Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structural uniformity of neocortex, revisited.

ABSTRACT: The number of neurons under a square millimeter of cortical surface has been reported to be the same across five cortical areas and five species [Rockel et al. (1980) Brain 103(2):221-244] despite differences in cortical thickness between the areas. Although the accuracy of this result has been the subject of sharp debate since its publication approximately 30 y ago, the experiments of Rockel et al. have never been directly replicated with modern stereological methods. We have replicated these experiments and confirm the accuracy of the original report. In addition, we have observed that the number of glial cells under a square millimeter of cortical surface depends on cortical thickness, but not on cortical area or species.

SUBMITTER: Carlo CN

PROVIDER: S-EPMC3557031 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Structural uniformity of neocortex, revisited.

Carlo C Nikoosh CN Stevens Charles F CF

Proceedings of the National Academy of Sciences of the United States of America 20130107 4

The number of neurons under a square millimeter of cortical surface has been reported to be the same across five cortical areas and five species [Rockel et al. (1980) Brain 103(2):221-244] despite differences in cortical thickness between the areas. Although the accuracy of this result has been the subject of sharp debate since its publication approximately 30 y ago, the experiments of Rockel et al. have never been directly replicated with modern stereological methods. We have replicated these e ...[more]

PMID: 23297199

Similar Datasets

Two Lineages of Pseudomonas aeruginosa Filamentous Phages: Structural Uniformity over Integration Preferences.

Project description:Pseudomonas aeruginosa filamentous (Pf) bacteriophages are important factors contributing to the pathogenicity of this opportunistic bacterium, including biofilm formation and suppression of bacterial phagocytosis by macrophages. In addition, the capacity of Pf phages to form liquid crystal structures and their high negative charge density makes them potent sequesters of cationic antibacterial agents, such as aminoglycoside antibiotics or host antimicrobial peptides. Therefore, Pf phages have been proposed as a potential biomarker for risk of antibiotic resistance development. The majority of studies describing biological functions of Pf viruses have been performed with only three of them: Pf1, Pf4, and Pf5. However, our analysis revealed that Pf phages exist as two evolutionary lineages (I and II), characterized by substantially different structural/morphogenesis properties, despite sharing the same integration sites in the host chromosomes. All aforementioned model Pf phages are members of the lineage I. Hence, it is reasonable to speculate that their interactions with P. aeruginosa and impact on its pathogenicity may be not completely extrapolated to the lineage II members. Furthermore, in order to organize the present numerical nomenclature of Pf phages, we propose a more informative approach based on the insertion sites, that is, Pf-tRNA-Gly, -Met, -Sec, -tmRNA, and -DR (direct repeats), which are fully compatible with one of five types of tyrosine integrases/recombinases XerC/D carried by these viruses. Finally, we discuss possible evolutionary mechanisms behind this division and consequences from the perspective of virus-virus, virus-bacterium, and virus-human interactions.

| S-EPMC7549136 | biostudies-literature

Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited.

Project description:In the past few years, our understanding of the RNA virosphere has changed dramatically due to the growth and spurt of metagenomics, exponentially increasing the number of RNA viral sequences, and providing a better understanding of their range of potential hosts. As of today, the only conserved protein among RNA viruses appears to be the monomeric RNA-dependent RNA polymerase. This enzyme belongs to the right-hand DNA-and RNA polymerases, which also includes reverse transcriptases and eukaryotic replicative DNA polymerases. The ubiquity of this protein in RNA viruses makes it a unique evolutionary marker and an appealing broad-spectrum antiviral target. In this work pairwise structural comparisons of viral RdRps and RTs were performed, including tertiary structures that have been obtained in the last few years. The resulting phylogenetic tree shows that the RdRps from (+)ss- and dsRNA viruses might have been recruited several times throughout the evolution of mobile genetic elements. RTs also display multiple evolutionary routes. We have identified a structural core comprising the entire palm, a large moiety of the fingers and the N-terminal helices of the thumb domain, comprising over 300 conserved residues, including two regions that we have named the "knuckles" and the "hypothenar eminence". The conservation of an helix bundle in the region preceding the polymerase domain confirms that (-)ss and dsRNA Reoviruses' polymerases share a recent ancestor. Finally, the inclusion of DNA polymerases into our structural analyses suggests that monomeric RNA-dependent polymerases might have diverged from B-family polymerases.

| S-EPMC9153872 | biostudies-literature

The pyrroloquinoline quinone biosynthesis pathway revisited: a structural approach.

Project description:BackgroundThe biosynthesis pathway of Pyrroloquinoline quinone, a bacterial redox active cofactor for numerous alcohol and aldose dehydrogenases, is largely unknown, but it is proven that at least six genes in Klebsiella pneumoniae (PqqA-F) are required, all of which are located in the PQQ-operon.ResultsNew structural data of some PQQ biosynthesis proteins and their homologues provide new insights and functional assignments of the proteins in the pathway. Based on sequence analysis and homology models we propose the role and catalytic function for each enzyme involved in this intriguing biosynthesis pathway.ConclusionPQQ is derived from the two amino acids glutamate and tyrosine encoded in the precursor peptide PqqA. Five reactions are necessary to form this quinone cofactor. The PqqA peptide is recognised by PqqE, which links the C9 and C9a, afterwards it is accepted by PqqF which cuts out the linked amino acids. The next reaction (Schiff base) is spontaneous, the following dioxygenation is catalysed by an unknown enzyme. The last cyclization and oxidation steps are catalysed by PqqC. Taken together the known facts of the different proteins we assign a putative function to all six proteins in PQQ biosynthesis pathway.

| S-EPMC2294125 | biostudies-literature

The chlamydiales pangenome revisited: structural stability and functional coherence.

