Organizational Heterogeneity of Vertebrate Genomes

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as “texts” using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences

Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome

Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min) remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and provide a general model for their replication kinetics

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to "epigenetic solitons" which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.Comment: Accepted version; Supplementary movies can be found at http://www2.ph.ed.ac.uk/~dmichiel/KnottedSolitons.html and https://www.youtube.com/watch?v=Osghh9nEhe

Pulse EPR detection of lipid exchange between protein-rich raft and bulk domains in the membrane: methodology development and its application to studies of influenza viral membrane.

A pulse saturation-recovery electron paramagnetic resonance (EPR) method has been developed that allows estimation of the exchange rates of a spin-labeled lipid between the bulk domain and the protein-rich membrane domain, in which the rate of collision between the spin label and molecular oxygen is reduced (slow-oxygen transport domain, or SLOT domain). It is based on the measurements of saturation-recovery signals of a lipid spin label as a function of concentrations of both molecular oxygen and the spin label. Influenza viral membrane, one of the simplest paradigms for the study of biomembranes, showed the presence of two membrane domains with slow and fast collision rates with oxygen (a 16-fold difference) at 30 degrees C. The outbound rate from and the inbound rate into the SLOT domain (or possibly the rate of the domain disintegration and formation) were estimated to be 7.7 x 10(4) and 4.6 x 10(4) s(-1), (15 micros residency time), respectively, indicating that the SLOT domain is highly dynamic and that the entire SLOT domain represents about one-third of the membrane area. Because the oxygen transport rate in the SLOT domain is a factor of two smaller than that in purple membrane, where bacteriorhodopsin is aggregated, we propose that the SLOT domain in the viral membrane is the cholesterol-rich raft domain stabilized by the trimers of hemagglutinin and/or the tetramers of neuraminidase

A importância da interação entre odontopediatrias e pediatrias no manejo de dentes natais e neonatais The importance of interaction of pediatric dentists and pediatricians in the management of natal and neonatal teeth

OBJETIVO: Apresentar revisão de literatura sobre dentes natais e neonatais, abordando características clínicas, fatores etiológicos, medidas terapêuticas e a importância do conhecimento desta anomalia, por odontopediatras e pediatras. FONTES DE DADOS: Foram selecionados os artigos mais relevantes sobre o tema, desde 1950 até 2006, pesquisados no Medline e na Bibliografia Brasileira em Odontologia (BBO), além de livros de pertinentes. SÍNTESE DOS DADOS: Os dentes natais e neonatais consistem em uma anomalia de erupção, sendo caracterizados por seu irrompimento na cavidade oral durante o período intra-uterino ou no primeiro mês de vida respectivamente, podendo fazer parte da dentição decídua normal ou supranumerária. Esses dentes, em geral, apresentam bordos cortantes e podem estar relacionados ao aparecimento de ulcerações na base da língua do bebê e/ou no seio materno, comprometendo a amamentação. A fraca implantação óssea desses dentes favorece sua grande mobilidade, tornando-se, assim, um fator de risco à sua aspiração ou deglutição pela criança. A abordagem terapêutica depende da dentição à qual pertence o dente e dos possíveis problemas que este pode causar à saúde da criança ou da mãe. CONCLUSÕES: O conhecimento sobre as características clínicas e os possíveis distúrbios aos quais os dentes natais e neonatais estão relacionados por odontopediatras e pediatras possibilita a interação necessária para o diagnóstico precoce e a abordagem integral da criança.<br>OBJECTIVE: To review available data about natal and neonatal teeth, emphasizing clinical characteristics, etiological factors, treatment, and the importance of the knowledge about this anomaly by pediatric dentists and pediatricians. DATA SOURCES: The most relevant articles published on the subject were selected, from 1950 to 2006, browsed on Medline, Brazilian Bibliografy of Odontology (BBO) and Dentistry books. DATA SYNTHESIS: Natal and neonatal teeth are considered eruption anomalies, characterized by eruption into oral cavity during the intrauterine period or during the first month after birth, respectively, being part of the regular deciduous or the supernumerary dentitions. As these teeth usually present cutting edges, they can be related to traumatic injury to newborn’s tongue and/or to mother’s nipples, compromising breastfeeding. In general, the weak attachment of these teeth to alveolar bone favors a high degree of mobility, which exposes the infant to the risk of aspiration or swallowing them. The management depends on which dentition these teeth belong and/or on complications that may affect either infant’s or mother’s health. CONCLUSIONS: The knowledge about the clinical characteristics and the possible complications related to natal and neonatal teeth by pediatric dentists and pediatricians provides the necessary interaction to early diagnosis and infant general management