Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells.

Gene transfer in eukaryotic cells and organisms suffers from epigenetic effects that result in low or unstable transgene expression and high clonal variability. Use of epigenetic regulators such as matrix attachment regions (MARs) is a promising approach to alleviate such unwanted effects. Dissection of a known MAR allowed the identification of sequence motifs that mediate elevated transgene expression. Bioinformatics analysis implied that these motifs adopt a curved DNA structure that positions nucleosomes and binds specific transcription factors. From these observations, we computed putative MARs from the human genome. Cloning of several predicted MARs indicated that they are much more potent than the previously known element, boosting the expression of recombinant proteins from cultured cells as well as mediating high and sustained expression in mice. Thus we computationally identified potent epigenetic regulators, opening new strategies toward high and stable transgene expression for research, therapeutic production or gene-based therapies.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Covariance Matrix Estimation and Mean-Variance Optimization in application to International Diversification

Tutkimus keskittyy kansainväliseen hajauttamiseen suomalaisen sijoittajan näkökulmasta. Tutkimuksen toinen tavoite on selvittää tehostavatko uudet kovarianssimatriisiestimaattorit minimivarianssiportfolion optimointiprosessia. Tavallisen otoskovarianssimatriisin lisäksi optimoinnissa käytetään kahta kutistusestimaattoria ja joustavaa monimuuttuja-GARCH(1,1)-mallia. Tutkimusaineisto koostuu Dow Jonesin toimialaindekseistä ja OMX-H:n portfolioindeksistä. Kansainvälinen hajautusstrategia on toteutettu käyttäen toimialalähestymistapaa ja portfoliota optimoidaan käyttäen kahtatoista komponenttia. Tutkimusaieisto kattaa vuodet 1996-2005 eli 120 kuukausittaista havaintoa. Muodostettujen portfolioiden suorituskykyä mitataan Sharpen indeksillä. Tutkimustulosten mukaan kansainvälisesti hajautettujen investointien ja kotimaisen portfolion riskikorjattujen tuottojen välillä ei ole tilastollisesti merkitsevää eroa. Myöskään uusien kovarianssimatriisiestimaattoreiden käytöstä ei synnytilastollisesti merkitsevää lisäarvoa verrattuna otoskovarianssimatrisiin perustuvaan portfolion optimointiin.

Different concentrations of Mg++ ions affect nuclear matrix protein distribution during thermal stabilization of isolated nuclei.

The nuclear matrix, a proteinaceous network believed to be a scaffolding structure determining higher-order organization of chromatin, is usually prepared from intact nuclei by a series of extraction steps. In most cell types investigated the nuclear matrix does not spontaneously resist these treatments but must be stabilized before the application of extracting agents. Incubation of isolated nuclei at 37C or 42C in buffers containing Mg++ has been widely employed as stabilizing agent. We have previously demonstrated that heat treatment induces changes in the distribution of three nuclear scaffold proteins in nuclei prepared in the absence of Mg++ ions. We studied whether different concentrations of Mg++ (2.0-5 mM) affect the spatial distribution of nuclear matrix proteins in nuclei isolated from K562 erythroleukemia cells and stabilized by heat at either 37C or 42C. Five proteins were studied, two of which were RNA metabolism-related proteins (a 105-kD component of splicing complexes and an RNP component), one a 126-kD constituent of a class of nuclear bodies, and two were components of the inner matrix network. The localization of proteins was determined by immunofluorescent staining and confocal scanning laser microscope. Mg++ induced significant changes of antigen distribution even at the lowest concentration employed, and these modifications were enhanced in parallel with increase in the concentration of the divalent cation. The different sensitivity to heat stabilization and Mg++ of these nuclear proteins might reflect a different degree of association with the nuclear scaffold and can be closely related to their functional or structural role.

