Genetic and Chemical Diversity of Edible Mushroom Pleurotus Species

The genus Pleurotus is one of the most widely cultivated and edible mushrooms with various cultivators. Three molecular characteristics were used to evaluate the genetic diversity of 132 tested samples. Phylogenetic analysis showed five clades for tested samples of the genus Pleurotus by the combined ITS and LSU sequences with strong bootstraps and Bayesian posterior probability supports. A total of 94 polymorphic fragments ranging from 10 to 100 bp were observed by using an intersimple sequence repeat (ISSR) marker. The DNA fragment pattern showed that P. ostreatus cultivator (strain P9) was clearly distinguished from wild strain based on their clear banding profiles produced. DNA GC content of the genus Pleurotus varied from 55.6 mol% to 43.3 mol%. Their chemical composition was also determined, including sugar, amino acid, polar lipid, mycolic acid, quinone, and fatty acid, which presented some high homogeneity. Most of the tested samples contained mycolic acid; glucose and arabinose as the main sugars; aspartic acid, arginine, lysine, tyrosine, and alanine as the main amino acids; and C16:0, C18:0, C18:2cis-9,12, anteiso-C14:0, and summed feature 8 as the main fatty acids. In addition, their polar lipid profiles were investigated for the first time, which significantly varied among Pleurotus species. The genus Pleurotus contained menaquinone-6 as the sole respiratory quinone, which showed a significant difference with that of its closely related genera. These results of this study demonstrated that the combined method above could efficiently differentiate each Pleurotus species and thus be considered an efficient tool for surveying the genetic diversity of the genus Pleurotus.

Taxonomic and phylogenic appraisal of a novel species and a new record of Stictidaceae from coffee in Yunnan Province, China

Coffee, an important economic crop, is often threatened by fungal infections. During a survey of coffee fungi in Yunnan Province, China, two saprobic Stictidaceae species were collected. Maximum likelihood (ML) and Bayesian posterior probability of combined LSU, ITS and mtSSU genes supported the placement of our fungal collections within Fitzroyomyces and Ostropomyces with high statistical support. A new species, Fitzroyomyces yunnanensis sp. nov. and a new record, Ostropomyces pruinosellus are introduced. These two species were recorded on coffee wood in sexual and asexual states, respectively. Their taxonomic placements were further supported by detailed morphological and phylogenetic comparisons of allied taxa.

Bayesian Online Change Point Detection in Finance

It is quite common that the structure of a time series changes abruptly. Identifying these change points and describing the model structure in the segments between these change points is an important task in financial time series analysis. Change point detection is the identification of abrupt changes in the generative parameters of sequential data. In application areas such as finance, online rather than offline detection of change points in time series is mostly required, due to their use in predictive tasks, possibly embedded in automatic trading systems. However, the complex structure of the data generation processes makes this a challenging endeavor. This paper is concerned with online change point detection in financial time series using the Bayesian setting. To this end, the Bayesian posterior probability of change at a specific time is proposed and some procedures are presented for selecting the priors and estimation of parameters. Applications in simulated financial time series are given. Finally, conclusions are proposed.

Ecological surveillance of bat coronaviruses in Sarawak, Malaysian Borneo

Objective Coronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at − 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidirectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed. Results CoV-RNA was detected in ten specimens (47.6%, n = 21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses.

Efficacy and safety of nivolumab in Japanese patients with first recurrence of glioblastoma: an open-label, non-comparative study

