Sufficient structural information on mammalian cytochromes P450 has now been published (including seventeen X-ray structures of these enzymes by June 2006) to allow characteristic features of these enzymes to be identified, including: (i) the presence of a common fold, typical of all P450s, (ii) similarities in the positioning of the heme cofactor, (iii) the spatial arrangement of certain structural elements, and (iv) the access/egress paths for substrates and products, (v) probably common orientation in the membrane, (vi) characteristic properties of the active sites with networks of water molecules, (vii) mode of interaction with redox partners and (viii) a certain degree of flexibility of the structure and active site determining the ease with which the enzyme may bind the substrates. As well as facilitating the identification of common features, comparison of the available structures allows differences among the structures to be identified, including variations in: (i) preferred access/egress paths to/from the active site, (ii) the active site volume and (iii) flexible regions. The availability of crystal structures provides opportunities for molecular dynamic simulations, providing data that are apparently complementary to experimental findings but also allow the dynamic behavior of access/egress paths and other dynamic features of the enzymes to be explored.
- MeSH
- Financing, Organized MeSH
- Protein Conformation MeSH
- Humans MeSH
- Membrane Proteins chemistry MeSH
- Models, Molecular MeSH
- Molecular Sequence Data MeSH
- Mammals MeSH
- Protein Folding MeSH
- Amino Acid Sequence MeSH
- Sequence Homology, Amino Acid MeSH
- Cytochrome P-450 Enzyme System chemistry MeSH
- Protein Structure, Tertiary MeSH
- Binding Sites MeSH
- Water chemistry MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
Structural variations (SVs) such as copy number and presence-absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species.
- Publication type
- Journal Article MeSH
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
BACKGROUND: Structural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exact genomic position. Breakpoint uncertainty is a characteristic issue of structural variants detected via short-read sequencing methods and complicates subsequent population analyses. The commonly used heuristic strategy reduces this issue by clustering/merging nearby structural variants of the same type before the data from individual samples are merged. RESULTS: We compared the two most used dissimilarity measures for SV clustering in terms of Mendelian inheritance errors (MIE), kinship prediction, and deviation from Hardy-Weinberg equilibrium. We analyzed the occurrence of Mendelian-inconsistent SV clusters that can be collapsed into one Mendelian-consistent SV as a new measure of dataset consistency. We also developed a new method based on constrained clustering that explicitly identifies these types of clusters. CONCLUSIONS: We found that the dissimilarity measure based on the distance between SVs breakpoints produces slightly better results than the measure based on SVs overlap. This difference is evident in trivial and corrected clustering strategy, but not in constrained clustering strategy. However, constrained clustering strategy provided the best results in all aspects, regardless of the dissimilarity measure used.
- MeSH
- Genome, Human * MeSH
- Genomics MeSH
- Humans MeSH
- Uncertainty MeSH
- Cluster Analysis MeSH
- Genomic Structural Variation * MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
MicroRNA (miRNA) expression is deregulated in many tumors including chronic lymphocytic leukemia (CLL). Although the particular mechanism(s) responsible for their aberrant expression is not well characterized, the presence of mutations and single-nucleotide polymorphisms (SNPs) in miRNA genes, possibly affecting their secondary structure and expression, has been described. In CLL; however, the impact and frequency of such variations have yet to be elucidated. Using a custom resequencing microarray, we screened sequence variations in 109 cancer-related pre-miRNAs in 98 CLL patients. Additionally, the primary regions of miR-29b-2/29c and miR-16-1 were analyzed by Sanger sequencing in another cohort of 213 and 193 CLL patients, respectively. Altogether, we describe six novel miR-sequence variations and the presence of SNPs (n = 27), most of which changed the miR-secondary structure. Moreover, some of the identified SNPs have a significantly different frequency in CLL when compared with a control population. Additionally, we identified a novel variation in miR-16-1 that had not been described previously in CLL patients. We show that this variation affects the expression of mature miR-16-1. We also show that the expression of another miRNA with pathogenetic relevance for CLL, namely miR-29b-2, is influenced by the presence of a polymorphic insertion, which is more frequent in CLL than in a control population. Altogether, these data suggest that sequence variations may occur during CLL development and/or progression.