Application des méthodes géophysiques à l'étude de deux sites (Kappelen et Grenchen) de l'aquifère poreux complexe du Seeland

L'aquifère du Seeland représente une richesse en ressources hydriques qu'il est impératif de préserver contre tout risque de détérioration. Cet aquifère prolifique est constitué principalement de sédiments alluviaux post-glaciaires (graviers, sables et limons). Il est soumis aux contraintes environnementales des pratiques d'agriculture intensive, du réseau routier, des villes et de leurs activités industrielles. La connaissance optimale de ces ressources est donc primordiale pour leur protection. Dans cette optique, deux sites Kappelen et Grenchen représentatifs de l'aquifère du Seeland ont été étudiés. L'objectif de ce travail est de caractériser d'un point de vue hydrogéophysique l'aquifère au niveau de ces deux sites, c'est-à-dire, comprendre la dynamique des écoulements souterrains par l'application des méthodes électriques de surface associées aux diagraphies en intégrant des méthodes hydrogéologiques. Pour le site de Kappelen, les méthodes électriques de surface ont permis d'identifier les différents faciès géoélectriques en présence et de mettre en évidence leur disposition en une structure tabulaire et horizontale. Il s'agit d'un aquifère libre constitué d'une série de graviers allant jusqu'à 15 m de profondeur reposant sur de la moraine argileuse. Les diagraphies électriques, nucléaires et du fluide ont servis à la détermination des caractéristiques pétrophysiques et hydrauliques de l'aquifère qui contrôlent son comportement hydrodynamique. Les graviers aquifères de Kappelen présentent deux minéraux dominants: quartz et calcite. Les analyses minéralogiques indiquent que ces deux éléments constituent 65 à 75% de la matrice. La porosité totale obtenue par les diagraphies nucléaires varie de 20 à 30 %, et de 22 à 29 % par diagraphies électrique. Avec les faibles valeurs de Gamma Ray ces résultats indiquent que l'aquifère des graviers de Kappelen est dépourvu d'argile minéralogique. La perméabilité obtenue par diagraphies du fluide varie de 3.10-4 à 5.10-2 m/s, et par essais de pompage de 10-4 à 10-2 m/s. Les résultats des analyses granulométriques indiquent une hétérogénéité granulométrique au niveau des graviers aquifères. La fraction de sables, sables très fins, silts et limons constitue de 10 à 40 %. Ces éléments jouent un rôle important dans le comportement hydraulique de l'aquifère. La porosité efficace de 11 à 25% estimée à partir des résultats des analyses granulométriques suppose que les zones les plus perméables correspondent aux zones les plus graveleuses du site. Etablie sur le site de Kappelen, cette méthodologie a été utilisée sur le site de Grenchen. Les méthodes électriques de surface indiquent que l'aquifère captif de Grenchen est constitué des sables silteux comprenant des passages sableux, encadrés par des silts argileux imperméables. L'aquifère de Grenchen est disposé dans une structure relativement tabulaire et horizontale. Son épaisseur totale peut atteindre les 25 m vers le sud et le sud ouest ou les passages sableux sont les plus importants. La détermination des caractéristiques pétrophysiques et hydrauliques s'est faite à l'aide des diagraphies. Les intensités Gamma Ray varient de 30 à 100 cps, les plus fortes valeurs n'indiquent qu'une présence d'éléments argileux mais pas de bancs d'argile. Les porosités totales de 15 à 25% et les densités globales de 2.25 à 2.45 g/cm3 indiquent que la phase minérale (matrice) est composée essentiellement de quartz et de calcaire. Les densités de matrice varient entre 2.65 et 2.75 g/cm3. La perméabilité varie de 2 10-6 à 5 10-4 m/s. La surestimation des porosités totales à partir des diagraphies électriques de 25 à 42% est due à la présence d'argiles. -- The vast alluvial Seeland aquifer