The acid dissociation constant is an important molecular property, and it can be successfully predicted by Quantitative Structure-Property Relationship (QSPR) models, even for in silico designed molecules. We analyzed how the methodology of in silico 3D structure preparation influences the quality of QSPR models. Specifically, we evaluated and compared QSPR models based on six different 3D structure sources (DTP NCI, Pubchem, Balloon, Frog2, OpenBabel, and RDKit) combined with four different types of optimization. These analyses were performed for three classes of molecules (phenols, carboxylic acids, anilines), and the QSPR model descriptors were quantum mechanical (QM) and empirical partial atomic charges. Specifically, we developed 516 QSPR models and afterward systematically analyzed the influence of the 3D structure source and other factors on their quality. Our results confirmed that QSPR models based on partial atomic charges are able to predict pKa with high accuracy. We also confirmed that ab initio and semiempirical QM charges provide very accurate QSPR models and using empirical charges based on electronegativity equalization is also acceptable, as well as advantageous, because their calculation is very fast. On the other hand, Gasteiger-Marsili empirical charges are not applicable for pKa prediction. We later found that QSPR models for some classes of molecules (carboxylic acids) are less accurate. In this context, we compared the influence of different 3D structure sources. We found that an appropriate selection of 3D structure source and optimization method is essential for the successful QSPR modeling of pKa. Specifically, the 3D structures from the DTP NCI and Pubchem databases performed the best, as they provided very accurate QSPR models for all the tested molecular classes and charge calculation approaches, and they do not require optimization. Also, Frog2 performed very well. Other 3D structure sources can also be used but are not so robust, and an unfortunate combination of molecular class and charge calculation approach can produce weak QSPR models. Additionally, these 3D structures generally need optimization in order to produce good quality QSPR models.

• MeSH
• chemické jevy * MeSH
• kvantitativní vztahy mezi strukturou a aktivitou * MeSH
• kvantová teorie MeSH
• molekulární konformace * MeSH
• molekulární modely * MeSH
• počítačová simulace MeSH
• racionální návrh léčiv MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

The representation of carbohydrates in 3D space using symbols is a powerful visualization method, but such representations are lacking in currently available visualization software. The work presented here allows researchers to display carbohydrate 3D structures as 3D-SNFG symbols using LiteMol from a web browser (e.g., v.litemol.org/?loadFromCS=5T3X ). Any PDB ID can be substituted at the end of the URL. Alternatively, the user may enter a PDB ID or upload a structure. LiteMol is available at https://v.litemol.org and automatically depicts any carbohydrate residues as 3D-SNFG symbols. To embed LiteMol in a webpage, visit https://github.com/dsehnal/LiteMol .

• Klíčová slova
• 3D-SNFG, LiteMol, SNFG, carbohydrate, glycan, glycoprotein, oligosaccharide, structure, symbol nomenclature for glycans, visualization,
• MeSH
• molekulární konformace * MeSH
• polysacharidy chemie   MeSH
• sacharidy chemie   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• polysacharidy MeSH
• sacharidy MeSH

A complex study of the spatial arrangement of different genetic elements (genes, centromeres and chromosomal domains) in the cell nucleus is presented and the principles of this arrangement are discussed. We show that the radial location of genetic elements in the three-dimensional (3D) space between the center of the nucleus and the nuclear membrane is element specific and dependent on the position of the element on the chromosome. In contrast, mutual angular positioning of both homologous and heterologous genetic elements is, in the majority of cases, random. In several cases, tethering of heterologous genetic elements was observed. This close proximity of specific loci may be responsible for their mutual rearrangement and the development of cancer. Comparison of our results with transcriptome maps shows that the nuclear location of chromosomal domains with highly expressed genes is more central when compared with chromosomes with low expression. The higher-order chromatin structure is strikingly similar in various human cell types, which correlates with the fact that the profiles of gene expression are also similar.

