Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution

Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.

PacBio high-throughput multi-locus sequencing reveals high genetic diversity in mushroom-forming fungi

Multi-locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi-locus pooled sequencing method using PacBio long-read high-throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein-coding genes rpb1, rpb2 and tef1. Within-sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants of rpb2 and tef1 from corticioid Cantharellales. Our method is a cost-effective approach for generating accurate multi-locus sequence data coupled with recovery of alleles from polymorphic samples and multi-organism specimens. These results have important implications for understanding intra-individual genomic variation among genetic loci commonly used in species delimitation of fungi.

Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi

Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species' breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.

The usefulness of non-invasive co-oximetry haemoglobin measurement for screening pre-operative anaemia

Pre-operative anaemia (haemoglobin < 13.0 g.dl^-1 ) is a modifiable peri-operative risk-factor. This is screened for using formal laboratory testing. A non-invasive finger-probe sensor that can accurately measure haemoglobin is a possible alternative. This study considers the accuracy of non-invasive haemoglobin measurement using the Rad-67™ Rainbow (Masimo Corp., Irvine, CA, USA) compared with formal laboratory testing and its usefulness in detecting pre-operative anaemia. A total of 392 patients had measurements taken for non-invasive haemoglobin and perfusion index values using the Rad-67 Rainbow, alongside further peri-operative parameters and a formal laboratory haemoglobin test. Bland-Altman and sensitivity analysis showed that the limits of agreement between non-invasive and formal laboratory haemoglobin testing were between -1.95 g.dl^-1 and 2.23 g.dl^-1 (p < 0.001). The overall performance of non-invasive haemoglobin measurement was better in men than women (ROC 91.1% vs. 78.2%) and less biased in men, mean -0.08 (SD 1.09, 95%Cl -0.23-0.07) compared with women (mean 0.38 (SD 0.99, 95%CI 0.24-0.52)). Pre-operative anaemia was more prevalent in women than men (50.3% vs. 14.4%). The sensitivity of non-invasive anaemia detection (haemoglobin < 13 g.dl^-1 ) was 66% for women and 52% for men. A non-invasive haemoglobin value of 14.0 g.dl^-1 had an overall 91% sensitivity for detecting pre-operative anaemia (82% in men and 93% in women). The Rad-67 Rainbow is inadequate for the estimation of formal laboratory haemoglobin and lacks sensitivity for detecting pre-operative anaemia, especially in women. Further advancement in technology and accuracy is needed before it can be recommended as a routine pre-operative screening test.

Rhinovirus respiratory tract infection in hospitalized adult patients is associated with TH2 response irrespective of asthma

OBJECTIVES

We assessed the immunological response of hospitalized adult patients with rhinovirus infection, including critically-ill patients.

METHODS

The differential white blood cell (WBC) count and the levels of 29 plasma cytokines/chemokines were compared between 50 adult hospitalized patients with rhinovirus infection and 100 age-matched controls with influenza virus infection.

RESULTS

The demographics and comorbidities were similar between rhinovirus and influenza patients, but severe disease was more common for the rhinovirus cohort. Rhinovirus patients had significantly higher WBC counts than influenza patients, especially for eosinophil (P = 3.1 × 10^-8). The level of the T_H2 cytokine IL-5 was significantly higher among rhinovirus patients, while the levels of 9 other cytokines/chemokines were significantly lower among rhinovirus patients. The levels of CXCL-10 (IP-10), CCL-2 (MCP-1), IFN-α2, IFN-γ, IL-10, and IL-15 remained significantly lower among rhinovirus patients after correction for multiple comparisons. Notably, CXCL-10 had the highest area under the receiver operating characteristic curve (AUC) in differentiating rhinovirus from influenza patients (AUC, 0.918). In the patient subgroup without asthma, the difference in the WBC count and cytokine/chemokine levels between rhinovirus and influenza patients remained statistically significant.

CONCLUSIONS

Rhinovirus infection was characterized by a prominent T_H2 response, even in patients without asthma. CXCL-10 (IP-10) is a potential biomarker in differentiating rhinovirus from influenza infection.

Lipid metabolites as potential diagnostic and prognostic biomarkers for acute community acquired pneumonia

Early diagnosis of acute community-acquired pneumonia (CAP) is important in patient triage and treatment decisions. To identify biomarkers that distinguish patients with CAP from non-CAP controls, we conducted an untargeted global metabolome analysis for plasma samples from 142 patients with CAP (CAP cases) and 97 without CAP (non-CAP controls). Thirteen lipid metabolites could discriminate between CAP cases and non-CAP controls with area-under-the-receiver-operating-characteristic curve of >0.8 (P ≤ 10⁻⁹). The levels of glycosphingolipids, sphingomyelins, lysophosphatidylcholines and L-palmitoylcarnitine were higher, while the levels of lysophosphatidylethanolamines were lower in the CAP cases than those in non-CAP controls. All 13 metabolites could distinguish CAP cases from the non-infection, extrapulmonary infection and non-CAP respiratory tract infection subgroups. The levels of trihexosylceramide (d18:1/16:0) were higher, while the levels of lysophosphatidylethanolamines were lower, in the fatal than those of non-fatal CAP cases. Our findings suggest that lipid metabolites are potential diagnostic and prognostic biomarkers for CAP.

