The ENCODE (ENCyclopedia Of DNA Elements) Project.

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.

Selectively impaired development of intestinal T cell receptor gamma delta+ cells and liver CD4+ NK1+ T cell receptor alpha beta+ cells in T cell factor-1-deficient mice.

T cell factor-1 (Tcf-1) is a transcription factor that binds to a sequence motif present in several T cell-specific enhancer elements. In Tcf-1-deficient (Tcf-1-/-) mice, thymocyte development is partially blocked at the transition from the CD4-8+ immature single-positive stage to the CD4+8+ double-positive stage, resulting in a marked decrease of mature peripheral T cells in lymph node and spleen. We report here that the development of most intestinal TCR gamma delta+ cells and liver CD4+ NK1.1+TCR alpha beta+ (NK1+T) cells, which are believed to be of extrathymic origin, is selectively impaired in Tcf-1-/- mice. In contrast, thymic and thymus-derived (splenic) TCR gamma delta+ cells are present in normal numbers in Tcf-1-/- mice, as are other T cell subsets in intestine and liver. Collectively, our data suggest that Tcf-1 is differentially required for the development of some extrathymic T cell subsets, including intestinal TCR gamma delta+ cells and liver CD4+ NK1+T cells.

Chronic nitric oxide synthase inhibition and carotid artery distensibility in renal hypertensive rats.

The goal of the present study was to examine the viscoelastic properties of the carotid artery in genetically identical rats exposed to similar levels of blood pressure sustained by different mechanisms. Eight-week old male Wistar rats were examined 2 weeks after renal artery clipping (two-kidney, one clip [2K1C] Goldblatt rats, n = 53) or sham operation (n = 49). One half of the 2K1C and sham rats received the nitric oxide synthase inhibitor NG-nitro-L-arginine methyl ester (L-NAME, 1.48 mmol/L) in their drinking water for 2 weeks after the surgical procedure. Mean blood pressure increased significantly in the 2K1C-water (182 mm Hg), 2K1C-L-NAME (197 mm Hg), and sham-L-NAME (170 mm Hg) rats compared with the sham-water rats (127 mm Hg). Plasma renin activity was not altered by L-NAME but significantly enhanced after renal artery clipping. A significant and similar increase in the cross-sectional area of the carotid artery was observed in L-NAME and vehicle-treated 2K1C rats. L-NAME per se did not modify cross-sectional area in the sham rats. There was a significant upward shift of the distensibility-pressure curve in the L-NAME- and vehicle-treated 2K1C rats compared with the sham-L-NAME rats. L-NAME treatment did not alter the distensibility-pressure curve in the 2K1C rats. These results demonstrate that the mechanisms responsible for artery wall hypertrophy in renovascular hypertension are accompanied by an increase in arterial distensibility that is not dependent on the synthesis of nitric oxide.

Development of bacteria-based bioassays for arsenic detection in natural waters.

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.

Phase-sensitive black-blood coronary vessel wall imaging.

Black-blood MR coronary vessel wall imaging may become a powerful tool for the quantitative and noninvasive assessment of atherosclerosis and positive arterial remodeling. Although dual-inversion recovery is currently the gold standard, optimal lumen-to-vessel wall contrast is sometimes difficult to obtain, and the time window available for imaging is limited due to competing requirements between blood signal nulling time and period of minimal myocardial motion. Further, atherosclerosis is a spatially heterogeneous disease, and imaging at multiple anatomic levels of the coronary circulation is mandatory. However, this requirement of enhanced volumetric coverage comes at the expense of scanning time. Phase-sensitive inversion recovery has shown to be very valuable for enhancing tissue-tissue contrast and for making inversion recovery imaging less sensitive to tissue signal nulling time. This work enables multislice black-blood coronary vessel wall imaging in a single breath hold by extending phase-sensitive inversion recovery to phase-sensitive dual-inversion recovery, by combining it with spiral imaging and yet relaxing constraints related to blood signal nulling time and period of minimal myocardial motion.

The application of Fick's law to evaluate the period of stay of mega-olivines in alkaline lavas

The integration of the differential equation of the second law of Fick applied to the diffusion of chemical elements in a semi-infinite solid made it easier to estimate the time of stay of olivine mega-cristals in contact with the host lava The results of this research show the existence of two groups of olivine. The first remained in contact with the magmatic liquid during 19 to 22 days, while the second remained so during only 5 to 9 days. This distinction is correlative to that based on the qualitative observation.

Hypertension increases connexin43 in a tissue-specific manner.