Background An open-label, non-comparative study assessed the efficacy and safety of nivolumab in Japanese patients with first recurrence glioblastoma. Methods Patients with first recurrence of histologically confirmed World Health Organization Grade IV glioma, after treatment with temozolomide and radiotherapy, received nivolumab 3 mg/kg every 2 weeks until confirmed disease progression (Response Assessment in Neuro-Oncology criteria) or toxicity. Primary endpoint was 1-year overall survival rate assessed by Bayesian approach. The prespecified efficacy criterion was that the Bayesian posterior probability threshold for exceeding the 1-year overall survival of bevacizumab (34.5%) from the Japanese phase 2 study (JO22506) would be 93%. Results Of the 50 enrolled patients, 44 (88.0%) had recurrent malignant glioma (glioblastoma, gliosarcoma), and of these, 26 (59.1%) had at least one measurable lesion at baseline. The Bayesian posterior mean 1-year overall survival (90% Bayesian credible intervals) with nivolumab was 54.4% (42.27–66.21), and the Bayesian posterior probability of exceeding the threshold of the 1-year overall survival rate of bevacizumab (34.5%) was 99.7%. Median (90% confidence interval) overall and progression-free survival was 13.1 (10.4–17.7) and 1.5 (1.4–1.5) months, respectively. One partial response was observed (objective response rate 1/26 evaluable patients [3.8%]). Treatment-related adverse event rates were 14.0% for Grade 3–4 and 2.0% for Grade 5; most adverse events resolved and were manageable. Conclusions The 1-year overall survival with nivolumab monotherapy in Japanese patients with glioblastoma met the prespecified efficacy criterion. The safety profile of nivolumab was consistent with that observed in other tumor types. Clinical Trial Registration JapicCTI-152967.

First Report of Diaporthe cercidis Causing Leaf Blotch of Acer pictum subsp. mono in China

Acer pictum subsp. mono (Maxim.) H. Ohashi is a common deciduous tree species that is widely distributed in Northeast and Northern China, including all provinces of the Yangtze River Basin (Liu et al. 2014). A foliar disease, with an incidence of ~90% (19/21 trees), occurred on A. pictum subsp. mono in a community park, Nanjing, Jiangsu, China in July 2019. On average, ~80% of the leaves per individual tree were infected by this disease. The symptoms initially appeared as brown, necrotic lesions at leaf tips, and half the leaf would become dark brown with time, and finally almost all of leaves were infected. Small pieces of leaf tissue (3 to 5 mm2) cut from the lesion margins were surface-sterilized in 75% ethanol for 30 s and 1% NaClO for 90 s, rinsed with sterile H2O three times, and placed on potato dextrose agar (PDA) at 25°C in the dark. The same fungus was isolated from 92% of the samples. The pure cultures were obtained by single-spore isolation. Three representative isolates (WJF1, WJF3 and WJF4) were obtained, and WJF1 was deposited in China’s Forestry Culture Collection Center (CFCC 54806), and WJF3 and WJF4 were deposited at the Nanjing Forestry University (NFU 083 and NFU 084). The culture on PDA was white, with white vigorous aerial mycelia at the edge. Black pycnidia developed on the alfalfa stems at 25°C under a 14/10 h light/dark cycle for 20 days. Conidiophores were hyaline, branched, septate, straight, 16.4–34.7 × 1.5–3.0 μm (n = 30). Conidiogenous cells were 9.0–24.6 × 1.3–2.3 μm (n = 30). Alpha conidia were 7.0 ± 0.6 × 2.2 ± 0.2 μm (n = 30), fusiform, hyaline, smooth and multi-guttulate. Beta conidia were 25.5 ± 4.3 × 1.3 ± 0.1 μm (n = 30), hyaline, smooth and hamate. Morphological characters of all three isolates matched those of Diaporthe spp. (Gomes et al. 2013). DNA of three isolates were extracted and the internal transcribed spacer region (ITS), partial sequences of elongation factor 1-alpha (EF1-α), calmodulin (CAL), beta-tubulin (β-tub) and histone H3 (HIS) genes were amplified with primers ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R and CAL228F/CAL737R (Carbone et al. 1999), βt2a/βt2b and CYLH3F/H3-1b (Glass and Donaldson, 1995, Crous et al. 2004), respectively. The sequences of WJF1, WJF3 and WJF4 were deposited in GenBank (WJF1: Accession Nos. MW301339 for ITS, MW363932 to MW363935 for EF1-α, β-tub, HIS, and CAL; WJF3: MW453062 and MW561566 to MW561569; WJF4: MW453063 and MW561570 to MW561573). BLAST results showed that the ITS, EF1-α, β-tub, HIS, and CAL sequences of WJF1 were similar with sequences of Phomopsis liquidambari C.Q. Chang, Z.D. Jiang & P.K. Chi JQ676191 (identity = 540/540; 100%), D. huangshanensis H. Zhou & C.L. Hou MN224671 (identity = 291/292; 99%), D. pescicola Dissan., J.Y. Yan, Xing H. Li & K.D. Hyde MK691230 (identity = 438/438; 100%), D. spinosa Y.S. Guo & G.P. Wang MK726170 (identity = 437/438; 99%), D. cercidis C.M. Tian & Qin Yang MK691114 (identity = 452/452; 100%), respectively. BLAST results of WJF3 and WJF4 are list in Table 1. A maximum likelihood and Bayesian posterior probability analyses using IQtree v. 1.6.8 and Mr. Bayes v. 3.2.6 with the concatenated sequences placed WJF1, WJF3 and WJF4 in the clade of D. cercidis. Based on the five-locus phylogeny and morphology, WJF1, WJF3 and WJF4 were identified as D. cercidis. The pathogenicity of three isolates were tested on potted 3-yr-old seedlings of A. pictum subsp. mono, grown in a greenhouse. Healthy leaves were wounded with a sterile needle and then inoculated with 10 μL of conidial suspensions (106 conidia/mL). Control leaves were treated with sterilized H2O. A total of twelve seedlings were used for the tests, 3 seedlings per treatment, and five leaves were inoculated per seedling. Each plant was covered with a plastic bag after inoculation and sterilized H2O was sprayed into the bag twice/day to maintain humidity and kept in a greenhouse at the day/night temperatures at 25 ± 2°C/16 ± 2°C. In 5 days, all the inoculated leaves had lesions similar to those observed in the field. D. cercidis was reisolated from the lesions of the inoculated leaves and was confirmed based on morphological characteristics and ITS sequence analysis. No symptoms were observed on the control leaves, and no fungus was isolated from them. D. cercidis was previously reported on twigs of Cercis chinensis (Yang et al. 2018) and causing pear shoot canker (Guo et al. 2020). This is the first report of D. cercidis causing leaf blotch on A. pictum subsp. mono. Identification of the pathogen is imperative for diagnosing and controlling this potentially high risk disease on A. pictum subsp. mono and also for the future studies.

