Complex formation regulates the glycosylation of the reversibly glycosylated polypeptide

Reversible glycosylated polypeptides (RGPs) are highly conserved plant-specific proteins, which can perform self-glycosylation. These proteins have been shown essential in plants yet its precise function remains unknown. In order to understand the function of this self-glycosylating polypeptide, it is important to establish what factors are involved in the regulation of the RGP activity. Here we show that incubation at high ionic strength produced a high self-glycosylation level and a high glycosylation reversibility of RGP from Solanum tuberosum L. In contrast, incubation at low ionic strength led to a low level of glycosylation and a low glycosylation reversibility of RGP. The incubation at low ionic strength favored the formation of high molecular weight RGP-containing forms, whereas incubation at high ionic strength produced active RGP with a molecular weight similar to the one expected for the monomer. Our data also showed that glycosylation of RGP, in its monomeric form, was highly reversible, whereas, a low reversibility of the protein glycosylation was observed when RGP was part of high molecular weight structures. In addition, glycosylation of RGP increased the occurrence of non-monomeric RGP-containing forms, suggesting that glycosylation may favor multimer formation. Finally, our results indicated that RGP from Arabidopsis thaliana and Pisum sativum are associated to golgi membranes, as part of protein complexes. A model for the regulation of the RGP activity and its binding to golgi membranes based on the glycosylation of the protein is proposed where the sugars linked to oligomeric form of RGP in the golgi may be transferred to acceptors involved in polysaccharide biosynthesis.     

Diversity and symbiotic effectiveness of <Emphasis Type="Italic">Adesmia</Emphasis> spp. root nodule bacteria in central and southern Chile

Legumes in the genus Adesmia are wild species with forage and medicinal potential. Their nitrogen fixation efficiency depends on their association with soil bacteria known as rhizobia. The aim of this work was to assess the diversity and symbiotic effectiveness of root nodule bacteria from Adesmia boronioides, Adesmia emarginata and Adesmia tenella from different regions of Chile. Adesmia spp. nodules were collected from seven sites obtaining 47 isolates, which resulted in 19 distinct strains. The diversity of the strains was determined via partial sequencing of the dnaK, 16srRNA and nodA genes. The strains were authenticated as root nodule bacteria on their original host and assessed for symbiotic effectiveness on A. emarginata and A. tenella. The strains from Adesmia tenella clustered within the Mesorhizobium clade. Adesmia boronioides nodulated with Mesorhizobium sp., Rhizobium leguminosarum and Bradyrhizobium sp. The rhizobia from A. emarginata were identified as Burkholderia spp, which was symbiotically ineffective on this species and on A. tenella. Strains isolated from Adesmia emarginata nodules, but unable to induce nodulation, were identified as Labrys methylaminiphilus. Labrys strain AG-49 significantly increased root dry weight in A. emarginata. The nodA genes from Adesmia strains were unique and correlated to legume host. A. emarginata was effectively nodulated by Bradyrhizobium AG-64 and A. tenella by Mesorhizobium strains AG-51 and AG.52. It is concluded that Adesmia emarginata, A. tenella and A. boronioides are associated to diverse bacterial symbionts and selection of an effective inoculant is a key step to assist Adesmia spp. adaptation and restoration.     

Phosphatidic Acid Induces Ligand-independent Epidermal Growth Factor Receptor Endocytic Traffic through PDE4 Activation

Endocytosis modulates EGFR function by compartmentalizing and attenuating or enhancing its ligand-induced signaling. Here we show that it can also control the cell surface versus intracellular distribution of empty/inactive EGFR. Our previous observation that PKA inhibitors induce EGFR internalization prompted us to test phosphatidic acid (PA) generated by phospholipase D (PLD) as an endogenous down-regulator of PKA activity, which activates rolipram-sensitive type 4 phosphodiesterases (PDE4) that degrade cAMP. We found that inhibition of PA hydrolysis by propranolol, in the absence of ligand, provokes internalization of inactive (neither tyrosine-phosphorylated nor ubiquitinated) EGFR, accompanied by a transient increase in PA levels and PDE4s activity. This EGFR internalization is mimicked by PA micelles and is strongly counteracted by PLD2 silencing, rolipram or forskolin treatment, and PKA overexpression. Accelerated EGFR endocytosis seems to be mediated by clathrin-dependent and -independent pathways, leading to receptor accumulation in juxtanuclear recycling endosomes, also due to a decreased recycling. Internalized EGFR can remain intracellular without degradation for several hours or return rapidly to the cell surface upon discontinuation of the stimulus. This novel regulatory mechanism of EGFR, also novel function of signaling PA, can transmodulate receptor accessibility in response to heterologous stimuli.     

