scholarly journals DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions

2019 ◽  
Author(s):  
Angus M. Sidore ◽  
Calin Plesa ◽  
Joyce A. Samson ◽  
Sriram Kosuri
Keyword(s):  
Error Correction ◽  
Low Cost ◽  
Gene Synthesis ◽  
High Fidelity ◽  
Functional Testing ◽  
Gene Length ◽  
Genetic Elements ◽  
Gene Libraries

AbstractMultiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here we improve DropSynth, a low-cost, multiplexed method which builds gene libraries by compartmentalizing and assembling microarray-derived oligos in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction, and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.

scholarly journals DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions

2020 ◽  
Vol 48 (16) ◽  
pp. e95-e95 ◽  
Author(s):  
Angus M Sidore ◽  
Calin Plesa ◽  
Joyce A Samson ◽  
Nathan B Lubock ◽  
Sriram Kosuri
Keyword(s):  
Error Correction ◽  
Low Cost ◽  
Gene Synthesis ◽  
High Fidelity ◽  
Functional Testing ◽  
Gene Length ◽  
Genetic Elements ◽  
Gene Libraries

Abstract Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene libraries by compartmentalizing and assembling microarray-derived oligonucleotides in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.

scholarly journals Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes

2017 ◽  
Author(s):  
Calin Plesa ◽  
Angus M. Sidore ◽  
Nathan B. Lubock ◽  
Di Zhang ◽  
Sriram Kosuri
Keyword(s):  
Low Cost ◽  
Short Length ◽  
Gene Synthesis ◽  
Test Sequence ◽  
Functional Assay ◽  
Functional Assays ◽  
Emulsion Droplets ◽  
Gene Libraries ◽  
Potential Applications ◽  
Generation Sequencing

AbstractNext-generation sequencing has engendered an expanding suite of functional assays that can test sequence-function relationships at unprecedented scales in pooled formats (multiplex). Such assays are currently constrained by the short length of oligonucleotide (oligo) pools, which limit potential applications. Here we report a simple, low-cost, and scalable method called DropSynth that assembles gene libraries from oligo pools for use in multiplexed functional assays. DropSynth utilizes a library of barcoded beads to isolate and concentrate oligos needed for a gene’s synthesis in a pooled format. These bead-bound oligos are then emulsified, processed, and assembled into genes within the emulsion droplets. We synthesized ~1000 phylogenetically diverse orthologs of phosphopantetheine adenylyltransferase (PPAT) and tested their fitness in a multiplexed functional assay. While the majority of orthologs complement, those that do not are broadly distributed across the phylogenetic tree. Synthetic errors in our assemblies allow us to explore local landscapes around the designed orthologs revealing constrained mutations for complementing orthologs as well as gain-of-function mutations for low-fitness orthologs. This broad mutational scanning approach is complementary to deep mutational scanning and helps us understand proteins by probing evolutionarily divergent sequences that share function.

scholarly journals Novel Neonatal Simulator Provides High-Fidelity Ventilation Training Comparable to Real-Life Newborn Ventilation

Children ◽  
2021 ◽  
Vol 8 (10) ◽  
pp. 940
Author(s):  
Joanna Haynes ◽  
Peder Bjorland ◽  
Øystein Gomo ◽  
Anastasia Ushakova ◽  
Siren Rettedal ◽  
...  
Keyword(s):  
Skill Acquisition ◽  
Low Cost ◽  
Negative Relationship ◽  
Real Life ◽  
Neonatal Resuscitation ◽  
Healthcare Personnel ◽  
Positive Pressure ◽  
High Fidelity ◽  
High Resource ◽  
Clinical Conditions

Face mask ventilation of apnoeic neonates is an essential skill. However, many non-paediatric healthcare personnel (HCP) in high-resource childbirth facilities receive little hands-on real-life practice. Simulation training aims to bridge this gap by enabling skill acquisition and maintenance. Success may rely on how closely a simulator mimics the clinical conditions faced by HCPs during neonatal resuscitation. Using a novel, low-cost, high-fidelity simulator designed to train newborn ventilation skills, we compared objective measures of ventilation derived from the new manikin and from real newborns, both ventilated by the same group of experienced paediatricians. Simulated and clinical ventilation sequences were paired according to similar duration of ventilation required to achieve success. We found consistencies between manikin and neonatal positive pressure ventilation (PPV) in generated peak inflating pressure (PIP), mask leak and comparable expired tidal volume (eVT), but positive end-expiratory pressure (PEEP) was lower in manikin ventilation. Correlations between PIP, eVT and leak followed a consistent pattern for manikin and neonatal PPV, with a negative relationship between eVT and leak being the only significant correlation. Airway obstruction occurred with the same frequency in the manikin and newborns. These findings support the fidelity of the manikin in simulating clinical conditions encountered during real newborn ventilation. Two limitations of the simulator provide focus for further improvements.

