757 research outputs found
Cardiac cell modelling: Observations from the heart of the cardiac physiome project
In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field
Design and Analysis of Infectious Disease Studies
The fourth workshop on this theme is devoted to the statistical problems of planning and analyzing studies in infectious disease epidemiology
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Predicting light-induced stomatal movements based on the redox state of plastoquinone: theory and validation.
Prediction of stomatal conductance is a key element to relate and scale up leaf-level gas exchange processes to canopy, ecosystem and land surface models. The empirical models that are typically employed for this purpose are simple and elegant formulations which relate stomatal conductance on a leaf area basis to the net rate of CO2 assimilation, humidity and CO2 concentration. Although light intensity is not directly modelled as a stomatal opening cue, it is well-known that stomata respond strongly to light. One response mode depends specifically on the blue-light part of the light spectrum, whereas the quantitative or 'red' light response is less spectrally defined and relies more on the quantity of incident light. Here, we present a modification of an empirical stomatal conductance model which explicitly accounts for the stomatal red-light response, based on a mesophyll-derived signal putatively initiated by the chloroplastic plastoquinone redox state. The modified model showed similar prediction accuracy compared to models using a relationship between stomatal conductance and net assimilation rate. However, fitted parameter values with the modified model varied much less across different measurement conditions, lessening the need for frequent re-parameterization to different conditions required of the current model. We also present a simple and easy to parameterize extension to the widely used Farquhar-Von Caemmerer-Berry photosynthesis model to facilitate coupling with the modified stomatal conductance model, which should enable use of the new stomatal conductance model to simulate ecosystem water vapour exchange in terrestrial biosphere models
A gradient-forming MipZ protein mediating the control of cell division in the magnetotactic bacterium Magnetospirillum gryphiswaldense
Cell division needs to be tightly regulated and closely coordinated with other cellular processes to ensure the generation of fully viable offspring. Here, we investigate division site placement by the cell division regulator MipZ in the alphaproteobacterium Magnetospirillum gryphiswaldense, a species that forms linear chains of magnetosomes to navigate within the geomagnetic field. We show that M. gryphiswaldense contains two MipZ homologs, termed MipZ1 and MipZ2. MipZ2 localizes to the division site, but its absence does not cause any obvious phenotype. MipZ1, by contrast, forms a dynamic bipolar gradient, and its deletion or overproduction cause cell filamentation, suggesting an important role in cell division. The monomeric form of MipZ1 interacts with the chromosome partitioning protein ParB, whereas its ATP-dependent dimeric form shows non-specific DNA-binding activity. Notably, both the dimeric and, to a lesser extent, the monomeric form inhibit FtsZ polymerization in vitro. MipZ1 thus represents a canonical gradient-forming MipZ homolog that critically contributes to the spatiotemporal control of FtsZ ring formation. Collectively, our findings add to the view that the regulatory role of MipZ proteins in cell division is conserved among many alphaproteobacteria. However, their number and biochemical properties may have adapted to the specific needs of the host organism
A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile Acetobacter aceti
The characteristic ability of acetic acid bacteria to aerobically oxidize ethanol to acetic acid has been harnessed for millennia to produce vinegar. Acetic acid permeates cell membranes at low pH and generally inhibits bacterial growth at low millimolar concentrations. The strains used for vinegar production, however, thrive in near-molar concentrations. This remarkable resistance results from the combined contributions of several molecular mechanisms. This study examines the inherent acid stability of proteins from the industrial vinegar-production strain Acetobacter aceti 1023 and the process by which cytoplasmic acetic acid is overoxidized to carbon dioxide. Acetate overoxidation in A. aceti strain 1023 is catalyzed by a variant citric acid cycle: CAC) that lacks succinyl-coenzyme A: CoA) synthetase. The acetic-acid-resistance protein succinyl-CoA:acetate CoA-transferase: SCACT, AarC) circumvents this deficiency and bypasses substrate-level phosphorylation and/or adenylation of acetate. Continuous acetate dissimilation by this specialized CAC is dependent upon only favorable oxidation of reduced cofactors. Biphasic growth of A. aceti strain 1023 in yeast extract-peptone-dextrose-ethanol medium is accompanied by distinct stages of acetate production, conservation, and depletion. Acetate is initially accumulated as ethanol is oxidized in the first log phase, transiently maintained in the first stationary phase, and ultimately consumed in the second log phase. The high levels