• MeSH
• buněčné jádro genetika   metabolismus   MeSH
• DNA chemie   MeSH
• exprese genu fyziologie   MeSH
• genom lidský * MeSH
• hybridizace in situ fluorescenční MeSH
• konformace nukleové kyseliny * MeSH
• lidé MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH

3D electron crystallography has emerged as a method with great potential for the structure determination of small molecules and macromolecules complementing traditional single-crystal X-ray crystallography and powder X-ray diffraction (PXRD). It offers the unique capability of determining the structures of small molecules and macromolecules from micro- and nanocrystals. In this study, using 3D electron diffraction (3D ED), we determined the single-crystal structure of commercially sourced arginine directly from its bottle. The 3D ED analysis of micro-sized single crystals identified two distinct forms: the L-arginine enantiomer and the racemic mixture DL-arginine. At the time of writing, neither the Cambridge Structural Database nor the Crystallographic Open Database contain a single-crystal structure of isolated L-arginine (sum formula C6H14N4O2), which has been solved in this work by 3D ED. We also present a comparison of the structures of these molecules solved by 3D ED and PXRD.

• Klíčová slova
• 3D ED, 3D electron crystallography, crystal structure, l-arginine, trace impurity,
• Publikační typ
• časopisecké články MeSH

The spatial arrangement of some genetic elements relative to chromosome territories and in parallel with the cell nucleus was investigated in human lymphocytes. The structure of the chromosome territories was studied in chromosomes containing regions (clusters) of highly expressed genes (HSA 9, 17) and those without such clusters (HSA 8, 13). In chromosomes containing highly expressed regions, the elements pertaining to these regions were found close to the centre of the nucleus on the inner sides of chromosome territories; those pertaining to regions with low expression were localized close to the nuclear membrane on the opposite sides of the territories. In chromosomes with generally low expression (HSA 8, 13), the elements investigated were found symmetrically distributed over the territories. Based on the investigations of the chromosome structure, the following conclusions are suggested: (1) Chromosome territories have a non-random internal 3D structure with defined average mutual positions between elements. For example, RARalpha, TP53 and Iso-q of HSA 17 are nearer to each other than they are to the HSA 17 centromere. (2) The structure of a chromosome territory reflects the number and chromosome location of clusters of highly expressed genes. (3) Chromosome territories behave to some extent as solid bodies: if the territory is found closer to the nuclear centre, the individual genetic elements of this chromosome are also found, on average, closer the centre of the nucleus. (4) The positions of centromeres are, on average, nearer to the fluorescence weight centre of the territory (FWCT) than to genes. (5) Active genes are not found near the centromeres of their own territory. A simple model of the structure of chromosome territory is proposed.

• MeSH
• buněčné jádro genetika   MeSH
• centromera genetika   MeSH
• euchromatin genetika   MeSH
• geny MeSH
• heterochromatin genetika   MeSH
• hybridizace in situ fluorescenční MeSH
• jaderný obal genetika   MeSH
• kompartmentace buňky MeSH
• lidé MeSH
• lidské chromozomy, pár 17 ultrastruktura   MeSH
• lidské chromozomy ultrastruktura   MeSH
• lymfocyty diagnostické zobrazování   MeSH
• metoda Monte Carlo MeSH
• modely genetické MeSH
• počítačová simulace MeSH
• počítačové zpracování obrazu MeSH
• ultrasonografie MeSH
• zobrazování trojrozměrné * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• euchromatin MeSH
• heterochromatin MeSH

