Structural and biochemical insights of CypA and AIF interaction

The Cyclophilin A (CypA)/Apoptosis Inducing Factor (AIF) complex is implicated in the DNA degradation in response to various cellular stress conditions, such as oxidative stress, cerebral hypoxia-ischemia and traumatic brain injury. The pro-apoptotic form of AIF (AIF(Δ1-121)) mainly interacts with CypA through the amino acid region 370-394. The AIF(370-394) synthetic peptide inhibits complex formation in vitro by binding to CypA and exerts neuroprotection in a model of glutamate-mediated oxidative stress. Here, the binding site of AIF(Δ1-121) and AIF(370-394) on CypA has been mapped by NMR spectroscopy and biochemical studies, and a molecular model of the complex has been proposed. We show that AIF(370-394) interacts with CypA on the same surface recognized by AIF(Δ1-121) protein and that the region is very close to the CypA catalytic pocket. Such region partially overlaps with the binding site of cyclosporin A (CsA), the strongest catalytic inhibitor of CypA. Our data point toward distinct CypA structural determinants governing the inhibitor selectivity and the differential biological effects of AIF and CsA, and provide new structural insights for designing CypA/AIF selective inhibitors with therapeutic relevance in neurodegenerative diseases

디젤 가솔린 융합 연소에서 단열 피스톤의 효과

학위논문 (석사)-- 서울대학교 대학원 : 공과대학 기계항공공학부, 2019. 2. 민경덕.The regulation for diesel engine has been more stringent as concerns about the environment have increased. Specifically, the EURO-6c regulation has been implemented since September 2017, then driving test cycle changed from NEDC to WLTP and RDE test was added. To satisfy these regulations, it is necessary to advance combustion for reducing emissions and achieving a high thermal efficiency simultaneously. Dual-fuel combustion which uses two different fuels can be regarded as a type of advanced combustion technology. In this study, the effects of thermally insulated piston on diesel and gasoline dual-fuel combustion were investigated. The experiments were implemented in a light-duty single cylinder diesel engine satisfying the EURO-6 regulation adapted for dual-fuel operation. The engine was operated under low load conditions and high load conditions, with compression ratio of 14. To achieve the low thermal conductivity and volumetric heat capacity for thermal insulation, it is necessary to reduce the density of the insulation coating materials. Therefore, a porous alumina structure formed by anodizing aluminum alloy was selected as thermal insulation materials because it has a lot of pores, then it makes a low density relative to dense aluminum oxide. The thermally insulated piston used in this study was coated with silica coated porous anodized aluminum to block the high temperature in-cylinder gas, which was called anodizing piston. The experiments were conducted to satisfy the various constraints. The gISNOx was restricted below 0.3 g/kWh, the soot emission was limited to below 0.2 FSN, and the mPRR was confined to below 10 bar/deg. The experimental results validated that the combustion stability was improved under low load conditions, and the GIE and IMEP was increased by the enhanced thermal insulation performance due to the high combustion temperature under high load conditions.환경에 대한 관심이 증가함에 따라 디젤 엔진에 대한 규제도 점차 강화되고 있다. 특히, 2017년 9월부터는 EURO-6c 규제가 시행되었다. 이에 따라 운전 시험 모드는 NEDC에서 WLTP로 바뀌었으며, 실도로 주행 배기가스(RDE) 측정 시험도 추가되었다. 이러한 규제를 만족하기 위해 배기 배출물을 줄이면서 동시에 높은 열효율을 가질 수 있는 신 연소 기술이 요구되었다. 그 중 두 가지의 연료를 사용하는 융합 연소는 신 연소 기술의 한 가지로 여겨지고 있다. 본 연구에서는 디젤 가솔린 융합 연소에서 단열 피스톤의 효과를 조사하였다. 본 실험은 EURO-6 규제를 만족하면서 융합 연소가 가능하게 만든 단기통 승용 디젤 엔진으로 진행하였다. 그리고 이 엔진은 압축비 14에서 저부하 영역과 고부하 영역으로 나누어 운전하였다. 단열에 필요한 낮은 열전도도와 낮은 체적 열용량을 얻기 위해서는 단열 코팅 재료의 밀도를 줄여야 한다. 따라서 알루미늄 합금의 양극 산화 처리에 의한 다공성 알루미늄 구조를 단열 재료로 사용하였다. 이 구조는 기공이 많아 일반 알루미늄 합금에 비해 상대적으로 낮은 밀도를 갖고 있기 때문이다. 그리고 본 연구에서는 뜨거운 실린더 내 가스가 기공으로 들어오는 것을 막기 위해 다공성 양극 산화처리 알루미늄에 실리콘을 코팅한 피스톤을 사용하였다. 이 피스톤을 anodizing piston 이라 불렀다. 본 실험은 다양한 제한 조건을 만족하기 위해 진행되었다. gISNOx 는 0.3 g/kWh 이하로, soot 배출물은 0.2 FSN 미만으로 제한하였고, 최대압력상승률 (mPRR)은 10 bar/deg 미만으로 제한하였다. 실험 결과는 저부하 조건에서는 연소 안정성의 증가를, 고부하 운전조건에서는 높은 연소 온도로 인한 GIE와 IMEP의 증가를 확인하였다.Chapter 1. Introduction 1 1.1 Research Background 1 1.2 Previous Research 2 1.3 Research Objective 5 Chapter 2. Experimental Setup and Conditions. 7 2.1 Experimental Setup. 7 2.2 Thermal Insulation Material. 13 2.3 Experimental Conditions. 20 Chapter 3. Experimental Results and Discussion 25 3.1 Low Load Condition 25 3.2 High Load Condition. 33 Chapter 4. Conclusion 43 Reference. 45 국 문 초 록. 48Maste