BACKGROUND: Connexin43 (Cx43), a membrane protein involved in the control of cell-to-cell communication, is thought to play a role in the contractility of the vascular wall and in the electrical coupling of cardiac myocytes. The aim of this study was to investigate the effects of experimental hypertension on Cx43 expression in rat aorta and heart. METHODS AND RESULTS: Rats were made hypertensive after one renal artery was clipped (two kidney, one-clip renal model) or after the administration of deoxycorticosterone and salt (DOCA-salt model). After 4 weeks, all rats showed a similar increase in intra-arterial mean blood pressure and in the thickness of both the aortic wall and the heart. Northern blot analysis of aorta mRNA and immunolabeling for Cx43 showed that hypertensive rats expressed twice as much Cx43 in aorta as the control animals. In contrast, no difference in Cx43 mRNA or in the immunolabeled protein was observed in heart. CONCLUSIONS: The results show that rats exhibiting a similar degree of blood pressure elevation, as the result of different mechanisms, feature a comparable increase in Cx43 gene expression, which was observed in the aortic but not in the cardiac muscle. These data suggest that localized mechanical forces induced by hypertension are major tissue-specific regulators of Cx43 expression.

The effects of arterial flow on platelet activation, thrombus growth, and stabilization.

Injury of an arterial vessel wall acutely triggers a multifaceted process of thrombus formation, which is dictated by the high-shear flow conditions in the artery. In this overview, we describe how the classical concept of arterial thrombus formation and vascular occlusion, driven by platelet activation and fibrin formation, can be extended and fine-tuned. This has become possible because of recent insight into the mechanisms of: (i) platelet-vessel wall and platelet-platelet communication, (ii) autocrine platelet activation, and (iii) platelet-coagulation interactions, in relation to blood flow dynamics. We list over 40 studies with genetically modified mice showing a role of platelet and plasma proteins in the control of thrombus stability after vascular injury. These include multiple platelet adhesive receptors and other junctional molecules, components of the ADP receptor signalling cascade to integrin activation, proteins controlling platelet shape, and autocrine activation processes, as well as multiple plasma proteins binding to platelets and proteins of the intrinsic coagulation cascade. Regulatory roles herein of the endothelium and other blood cells are recapitulated as well. Patient studies support the contribution of platelet- and coagulation activation in the regulation of thrombus stability. Analysis of the factors determining flow-dependent thrombus stabilization and embolus formation in mice will help to understand the regulation of this process in human arterial disease.

High prevalence of peripheral atherosclerosis in a rapidly developing country.

Cardiovascular disease is rapidly increasing in developing countries experiencing epidemiological transition. We investigated the prevalence of peripheral atherosclerosis in a rapidly developing country and compared our findings with data previously reported in Western populations. A cardiovascular risk factor survey was conducted in 1067 individuals aged 25-64 randomly selected from the general population of Seychelles. High-resolution ultrasonography of the right and left carotid and femoral arteries was performed in a random subgroup of 503 subjects (245 men and 258 women). In each of the four arteries, arterial wall thickness (in plaque-free segments) and atherosclerotic plaques (i.e. focal wall thickening at least 1.0 mm thick) were measured separately. The prevalence of peripheral atherosclerosis was high in this population. For instance, at least one plaque > or =1.0 mm was found in, respectively, 34.9 and 27.5% of men and women aged 25-34 and at least one plaque > or =2.5 mm was found in, respectively, 58.2 and 36.9% of men and women aged 55-64. With reference to data found in the literature, the prevalence of carotid atherosclerosis appeared to be significantly higher in Seychelles than in Western populations. This study provides further evidence for the importance of cardiovascular disease in developing countries. Determinants should be identified and relevant prevention and control programs implemented.

Variscan lamprophyres in the Lower Penninic domain (Central Alps): age and tectonic significance

Lamprophyre dykes have been recently discovered in blocks of gneiss embedded in a calcschist formation of wildflysch type that forms the top of the Mesozoic-Tertiary metasedimentary cover of the Antigorio nappe (the Teggiolo zone) in the Val Bavona (Lower Penninic, NW Ticino, Switzerland). The presence of the lamprophyres gives a clue to the possible source of these blocks. Similar dykes occur in the N part of the Maggia nappe where they are intruded into the Matorello granite and the surrounding gneisses. We studied these lamprophyres at two localities in the Teggiolo zone (Tamierpass and Lago del Zott) and at one locality in the Maggia nappe (Laghetti). Detailed mineralogical and geochemical investigations confirm their great similarity, particularly between the Tamier and Laghetti dykes. They all recrystallized during Alpine metamorphism under amphibolite facies conditions and lost their primary mineral assemblages and textures. The chemistry reveals a calc-alkaline affinity, a limited differentiation range, features of mineral accumulation and intense remobilization in some cases. The lamprophyres are characterized by a high mg# and relatively low contents in REE and other incompatible elements. In situ SHRIMP and LA-ICPMS U-Pb zircon dating yielded ages of 284.8 +/- 1.7 Ma (Tamier), 290.0 +/- 1.3 Ma (Zott) and 290.5 +/- 3.7 Ma (Laghetti). These ages are compatible with the general late- to post-Variscan magmatic evolution of the Helvetic and Lower Penninic domains. The lamprophyres are considered as melts derived from the lithospheric Variscan mantle, variously hybridized and differentiated at the contact with crustal material during late- to post-orogenic extension. These lamprophyres are chemically distinct from earlier lamprophyres of Visean age, emplaced together with their associated granites in transcurrent fault zones during the Variscan orogenic compression. The similarity of these different dykes suggests that the front of the Maggia nappe is a likely source of the gneissic blocks embedded in the calcschists at the top of the Teggiolo zone. They would have been provided by the advancing Maggia nappe during its thrusting over the Antigorio nappe and simultaneous closure of the Teggiolo sedimentary basin.

