Revealing the multiple structures of serine.
Ontology highlight
ABSTRACT:
SUBMITTER: Blanco S
PROVIDER: S-EPMC2154405 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Few questions in condensed matter science have proven as difficult to unravel as the interplay between structure and dynamics in supercooled liquids. To explore this link, much research has been devoted to pinpointing local structures and order parameters that correlate strongly with dynamics. Here we use an unsupervised machine learning algorithm to identify structural heterogeneities in three archetypical glass formers-without using any dynamical information. In each system, the unsupervised machine learning approach autonomously designs a purely structural order parameter within a single snapshot. Comparing the structural order parameter with the dynamics, we find strong correlations with the dynamical heterogeneities. Moreover, the structural characteristics linked to slow particles disappear further away from the glass transition. Our results demonstrate the power of machine learning techniques to detect structural patterns even in disordered systems, and provide a new way forward for unraveling the structural origins of the slow dynamics of glassy materials.
| S-EPMC7603397 | biostudies-literature
Project description:The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.
| S-EPMC4117781 | biostudies-literature
Project description:BackgroundAcross the globe multiple mini interviews (MMIs) have rapidly replaced the use of panel interviews in the selection of medical students and other health professionals. MMIs typically demonstrate better reliability and validity than panel interviews but there is limited research on whether these different types of interview process measure the same or different constructs. Our research aims to ascertain if MMIs are multidimensional or unidimensional, and whether MMIs conducted at different institutions assess the same or different constructs to each other or to panel interviews.MethodsParticipants were applicants to medical degrees who were shortlisted for interviews at three different institutions in 2013 (n = 165) and 2014 (n = 128). Two institutions used a bespoke MMI developed independently from each other and the third used a panel interview. Stations scores and overall (mean) interview scores were examined.ResultsExploratory principal components analysis and confirmatory factor analysis showed similar results in both years' data, supporting a unidimensional model. The two overall MMI scores were more strongly correlated to each other (r = .56 and .64 in 2013 and 2014 respectively) than either were to the panel interview scores (r = .07 and .15 in 2013; .39 and .48 in 2014).ConclusionsIt appears that both MMIs panel interviews tap a single latent construct, but not the same construct. We suggest that the MMI methodology might allow the measurement of an emergent construct such as adaptability.
| S-EPMC6080397 | biostudies-literature
Project description:The surface morphology and electronic structure of hexagonal graphene onion rings (HGORs), a modified graphene structure, were investigated to confirm the possibility as an efficient catalyst when compared to graphene. After confirming the formation of HGORs with a smaller width (~4.2 ?m) from scanning electron microscopy (SEM) and optical microscopy images, we compared the catalytic activities of HGORs and graphene by measuring the rate of oxidation of thiophenol using high-resolution photoemission spectroscopy (HRPES). In addition, we also assessed in 4-chlorophenol degradation and the OH radical formation with a benzoic acid to confirm the possibility for photocatalytic activities of HGORs. As a result, we confirmed that HGORs, which has an increased active site due to its three-dimensional structure formed by the reaction of graphene with hydrogen, can act as an effective catalyst. In addition, we could also realize the possibility of optical applicability by observing the 0.13?eV of band gap opening of HGORs.
| S-EPMC7005818 | biostudies-literature
Project description:Scholars across disciplines have long debated the existence of a common structure that underlies narratives. Using computer-based language analysis methods, several structural and psychological categories of language were measured across ~40,000 traditional narratives (e.g., novels and movie scripts) and ~20,000 nontraditional narratives (science reporting in newspaper articles, TED talks, and Supreme Court opinions). Across traditional narratives, a consistent underlying story structure emerged that revealed three primary processes: staging, plot progression, and cognitive tension. No evidence emerged to indicate that adherence to normative story structures was related to the popularity of the story. Last, analysis of fact-driven texts revealed structures that differed from story-based narratives.