Cardiovascular diseases are the leading cause of mortality worldwide. Given the limited endogenous regenerative capabilities of cardiac tissue, patient-specific anatomy, challenges in treatment options, and shortage of donor tissues for transplantation, there is an urgent need for novel approaches in cardiac tissue repair. 3D bioprinting is a technology based on additive manufacturing which allows for the design of precisely controlled and spatially organized structures, which could possibly lead to solutions in cardiac tissue repair. In this review, we describe the basic morphological and physiological specifics of the heart and cardiac tissues and introduce the readers to the fundamental principles underlying 3D printing technology and some of the materials/approaches which have been used to date for cardiac repair. By summarizing recent progress in 3D printing of cardiac tissue and valves with respect to the key features of cardiovascular tissue (such as contractility, conductivity, and vascularization), we highlight how 3D printing can facilitate surgical planning and provide custom-fit implants and properties that match those from the native heart. Finally, we also discuss the suitability of this technology in the design and fabrication of custom-made devices intended for the maturation of the cardiac tissue, a process that has been shown to increase the viability of implants. Altogether this review shows that 3D printing and bioprinting are versatile and highly modulative technologies with wide applications in cardiac regeneration and beyond.

• Klíčová slova
• 3D printing, Bioreactor, Cardiac tissue, Maturation, Valve,
• MeSH
• 3D tisk MeSH
• bioprinting * metody   MeSH
• lidé MeSH
• srdce MeSH
• tkáňové inženýrství * metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Invadopodia and podosomes have been intensively studied because of their involvement in the degradation of extracellular matrix. As both structures have been studied mostly on thin matrices, their commonly reported shapes and characteristics may differ from those in vivo. To assess the morphology of invadopodia in a complex 3D environment, we observed invadopodial formation in cells grown on a dense matrix based on cell-free dermis. We have found that invadopodia differ in morphology when cells grown on the dermis-based matrix and thin substrates are compared. The cells grown on the dermis-based matrix display invadopodia which are formed by a thick protruding base rich in F-actin, phospho-paxillin, phospho-cortactin and phosphotyrosine signal, from which numerous thin filaments protrude into the matrix. The protruding filaments are composed of an F-actin core and are free of phospho-paxillin and phospho-cortactin but capped by phosphotyrosine signal. Furthermore, we found that a matrix-degrading activity is localized to the base of invadopodia and not along the matrix-penetrating protrusions. Our description of invadopodial structures on a dermis-based matrix should greatly aid the development of new criteria for the identification of invadopodia in vivo, and opens up the possibility of studying the invadopodia-related signaling in a more physiological environment.

• MeSH
• aktiny metabolismus   MeSH
• buněčné kultury MeSH
• buněčné výběžky metabolismus   ultrastruktura   MeSH
• cytoskelet metabolismus   MeSH
• elektronová mikroskopie MeSH
• experimentální sarkom metabolismus   ultrastruktura   MeSH
• extracelulární matrix metabolismus   fyziologie   ultrastruktura   MeSH
• fluorescenční protilátková technika MeSH
• kortaktin metabolismus   MeSH
• krysa rodu Rattus MeSH
• lidé MeSH
• nádorové buněčné linie MeSH
• prasata MeSH
• signální transdukce MeSH
• zobrazování trojrozměrné MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aktiny MeSH
• kortaktin MeSH

