Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. Chimeras are hybrid products composed of distinct parental sequences that can lead to the misinterpretation of diversity estimates. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using a nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. To further investigate how chimeric molecules are formed, the nSSU gene secondary structure was analyzed in several individuals. For the first time in eukaryotes, chimera formation proved to be higher in both richer and more genetically diverse samples, thus providing a novel perspective of chimera formation in pyrosequenced environmental data sets. Findings contribute to a better understanding of the nature and mechanisms involved in chimera formation during PCR amplification of environmentally derived DNA. Moreover, given the similarities between biodiversity analyses using amplicon sequencing and those used to assess genomic variation, our findings have potential broad application for identifying genetic variation in homologous loci or multigene families in general.     

Altered fatty acid membrane composition modifies lymphocyte localization in vivo

In the present paper, we report the results of a study on the in vivo localization of 51Cr-labeled lymphocytes with an altered lipid bilayer. In vitro treatment of lymphocytes with fatty acids (arachidic and linolenic acids) modifies the relative composition of plasma membrane fatty acids. Phospholipids of the plasma membrane of lymphocytes incubated with arachidic acid show a preferential increase of fatty acids with chain length between C:12 and C:16. Cells incubated with linolenic acid show an increase percentage of fatty acids C:16 to C:20 and the relative amount of the fatty acids with chain length superior to C:20 is higher in cells treated with linolenic than with arachidic acid. We have found that these alterations in plasma membrane fatty acid composition can modify the normal pattern of lymphocyte localization in vivo after iv transfer into syngeneic hosts. The possible role of factors such as cell to cell adhesion and/or fluidity of plasma membranes in the control of lymphocyte migration are discussed.     

The antinociceptive effect of iontophoretic direct application of diclofenac to arthritic knee-joints of rats

This study compared the antinociceptive effect produced by cathodic iontophoresis of sodium diclofenac close to an arthritic knee-joint in rats with that of systemic application. Arthritic nocifensive incapacitation was induced by LPS (1 microg) injection into a knee-joint previously (72 h) primed with carrageenan (300 microg). Diclofenac (0.1, 0.25 and 0.5 mg/kg) given intraperitoneally 1 h after LPS injection caused dose-dependent inhibition of incapacitation. Diclofenac iontophoresis was performed by varying either the current density (0.1, 0.2, and 0.3 mA/cm2) or the duration of application (4, 10, 20 and 30 min) of a polyvinylpirrolydone-hydroxymethylcellulose gel containing 1% sodium diclofenac. A clear, current density-dependent effect was observed for 0.1, 0.2 and 0.3 mA/cm2 (10 min period), which was similar to the effect observed for the intraperitoneal application of 0.1, 0.25 and 0.5 mg/kg doses. Combining different application periods with different current densities, in a manner that resulted in the same total current (1.6 mA*min) application, did not produce similar therapeutic effects, but the antinociceptive effect was directly proportional to the current density. The ipsilateral iontophoresis (0.25 mA/cm2 x 10 min or 0.5 mA/cm2 x 4 min) of diclofenac produced an effect significantly greater than the same contralateral application (p<0.05). In conclusion, our results suggest that the therapeutic effect depends on the current density but not on the application time, and also that the iontophoretic, direct application to the inflamed knee-joint enhances the therapeutic effect probably as a result of the direct delivery of the drug.     

Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes

Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence‐capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence‐capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence‐capture recovered 80%–90% of the control sample species. DNA sequence‐capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low‐cost, whereas DNA‐sequence capture for biodiversity assessment is still in its infancy, is more time‐consuming but provides more taxonomic assignments.     

Role of B lymphocytes in the infarcted mass in patients with acute myocardial infarction

Despite early reperfusion, patients with ST segment elevation myocardial infarction (STEMI) may present large myocardial necrosis and significant impairment of ventricular function. The present study aimed to evaluate the role of subtypes of B lymphocytes and related cytokines in the infarcted mass and left ventricular ejection fraction obtained by cardiac magnetic resonance imaging performed after 30 days of STEMI. This prospective study included 120 subjects with STEMI submitted to pharmacoinvasive strategy. Blood samples were collected in subjects in the first (D1) and 30th (D30) days post STEMI. The amount of CD11b+ B1 lymphocytes (cells/ml) at D1 were related to the infarcted mass (rho = 0.43; P=0.033), measured by cardiac MRI at D30. These B1 cells were associated with CD4+ T lymphocytes at D1 and D30, while B2 classic lymphocytes at day 30 were related to left ventricular ejection fraction (LVEF). Higher titers of circulating IL-4 and IL-10 were observed at D30 versus D1 (P=0.013 and P<0.001, respectively). Titers of IL-6 at D1 were associated with infarcted mass (rho = 0.41, P<0.001) and inversely related to LVEF (rho = −0.38, P<0.001). After multiple linear regression analysis, high-sensitivity troponin T and IL-6 collected at day 1 were independent predictors of infarcted mass and, at day 30, only HDL-C. Regarding LVEF, high-sensitivity troponin T and high-sensitivity C-reactive protein were independent predictors at day 1, and B2 classic lymphocytes, at day 30. In subjects with STEMI, despite early reperfusion, the amount of infarcted mass and ventricular performance were related to inflammatory responses triggered by circulating B lymphocytes.     

The glyceraldehyde-3-phosphate dehydrogenase promoter of the food yeast Candida utilis strain NRRL Y-660 is functional in Agrobacterium tumefaciens

The glyceraldehyde-3-phosphate dehydrogenase promoter of the food yeast Candida utilis strain NRRL Y-660 was cloned to create a novel integrative vector for Agrobacterium tumefaciens-mediated transformation. The new binary vector harbors β-glucuronidase activity as reporter and kanamicin/geneticin resistance as selection marker. Recombinant clones of A. tumefaciens show kanamycin resistance and high β-glucuronidase activity under the control of the C. utilis promoter. This finding can be explained by the presence of a prokaryotic core in the yeast promoter, predicted by in silico analysis of the sequence. This is the first report about functionality of a yeast promoter in A. tumefaciens.