher
The surface composition and tensions of aqueous aerosols govern a set of processes that largely determine the fate of particles in the atmosphere. Predictive modeling of surface tension can provide significant contributions to studies of atmospheric aerosol effects on climate and human health. A previously derived surface tension model for single solute aqueous solutions used adsorption isotherms and statistical mechanics to enable surface tension predictions across the entire concentration range as a function of solute activity...
December 30, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27933691/single-fusion-events-at-polarized-liquid-liquid-interfaces
#13
Eduardo Laborda, Angela Molina, Vanesa Fernández Espín, Francisco Martínez-Ortiz, José García de la Torre, Richard G Compton
A new electrochemical framework for tracking individual soft particles in solution and monitoring their fusion with polarized liquid-liquid interfaces is reported. The physicochemical principle lies in the interfacial transfer of an ionic probe confined in the particles dispersed in solution and that is released upon their collision and fusion with the fluid interface. As a proof-of-concept, spike-like transients of a stochastic nature are reported in the current-time response of 1,2-dichloroethane(DCE)|water(W) submilli-interfaces after injection of DCE-in-W emulsions...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27860309/a-platform-for-electric-field-aided-and-wire-guided-droplet-manipulation
#14
Yanzhen Zhang, Gunther Wittstock
Small droplets can be manipulated based on controlling the adhesion work to a hydrophobic wire. The wire can be used to pick up, transport, and lay down droplets with volumes between picoliters to microliters avoiding the sliding of droplets over chip surfaces. Handling of droplets on surfaces with large steps such as engraved wells or channels is possible.
February 2017: Small
https://www.readbyqxmd.com/read/27812580/monitoring-few-molecular-binding-events-in-scalable-confined-aqueous-compartments-by-raster-image-correlation-spectroscopy-cadrics
#15
G Arrabito, F Cavaleri, V Montalbano, V Vetri, M Leone, B Pignataro
The assembly of scalable liquid compartments for binding assays in array formats constitutes a topic of fundamental importance in life sciences. This challenge can be addressed by mimicking the structure of cellular compartments with biological native conditions. Here, inkjet printing is employed to develop up to hundreds of picoliter aqueous droplet arrays stabilized by oil-confinement with mild surfactants (Tween-20). The aqueous environments constitute specialized compartments in which biomolecules may exploit their function and a wide range of molecular interactions can be quantitatively investigated...
November 4, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27783484/single-cell-total-rna-sequencing-through-isothermal-amplification-in-picoliter-droplet-emulsion
#16
Yusi Fu, He Chen, Lu Liu, Yanyi Huang
Prevalent single cell RNA amplification and sequencing chemistries mainly focus on polyadenylated RNAs in eukaryotic cells by using oligo(dT) primers for reverse transcription. We develop a new RNA amplification method, "easier-seq", to reverse transcribe and amplify the total RNAs, both with and without polyadenylate tails, from a single cell for transcriptome sequencing with high efficiency, reproducibility, and accuracy. By distributing the reverse transcribed cDNA molecules into 1.5 × 10(5) aqueous droplets in oil, the cDNAs are isothermally amplified using random primers in each of these 65-pL reactors separately...
November 15, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27782402/3d-printing-of-photoresponsive-biomaterials-for-control-of-bacterial-microenvironments
#17
Jodi L Connell, Eric T Ritschdorff, Jason B Shear
Advances in microscopic three-dimensional (µ3D) printing provide a means to microfabricate an almost limitless range of arbitrary geometries, offering new opportunities to rapidly prototype complex architectures for microfluidic and cellular applications. Such 3D lithographic capabilities present the tantalizing prospect for engineering micromechanical components - for example, pumps and valves - for cellular environments comprised of smart materials whose size, shape, permeability, stiffness, and other attributes might be modified in real time to precisely manipulate ultra-low-volume samples...
October 26, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27775138/spinning-micropipette-liquid-emulsion-generator-for-single-cell-whole-genome-amplification
#18
Zitian Chen, Yusi Fu, Fangli Zhang, Lu Liu, Naiqing Zhang, Dong Zhou, Junrui Yang, Yuhong Pang, Yanyi Huang
Many on-chip approaches that use flow-focusing to pinch the continuous aqueous phase into droplets have become the most popular methods that provide monodisperse emulsion droplets. However, not every lab can easily adapt a microfluidic workflow into their familiar protocols. We develop an off-chip approach, spinning micro-pipette liquid emulsion (SiMPLE) generator, to produce highly stable monodisperse water-in-oil emulsions using a moving micropipette to disperse the aqueous phase in an oil-filled microcentrifuge tube...
October 24, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27714122/optofluidic-sensing-from-inkjet-printed-droplets-the-enormous-enhancement-by-evaporation-induced-spontaneous-flow-on-photonic-crystal-biosilica
#19
Xianming Kong, Yuting Xi, Paul LeDuff, Erwen Li, Ye Liu, Li-Jing Cheng, Gregory L Rorrer, Hua Tan, Alan X Wang
Novel transducers for detecting an ultra-small volume of an analyte solution play pivotal roles in many applications such as chemical analysis, environmental protection and biomedical diagnosis. Recent advances in optofluidics offer tremendous opportunities for analyzing miniature amounts of samples with high detection sensitivity. In this work, we demonstrate enormous enhancement factors (10(6)-10(7)) of the detection limit for optofluidic analysis from inkjet-printed droplets by evaporation-induced spontaneous flow on photonic crystal biosilica when compared with conventional surface-enhanced Raman scattering (SERS) sensing using the pipette dispensing technology...
October 6, 2016: Nanoscale
https://www.readbyqxmd.com/read/27677315/label-free-analysis-and-sorting-of-microalgae-and-cyanobacteria-in-microdroplets-by-intrinsic-chlorophyll-fluorescence-for-the-identification-of-fast-growing-strains
#20
Roshni J Best, Jan J Lyczakowski, Sara Abalde-Cela, Ziyi Yu, Chris Abell, Alison G Smith
Microalgae and cyanobacteria are promising organisms for sustainable biofuel production, but several challenges remain to make this economically viable, including identification of optimized strains with high biomass productivity. Here we report on a novel methodology for the label-free screening and sorting of cyanobacteria and microalgae in a microdroplet platform. We show for the first time that chlorophyll fluorescence can be used to measure differences in biomass between populations of picoliter microdroplets containing different species of cyanobacteria, Synechocystis PCC 6803 and Synechococcus PCC 7002, which exhibit different growth dynamics in bulk culture...
October 21, 2016: Analytical Chemistry
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