• Journal of Microbiology and Biotechnology
• /
• v.18 no.6
• /
• pp.1121-1129
• /
• 2008

A series of steady-state and short-term experiments on a three-phase circulating-bed biofilm reactor (CBBR) for removing toluene from gas streams were conducted to investigate the effect of macroporous-carrier size (1-mm cubes versus 4-mm cubes, which have the same total surface area) on CBBR performance. Experimental conditions were identical, except for the carrier size. The CBBR with 1-mm carriers (the 1-mm CBBR) overcame the performance limitation observed with the CBBR with 4-mm carriers (the 4-mm CBBR): oxygen depletion inside the biofilm. The 1-mm CBBR consistently had the superior removal efficiencies of toluene and COD, higher than 93% for all, and the advantage was greatest for the highest toluene loading, $0.12\;M/m^2-day$. The 1-mm carriers achieved superior performance by minimizing the negative effects of oxygen depletion, because they had 4.7 to 6.8 times thinner biofilm depths. The 1-mm carriers continued to provide protection from excess biomass detachment and inhibition from toluene. Finally, the 1-mm CBBR achieved volumetric removal capacities up to 300 times greater than demonstrated by other biofilters treating toluene and related volatile hydrocarbons.

• Environmental Engineering Research
• /
• v.12 no.4
• /
• pp.157-175
• /
• 2007

The membrane biofilm reactor (MBfR) creates a natural partnership of a membrane and biofilm, because a gas-transfer membrane delivers a gaseous substrate to the biofilm that grows on the membrane's outer wall. $O_2$-based MBfRs (called membrane aerated biofilm reactors, or MABRs) have existed for much longer than $H_2$-based MBfRs, but the $O_2$-based MBfR is a versatile platform for reducing oxidized contaminants in many water-treatment settings: drinking water, ground water, wastewater, and agricultural drainage. Extensive bench-scale experimentation has proven that the $H_2$-based MBfR can reduce many oxidized contaminant to harmless or easily removed forms: e.g., ${NO_3}^-$ to $N_2$, ${ClO_4}^-$ to $H_2O$ and $Cl^-$, ${SeO_4}^{2-}$ to $Se^0$, and trichloroethene (TCE) to ethene and $Cl^-$. The MBfR has been tested at the pilot scale for ${NO_3}^-$ and ${ClO_4}^-$ and is now entering field-testing for many of the oxidized contaminants alone or in mixtures. For the MBfR to attain its full promise, several issues must be addressed by bench and field research: understanding interactions with mixtures of oxidized contaminants, treating waters with a high TDS concentration, developing modules that can be used in situ to augment pre-denitrification of wastewater, and keeping the capital costs low.

• Biodesign
• /
• v.5 no.4
• /
• pp.136-140
• /
• 2017

Lam6 is a member of sterol-specific ${\underline{l}ipid$ transfer proteins ${\underline{a}}nchored$ at ${\underline{m}ebrane$ contact sites (LAMs). Lam6 localizes to the ER-mitochondria contact sites by its PH-like domain and the C-terminal transmembrane helix. Here, we purified and crystallized the Lam6 PH-like domain from Saccharomyces cerevisiae. To aid crystallization of the Lam6 PH-like domain, T4 lysozyme was fused to the N-terminus of the Lam6 PH-like domain with a short dipeptide linker, GlySer. The fusion protein was crystallized under the condition of 0.1 M HEPES-HCl pH 7.0, 10% (w/v) PEG 8000, and 0.1 M $Na_3$ Citrate at 293K. X-ray diffraction data of the crystals were collected to $2.4{\AA}$ resolution using synchrotron radiation. The crystals belong to the orthorhombic space group $P2_12_12_1$ with unit cell parameters $a=59.5{\AA}$, $b=60.1{\AA}$, and $c=105.6{\AA}$. The asymmetric unit contains one T4L-Lam6 molecule with a solvent content of 58.7%. The initial attempt to solve the structure by molecular replacement using the T4 lysozyme structure was successful.

