Design and validation of a frugal, automated, solid-phase peptide synthesizer.
ABSTRACT: Solid phase peptide synthesis (SPPS) has enabled widespread use of synthetic peptides in applications ranging from pharmaceuticals to materials science. The demand for synthetic peptides has driven recent efforts to produce automated SPPS synthesizers which utilize fluid-handling components common to chemistry laboratories to drive costs down to several thousand dollars. Herein, we describe the design and validation of a more 'frugal' SPPS synthesizer that uses inexpensive, consumer-grade fluid-handling components to achieve a prototype price point between US$300 and $600. We demonstrated functionality by preparing and characterizing peptides with a variety of distinct properties including binding functionality, nanoscale self-assembly, and oxidation-induced fluorescence. This system yielded micromoles of peptide at a cost of approximately $1/residue, a cost which may be further reduced by optimization and bulk purchasing.
Project description:Frugal products possess a proper mix of features including minimal consumption of resources, good functionality under nominal conditions and low cost. Therefore, increasing use of frugal products, that are designed and also fabricated systematically, is crucial to all-round sustainable development. However, their low factor-of-safety rigorous-design makes them inherently prone to failure under conditions of overloading. And multitudes of such coupled-products would create topologies of interconnected complex systems in the foreseeable future whose individual products should be made to adapt against any events of failure to enhance functionality while maintaining low cost. Accordingly, this paper proposes a two-pronged methodology for adaptation of frugal products along with ramifications of complex systems of frugal products. The adaptation methodology is crucial to the functioning of individual and also networks of frugal products and this work accordingly explicates scenarios of ensuing networks. Other than application to various sectors including electric vehicles, a basic example of which is covered in this paper, the proposed adaptation-and-networking framework can also be applied to a growing numbers of sustainable products, which are frugal according to the terminology of this effort and hence prone to premature failure.
Project description:A DNA synthesizer was successfully employed for preparation of well-defined polymers by atom transfer radical polymerization (ATRP), in a technique termed AutoATRP. This method provides well-defined homopolymers, diblock copolymers, and biohybrids under automated photomediated ATRP conditions. PhotoATRP was selected over other ATRP methods because of mild reaction conditions, ambient temperature, tolerance to oxygen, and no need to introduce reducing agents or radical initiators. Both acrylate and methacrylate monomers were successfully polymerized with excellent control in the DNA synthesizer. Diblock copolymers were synthesized with different targeted degrees of polymerization and with high retention of chain-end functionality. Both hydrophobic and hydrophilic monomers were grafted from DNA. The DNA-polymer hybrids were characterized by SEC and DLS. The AutoATRP method provides an efficient route to prepare a range of different polymeric materials, especially polymer-biohybrids.
Project description:Heuristics are simple, yet effective, strategies that people use to make decisions. Because heuristics do not require all available information, they are thought to be easy to implement and to not tax limited cognitive resources, which has led heuristics to be characterized as fast-and-frugal. We question this monolithic conception of heuristics by contrasting the cognitive demands of two popular heuristics, Tallying and Take-the-Best. We contend that heuristics that are frugal in terms of information usage may not always be fast because of the attentional control required to implement this focus in certain contexts. In support of this hypothesis, we find that Take-the-Best, while being more frugal in terms of information usage, is slower to implement and fares worse under time pressure manipulations than Tallying. This effect is then reversed when search costs for Take-the-Best are reduced by changing the format of the stimuli. These findings suggest that heuristics are heterogeneous and should be unpacked according to their cognitive demands to determine the circumstances a heuristic best applies. (PsycINFO Database Record
Project description:Restoring natural speech in paralyzed and aphasic people could be achieved using a Brain-Computer Interface (BCI) controlling a speech synthesizer in real-time. To reach this goal, a prerequisite is to develop a speech synthesizer producing intelligible speech in real-time with a reasonable number of control parameters. We present here an articulatory-based speech synthesizer that can be controlled in real-time for future BCI applications. This synthesizer converts movements of the main speech articulators (tongue, jaw, velum, and lips) into intelligible speech. The articulatory-to-acoustic mapping is performed using a deep neural network (DNN) trained on electromagnetic articulography (EMA) data recorded on a reference speaker synchronously with the produced speech signal. This DNN is then used in both offline and online modes to map the position of sensors glued on different speech articulators into acoustic parameters that are further converted into an audio signal using a vocoder. In offline mode, highly intelligible speech could be obtained as assessed by perceptual evaluation performed by 12 listeners. Then, to anticipate future BCI applications, we further assessed the real-time control of the synthesizer by both the reference speaker and new speakers, in a closed-loop paradigm using EMA data recorded in real time. A short calibration period was used to compensate for differences in sensor positions and articulatory differences between new speakers and the reference speaker. We found that real-time synthesis of vowels and consonants was possible with good intelligibility. In conclusion, these results open to future speech BCI applications using such articulatory-based speech synthesizer.
