bio-imaging
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We present the MR properties of a novel bio-responsive phosphorus probe doped with iron for dual proton and phosphorus magnetic resonance imaging (1H/31P-MRI), which provide simultaneously complementary information. The probes consist of non-toxic biodegradable calcium phytate (CaIP6) nanoparticles doped with different amounts of cleavable paramagnetic Fe3+ ions. Phosphorus atoms in the phytate structure delivered an efficient 31P-MR signal, with iron ions altering MR contrast for both 1H and 31P-MR. The coordinated paramagnetic Fe3+ ions broadened the 31P-MR signal spectral line due to the short T2 relaxation time, resulting in more hypointense signal. However, when Fe3+ was decomplexed from the probe, relaxation times were prolonged. As a result of iron release, intensity of 1H-MR, as well as the 31P-MR signal increase. These 1H and 31P-MR dual signals triggered by iron decomplexation may have been attributable to biochemical changes in the environment with strong iron chelators, such as bacterial siderophore (deferoxamine). Analysing MR signal alternations as a proof-of-principle on a phantom at a 4.7 T magnetic field, we found that iron presence influenced 1H and 31P signals and signal recovery via iron chelation using deferoxamine.
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license. A copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/.
The pathogenic fungus Aspergillus fumigatus utilizes a cyclic ferrioxamine E (FOXE) siderophore to acquire iron from the host. Biomimetic FOXE analogues were labeled with gallium-68 for molecular imaging with PET. [68Ga]Ga(III)-FOXE analogues were internalized in A. fumigatus cells via Sit1. Uptake of [68Ga]Ga(III)-FOX 2-5, the most structurally alike analogue to FOXE, was high by both A. fumigatus and bacterial Staphylococcus aureus. However, altering the ring size provoked species-specific uptake between these two microbes: ring size shortening by one methylene unit (FOX 2-4) increased uptake by A. fumigatus compared to that by S. aureus, whereas lengthening the ring (FOX 2-6 and 3-5) had the opposite effect. These results were consistent both in vitro and in vivo, including PET imaging in infection models. Overall, this study provided valuable structural insights into the specificity of siderophore uptake and, for the first time, opened up ways for selective targeting and imaging of microbial pathogens by siderophore derivatization.
- MeSH
- Aspergillus fumigatus * metabolismus chemie MeSH
- aspergilóza * diagnostické zobrazování mikrobiologie MeSH
- biomimetické materiály chemie metabolismus MeSH
- cyklické peptidy MeSH
- deferoxamin chemie MeSH
- druhová specificita MeSH
- myši MeSH
- pozitronová emisní tomografie * metody MeSH
- radioizotopy galia * chemie MeSH
- siderofory * chemie metabolismus MeSH
- Staphylococcus aureus * metabolismus MeSH
- železité sloučeniny chemie MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.
- MeSH
- algoritmy * MeSH
- elektronová kryomikroskopie metody MeSH
- makromolekulární látky ultrastruktura MeSH
- molekulární biologie metody MeSH
- počítačové zpracování obrazu metody MeSH
- průběh práce MeSH
- výpočetní biologie MeSH
- zobrazení jednotlivé molekuly metody MeSH
- zobrazování trojrozměrné metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- lidé MeSH
- paternita * MeSH
- prenatální diagnóza * MeSH
- těhotenství MeSH
- výpočetní biologie * MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- dopisy MeSH
- komentáře MeSH
To be biologically active, proteins must adopt specific folded three-dimensional tertiary structures. Yet the genetic information for the proteins specifies only the primary structure, the linear sequence of amino acids in the polypeptide backbone. Many purified proteins can spontaneously refold in vitro after being completely unfolded, so the three-dimensional structure must be determined by the primary structure. How this occurs has become known as the protein-folding problem. It was primarily of academic interest, but the advent of protein engineering and the ability to produce any protein, often in an insoluble, unfolded, inactive and useless form, has made it also of great practical importance. The problem can be divided into two main questions. The first is by what kinetic process or pathway does protein adopt its native and biologically active folded conformation and the other, what is the physical basis of the stability of folded conformations. The present review summarizes the present state of knowledge of the problem and attempts to put it into perspective for what could follows.
- MeSH
- biologické modely MeSH
- Creutzfeldtova-Jakobova nemoc diagnóza MeSH
- encefalopatie bovinní spongioformní diagnóza MeSH
- konformace proteinů MeSH
- lidé MeSH
- molekulární biologie MeSH
- molekulární konformace MeSH
- proteiny diagnostické užití ultrastruktura MeSH
- sekvence aminokyselin MeSH
- techniky in vitro MeSH
- termodynamika MeSH
- výpočetní biologie MeSH
- zobrazování trojrozměrné využití MeSH
- Check Tag
- lidé MeSH
The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.