Regional coronary endothelial function is closely related to local early coronary atherosclerosis in patients with mild coronary artery disease: pilot study.

BACKGROUND: Coronary endothelial function is abnormal in patients with established coronary artery disease and was recently shown by MRI to relate to the severity of luminal stenosis. Recent advances in MRI now allow the noninvasive assessment of both anatomic and functional (endothelial function) changes that previously required invasive studies. We tested the hypothesis that abnormal coronary endothelial function is related to measures of early atherosclerosis such as increased coronary wall thickness. METHODS AND RESULTS: Seventeen arteries in 14 healthy adults and 17 arteries in 14 patients with nonobstructive coronary artery disease were studied. To measure endothelial function, coronary MRI was performed before and during isometric handgrip exercise, an endothelial-dependent stressor, and changes in coronary cross-sectional area and flow were measured. Black blood imaging was performed to quantify coronary wall thickness and indices of arterial remodeling. The mean stress-induced change in cross-sectional area was significantly higher in healthy adults (13.5%±12.8%, mean±SD, n=17) than in those with mildly diseased arteries (-2.2%±6.8%, P<0.0001, n=17). Mean coronary wall thickness was lower in healthy subjects (0.9±0.2 mm) than in patients with coronary artery disease (1.4±0.3 mm, P<0.0001). In contrast to healthy subjects, stress-induced changes in cross-sectional area, a measure of coronary endothelial function, correlated inversely with coronary wall thickness in patients with coronary artery disease (r=-0.73, P=0.0008). CONCLUSIONS: There is an inverse relationship between coronary endothelial function and local coronary wall thickness in patients with coronary artery disease but not in healthy adults. These findings demonstrate that local endothelial-dependent functional changes are related to the extent of early anatomic atherosclerosis in mildly diseased arteries. This combined MRI approach enables the anatomic and functional investigation of early coronary disease.

The contribution of the young Cretaceous Caribbean Oceanic Plateau to the genesis of late Cretaceous arc magmatism in the Cordillera Occidental of Ecuador

The eastern part of the Cordillera Occidental of Ecuador comprises thick buoyant oceanic plateaus associated with island-arc tholeiites and subduction-related calc-alkaline series, accreted to the Ecuadorian Continental Margin from Late Cretaceous to Eocene times. One of these plateau sequences, the Guaranda Oceanic Plateau is considered as remnant of the Caribbean-Colombian Oceanic Province (CCOP) accreted to the Ecuadorian Margin in the Maastrichtien. Samples studied in this paper were taken from four cross-sections through two arc-sequences in the northern part of the Cordillera Occidental of Ecuador, dated as (Rio Cala) or ascribed to (Macuchi) the Late Cretaceous and one arc-like sequence in the Chogon-Colonche Cordillera (Las Orquideas). These three island-arcs can clearly be identified and rest conformably on the CCOP. In all four localities, basalts with abundant large clinopyroxene phenocrysts can be found, mimicking a picritic or ankaramitic facies. This mineralogical particularity, although not uncommon in island arc lavas, hints at a contribution of the CCOP in the genesis of these island arc rocks. The complete petrological and geochemical study of these rocks reveals that some have a primitive island-arc nature (MgO values range from 6 to 11 wt.%). Studied samples display marked Nb, Ta and Ti negative anomalies relative to the adjacent elements in the spidergrams characteristic of subductionrelated magmatism. These rocks are LREE-enriched and their clinopyroxenes show a tholeiitic affinity (FeO(1)-TiO(2) enrichment and CaO depletion from core to rim within a single crystal). The four sampled cross-sections through the island-arc sequences display homogeneous initial Nd, and Pb isotope ratios that suggest a unique mantellic source for these rocks resulting from the mixing of three components: an East-Pacific MORB end-member, an enriched pelagic sediment component, and a HIMU component carried by the CCOP. Indeed, the ankaramite and Mg-basalt sequences that form part of the Caribbean-Colombian Oceanic Plateau are radiogenically enriched in (206)Pb/(204)Pb and (207)Pb/(204)Pb and contain a HIMU component similar to that observed in the Gorgona basalts and Galapagos lavas. The subduction zone that generated the Late Cretaceous arcs occurred far from the continental margin, in an oceanic environment. This implies that no terrigenous detrital sediments interacted with the source at this period. Thus, the enriched component can only result from the melting of subducted pelagic sediments. We have thus defined the East-Pacific MORB, enriched (cherts, pelagic sediments) and HIMU components in an attempt to constrain and model the genesis of the studied island-arc magmatism, using a compilation of carefully selected isotopic data from literature according to rock age and paleogeographic location at the time of arc edification. Tripolar mixing models reveal that proportions of 12-15 wt.% of the HIMU component, 7-15 wt.% of the pelagic sediment end-member and 70-75 wt.% of an East-pacific MORB end-member are needed to explain the measured isotope ratios. These surprisingly high proportions of the HIMU/CCOP component could be explained by the young age of the oceanic plateau (5-15 Ma) during the Late Cretaceous arc emplacement. The CCOP, basement of these arc sequences, was probably still hot and easily assimilated at the island-arc lava source. (C) 2008 Elsevier Ltd. All rights reserved,

