Communication: Site-selective bond excision of adenine upon electron transfer

This work demonstrates that selective excision of hydrogen atoms at a particular site of the DNA base adenine can be achieved in collisions with electronegative atoms by controlling the impact energy. The result is based on analysing the time-of-flight mass spectra yields of potassium collisions with a series of labeled adenine derivatives. The production of dehydrogenated parent anions is consistent with neutral H loss either from selective breaking of C-H or N-H bonds. These unprecedented results open up a new methodology in charge transfer collisions that can initiate selective reactivity as a key process in chemical reactions that are dominant in different areas of science and technology.

Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods

We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH₂ loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K⁺ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.

Magnetically confined electron beam system for high resolution electron transmission-beam experiments

A novel experimental setup has been implemented to provide accurate electron scattering cross sections from molecules at low and intermediate impact energies (1-300 eV) by measuring the attenuation of a magnetically confined linear electron beam from a molecular target. High-resolution electron energy is achieved through confinement in a magnetic gas trap where electrons are cooled by successive collisions with N₂. Additionally, we developed and present a method to correct systematic errors arising from energy and angular resolution limitations. The accuracy of the entire measurement procedure is validated by comparing the N₂ total scattering cross section in the considered energy range with benchmark values available in the literature.

A process to describe radiation damage at the molecular level. Application to the 125I seeds in water

The correlation between the absorbed energy and the induced biological damage still has unclear aspects, especially in the low energy and low dose rate irradiation regimes. From the knowledge of the molecular-induced effects (dissociations), it would be possible to better understand the side effects of radiation, such as induced cancers or damage to healthy tissue. With this in view, this paper presents results of a simulation of a ¹²⁵I-seed treatment with an event-by-event MC code (LEPTS) specifically designed to account for the low energy secondary particle interactions, such as electron attachment, vibro-rotational and neutral dissociation interactions. This calculation allowed us to analyze the potential radiation damage not only in connection with the energy deposition, but also in terms of induced molecular dissociations by taking into account ionizing and non-ionizing dissociative processes. We propose that this description of the molecular level damage be the basis for nanodosimetric evaluations.

Electron stimulated desorption from condensed pyrimidine and pyridazine

Low energy electron (LEE) interactions and the formation of transient negative ions play a dominant role in radiation-induced dissociation of condensed-phase biomolecules (e.g. in radiotherapy). Here we present data on the LEE-induced dissociation and desorption of the DNA/RNA-base and radiosensitizing agent analogues pyrimidine and pyridazine. Vapors of each molecule were condensed on either a Pt or Ar substrate to form a multilayer film or a submonolayer molecular target, respectively. These were irradiated with electrons of 0-80 eV and the desorbing anionic and cationic fragments analysed via time of flight mass spectrometry. The detected cations are the same species seen in gas-phase mass spectra, albeit of differing relative intensity. Anion yield functions exhibit strong maxima, indicating that transient negative ions contribute significantly, via dissociative electron attachment (DEA), to molecular dissociation below 20 eV. For both molecules, the <5 eV shape resonances, seen experimentally and predicted by theory, do not result in fragment desorption. The main anionic fragments are H^- and CN^- for both molecules, additionally the fragments C^-, CH^- C₂H^- and CHN^- desorb from pyrimidine and C^- and C₂H^- from pyridazine, with some resonances lying above the ionization limit. Pyrimidine shows higher anion desorption yields than pyridazine for all species except H^-. The anion signal also comprises dipolar dissociation (DD), investigated in both anionic and cationic yield functions. From analysis of anion and cation yields, fragmentation pathways are suggested. The direct ionization pathway provides information on the appearance energies for cations and their production processes in condensed phase.

Impact of using the new GOLD classification on the distribution of COPD severity in clinical practice

Objective

The objective of this study was to examine how COPD patients were classified by the Global Initiative for Chronic Obstructive Lung Disease (GOLD) spirometry-based severity system and the distribution of COPD severity using the new GOLD 2011 assessment framework.

Materials and methods

This was an observational, retrospective cohort study conducted in a single tertiary center on a prospective database, which aimed to evaluate the prevalence, incidence, severity, and comorbidities of COPD. Inclusion criteria were age ≥40 years and COPD diagnosis according to GOLD 2007 classification. Clinical factors were compared between the categories in GOLD 2007 and 2011 groups by using the χ² test for categorical data and the analysis of variance for continuous data.