| S-EPMC7413736 | biostudies-literature
Project description:Type I collagen gels are routinely used in biophysical studies and bioengineering applications. The structural and mechanical properties of these fibrillar matrices depend on the conditions under which collagen fibrillogenesis proceeds, and developing a fuller understanding of this process will enhance control over gel properties. Turbidity measurements have long been the method of choice for monitoring developing gels, whereas imaging methods are regularly used to visualize fully developed gels. In this study, turbidity and confocal reflectance microscopy (CRM) were simultaneously employed to track collagen fibrillogenesis and reconcile the information reported by the two techniques, with confocal fluorescence microscopy (CFM) used to supplement information about early events in fibrillogenesis. Time-lapse images of 0.5 mg/ml, 1.0 mg/ml, and 2.0 mg/ml acid-solubilized collagen I gels forming at 27°C, 32°C, and 37°C were collected. It was found that in situ turbidity measured in a scanning transmittance configuration was interchangeable with traditional turbidity measurements using a spectrophotometer. CRM and CFM were employed to reveal the structures responsible for the turbidity that develops during collagen self-assembly. Information from CRM and transmittance images was collapsed into straightforward single variables; total intensity in CRM images tracked turbidity development closely for all collagen gels investigated, and the two techniques were similarly sensitive to fibril number and dimension. Complementary CRM, CFM, and in situ turbidity measurements revealed that fibril and network formation occurred before substantial turbidity was present, and the majority of increasing turbidity during collagen self-assembly was due to increasing fibril thickness.
| S-EPMC4008796 | biostudies-other
Project description:The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.
| S-EPMC7718922 | biostudies-literature
Project description:Approximately 1% of the open reading frames in the human genome encode proteins that function as DNA or RNA helicases. These enzymes act in all aspects of nucleic acid metabolism where the complementary strands of DNA:DNA or DNA:RNA duplexes require to be transiently opened. However, they perform wider roles in nucleic acid metabolism due to their ability to couple the energy derived from hydrolysis of ATP to their unidirectional translocation along strands of DNARNA. In this way, helicases can displace proteins from DNARNA, drive the migration of DNA junctions (such as the Holliday junction recombination intermediate), or generate superhelical tension in nucleic acid duplexes. Here, we review a subgroup of DNA helicase enzymes, the RecQ family, that has attracted considerable interest in recent years due to their role not only in suppression of genome instability, but also in the avoidance of human disease. We focus particularly on the protein structural motifs and the multiple assembly states that characterize RecQ helicases and discuss novel biophysical techniques to study the different RecQ structures present in solution. We also speculate on the roles of the different domains and oligomeric forms in defining which DNA structures will represent substrates for RecQ helicase-mediated transactions.
| S-EPMC2714954 | biostudies-literature
Project description:The landscape of structural variants (SVs) in multiple myeloma remains poorly understood. Here, we performed comprehensive analysis of SVs in a large cohort of 752 multiple myeloma patients by low coverage long-insert whole genome sequencing. We identified 68 SV hotspots involving 17 new candidate driver genes, including the therapeutic targets BCMA (TNFRSF17), SLAMF and MCL1. Catastrophic complex rearrangements termed chromothripsis were present in 24% of patients and independently associated with poor clinical outcomes. Templated insertions were the second most frequent complex event (19%), mostly involved in super-enhancer hijacking and activation of oncogenes such as CCND1 and MYC. Importantly, in 31% of patients two or more seemingly independent putative driver events were caused by a single structural event, demonstrating that the complex genomic landscape of multiple myeloma can be acquired through few key events during tumor evolutionary history. Overall, this study reveals the critical role of SVs in multiple myeloma pathogenesis.
| S-EPMC7774871 | biostudies-literature
Project description:Development of heart diseases is driven by dynamic changes in both the activity and connectivity of gene pathways. Understanding these dynamic events is critical for understanding pathogenic mechanisms and development of effective treatment. Currently, there is a lack of computational methods that enable analysis of multiple gene networks, each of which exhibits differential activity compared to the network of the baseline/healthy condition. We describe the iMDM algorithm to identify both unique and shared gene modules across multiple differential co-expression networks, termed M-DMs (multiple differential modules). We applied iMDM to a time-course RNA-Seq dataset generated using a murine heart failure model generated on two genotypes. We showed that iMDM achieves higher accuracy in inferring gene modules compared to using single or multiple co-expression networks. We found that condition-specific M-DMs exhibit differential activities, mediate different biological processes, and are enriched for genes with known cardiovascular phenotypes. By analyzing M-DMs that are present in multiple conditions, we revealed dynamic changes in pathway activity and connectivity across heart failure conditions. We further showed that module dynamics were correlated with the dynamics of disease phenotypes during the development of heart failure. Thus, pathway dynamics is a powerful measure for understanding pathogenesis. iMDM provides a principled way to dissect the dynamics of gene pathways and its relationship to the dynamics of disease phenotype. With the exponential growth of omics data, our method can aid in generating systems-level insights into disease progression.
| S-EPMC4471235 | biostudies-other