Structural Divergence (structural + divergence)

Distribution by Scientific Domains


Selected Abstracts


Understanding the recent evolution of the human genome: insights from human,chimpanzee genome comparisons,

HUMAN MUTATION, Issue 2 2007
Hildegard Kehrer-Sawatzki
Abstract The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome. Hum Mutat 28(2), 99,130, 2007. © 2006 Wiley-Liss, Inc. [source]


Primitive complement system of invertebrates

IMMUNOLOGICAL REVIEWS, Issue 1 2004
Masaru Nonaka
Summary:, Most components of the human complement system have unmistakable domain architectures, making evolutionary tracing feasible. In contrast to the major genes of the adaptive immune system, which are present only in jawed vertebrates, complement component genes with unique domain structures are present not only in jawed vertebrates but also in jawless fish and non-vertebrate deuterostomes. Recent progress in genome analysis in several eukaryotes, occupying the phylogenetically critical positions, showed that most individual domains found in the complement components are metazoa specific, being found both in deuterostomes and in protostomes but not in yeast or plant. However, unique domain architecture of complement components is not present in protostomes, suggesting that the complement system has been established in the deuterostome lineage not by invention of new domains but by innovation of unique combination of the pre-existing domains. The recently assembled Ciona intestinalis draft genome contained the most modular complement genes, except for factor I. However, some possible C. intestinalis complement components show critical structural divergence from the mammalian counterparts, casting doubt on their mutual interaction. Thus, another integrative step seems to have been required to establish the modern complement system of higher vertebrates. [source]


Force field-dependant structural divergence revealed during long time simulations of Calbindin d9k

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010
Elad Project
Abstract The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S2 order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]


Structural stability of Sclerotium rolfsii ATCC 201126 ,-glucan with fermentation time: a chemical, infrared spectroscopic and enzymatic approach

JOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009
J.I. Fariña
Abstract Aims:,Sclerotium rolfsii ATCC 201126 exopolysaccharides (EPSs) recovered at 48 h (EPS I) and 72 h (EPS II) of fermentation, with differences in rheological parameters, hydrogel topography, salt tolerance, antisyneresis, emulsifying and suspending properties, were subjected to a polyphasic characterization in order to detect structural divergences. Methods and Results:, Fermenter-scale production led to productivity (Pr) and yield (YP/C) values higher at 48 h (Pr = 0·542 g l,1 h,1; YP/C = 0·74) than at 72 h (Pr = 0·336 g l,1 h,1; YP/C = 0·50). Both EPSs were neutral glucose-homopolysaccharides with a ,-(1,3)-glycosidic backbone and single ,-(1,6)-glucopyranosyl sidechains regularly attached every three residues in the main chain, as revealed by chemical analyses. The infra-red diagnostic peak at 890 cm,1 confirmed ,-glycosidic linkages, while gentiobiose released by ,-(1,3)-glucanases confirmed single ,-1,6-glycosidic branching for both EPSs. Conclusions:, The true modular repeating unit of S. rolfsii ATCC 201126 scleroglucan could be resolved. Structural stability was corroborated and no structural differences could be detected as to account for the variations in EPSs behaviour. Significance and Impact of the Study:, Recovery of S. rolfsii ATCC 201126 scleroglucan at 48 h might be considered based on better fermentation kinetic parameters and no detrimental effects on EPS structural features. [source]