Solid-phase synthesis and NMR studies of modified oligonucleotides forming triplex helix and of oligonucleopeptides mimicking the topoisomerase I-DNA covalent complex

Report for the scientific sojourn carried out at the Institut de Biologia Molecular de Barcelona of the CSIC –state agency – from april until september 2007. Topoisomerase I is an essential nuclear enzyme that modulates the topological status of DNA, facilitating DNA helix unwinding during replication and transcription. We have prepared the oligonucleotide-peptide conjugate Ac-NLeu-Asn-Tyr(p-3’TTCAGAAGC5’)-LeuC-CONH-(CH2)6-OH as model compound for NMR studies of the Topoisomerase I- DNA complex. Special attention was made on the synthetic aspects for the preparation of this challenging compound especially solid supports and protecting groups. The desired peptide was obtained although we did not achieve the amount of the conjugate needed for NMR studies. Most probably the low yield is due to the intrinsic sensitive to hydrolysis of the phosphate bond between oligonucleotide and tyrosine. We have started the synthesis and the structural characterization of oligonucleotides carrying intercalating compounds. At the present state we have obtained model duplex and quadruplex sequences modified with acridine and NMR studies are underway. In addition to this project we have successfully resolved the structure of a fusion peptide derived from hepatitis C virus envelope synthesized by the group of Dr. Haro and we have synthesized and started the characterization of a modified G-quadruplex.

Cerebrospinal fluid antimicroglial antibodies in Alzheimer disease: a putative marker of an ongoing inflammatory process.

Immunocompetent microglia play an important role in the pathogenesis of Alzheimer's disease (AD). Antimicroglial antibodies in the cerebrospinal fluid (CSF) in clinically diagnosed AD patients have been previously recorded. Here, we report the results of the analysis of the CSF from 38 autopsy cases: 7 with definite AD; 14 with mild and 10 with moderate Alzheimer's type pathology; and 7 controls. Antimicroglial antibodies were identified in 70% of patients with definite AD, in 80% of patients with moderate and in 28% of patients with mild Alzheimer's type pathology. CSF antimicroglial antibodies were not observed in any of the control cases. The results show that CSF antimicroglial antibodies are present in the majority of patients with definite AD and also in cases with moderate Alzheimer's type changes. They may also indicate dysregulation of microglial function. Together with previous observations, these findings indicate that compromised immune defense mechanisms play an important role in the pathogenesis of AD.

Segmental bioelectrical impedance analysis to assess perioperative fluid changes.

OBJECTIVES: Perioperative fluid accumulation determination is a challenge for the clinician. Bioelectrical impedance analysis (BIA) is a noninvasive method based on the electrical properties of tissues, which can assess body fluid compartments. The study aimed at assessing their changes in three types of surgery (thoracic, abdominal, and intracranial) requiring various regimens of fluid administration. DESIGN: Prospective descriptive trial. PATIENTS: A total of 26 patients scheduled for elective surgery were separated into three groups according to site of surgery: thoracic (n = 8), abdominal aortic (n = 8), and brain surgery (n = 10). SETTING: University teaching hospital. INTERVENTION: None. MEASUREMENTS: Whole body, segmental (arm, trunk, and legs) BIA at multiple frequency (0.5, 50, 100 kHz) was used to assess perioperative fluid accumulation after surgery. The fluid balances were calculated from the charts. RESULTS: The patients were aged 62+/-4 yrs. Fluid balances were 4.8+/-1.0 L, 4.1+/-0.5 L, and 1.9+/-0.3 L, respectively, in the three groups. In trunk surgery patients, fluid accumulation was detected as a drop in impedance in the operated area at all frequencies. In the operated area, there was an expansion of both intra- and extracellular compartments. A reduction in high frequencies' impedance in the legs was only detected after aortic surgery. Fluid accumulation and trunk impedance changes were strongly correlated. Neurosurgery only induced minor body fluid changes. CONCLUSIONS: Segmental BIA is able to detect and localize perioperative fluid accumulation. It may become a bedside tool to quantify and to localize fluid accumulation.

