A relational database for the FGSC

In our continuing effort to make more information about the materials at the FGSC available, we have developed a new database for the FGSC. This database has information about strains, lesions and a limited amount of information about cloned genes. There are also links to Genbank listings for many genes that are represented in the collection. The new database also manages the FGSC customer list and allows us to track orders

ScotPID - a model of collaboration

ScotPID is a national personal development initiative in Scotland, with thirteen higher education institutions taking part in the development of case studies which enhance personal development planning for students. As a model of collaboration, ScotPID involves all stakeholders: each core project group is composed of an academic, IT support manager, careers service adviser and undergraduate student, with support from QAA Scotland. The case study is developed by the contribution of all of the members of the team. The strength of the ScotPID collaboration is the varied background of the team members. However, collaboration between the ScotPID teams should also be encouraged, to strengthen the inter-institutional approach further

Long term viability of Neurospora crassa at the FGSC

Lyophilized samples of Neurospora crassa were tested following storage for many years. The oldest viable stock was preserved in 1946. Some samples that were preserved more recently were not viable. The characteristics that predispose a sample to viability remain unknown

REPUTATION AND STATE COMMODITY PROMOTION: THE CASE OF WASHINGTON APPLES

A dynamic multiple-indicator multiple-cause (MIMIC) framework was used to estimate the latent variable reputation with price premiums for Washington apples and attributes that covered the period July 1996 to November 1999. A maximum likelihood two-stage approach was employed. For comparison purposes, a hedonic regression was also estimated. Results from the first stage of the estimation procedure in the MIMIC reputation model suggest that price premiums are good indicators of reputation. The indicator coefficients, also called factor loadings, imply that the estimated reputation variable is common to the five indicators chosen and that the measurement of reputation is not likely to be obscured by a wide diversity in the indicators. The common factor issue suggests a possible existence of collective 'Washington' reputation. Results from the second stage of the MIMIC reputation model are compared to those from the Hedonic proxy model. In general, results from the MIMIC reputation model make more intuitive sense and are in line with the theoretical literature on reputation than the results from the Hedonic proxy model. Reputation is found to be stationary and that shocks to Washington's reputation are temporary. In the MIMIC reputation model, all the estimated coefficients on the explanatory cause variables had positive signs, except the Red Delicious variety variable. The magnitude of the coefficient on the logo term is large, suggesting a strong impact on reputation. The estimated constant term in the MIMIC reputation model is negative and relatively large, which suggests that reputation is declining. The concerns of declining perceived "eating" quality in Washington varieties thus appear to be real. It appears then that the apple industry is currently benefiting from past/accrued reputation. The current standards in the apple industry give room for some Washington producers to free ride on the collective reputation. Hence, there may be some justification for minimum quality standards. For efficient public policy purposes, our findings suggest that policymakers and the apple industry as a whole should consider reputation in their cost-benefit analysis for purposes of resource allocation.Marketing,

An integrated perspective on RNA aptamer ligand-recognition models : clearing muddy waters

Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor’s dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state. In this article, we question whether a polarized division of RNA binding mechanisms truly meets the conceptual needs of the field. We will review the history behind this classification of RNA-ligand interactions, and the way induced fit in particular has been rehabilitated by single-molecule studies of RNA aptamers. We will highlight several recent results from single-molecule experimental studies of riboswitches that reveal gaps or even contradictions between common definitions of the two terms, and we will conclude by proposing a more robust framework that considers the range of RNA behaviors unveiled in recent years as a reality to be described, rather than an increasingly unwieldy set of exceptions to the traditional models.PostprintPeer reviewe

Evidence for dominant suppression of repeat-induced point mutation (RIP) in crosses with the wild-isolated Neurospora crassa strains Sugartown and Adiopodoume-7

A convenient assay to score repeat-induced point mutation (RIP) in Neurospora employs the erg-3 locus as a mutagenesis target. Using this assay we screened 132 wild-isolated Neurospora crassa strains for ability to dominantly suppress RIP. RIP was exceptionally inefficient in crosses with the wild isolates Sugartown (P0854) and Adiopodoume-7 (P4305), thereby suggesting the presence of dominant RIP suppressors in these strains. In other experiments, we found no evidence for dominant RIP suppression by the Spore killer haplotypes Sk-2 and Sk-3