system in northwestern Switzerland is subjected to environmental challenges due to intensive agriculture, roads, cities and industrial activities. Optimal knowledge of the hydrological resources of this aquifer system is therefore important for their protection. Two representative sites, Kappelen and Grenchen, of the Seeland aquifer were investigated using surface-based geoelectric methods and geophysical borehole logging methods. By integrating of hydrogeological and hydrogeophysical methods, a reliable characterization of the aquifer system at these two sites can be performed in order to better understand the governing flow and transport process. At the Kappelen site, surface-based geoelectric methods allowed to identify various geoelectric facies and highlighted their tabular and horizontal structure. It is an unconfined aquifer made up of 15 m thick gravels with an important sandy fraction and bounded by a shaly glacial aquitard. Electrical and nuclear logging measurements allow for constraining the petrophysical and hydrological parameters of saturated gravels. Results indicate that in agreement with mineralogical analyses, matrix of the probed formations is dominated by quartz and calcite with densities of 2.65 and 2.71 g/cc, respectively. These two minerals constitute approximately 65 to 75 % of the mineral matrix. Matrix density values vary from 2.60 to 2.75 g/cc. Total porosity values obtained from nuclear logs range from 20 to 30 % and are consistent with those obtained from electrical logs ranging from 22 to 29 %. Together with the inherently low natural gamma radiation and the matrix density values obtained from other nuclear logging measurements, this indicates that at Kappelen site the aquifer is essentially devoid of clay. Hydraulic conductivity values obtained by the Dilution Technique vary between 3.10-4 and 5.10-2 m/s, while pumping tests give values ranging from 10-4 to 10-2 m/s. Grain size analysis of gravel samples collected from boreholes cores reveal significant granulometric heterogeneity of these deposits. Calculations based on these granulometric data have shown that the sand-, silt- and shale-sized fractions constitute between 10 and 40 % of the sample mass. The presence of these fine elements in general and their spatial distribution in particular are important as they largely control the distribution of the total and effective porosity as well as the hydraulic conductivity. Effective porosity values ranging from 11 to 25% estimated from grain size analyses indicate that the zones of higher hydraulic conductivity values correspond to the zones dominated by gravels. The methodology established at the Kappelen site was then applied to the Grenchen site. Results from surface-based geoelectric measurements indicate that it is a confined aquifer made up predominantly of shaly sands with intercalated sand lenses confined impermeable shally clay. The Grenchen confined aquifer has a relatively tabular and horizontal structure with a maximum thickness of 25 m in the south and the southwest with important sand passages. Petrophysical and hydrological characteristics were performed using electrical and nuclear logging. Natural gamma radiation values ranging from 30 to 100 cps indicate presence of a clay fraction but not of pure clay layers. Total porosity values obtained from electrical logs vary form 25 to 42%, whereas those obtained from nuclear logs values vary from 15 to 25%. This over-estimation confirms presences of clays. Density values obtained from nuclear logs varying from 2.25 to 2.45 g/cc in conjunction with the total porosity values indicate that the dominating matrix minerals are quartz and calcite. Matrix density values vary between 2.65 and 2.75 g/cc. Hydraulic conductivity values obtained by the Dilution Technique vary from 2 10-6 to 5 10-4 m/s.

