• Journal of Microbiology and Biotechnology
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• 제24권3호
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• pp.408-420
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• 2014

Yeast surface-displayed antibody libraries provide an efficient and quantitative screening resource for given antigens, but suffer from typically modest library sizes owing to low yeast transformation efficiency. Yeast mating is an attractive method for overcoming the limit of yeast transformation to construct a large, combinatorial antibody library, but the optimal conditions have not been reported. Here, we report a large synthetic human Fab (antigen binding fragment) yeast surface-displayed library generated by stepwise optimization of yeast mating conditions. We first constructed HC (heavy chain) and LC (light chain) libraries, where all of the six CDRs (complementarity-determining regions) of the variable domains were diversified mimicking the human germline antibody repertoires by degenerate codons, onto single frameworks of VH3-23 and $V{\kappa}1$-16 germline sequences, in two haploid cells of opposite mating types. Yeast mating conditions were optimized in the order of cell density, media pH, and cell growth phase, yielding a mating efficiency of ~58% between the two haploid cells carrying HC and LC libraries. We constructed two combinatorial Fab libraries with CDR-H3 of 9 or 11 residues in length with colony diversities of more than $10^9$ by one round of yeast mating between the two haploid HC and LC libraries, with modest diversity sizes of ${\sim}10^7$. The synthetic human Fab yeast-displayed libraries exhibited relative amino acid compositions in each position of the six CDRs that were very similar to those of the designed repertoires, suggesting that they are a promising source for human Fab antibody screening.

• Molecules and Cells
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• 제27권2호
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• pp.225-235
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• 2009

Antibody phage display provides a powerful and efficient tool for the discovery and development of monoclonal antibodies for therapeutic and other applications. Antibody clones from synthetic libraries with optimized design features have several distinct advantages that include high stability, high levels of expression, and ease of downstream optimization and engineering. In this study, a fully synthetic human scFv library with six diversified CDRs was constructed by polymerase chain reaction assembly of overlapping oligonucleotides. In order to maximize the functional diversity of the library, a ${\beta}$-lactamase selection strategy was employed in which the assembled scFv gene repertoire was fused to the 5'-end of the ${\beta}$-lactamase gene, and in-frame scFv clones were enriched by carbenicillin selection. A final library with an estimated total diversity of $7.6{\times}10^9$, greater than 70% functional diversity, and diversification of all six CDRs was obtained after insertion of fully randomized CDR-H3 sequences into this proofread repertoire. The performance of the library was validated using a number of target antigens, against which multiple unique scFv sequences with dissociation constants in the nanomolar range were isolated.

• 제어로봇시스템학회논문지
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• 제18권5호
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• pp.465-470
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• 2012

This paper proposes a distributed autonomous control method of swarm robot behavior strategy based on artificial immune system and an optimization strategy for artificial immune system. The behavior strategies of swarm robot in the system are depend on the task distribution in environment and we have to consider the dynamics of the system environment. In this paper, the behavior strategies divided into dispersion and aggregation. For applying to artificial immune system, an individual of swarm is regarded as a B-cell, each task distribution in environment as an antigen, a behavior strategy as an antibody and control parameter as a T-cell respectively. The executing process of proposed method is as follows: When the environmental condition changes, the agent selects an appropriate behavior strategy. And its behavior strategy is stimulated and suppressed by other agent using communication. Finally much stimulated strategy is adopted as a swarm behavior strategy. In order to decide more accurately select the behavior strategy, the optimized parameter learning procedure that is represented by stimulus function of antigen to antibody in artificial immune system is required. In this paper, particle swarm optimization algorithm is applied to this learning procedure. The proposed method shows more adaptive and robustness results than the existing system at the viewpoint that the swarm robots learning and adaptation degree associated with the changing of tasks.

• International Journal of Fuzzy Logic and Intelligent Systems
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• 제4권1호
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• pp.7-11
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• 2004

This paper proposes a new immunotronic approach for the fault detection in hardware. The suggested method is, inspired by biology and its implementation is based on genetic algorithm. Tolerance conditions in the immunotronic system for fault detection correspond to the antibodies in the biological immune system. A novel algorithm of generating tolerance conditions is suggested based on the principle of the antibody diversity and GA optimization is employed to select mature tolerance conditions in immunotronic fault detection system. The suggested method is applied to the fault detection for MCNC benchmark FSMs (finite state machines) and its effectiveness is demonstrated by the computer simulation.