The fungal cell death regulator czt-1 is allelic to acr-3

Fungal infections have far-reaching implications that range from severe human disease to a panoply of disruptive agricultural and ecological effects, making it imperative to identify and understand the molecular pathways governing the response to antifungal compounds. In this context, CZT-1 (cell death-activated zinc cluster transcription factor) functions as a master regulator of cell death and drug susceptibility in Neurospora crassa. Here we provide evidence indicating that czt-1 is allelic to acr-3, a previously described locus that we now found to harbor a point mutation in its coding sequence. This nonsynonymous amino acid substitution in a low complexity region of CZT-1/ACR-3 caused a robust gain-of-function that led to reduced sensitivity to acriflavine and staurosporine, and increased expression of the drug efflux pump abc-3. Thus, accumulating evidence shows that CZT-1 is an important broad regulator of the cellular response to various antifungal compounds that appear to share common molecular targets.A.P.G. was recipient of a fellowship from Fundação Calouste Gulbenkian (104210) and a short-term fellowship from EMBO (329-2012). This work was supported by FCT Portugal (PEst-C/SAU/LA0002/2013 and FCOMP-01-0124-FEDER-037277 to A.V.), the European POCI program of QCAIII co-participated by FEDER (NORTE-07-0124-FEDER-000003) and the National Science Foundation (DBI 0742713 to the Fungal Genetics Stock Center – K.M.)

An evaluation of the status of living collections for plant, environmental, and microbial research

Citation: McCluskey, K., Parsons, J. P., Quach, K., & Duke, C. S. (2017). An evaluation of the status of living collections for plant, environmental, and microbial research. Journal of Biosciences, 42(2), 321-331. https://doi.org/10.1007/s12038-017-9685-6While living collections are critical for biological research, support for these foundational infrastructure elements is inconsistent, which makes quality control, regulatory compliance, and reproducibility difficult. In recent years, the Ecological Society of America has hosted several National Science Foundation–sponsored workshops to explore and enhance the sustainability of biological research infrastructure. At the same time, the United States Culture Collection Network has brought together managers of living collections to foster collaboration and information exchange within a specific living collections community. To assess the sustainability of collections, a survey was distributed to collection scientists whose responses provide a benchmark for evaluating the resiliency of these collections. Among the key observations were that plant collections have larger staffing requirements and that living microbe collections were the most vulnerable to retirements or other disruptions. Many higher plant and vertebrate collections have institutional support and several have endowments. Other collections depend on competitive grant support in an era of intense competition for these resources. Opportunities for synergy among living collections depend upon complementing the natural strong engagement with the research communities that depend on these collections with enhanced information sharing, communication, and collective action to keep them sustainable for the future. External efforts by funding agencies and publishers could reinforce the advantages of having professional management of research resources across every discipline. © 2017 Indian Academy of Science

Pisatin demethylation by fungal pathogens and nonpathogens of pea: Association with pisatin tolerance and virulence

Previous studies have indicated that detoxification of their hosts’ phytoalexins is a tolerance mechanism for some true fungi, but not the fungus-like Oomycota, and may be involved in determining the virulence of a pathogen. In the present study, the associations between demethylation of the pea phytoalexin pisatin, tolerance to pisatin, and viru­lence on pea were examined for 50 fungal isolates which represent 17 species of pathogens and nonpathogens of pea. All isolates of Pythium coloratum and P. irregulare failed to metabolize and were sensitive to pisatin, consistent with previous observations that members of the Oomycota generally lack the ability to metabolize and are sensitive to their hosts’ phytoalexins. Among true fungi tested, the ability to demethylate pisatin was common, regardless of whether the particular isolate was pathogenic on pea or not. However, when the rate of pisatin demethylation was compared to virulence, all but one of the moderate to highly virulent isolates rapidly demethylated pisatin. In addition, the more rapidly demethylating isolates were generally more tolerant of pisatin. These results suggest that a specialized en­zyme system for quickly detoxifying pisatin might be present in most pea pathogens. In previous studies a specific cy­tochrome P450 enzyme for demethylating pisatin was identified in the pea pathogen Nectria haematococca mating pop­ulation VI, and genes (PDA genes) encoding that enzyme have been cloned from this fungus. When DNA specific for these genes was used to probe genomic DNA from other fungi that demethylate pisatin, significant hybridization was detected with only one fungus, the pea pathogen Fusarium oxysporum f. sp. pisi. If the other pea pathogens possess a specific cytochrome P450 system for detoxification of pisatin, the genes encoding these enzymes apparently share lim­ited nucleotide similarity with N. haematococca PDA genes