Characterization of insulators and barrier elements for gene therapy

Gene transfer that relies on integrating vectors often suffers from epigenetic or regulatory effects that influence the expression of the therapeutic gene and=or of cellular genes located near the vector integration site in the chromosome. Insulator elements act to block gene activation by enhancers, while chromatin domain boundary or barrier sequences prevent gene-silencing effects. At present, the modes of action of insulator and barriers are poorly understood, and their use in the context of gene therapies remains to be documented. Using combinations of reporter genes coding for indicator fluorescent proteins, we constructed assay systems that allow the quantification of the insulator or barrier activities of genetic elements in individual cells. This presentation will illustrate how these assay systems were used to identify short DNA elements that insulate nearby genes from activation by viral vector elements, and=or that block the propagation of a silent chromatin structure that leads to gene silencing. We will show that some barrier elements do not merely block repressive effects, but that they can act to stabilize and sustain transgene expression. We will illustrate that this may be beneficial when transgenes are introduced into stem or precursor cells using non-viral vectors, where later differentiation may lead to the silencing of the therapeutic gene. We will show that these elements can be used to maintain efficient transgene expression upon the differentiation of murine precursor cells towards myofibers, in a model of cell therapy for muscle dystrophies.

Hand development and sequence of ossification in the forelimb of the European shrew Crocidura russula (Soricidae) and comparisons across therian mammals.

Hand development in the European shrew Crocidura russula is described, based on the examination of a cleared and double-stained ontogenetic series and histological sections of a c. 20-day-old embryo and a neonate. In the embryo all carpal elements are still mesenchymal condensations, and there are three more elements than in the adult stage: the 'lunatum', which fuses with the scaphoid around birth; a centrale, which either fuses with another carpal element or just disappears later in ontogeny; and the anlage of an element that later fuses with the radius. Carpal arrangement in the neonate and the adult is the same. In order to compare the relative timing of the onset of ossification in forelimb bones in C. russula with that of other therians, we built up two matrices of events based on two sets of data and used the event-pair method. In the first analysis, ossification of forelimb elements in general was examined, including that of the humerus, radius, ulna, the first carpal and metacarpal to ossify, and the phalanges of the third digit. The second analysis included each carpal, humerus, radius, ulna, the first metacarpal and the first phalanx to ossify. Some characters (= event-pairs) provide synapomorphies for some clades examined. There have been some shifts in the timing of ossification apparently not caused by ecological and/or environmental influences. In two species (Oryctolagus and Myotis), there is a tendency to start the ossification of the carpals relatively earlier than in all other species examined, the sauropsid outgroups included.

Use of human MAR elements to improve retroviral vector production.

Retroviral vectors have many favorable properties for gene therapies, but their use remains limited by safety concerns and/or by relatively lower titers for some of the safer self-inactivating (SIN) derivatives. In this study, we evaluated whether increased production of SIN retroviral vectors can be achieved from the use of matrix attachment region (MAR) epigenetic regulators. Two MAR elements of human origin were found to increase and to stabilize the expression of the green fluorescent protein transgene in stably transfected HEK-293 packaging cells. Introduction of one of these MAR elements in retroviral vector-producing plasmids yielded higher expression of the viral vector RNA. Consistently, viral titers obtained from transient transfection of MAR-containing plasmids were increased up to sixfold as compared with the parental construct, when evaluated in different packaging cell systems and transfection conditions. Thus, use of MAR elements opens new perspectives for the efficient generation of gene therapy vectors.