- MeSH
- Alleles MeSH
- Chromosome Aberrations MeSH
- Leukemia, Lymphocytic, Chronic, B-Cell genetics MeSH
- Adult MeSH
- Gene Frequency MeSH
- Genetic Variation * MeSH
- Polymorphism, Single Nucleotide MeSH
- Nucleic Acid Conformation MeSH
- Middle Aged MeSH
- Humans MeSH
- MicroRNAs chemistry genetics MeSH
- Mutation MeSH
- Gene Expression Regulation, Leukemic MeSH
- Sequence Analysis, DNA MeSH
- Aged MeSH
- Immunoglobulin Heavy Chains genetics MeSH
- Germ-Line Mutation MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
High-resolution melting (HRM) analysis is a simple, sensitive, and cost-effective screening method. HRM enables the detection of homozygous or heterozygous point sequence variants and small deletions within specific PCR products by observing temperature and shape changes in melting curve profiles using fluorescent dyes. Herein, an updated protocol for routine variant screening of nuclear genes encoding assembly factors and structural subunits of cytochrome c oxidase (COX) is described. Nonetheless, the general recommendations given for HRM analysis can be applicable for examining any genetic region of interest.
- MeSH
- Genetic Variation * MeSH
- Genotype MeSH
- Humans MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Protein Subunits chemistry genetics metabolism MeSH
- Polymerase Chain Reaction methods MeSH
- Electron Transport Complex IV chemistry metabolism MeSH
- Nucleic Acid Amplification Techniques * methods MeSH
- Transition Temperature MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Cíl studie: posoudit schopnost strukturální analýzy terče zrakového nervu (ZN) pomocí Heidelberskéhoretinálníhotomografu (HRT),detekovat glaukomové změny ZN a nalézt topografické parametry, které jsou glaukomem nejvíce ovlivněny a které jsou významné pro časnou diagnostiku glaukomatózních změn ZN. Metodika: 68 zdravých očí (kontrolní soubor) a 42 očí s glaukomem otevřeného úhlu (studovaný soubor) osob nad 35 let bylo vyšetřeno pomocí laserové skenovací tomografie (HRT II). Ve studii byly sledovány tyto topografické parametry terče ZN: plocha disku, exkavace a neuroretinálního lemu, objem exkavace a neuroretinálníholemu, cup/discarea ratio,průměrnáhloubkaexkavace,maximálníhloubka exkavace, průměrná tloušťka vrstvy nervových vláken sítnice, plocha průřezu vrstvy nervových vláken sítnice, rozdíl mezi nejvyšším a nejnižším místem na sítnici podle konturní linie (height variation contour), hodnota pro 3D tvar oblasti pod referenční rovinou (cup shape measure) a diskriminační funkce dle F. S. Mikelberga a R. Burka používané pro klasifikaci nálezu na ZN. Statistickou analýzou byla testována významnost rozdílů těchto parametrů u zdravých očí a očí s glaukomem otevřeného úhlu pro celou oblast terče ZN a v 6 sektorech terče. Dále byla zjišťována významnost závislosti hodnot topografických parametrů na věku. Výsledky: Významné rozdíly topografických parametrů pro celou plochu terče mezi kontrolním a studovaným souborem byly nalezeny u těchto parametrů: objem neuroretinálního lemu, průměrná tloušťka vrstvy nervových vláken sítnice, plocha průřezu vrstvy nervových vláken sítnice a diskriminační funkce FSM. Významné rozdíly byly nalezeny i mezi jednotlivými sektory terče ZN, s výjimkou sektoru temporálního horního a nazálního horního. Nejčastěji odlišným parametrem mezi oběma soubory byl objem neuroretinálního lemu. Významná závislost topografických parametrů terče na věku byla zjištěna u těchto parametrů: plocha neuroretinálního lemu, cup shapemeasure a průměrná tloušťka vrstvy nervových vláken sítnice. Závěr: Výsledky naší studie ukázaly, že HRT je schopno rozlišit normální a patologický nález na ZN na základě topografických parametrů terče zrakového nervu významně odlišných mezi oběma testovanými soubory. Tyto parametry jsou důležité pro stanovení diagnózy glaukomu a při longitudinálním sledování pacientů s glaukomem otevřeného úhlu s ohledem na progresi tohoto onemocnění.
