Exonic Sequences in the 5′ Untranslated Region of α-Tubulin mRNA Modulate trans Splicing in Trypanosoma brucei

Previous studies have identified a conserved AG dinucleotide at the 3′ splice site (3′SS) and a polypyrimidine (pPy) tract that are required for trans splicing of polycistronic pre-mRNAs in trypanosomatids. Furthermore, the pPy tract of the Trypanosoma brucei α-tubulin 3′SS region is required to specify accurate 3′-end formation of the upstream β-tubulin gene and trans splicing of the downstream α-tubulin gene. Here, we employed an in vivo cis competition assay to determine whether sequences other than those of the AG dinucleotide and the pPy tract were required for 3′SS identification. Our results indicate that a minimal α-tubulin 3′SS, from the putative branch site region to the AG dinucleotide, is not sufficient for recognition by the trans-splicing machinery and that polyadenylation is strictly dependent on downstream trans splicing. We show that efficient use of the α-tubulin 3′SS is dependent upon the presence of exon sequences. Furthermore, β-tubulin, but not actin exon sequences or unrelated plasmid sequences, can replace α-tubulin exon sequences for accurate trans-splice-site selection. Taken together, these results support a model in which the informational content required for efficient trans splicing of the α-tubulin pre-mRNA includes exon sequences which are involved in modulation of trans-splicing efficiency. Sequences that positively regulate trans splicing might be similar to cis-splicing enhancers described in other systems.     

Expression of Parkin,APC, APE1, and Bcl-xL in Colorectal Polyps

Colorectal cancer can develop through molecular, chromosomal, and epigenetic cumulative changes that transform the normal intestinal epithelium into the colorectal polyps, called conventional adenomas (CAs) or serrated polyps (SPs), recognized as precursors of invasive colorectal neoplasia. These benign lesions need to explore the morphology, histological diagnosis, and biomarkers profile to accurately characterize lesions with potential for evolution to cancer. This study aimed to correlate the immunohistochemical expression of Parkin and Adenomatous Polyposis Coli (APC; tumor suppressors), Human Apurinic/Apyrimidinic endonuclease 1 (APE1), and B-cell lymphoma-extra-large (Bcl-xL; oncogenic proteins) in sporadic colorectal polyps with clinical, endoscopic, and diagnostic data. Immunohistochemical analysis was performed on tissue microarray samples of 306 polyps. Based on the Allred score, the expressions were graduated in the cytoplasm and nucleus of superficial and cryptic cells. There was higher Parkin nuclear expression (p=0.006 and 0.010) and APC cytoplasmic expression in cryptic cells (p<0.001) in SPs. CAs, APE1 (p<0.001) and Bcl-xL (p<0.001) were more expressed in the nuclei and cytoplasms, respectively. These results are related to the biological role proposed for these proteins in cellular functions. They can contribute to the diagnosis criteria for polyps and improve the knowledge of biomarkers that could predict cancer development:     

Associations of Spiders of the Genus Peucetia (Oxyopidae) with Plants Bearing Glandular Hairs

Two common South American species of lynx spiders, Peucetia rubrolineata and P. flava (Oxyopidae), were surveyed on three localities in southeastern Brazil to determine plant choice. Both species were found to be associated with plants bearing glandular trichomes. A literature review and complementary data show that ten Peucetia species are associated with up to 55 plant species bearing glandular trichomes in at least 20 distinct vegetation types (phytophysiognomies) in more than 36 localities in the Neotropical, Neartic, Afrotropical, and Paleartic regions. The main plant families used by the spiders were Solanaceae, Asteraceae, and Melastomataceae. The specialization of the Peucetia species for plants bearing glandular trichomes may have evolved because insects adhered to these sticky structures may be used as prey by the spiders.     

Detection of resistance genes and susceptibility patterns in Bacteroides and Parabacteroides strains

Susceptibility to five antimicrobials was determined for Bacteroides spp. (n = 52) and Parabacteroides distasonis (n = 8). All isolates were susceptible to metronidazole. The resistance rates to ampicillin, cefoxitin, tetracycline and clindamycin were 98%, 9.6%, 65.3% and 19.2% of the Bacteroides strains, respectively. The genes cepA, cfiA, cfxA, tetQ, ermF and nim were found in 69.2%, 17.3% 9.6%, 50%, 7.7% and 3.8% for these strains respectively. All P. distasonis strains were resistant to ampicilin. Cefoxitin, tetracycline and clindamycin resistance rates were 75%, 87.5% and 50%, respectively. The ermF and nim genes were absent and 37.5%, 12.5%, 12.5% and 87.5% of this strains possessed cepA, cfiA, cfxA and tetQ genes, respectively. Ten cfiA gene positive strains of Bacteroides and Parabacteroides were submitted to E-test with imipenem and amoxicillin–clavulanate. The resistance rate to imipenem was 4.1% and 8.3% to amoxicillin–clavulanate. This feature is for the first time described in Brazil.     

A new method for the improvement of data production in phytochemical analysis

Introduction – The use of the average analytical signal for the construction of curves by the least squares method (LSM) over the standard addition method (SAM) is widespread. It would be advantageous, however, to find a way to avoid intermediary averages, which are known to be the cause of significant increases in standard deviations (SD). Objective – To develop a protocol that uses all gathered data to create curves by LSM over SAM. To use Excel^® for the estimation of y = mx + b and R² rather than using LSM equations for the SD of m, x and b. Methodology – The level of lead (II) in the bark (cork) of Quercus suber Linnaeus was determined using differential pulse anodic stripping voltammetry (DPASV). Three current samples were taken for each of the four standard additions. These signals were combined for adjustment by LSM. The results were compared with those obtained after averaging the current for each addition, and the expression of uncertainty in the measurements determined. Results – The new method shows an expanded uncertainty of ± 0.3321 μg/g (nearly 1.42%). The difference between the results obtained by the new and the old method is 0.01 μg/g (23.41 and 23.40 μg/g). The limit of detection changed approximately from 4.8 to 4 μg/g and the relative SD approximately from 9 to 6%. Conclusion – The absence of intermediary averages in curves improved the determination of lead (II) in cork by DPASV. Estimation of SD only with LSM equations produced results that were significantly worse. The changes are large enough to transform an apparently internally non‐validated procedure (repeatability for precision) into an internally validated procedure. Copyright © 2009 John Wiley & Sons, Ltd.     

