Fluorescence resonance energy transfer-based technologies in the study of protein-protein interactions at the cell surface

Understanding of the molecular mechanisms of protein-protein interactions (PPIs) at the cell surface of living cells is fundamental to comprehend the functional meaning of a large number of cellular processes. Here we discuss how new methodological strategies derived from non-invasive fluorescence-based approaches (i.e. fluorescence resonance energy transfer, FRET) have been successfully developed to characterize plasma membrane PPIs. Importantly, these technologies alone - or in concert with complementary methods (i.e. SNAP-tag/TR-FRET, TIRF/FRET) - can become extremely powerful approaches for visualizing cell surface PPIs, even between more than two proteins and also in native tissues. Interestingly, these methods would also be relevant in drug discovery in order to develop new high-throughput screening approaches or to identify new therapeutic targets. Accordingly, herein we provide a thorough assessment on all biotechnological aspects, including strengths and weaknesses, of these fluorescence-based methodologies when applied in the study of PPIs occurring at the cell surface of living cells.     

Azospirillum brasilense inoculation,auxin induction and culture medium composition modify the profile of antioxidant enzymes during in vitro rhizogenesis of pink lapacho

Optimal in vitro plant growth can be stimulated by selecting specific nutritional and environmental conditions. However, the culture conditions, dissection, and disinfection of plant material are stressful and may induce disruption of the plant physiological homeostasis. This can be modified by inoculation with rhizobacteria as Azospirillum brasilense, by the culture medium type, and by auxin induction. Here, we performed rooting experiments in two auxin-free culture media with ‘pink lapacho’ (Handroanthus impetiginosus) shoots previously induced with 0, 10, 30, or 50 μM indole butyric acid (IBA) for 3 days and inoculated with A. brasilense Cd and Az39. Peroxidase (PO), phenylalanine ammonia-lyase (PAL), and polyphenol oxidase (PPO) activities were determined on days 0, 3, 6, 9, 12, and 15. Also, weekly absolute rooting percentage was evaluated. All enzymatic activities were higher in A. brasilense-inoculated shoots, linked to early and high rooting percentage. The culture medium type and IBA concentration also affected enzymatic activities. The positive correlation between PO and PAL activities on day 9 and successful final in vitro rooting of H. impetiginosus allows using these activities as early markers of rhizogenesis reducing the selection time of easy-to-root plants. The changes in enzymatic levels performed here are discussed on the basis of their role in rooting and in vitro stress and contribute to the knowledge of the physiology of trees and their interaction with rhizobacteria.     

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

Background  

The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis.     

Structure and dynamics of an amphibian metacommunity in two regions

1. The concept of metacommunity is based on the hypothesis that species occurrence depends on species dynamics and interactions on local and regional scales via the movements of individuals between localities. Metacommunity approaches are currently being applied to pond breeding taxa such as amphibians. 2. Given that animal movement is also influenced by the physical quality of the matrix to be crossed to reach a breeding habitat and by the affinity of the species for specific terrestrial habitats, matrix characteristics may enhance or hinder dispersal success. These characteristics would, in turn, affect the composition of larval assemblages at local level and, consequently, determine metacommunity structure and dynamics. 3. Here we compared the structures and dynamics of two metacommunities with the same pool of anurans along similar freshwater gradients in two regions that are well differentiated in terms of their respective terrestrial matrix. 4. Abundance of tadpole species and species assemblage in the two regions were determined principally by local processes (at pond level); however, the structure and dynamics of the communities differed. In one region species abundance was explained in part by landscape factors and consequently showed lower co-occurrence and lower colonization rates (species sorting models) indicating that terrestrial habitat could restrict animal movements, whereas in the other region higher co-occurrence and higher colonization rates (mass effect models) indicated low dispersal limitations.     

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

Background  

Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive.     

Improvement of aroma in transgenic potato as a consequence of impairing tuber browning

Sensory analysis studies are critical in the development of quality enhanced crops, and may be an important component in the public acceptance of genetically modified foods. It has recently been established that odor preferences are shared between humans and mice, suggesting that odor exploration behavior in mice may be used to predict the effect of odors in humans. We have previously found that mice fed diets supplemented with engineered nonbrowning potatoes (-PPO) consumed more potato than mice fed diets supplemented with wild-type potatoes (WT). This prompted us to explore a possible role of potato odor in mice preference for nonbrowning potatoes. Taking advantage of two well established neuroscience paradigms, the "open field test" and the "nose-poking preference test", we performed experiments where mice exploration behavior was monitored in preference assays on the basis of olfaction alone. No obvious preference was observed towards -PPO or WT lines when fresh potato samples were tested. However, when oxidized samples were tested, mice consistently investigated -PPO potatoes more times and for longer periods than WT potatoes. Congruently, humans discriminated WT from -PPO samples with a considerably better performance when oxidized samples were tested than when fresh samples were tested in blind olfactory experiments. Notably, even though participants ranked all samples with an intermediate level of pleasantness, there was a general consensus that the -PPO samples had a more intense odor and also evoked the sense-impression of a familiar vegetable more often than the WT samples. Taken together, these findings suggest that our previous observations might be influenced, at least in part, by differential odors that are accentuated among the lines once oxidative deterioration takes place. Additionally, our results suggest that nonbrowning potatoes, in addition to their extended shelf life, maintain their odor quality for longer periods of time than WT potatoes. To our knowledge this is the first report on the use of an animal model applied to the sensory analysis of a transgenic crop.