Results

In total, 420 COPD patients were included in the analysis. The distribution of patients into GOLD 2007 categories was as follows: 6.4% (n=27) of them were classified into subgroup I, 42.1% (n=177) into subgroup II, 37.9% (n=159) into subgroup III, and 13.6% (n=57) into subgroup IV. The distribution of patients into GOLD 2011 categories was as follows: 16.4% (n=69) of them were classified into subgroup A (low risk and fewer symptoms), 32.1% (n=135) into subgroup B (low risk and more symptoms), 21.6% (n=91) into subgroup C (high risk and fewer symptoms), and 29.7% (n=125) into subgroup D (high risk and more symptoms). After the application of the new GOLD 2011 (modified Medical Research Council [mMRC] system), 22% (n=94) of patients were upgraded to a higher level than their spirometry level, and 16.2% (n=68) of them were downgraded in their severity category, meaning that almost 40% of patients changed their severity assessment category. In total, 22% of patients in stage I were allocated to group B, and 35% of patients in stage IV were allocated to group C. Patients in stage III were the most frequently upgraded to a higher risk group (D), taking into account mMRC and exacerbation history.

Conclusion

Classifying patients using the new GOLD 2011 criteria reallocated a relevant proportion of patients to a different risk category and identified larger proportions of patients in the mildest and more severe groups compared with GOLD 2007 classification.

Polymorphisms associated with resistance to protease inhibitors in naïve patients infected with hepatitis C virus genotype 1 in Argentina: Low prevalence of Q80K

Incorporation of direct acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) significantly increases sustained virologic response rates. However, despite the greater potency offered by these antivirals, drug resistance plays a key role in patients with failure to DAA. Nevertheless, there is no information about the prevalence of resistance-associated substitutions (RASs) in Argentina. The aim of this study was to analyze HCV variants resistant to protease inhibitors (PI) in naïve patients infected with HCV genotype 1 from Argentina. In this retrospective cross-sectional study, 103 patients infected with HCV-1 were included. Eighteen positions related with RASs were analyzed by Sanger at baseline and phylogenetic analysis was performed to determine the diversification of this samples. The analyzed RASs were present in 38 out of 103 patients (36.9%) infected with HCV-1. Patients infected with subtype HCV-1b had higher prevalence of baseline RASs than patients infected with HCV-1a [51.6% vs. 12.8%, respectively (p<0.001)]. The Q80K polymorphism was not found in HCV-1a samples, even when 51% of them belonged to cluster 1, which is associated with a high frequency of Q80K. Phylogenetic analysis showed that Argentinean samples were intermingled with sequences from other geographic regions. RASs to PI were highly prevalent and subtype dependent in treatment-naïve Argentinean patients. Surprisingly, Q80K polymorphism was not detected in our study population. The phylogenetic analysis showed no relationship between our samples and other samples from Brazil which also present a low prevalence of Q80K. This study supports the need for surveillance of resistance in patients who will be treated with DAA in each particular country since the observed RASs have very different prevalence worldwide.

NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b

OBJECTIVE

To evaluate the use of hepatitis C virus (HCV) NS3 sequencing as alternative to the comercially available Versant HCV 2.0 reverse hybridization line-probe assay (LiPA 2.0) to determine HCV genotype 1 (HCV-1) subtypes.

PATIENTS AND METHODS

A cohort of 104 patients infected by HCV-1 according to LiPA 2.0 was analyzed in a cross-sectional study conducted in patients seen from January 2012 to June 2016 at an outpatient clinic in Buenos Aires, Argentina.

RESULTS

The samples were included within well supported subtype clades: 64 with HCV-1b and 39 with HCV-1a infection. Twenty of the HCV-1a infected patientes were included in a supported sub-clade "1" and 19 individuals were among the basal sub-clade "2". LiPA 2.0 failed to subtype HCV-1 in 20 (19.2%) individuals. Subtype classification determined by NS3 direct sequencing showed that 2/18 (11.1%) of the HCV-1a-infected patients as determined by LiPA 2.0 were in fact infected by HCV-1b. Of the HCV-1b-infected according to LiPA 2.0, 10/66 (15.2%) patients showed HCV-1a infection according to NS3 sequencing. Overall misclassification was 14.3% (κ-index for the concordance with NS3 sequencing = 0.635). One (1%) patient was erroneously genotyped as HCV-1 and was revealed as HCV genotype 4 infection.

CONCLUSIONS

Genomic sequencing of the HCV NS3 region represents an adequate alternative since it provides reliable genetic information. It even distinguishes between HCV-1a clades related to resistance-associated substitutions to HCV protease inhibitors, it provides reliable genetic information for genotyping/subgenotyping and simultaneously allows to determine the presence of resistance-associated substitutions to currently recommended DAAs.

