• Journal of The Korean Association For Science Education
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• v.27 no.6
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• pp.477-487
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• 2007

Previous studies show that students have difficulties in understanding and using molecular visualization tools. This study focuses on the ways in which first year chemistry undergraduates use ball-and-stick molecular models to explain the concept of addition reaction and the difficulties that they face using the models. Video recordings of interviews with undergraduates manipulating ball-and-stick models to solve problems related to reaction mechanisms are analysed to determine if they are able to elucidate their understanding with use of models. The results showed that students have difficulties with viewing the ball-and-stick models from the proper perspective and understanding the relationship between the various structures that they have created using the models. They also find the use of ball-and-stick models tedious and prefer drawing molecular structures on paper to explain their ideas. Implications for the teaching using ball-and-stick molecular models are discussed.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2433-2442
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• 2011

The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

• Journal of Microbiology
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• v.43 no.spc1
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• pp.118-131
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• 2005

Vibrio vulnificus is an opportunistic pathogen of humans that has the capability of causing rare, yet devastating disease. The bacteria are naturally present in estuarine environments and frequently contaminate seafoods. Within days of consuming uncooked, contaminated seafood, predisposed individuals can succumb to sepsis. Additionally, in otherwise healthy people, V. vulnificus causes wound infection that can require amputation or lead to sepsis. These diseases share the characteristics that the bacteria multiply extremely rapidly in host tissues and cause extensive damage. Despite the analysis of virulence for over 20 years using a combination of animal and cell culture models, surprisingly little is known about the mechanisms by which V. vulnificus causes disease. This is in part because of differences observed using animal models that involve infection with bacteria versus injection of toxins. However, the increasing use of genetic analysis coupled with detailed animal models is revealing new insight into the pathogenesis of V. vulnificus disease.

• Journal of Korean Society for Atmospheric Environment
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• v.25 no.3
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• pp.219-236
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• 2009

Particle-phase organic tracers (molecular markers) have been shown to be an effective method to assess and quantify the impact of sources of carbonaceous aerosols. These molecular markers have been used in chemical mass balance (CMB) models to apportion primary sources of organic aerosols in regions where the major organic aerosol source categories have been identified. As in the case of all CMB models, all important sources of the tracer compounds must be included in a Molecular Marker CMB (MM-CMB) model or the MMCMB model can be subject to biases. To this end, the application of the MM-CMB models to locations where reasonably accurate emissions inventory of organic aerosols are not available, should be performed with extreme caution. Of great concern is the potential presence of industrial point sources that emit carbonaceous aerosols and have not been well characterized or inventoried. The current study demonstrates that emissions from industrial point sources in the St. Louis, Missouri area can greatly bias molecular marker CMB models if their emissions are not correctly addressed. At a sampling site in the greater St. Louis Area, carbonaceous aerosols from industrial point sources were found to be important source of carbonaceous aerosols during specific time periods in addition to common urban sources (i.e. mobile sources, wood burning, and road dust). Since source profiles for these industrial sources have not been properly characterized, method to identify time periods when point sources are impacting a sampling site, needs to avoid obtaining biases source apportionment results. The use of real time air pollution measurements, along with molecular marker measurements, as a screening tool to identify when point sources are impacting a receptor site is presented.

• Biomolecules & Therapeutics
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• v.15 no.1
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• pp.7-15
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• 2007

There have been various animal models of skin inflammation. These models have been used for establishing anti-inflammatory activity of the topical agents including cosmetics. Here, the molecular mechanisms of most widely-used animal models of skin inflammation including contact irritation, acute and chronic inflammation, and delayed-type hypersensitivity are summarized. Against these animal models, varieties of plant flavonoids showed anti-inflammatory activity. The action mechanisms of anti-inflammation by topical flavonoids are presented. A therapeutic potential of flavonoids is discussed.