Fluorescence of the bladder washout fluid following cystoscopy: a preliminary study

During fluorescence cystoscopy, it is observed that the acquired images are sometimes blurred by a greenish background originating from the bladder washout fluid. Several fluorophores are involved in this overall liquid fluorescence, and their exact origin and relative contributions remain unknown. In this study, the bladder washout fluid is sampled at different times during fluorescence cystoscopy examinations. In total, 32 samples from 12 patients are analyzed with a spectrofluorimeter (excitation range: 350-445 nm, emission range 380-700 nm). This study shows clearly that the position of the fluorescence peaks (excitation/emission wavelengths: 450/525 nm, 405/625 nm) and shoulder (440/525 nm) is reproducible between different patients. It also suggests that an excitation at wavelengths higher than 400 nm helps to suppress this solution background fluorescence. Additionally, the pH of the solution seems to influence the position of the fluorescence peaks, and this suggests that changing the pH of the examination liquid could help in avoiding the greenish background.

Behavior study of pipes after forming, coating and bending

A study of the main types of coatings and its processes that modern industry commonly apply to prevent to the corrosion due to the environmental effects to energetic market pipelines have been done. Extracting main time and temperature range values, coating heat treatment recreation have been applied to x65 pipelines steel grade samples obtained from a pipe which was formed using UOE forming process. Experimental tensile tests and Charpy V‐Notch Impact test have been carried out for a deeply knowledge of the influence on the steel once this recreations are applied. The Yield Strength and toughness have been improved despite lower values in rupture strain and ductile‐brittle temperature transition have been obtained. Finite Element Method have been applied to simulate the entirely pipe cold bending process to predict the mechanical properties and behaviour of the pipe made from x65 steel grade under different conditions.

Estudi òptic dels minerals

El Grup Consolidat d’Innovació Docent de Mineralogia i òptica cristal·lina de la Universitat de Barcelona ha desenvolupat un CD interactiu que simula el funcionament d’un microscopi petrogràfic, per tal de facilitar a l’alumne un material d’autoaprenentatge, ha de servir per a reforçar els coneixements dels minerals formadors de roques en làmina prima. Aquest material te tres entrades diferents, en català, castellà i anglès. Cada mineral té una fitxa general amb les seves propietats òptiques i una complementaria amb les característiques cristal·logràfiques, camp d’estabilitat, diagrames de fases i característiques morfològiques del mineral a observar, les quals marquen els trets determinatius d’aquell mineral per tal de facilitar el seu reconeixement. Per tal de complementar les dades s’han introduït links directes amb la planes web: “webmineral” i “mindat” on hi ha les corresponents estructures i morfologies “interactives” de cadascun dels minerals que apareixen en el programa. En l’aplicació informàtica hi ha 169 filmacions corresponents a 43 dels principals minerals que formen les roques, una filmació correspon a la imatge només amb el polaritzador, i l'altre a la imatge amb el polaritzador més l'analitzador. Cadascuna d'aquestes imatges es presenta amb un gir de 360º; es pot aturar i després continuar girant, simulant el que veuríem al microscopi. D'aquesta manera es pot determinar el pleocroisme, la presència de macles, el color d'interferència i l'angle d'extinció.. S’ha intentat sempre que hi hagués diferents exemples d’un mateix mineral en diverses paragènesis. També s'incorpora una fitxa que l'usuari pot omplir amb les característiques texturals i òptiques del mineral agrupades segons les observacions que es fan, bé amb el polaritzador, amb el polaritzador i l'analitzador o bé amb les condicions específiques per veure la figura d'interferència i el signe òptic. Aquesta fitxa, un cop plena, es pot imprimir. En tot moment hi ha un menú d’ajuda on l’usuari pot remetre i fer la consulta adient per poder continuar.

A stable and 40Ar/39Ar isotope study of a major thrust in the Helvetic nappes (Swiss Alps) - Evidence for fluid-flow and constraints on nappe kinematics

Stable isotope and Ar-40/Ar-39 measurements,were made on samples associated with a major tectonic discontinuity in the Helvetic Alps, the basal thrust of the Diablerets nappe (external zone of the Alpine Belt) in order to determine both the importance of fluids in this thrust zone and the timing of thrusting. A systematic decrease in the delta(18)O values (up to 6 parts per thousand) of calcite, quartz, and white mica exists within a 10- to 70-m-wide zone over a distance of 37 km along the thrust, and they become more pronounced toward the root of the nappe. A similar decrease in the delta(13)C values of calcite is observed only in the deepest sections (up to 3 parts per thousand). The delta D-SMOW (SMOW = standard mean ocean water) values of white mica are -54 parts per thousand +/- 8 parts per thousand (n = 22) and are independent of the distance from the thrust. These variations are interpreted to reflect syntectonic solution reprecipitation during fluid passage along the thrust. The calculated delta(18)O and delta D values (versus SMOW) for the fluid in equilibrium with the analyzed minerals is 12 parts per thousand to 16 parts per thousand and -30 parts per thousand to +5 parts per thousand, respectively, for assumed temperatures of 250 to 450 degrees C. The isotopic and structural data are consistent with fluids derived from the deep-seated roots of the Helvetic nappes where large volumes of Mesozoic sediments were metamorphosed to the amphibolite facies, It is suggested that connate and metamorphic waters, overpressured by rapid tectonic burial in a subductive system escaped by upward infiltration along moderately dipping pathways until they reached the main shear zone at the base of the moving pile, where they were channeled toward the surface, This model also explains the mechanism by which large amounts of fluid were removed from the Mesozoic sediments during Alpine metamorphism. White mica Ar-49/Ar-39 ages vary from 27 Ma far from the Diablerets thrust to 15 Ma along the thrust. An older component is observed in micas far from the thrust, interpreted as a detrital signature, and indicates that regional metamorphic temperatures were less than about 350 degrees C. The;plateau and near plateau ages nearest the thrust are consistent with either neocrystallization of white mica or argon loss by recrystallization during thrusting, which may have been enhanced in the zones of highest fluid flow. The 15 Ma Ar-40/Ar-39 age plateau measured on white mica sampled exactly on the thrust surface dates the end of both fluid flow and tectonic transport.

Producing on-line ultrapure dialysis fluid.

The process of on-line generation of ultrapure dialysis fluid is a core prerequisite for the safe execution of modern renal replacement therapies such as on-line hemodiafiltration and high-flux hemodialysis. In these extracorporeal treatments with variable degrees of convection, significant volumes of plasma water are removed and replaced with dialysis fluid, which must occur without causing harm to the patient. Historically, on-line generation of sterile and pyrogen-free physiological substitution fluid by the process of membrane ultrafiltration of fresh dialysis fluid has its origin in hemofiltration, a purely convective therapy. Development of this and later therapies is described in the historical context of a successful effort over decades to overcome the above formidable challenge, which was provided jointly by pioneering clinical investigators and a resourceful dialysis industry.

Mycoplasma hominis in mid-trimester amniotic fluid : relation to pregnangy outcome

RESUME Introduction : Les naissances prématurées compliquent 6-10 % des grossesses dans les pays industrialisés et contribuent de façon notable aux taux de mortalité périnatale et de morbidité néonatale. Il a été démontré que la colonisation bactérienne du liquide amniotique joue un rôle dans l'étiologie des accouchements prématurés spontanés et des ruptures prématurées des membranes. Le but de ce travail était d'évaluer la présence de Mycoplasma hominis dans le liquide amniotique prélevé au 2eme trimestre de grossesse chez des patientes asymptomatiques et de déterminer son association avec une issue défavorable de la grossesse. Matériels et méthodes : Les échantillons de liquide amniotique de 456 patientes ayant subi une amniocentèse trans-abdominale entre les 15eme et I7eme semaines de grossesse pour diverses indications ont été testés par PCR (Polymerase Chain Reaction) afin d'identifier Mycoplasma hominis. Les produits ainsi amplifiés étaient ensuite détectés par ELISA (Enzyme-Linked Immunosorbent Assay). Les données cliniques étaient obtenues après l'accouchement. Résultats : Mycoplasma hominis a été identifié dans 29 (6,4%) des échantillons de liquide amniotique. Le taux de menace d'accouchement prématuré chez les patientes positives pour Mycoplasma hominis (14,3%) était plus élevé que chez les patientes négatives (3,3 %) (p=0,01). De même, les naissances prématurées spontanées avec membranes intactes étaient plus fréquentes chez les patientes positives (10,7%) que chez les patientes négatives (1,9 %) (p=0,02). Le taux de menace d'accouchement prématuré lors d'une grossesse antérieure était plus de trois fois plus élevé chez les patientes positives, cependant ce résultat n'était pas statistiquement significatif. Finalement, la présence du mycoplasme n'était pas corrélée à la gestose, au retard de croissance intra-utérin ou aux anomalies chromosomiques foetales. Conclusions : Les résultats montrent que la présence de Mycoplasma hominis dans le liquide amniotique prélevé entre les 15eme et I7eme semaines d' aménorrhée chez des patientes asymptomatiques est associée à un taux plus élevé de menace d'accouchement prématuré et de naissances prématurées spontanées. La détection de ce microorganisme au 2eme trimestre de la grossesse peut donc identifier les patientes à risque de menace d'accouchement et de naissance prématurées. Abstract Objective: The relationship between detection of Mycoplasma hominis in mid-trimester amniotic fluid and subsequent pregnancy outcome was investigated. Study design: Amniotic fluids from 456 women of European background who underwent a transabdominal amniocentesis at weeks 15-17 of pregnancy were tested for M. hominis by polymerase chain reaction (PCR). The amplicons were hybridized to an internal probe and detected by ELISA. Pregnancy outcomes and clinical data were subsequently obtained. Results: M. hominis were identified in 29 (6.4%) of the amniotic fluids. The rate of preterm labor in women positive for M. hominis (14.3%) was higher than in the negative women (3.3%) (p = 0.01). Similarly, a spontaneous preterm birth with intact membranes occurred in 10.7% of the M. hominis-posltive women as opposed to only 1.9% of the negative women (p = 0.02). The presence of this mycoplasma was not correlated with fetal chromosomal aberrations, intrauterine growth restriction or preeclampsia. Conclusions: Detection of M. hominis in second-trimester amniotic fluids can identify women at increased risk for subsequent preterm labor and delivery.

Hydrocarbon biomarkers in the Topla-Mezica zinc-lead deposits, northern Karavanke/Drau Range, Slovenia: Paleoenvironment at the site of ore formation

The Mississippi Valley-type zinc and lead deposits at Topla (250,150 metric tons (t) of ore grading 1.0 wt % Zn and 3.3 wt % Pb) and Mezica (19 million metric tons (Mt) of ore grading 5.3 wt % Pb and 2.7 wt % Zn) occur within the Middle to Upper Triassic platform carbonate rocks of the northern Karavanke/Drau Range geotectonic units of the Eastern Alps, Slovenia. The ore and host rocks of these deposits have been investigated by a combination of inorganic and organic geochemical methods to determine major, trace, and rare earth element (REE) concentrations, hydrocarbon distribution, and stable isotope ratios of carbonates, kerogen, extractable organic matter, and individual hydrocarbons. These data combined with sedimentological evidence provide insight into the paleoenvironmental conditions at the site of ore formation. The carbonate isotope composition, the REE patterns, and the distribution of hydrocarbon biomarkers (normal alkanes and steranes) suggest a marine depositional environment. At Topla, a relatively high concentration of redox sensitive trace elements (V, Mo, U) in the host dolostones and REE patterns parallel to that of the North American shale composite suggest that sediments were deposited in a reducing environment. Anoxic conditions enhanced the preservation of organic matter and resulted in relatively higher total organic carbon contents (up to 0.4 wt %). The isotopic composition of the kerogen (delta C-13(kerogon) = -29.4 to -25.0 parts per thousand, delta N-15(kerogen) = -.13.6 to 6.8 parts per thousand) suggests that marine algae and/or bacteria were the main source of organic carbon with a very minor contribution from detrital continental plants and a varying degree of alteration. Extractable organic matter from Topla ore is generally depleted in C-13 compared to the associated kerogen, which is consistent with an indigenous source of the bitumens. The mineralization correlates with delta N-15(kerogen) values around 0 per mil, C-13 depleted kerogen, C-13 enriched n-heptadecane, and relatively high concentrations of bacteria] hydrocarbon biomarkers, indicating a high cyanobacterial biomass at the site of ore formation. Abundant dissimilatory sulfate-reducing bacteria, feeding on the cyanobacterial remains, led to accumulation of biogenic H2S in the pore water of the sediments. This biogenic H2S was mainly incorporated into sedimentary organic matter and diagenetic pyrite. Higher bacterial activity at the ore site also is indicated by specific concentration ratios of hydrocarbons, which are roughly correlated with total Pb plus Zn contents. This correlation is consistent with mixing of hydrothermal metal-rich, fluids and local bacteriogenic sulfide sulfur. The new geochemical data provide supporting evidence that Topla is a low-temperature Mississippi Valley-type deposit formed in an anoxic supratidal saline to hypersaline environment. A laminated cyanobacterial mat, with abundant sulfate-reducing bacteria was the main site of sulfate reduction.

Rapid detection of enterovirus in cerebrospinal fluid by a fully-automated PCR assay is associated with improved management of aseptic meningitis in adult patients.

BACKGROUND: Enterovirus (EV) is the most frequent cause of aseptic meningitis (AM). Lack of microbiological documentation results in unnecessary antimicrobial therapy and hospitalization. OBJECTIVES: To assess the impact of rapid EV detection in cerebrospinal fluid (CSF) by a fully-automated PCR (GeneXpert EV assay, GXEA) on the management of AM. STUDY DESIGN: Observational study in adult patients with AM. Three groups were analyzed according to EV documentation in CSF: group A=no PCR or negative PCR (n=17), group B=positive real-time PCR (n=20), and group C=positive GXEA (n=22). Clinical, laboratory and health-care costs data were compared. RESULTS: Clinical characteristics were similar in the 3 groups. Median turn-around time of EV PCR decreased from 60h (IQR (interquartile range) 44-87) in group B to 5h (IQR 4-11) in group C (p<0.0001). Median duration of antibiotics was 1 (IQR 0-6), 1 (0-1.9), and 0.5 days (single dose) in groups A, B, and C, respectively (p<0.001). Median length of hospitalization was 4 days (2.5-7.5), 2 (1-3.7), and 0.5 (0.3-0.7), respectively (p<0.001). Median hospitalization costs were $5458 (2676-6274) in group A, $2796 (2062-5726) in group B, and $921 (765-1230) in group C (p<0.0001). CONCLUSIONS: Rapid EV detection in CSF by a fully-automated PCR improves management of AM by significantly reducing antibiotic use, hospitalization length and costs.

Morphometric Analysis of McCoy Cells Inoculated with Cerebrospinal Fluid from Patients with Rabies

To demonstrate the potential of McCoy cells for the isolation of rabies virus from the cerebrospinal (CSF) fluid of a patient with a diagnosis of rabies, McCoy cells were inoculated with CSF from a patient with a clinical diagnosis of rabies and investigated in terms of morphometric aspect using the JAVA analysis system for the quantification of the increased size of infected cells compared to noninfected cells. The cells were also examined in terms of specific staining for the diagnosis of rabies by the method of Sellers for the observation of intracytoplasmic inclusions and by specific immunofluorescence staining for rabies virus. Infected cells showed changes in cell permeability and morphologic modifications which differed significantly compared to normal cells (P<0.001) when analyzed by the Mann-Whitney and Kruskal-Wallis tests. Intense activity of the endoplasmic reticulum was also observed, as indicated by the presence of intracytoplasmic inclusions visualized by specific staining. The present study demonstrated the isolation of rabies virus from the CSF of a patient with rabies, showing that McCoy cells can be used for the laboratory diagnosis of patients suspected to have rabies.

An approximate solution method for boundary layer flow of a power law fluid over a flat plate

The work in this paper deals with the development of momentum and thermal boundary layers when a power law fluid flows over a flat plate. At the plate we impose either constant temperature, constant flux or a Newton cooling condition. The problem is analysed using similarity solutions, integral momentum and energy equations and an approximation technique which is a form of the Heat Balance Integral Method. The fluid properties are assumed to be independent of temperature, hence the momentum equation uncouples from the thermal problem. We first derive the similarity equations for the velocity and present exact solutions for the case where the power law index n = 2. The similarity solutions are used to validate the new approximation method. This new technique is then applied to the thermal boundary layer, where a similarity solution can only be obtained for the case n = 1.