New heteroaryl nitrones with spin trap properties: Identification of a 4-furoxanyl derivative with excellent properties to be used in biological systems

A new series of heteroaryl nitrones, 1–7, bearing furoxanyl and thiadiazolyl moieties, were evaluated for their free radical-trapping properties. The physicochemical characterization by electron paramagnetic resonance (EPR) demonstrated its capability to trap and stabilize oxygen-, carbon-, sulfur-, and nitrogen-centered free radicals. The 4-furoxanyl nitrone 3 (FxBN), α(Z)-(3-methylfuroxan-4-yl)-N-tert-butylnitrone, showed appropriate solubility in aqueous solution and taking into account that this physicochemical property is very important for biological applications, we studied it deeply in terms of its trapping and kinetic behaviors. For this, kinetic studies of the hydroxyl adduct decay gave rate constants k_ST of 1.22 × 10¹⁰ dm³ mol^?1 s^?1 and half-live up to 7200 s at physiological pH, without any artifactual signals. The ability of FxBN to directly traps and stabilizes superoxide free radical, with a half-life of 1620 s at physiological pH, was also demonstrated. Besides, FxBN-hydroxyl and -superoxide adducts exhibited distinct and characteristic EPR spectral patterns. Finally, we confirmed the ability of FxBN to act as spin trap in a specific biological system, that is, in the free radical production of experimental anti-trypanosomatid drugs using Trypanosoma cruzi microsomes as biological system. Moreover, previous observations of low FxBN toxicity transform it in a good candidate for in vivo spin trapping.     

Effect of location and stage of development of dominant follicle on ovulation and embryo survival rate in alpacas

This study was designed to determine the effect of location of the preovulatory dominant follicle and stage of ovarian follicle development on ovulation rate and embryo survival in alpacas. In Experiment 1, mature lactating alpacas were randomly assigned to one of two groups according to the location of the dominant follicle detected by ultrasonography: (a) Right ovary (RO, n=96) or (b) Left ovary (LO, n=108). All females were mated once by an intact adult male. Ovulation rate, CL diameter and embryo survival rate (heartbeat) were assessed by ultrasonography on Days 2 (Day 0=mating), 8 and 30, respectively. Ovulation rate (96.5 and 96.3% for RO and LO group, respectively), corpus luteum (CL) diameter (10.2 and 10.6 mm for RO and LO group, respectively) and pregnancy rate (60.2 and 56.7% for RO and LO group, respectively) did not differ among groups. In Experiment 2, lactating alpacas (n=116) were submitted to ultrasonic-guided follicle ablation to synchronize follicular wave emergence. Afterwards, daily ultrasonography examinations were performed and females were randomly assigned to the following groups according to the growth phase and diameter of the dominant follicle: (a) early growing (5-6 mm, n=27), (b) growing (7-12 mm, n=30); (c) static (7-12 mm, n=30), or (d) regressing phase (12-7 mm, n=29). All alpacas were mated with a proven intact male, except five alpacas from early growing group that rejected the male. Females were examined by ultrasonography on Day 2 (ovulation rate), Day 8 (CL diameter), and Days 15, 20, 25, 30 and 35 (embryo survival by the presence of embryo proper and heartbeat). No differences were detected in ovulation rate among groups (96%, 97%, 100%, and 97%) or in CL size (10.3, 11.7, 11.1, and 11.1 mm, for early growing, growing, early static and regressing, respectively). Although, embryo survival rate at Day 35 after mating was numerically greatest in growing (65.5%), intermediate in early growing (52.4%) and static (53.3%), and least in regressing phase (42.9%), there were no differences among groups. Results suggest that neither location nor stage of development of the dominant follicle has an influence on ovulation and embryo survival rate in alpacas.     

StAR: a simple tool for the statistical comparison of ROC curves

Background  

As in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance of binary classifiers is typically carried out through the analysis of their receiver operating characteristic (ROC) curves. The area under the ROC curve (AUC) constitutes a popular indicator of the performance of a binary classifier. However, the assessment of the statistical significance of the difference between any two classifiers based on this measure is not a straightforward task, since not many freely available tools exist. Most existing software is either not free, difficult to use or not easy to automate when a comparative assessment of the performance of many binary classifiers is intended. This constitutes the typical scenario for the optimization of parameters when developing new classifiers and also for their performance validation through the comparison to previous art.