Yuxiensis granularis gen. et sp. nov., a Novel Quellkörper-Bearing Fungal Taxon Added to Scortechiniaceae and Inclusion of Parasympodiellaceae in Coronophorales Based on Phylogenetic Evidence

An undetermined saprobic fungal taxon from Yunnan (China) is revealed as a new genus in Scortechiniaceae (Coronophorales). The novel taxon, Yuxiensis, is characterized by immersed to erumpent, semi-globose ascomata, which are not surrounded by any tomentum or conspicuous subiculum, a subcylindrical quellkörper in the centrum, clavate asci with long pedicels and allantoid hyaline ascospores with granular contents. Maximum likelihood and Bayesian posterior probability analyses based on LSU, ITS, tef1 and rpb2 sequence data depict a close phylogenetic relationship of the new genus to Pseudocatenomycopsis, hence, confirming its placement in Scortechiniaceae. Parasympodiellaceae, thus far belonging to Parasympodiellales, is transferred to Coronophorales based on multi-gene phylogenetic evidence. Additionally, the incertae sedis monotypic genus Arthrocristula is treated as a synonym of Parasympodiella, with Arthrocristula hyphenata recombined as Parasympodiella hyphenata comb. nov., as the type strain of Arthrocristula hyphenata clusters inside the Parasympodiellaceae clade along with other Parasympodiella taxa.

A new species of Paralaophonte Lang 1948 (Harpacticoida: Laophontidae), with notes on the phylogeny of the genus and its relationships with Loureirophonte Jakobi 1953 using Bayesian inference

