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 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 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 Visualization of Surface Acoustic Waves in Thin Liquid Films

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
R. W. Rambach ◽  
J. Taiber ◽  
C. M. L. Scheck ◽  
C. Meyer ◽  
J. Reboud ◽  
...  
Keyword(s):  
Liquid Film ◽  
Acoustic Waves ◽  
Low Cost ◽  
Thin Liquid Film ◽  
Surface Acoustic Waves ◽  
Liquid Films ◽  
Theoretical Description ◽  
Propagation Path ◽  
Microfluidic Channels ◽  
Potential Applications

Abstract We demonstrate that the propagation path of a surface acoustic wave (SAW), excited with an interdigitated transducer (IDT), can be visualized using a thin liquid film dispensed onto a lithium niobate (LiNbO3) substrate. The practical advantages of this visualization method are its rapid and simple implementation, with many potential applications including in characterising acoustic pumping within microfluidic channels. It also enables low-cost characterisation of IDT designs thereby allowing the determination of anisotropy and orientation of the piezoelectric substrate without the requirement for sophisticated and expensive equipment. Here, we show that the optical visibility of the sound path critically depends on the physical properties of the liquid film and identify heptane and methanol as most contrast rich solvents for visualization of SAW. We also provide a detailed theoretical description of this effect.

scholarly journals Pancreatic cancer prognosis is predicted by an ATAC-array technology for assessing chromatin accessibility

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
S. Dhara ◽  
S. Chhangawala ◽  
H. Chintalapudi ◽  
G. Askan ◽  
V. Aveson ◽  
...  
Keyword(s):  
Low Cost ◽  
Disease Free Survival ◽  
Chromatin Accessibility ◽  
Cancer Prognosis ◽  
Ductal Adenocarcinoma ◽  
Binding Motifs ◽  
Free Survival ◽  
Array Technology ◽  
Treatment Naïve ◽  
Generation Sequencing

AbstractUnlike other malignancies, therapeutic options in pancreatic ductal adenocarcinoma (PDAC) are largely limited to cytotoxic chemotherapy without the benefit of molecular markers predicting response. Here we report tumor-cell-intrinsic chromatin accessibility patterns of treatment-naïve surgically resected PDAC tumors that were subsequently treated with (Gem)/Abraxane adjuvant chemotherapy. By ATAC-seq analyses of EpCAM+ PDAC malignant epithelial cells sorted from 54 freshly resected human tumors, we show here the discovery of a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identify two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further develop a chromatin accessibility microarray methodology termed “ATAC-array”, an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validate ATAC-array technology in both the original ATAC-seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a low-cost, clinically feasible technology for assessing chromatin accessibility profiles.

scholarly journals Recent Findings in Azaphilone Pigments

2021 ◽  
Vol 7 (7) ◽  
pp. 541
Author(s):  
Lúcia P. S. Pimenta ◽  
Dhionne C. Gomes ◽  
Patrícia G. Cardoso ◽  
Jacqueline A. Takahashi
Keyword(s):  
Water Solubility ◽  
Biological Activities ◽  
Low Cost ◽  
Scale Up ◽  
Structural Diversity ◽  
Downstream Processing ◽  
Global Market ◽  
Yield Improvement ◽  
Potential Applications ◽  
New Compounds

Filamentous fungi are known to biosynthesize an extraordinary range of azaphilones pigments with structural diversity and advantages over vegetal-derived colored natural products such agile and simple cultivation in the lab, acceptance of low-cost substrates, speed yield improvement, and ease of downstream processing. Modern genetic engineering allows industrial production, providing pigments with higher thermostability, water-solubility, and promising bioactivities combined with ecological functions. This review, covering the literature from 2020 onwards, focuses on the state-of-the-art of azaphilone dyes, the global market scenario, new compounds isolated in the period with respective biological activities, and biosynthetic pathways. Furthermore, we discussed the innovations of azaphilone cultivation and extraction techniques, as well as in yield improvement and scale-up. Potential applications in the food, cosmetic, pharmaceutical, and textile industries were also explored.