• Biotechnology and Bioprocess Engineering:BBE
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• 제7권3호
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• pp.163-170
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• 2002

This report describes the use of a transtubular bioreactor to study the relative effects of diffusion versus perfusion of medium on antibody production by a hybridoma cell line. The study was performed with a high-density cell culture maintained in a serum-free, low-protein medium for 77 days. It was determined that the reactor possessed a macro-mixing pattern residence time distribution similar to a continuous stirred tank reactor (CSTR), However, due to the arrangement of the medium lines in the reactor, the flow patterns for nutrient distribution consist of largely independent medium path lengths ranging from short to long. When operated with cyclic, reversing, transtubular medium flow, some regions of the reactor (with short residence times) are more accessible to medium than others (with long residence times). From this standpoint, the reactor can be divided into three regions: a captive volume, which consists of medium primarily delivered via diffusion; a lapped volume, which provides nutrients through unilateral convection; and a swept volume, which operates through bilateral convection. The relative sizes of these three volumes were modified experimentally by changing the period over which the direction of medium flow was reversed from 15 min (larger captive volume) to 9 h (larger swept volume). The results suggest that antibody concentration increases as the size of the diffusion-limited (captive) volume is increased to a maximum at around 30 min with a sharp decrease thereafter. As reflected by changes in measured consumption of glucose and production of lactate, no significant difference in cellular metabolism occurred as the reactor was moved between these different states. These results indicate that the mode of operation of the transtubular bioreactor may influence antibody productivity under serum-free, low-protein conditions with minimal effects on cellular metabolism.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제15권5호
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• pp.1666-1689
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• 2021

The red line of Permanent Basic Farmland is the most important part in the "three-line" demarcation of China's national territorial development plan. The scientific and reasonable delineation of the red line is a major strategic measure being taken by China to improve its ability to safeguard the practical interests of farmers and guarantee national food security. The delineation of Permanent Basic Farmland zoning (DPBFZ) is essentially a multi-objective optimization problem. However, the traditional method of demarcation does not take into account the synergistic development goals of conservation of cultivated land utilization, ecological conservation, or urban expansion. Therefore, this research introduces the idea of artificial immune optimization and proposes a multi-objective model of DPBFZ red line delineation based on a clone selection algorithm. This research proposes an objective functional system consisting of these three sub-objectives: optimal quality of cropland, spatially concentrated distribution, and stability of cropland. It also takes into consideration constraints such as the red line of ecological protection, topography, and space for major development projects. The mathematical formal expressions for the objectives and constraints are given in the paper, and a multi-objective optimal decision model with multiple constraints for the DPBFZ problem is constructed based on the clone selection algorithm. An antibody coding scheme was designed according to the spatial pattern of DPBFZ zoning. In addition, the antibody-antigen affinity function, the clone mechanism, and mutation strategy were constructed and improved to solve the DPBFZ problem with a spatial optimization feature. Finally, Tongxu County in Henan province was selected as the study area, and a controlled experiment was set up according to different target preferences. The results show that the model proposed in this paper is operational in the work of delineating DPBFZ. It not only avoids the adverse effects of subjective factors in the delineation process but also provides multiple scenarios DPBFZ layouts for decision makers by adjusting the weighting of the objective function.

• 생약학회지
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• 제46권4호
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• pp.279-282
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• 2015

In order to quantify compound K(CK), anticancer component of Panax ginseng C. A. Meyer, high titer rabbit polyclonal antibodies (pAbs) were raised against a conjugate of CK and bovine serum albumin coupled by a periodate oxidation method. Coating antigen (CK-OVA) was also prepared by the same method with OVA. As a result of optimization of antiserum dilution (2,000 fold), coating antigen ($25{\mu}g/ml$) and other condition (incubation time, temperature and washing method), ELISA method for the determination of CK was established. The measuring range extended from 0.5 ng/ml to 25 ng/ml of CK. The antibodies exhibited minor or even no cross reactivities with protopanaxatriol (1.56%) and other tested ginsenosides, $GRb_1$ (0.11%), $GRg_1$ (0.07%) except protopanaxadiol (87.2%) from the structural similarity. And the antibody showed good correlation (r=0.987) between the assay values obtained by this ELISA method and HPLC. Therefore, the ELISA method could be very useful tools for the determination of CK in biological fluids because of their high sensitivity and specificity.