La inhibición de P2X7 mejora el deterioro del sistema ubiquitina-proteasoma asociado con enfermedades neurológicas

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Veterinaria, Departamento de Bioquímica y Biología Molecular IV, leída el 12-11-2021The Ubiquitin Proteasome System (UPS) is the primary intracellular pathway leading to the degradation of misfolded, disassembled, or damaged proteins (Kaushik & Cuervo 2015). The destruction of a target protein is handled by the 26S proteasome complex following the covalent binding of multiple copies of ubiquitin molecules to a substrate protein via an enzymatic cascade (Hershko and Ciechanover,1998). UPS dysfunction has been linked to several neurological disorders, including Alzheimer's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, and epilepsy (Stefanis and Keller, 2017; Upadhya et al., 2007, Engel et al., 2017). The impact of the UPS in these diseases may be linked to deficiencies in the clearance of misfolded proteins, which can lead to intracellular protein aggregation, cytotoxicity, and cell death (Leight et al., 1991; Neumann et al., 2006)...El Sistema Ubiquitina-Proteasoma (UPS) es el principal sistema encargado de controlar la proteostasis celular (Kaushik y Cuervo 2015). La destrucción de una proteína diana es operada por el complejo de proteasoma 26S después de la unión covalente de múltiples copias de moléculas de ubiquitina a una proteína sustrato a través de una cascada enzimática (Hershko y Ciechanover, 1998). La disfunción del UPS se ha relacionado con una variedad de enfermedades neurológicas, incluida la enfermedad de Alzheimer, la Esclerosis Lateral Amiotrófica, la enfermedad de Huntington y la Epilepsia (Stefanis y Keller, 2007; Upadhya et al., 2007; Engel et al, 2017). El impacto del UPS en estas enfermedades puede estar relacionado con deficiencias en la eliminación de proteínas mal plegadas, lo que puede conducir a la agregación de proteínas intracelulares, citotoxicidad y muerte celular (Leight et al., 1991; Neumann et al., 2006)...Fac. de VeterinariaTRUEunpu

Control of NOx emissions from diesel engines using exhaust gas re-circulation

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The diesel engine currently accounts for 32 per cent of the new passenger car sales in Europe. In the US, diesel-power is responsible for 94 per cent of all freight movement. Comparing European Stage III standard petrol and diesel passenger car emissions, diesel NOx emissions are still considered a concern. This thesis investigates the mechanisms by which oxides of nitrogen are formed during diesel combustion. It reviews the current methods of controlling NOx emissions, such as retarding fuel injection timing, exhaust gas re-circulation (EGR), water injection and exhaust after-treatment. Modelling using a phenomenological model, is used to demonstrate the extended Zeldovich mechanism and formation trends, the effects of EGR and the significance of the Zeldovich mechanism rate constants. Modified Zeldovich rate constants are proposed to improve the correlation to measured data. Clearly, EGR is currently the most effective method of reducing NOx emissions from passenger car diesel engines. The way EGR works in suppressing NOx formation is reviewed in detail. Experimentation on a 1.8 litre inline 4-cylinder 4-valve per cylinder DI diesel with a variable nozzle turbine (VNT) turbocharger was used to demonstrate the concept of "additional" EGR on this small automotive engine. "Additional" EGR is the concept whereby a proportion of the EGR is added to the total charge, so that the volumetric efficiency increases as EGR is introduced. By using "additional" EGR, the benefits of lower NOx emissions combined with reduced particulates emissions and improved fuel consumption were clearly demonstrated at two test conditions. The reasons for achieving lower NOx emissions when using a VNT turbocharger and EGR have been explained. Finally, several methods of calculating EGR proportion were used and compared against true mass flow. The use of a CO2 balance was found to be the most accurate method.This study is funded by the Ford Motor Company