Aflatoxins and Saccharomyces cerevisiae: yeast modulates the intestinal effect of aflatoxins, while aflatoxin B1 influences yeast ultrastructure

The gastrointestinal tract (GIT) is the main site where absorption of food components takes place and the first system coming into contact with mycotoxins of dietary origin. The aim of this work was to study the effect of probiotic Saccharomyces cerevisiae RC016 on intestinal villi of rats exposed to aflatoxins for 60 days. Moreover, the effect of in vitro aflatoxin B1 (AFB1) exposure on yeast cell ultrastructure was evaluated. Six treatments were applied (n=6) to inbred male Wistar rats: (1) uncontaminated feed control (F); (2) yeast control; (3) F + 40 μg/kg AFB1 + 20 μg/kg aflatoxin G1 (AFG1); (4) F + 100 μg/kg AFB1 + 50 μg/kg AFG1; (5) F + 40 μg/kg AFB1 + 20 μg/kg AFG1 + daily oral dose 108 viable S. cerevisiae cells; and (6) F + 100 μg/kg AFB1 + 50 μg/kg AFG1 + daily oral dose 108 viable S. cerevisiae cells. Morphometric measurements (villus length and width, crypt depth, quantification of goblet cells) were assessed using image analysis. S. cerevisiae RC016 cells were exposed to 20 μg/ml of AFB1 in intestinal solutions or in phosphate buffered saline and cells processed for transmission electron microscopy and high resolution light microscopy studies. Dietary exposure to the yeast did not induce significant differences in villus width but increased villus length and crypt depth. Aflatoxin-contaminated diets induced an increase in villus length, width and crypt depth and a significant decrease in the number of goblet cells which were improved by the addition of S. cerevisiae RC016. A significant increase in the yeast cell diameter was observed when RC016 was exposed to aflatoxins, suggesting this as an advantage since a larger cell would be able to adsorb mycotoxins more efficiently. The ability of this strain to act as probiotic and aflatoxin binder makes it a candidate for the formulation of new additives to improve animal performance.

Estado de conservación de Lagothrix flavicauda y otros primates en bosques montanos de San Martín y Huánuco, Perú

Lagothrix flavicauda es endémica y vive en simpatría con otros primates en bosques montanos de Amazonas, San Martín, La Libertad y Huánuco. Información detallada sobre su abundancia y estado de conservación, así como de los sitios con poblaciones saludables son desconocidas, excepto para Amazonas donde fueron ejecutados la mayoría de los estudios. Para obtener la información sobre los aspectos mencionados fueron conducidos censos por transecto entre noviembre y diciembre del 2015, febrero a mayo del 2016 y entre junio y julio del 2016 en seis sitios de muestreo localizados entre las regiones de San Martín y Huánuco. Como resultado de los censos fueron avistados 49 grupos pertenecientes a 7 especies, siendo L. flavicauda la más observada con 14 grupos. Grupos más grandes se observaron en L. flavicauda (promedio 13.5±2.2 individuos) y Cebus yuracus (promedio 12.5±3.6 individuos) y más pequeños en Alouatta seniculus (promedio 3.0±2.4 individuos), ambos en Huánuco. La abundancia relativa fue más alta para L. flavicauda en San Martín (2.4 individuos/10 km) y más baja para A. seniculus en Huánuco (0.2 individuos/10 km). Con el registro de L. flavicauda en el lado oriental del río Huallaga su distribución en Huánuco se amplía hasta el río Pozuzo, pero en el lado occidental podemos considerarlo localmente extinta en gran parte de su distribución. En los sitios de muestreo, la deforestación y la caza son las principales amenazas para los primates y otros componentes de la fauna silvestre.

Gut-borne Saccharomyces cerevisiae, a promising candidate for the formulation of feed additives, modulates immune system and gut microbiota

The aim was to evaluate the effect of Saccharomyces cerevisiae RC016 on immune parameters and gut microbiota in healthy mice. Animals received S. cerevisiae RC016 for 10 days. Microbial translocation to liver and changes in some bacterial populations in caecum were determined. Immune stimulation was assessed at gut level (measure of immunoglobulin A (IgA)+ cells and luminal cytokine profile) and by evaluating the activity of peritoneal macrophages. Oral administration of S. cerevisiae RC016 did not induce microbial translocation to liver. Mice that received yeast increased the number of IgA+ cells in their intestines, the phagocytic activity of peritoneal macrophages and decreased tumour necrosis factor alpha (TNF-α) levels in the small intestine with increases of interleukin-10/TNF-αratio. Administration of S. cerevisiae RC016 caused the decline of a logarithmic unit for Enterobacteriaceae counts compared to the control. The immune and gut microbiota modulation observed demonstrates that S. cerevisiae RC016 is a promising candidate for the formulation of feed additives to improve animal productivity. The beneficial in vivo effects observed for the potential probiotic S. cerevisiae RC016 with previously reported mycotoxin-binding properties, demonstrated that this strain could be suitable to be included in a novel product to improve animal productivity, with both probiotic and mycotoxin-binding properties. However, studies in the specific host will be necessary to confirm this potential.