scholarly journals Color-Variable Photodynamic Antimicrobial Wool/Acrylic Blended Fabrics

Materials ◽  
2020 ◽  
Vol 13 (18) ◽  
pp. 4141
Author(s):  
Tingting Wang ◽  
Wangbingfei Chen ◽  
Tingting Dong ◽  
Zihao Lv ◽  
Siming Zheng ◽  
...  
Keyword(s):  
Low Cost ◽  
Pathogen Transmission ◽  
Cationic Dyes ◽  
Light Illumination ◽  
Antibacterial Studies ◽  
Wool Fibers ◽  
Visible Light Illumination ◽  
Potential Applications ◽  
Dyed Fabrics ◽  
Acrylic Fibers

Towards the goal of developing scalable, economical and effective antimicrobial textiles to reduce infection transmission, here we prepared color-variable photodynamic materials comprised of photosensitizer (PS)-loaded wool/acrylic (W/A) blends. Wool fibers in the W/A blended fabrics were loaded with the photosensitizer rose bengal (RB), and the acrylic fibers were dyed with a variety of traditional cationic dyes (cationic yellow, cationic blue and cationic red) to broaden their color range. Investigations on the colorimetric and photodynamic properties of a series of these materials were implemented through CIELab evaluation, as well as photooxidation and antibacterial studies. Generally, the photodynamic efficacy of these dual-dyed fabrics was impacted by both the choice, and how much of the traditional cationic dye was employed in the dyeing of the W/A fabrics. When compared with the PS-only singly-dyed material, RB-W/A, that showed a 99.97% (3.5 log units; p = 0.02) reduction of Staphylococcus aureus under visible light illumination (λ ≥ 420 nm, 60 min), the addition of cationic dyes led to a slight decrease in the photoinactivation ability of the dual-dyed fabrics, but was still able to achieve a 99.3% inactivation of S. aureus. Overall, our findings demonstrate the feasibility and potential applications of low cost and color variable RB-loaded W/A blended fabrics as effective self-disinfecting textiles against pathogen transmission.

Synthesis and characterization of hyperbranched poly (sulfone-amine) modified β-cyclodextrin

e-Polymers ◽  
2006 ◽  
Vol 6 (1) ◽  
Author(s):  
Liang Chen ◽  
Peng He ◽  
Zhifeng Jia ◽  
Xinyuan Zhu ◽  
Deyue Yan
Keyword(s):  
Drug Delivery ◽  
Low Cost ◽  
Food Additives ◽  
Synthesis And Characterization ◽  
Good Solubility ◽  
Low Viscosity ◽  
Hyperbranched Poly ◽  
Potential Applications ◽  
Inclusion Ability

AbstractAn economical strategy to prepare hyperbranched poly(sulfone-amine) modified β-cyclodextrins (HPSA-m-CDs) from natural β-cyclodextrin (β-CD) and other commercially available materials has been reported. The final product has many good properties of hyperbranched poly(sulfone-amine)s (good solubility, low viscosity etc.), while its inclusion ability can also be well kept. It is a feasible approach to prepare functionalized modified cyclodextrin at very low cost, and may have potential applications in the fields of catalysis, drug delivery, food additives, etc.

A review of passive self-sensing tag

Sensor Review ◽  
2017 ◽  
Vol 37 (3) ◽  
pp. 338-345 ◽  
Author(s):  
Yawei Xu ◽  
Lihong Dong ◽  
Haidou Wang ◽  
Jiannong Jing ◽  
Yongxiang Lu
Keyword(s):  
Radio Frequency Identification ◽  
Large Scale ◽  
Low Cost ◽  
Integrated Sensor ◽  
Content Type ◽  
Passive Sensing ◽  
Static Information ◽  
Potential Applications ◽  
Frequency Identification ◽  
Identification Tags

