• Journal of Microbiology and Biotechnology
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• v.32 no.8
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• pp.1026-1033
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• 2022

This study presents a novel DNA part characterization technique that increases throughput by combinatorial DNA part assembly, solid plate-based quantitative fluorescence assay for phenotyping, and barcode tagging-based long-read sequencing for genotyping. We confirmed that the fluorescence intensities of colonies on plates were comparable to fluorescence at the single-cell level from a high-end, flow-cytometry device and developed a high-throughput image analysis pipeline. The barcode tagging-based long-read sequencing technique enabled rapid identification of all DNA parts and their combinations with a single sequencing experiment. Using our techniques, forty-four DNA parts (21 promoters and 23 RBSs) were successfully characterized in 72 h without any automated equipment. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increasing part diversity and be useful for building genetic circuits and metabolic pathways in synthetic biology.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.202-202
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• 2006

With a modern size exclusion chromatography (SEC) column, molecular weight analysis of a polymer sample takes about 10 min. However, it is desirable to reduce the analysis time further, in particular, for high throughput measurements required in combinatorial analyses or 2D-HPLC analyses. We implemented the high temperature SEC for the purpose. By inserting a narrow bore tubing between the column and the detector, a sufficient backpressure can be maintained to prevent the mobile phase from boiling and the effluent is cooled down enough when it reaches the detector. Therefore, a normal SEC detector can be used without any modification. The SEC resolution is greatly improved at the elevated temperature at high flow rate which allows high speed operation.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2009.06a
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• pp.693-694
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• 2009

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.385-399
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• 2005

The phenotypic response of a cell results from a well orchestrated web of complex interactions which propagate from the genetic architecture through the metabolic flux network. To rationally design cell factories which carry out specific functional objectives by controlling this hierarchical system is a challenge. Transcriptome analysis, the most mature high-throughput measurement technology, has been readily applied In strain improvement programs in an attempt to Identify genes involved in expressing a given phenotype. Unfortunately, while differentially expressed genes may provide targets for metabolic engineering, phenotypic responses are often not directly linked to transcriptional patterns, This limits the application of genome-wide transcriptional analysis for the design of cell factories. However, improved tools for integrating transcriptional data with other high-throughput measurements and known biological interactions are emerging. These tools hold significant promise for providing the framework to comprehensively dissect the regulatory mechanisms that identify the cellular control mechanisms and lead to more effective strategies to rewire the cellular control elements for metabolic engineering.

• Proceedings of the KSME Conference
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• 2003.04a
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• pp.1036-1042
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• 2003

The hot embossing process has been mentioned as one of major nanoreplication techniques. This is due to its simple process, low cost, high replication fidelity and relatively high throughput. As the initial step of quantitating the embossing process , simple parametric study about embossing time have been carried out using high-resolution masters which patterned by the DRIE process and laser machining. Under the various embossing time, the viscous flow of thin PMMA films into microcavities during compression force has been investigated. Also, a study about simulating the viscous flow during embossing process has planned and continuum scale FDM analysis was applied on this simulation. With currently available test data and condition, simple FDM analysis using FLOW3D was made attempt to match simulation and experiment.

• Mass Spectrometry Letters
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• v.4 no.3
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• pp.47-50
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• 2013

An ultra-fast generic LC-MS/MS method was developed for high-throughput quantification of discovery pharmacokinetic (PK) samples and its reliability was verified. The method involves a simple protein precipitation for sample preparation and the analysis by ultra-fast generic LC-MS/MS with the ballistic gradient program and selected reaction monitoring (SRM) mode. Approximately 290 new chemical entities (NCEs) (over 10,000 samples) from 5 therapeutic programs were analyzed. The calibration curves showed good linearity in the concentration range of 1, 2 or 5 to 2000 ng/mL. No significant ion suppression was observed in the elution region of all the NCEs. When approximately 300 plasma samples were continuously analyzed, the peak area of internal standard was constant and reproducible. In the repeated analysis of samples, the plasma concentrations and the area under the curve (AUC) were consistent with the results from the first analysis. These results showed that the present ultra-fast generic LC-MS/MS method is reliable in terms of selectivity, sensitivity, and reproducibility and could be useful for high-throughput quantification and other bioanalysis in drug discovery.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.2
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• pp.69-75
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• 2004

In recent years, the importance of proteomic works, such as protein expression, detection and identification, has grown in the fields of proteomic and diagnostic research. This is because complete genome sequences of humans, and other organisms, progress as cellular processing and controlling are performed by proteins as well as DNA or RNA. However, conventional I protein analyses are time-consuming; therefore, high throughput protein analysis methods, which allow fast, direct and quantitative detection, are needed. These are so-called protein microarrays or protein chips, which have been developed to fulfill the need for high-throughput protein analyses. Although protein arrays are still in their infancy, technical development in immobilizing proteins in their native conformation on arrays, and the development of more sensitive detection methods, will facilitate the rapid deployment of protein arrays as high-throughput protein assay tools in proteomics and diagnostics. This review summarizes the basic technologies that are needed in the fabrication of protein arrays and their recent applications.

• BMB Reports
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• v.50 no.4
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• IEIE Transactions on Smart Processing and Computing
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• v.3 no.5
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• pp.275-284
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• 2014

This paper considers two-tier networks consisting of macrocells and femtocells operating in the same spectrum. This paper proposes a femtocell spectrum reuse scheme that determines the shared spectrum and transmit power for the femtocells to mitigate the effects of cross-tier interference between the macrocells and femtocells. The proposed scheme provides macrocell throughput that is unaffected by the increasing number of femtocells per cell site and improves the femtocell signal quality at the same time by limiting the cross-tier interference. This study analyzed the per-tier signal-to-interference ratio (SIR) and outage probability of the proposed scheme to investigate the macrocell and femtocell performance. The total throughput of the proposed scheme was analyzed based on the outage probabilities. The analysis and numerical results proved that high femtocell throughput can be achieved using only a small fraction of the spectrum while protecting the macrocell throughput. As a result, an improved total throughput was achieved enforcing higher spatial reuse.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.6 no.12
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• pp.3237-3256
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• 2012

In the context of effective usage of a scarce spectrum resource, emerging wireless communication standards will demand spectrum sharing with existing systems as well as multiple access with higher spectral efficiency. We mathematically analyze the sum throughput of a spectrum sharing space-division multiple access (SDMA) system, which forms a transmit null in the direction of other coexisting systems while satisfying orthogonal beamforming constraints. For a large number of users N, the SDMA throughput scales as log N at high signal-to-noise ratio (SNR) ((J-1) loglog N at normal SNR), where J is the number of transmit antennas. This indicates that multiplexing gain of the spectrum sharing SDMA is $\frac{J-1}{J}$ times less than that of the non-spectrum sharing SDMA only using orthogonal beamforming, whereas no loss in multiuser diversity gain. Although the spectrum sharing SDMA always has lower throughput compared to the non-spectrum sharing SDMA in the non-coexistence scenario, it offers an intriguing opportunity to reuse spectrum already allocated to other coexisting systems.