Project description:The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.

| S-EPMC3899948 | biostudies-literature

The structural-demographic theory revisited: An empirical test for industrialized societies

Project description: Not available

| S-EPMC10621949 | biostudies-literature

High-Temperature Magnetism as a Probe for Structural and Compositional Uniformity in Ligand-Capped Magnetite Nanoparticles.

Project description:To investigate magnetostructural relationships in colloidal magnetite (Fe3O4) nanoparticles (NPs) at high temperature (300-900 K), we measured the temperature dependence of magnetization (M) of oleate-capped magnetite NPs ca. 20 nm in size. Magnetometry revealed an unusual irreversible high-temperature dependence of M for these NPs, with dip and loop features observed during heating-cooling cycles. Detailed characterizations of as-synthesized and annealed Fe3O4 NPs as well as reference ligand-free Fe3O4 NPs indicate that both types of features in M(T) are related to thermal decomposition of the capping ligands. The ligand decomposition upon the initial heating induces a reduction of Fe3+ to Fe2+ and the associated dip in M, leading to more structurally and compositionally uniform magnetite NPs. Having lost the protective ligands, the NPs continually sinter during subsequent heating cycles, resulting in divergent M curves featuring loops. The increase in M with sintering proceeds not only through elimination of a magnetically dead layer on the particle surface, as a result of a decrease in specific surface area with increasing size, but also through an uncommonly invoked effect resulting from a significant change in Fe3+/Fe2+ ratio with heat treatment. The interpretation of irreversible features in M(T) indicates that reversible M(T) behavior, conversely, can be expected only for ligand-free, structurally and compositionally uniform magnetite NPs, suggesting a general applicability of high-temperature M(T) measurements as an analytical method for probing the structure and composition of magnetic nanomaterials.

| S-EPMC4259497 | biostudies-literature

Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures.

Project description:Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the "standard" GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature.

| S-EPMC3494683 | biostudies-literature

The Importance of Structural Uniformity and Chemical Homogeneity in Cobalt-Free Lithium Excess Nickel Manganese Oxide Cathodes.

Project description:This study explores the relationships between material quench rate during processing and the resulting structural and electrochemical properties of Li[Ni0.25 Li0.167 Mn0.583 ]O2 . Samples of this lithium-rich material are prepared with highly contrasting postfiring cooling methods: a rapid water emersion quench or closed-door oven cooling. The contrasting approaches result in samples with different structural, chemical, and electrochemical behaviors; after cycling the rapidly quenched material yields greater capacity, greater stability, and initially lower, but more stable voltages than the slower cooled samples. Through the use of scanning tunneling electron microscopy, X-Ray Diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) it is demonstrated that rapidly quenched powders are more structurally uniform and chemically homogenous before cycling. By comparing these precycling sample to postcycling samples, it is then examined how this increased structural uniformity and chemical homogeneity leads to the superior electrochemical properties of the rapidly quenched samples.

| S-EPMC10238218 | biostudies-literature

1,2,3,4-Tetrahydro-1,4,5,8-tetraazaanthracene revisited: properties and structural evidence of aromaticity loss.

Project description:The synthesis and properties of 1,2,3,4-tetrahydro-1,4,5,8-tetraazaanthracene (THTAA) - a heterocycle involving both >N-H donating and =N- accepting moieties - have been reinvestigated. Unlike previously reported, THTAA is a thermally stable compound that can be re-sublimed at 300-310 °C without decomposition. Controlled introduction of substituents at the nitrogen atoms of THTAA led to variation of its electron donor/acceptor capability that allowed fine-tuning the absorption properties. The propensity of these compounds and a number of its derivatives to form infinite chains involving >N-H···N= and >N-H···Hal-···N+ atoms is demonstrated by X-ray structure analysis. The DFT level optimized and experimental geometry of THTAA and its derivatives show considerable loss of aromaticity within the quinoxaline moiety.

| S-EPMC6720741 | biostudies-literature

Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites.

Project description:The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature. The resulting model, with an increase in resolution from 3.1 to 2.8 A, gives an overall improvement of the molecular structure, in particular the side chains. In addition, it enables the clear definition of previously unidentified Ca2+-binding and Na+-binding sites. The Ca2+ cation is located in domain 1 in a configuration very similar to that found in the activated bovine factor Va. The Na+ sites appear to play a structural role in providing rigidity to the three protuberances on the top surface of the molecule. These features probably help to steer substrates towards the mononuclear copper sites prior to their oxidation and to restrict the size of the approaching substrate. The trinuclear copper centre appears to differ from the room-temperature structure in that a dioxygen moiety is bound in a similar way to that found in the endospore coat protein CotA from Bacillus subtilis.

| S-EPMC2483498 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data