scholarly journals SOFTWARE IMPLEMENTED HARDWARE-TRANSIENT FAULTS DETECTION

2014 ◽  
pp. 26-30
Author(s):  
Goutam Kumar Saha
Keyword(s):  
Error Correction ◽  
Fault Tolerant ◽  
Low Cost ◽  
Transient Faults ◽  
Fault Tolerant System ◽  
Cost Approach ◽  
Run Time ◽  
Commodity Systems ◽  
Fail Safe ◽  
Register Error

This paper examines a software implemented self-checking technique that is capable of detecting processorregisters' hardware-transient faults. The proposed approach is intended to detect run-time transient bit-errors in memory and processor status register. Error correction is not considered here. However, this low-cost approach is intended to be adopted in commodity systems that use ordinary off-the-shelf microprocessors, for the purpose of operational faults detection towards gaining fail-safe kind of fault tolerant system.

scholarly journals A novel, low-cost, reusable, high-fidelity neurosurgical training simulator for cerebrovascular bypass surgery

2019 ◽  
Vol 130 (5) ◽  
pp. 1663-1671
Author(s):  
Ulas Cikla ◽  
Balkan Sahin ◽  
Sahin Hanalioglu ◽  
Azam S. Ahmed ◽  
David Niemann ◽  
...  
Keyword(s):  
Bypass Surgery ◽  
Low Cost ◽  
Artery Bypass ◽  
Superficial Temporal Artery ◽  
Temporal Artery ◽  
High Fidelity ◽  
Skin Closure ◽  
Neurosurgical Training ◽  
Training Simulator ◽  
Live Animal

OBJECTIVECerebrovascular bypass surgery is a challenging yet important neurosurgical procedure that is performed to restore circulation in the treatment of carotid occlusive diseases, giant/complex aneurysms, and skull base tumors. It requires advanced microsurgical skills and dedicated training in microsurgical techniques. Most available training tools, however, either lack the realism of the actual bypass surgery (e.g., artificial vessel, chicken wing models) or require special facilities and regulations (e.g., cadaver, live animal, placenta models). The aim of the present study was to design a readily accessible, realistic, easy-to-build, reusable, and high-fidelity simulator to train neurosurgeons or trainees on vascular anastomosis techniques even in the operating room.METHODSThe authors used an anatomical skull and brain model, artificial vessels, and a water pump to simulate both extracranial and intracranial circulations. They demonstrated the step-by-step preparation of the bypass simulator using readily available and affordable equipment and consumables.RESULTSAll necessary steps of a superficial temporal artery–middle cerebral artery bypass surgery (from skin opening to skin closure) were performed on the simulator under a surgical microscope. The simulator was used by both experienced neurosurgeons and trainees. Feedback survey results from the participants of the microsurgery course suggested that the model is superior to existing microanastomosis training kits in simulating real surgery conditions (e.g., depth, blood flow, anatomical constraints) and holds promise for widespread use in neurosurgical training.CONCLUSIONSWith no requirement for specialized laboratory facilities and regulations, this novel, low-cost, reusable, high-fidelity simulator can be readily constructed and used for neurosurgical training with various scenarios and modifications.

XPS Jensen Lung as a Low-Cost, High-Fidelity Training Adjunct to Ex-Vivo Lung Perfusion

2018 ◽  
Vol 37 (4) ◽  
pp. S243-S244
Author(s):  
B. Shukrallah ◽  
C. Eggeman ◽  
D. Mast ◽  
D. Igoe ◽  
J. Ralston ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Low Cost ◽  
Lung Perfusion ◽  
High Fidelity ◽  
Ex Vivo Lung Perfusion

Realization of Three-Dimensional Nanostructure Fabrication by Nanoimprint on Silicon Substrate

2011 ◽  
Vol 211-212 ◽  
pp. 1105-1109
Author(s):  
Xi Qiu Fan
Keyword(s):  
Silicon Substrate ◽  
Low Cost ◽  
Three Dimensional ◽  
Microlens Array ◽  
Optical Lithography ◽  
High Fidelity ◽  
Fabrication Method ◽  
Nanostructure Fabrication ◽  
Large Area ◽  
3D Nanostructures

Traditional optical lithography techniques to fabricate three-dimensional (3D) nanostructures are complicated and time consuming. Due to the capability to replicate nanostructures repeatedly in a large area with high resolution and uniformity, nanoimprint (NI) has been recognized as one of the promising approaches to fabricate 3-D nanostructures with high throughput and low cost. This paper introduces a novel 3-D nanostructure fabrication method by nanoimprint on silicon substrate. Nanoscale gratings and microlens array are taken as examples of 3-D nanostructures fabricated by nanoimprint. High fidelity demonstrates the possibility of nanoimprint to fabricate 3-D nanostructures on silicon substrate.

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