Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach

Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Explaining oscillations and variability in the p53-Mdm2 system

<p>Abstract</p> <p>Background</p> <p>In individual living cells p53 has been found to be expressed in a series of discrete pulses after DNA damage. Its negative regulator Mdm2 also demonstrates oscillatory behaviour. Attempts have been made recently to explain this behaviour by mathematical models but these have not addressed explicit molecular mechanisms. We describe two stochastic mechanistic models of the p53/Mdm2 circuit and show that sustained oscillations result directly from the key biological features, without assuming complicated mathematical functions or requiring more than one feedback loop. Each model examines a different mechanism for providing a negative feedback loop which results in p53 activation after DNA damage. The first model (ARF model) looks at the mechanism of p14^ARFwhich sequesters Mdm2 and leads to stabilisation of p53. The second model (ATM model) examines the mechanism of ATM activation which leads to phosphorylation of both p53 and Mdm2 and increased degradation of Mdm2, which again results in p53 stabilisation. The models can readily be modified as further information becomes available, and linked to other models of cellular ageing.</p> <p>Results</p> <p>The ARF model is robust to changes in its parameters and predicts undamped oscillations after DNA damage so long as the signal persists. It also predicts that if there is a gradual accumulation of DNA damage, such as may occur in ageing, oscillations break out once a threshold level of damage is acquired. The ATM model requires an additional step for p53 synthesis for sustained oscillations to develop. The ATM model shows much more variability in the oscillatory behaviour and this variability is observed over a wide range of parameter values. This may account for the large variability seen in the experimental data which so far has examined ARF negative cells.</p> <p>Conclusion</p> <p>The models predict more regular oscillations if ARF is present and suggest the need for further experiments in ARF positive cells to test these predictions. Our work illustrates the importance of systems biology approaches to understanding the complex role of p53 in both ageing and cancer.</p

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Valoración y análisis en pacientes con diagnóstico de evento vascular cerebral isquémico en el servicio de urgencias

Introducción: El evento vascular cerebral (EVC) se considera la tercera enfermedad con mayor mortalidad en México, y sus repercusiones son amplias. Objetivo: Valorar y analizar los pacientes con EVC isquémico atendidos en el servicio de urgencias del Hospital General Regional No. 20, Instituto Mexicano del Seguro Social, en Tijuana, Baja California, México. Método: Se realizó un estudio retrospectivo, descriptivo y transversal en pacientes que cumplieron los criterios de inclusión. Las variables fueron edad, sexo, antecedente familiar de infarto agudo de miocardio (IAM), antecedente familiar de EVC, antecedente personal de IAM, antecedente personal de trombosis, diabetes mellitus, hipertensión arterial sistémica, dislipidemia, enfermedad renal crónica, obesidad, fibrilación auricular, tabaquismo y alcoholismo. El análisis de los datos se realizó con estadística descriptiva, medidas de tendencia central y de dispersión para variables de frecuencia. Para el análisis de los resultados se usó el programa estadístico SPSS. Resultados: El sexo predominante fue el femenino, con un 51%, y el grupo etario ≥ 75 años correspondió al 40% de los casos. En cuanto a las prevalencias, la nula escolaridad se encontró en un 47%, el tabaquismo en un 27.8%, la obesidad en un 13.9%, la dislipidemia y la hipertensión en un 77.8%, la diabetes mellitus en un 50% y la fibrilación auricular en un 4.2%. Conclusiones: La muestra obtenida presenta una alta prevalencia de hipertensión, dislipidemia y diabetes mellitus. La importancia de la prevención y el manejo oportuno de dichas patologías en nuestra entidad puede ser un factor determinante para poder combatir la creciente incidencia del EVC

X-ray structure analysis of symmetrically substituted 1,1′-diformylruthenocene

1,1′-Diformylruthenocene, [Ru(C6H5O)2], crystallizes in the orthorhombic system in the P212121 space group at room temperature. There are two crystallographically independent molecules in the asymmetric unit. The cyclopentadienyl rings have eclipsed configuration. The molecules self-assemble in a two-dimensional structure by C—H...O and C—H...π interactions with cisoid relative orientations of the two formyl groups. The crystal studied was refined as an inversion twin