FYPO: the fission yeast phenotype ontology.

MOTIVATION: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. RESULTS: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. AVAILABILITY: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/)

Toxoplasma gondii Lysine Acetyltransferase GCN5-A Functions in the Cellular Response to Alkaline Stress and Expression of Cyst Genes

Parasitic protozoa such as the apicomplexan Toxoplasma gondii progress through their life cycle in response to stimuli in the environment or host organism. Very little is known about how proliferating tachyzoites reprogram their expressed genome in response to stresses that prompt development into latent bradyzoite cysts. We have previously linked histone acetylation with the expression of stage-specific genes, but the factors involved remain to be determined. We sought to determine if GCN5, which operates as a transcriptional co-activator by virtue of its histone acetyltransferase (HAT) activity, contributed to stress-induced changes in gene expression in Toxoplasma. In contrast to other lower eukaryotes, Toxoplasma has duplicated its GCN5 lysine acetyltransferase (KAT). Disruption of the gene encoding for TgGCN5-A in type I RH strain did not produce a severe phenotype under normal culture conditions, but here we show that the TgGCN5-A null mutant is deficient in responding to alkaline pH, a common stress used to induce bradyzoite differentiation in vitro. We performed a genome-wide analysis of the Toxoplasma transcriptional response to alkaline pH stress, finding that parasites deleted for TgGCN5-A fail to up-regulate 74% of the stress response genes that are induced 2-fold or more in wild-type. Using chromatin immunoprecipitation, we verify an enrichment of TgGCN5-A at the upstream regions of genes activated by alkaline pH exposure. The TgGCN5-A knockout is also incapable of up-regulating key marker genes expressed during development of the latent cyst form, and is impaired in its ability to recover from alkaline stress. Complementation of the TgGCN5-A knockout restores the expression of these stress-induced genes and reverses the stress recovery defect. These results establish TgGCN5-A as a major contributor to the alkaline stress response in RH strain Toxoplasma

Linking Yeast Gcn5p Catalytic Function and Gene Regulation Using a Quantitative, Graded Dominant Mutant Approach

Establishing causative links between protein functional domains and global gene regulation is critical for advancements in genetics, biotechnology, disease treatment, and systems biology. This task is challenging for multifunctional proteins when relying on traditional approaches such as gene deletions since they remove all domains simultaneously. Here, we describe a novel approach to extract quantitative, causative links by modulating the expression of a dominant mutant allele to create a function-specific competitive inhibition. Using the yeast histone acetyltransferase Gcn5p as a case study, we demonstrate the utility of this approach and (1) find evidence that Gcn5p is more involved in cell-wide gene repression, instead of the accepted gene activation associated with HATs, (2) identify previously unknown gene targets and interactions for Gcn5p-based acetylation, (3) quantify the strength of some Gcn5p-DNA associations, (4) demonstrate that this approach can be used to correctly identify canonical chromatin modifications, (5) establish the role of acetyltransferase activity on synthetic lethal interactions, and (6) identify new functional classes of genes regulated by Gcn5p acetyltransferase activity—all six of these major conclusions were unattainable by using standard gene knockout studies alone. We recommend that a graded dominant mutant approach be utilized in conjunction with a traditional knockout to study multifunctional proteins and generate higher-resolution data that more accurately probes protein domain function and influence

Site-specific seeding using multi-sensor and data fusion techniques : a review

Site-specific seeding (SSS) is a precision agricultural (PA) practice aiming at optimizing seeding rate and depth, depending on the within field variability in soil fertility and yield potential. Unlike other site-specific applications, SSS was not adopted sufficiently by farmers due to some technological and practical challenges that need to be overcome. Success of site-specific application strongly depends on the accuracy of measurement of key parameters in the system, modeling and delineation of management zone maps, accurate recommendations and finally the right choice of variable rate (VR) technologies and their integrations. The current study reviews available principles and technologies for both map-based and senor-based SSS. It covers the background of crop and soil quality indicators (SQI), various soil and crop sensor technologies and recommendation approaches of map-based and sensor-based SSS applications. It also discusses the potential of socio-economic benefits of SSS against uniform seeding. The current review proposes prospective future technology synthesis for implementation of SSS in practice. A multi-sensor data fusion system, integrating proper sensor combinations, is suggested as an essential approach for putting SSS into practice

Iron regulates hexose transporters in Schizosaccharomyces pombe

This study focuses on the effect of iron on hexose transporters which perform glucose uptake. For this aim, we investigated the role of iron in glucose utilization and expression of hexose transporters in Schizosaccharomyces pombe. We applied different iron concentrations (1, 2, 5, 10mM) to the cells grown up to mid-logarithmic phase. According to analysis of cell viability and morphology, we determined 2mM and 5mM as non-toxic and toxic doses, respectively. Besides, glucose consumption efficiency increased (1.5-fold) in the cells which were exposed to these iron concentrations. qRT-PCR analysis of hexose transporter genes showed that the expression of ght2 and ght8 genes were downregulated under both non-toxic and toxic iron conditions, but that of ght5 gene was significantly decreased only by toxic iron dose. In conclusion, it was suggested for the first time in this study that the Ght5 protein, as being high affinity hexose transporter, might play a role in sensing and signaling of iron stress