•

Thirteen lipid metabolites could discriminate CAP cases from non-CAP controls.

•

The levels of 2 lipid metabolites differ between fatal and non-fatal CAP cases.

•

Lipid metabolites are potential diagnostic and prognostic biomarkers for CAP.

Two rare ophiocordycipitaceous fungi newly recorded in Taiwan

BACKGROUND

Ophiocordycipitaceae is a highly diverse fungal family parasitizing a wide range of arthropods and hypogeous fungi. We collected two ophiocordycipitaceous species previously unknown in Taiwan: one emerged from hypogeous fruiting bodies of an Elaphomyces fungus and the other was associated with dragonflies.

RESULTS

Based on gross morphology, microscopic features, ITS sequences, and hosts, the two ophiocordycipitaceous fungi were identified as Tolypocladium japonicum and Ophiocordyceps odonatae. We isolated axenic cultures of these two fungi, and their anamorphs were obtained. The simplicillium-like anamorph of T. japonicum is described herein for the first time. The anamorph of O. odonatae produce conidia holoblastically in sympodial sequence and is assignable to Hymenostilbe. A dichotomous key to the species of Ophiocordycipitaceae reported in Taiwan is provided.

CONCLUSION

A thorough literature study indicates that the two fungi reported herein have rarely been collected. Our identifications of T. japonicum and O. odonatae agree well with descriptions in the literature and are highly supported by DNA sequence analysis.

Lipid mediators of inflammation as novel plasma biomarkers to identify patients with bacteremia

OBJECTIVES

Rapid diagnostic tests for bacteremia are important for early treatment to improve clinical outcome. We sought to identify plasma biomarkers that can identify patients with bacteremia using an untargeted global metabolomic analysis.

METHODS

Plasma metabolomic profiles were analyzed for 145 adult patients with (cases) and without (controls) bacteremia using ultra-high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). All metabolites were compared between cases and controls using a 2-tier filtering approach, and each metabolite underwent receiver operating characteristic (ROC) curve analysis. Individual metabolites that distinguish between cases and controls were characterized. Subgroup analysis was performed to identify metabolites with prognostic significance.

RESULTS

After 2-tier filtering, 128 molecular features were identified to be potential biomarkers that could distinguish cases from controls. Five metabolites had an area under the ROC curve (AUC) of >0.8 in ROC curve analysis, including a sphingolipid, an acylcarnitine, a fatty acid ester, and 2 glycerophosphocholines. These metabolites could distinguish cases from controls in the unsupervised hierarchical clustering analysis. Subgroup analysis of bacteremic patients showed that the level of trans-2,3,4-trimethoxycinnamate was lower in fatal than non-fatal cases.

CONCLUSIONS

Plasma lipid mediators of inflammation can distinguish bacteremia cases from non-bacteremia controls. These biomarkers may be used as targets for rapid test in clinical practice.

[Citation analysis of Acta Pharmacologica Sinica 1984-1989]

Citation analysis was made bibliometrically on the collection and dispersion of the references in Acta Pharmacologica Sinica 1984-1989. Core periodicals were sorted out: 31 in foreign languages and 6 in Chinese. Suggestions are proposed to the information services.

Regulation of cellular interferon production: enhancement by antimetabolites

Cycloheximide, at a protein-inhibitory concentration, when given to rabbit kidney cell cultures that had been exposed either to UV-irradiated Newcastle Disease virus or to a complex of polyinosinic and polycytidylic acids (poly I.poly C), enhanced the production of interferon. The enhancement was greater if, in addition to cycloheximide, the cells were also treated with actinomycin D. On the basis of these findings, a mechanism, consisting primarily of the production of a control protein which normally checks interferon production, is postulated for interferons stimulated by these two substances.

Characterization of virus- and endotoxin-induced interferons obtained from the serum and urine of rabbits

Interferons induced in the rabbit by Newcastle disease virus or by endotoxin have been further characterized as to their physicochemical stability and molecular size by Sephadex G-100 gel filtration. Endotoxin-induced interferon obtained from serum was more labile than virus-induced interferon. Both endotoxin and virus induced interferons obtained from serum contained two peaks: a minor high molecular weight (>100,000) peak and a major lower molecular weight peak. The molecular weight of the major peak induced by endotoxin was 54,000, and that induced by Newcastle disease virus was 46,000. The gel filtration pattern of interferon recovered from the urine of animals inoculated with virus reflected faithfully the pattern found in serum except that there was proportionately less of the high molecular weight peak. However, the urine interferon from endotoxin-inoculated animals contained only one broad peak with a molecular weight of 35,000. This was not the peak fraction present in the serum of such animals. It is postulated that this may represent the basic unit of endotoxin-induced interferon, and that the serum components are either polymers or conjugates of this basic unit.