Internal amplification controls have not been employed in fungal PCR hence potential false negative results

Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.Fundação para a Ciência e a Tecnologia (FCT

Ultracold molecules for quantum simulation: rotational coherence in CaF and RbCs

Polar molecules offer a new platform for quantum simulation of systems with long-range interactions, based on the electrostatic interaction between their electric dipole moments. Here, we report the development of coherent quantum state control using microwave fields in $^{40}$Ca$^{19}$F and $^{87}$Rb$^{133}$Cs molecules, a crucial ingredient for many quantum simulation applications. We perform Ramsey interferometry measurements with fringe spacings of $\sim 1~\rm kHz$ and investigate the dephasing time of a superposition of $N=0$ and $N=1$ rotational states when the molecules are confined. For both molecules, we show that a judicious choice of molecular hyperfine states minimises the impact of spatially varying transition-frequency shifts across the trap. For magnetically trapped $^{40}$Ca$^{19}$F we use a magnetically insensitive transition and observe a coherence time of 0.61(3)~ms. For optically trapped $^{87}$Rb$^{133}$Cs we exploit an avoided crossing in the AC Stark shifts and observe a maximum coherence time of 0.75(6)~ms

Social–environmental drivers inform strategic management of coral reefs in the Anthropocene

Without drastic efforts to reduce carbon emissions and mitigate globalized stressors, tropical coral reefs are in jeopardy. Strategic conservation and management requires identification of the environmental and socioeconomic factors driving the persistence of scleractinian coral assemblages—the foundation species of coral reef ecosystems. Here, we compiled coral abundance data from 2,584 Indo-Pacific reefs to evaluate the influence of 21 climate, social and environmental drivers on the ecology of reef coral assemblages. Higher abundances of framework-building corals were typically associated with: weaker thermal disturbances and longer intervals for potential recovery; slower human population growth; reduced access by human settlements and markets; and less nearby agriculture. We therefore propose a framework of three management strategies (protect, recover or transform) by considering: (1) if reefs were above or below a proposed threshold of >10% cover of the coral taxa important for structural complexity and carbonate production; and (2) reef exposure to severe thermal stress during the 2014–2017 global coral bleaching event. Our findings can guide urgent management efforts for coral reefs, by identifying key threats across multiple scales and strategic policy priorities that might sustain a network of functioning reefs in the Indo-Pacific to avoid ecosystem collapse

First report of an entomophthoralean fungus on an arthropod host in Antarctica

A species of the fungus Neozygites (Zygomycetes: Entomophthorales) is recorded from the Antarctic mite Alaskozetes antarcticus (Acarina: Oribatidales) collected off the west coast of the Antarctic peninsula. The features of the fungus were similar to those recorded for Neozygites acaridis, and to other species of the genus recorded from mites in tropical and cool-temperate regions. This is the first report of any entomophthoralean fungus from the Antarctic region

Soil fungal community composition at Mars Oasis, a southern maritime Antarctic site

PCR amplification of ITS1-5.8S-ITS2 regions of rDNA followed by cloning was used to determine the fungi present in soil from three sites at Mars Oasis in the southern maritime Antarctic. The soils sampled were adjacent to, or distant from, a meltwater pond, and had moisture contents of 8 %, 3.6 % and 2.5 %. Sequences bearing close similarity to Chytridiales were commonly recorded in clone libraries from the wettest soil. In contrast, sequences from the driest soil matched closely with ectomycorrhizal members of the Helotiales and less closely with Serendipita-like Sebacinales, Tetracladium and ascomycetous black yeasts, such as Rhinociadiella- and Cladophialophora-like fungi and members of the Verrucariales. Sequences loosely similar to Tetracladium, Arrhenia and Omphalina were frequently recovered from the soil of moderate moisture content. our study corroborates research from the Dry Valleys indicating that soil moisture has an important influence on the composition of Antarctic soil fungal communities. (C) 2008 Elsevier Ltd and The British Mycological Societ

Growth and spread of the woodchip associated fungus Leratiomyces ceres in undisturbed garden soils

A survey was undertaken to determine the extent of Leratiomyces ceres (syn. Stropharia aurantiaca sensu auct.) in soil surrounding apparently isolated occurrences of fungal fruit bodies on woodchip mulch. A molecular detection system with specific primers identified the fungus in the soil below woodchip in which fruit bodies had been noted in the previous year, and also in adjacent soil beyond the mulched area where fruiting had not been observed. The results indicate that L. ceres is widespread in the soil in the survey area, and possible reasons for this finding, and their implication for distribution studies are discussed. (C) 2009 Elsevier Ltd and The British Mycological Society. All rights reserved

A new species of Paecilomyces isolated from the Antarctic springtail Cryptopygus antarcticus

A monophialidic species of Paecilomyces was isolated from the Antarctic springtail Cryptopygus antarcticus in the peninsular Antarctic. The fungus emerged through the carapace of dead arthropods during incubation at 4oC, and produced colonies on agar media at both 4 and 17oC. The fungus was morphologically similar to a number of existing monophialidic species of Paecilomyces, but differed in colony pigmentation, the size of phialides and conidial features. Analysis of the ribosomal DNA internally transcribed spacer (ITS) and 18s subunit sequences showed the fungus to be distinct from other Paecilomyces species, and suggested a close relationship with Cordyceps species. The new species Paecilomyces antarcticus is described