Scales and causes of heterogeneity in bars in a large multi-channel river: Rio Parana, Argentina

To date, published studies of alluvial bar architecture in large rivers have been restricted mostly to case studies of individual bars and single locations. Relatively little is known about how the depositional processes and sedimentary architecture of kilometre-scale bars vary within a multi-kilometre reach or over several hundreds of kilometres downstream. This study presents Ground Penetrating Radar and core data from 11, kilometre-scale bars from the Rio Parana, Argentina. The investigated bars are located between 30km upstream and 540km downstream of the Rio Parana - Rio Paraguay confluence, where a significant volume of fine-grained suspended sediment is introduced into the network. Bar-scale cross-stratified sets, with lengths and widths up to 600m and thicknesses up to 12m, enable the distinction of large river deposits from stacked deposits of smaller rivers, but are only present in half the surface area of the bars. Up to 90% of bar-scale sets are found on top of finer-grained ripple-laminated bar-trough deposits. Bar-scale sets make up as much as 58% of the volume of the deposits in small, incipient mid-channel bars, but this proportion decreases significantly with increasing age and size of the bars. Contrary to what might be expected, a significant proportion of the sedimentary structures found in the Rio Parana is similar in scale to those found in much smaller rivers. In other words, large river deposits are not always characterized by big structures that allow a simple interpretation of river scale. However, the large scale of the depositional units in big rivers causes small-scale structures, such as ripple sets, to be grouped into thicker cosets, which indicate river scale even when no obvious large-scale sets are present. The results also show that the composition of bars differs between the studied reaches upstream and downstream of the confluence with the Rio Paraguay. Relative to other controls on downstream fining, the tributary input of fine-grained suspended material from the Rio Paraguay causes a marked change in the composition of the bar deposits. Compared to the upstream reaches, the sedimentary architecture of the downstream reaches in the top ca 5m of mid-channel bars shows: (i) an increase in the abundance and thickness (up to metre-scale) of laterally extensive (hundreds of metres) fine-grained layers; (ii) an increase in the percentage of deposits comprised of ripple sets (to >40% in the upper bar deposits); and (iii) an increase in bar-trough deposits and a corresponding decrease in bar-scale cross-strata (<10%). The thalweg deposits of the Rio Parana are composed of dune sets, even directly downstream from the Rio Paraguay where the upper channel deposits are dominantly fine-grained. Thus, the change in sedimentary facies due to a tributary point-source of fine-grained sediment is primarily expressed in the composition of the upper bar deposits.

Tumor heterogeneity and cancer stem cell paradigm: updates in concept, controversies and clinical relevance.

Although tumor heterogeneity is widely accepted, the existence of cancer stem cells (CSCs) and their proposed role in tumor maintenance has always been challenged and remains a matter of debate. Recently, a path-breaking chapter was added to this saga when three independent groups reported the in vivo existence of CSCs in brain, skin and intestinal tumors using lineage-tracing and thus strengthens the CSC concept; even though certain fundamental caveats are always associated with lineage-tracing approach. In principle, the CSC hypothesis proposes that similar to normal stem cells, CSCs maintain self renewal and multilineage differentiation property and are found at the central echelon of cellular hierarchy present within tumors. However, these cells differ from their normal counterpart by maintaining their malignant potential, alteration of genomic integrity, epigenetic identity and the expression of specific surface protein profiles. As CSCs are highly resistant to chemotherapeutics, they are thought to be a crucial factor involved in tumor relapse and superficially appear as the ultimate therapeutic target. However, even that is not the end; further complication is attributed by reports of bidirectional regeneration mechanism for CSCs, one from their self-renewal capability and another from the recently proposed concept of dynamic equilibrium between CSCs and non-CSCs via their interconversion. This phenomenon has currently added a new layer of complexity in understanding the biology of tumor heterogeneity. In-spite of its associated controversies, this area has rapidly emerged as the center of attention for researchers and clinicians, because of the conceptual framework it provides towards devising new therapies.

Recruitment of Matrix Metalloproteinase-9 (MMP-9) to the Fibroblast Cell Surface by Lysyl Hydroxylase 3 (LH3) Triggers Transforming Growth Factor-β (TGF-β) Activation and Fibroblast Differentiation.