• Biodesign
• /
• v.6 no.4
• /
• pp.96-99
• /
• 2018

The gram-positive bacterium Staphylococcus aureus is a common cause of abscesses, sinusitis and food poisoning. The emergence of antibiotic-resistant strains has caused significant clinical issues worldwide. The HslU-HslV complex was first identified as a prokaryotic homolog of eukaryotic proteasomes. HslU is an unfoldase that mediates the unfolding of the substrate proteins, and it works with the protease HslV in the complex. To date, the protein complex has been mostly studied in gram-negative bacteria. In this study, we report the purification and crystallization of the full-length HslU from S. aureus. The crystal diffracted X-rays to a $3.5{\AA}$ resolution, revealing that the crystals belong to space group $P2_1$, with unit cell parameters of a = 166.5, b = 189.6, $c=226.6{\AA}$, and ${\beta}=108.1^{\circ}$. We solved the phage problem by molecular replacement using the structure of HslU from Haemophilus influenzae as a search model. The cell content analysis with this molecular replacement solution revealed that 24 molecules are contained in the asymmetric unit. This structure provides insight into the structural and mechanistic difference of the HslUV complex of gram-positive bacteria.

• Biodesign
• /
• v.6 no.4
• /
• pp.100-102
• /
• 2018

Autophagy is a degradation pathway that targets many cellular components and plays a particularly important role in protein degradation and recycling. This process is very complex and several proteins participate in this process. One of them, P62/SQSTM1, is related to the N-end rule and induces protein degradation through autophagy. The P62/SQSTM1 makes a huge oligomer, and this oligomerization is known to play an important role in its mechanism. This oligomerization takes two steps. First, the PB1 domain of P62/SQSTM1 makes the base oligomer, and then, when the ligand binds to the ZZ domain of P62/SQSTM1, it induces a higher oligomer by the disulfide bond of the two cysteines. To understand the oligomerization mechanism of P62/SQSTM1, we need to know the dimerization of the PB1 domain. In this study, crystals of PB1 dimer were made and the crystals were diffracted by X-ray to collect usable data up to 3.2A. We are analyzing the structure using the molecular replacement (MR) method.

• Biodesign
• /
• v.7 no.2
• /
• pp.35-37
• /
• 2019

Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen, which causes a bacterial blight of rice. The bacterial blight is one of the most devastating diseases of rice in most of the rice growing countries and there is no effective pesticide against bacterial blight. The β-ketoacyl-acyl carrier protein synthase III (FabH) plays a key role in fatty acid synthesis (FAS) and is a promising drug target for the development of antibacterial agents. Xoo0878 gene, a fabH gene, from Xoo was cloned and its gene product Xoo0878 was expressed, purified and crystallized. Xoo0878 crystal diffracted to 2.1Å resolution and belonged to the triclinic space group P1, with unit-cell parameters a = 57.3Å, b = 64.7Å, c = 104.2Å and α = 81.6°, β = 84.7°, γ = 74.4°. There are four monomers in the asymmetric unit, with a corresponding crystal volume per protein weight of 2.65 ų Da^-1 and a solvent content of 53.6%. Xoo0878 structure will be useful to develop new antibacterial agents against Xoo.

• Biodesign
• /
• v.5 no.3
• /
• pp.122-125
• /
• 2017

Receptor for advanced glycation end products (RAGE) is one of the single transmembrane domain containing receptors and causes various inflammatory diseases including diabetes and atherosclerosis. RAGE extracellular domain has three consecutive IgG-like domains (V-C₁-C₂ domain) which interact with various soluble ligands including heparan sulfate or HMGB1. Studies have shown that each ligand induces different oligomeric forms of RAGE which results in a ligand-specific signal transduction. The structure of mouse RAGE bound to heparan sulfate has been previously determined but the electron density map of heparan sulfate was too ambiguous that the exact position of heparin sulfate could not be defined. Furthermore, the complex structure of human RAGE and heparin sulfate still remains elusive. Therefore, to determine the structure, human RAGE was overexpressed using bacterial expression system and crystallized using the sitting drop method in the condition of 0.1 M sodium acetate trihydrate pH 4.6, 8 % (w/v) polyethylene glycol 4,000 at 290 K. The crystal diffracted to 3.6 Å resolution and the space group is C121 with unit cell parameters a= 206.04 Å, b= 68.64 Å, c= 98.73 Å, α= 90.00°, β= 90.62°, γ= 90.00°.