• Interdisciplinary Bio Central
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• v.3 no.4
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• pp.15.1-15.11
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• 2011

Background: Histone deacetylase (HDAC) 8 is one of its family members catalyzes the removal of acetyl groups from N-terminal lysine residues of histone proteins thereby restricts transcription factors from being expressed. Inhibition of HDAC8 has become an emerging and effective anti-cancer therapy for various cancers. Application computational methodologies may result in identifying the key components that can be used in developing future potent HDAC8 inhibitors. Results: Facilitating the discovery of novel and potential chemical scaffolds as starting points in the future HDAC8 inhibitor design, quantitative structure-activity relationship models were generated with 30 training set compounds using genetic function approximation (GFA) and Bayesian algorithms. Six GFA models were selected based on the significant statistical parameters calculated during model development. A Bayesian model using fingerprints was developed with a receiver operating characteristic curve cross-validation value of 0.902. An external test set of 54 diverse compounds was used in validating the models. Conclusions: Finally two out of six models based on their predictive ability over the test set compounds were selected as final GFA models. The Bayesian model has displayed a high classifying ability with the same test set compounds and the positively and negatively contributing molecular fingerprints were also unveiled by the model. The effectively contributing physicochemical properties and molecular fingerprints from a set of known HDAC8 inhibitors were identified and can be used in designing future HDAC8 inhibitors.

• Korean Journal of Audiology
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• v.24 no.2
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• pp.53-60
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• 2020

Several novel animal models that represent the pathophysiological process of endolymphatic hydrops (ELH) of Meniere's disease (MD) have been developed. Animal models are important to identify and characterize the pathophysiology of ELH and to corroborate molecular and genetic findings in humans. This review of the current animal models will be useful in understanding the pathophysiology of and developing proper treatments for MD. Surgical animal models will be replaced by medication-induced animal models. Study models previously developed in guinea pigs will be developed in several smaller animals for ease of conducting molecular analysis. In this review, we provided updated resources including our previous studies regarding the current and desirable animal models for MD.

• Journal of Audiology & Otology
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• v.24 no.2
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• pp.53-60
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• 2020

Several novel animal models that represent the pathophysiological process of endolymphatic hydrops (ELH) of Meniere's disease (MD) have been developed. Animal models are important to identify and characterize the pathophysiology of ELH and to corroborate molecular and genetic findings in humans. This review of the current animal models will be useful in understanding the pathophysiology of and developing proper treatments for MD. Surgical animal models will be replaced by medication-induced animal models. Study models previously developed in guinea pigs will be developed in several smaller animals for ease of conducting molecular analysis. In this review, we provided updated resources including our previous studies regarding the current and desirable animal models for MD.

• Korea-Australia Rheology Journal
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• v.14 no.4
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• pp.161-174
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• 2002

A new technique for numerical calculation of viscoelastic flow based on the combination of Neural Net-works (NN) and Brownian Dynamics simulation or Stochastic Simulation Technique (SST) is presented in this paper. This method uses a "universal approximator" based on neural network methodology in combination with the kinetic theory of polymeric liquid in which the stress is computed from the molecular configuration rather than from closed form constitutive equations. Thus the new method obviates not only the need for a rheological constitutive equation to describe the fluid (as in the original Calculation Of Non-Newtonian Flows: Finite Elements St Stochastic Simulation Techniques (CONNFFESSIT) idea) but also any kind of finite element-type discretisation of the domain and its boundary for numerical solution of the governing PDE's. As an illustration of the method, the time development of the planar Couette flow is studied for two molecular kinetic models with finite extensibility, namely the Finitely Extensible Nonlinear Elastic (FENE) and FENE-Peterlin (FENE-P) models.P) models.

• BMB Reports
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• v.52 no.1
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• pp.70-85
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• 2019

Reduction of insulin/insulin-like growth factor 1 (IGF1) signaling (IIS) extends the lifespan of various species. So far, several longevity mouse models have been developed containing mutations related to growth signaling deficiency by targeting growth hormone (GH), IGF1, IGF1 receptor, insulin receptor, and insulin receptor substrate. In addition, p70 ribosomal protein S6 kinase 1 (S6K1) knockout leads to lifespan extension. S6K1 encodes an important kinase in the regulation of cell growth. S6K1 is regulated by mechanistic target of rapamycin (mTOR) complex 1. The v-myc myelocytomatosis viral oncogene homolog (MYC)-deficient mice also exhibits a longevity phenotype. The gene expression profiles of these mice models have been measured to identify their longevity mechanisms. Here, we summarize our knowledge of long-lived mouse models related to growth and discuss phenotypic characteristics, including organ-specific gene expression patterns.