Size Controlled Metal Oxide Nanoparticles:Synthesis, Characterization, and Application to Catalysis

The research in this dissertation focuses on the synthesis of size-controlled metal oxide nanoclusters (\u3c 10 nm) on amorphous silica and their catalytic performance in thermal degradation of chlorinated benzenes with regard to the cluster size effect. Furthermore, with the concern that metal can condense as the nano-size nuclei core for particle growth in combustion process, a flow reactor was built to investigate the effect of metal oxide nanoparticles on the formation of soot in fuel-rich combustion. The synthesis of copper oxide nanoclusters was carried by calcination of silica impregnated with dendrimer-metal complexes. The 4th generation poly(propylene imine) dendrimer DAB-Am32 was used in this template-based method. The sizes of copper oxide nanoclusters were exquisitely controlled in the range of 1-5 nm with narrow size distribution by changing the stoichiometric ratio of metal ion to the terminal primary amines of dendrimer, the equivalent metal oxide loading on surface, and the impregnation procedure. XANES and XPS studies revealed that CuO was the dominant component of copper oxide nanoclusters. This method was also experimentally proven to be valid in the preparation of other metal oxide nanoparticles, e.g., Ni and Fe, and with other oxide substrates, e.g., titanium oxide. Chlorinated benzenes were selected as the model compound for studying the activity of metal (Cu and Fe) oxide catalysts with regard to their cluster sizes. Compared to the surrogate of coarse metal oxide samples, which was prepared by incipient wetness method, their nanosize analogues showed superior catalytic activity on the conversion of chlorinated benzenes under both pyrolytic and oxidative thermal condition. Furthermore, such catalytic size effect was also observed on the selectivity of products yields. Sooting combustion was performed using a two-zone flow reactor with precise control on experimental parameters. Gas suspended metal oxide nanoparticles were generated by burning off the organic backbone of the dendrimer-metal complexes in zone 1 and immediately transferred to zone 2, where the hydrocarbon combustion occurred. TEM results of the particulate sample collected at the outlet of reactor indicated that metal oxide nanoparticles promoted soot formation. GC/MS analysis of the extracted organic materials from soot samples suggested the formation of PAH was also promoted by metal addition as well

The unique disulfide linked activation loop of DYRK kinases and possible redox activity control

The cysteine of HCD (C286) in DYRK1A is involved in disulfide bridge formation with a cysteine (C312) in the DFGSSC sequence. The purpose of this project was to investigate how the state of the disulfide bridge would affect enzyme catalytic and ligand binding properties of the protein kinase. A mutant, DYRK1A C312A, was thus designed to eliminate the disulfide bridge. The mutant was expressed and purified following the same protocol as for DYRK1A wt, including HisTrap purification, TEV cleavage and size exclusion chromatography. Crystallization trials were performed for both the wt and the mutant with the kinase inhibitor Staurosporine. DYRK1A wt with STU crystallized and diffracted with at a resolution of 2.33 Å. The DYRK1A C312A mutant with STU crystallized and diffracted with a resolution of 2.59 Å. The structure was solved by molecular replacement in Molrep (CCP4) and refined by Refmac5 and Phenix. Molecular dynamics (MD) simulations (SCHRODINGER) were performed with the intent to compare diverse disulfide bridge states. Ligand binding and enzyme catalytic properties were analyzed using a combination of techniques, including activity assays, microscale thermophoresis, and isothermal calorimetry. The Thermofluor assay confirmed that both the wt and the mutant bind tightly to STU and AZ-191. It also showed that the mutant consistently has a slightly lower melting temperature than the wt, which would indicate that it is less stable. Solvent accessible surface area (SASA) analysis support the theory of accessibility to conserved cysteine residues

The Effect Of Biodiesel Blends On A Multi-Cylinder Engine And The Impact On Aftertreatment