• Environmental Engineering Research
• /
• v.20 no.4
• /
• pp.347-355
• /
• 2015

The growth kinetics of phototrophic microorganisms can be controlled by the light irradiance, the concentration of an inorganic nutrient, or both. A multi-component kinetic model is proposed and tested in novel batch experiments that allow the kinetic parameters for each factor to be estimated independently. For the cyanobacterium Synechocystis sp. PCC6803, the estimated parameters are maximum specific growth rate $({\mu}_{max})=2.8/d$, half-maximum-rate light irradiance $(K_L)=11W/m^2$, half-inhibition-rate light irradiance $(K_{L,I})=39W/m^2$, and half-maximum-rate concentration for inorganic carbon $(K_{S,Ci})=0.5mgC/L$, half-maximum-rate concentration for inorganic nitrogen $(K_{S,Ni})=1.4mgN/L$, and half-maximum-rate concentration for inorganic phosphorus $(K_{S,Pi})=0.06mgP/L$. Compared to other phototrophs having ${\mu}max$ estimates, PCC6803 is a fast-growing r-strategist relying on reaction rate. Its half-maximum-rate and half-inhibition rate values identify the ranges of light irradiance and nutrient concentrations that PCC6803 needs to achieve a high specific growth rate to be a sustainable bioenergy source. To gain the advantages of its high maximum specific growth rate, PCC6803 needs to have moderate light illumination ($7-62W/m^2$ for ${\mu}_{syn}{\geq}1/d$) and relatively high nutrient concentrations: $N_i{\geq}2.3 mgN/L$, $P_i{\geq}0.1mgP/L$, and $C_i{\geq}1.0mgC/L$.

• Environmental Engineering Research
• /
• v.15 no.2
• /
• pp.71-78
• /
• 2010

To understand the effects of acclimation schemes on the formation of anode biofilms, different electrical performances are characterized in this study, with the roles of suspended and attached bacteria in single-chamber microbial fuel cells (MFCs). The results show that the generation of current in single-chamber MFCs is significantly affected by the development of a biofilm matrix on the anode surface containing abundant immobilized microorganisms. The long-term operation with suspended microorganisms was demonstrated to form a dense biofilm matrix that was able to reduce the activation loss in MFCs. Also, a Pt-coated anode was not favorable for the initial or long-term bacterial attachment due to its high hydrophobicity (contact angle = $124^{\circ}$), which promotes easy detachment of the biofilm from the anode surface. Maximum power ($655.0\;mW/m^2$) was obtained at a current density of $3,358.8\;mA/m^2$ in the MFCs with longer acclimation periods. It was found that a dense biofilm was able to enhance the charge transfer rates due to the complex development of a biofilm matrix anchoring the electrochemically active microorganisms together on the anode surface. Among the major components of the extracellular polymeric substance, carbohydrates ($85.7\;mg/m^2_{anode}$) and proteins ($81.0\;mg/m^2_{anode}$) in the dense anode biofilm accounted for 17 and 19%, respectively, which are greater than those in the sparse anode biofilm.

• Journal of Korean Society on Water Environment
• /
• v.22 no.1
• /
• pp.23-29
• /
• 2006

Biosorption technology was used to remove hazardous materials from wastewater, herbicide, heavy metals, and radioactive compounds, based on binding capacities of various biological materials. Biosorption process can be explained by two steps; the first step is that target contaminants is in contact with microorganisms and the second is that the adsorbed target contaminants is infiltrated with inner cell through metabolically mediated or physico-chemical pathways of uptake. Until recently, no information is available to explain the definitive mechanism of biosorption. The purpose of this study is to evaluate biosorption capabilities of organic matters using activated sludge and to investigate affecting factors upon biosorption. Over 49% of organic matter could be removed by positive biosorption reaction under anoxic condition within 10 minutes. The biosorption capacities were constant at around 50 mg-COD/mg-MLSS for all batch experiments. As starvation time increased under aerobic or anaerobic conditions, biosorption capacity increased since higher stressed microorganisms by starvation was more brisk. Starvation stress of microorganisms was higher at aerobic condition than anaerobic one. As temperature increased or easily biodegradable carbon sources were used, biosorption capacities increased. Consequently, biosorption can be estimated by biological -adsorbed capability of the bacterial cell-wall and we can achieve the cost-effective and non -residual denitrification with applying biosorption to the bio-reduction of nitrate.