Early studies during the 1990’s supported a close relationship between the genera Paralaophonte and Loureirophonte. Subsequent studies carried out during the first decade of the 2000’s suggested the monophyly of the latter and that it could be nested within Paralaophonte, rendering the latter paraphyletic. However, efforts to synonymize these two genera were hampered by the lack of phylogenetic analyses at the species level. Here we describe a new species of Paralaophonte from north-western Mexico, P. ullama sp. nov., and we formally synonymize Loureirophonte with Paralaophonte for which we propose two monophyletic subgenera, Pa. (Paralaophonte) and Pa. (Loureirophonte). The detection of the species most closely related to P. ullama sp. nov. is controversial. Our Bayesian analysis indicates that the new species might be related to Pa. (Pa.) gurneyi, and to Pa. (Pa.) ormieresi and Pa. (Pa.) septemarticulata, with which they form a larger clade supported by a very low Bayesian Posterior Probability value. However, the precise nature of the relationship between the new species and Pa. (Pa.) gurneyi is hampered by the gap in our knowledge of the armature formulae of the swimming legs of the latter, and by the lack of the male of the new species. On the other hand, the new species share several characters with Pa. (Pa.) problematica, Pa. (Pa.) pacificavicinum, Pa. (Pa.) pacificaemulator, and Pa. (Pa.) pacifica, with which it might be related. Our Bayesian analysis of forty-two morphological characters at the species level confirmed earlier suspicions about the relationships between Paralaophonte and Loureirophonte, the latter being nested within the former, and showed the monophyly of the Paralaophonte-Loureirophonte clade with high Bayesian Posterior Probability value, thus confirming the synonymy of these genera. The Paralaophonte-Loureirophonte clade is defined by the synapomorphic dimorphism in the second endopodal segment of the second swimming leg of the male. We did not detect any (aut)apomorphy for Pa. (Paralaophonte). Paralaophonte (Loureirophonte) is defined by the presence of one seta only on the second endopodal segment of the second swimming leg, and the one-segmented endopod of the fourth swimming leg.

A Bayesian method for synthesizing multiple diagnostic outcomes of COVID-19 tests

The novel coronavirus disease 2019 (COVID-19) has spread worldwide and threatened human life. Diagnosis is crucial to contain the spread of SARS-CoV-2 infections and save lives. Diagnostic tests for COVID-19 have varying sensitivity and specificity, and the false-negative results would have substantial consequences to patient treatment and pandemic control. To detect all suspected infections, multiple testing is widely used. However, it may be challenging to build an assertion when the testing results are inconsistent. Considering the situation where there is more than one diagnostic outcome for each subject, we proposed a Bayesian probabilistic framework based on the sensitivity and specificity of each diagnostic method to synthesize a posterior probability of being infected by SARS-CoV-2. We demonstrated that the synthesized posterior outcome outperformed each individual testing outcome. A user-friendly web application was developed to implement our analytic framework with free access via http://www2.ccrb.cuhk.edu.hk/statgene/COVID_19/ . The web application enables the real-time display of the integrated outcome incorporating two or more tests and calculated based on Bayesian posterior probability. A simulation-based assessment demonstrated higher accuracy and precision of the Bayesian probabilistic model compared with a single-test outcome. The online tool developed in this study can assist physicians in making clinical evaluations by effectively integrating multiple COVID-19 tests.

3D Underwater Uncooperative Target Tracking for a Time-Varying Non-Gaussian Environment by Distributed Passive Underwater Buoys

Accurate 3D passive tracking of an underwater uncooperative target is of great significance to make use of the sea resources as well as to ensure the safety of our maritime areas. In this paper, a 3D passive underwater uncooperative target tracking problem for a time-varying non-Gaussian environment is studied. Aiming to overcome the low observability drawback inherent in the passive target tracking problem, a distributed passive underwater buoys observing system is considered and the optimal topology of the distributed measurement system is designed based on the nonlinear system observability analysis theory and the Cramer–Rao lower bound (CRLB) analysis method. Then, considering the unknown underwater environment will lead to time-varying non-Gaussian disturbances for both the target’s dynamics and the measurements, the robust optimal nonlinear estimator, namely the adaptive particle filter (APF), is proposed. Based on the Bayesian posterior probability and Monte Carlo techniques, the proposed algorithm utilizes the real-time optimal estimation technique to calculate the complex noise online and tackle the underwater uncooperative target tracking problem. Finally, the proposed algorithm is tested by simulated data and comprehensive comparisons along with detailed discussions that are made to demonstrate the effectiveness of the proposed APF.