Three-dimensional (3D) sonography is the next logical step in diagnostic ultrasound examination. The true value of 3D ultrasonography, however, becomes evident only if 3D structures can be assessed without preconceptions ensuing from 2D interpretations. 3D ultrasonography can greatly improve our understanding of locomotor apparatus anatomy and pathology. The authors used spatial analysis to evaluate the data obtained by examination of patients with orthopedic diagnoses. The Voluson 530 MT and SONOReal system were used for examination. The Voluson permits a choice of either a 2D or a 3D imaging program for musculoskeletal system examination. The SONOReal, owing to a positional sensor of the probe, can be attached to any ultrasound transducer. In the period from 1990 to 2004, a total of 19 000 patients were examined by ultrasonography and, in 6 500 of them, the diagnosis was verified by another method, which showed a 99 % reliability of ultrasound examination. In 350 patients 2D imaging was followed by 3D examination; in 53 of them, 3D coronal and multiplanar imaging made the diagnosis based on 2D imaging more accurate and, in 12 patients, it provided new information on the patient's diagnosis. 3D reconstructions were made in 101 patients, of these 40 had been examined by other imaging methods (magnetic resonance, computer-assisted tomography) or arthroscopy. The results of examination showed a 100% correlation. Spatial reconstruction is based on the volume rendering method. This is an extension of the planar reconstruction method. Additional image processing techniques are used for a region of interest within a 3D volume data set. 3D ultrasound revealed a spatial relationship between lesions and their surfaces. The surface mode requires that the interface between tissues with different acoustic impedances should be a start line of 3D rendering. The acoustic threshold is a condition that restricts imaging circumstances in which surface rendering will be successful. Exploring 3D reconstructions with power Doppler scanning, which is more sensitive for tracking vessels, is a unique technique that can hardly be compared with any other imaging modality. 3D-volume imaging gives the examiner freedom to generate anatomical views from an infinite number of perspectives and allows us to explore anatomic relationships in the ways not available in any conventional 2D imaging. A spatial reconstruction presents a nearly perfect anatomical model. The possibility of storing volume data is considered a further progressive trend. It greatly contributes to enhancement of the scope of follow-up examinations, permits comparisons of expert conclusions and can serve educational purposes. The digital technology offers various networking solutions and plays a role in the development of 3D telemedicine. Although the diagnostic efficacy of 3D imaging is not greatly enhanced when compared with a 2D examination done by a well-trained specialist, the features of coronary sections and spatial reconstructions represent great progress of this imaging technology.

• MeSH
• lidé MeSH
• muskuloskeletální systém diagnostické zobrazování   MeSH
• počítačové zpracování obrazu MeSH
• ultrasonografie MeSH
• zobrazování trojrozměrné * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Unique 3D tomography apparatus was built and successfully tested in Research Centre Rez. The apparatus allows three-dimensional view into the interior of low-dimension radioactive samples with a diameter up to several tens of millimeters with a betterresolution then 1 mm3 and is designed to detect domains with different levels of radioactivity. Structural inhomogeneities such as cavities, cracks or regions with different chemical composition can be detected using this equipment. The SPECT scanner has been successfully tested on several samples composed of a 3-mm radionuclide source located eccentrically within homogeneous steel bushings. To detect fine cracks inside a small sample, an ultrafine scan of the sample was carried out in the course of 24 hours with a 0.5-mm longitudinal and transverse step and 18° angular step. The exact location and orientation of a fine crack artificially formed inside a sample has been detected.

• MeSH
• algoritmy MeSH
• difuze MeSH
• geologie MeSH
• jednofotonová emisní výpočetní tomografie * MeSH
• oxid křemičitý MeSH
• počítačové zpracování obrazu metody   MeSH
• poréznost MeSH
• radioizotopy kobaltu MeSH
• radiometrie přístrojové vybavení   metody   MeSH
• radon MeSH
• scintilace - počítání MeSH
• software MeSH
• teoretické modely MeSH
• wolfram MeSH
• záření gama MeSH
• zobrazování trojrozměrné * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• granite MeSH Prohlížeč
• oxid křemičitý MeSH
• radioizotopy kobaltu MeSH
• radon MeSH
• wolfram MeSH

3D printing technique is currently one of the promising emerging technologies. It is used in many areas of human activity, including acoustic applications. This paper focuses on studying the sound reflection behavior of four different types of 3D-printed open-porous polylactic acid (PLA) material structures, namely cartesian, octagonal, rhomboid and starlit structures. Sound reflection properties were evaluated by means of the normal incidence sound reflection coefficient based on the transfer function method using an acoustic impedance tube. In this study, various factors affecting the sound reflection performance of the investigated PLA samples were evaluated. It can be concluded that the sound reflection behavior of the tested PLA specimens was strongly affected by different factors. It was influenced, not only by the type of 3D-printed open-porous material structure, but also by the excitation frequency, the total volume porosity, the specimen thickness, and the air gap size behind the tested specimen inside the acoustic impedance tube.

• Klíčová slova
• 3D printing technique, air gap, excitation frequency, polylactic acid, porosity, sound reflection, thickness,
• Publikační typ
• časopisecké články MeSH