of AarC and SCACT activity present prior to the acetate depletion phase suggest that regulation of CAC enzyme levels is not the only mechanism by which premature acetate overoxidation is avoided. Acetate catabolism may be further minimized during ethanol oxidation by the maintenance of a low cytoplasmic acetate concentration. A. aceti employs multiple means of active acetic acid efflux which may be driven by the energetically favorable oxidation of ethanol. Selective pressure to function in a primary metabolic role increased the specificity and catalytic rapidity of AarC relative to other class I CoA-transferases. Catalysis relies upon a novel oxyanion hole configuration composed partly of the distal amide nitrogen of CoA to stabilize tetrahedral oxyanion intermediates. Structural alignments suggest this mechanism is employed by all class I enzymes. Favorable hydrogen-bonding and electrostatic interactions between the protein and the diphosphate moiety of CoA induce a protein conformational change that was previously predicted to accelerate CoA transfer. This motion is influenced by an auxiliary binding site that preconcentrates carboxylate substrates
DEVELOPTMENT OF HYDROGEL-SOLID HYBRIDS FOR ELECTRO-MICROFLUIDICS AND SINGLE CELL ANALYSIS
학위논문 (박사) -- 서울대학교 대학원 : 공과대학 협동과정 바이오엔지니어링전공, 2020. 8. 권성훈.Agarose and other noncovalent hydrogels have good biocompatibility but their applications were restricted since they tend to have low interfacial bonding strength with other polymers or solids. Previously introduced noncovalent hydrogel-to-solid fixation strategies relied heavily on mechanical clamping which is a temporary approach and difficult to apply to kinetic parts or morphologically non-trivial adhesions. Here, we introduce a facile method that increased interfacial bonding strength of agarose hydrogel against solids via an interface-toughening hydrogel. The method showed applicability to several other noncovlanet hydrogels as well, including gelatin, alginate, agar, and chitosan. The bonding method requires no mechanical clamping, liquid glue or bulk modification of the noncovalent hydrogels polymer backbone. It is also compatible with forming micropatterns within the bonding interface. With this new bonding technique, we were able to fabricate various noncovalent hydrogel-solid integrated structures with novel functionalities for in vitro assay, soft robotics and biologically inspired systems.아가로스를 비롯한 noncovalent 하이드로겔들은 biocompatibility가 좋은 반면에 다른 고체 표면과의 접착력이 약해 그 활용성이 낮은 편이었다. 기존의 noncovalent 하이드로겔 접착 방법은 주로 기계적 고정방법에 많이 의존했는데 이는 일시적인 접착일 뿐이고, 동적 부품이나 복잡한 표면에는 적용이 어려웠다. 본 논문에선 접착면 toughness 증강을 도모하는, 그리고 활용성, 범용성이 좋은 하이드로겔 접착방법을 제시한다. 본 접착방법은 gelatin, alginate, agar, 그리고 chitosan등의 noncovalent hydrogel에 대해 적용 가능하다는 것을 보여줬다. 본 방법은 기계적 고정이 전혀 필요 없고, 액상 접착제나 하이드로겔 polymer backbone 수정을 요구하지 않는다. 또한 접착표면상에 미세구조들을 유지할 수 있다. 이 접착방법을 사용해서 전기미세유체, 단일세포전사체분석 등의 활용 예시들을 보여줬다. 본 접착방법은 이 외에도 in vitro 어세이, 소프트 로보틱스, 생체모방 등의 분야에 활용 가능할 것으로 예상한다.Chapter 1 1
Chapter 2 6
2.1 Fabrication of hybrid hydrogel films 7
2.2 Fabrication of hybrid hydrogel and noncovalent hydrogel double layer structure 8
2.3 Performing various hydrogel-to-hybrid gel bonding 8
2.4 Agarose hydrogel to tough hydrogel bonding procedure. 9
2.5 Preparing solids and elastomers to bond with hybrid gels. 10
Chapter 3 11
3.1 FTIR measurement of imine bond formation 12
3.1.1 Sample preparation for FTIR measurement 12
3.1.2 FTIR Measurement result 12
3.2 13C-NMR chemical shift measurement 15
3.2.1 Sample preparation for NMR measurement 15
3.2.2 NMR measurement result 16
3.3 SEM/EDS measurement of monomer diffusion layer 19
3.3.1 Sample preparation for SEM measurement 19
3.3.2 SEM measurement result 19
3.3.3 EDS measurement result 21
Chapter 4 25
4.1 Bonding strength measurement 26
4.1.1 The effect of monomer concentration 26
4.1.2 The effect of agarose chain aldehyde modification 30
4.1.3 The effect of monomer diffusion 31
4.1.4 Fracture energy analysis 33
4.2 Noncovalent hydrogel to solid bonding 35
4.2.1 Noncovalent hydrogel to solid surface bonding 35
4.2.2 Noncovalent hydrogel to elastomer surface bonding 37
4.2.3 Noncovalent hydrogel to tough hydrogel bonding 41
Chapter 5 45
5.1 Zig-free hydrogel microfluidic system 46
5.2 Electrophoretic oligonucleotide retrieval system 52
5.3 Discussion 57
Chapter 6 59
6.1 Introduction of the field and the proposed approach 60
6.2 Device design 62
6.2.1 Optimization of cell assembly protocol 66
6.2.2 Optimization of electrophoretic mRNA capture protocol 70
6.2.3 Crosslinking mRNA capturing probe onto magnetic microparticles 74
6.2.4 Optimizing RT-PCR protocol for single cell or small number of cells using mouth pipetting 75
6.2.5 Critical limitation of the approach 80
Chapter 7 81
7.1 Single cell electrophoresis protocol optimization 82
7.1.1 Optimization of barcoded mRNA-capturing microparticle synthesis 82
7.1.2 Optimization of cell assembly and bead assembly 87
7.1.3 Optimization of electrophoretic mRNA capture protocol 93
7.2 Single cell RNA retrieval demonstration 96
7.2.1 Single cell mRNA retrieval test 96
7.2.2 Bead harvest and RT-PCR 105
7.2.3 Validation using Sanger sequencing 107
7.2.4 Discussion 110
Chapter 8 : Summary 115
Bibliography 117
Abstract(국문초록) 120Docto
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