Purpose Radio frequency identification tags for passive sensing have attracted wide attention in the area of Internet of Things (IoT). Among them, some tags can sense the property change of objects without an integrated sensor, which is a new trend of passive sensing based on tag. The purpose of this paper is to review recent research on passive self-sensing tags (PSSTs). Design/methodology/approach The PSSTs reported in the past decade are classified in terms of sensing mode, composition and the ways of power supply. This paper presents operation principles of PSSTs and analyzes the characteristics of them. Moreover, the paper focuses on summarizing the latest sensing parameters of PSSTs and their matching equipment. Finally, some potential applications and challenges faced by this emerging technique are discussed. Findings PSST is suitable for long-term and large-scale monitoring compared to conventional sensors because it gets rid of the limitation of battery and has relatively low cost. Also, the static information of objects stored in different PSSTs can be identified by a single reader without touch. Originality/value This paper provides a detailed and timely review of the rapidly growing research in PSST.

Sintering and Hot-Pressing of Ti2AlC Obtained by SHS Process

2010 ◽  
Vol 63 ◽  
pp. 282-286 ◽  
Author(s):  
Leszek Chlubny ◽  
Jerzy Lis ◽  
Mirosław M. Bućko
Keyword(s):  
Hot Pressing ◽  
High Efficiency ◽  
Layer Structure ◽  
Low Cost ◽  
Max Phases ◽  
Fine Powders ◽  
High Temperature Synthesis ◽  
Low Energy Consumption ◽  
Potential Applications ◽  
Xrd Method

Some of ternary materials in the Ti-Al-C system are called MAX-phases and are characterised by heterodesmic layer structure. Their specific structure consisting of covalent and metallic chemical bonds influence its semi-ductile features locating them on the boundary between metals and ceramics, which may lead to many potential applications, for example as a part of a ceramic armour. Ti2AlC is one of this nanolaminate materials. Self-propagating High-temperature Synthesis (SHS) was applied to obtain sinterable powders of Ti2AlC Utilization of heat produced in exothermal reaction in adiabatic conditions to sustain process until all substrates are transformed into product is one of the advantages of the method that result in low energy consumption and low cost combined with high efficiency. Different substrates were used to produce fine powders of ternary material. Phase compositions of obtained powder were examined by XRD method. Than selected powders were used for sintering in various temperature both in a presureless sintering and hot-pressing in argon atmosphere. Properties and phase composition of obtained products were examined.

Pseudoelasticity of Cu-13.8Al-Ni Alloys Containing V and Nb

2008 ◽  
Vol 59 ◽  
pp. 101-107 ◽  
Author(s):  
Rodinei Medeiros Gomes ◽  
Ana Cris R. Veloso ◽  
V.T.L. Buono ◽  
Severino Jackson Guedes de Lima ◽  
Tadeu Antonio de Azevedo Melo
Keyword(s):  
Mechanical Properties ◽  
Shape Memory ◽  
Shape Recovery ◽  
Cold Water ◽  
Low Cost ◽  
Tensile Tests ◽  
Grain Refiner ◽  
Good Shape ◽  
Potential Applications ◽  
Superelastic Behavior

Polycrystalline copper-based shape memory alloys have been of particular interest in relation to Ni-Ti because of their low cost and good shape memory effect. Nevertheless the absence of a pronounced pseudoelasticity effect restricts the number of potential applications. In this work, the influence of Nb and V on the microstructure and the mechanical properties was investigated. Samples of Cu-13.8 Al-Ni containing V and Nb alloy were prepared by induction and solution treated at 850°C and then further quenched into cold water. The addition of Nb and V promotes the formation of precipitates which act as grain refiner and subsequently improve the mechanical properties. The tensile tests were performed at temperatures slightly inferior to Mf and superior to Af, to investigate the shape recovery and pseudoelasticity, respectively. Based on the analyses of the Cu-13,8Al-2Ni-1Nb (wt%) alloy was detected rupture strains greater than 14%, besides observation of the superelasticity of these alloys and quantification of this property by means of cycling, from 0 to strains between 1 and 7%. The studies performed on alloy Cu-13.8Al- 3,5Ni-1V (wt%) made it possible to determine rupture strains in the order of 3% and its superelastic behavior through cycling for deformations between 1 and 3%.

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