Application of direct PCR in rapid rDNA ITS haplotype determination of the hyperparasitic fungus Sphaeropsis visci (Botryosphaeriaceae)

Many foliar endophytic fungi of Quercus gambelii are capable of psychrotolerant saprotrophic growth

Many endophytic fungi have the potential to function as saprotrophs when living host tissues senesce and enter the litter pool. The consumption of plant litter by fungi obviously requires moisture but, in the arid, western USA, the native range of Quercus gambelii Nutt., most of the precipitation occurs during the coldest months of the year. Therefore, we hypothesized that the endophytic fungi of Q. gambelii have the potential to function as psychrotolerant saprotrophs, which we defined in this study as an organism capable of significant growth on leaf litter at 5°C. We further hypothesized that a tradeoff exists between growth of endophytic fungi at 5°C and at 17°C such that fungal isolates are either cold- or warm-temperature specialists. Consistent with our first hypothesis, we found that 36 of our 40 isolates consumed leaf litter at 5°C, but there was a surprisingly high degree of variability among isolates in this ability, even among isolates of a given species. Contrary to our second hypothesis, there was no tradeoff between saprotrophic growth at 5°C and saprotrophic growth at 17°C. Indeed, the isolates that grew poorly as saprotrophs at 5°C were generally those that grew poorly as saprotrophs at 17°C. By virtue of being endophytic, endophytic fungi have priority in litter over decomposer fungi that colonize plant tissues only after they enter the litter pool. Moreover, by virtue of being psychrotolerant, some endophytic fungi may function as saprotrophs during the cold months of the year when moisture is temporarily available. Therefore, we suggest that some endophytic fungi of Q. gambelii could play significant ecosystem roles in litter decomposition and nutrient cycling.

Multiplex polymerase chain reaction assays for the detection of the zearalenone chemotype of Fusarium species in white and brown rice

Early detection of the zearalenone (ZEA) chemotype of Fusarium species could be a precautionary measure for preventing ZEA contamination in rice. In this study, a multiplex polymerase chain reaction (mPCR) assay for detecting ZEA-producing fungi in rice was established using a set of four primers targeting the ZEA biosynthesis genes PKS3, PKS13, ZEB1, and ZEB2. Two mPCR approaches were used: one that amplified the DNA obtained from Fusarium isolates (conventional method) and another that directly amplified the target DNA from rice samples without time-consuming DNA isolation (direct method). The two mPCR methods showed high sensitivity in detecting ZEA-producing species, with a detection limit of 1.25 pg/μL of genomic DNA and 10² and 10³ spores/g of white and brown rice, respectively. Both methods were specific for ZEA-producing species and gave four band patterns. The application of the two mPCR methods to 51 Fusarium isolates and 41 rice samples revealed that 31% (16 of 51) and 24% (10 of 41) of the samples were contaminated with ZEA-producing species, respectively. The mPCR results were further evaluated using high-performance liquid chromatography; in general, the two methods yielded similar results. These findings indicate that both mPCR methods are suitable for the detection of ZEA-producing Fusarium species in white and brown rice; however, the direct method yielded more rapid results.

Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag

With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant.