Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy.

Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.

Histopathologic characteristics of gastric adenocarcinoma in Mexican patients: a 10-year experience at the Hospital Juárez of Mexico.

BACKGROUND: Gastric cancer is the second cause of death by cancer worldwide. Histologic classification may predict tumor biology, clinical behavior, and outcome. According to the Lauren classification, the disease is divided into 2 types, diffuse and intestinal, and the latter has a better prognosis. AIM: To determine the frequency of gastric adenocarcinoma and compare the histopathologic characteristics of intestinal and diffuse-type gastric adenocarcinoma in Mexican patients treated at a tertiary referral hospital. METHODOLOGY: A retrospective study evaluated the pathology reports of patients with gastric adenocarcinoma corresponding to the time frame of January 2003 to December 2012. Adenocarcinomas of the gastric cardia were excluded. Frequencies were expressed as percentages and the categorical variables were compared with the chi-square test. Statistical significance was set at a P<.05. RESULTS: A total of 417 cases of gastric adenocarcinoma were found, 230 (55.2%) of which were diffuse-type and 118 (28.2%) were intestinal-type. The mean age of the patients with diffuse type gastric cancer was 54.02±14.93 and 119 (51.3%) of those patients were men. The mean age of the patients with intestinal-type gastric cancer was 63.43±13.78, and 69 (62.2%) were men. Ninety-two of the diffuse-type patients were under the age of 50 years, compared with 22 of the patients with intestinal-type carcinoma. CONCLUSIONS: This is the first study on the Mexican population to analyze the differences in the histologic types of adenocarcinoma. Diffuse-type gastric carcinoma was the most frequent subtype in our study population and it is associated with worse outcome.

Indoor radon risk mapping of the Canary Islands using a methodology for volcanic islands combining geological information and terrestrial gamma radiation data.

Within the framework of the recent approval of the National Plan Against Radon by the Council of Ministers of the Spanish Government, one of its five axes focuses on the delimitation of priority action areas. In line with this objective, this paper presents the indoor radon risk maps of the Canary Islands. Due to the volcanic origin of the Canary Islands, there is a great deal of geological heterogeneity in the soils on which buildings settle, making it very difficult to delimit radon-risk areas in the process of creating maps. Following a methodology developed in previous works for a study area formed of a set of representative municipalities, this paper presents radon risk maps of the Canary Islands based on lithostratigraphic information and high-resolution terrestrial gamma radiation maps. The goodness of fit of these maps is verified based on a statistical analysis of indoor radon concentration measurements carried out at representative building enclosures. In order to analyse the level of risk to the population, these maps were combined with built up areas (urban fabric) maps and estimations of the annual effective doses due to radon was obtained by applying a dosimetric model. This methodology improves the capability to delimit indoor radon risk areas, with a greater margin of safety. In this respect, it is estimated that areas classified as low risk have indoor radon concentrations 41 % below the current reference level of 300 Bq/m3 established by national regulations in compliance with the precepts laid down in the European EURATOM Directive.

Multiparametric analysis for the determination of radon potential areas in buildings on different soils of volcanic origin.

The transposition of the European EURATOM directive into the regulations of the different member states of the European Union involved governments making great efforts to define priority action maps against indoor radon exposure in buildings over a short time period. In Spain, the Technical Building Code established 300 Bq/m3 as a reference level and set up a classification of municipalities in which remediation measures should be adopted for radon exposure in buildings. Oceanic volcanic islands, such as the Canary Islands, present high geological heterogeneity in a small space due to their volcanic origin. This variability poses a challenge to the elaboration of radiological risk maps, which makes it necessary to have a high density of data to collect local variations. This paper presents a methodology to obtain accurate radon risk maps based on geological criteria and terrestrial gamma radiation. The predictive efficiency of these maps is statistically verified using indoor radon concentration data measured in buildings. Other radiological variables, which are commonly used as criteria for radon risk prediction found in the literature, were also applied, such as the geogenic radon potential and the activity concentration of natural radioisotopes in soils. The higher resolution of the maps obtained allows for a more detailed classification of radon risk zones in the study area than the current risk maps published in the Spanish building regulations.

Methodology for determination of radon prone areas combining the definition of a representative building enclosure and measurements of terrestrial gamma radiation.

The recommendations of the European Atomic Energy Community (EURATOM) have recently been incorporated into Spanish regulations in the Basic Document of Health Standards of the Technical Building Code (CTE), section HS6, on protection against radon exposure. This further accentuates the need to delimit radon prone areas as a strategy to address measures which minimise the effects of this gas on the population. In this research, measurements of terrestrial gamma radiation and indoor radon of dwellings have been carried out in the same location to delimit these risk areas. A new methodology has been developed including a definition of a Representative Building Enclosure (RBE) and it is proposed a Building Storey Index (IBS) which allows normalizing measurements of indoor radon activity concentration taken in different levels from the ground to the RBE. The results show the need to consider the type of contact that exists between the building and the ground as a determining factor of radon risk. Terrestrial gamma radiation is used as a proxy for radioisotopic composition of soils to characterise the indoor radon risk at different geological formation.

A DNA biosensor based on peptide nucleic acids on gold surfaces.

We present a DNA biosensor based on self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) molecules adsorbed on gold surfaces. Previous works have shown that PNA molecules at an optimal concentration can be self-assembled with their molecular axes normal to the surface. In such structural configuration BioSAMs of PNAs maintain their capability for recognizing complementary DNA. We describe the combined use of PM-RAIRS and synchrotron radiation XPS for the detection and spectroscopic characterization of PNA-DNA hybridization process on gold surfaces. RAIRS and XPS are powerful techniques for surface characterization and molecular detection, which do not require a fluorescence labeling of the target. We present a characterization of the spectroscopic IR and XPS features, some of them associated to the phosphate groups of the DNA backbone, as an unambiguous signature of the PNA-DNA heteroduplex formation. The N(1s) XPS core level peak after DNA hybridization is decomposed in curves components, and every component assigned to different chemical species. Therefore, the results obtained by means of two complementary structural characterization techniques encourage the use of PNA-based biosensors for the detection of DNA molecules on natural samples.

Conformational changes induced in the Saccharomyces cerevisiae GTPase-associated rRNA by ribosomal stalk components and a translocation inhibitor.

The yeast ribosomal GTPase associated center is made of parts of the 26S rRNA domains II and VI, and a number of proteins including P0, P1alpha, P1beta, P2alpha, P2beta and L12. Mapping of the rRNA neighborhood of the proteins was performed by footprinting in ribosomes from yeast strains lacking different GTPase components. The absence of protein P0 dramatically increases the sensitivity of the defective ribosome to degradation hampering the RNA footprinting. In ribosomes lacking the P1/P2 complex, protection of a number of nucleotides is detected around positions 840, 880, 1100, 1220-1280 and 1350 in domain II as well as in several positions in the domain VI alpha-sarcin region. The protection pattern resembles the one reported for the interaction of elongation factors in bacterial systems. The results exclude a direct interaction of these proteins with the rRNA and are compatible with an increase in the ribosome affinity for EF-2 in the absence of the acidic P proteins. Interestingly, a sordarin derivative inhibitor of EF-2 causes an opposite effect, increasing the reactivity in positions protected by the absence of P1/P2. Similarly, a deficiency in protein L12 exposes nucleotides G1235, G1242, A1262, A1269, A1270 and A1272 to chemical modification, thus situating the protein binding site in the most conserved part of the 26S rRNA, equivalent to the bacterial protein L11 binding site.

Kinetic analysis of phospholipase C from catharanthus roseus transformed roots using different assays

The properties of phospholipase C (PLC) partially purified from Catharanthus roseus transformed roots were analyzed using substrate lipids dispersed in phospholipid vesicles, phospholipid-detergent mixed micelles, and phospholipid monolayers spread at an air-water interface. Using [(33)P]phosphatidylinositol 4,5-bisphosphate (PIP(2)) of high specific radioactivity, PLC activity was monitored directly by measuring the loss of radioactivity from monolayers as a result of the release of inositol phosphate and its subsequent dissolution on quenching in the subphase. PLC activity was markedly affected by the surface pressure of the monolayer, with reduced activity at extremes of initial pressure. The optimum surface pressure for PIP(2) hydrolysis was 20 mN/m. Depletion of PLC from solution by incubation with sucrose-loaded PIP(2) vesicles followed by ultracentrifugation demonstrated stable attachment of PLC to the vesicles. A mixed micellar system was established to assay PLC activity using deoxycholate. Kinetic analyses were performed to determine whether PLC activity was dependent on both bulk PIP(2) and PIP(2) surface concentrations in the micelles. The interfacial Michaelis constant was calculated to be 0.0518 mol fraction, and the equilibrium dissociation constant of PLC for the lipid was 45.5 &mgr;M. These findings will add to our understanding of the mechanisms of regulation of plant PLC.

Prevalence of genotypic resistance to nucleoside analogues and protease inhibitors in Spain. The ERASE-2 Study Group.

OBJECTIVE: To examine the prevalence of resistance mutations to nucleoside reverse transcriptase inhibitors (NRTI) and protease inhibitors (PI) in a representative HIV-1 population in Spain. METHODS: A cross-sectional study was conducted including 601 HIV-infected patients who attended 20 Spanish hospitals in June 1998. Drug resistant mutations were examined using hybridization line probe assays (LiPA). The 6 bp insert at position 69 and the codon 75 mutant were examined by sequencing analysis in specimens lacking reactivity to 69/70 and 74 bands on LiPA, respectively. RESULTS: Primary resistance to NRTI was recognized in nine out of 52 (17%) naive individuals, whereas primary resistance to PI was found in seven out of 126 (6%) PI-naïve patients. The codons most frequently involved in NRTI resistance were at positions 70 (66%), 184 (44%), 215 (33%), and 41 (11%), whereas the most common PI resistance mutation was at codon 82 (6/7 subjects). In pre-treated patients, the overall prevalence of resistant genotypes was 72.9% for NRTI and 27.2% for PI. The most frequent NRTI mutations occurred at codons 184 (38.5%), 215 (30.1%), and 41 (22.5%), whereas the most frequent PI mutations in pre-treated subjects were found at positions 82 (15.8%) and 84 (11.4%). Overall, patients who began triple combinations as initial therapy showed a lower number of key resistance mutations than those who began highly active antiretroviral therapy (HAART) after being exposed to NRTI for a period of time (mean number of mutations, 0.1 versus 1.8, P< 0.05). Codon 75 mutant was found in three out of 387 patients (0.7%), whereas no insertions at codon 69 were recognized. CONCLUSION: The prevalence of primary genotypic resistance to NRTI and PI in Spain was 17% and 6%, respectively. Zidovudine, lamivudine, indinavir and ritonavir were the drugs most frequently affected. These data support the use of resistance testing prior to the introduction of first-line antiretroviral therapies in Spain. Among pre-treated subjects, drug resistance genotypes were less prevalent in those who began HAART as initial therapy.

Different outcome in the first two patients with an HIV-1 multinucleoside drug-resistant T69SSS insertion in Spain.

A novel multidrug-resistance mechanism has been described in human immunodeficiency virus type 1 (HIV-1), which involves the insertion of 6 bp between codons 69 and 70 in the reverse transcriptase (RT) gene. Herein, we report the first two patients in Spain carrying viral populations with the 69-SS insert coupled to the T69S mutation. Both patients were selected because of the lack of signal at positions 69/70 in the LiPA RT test despite being reactive to the remaining probes on the LiPA strip. The presence of the T69SSS complex was confirmed by sequence analysis. A common feature for both subjects was their past history with zidovudine monotherapy and zidovudine plus either didanosine or zalcitabine later on in the presence of persistent virus replication. Remarkably, the introduction of triple therapy in patient 1 soon after the emergence of the insert-containing viral strain produced its total displacement, which correlated with a sustained suppression in viral load.

Dynamics of dominance of a dipeptide insertion in reverse transcriptase of HIV-1 from patients subjected to prolonged therapy.

A small proportion (0.8%) of individuals of a cohort of HIV-1 infected patients subjected to prolonged therapy with nucleoside analogues included a recently recognised dipeptide insertion in their RT (Ser-Ser or Ser-Gly between RT codons 69 and 70). To study the dynamics of dominance of genomes with this genetic change, sequential HIV-1 isolates from two patients were analyzed with regard to consensus sequences and complexity of mutant spectra. The two patients displayed completely different, complex evolutionary patterns leading to temporary dominance of dipeptide insertions. In one patient, a virus very closely related to an ancestor virus from the same patient overtook the population at late times, displacing genomes encoding a Ser-Ser insertion. In another patient the sequential dominance of genomes with Ser-Ser insertion-->no insertion-->Ser-Gly insertion was observed. These three types of genomes coexisted in the mutant spectrum of one HIV-1 isolate. Complexity was also reflected in the shape of phylogenetic trees derived with genomes from the mutant spectrum at each time point. The results suggest that HIV-1 genomes encoding a dipeptide insertion between RT codons 69 and 70 do not show a clear selective advantage over other genomes lacking the insertion. Such an absence of a clear selective advantage will favor that such genomes encoding this RT insertion become dominant only in a transient fashion, and following disparate kinetics in different patients.

Effects of p-chloro-phenylalanine on the behaviors induced by apomorphine and amphetamine in adult cats.

1. The effects of serotonin depletion on the behaviors evoked by apomorphine or amphetamine are analyzed. Amphetamine (5 mg/kg, s.c.) or apomorphine (2 mg/kg, s.c.) were administered to fourteen adult mongrel cats. Inhibition of tryptophan hydroxylase was achieved by intraperitoneal injection of p-chlorophenylalanine (100 mg/kg daily for three consecutive days). Serotonin depleted animals were tested with either apomorphine or amphetamine (same doses as above). 2. Behaviors evoked by both drugs were recorded and quantified. The following behaviors were rated: motility (locomotion), alertness, fear, indifference, olfaction and lateral head movements. 3. Biochemical analysis of the raphe dorsalis and caudate nuclei of p-CPA treated animals showed an average drop in serotonin concentration of 77%. Serotonin depletion induced statistically significant changes in the following behaviors in amphetamine-treated cats: locomotion, fear, lateral head movements and alertness. Serotonin depleted cats tested with apomorphine showed significant changes only in olfaction and indifference behaviors. 4. Serotonin appears to play a significant modulatory role in some of the behaviors evoked by amphetamine, specially locomotion. Such role is less evident for the behaviors evoked by apomorphine.

Effects of disulfiram, phenoxybenzamine and propranolol on the behaviors evoked by apomorphine and amphetamine in adult cats.

The aim of this work was to study the role that the noradrenergic system could play in the mechanism of production of the behaviors evoked by parenteral injection of apomorphine and amphetamine in adult cats. Ten cats were injected s.c. with 2 mg/kg of apomorphine and 2.5 mg/kg of amphetamine in separate sessions. The behaviors were recorded, until control conditions were again attained. In a second stage, disulfiram was administered ip., followed by apomorphine and amphetamine in the same doses as cited above. The effects on behaviors produced by disulfiram and those of apomorphine and amphetamine were recorded by three independent observers. Comparisons of the pre- and post-disulfiram behavioral results were analyzed with the help of the non-parametric Wilcoxon signed rank test. In another group of ten cats a similar procedure was carried on employing the alpha and beta noradrenergic blocking agents, phenoxybenzamine and propranolol. The noradrenergic blocking drugs, especially disulfiram and phenoxybenzamine produced by themselves a decrease in motility, in alertness and an increase in indifference and inappetence. Apomorphine and amphetamine administered after the blocking drugs showed slight behavioural modifications, reflection most of them the changes produced by the three blocking drugs. It is concluded that probably the nor-adrenergic system could be involved in the hypomotility elicited by amphetamine. NA is not involved in the induction of the other behaviors evoked by apomorphine and amphetamine.

Effect of different inhibitors on phospholipase C activity in Catharanthus roseus transformed roots.

We have previously reported that Catharanthus roseus transformed roots contain at least two phosphatidylinositol 4,5-bisphosphate-phospholipase C (PLC) activities, one soluble and one membrane associated. In this paper, the effect of neomycin and several divalent cations was analyzed, both in the soluble and the membrane-associated PLC activity in C. roseus transformed roots. In this system, neomycin, an aminoglycoside antibiotic, inhibited PLC in a concentration-dependent fashion. The neomycin IC50 (100 microM) was the same for the inhibition of the soluble and the membrane associated PLC activity. The effect of different divalent cations such as Ni2+, Cu2+, and Zn2+ was studied as well. In order to see the effect of these cations on PLC activity, we selected two conditions: a) in the presence of and b) in the absence of calcium. In the presence of calcium, these three divalent cations were able to inhibit PLC activity in both fractions in a concentration-dependent manner; however, the IC50s were different for the membrane and the soluble activities. For the soluble activity, the inhibition due to the three cations was very similar (IC50s between 0.2 and 0.3 mM). For the membrane associated PLC activity, Cu2+ was the most potent inhibitor (IC50 3.6 microM), then Ni2+ and then Zn2+. In the absence of calcium, higher concentrations of Cu2+ and Zn2+ demonstrated some inhibitory effect. We discuss the possible physiological role of these inhibitors on PLC activity.

Nucleotide sequence of the 235 rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA.

23S rRNA gene from the halophilic archaeon Haloferax mediterranei (strain ATCC 33500) was cloned and sequenced. Proceeding from the 2,912 nucleotides long sequence, the secondary structure of Haloferax genus large subunit rRNA was proposed. Haloferax mediterranei intergenic spacers 16S/23S and 23S/5S were also sequenced, and found to be 382 and 116 nucleotides long respectively. The 16S/23S spacer showed an Ala-tRNA intervening sequence, which is a common feature in Euryarchaeota. Sequence analysis of 23S rRNA and 16S rRNA was performed for the six organisms from the family Halobacteriaceae with both available gene sequences. Phylogenetic trees with completely different topology were obtained using both molecules.

[Prognostic value assessment of the early response of blood estradiol, FSH, and LH using leuprolide acetate during ovarian hyperstimulation in assisted reproduction]. / Evaluación del valor pronóstico de la respuesta temprana de estradiol sérico, FSH y LH con el uso de acetato de leuprolide durante la hiperestimulación ovárica en reproducción asistida.

OBJECTIVE: Evaluate the prognostic value of the early response of the serum estradiol FSH y LH action of leuprolide acetate during the folicular phase, used as an adjuvant to ovarian stimulation in IVF-ET. STUDY DESIGN: Were analyzed 31 cycles of stimulation in 26 patients with sterility primary and secondary. Where measured estradiol, FSH, LH on cycle day 2 to 5 for to establish the patterns of response to GnRHa administration. Were compared the response patterns in relation to the number of oocyte captured, estradiol in the day of application of hCG, number of embryos and fertilization rate using (t-student, wilcoxon test and X2). RESULTS: Where observed four distincts patterns of response of estradiol. Pattern A: 133 cycles, presented a prompt elevation of estradiol, followed by a fall on the 4th cycle's day. Pattern B: 9 cycles delayed elevation of the estradiol, followed by a fall on the 6th cycles day. Pattern C: 7 cycles showed persistent elevation of the estradiol. Pattern D: 2 cycles no response of the estradiol (canceled cycles). Was found a significative difference in the estradiol level the day of application of hCG, number of captured oocytes and number of embrions in the pattern A in relation with B and C. No significative difference were found in the fertilization rate. The seric level of FSH and LH were no predictives. We concluded that the response pattern of the estradiol to the leuprolide acetate is the good prognosis indicator of the results of IVF-ET.

Deep subsurface sulfate reduction and methanogenesis in the Iberian Pyrite Belt revealed through geochemistry and molecular biomarkers.

The Iberian Pyrite Belt (IPB, southwest of Spain), the largest known massive sulfide deposit, fuels a rich chemolithotrophic microbial community in the Río Tinto area. However, the geomicrobiology of its deep subsurface is still unexplored. Herein, we report on the geochemistry and prokaryotic diversity in the subsurface (down to a depth of 166 m) of the Iberian Pyritic belt using an array of geochemical and complementary molecular ecology techniques. Using an antibody microarray, we detected polymeric biomarkers (lipoteichoic acids and peptidoglycan) from Gram-positive bacteria throughout the borehole. DNA microarray hybridization confirmed the presence of members of methane oxidizers, sulfate-reducers, metal and sulfur oxidizers, and methanogenic Euryarchaeota. DNA sequences from denitrifying and hydrogenotrophic bacteria were also identified. FISH hybridization revealed live bacterial clusters associated with microniches on mineral surfaces. These results, together with measures of the geochemical parameters in the borehole, allowed us to create a preliminary scheme of the biogeochemical processes that could be operating in the deep subsurface of the Iberian Pyrite Belt, including microbial metabolisms such as sulfate reduction, methanogenesis and anaerobic methane oxidation.

Pérdida celular endotelial corneal asociada a facoemulsificación y experiencia del oftalmólogo: análisis prospectivo de datos secundarios individuales / Corneal endothelial cell loss associated to phacoemulsification and ophthalmologist experience: prospective analysis of individual secondary data

Resumen Introducción La facoéresis es el procedimiento en que se extrae quirúrgicamente el cristalino para tratar las cataratas. La pérdida endotelial corneal es una complicación reconocida. Si bien se han descrito diversos factores asociados a este daño, la experiencia del cirujano ha sido poco explorada. Objetivos Evaluar la asociación entre la experiencia del cirujano y otras variables asociadas a la pérdida celular endotelial en el contexto de la facoéresis. Métodos Se analizaron registros clínicos de 198 cirugías de cataratas, evaluando el efecto de la experiencia del cirujano y otras variables asociadas: energía disipada acumulada, tipo de viscoelástico empleado, uso de azul tripán, cantidad de fluídica, tiempo de ultrasonido, energía de facoemulsificación combinada y recuento celular endotelial pre y postoperatorio. Resultados No se observaron diferencias en el conteo postoperatorio de células endoteliales. Los oftalmólogos con más de cinco años de experiencia presentaron menor uso de azul tripán pero mayor cantidad de energía disipada acumulada en cada procedimiento, mientras que los oftalmólogos con menor experiencia utilizaron mayor cantidad de fluídica. Conclusiones Aunque hubo diferencias en el manejo de algunos factores influyentes sobre la pérdida endotelial cornal según la experiencia de los oftalmólogos, no se hallaron diferencias en relación a dicha pérdida como resultado final.

Abstract Introduction Phacoeresis is the procedure through which the lens is surgically removed to treat cataracts. A corneal endothelial loss is a recognized sequel. Although several factors associated with this harm have been described, the surgeon's prior experience has been scarcely evaluated. Objectives To assess the association between the surgeon's experience and other variables associated with a corneal endothelial cell loss in the context of phacoeresis. Methods Clinical records of 198 patients undergoing cataract operations were prospectively reviewed. The experience of the surgeon and other variables were recorded, including cumulative dissipated energy, viscoelastic type, the use of trypan blue, amount of fluidics, ultrasound time, combined phacoemulsification energy, and pre- and postoperative corneal endothelial cell counts. Results No differences were observed in the postoperative corneal endothelial cell count between surgeons with more or less than five years of experience. Nevertheless, ophthalmologists with more than five years' experience used less trypan blue, but more cumulative dissipated energy in each procedure, while less experienced ophthalmologists used less fluidics. Conclusions Although there were differences in the surgical management regarding the surgeons' experience in factors known to influence corneal endothelial cell loss, no differences in endothelial cell loss were observed as an outcome.