• Bulletin of the Korean Chemical Society
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• 제22권9호
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• pp.953-957
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• 2001

The specificity of conjugation site for coating ligands was investigated using toluene-bovine serum albumin (BSA) conjugates in which BSA was conjugated at the position of o-, m-, and ${\rho}-toluic$ acid. Toluene-BSA conjugated at ${\rho}-position$ showed a binding activity of about 89-95%, whereas, those conjugated at o- and m-position of toluene exhibited a binding activity of 5 and 11%, respectively. On the basis of the above result, coating ligands with various proteins (OVA, BSA, KLH) were compared by conjugating with $\rho-toluic$ acid, and toluene-KLH was considered as the best coating ligand for this ELISA. Indirect competitive ELISA method was developed using anti-toluene antibody and $\rho-position$ conjugated toluene-KLH. The dose-response curve constructed after kinetic and optimization studies showed a 1${\times}$10-4 - 1${\times}$102 mM detectable response range with 0.1 ${\mu}M$ detectability. In specificity test of the antibody, the binding capabilities of aromatic compounds substituted with nitro-, alkyl-, chloro-, and hydroxyl group were larger rather than those of aromatic compounds (benzene, toluene and xylene) themselves. Also, tests with soil and water samples that had been spiked with toluene resulted in 102.7-113.7% recovery.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2003년도 학술발표대회 발표논문초록집
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• pp.79-79
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• 2003

Embryonic stem cells are capable of differentiating into a variety of cell lineages. However, the ultimate results of differentiation in vitro greatly depend on the duration of treatment and kinds of differentiating inducers added. In order to investigate the efficiencies of various differentiation inducers and the methods of treatment, we examined differentiation patterns of human embryonic stem cell (hESC, MB03) according to several different protocols. Exp. I) Upon differentiation using retinoic acid and ascorbic acid (RA/AA), embryoid bodies (EB, for 4days) derived from hESC was exposed to Rh (10$^{-6}$ M) and AA (50 mM) for 4 days, and were allowed to differentiate in N2 medium for 7, 14, 21, or 28 days. Exp. II) When bFGF was used, neuronal precursor cells were selected for 8 days in N2 medium after EB formation. After selection, cells were expanded at the presence of bFGF (20 ng/ml) for another 6 days followed by a final differentiation in N2 medium for 7, 14, 21 or 28 days. Exp. III) In addition, to examine the effects of neurotrophic factors in the production of mature neurons, groups of cells were exposed to either BDNF (5 ng/ml) or TGF-$\alpha$(10 ng/ml) during the 28 days of final differentiation. Differentiation patterns of RA/AA or bFGF treated groups were very similar; approximately 82% and 83% of the cells, respectively, were positive for anti-NF200 antibody, while it was about 10% and 11%, respectively, for anti-NF160 antibody in 28 days in N2 medium. Alsor, cells expressing TH were as low as 5%, while the cells doubled when matured at the presence of either BDNF or TGF-$\alpha$. Cells immunoreactive to anti-GAD antibody were approximately 20%. These results suggest that a maturation step rather than differentiation induction step, which is formation of EB, effects more decisively to the ultimate differentiation pattern.

• Journal of Gastric Cancer
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• 제23권1호
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• pp.224-249
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• 2023

Gastric cancer is heterogeneous in morphology, biology, genomics, and treatment response. Alterations in human epidermal growth factor receptor 2 (HER2) overexpression, microsatellite instability (MSI) status, programmed death-ligand 1 (PD-L1) levels, and fibroblast growth factor receptor 2 (FGFR2) can be used as biomarkers. Since the combination of fluoropyrimidine/platinum plus trastuzumab that was investigated in the ToGA trial was approved as a standard of care in HER2-positive patients in 2010, no other agents showed efficacy in the first- (HELOISE, LOGiC, JACOB trials) and second- (TyTAN, GATSBY, T-ACT trials) line treatments. Despite the success in treating breast cancer, various anti-HER2 agents, including a monoclonal antibody (pertuzumab), an antibody-drug conjugate (ADC; trastuzumab emtansine [T-DM1]), and a small molecule (lapatinib) failed to translate into clinical benefits until the KEYNOTE-811 (first-line) and DESTINY-Gastri01 (≥second-line) trials were conducted. The incorporation of HER2-directed treatment with immune checkpoint inhibitors in the form of a monoclonal antibody or ADC is now approved as a standard treatment. Despite the promising results of new agents (engineered monoclonal antibodies, bi-specific antibodies, fusion proteins, and small molecules) in the early phase of development, the management of HER2-positive gastric cancer requires further optimization to achieve precision medicine with a chemotherapeutic backbone. Treatment resistance is a complex process that can be overcome using a combination of chemotherapy, targeted agents, and immune checkpoint inhibitors, including novel agents. HER2 status must be reassessed in patients undergoing anti-HER2 treatment with disease progression after the first-line treatment. As a general guideline, patients who need systemic treatment should receive chemotherapy plus targeted agents, anti-angiogenic agents, immune checkpoint inhibitors, or their combinations.