Project description:For decades, researchers have endeavored to develop a general automated system to synthesize oligosaccharides that is comparable to the preparation of oligonucleotides and oligopeptides by commercially available machines. Inspired by the success of automated oligosaccharide synthesis through chemical glycosylation, a fully automated system is reported for oligosaccharides synthesis through enzymatic glycosylation in aqueous solution. The designed system is based on the use of a thermosensitive polymer and a commercially available peptide synthesizer. This study represents a proof-of-concept demonstration that the enzymatic synthesis of oligosaccharides can be achieved in an automated manner using a commercially available peptide synthesizer.
Project description:A stable 50-mJ three-channel optical waveform synthesizer is demonstrated and used to reproducibly generate a high-order harmonic supercontinuum in the soft x-ray region. This synthesizer is composed of pump pulses from a 10-Hz repetition-rate Ti:sapphire pump laser and signal and idler pulses from an infrared two-stage optical parametric amplifier driven by this pump laser. With full active stabilization of all relative time delays, relative phases, and the carrier-envelope phase, a shot-to-shot stable intense continuum harmonic spectrum is obtained around 60 eV with pulse energy above 0.24 ?J. The peak power of the soft x-ray continuum is evaluated to be beyond 1 GW with a 170-as transform limit duration. We found a characteristic delay dependence of the multicycle waveform synthesizer and established its control scheme. Compared with the one-color case, we experimentally observe an enhancement of the cutoff spectrum intensity by one to two orders of magnitude using three-color waveform synthesis.
Project description:Frequency combs have made optical metrology accessible to hundreds of laboratories worldwide and they have set new benchmarks in multi-species trace gas sensing for environmental, industrial and medical applications. However, current comb spectrometers privilege either frequency precision and sensitivity through interposition of a cw probe laser with limited tuning range, or spectral coverage and measurement time using the comb itself as an ultra-broadband probe. We overcome this restriction by introducing a comb-locked frequency-swept optical synthesizer that allows a continuous-wave laser to be swept in seconds over spectral ranges of several terahertz while remaining phase locked to an underlying frequency comb. This offers a unique degree of versatility, as the synthesizer can be either repeatedly scanned over a single absorption line to achieve ultimate precision and sensitivity, or swept in seconds over an entire rovibrational band to capture multiple species. The spectrometer enables us to determine line center frequencies with an absolute uncertainty of 30?kHz and at the same time to collect absorption spectra over more than 3?THz with state-of-the-art sensitivity of a few 10-10?cm-1. Beyond precision broadband spectroscopy, the proposed synthesizer is an extremely promising tool to force a breakthrough in terahertz metrology and coherent laser ranging.
Project description:Scientists have unprecedented access to a wide variety of high-quality datasets. These datasets, which are often independently curated, commonly use unstructured spreadsheets to store their data. Standardized annotations are essential to perform synthesis studies across investigators, but are often not used in practice. Therefore, accurately combining records in spreadsheets from differing studies requires tedious and error-prone human curation. These efforts result in a significant time and cost barrier to synthesis research. We propose an information retrieval inspired algorithm, Synthesize, that merges unstructured data automatically based on both column labels and values. Application of the Synthesize algorithm to cancer and ecological datasets had high accuracy (on the order of 85-100%). We further implement Synthesize in an open source web application, Synthesizer (https://github.com/lisagandy/synthesizer). The software accepts input as spreadsheets in comma separated value (CSV) format, visualizes the merged data, and outputs the results as a new spreadsheet. Synthesizer includes an easy to use graphical user interface, which enables the user to finish combining data and obtain perfect accuracy. Future work will allow detection of units to automatically merge continuous data and application of the algorithm to other data formats, including databases.
Project description:Reliable and rapid access to defined biopolymers by automated DNA and peptide synthesis has fundamentally altered biological research and medical practice. Similarly, the procurement of defined glycans is key to establishing structure-activity relationships and thereby progress in the glycosciences. Here, we describe the rapid assembly of oligosaccharides using the commercially available Glyconeer 2.1 automated glycan synthesizer, monosaccharide building blocks, and a linker-functionalized polystyrene solid support. Purification and quality-control protocols for the oligosaccharide products have been standardized. Synthetic glycans prepared in this way are useful reagents as the basis for glycan arrays, diagnostics, and carbohydrate-based vaccines.
Project description:Electrochemical 18F-fluorination of organic compounds provides a means to synthesize Positron-Emission-Tomography (PET) tracers difficult to obtain otherwise. Here, the first automated synthesizer that enables radiolabeling through carrier-added electrochemical 18F-fluorination is described. The system provides capabilities for all necessary operations such as drying of cyclotron derived [18F]fluoride, electrochemical incorporation of the radioisotope into a precursor molecule, subsequent reactions such as protecting group removals, HPLC-purification and formulation of the final tracer. Demonstrated is the aliphatic electrochemical 18F-fluorination of methyl 2-(phenylthio)acetate.