- MeSH
- algoritmy MeSH
- aminokyseliny chemie MeSH
- biologické modely MeSH
- databáze proteinů MeSH
- internet MeSH
- ionty MeSH
- koncentrace vodíkových iontů MeSH
- ligandy MeSH
- počítačová simulace MeSH
- posttranslační úpravy proteinů MeSH
- proteiny chemie MeSH
- rozpouštědla MeSH
- sbalování proteinů MeSH
- simulace molekulární dynamiky MeSH
- simulace molekulového dockingu MeSH
- software MeSH
- strojové učení MeSH
- strukturní homologie proteinů MeSH
- voda MeSH
- výpočetní biologie metody MeSH
- zobrazování trojrozměrné metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
IMPORTANCE: Large-scale neuroimaging studies have revealed group differences in cortical thickness across many psychiatric disorders. The underlying neurobiology behind these differences is not well understood. OBJECTIVE: To determine neurobiologic correlates of group differences in cortical thickness between cases and controls in 6 disorders: attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), bipolar disorder (BD), major depressive disorder (MDD), obsessive-compulsive disorder (OCD), and schizophrenia. DESIGN, SETTING, AND PARTICIPANTS: Profiles of group differences in cortical thickness between cases and controls were generated using T1-weighted magnetic resonance images. Similarity between interregional profiles of cell-specific gene expression and those in the group differences in cortical thickness were investigated in each disorder. Next, principal component analysis was used to reveal a shared profile of group difference in thickness across the disorders. Analysis for gene coexpression, clustering, and enrichment for genes associated with these disorders were conducted. Data analysis was conducted between June and December 2019. The analysis included 145 cohorts across 6 psychiatric disorders drawn from the ENIGMA consortium. The numbers of cases and controls in each of the 6 disorders were as follows: ADHD: 1814 and 1602; ASD: 1748 and 1770; BD: 1547 and 3405; MDD: 2658 and 3572; OCD: 2266 and 2007; and schizophrenia: 2688 and 3244. MAIN OUTCOMES AND MEASURES: Interregional profiles of group difference in cortical thickness between cases and controls. RESULTS: A total of 12 721 cases and 15 600 controls, ranging from ages 2 to 89 years, were included in this study. Interregional profiles of group differences in cortical thickness for each of the 6 psychiatric disorders were associated with profiles of gene expression specific to pyramidal (CA1) cells, astrocytes (except for BD), and microglia (except for OCD); collectively, gene-expression profiles of the 3 cell types explain between 25% and 54% of variance in interregional profiles of group differences in cortical thickness. Principal component analysis revealed a shared profile of difference in cortical thickness across the 6 disorders (48% variance explained); interregional profile of this principal component 1 was associated with that of the pyramidal-cell gene expression (explaining 56% of interregional variation). Coexpression analyses of these genes revealed 2 clusters: (1) a prenatal cluster enriched with genes involved in neurodevelopmental (axon guidance) processes and (2) a postnatal cluster enriched with genes involved in synaptic activity and plasticity-related processes. These clusters were enriched with genes associated with all 6 psychiatric disorders. CONCLUSIONS AND RELEVANCE: In this study, shared neurobiologic processes were associated with differences in cortical thickness across multiple psychiatric disorders. These processes implicate a common role of prenatal development and postnatal functioning of the cerebral cortex in these disorders.
- MeSH
- analýza hlavních komponent MeSH
- bipolární porucha diagnostické zobrazování patologie MeSH
- depresivní porucha unipolární diagnostické zobrazování patologie MeSH
- dítě MeSH
- dospělí MeSH
- exprese genu fyziologie MeSH
- hyperkinetická porucha diagnostické zobrazování patologie MeSH
- kohortové studie MeSH
- lidé středního věku MeSH
- lidé MeSH
- magnetická rezonanční tomografie MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mozková kůra cytologie diagnostické zobrazování růst a vývoj patologie MeSH
- obsedantně kompulzivní porucha diagnostické zobrazování patologie MeSH
- poruchy autistického spektra diagnostické zobrazování patologie MeSH
- předškolní dítě MeSH
- schizofrenie diagnostické zobrazování patologie MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- studie případů a kontrol MeSH
- výpočetní biologie MeSH
- vývoj člověka fyziologie MeSH
- vývoj plodu fyziologie MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
632 stran : ilustrace, tabulky ; 28 cm
- MeSH
- chorobopisy - počítačové systémy MeSH
- diagnostické zobrazování MeSH
- management znalostí MeSH
- metody pro podporu rozhodování MeSH
- počítačové zpracování signálu MeSH
- řízení zdravotnictví MeSH
- studium lékařství MeSH
- výpočetní biologie MeSH
- zdravotnické informační systémy MeSH
- Publikační typ
- sborníky MeSH
- Konspekt
- Lékařské vědy. Lékařství
- NLK Obory
- lékařská informatika
- NLK Publikační typ
- ročenky
The light-driven splitting of water to oxygen (O2) is catalyzed by a protein-bound tetra-manganese penta-oxygen calcium (Mn4O5Ca) cluster in Photosystem II. In the current study, we used a large-scale integration (LSI)-based amperometric sensor array system, designated Bio-LSI, to perform two-dimensional imaging of light-induced O2 evolution from spinach leaves. The employed Bio-LSI chip consists of 400 sensor electrodes with a pitch of 250 μm for fast electrochemical imaging. Spinach leaves were illuminated to varying intensities of white light (400-700 nm) which induced oxygen evolution and subsequent electrochemical images were collected using the Bio-LSI chip. Bio-LSI images clearly showed the dose-dependent effects of the light-induced oxygen release from spinach leaves which was then significantly suppressed in the presence of urea-type herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). Our results clearly suggest that light-induced oxygen evolution can be monitored using the chip and suggesting that the Bio-LSI is a promising tool for real-time imaging. To the best of our knowledge, this report is the first to describe electrochemical imaging of light-induced O2 evolution using LSI-based amperometric sensors in plants.