Purpose: Assess the possibilities of structural analysis of the optic nerve head by Heidelberg Retina Tomograph (HRT) and its use in detection of glaucomatous changes of the optic nerve in particular. Indicate the topographical parameters that are most influenced by glaucoma and are therefore vital in early diagnosis of glaucomatous changes of the optic nerve. Patients and methods: Laser scanning tomography (HRT II) was used to examine 68 healthy eyes (control group) and 42 eyes with open angle glaucoma (study group). All the examined subjects were older than 35 years of age. The analysis concerned the following topographical parameters of the optic nerve head: disc area, cup area and rim area, cup volume, rim volume, cup/disc area ratio, mean cup depth, maximum cup depth, mean retinal nerve fiber layer thickness (RNFL), RNFL cross sectional area, height variation contour and cup shape measure and discriminant functions used for classification of the optic nerve head finding according to F. S. Mikelberg and R. Burk. Statistical analysis was employed to ascertain the significant difference in these topographical parameters for the healthy eyes and the eyes with glaucoma. This method was used for both the whole optic disc and the 6 sectors of the optic nerve head. Another aim of the analysis was also to find out the correlation between the topographical parameters and age. Results: Significant difference in the topographical parameters for thewhole optic disc was spotted in the following parameters: rim volume, mean RNFL thickness, RNFLcross sectional area and discriminant functionFSM. Significant differences were also found in between individual sectors of the optic nerve head, except for the upper temporal and upper nasal sector. The parameter, which varied most frequently between the groups, was rim volume. Significant correlations between age and topographical parameters were found forthe following parameters: rim area, cup shape measure and mean RNFL thickness. Conclusion: Results of our study showed, that HRT is able to distinguish between normal and the pathological findings of optic nerve head according to topographical parameters significantly different between the two examined groups. These parameters are important in the diagnosis of glaucoma and also in the follow-up of patients with open angle glaucoma.
- MeSH
- Anatomy, Regional MeSH
- Adult MeSH
- Glaucoma, Open-Angle diagnosis etiology MeSH
- Middle Aged MeSH
- Humans MeSH
- Optic Nerve anatomy & histology MeSH
- Aged MeSH
- Tomography methods instrumentation MeSH
- Visual Fields MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Aged MeSH
- Publication type
- Review MeSH
- Comparative Study MeSH
The 14-3-3 proteins, a family of conserved regulatory molecules, participate in a wide range of cellular processes through binding interactions with hundreds of structurally and functionally diverse proteins. Several distinct mechanisms of the 14-3-3 protein function were described, including conformational modulation of the bound protein, masking of its sequence-specific or structural features, and scaffolding that facilitates interaction between two simultaneously bound proteins. Details of these functional modes, especially from the structural point of view, still remain mostly elusive. This review gives an overview of the current knowledge concerning the structure of 14-3-3 proteins and their complexes as well as the insights it provides into the mechanisms of their functions. We discuss structural basis of target recognition by 14-3-3 proteins, common structural features of their complexes and known mechanisms of 14-3-3 protein-dependent regulations.
- MeSH
- DNA-Binding Proteins MeSH
- Eukaryota metabolism MeSH
- Phosphorylation MeSH
- Genetic Variation MeSH
- Protein Interaction Domains and Motifs MeSH
- Protein Conformation MeSH
- Humans MeSH
- Models, Molecular MeSH
- Protein Isoforms chemistry metabolism MeSH
- 14-3-3 Proteins chemistry genetics metabolism MeSH
- Protein Structure, Tertiary MeSH
- Protein Binding MeSH
- Binding Sites MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
