Common antigenic determinants in the glycoproteins of plants,molluscs and insects

An antiserum raised against -fructosidase isolated from the cell walls of suspension-cultured carrot cells cross-reacts with many plant proteins and hemocyanin ofHelix pomatia. The shared epitope appears to be a small complex glycan with a (1–2)-linked xylose residue attached to the -linked mannose residue of the core of an asparagine-linked oligosaccharide. There is strong cross-reactivity with the proteins of many seed plants, molluscs and insects, and no cross-reactivity with the proteins of fungi, algae, mosses, ferns, or any of the vertebrates tested. Xylose-containing glycans appear to increase the immunogenicity of the proteins to which they are attached, and we suggest that they may be responsible for some allergic responses of people that are repeatedly exposed to plant or insect proteins.     

Fatal-Mixed Cutaneous Zygomycosis–Aspergillosis: A Case Report

Mucorales and Aspergillus are molds responsible for infections in immunocompromised patients. In this report, we describe a case of a rare extensively mixed cutaneous infection caused by Lichtheimia ramosa, Aspergillus fumigatus and Aspergillus terreus in a neutropenic patient suffering from an acute leukemia. The fatal outcome of this patient can be attributed to its hematologic malignancy, the extensive nature of the lesions and the resistance of the strains to antifungals.     

Anoctamin 1 dysregulation alters bronchial epithelial repair in cystic fibrosis

Cystic fibrosis (CF) airway epithelium is constantly subjected to injury events due to chronic infection and inflammation. Moreover, abnormalities in CF airway epithelium repair have been described and contribute to the lung function decline seen in CF patients. In the last past years, it has been proposed that anoctamin 1 (ANO1), a Ca^2 +-activated Cl^? channel, might offset the CFTR deficiency but this protein has not been characterized in CF airways. Interestingly, recent evidence indicates a role for ANO1 in cell proliferation and tumor growth. Our aims were to study non-CF and CF bronchial epithelial repair and to determine whether ANO1 is involved in airway epithelial repair. Here, we showed, with human bronchial epithelial cell lines and primary cells, that both cell proliferation and migration during epithelial repair are delayed in CF compared to non-CF cells. We then demonstrated that ANO1 Cl^? channel activity was significantly decreased in CF versus non-CF cells. To explain this decreased Cl^? channel activity in CF context, we compared ANO1 expression in non-CF vs. CF bronchial epithelial cell lines and primary cells, in lung explants from wild-type vs. F508del mice and non-CF vs. CF patients. In all these models, ANO1 expression was markedly lower in CF compared to non-CF. Finally, we established that ANO1 inhibition or overexpression was associated respectively with decreases and increases in cell proliferation and migration. In summary, our study demonstrates involvement of ANO1 decreased activity and expression in abnormal CF airway epithelial repair and suggests that ANO1 correction may improve this process.     

Ecological assembly rules in plant communities—approaches,patterns and prospects

Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co‐occur randomly but are restricted in their co‐occurrence by interspecific competition. This concept can be redefined in a more general framework where the co‐occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta‐analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co‐occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta‐analyses suggest that non‐random co‐occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general conclusions about the non‐random aspect of assembly in plant communities.     

Number,position, diameter and initial direction of growth of primary roots in Musa

To understand soil colonization by a root system, information is needed on the architecture of the root system. In monocotyledons, soil exploration is mainly due to the growth of adventitious primary roots. Primary root emergence in banana was quantified in relation to shoot and corm development. Root emergence kinetics were closely related to the development of aerial organs. Root position at emergence on the corm followed an asymptotic function of corm dry weight, so that the age of each root at a given time could be deduced from its position. Root diameter at emergence was related to the position of the roots on the corm, with younger roots being thicker than older ones. However, root diameters were not constant along a given root, but instead decreased with the distance to the base; roots appear to be conical in their basal and apical parts. Root growth directions at emergence were variable, but a high proportion of the primary roots emerged with a low angle to the horizontal. Further research is needed to evaluate whether these initial trajectories are conserved during root development. Results presented in this study are in good agreement with those reported for other monocotyledons such as maize and rice. They give quantitative information that will facilitate the development of models of root system architecture in banana.     