Recently, topics including global warming, increased environmental awareness, recycling, and organically produced meat and vegetables have been prevalent in the media and research arenas. The rapidly increasing cost for fossil fuels and the pursuit of environmental conservation has brought about the interest in a renewable and clean burning fuel, specifically biodiesel. Biodiesel, or vegetable oil ester as it was originally referred to, has been improving and progressing since the early 1900\u27s. Fortunately, significant advancement in the understanding of raw vegetable oil as a fuel as well as converting it to ethyl or methyl esters, now known as biodiesel, has been evolving for nearly a century after. The objective of this study is predicated on the potential marketing of biodiesel blends, up to 20% by volume, without modification to standard production available engines to be used by the average consumer. The NextEnergy Biodiesel program is a collaborative effort involving a variety of disciplines and expertise. Objectives include developing manufacturing methods for soy-based biodiesel, evaluating and recording parameters such as cetane number, oxidative stability, and lubricity made from different feedstocks to be used for engine testing. The evaluations of these selected fuels are then blended with ULSD and tested in single and multi-cylinder engines. The proceeding work specifically focuses on results from a multi-cylinder engine coupled with a diesel oxidation catalyst, diesel particulate filter and a selective catalytic reduction catalyst and the effect that biodiesel blends has on their performance and effectiveness

Preparation, characterization and carrier gas transport characteristics of inorganic and organic membranes for application in lactic acid esterification with ethanol.

Ethyl lactate (EL) plays a major role as green solvent and also a replacement for most petrochemical solvents. The esterification process of lactic acid and ethanol to produce EL is an equilibrium-limiting reaction and the selective removal of one of the reaction products can be improved using a membrane reactor and when coupled with a heterogeneous catalyst offers an opportunity for process intensification. This thesis investigates the batch process esterification reaction involving lactic acid (LA) and ethanol (EL) in the presence of a water selective membrane using different cation-exchange resin catalysts. The product was analysed using gas chromatograph coupled with mass spectrometry detector (GC-MS). The analytical methods used for the characterisation of the cation-exchange resins and membrane include Fourier transform infrared coupled with attenuated total reflectance (FTIR-ATR), scanning electron microscopy attached to energy dispersive analyser (SEM/EDAX), Liquid nitrogen physisorption and nuclear magnetic resonance (NMR) respectively. A novel method was developed for carrying out esterification reaction in a gaseous phase system using a flat sheet polymeric membrane. Prior to the esterification reaction, different carrier gases were tested with ceramic membrane to determine the suitable carrier gases for the analysis of esterification product. The four carrier gases used for the permeation test were argon (Ar), helium (He), carbon dioxide (CO2) and nitrogen (N2). A 15nm pore size commercially available tubular ceramic support, consisting of 77%Al2O3 and 23%TiO2 with the porosity of 45% was used for the carrier gas investigation. The support was modified with silica based on the sol-gel dip-coating techniques. The dip-coated membrane exhibited a higher molar flux with He (0.046mol m-2s-1) and Ar (0.037mol m-2s-1) with a much lower flux for N2 (0.037mol m-2s-1) and CO2 (0.035 mol m-2s-1) at 0.30 bar. Helium gas with the highest permeation rate were identified as the suitable carrier gas for the analysis of esterification product with GC-MS. The esterification reaction in the presence of four cation-exchange resins to produce ethyl lactate was carried out between 60-160 oC in a batch and membrane processes to determine the effectiveness resin catalysts for LA esterification. The effect of external mass transfer diffusion limitation between the liquid components and the resin catalysts was avoided by increasing the agitation time of the esterification reaction. The percentage conversion rate of the lactic acid feed from the batch process esterification was found to be in the range of 98.6 to 99.8%. The reaction kinetics of the esterification reaction was described based on two simplified mechanisms of Langmuir Hinshelwood model to describe the adsorption components on the surface of the catalysts. The lactic acid feed gave a conversion rate of up to 100 % confirming the effectiveness of the acetate membrane impregnated resin catalysts in the selective removal of water for the separation of ethyl lactate. The significance of producing ethyl lactate through batch process intensified by a water-selective membrane processes can be recommended for industrial LA production

Cholinesterase Research

This collection of 10 papers includes original as well as review articles focused on the cholinesterase structural aspects, drug design and development of novel cholinesterase ligands, but also contains papers focused on the natural compounds and their effect on the cholinergic system and unexplored effects of donepezil