Solid tumor growth triggers a wound healing response. Similar to wound healing, fibroblasts in the tumor stroma differentiate into myofibroblasts (also referred to as cancer-associated fibroblasts) primarily, but not exclusively, in response to transforming growth factor-β (TGF-β). Myofibroblasts in turn enhance tumor progression by remodeling the stroma. Among proteases implicated in stroma remodeling, matrix metalloproteinases (MMPs), including MMP-9, play a prominent role. Recent evidence indicates that MMP-9 recruitment to the tumor cell surface enhances tumor growth and invasion. In the present work, we addressed the potential relevance of MMP-9 recruitment to and activity at the surface of fibroblasts. We show that recruitment of MMP-9 to the fibroblast cell surface occurs through its fibronectin-like (FN) domain and that the molecule responsible for the recruitment is lysyl hydroxylase 3 (LH3). Functional assays suggest that both pro- and active MMP-9 trigger α-smooth muscle actin expression in cultured fibroblasts, reflecting myofibroblast differentiation, possibly as a result of TGF-β activation. Moreover, the recombinant FN domain inhibited both MMP-9-induced TGF-β activation and α-smooth muscle actin expression by displacing MMP-9 from the fibroblast cell surface. Together our results uncover LH3 as a new docking receptor of MMP-9 on the fibroblast cell surface and demonstrate that the MMP-9 FN domain is essential for the interaction. They also show that the recombinant FN domain inhibits MMP-9-induced TGF-β activation and fibroblast differentiation, providing a potentially attractive therapeutic reagent toward attenuating tumor progression where MMP-9 activity is strongly implicated.

The effects of milk as a food matrix for polyphenols on the excretion profile of cocoa (-)-Epicatechin metabolites in healthy humans subjects

The effect of different food matrices on the metabolism and excretion of polyphenols is uncertain. The objective of the study was to evaluate the possible effect of milk on the excretion of (2)-epicatechin metabolites from cocoa powder after its ingestion with and without milk. Twenty-one volunteers received the following three test meals each in a randomised cross-over design with a 1-week interval between meals: (1) 250 ml whole milk as a control; (2) 40 g cocoa powder dissolved in 250 ml whole milk (CC-M); (3) 40 g cocoa powder dissolved in 250 ml water (CC-W). Urine was collected before consumption and during the 0-6, 6-12 and 12-24 h periods after consumption. (2)-Epicatechin metabolite excretion was measured using liquid chromatography-MS. One (2)-epicatechin glucuronide and three (2)-epicatechin sulfates were detected in urine excreted after the intake of the two cocoa beverages (CC-M and CC-W). The results show that milk does not significantly affect the total amount of metabolites excreted in urine. However, differences in metabolite excretion profiles were observed; there were changes in the glucuronide and sulfate excretion rates, and the sulfation position between the period of excretion and the matrix. The matrix in which polyphenols are consumed can affect their metabolism and excretion, and this may affect their biological activity. Thus, more studies are needed to evaluate the effect of these different metabolite profiles on the body.

Welfare spending and ethnic heterogeneity. Evidence from a massive immigration wave

[spa] En este trabajo se analiza la relación entre la heterogeneidad étnica y la redistribución, utilizando la reciente y masiva llegada de inmigrantes a España. En concreto, se estudia el efecto de los cambios en la densidad de inmigrantes, observada entre 1998 y 2006, sobre los cambios en el gasto social municipal. La densidad de inmigrantes se instrumenta utilizando los patrones de establecimiento por país de origen para asignar los flujos predichos de inmigrantes a cada municipio. Los resultados evidencian que el gasto social incrementó menos en los municipios con mayores incrementos en la densidad de inmigrantes. También se proporciona evidencia de la existencia de una relación positiva entre la densidad de inmigrantes y el porcentaje de voto obtenidos por los partidos de derecha. Por tanto, estos resultados son consistentes con las teorías que predicen una relación negativa entre la heterogeneidad étnica y la redistribución.