The relationships between static and dynamic variables in the description of root growth. Consequences for field interpretation of rooting variability

Field root investigations are often limited by the static nature of classical observations, resulting in the need to develop alternative methodologies that allow dynamic interpretation of root architecture variability on the basis of static measurements. The objectives of this work were (i) to evaluate the use of selected morphological indicators, namely root apical diameter (Da) and the length of the apical unbranched zone (LAUZ), in predicting primary and lateral root growth patterns in banana trees, (ii) to propose a field methodology for the assessment of root dynamics based on static measurements. Banana trees (Musa acuminata cv `Grande Naine') were grown in 5 rhizotrons as well as in field conditions, respectively on pouzzolane and Mollic Andosols. In rhizotrons, root growth analysis was carried out by reporting root elongation, Da and LAUZ, three times a week. In field conditions, 4 series of excavations were made at three-week intervals. Apart from root growth rate, measurements were the same as those in the rhizotrons. LAUZ was confirmed as a stable and good predictor of root growth rate for the different types of roots. In the rhizotrons, the root growth of lateral roots was found to be well correlated to the product of Da and the growth rate of the bearing root. Evaluation in field conditions from static observations attested consistent relationships between measured and predicted root length for lateral roots (slopes close to 1:1). The apical diameter can be considered as a good indicator of root growth potential, while actual lateral root growth depends on the bearing root elongation rate. Morphological static indicators calibrated from growth dynamics in rhizotrons are of major interest in explaining growth variability in field conditions. Especially the `growth rate-LAUZ' relationship can be considered a useful tool in interpreting field patterns of growing roots in relation to various soil conditions.     

Gene mention normalization and interaction extraction with context models and sentence motifs

Background:

The goal of text mining is to make the information conveyed in scientific publications accessible to structured search and automatic analysis. Two important subtasks of text mining are entity mention normalization - to identify biomedical objects in text - and extraction of qualified relationships between those objects. We describe a method for identifying genes and relationships between proteins.

Results:

We present solutions to gene mention normalization and extraction of protein-protein interactions. For the first task, we identify genes by using background knowledge on each gene, namely annotations related to function, location, disease, and so on. Our approach currently achieves an f-measure of 86.4% on the BioCreative II gene normalization data. For the extraction of protein-protein interactions, we pursue an approach that builds on classical sequence analysis: motifs derived from multiple sequence alignments. The method achieves an f-measure of 24.4% (micro-average) in the BioCreative II interaction pair subtask.

Conclusion:

For gene mention normalization, our approach outperforms strategies that utilize only the matching of genes names against dictionaries, without invoking further knowledge on each gene. Motifs derived from alignments of sentences are successful at identifying protein interactions in text; the approach we present in this report is fully automated and performs similarly to systems that require human intervention at one or more stages.

Availability:

Our methods for gene, protein, and species identification, and extraction of protein-protein are available as part of the BioCreative Meta Services (BCMS), see http://bcms.bioinfo.cnio.es/.

     

A functional selection of viral genetic elements in cultured cells to identify hepatitis C virus RNA translation inhibitors

We developed a functional selection system based on randomized genetic elements (GE) to identify potential regulators of hepatitis C virus (HCV) RNA translation, a process initiated by an internal ribosomal entry site (IRES). A retroviral HCV GE library was introduced into HepG2 cells, stably expressing the Herpes simplex virus thymidine kinase (HSV-TK) under the control of the HCV IRES. Cells that expressed transduced GEs inhibiting HSV-TK were selected via their resistance to ganciclovir. Six major GEs were rescued by PCR on the selected cell DNA and identified as HCV elements. We validated our strategy by further studying the activity of one of them, GE4, encoding the 5′ end of the viral NS5A gene. GE4 inhibited HCV IRES-, but not cap-dependent, reporter translation in human hepatic cell lines and inhibited HCV infection at a post-entry step, decreasing by 85% the number of viral RNA copies. This method can be applied to the identification of gene expression regulators.