Effects of species and habitat positional errors on the performance and interpretation of species distribution models

Aim A key assumption in species distribution modelling is that both species and environmental data layers contain no positional errors, yet this will rarely be true. This study assesses the effect of introduced positional errors on the performance and interpretation of species distribution models. Location Baixo Alentejo region of Portugal. Methods Data on steppe bird occurrence were collected using a random stratified sampling design on a 1‐km² pixel grid. Environmental data were sourced from satellite imagery and digital maps. Error was deliberately introduced into the species data as shifts in a random direction of 0–1, 2–3, 4–5 and 0–5 pixels. Whole habitat layers were shifted by 1 pixel to cause mis‐registration, and the cumulative effect of one to three shifted layers investigated. Distribution models were built for three species using three algorithms with three replicates. Test models were compared with controls without errors. Results Positional errors in the species data led to a drop in model performance (larger errors having larger effects – typically up to 10% drop in area under the curve on average), although not enough for models to be rejected. Model interpretation was more severely affected with inconsistencies in the contributing variables. Errors in the habitat layers had similar although lesser effects. Main conclusions Models with species positional errors are hard to detect, often statistically good, ecologically plausible and useful for prediction, but interpreting them is dangerous. Mis‐registered habitat layers produce smaller effects probably because shifting entire layers does not break down the correlation structure to the same extent as random shifts in individual species observations. Spatial autocorrelation in the habitat layers may protect against species positional errors to some extent but the relationship is complex and requires further work. The key recommendation must be that positional errors should be minimised through careful field design and data processing.     

Conventional sampling plan for the green leafhopper Empoasca kraemeri in common beans

Abstract:  A conventional sampling plan for the leafhopper Empoasca kraemeri Ross & Moore (Auchenorrhyncha: Cicadellidae) in common beans (Phaseolus vulgaris L.) is presented based on samples from 51 commercial fields. The research encompassed three phases. The first phase had the objective of determining the most suitable leaf to be used as a precise and representative sampling unit. In the second phase of the project, the available sampling methods for E. kraemeri were compared, including the approach identified in the first phase. In the third phase, the theoretical frequency distribution of the sampling data was assessed and the number of samples necessary for the sampling plan was established. The best leaves to sample adult leafhoppers were the fourth and the fifth from the apex, while the best leaf for sampling nymphs was the fifth from the apex. The best sampling technique for nymphs and adults was the beating of the apical leaves against a plastic tray. The sampling data obtained with this technique were fit to a negative binomial distribution with common aggregation parameter for adults ( K _common = 1.04) and nymphs ( K _common = 0.47). This sampling plan required 16.8 and 31.2 min to be carried out at an expense of US$ 0.31 and US$ 0.54 for sampling adults and nymphs in a field, respectively.     

Tolerance to herbivory in lupin genotypes with different alkaloid concentration: Interspecific differences between Lupinus albus L. and L. angustifolius L.

Lupin genotypes accumulate alkaloids that act as feeding deterrents for several kinds of herbivores. Breeding sweet (low alkaloid) genotypes resulted in a greater dependence on pesticides. Besides the concentration of defensive chemicals, plants possess another way to deal with herbivory, to allocate post-damage resources to growth in order to reach compensation in biomass (tolerance).

These two ways to deal with herbivores were postulated as alternative strategies, as scarce resources allocated to one function (growth or secondary metabolism) would not be available for the other function. Genotypes could differ in the way they respond to herbivory; identifying those genotypes with greater ability to overcome the damage would be useful to decrease the use of pesticides.

The aim of this work was to compare tolerance to herbivory in Lupinus albus and Lupinus angustifolius genotypes with contrasting alkaloid concentration. Tolerance was evaluated by comparing growth and grain yield of field-grown cut and uncut plants. Cutting treatments were performed at flowering by cutting 50% of the upper shoot biomass (including the main apex, stems, flowers and leaves). Differences between species were found in their tolerance to herbivory. While L. angustifolius showed full compensation in growth or grain yield that allowed cut plants to equal controls biomass or yield after damage, simulated herbivory reduced growth and grain yield in L. albus.     

Antifungal effect of different methyl and propyl paraben mixtures on the treatment of paper biodeterioration

With many important artistic works and documents made of paper, and thus susceptible to biodeterioration by fungi, research is required in an effort to replace toxic chemical products with other more benign ones. In this work the antifungal effect of methyl and propyl paraben mixtures at different concentrations was evaluated. The fungi used in the experiments were a Cladosporium species and Penicillium corylophilum, both of which are well known as paper-biodeteriorating fungi. The results demonstrate that a mixture of 0.5% methyl paraben and 1% propyl paraben, in 85% ethanolic solution, is the lowest concentration necessary to provide an efficient antifungal action. A deacidification agent, 5% calcium propionate, was added to this mixture to produce a multi-purpose formulation to treat acidification and fungal contamination of paper documents. Tests carried out on paper samples before and after application of this mixture showed only a minor increase in yellowing and a slight decrease in tensile strength, while substantially raising the pH, and thus the alkaline reserve, and also a slight increase in the percentage of deformation.