Welfare spending and ethnic heterogeneity. Evidence from a massive immigration wave

[spa] En este trabajo se analiza la relación entre la heterogeneidad étnica y la redistribución, utilizando la reciente y masiva llegada de inmigrantes a España. En concreto, se estudia el efecto de los cambios en la densidad de inmigrantes, observada entre 1998 y 2006, sobre los cambios en el gasto social municipal. La densidad de inmigrantes se instrumenta utilizando los patrones de establecimiento por país de origen para asignar los flujos predichos de inmigrantes a cada municipio. Los resultados evidencian que el gasto social incrementó menos en los municipios con mayores incrementos en la densidad de inmigrantes. También se proporciona evidencia de la existencia de una relación positiva entre la densidad de inmigrantes y el porcentaje de voto obtenidos por los partidos de derecha. Por tanto, estos resultados son consistentes con las teorías que predicen una relación negativa entre la heterogeneidad étnica y la redistribución.

Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome.

Cerebral, ocular, dental, auricular, skeletal anomalies (CODAS) syndrome (MIM 600373) was first described and named by Shehib et al, in 1991 in a single patient. The anomalies referred to in the acronym are as follows: cerebral-developmental delay, ocular-cataracts, dental-aberrant cusp morphology and delayed eruption, auricular-malformations of the external ear, and skeletal-spondyloepiphyseal dysplasia. This distinctive constellation of anatomical findings should allow easy recognition but despite this only four apparently sporadic patients have been reported in the last 20 years indicating that the full phenotype is indeed very rare with perhaps milder or a typical presentations that are allelic but without sufficient phenotypic resemblance to permit clinical diagnosis. We performed exome sequencing in three patients (an isolated case and a brother and sister sib pair) with classical features of CODAS. Sanger sequencing was used to confirm results as well as for mutation discovery in a further four unrelated patients ascertained via their skeletal features. Compound heterozygous or homozygous mutations in LONP1 were found in all (8 separate mutations; 6 missense, 1 nonsense, 1 small in-frame deletion) thus establishing the genetic basis of CODAS and the pattern of inheritance (autosomal recessive). LONP1 encodes an enzyme of bacterial ancestry that participates in protein turnover within the mitochondrial matrix. The mutations cluster at the ATP-binding and proteolytic domains of the enzyme. Biallelic inheritance and clustering of mutations confirm dysfunction of LONP1 activity as the molecular basis of CODAS but the pathogenesis remains to be explored.

1D.03: Inactive matrix GLA protein is associated with renal resistive index in a population-based study

OBJECTIVE: Renal resistive index (RRI) varies directly with renal vascular stiffness and pulse pressure. RRI correlates positively with arteriolosclerosis in damaged kidneys and predicts progressive renal dysfunction. Matrix Gla-protein (MGP) is a vascular calcification inhibitor that needs vitamin K to be activated. Inactive MGP, known as desphospho-uncarboxylated MGP (dp-ucMGP), can be measured in plasma and has been associated with various cardiovascular (CV) markers, CV outcomes and mortality. In this study we hypothesize that increased RRI is associated with high levels of dp-ucMGP. DESIGN AND METHOD: We recruited participants via a multi-center family-based cross-sectional study in Switzerland exploring the role of genes and kidney hemodynamics in blood pressure regulation. Dp-ucMGP was quantified in plasma samples by sandwich ELISA. Renal doppler sonography was performed using a standardized protocol to measure RRIs on 3 segmental arteries in each kidney. The mean of the 6 measures was reported. Multiple regression analysis was performed to estimate associations between RRI and dp-ucMGP adjusting for sex, age, pulse pressure, mean pressure, renal function and other CV risk factors. RESULTS: We included 1035 participants in our analyses. Mean values were 0.64 ± 0.06 for RRI and 0.44 ± 0.21 (nmol/L) for dp-ucMGP. RRI was positively associated with dp-ucMGP both before and after adjustment for sex, age, body mass index, pulse pressure, mean pressure, heart rate, renal function, low and high density lipoprotein, smoking status, diabetes, blood pressure and cholesterol lowering drugs, and history of CV disease (P < 0.001). CONCLUSIONS: RRI is independently and positively associated with high levels of dp-ucMGP after adjustment for pulse pressure and common CV risk factors. Further studies are needed to determine if vitamin K supplementation can have a positive effect on renal vascular stiffness and kidney function.