• Journal of Microbiology and Biotechnology
• /
• v.30 no.12
• /
• pp.1919-1926
• /
• 2020

CRISPR interference (CRISPRi) has been developed as a transcriptional control tool by inactivating the DNA cleavage ability of Cas9 nucleases to produce dCas9 (deactivated Cas9), and leaving dCas9 the ability to specifically bind to the target DNA sequence. CRISPR/Cas9 technology has limitations in designing target-specific single-guide RNA (sgRNA) due to the dependence of protospacer adjacent motif (PAM) (5'-NGG) for binding target DNAs. Reportedly, Cas9-NG recognizing 5'-NG as the PAM sequence has been constructed by removing the dependence on the last base G of PAM through protein engineering of Cas9. In this study, a dCas9-NG protein was engineered by introducing two active site mutations in Cas9-NG, and its ability to regulate transcription was evaluated in the gal promoter in E. coli. Analysis of cell growth rate, D-galactose consumption rate, and gal transcripts confirmed that dCas9-NG can completely repress the promoter by recognizing DNA targets with PAM of 5'-NGG, NGA, NGC, NGT, and NAG. Our study showed possible PAM sequences for dCas9-NG and provided information on target-specific sgRNA design for regulation of both gene expression and cellular metabolism.

• Journal of Advanced Marine Engineering and Technology
• /
• v.32 no.4
• /
• pp.603-610
• /
• 2008

In this paper, analytical methods for calculating the average probability of bit error of direct sequence pulse amplitude modulation ultra wideband (DS-PAM UWB) system and time hopping pulse position modulation ultra wideband (TH-PPM UWB) system are given. For the multi-user DS-PAM UWB system, the bipolar pulse amplitude modulation is used in order to achieve better performance. As we know, more attention is paid to the TH-PPM UWB systems recently. In this paper. we first introduce the accurate BER calculation methods of the multi-user DS-PAM UWB and TH-PPM UWB systems and then give the performance analysis over the ideal AWGN channel and a correlation receiver. Furthermore, we also introduce their applications in image transmission and data transmission and give the simulation results. The analytical method yields simple and exact formulas relating the performance to the system parameters.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
• /
• 2009.05a
• /
• pp.447-450
• /
• 2009

In this paper, binary pulse-antipodal modulation (2PAM) direct-sequence (DS) ultra-wideband (UWB) system is applied to multiple input multiple output (MIMO) system using vertical bell lab layered space-time (V-BLAST) structure to achieve high-data-rate communications over indoor wireless channels. The relationship between antenna dimension and BER performance of 2PAM DS UWB MIMO system is discussed. In the receiver of UWB-MIMO system, various MIMO detection algorithms such as zero-forcing (ZF), ZF-ordered successive interference cancellation (OSIC), minimum-mean-square-error (MMSE), MMSE-OSIC and maximum likelihood (ML) are comparatively studied.

• Interdisciplinary Bio Central
• /
• v.6 no.4
• /
• pp.3.1-3.10
• /
• 2014

Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic ($ROC_{50}$) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.

• Journal of the Institute of Electronics Engineers of Korea SD
• /
• v.46 no.11
• /
• pp.84-91
• /
• 2009

A high speed serial link transmitter using multi-level signaling is proposed. To achieve high data rate m high speed serial link, 4-pulse amplitude modulation (PAM) is used. By transmitting 2 bit data in each symbol time, high speed data transmission, two times than binary signaling, is achieved. The transmitter transmits current-mode output instead of voltage-mode output Current-mode output is much faster than voltage-mode output, so higher data transmission is available by increasing switching speed of driver. $2^5-1$ pseudo-random bit sequence (PRBS) generator is contained to perform built-in self test (BIST). The 4-PAM transmitter is designed in Dongbu HiTek $0.18{\mu}m$ CMOS technology and achieves 8 Gb/s, 160 mV of eye height with 1.8 V supply voltage. The transmitter consumes only 98 mW for 8 Gb/s transmission.

• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.9 no.8
• /
• pp.1656-1662
• /
• 2005

This paper introduces M-PPAM(M-ary Pulse Position and Amplitude Modulation) architecture, combined PPM(Pulse Position Modulation) with PAM(Pulse Amplitude Modulation). Since M-PPAM can transmit several bits using one pulse, it is mon effective than PPM or PAM. Also, to obtain the same data transmission rate with PPM or PAM, M-PPAM can use a long pulse repetition period. This method will be able to use in the multi-path fading environment such as indoor condition. To accomodate multiple users, direct sequence technique is used. This paper has provided the modeling method of the M-PPAM DS-UWB receiver covering multi-user interference(MUI) with the Standard Gaussian Approximation under Gaussian channel. The performance of the receiver is simulated.

• Journal of Korea Technical Association of The Pulp and Paper Industry
• /
• v.41 no.2
• /
• pp.13-19
• /
• 2009

In order to produce high quality paper at the lowest cost in high speed, typically various polyelectrolytes as retention aids were used. Retention systems such as single polymer system, dual polymer system, and microparticle system were used. The objective of this study was to analyze the changes of retention, drainage, formation and fracture toughness depending on types of retention system, molecular weight of C-PAM and dosage sequences of agents. When single polymer system was applied, retention was increased with poor formation and drainage. When common microparticle system(C-PAM/bentonite) was used, high molecular weight PAM gave high retention and fast drainage, but poor formation. When the microparticle system with reverse dosage sequence(bentonite/C-PAM) was used, low molecular weight PAM gave high retention, fast drainage and good formation. When various retention agents were applied, fracture toughness was increased than that of blank. When using high molecular weight PAM and consequently causing excessive flocculation, fracture toughness was decreased.

• The Journal of the Institute of Internet, Broadcasting and Communication
• /
• v.9 no.2
• /
• pp.117-122
• /
• 2009

In this paper, the performance of double binary turbo code is analyzed and simulated in ultra wide-band (UWB) systems employing multiple-antenna scheme. We consider both pulse position modulation-time hopping (PPM-TH) and pulse amplitude modulation-direct sequence (PAM-DS) UWB systems. The space time block code (STBC) scheme is adopted as a transmit diversity method. Also, receive diversity scheme is applied. And double binary turbo code is applied to the UWB system.

• ETRI Journal
• /
• v.29 no.3
• /
• pp.322-328
• /
• 2007

We propose a direct-sequence pulse-amplitude modulation (DS-PAM) ultra-wideband (UWB) system which employs a non-linear chirp waveform instead of the conventional Gaussian monocycle in this paper. In the approved frequency for UWB, there exist myriad narrowband interferers. Specifically, we focus on the mutual interference between UWB systems and 802.11a WLAN. This paper offers a method to suppress this in-band narrowband interference by introducing a kind of non-linear chirp waveform. Using the proposed non-linear chirp waveform, the effects of one or more narrowband interference sources with different frequencies can be suppressed. System performance of UWB systems in the narrowband interference environment can be improved. Computer simulations with additive white Gaussian noise successfully demonstrate an increase in performance with the proposed system as compared to traditional linear chirp systems.

• Bioinformatics and Biosystems
• /
• v.2 no.1
• /
• pp.7-11
• /
• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.