Species Diversity, Phylogeny, Divergence Time, and Biogeography of the Genus Sanghuangporus (Basidiomycota)

“Sanghuang” is a popular fungus used as a Chinese traditional medicine. In fact, it represents a group of fungi belonging to the genus Sanghuangporus, but little is known about its origin and biogeography. The aim of this study was to characterize the molecular relationships, origin and biogeographical distribution of Sanghuangporus. The multi-locus phylogenetic analyses were used to infer the phylogenetic relationships. In addition, based on Bayesian evolutionary analysis using sequences from the internal transcribed spacer (ITS), nuclear large subunit rDNA (nLSU), translation elongation factor 1-α (EF1-α), and the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), we used a fungus fossil-based approach to gain insight into the divergence time of species in Sanghuangporus. The molecular phylogeny strongly supports the monophyly of Sanghuangporus (MP = 100%, ML = 100%, and BPP = 1.00), and 13 species are recognized in this genus. The Bayesian uncorrelated lognormal relaxed molecular clock using BEAST and reconstructed ancestral areas indicate that the maximum crown age of Sanghuangporus is approximately 30.85 million years. East Asia is the likely ancestral area (38%). Dispersal and differentiation to other continents then occurred during the late Middle Miocene and Pliocene. The ancestor of Sanghuangporus probably originated in palaeotropical Northeast Asia and covered Northeast Asia and East Africa during the Oligocene-Miocene, hosted by plants that expanded via the “Gomphotherium Landbridge.” Six kinds of dispersal routes are proposed, including intercontinental dispersal events of three clades between Northeast Asia and East Africa, between East Asia and North America, and between Northeast Asia and Europe

Molecular phylogeny and taxonomy of the remarkable genus Leptoporus (Polyporales, Basidiomycota) with description of a new species from Southwest China

Leptoporus is a rare and remarkable genus, mainly occurring in coniferous forests in the Northern Hemisphere. Recent phylogenetic studies showed that Leptoporus belongs to Irpicaceae in the phlebioid clade. It is worth noting that most species in the phlebioid clade can cause white-rot decay, except for the Leptoporus species, which can cause a brown-rot decay. In this study, we performed phylogenetic and taxonomic studies of Leptoporus and related genera. Molecular phylogenetic analyses were conducted based on sequences from multiple loci including the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), the largest subunit of RNA polymerase II gene (RPB1), the second largest subunit of RNA polymerase II gene (RPB2), and the translation elongation factor 1-α gene (TEF1). Combined with morphological characteristics, a new species, Leptoporus submollis sp. nov., is discovered and illustrated from Southwest China

Ginseng and Ganoderma lucidum Use after Breast Cancer Diagnosis and Quality of Life: A Report from the Shanghai Breast Cancer Survival Study

Objective: To evaluate associations between quality of life (QOL) and use of ginseng and Ganoderma lucidum (G. lucidum) among breast cancer survivors. Methods: Included in this study were 4,149 women with breast cancer who participated in the Shanghai Breast Cancer Survival Study. Ginseng use was assessed at 6-, 18-, and 36-month post-diagnosis surveys; G. lucidum use was assessed at the 6- and 36-month surveys. QOL was evaluated at the 6- and 36-month surveys. Multiple linear regression models were used to examine associations between ginseng and G.lucidum use and QOL assessed at the 36-month survey, with adjustment for potential confounders and baseline QOL. Results: At 6 months post-diagnosis, 14.2 % of participants reported regular use of ginseng and 58.8 % reported use of G. lucidum. We found no significant associations between ginseng use at 6, 18, and 36 months post-diagnosis and participants’ total QOL score or individual scores for psychological, physical, or social well-being. Post-diagnosis G. lucidum use was positively associated with social well-being (adjusted mean difference: 1.26; 95 % CI: 0.66, 1.86), but was inversely associated with physical well-being (adjusted mean difference: 21.16; 95 % CI: 21.86, 20.47) with a dose-response pattern observed for cumulative number of times of use (P for trend,0.001 for both). Conclusion: We found no evidence that post-diagnosis ginseng use improved the QOL of breast cancer survivors. Post

Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties

Non-synonymous SNPs (nsSNPs), also known as Single Amino acid Polymorphisms (SAPs) account for the majority of human inherited diseases. It is important to distinguish the deleterious SAPs from neutral ones. Most traditional computational methods to classify SAPs are based on sequential or structural features. However, these features cannot fully explain the association between a SAP and the observed pathophysiological phenotype. We believe the better rationale for deleterious SAP prediction should be: If a SAP lies in the protein with important functions and it can change the protein sequence and structure severely, it is more likely related to disease. So we established a method to predict deleterious SAPs based on both protein interaction network and traditional hybrid properties. Each SAP is represented by 472 features that include sequential features, structural features and network features. Maximum Relevance Minimum Redundancy (mRMR) method and Incremental Feature Selection (IFS) were applied to obtain the optimal feature set and the prediction model was Nearest Neighbor Algorithm (NNA). In jackknife cross-validation, 83.27% of SAPs were correctly predicted when the optimized 263 features were used. The optimized predictor with 263 features was also tested in an independent dataset and the accuracy was still 80.00%. In contrast, SIFT, a widely used predictor of deleterious SAPs based on sequential features, has a prediction accuracy of 71.05% on the same dataset. In our study, network features were found to be most important for accurate prediction and can significantly improve the prediction performance. Our results suggest that the protein interaction context could provide important clues to help better illustrate SAP's functional association. This research will facilitate the post genome-wide association studies

Residues 318 and 323 in capsid protein are involved in immune circumvention of the atypical epizootic infection of infectious bursal disease virus

Recently, atypical infectious bursal disease (IBD) caused by a novel variant infectious bursal disease virus (varIBDV) suddenly appeared in immunized chicken flocks in East Asia and led to serious economic losses. The epizootic varIBDV can partly circumvent the immune protection of the existing vaccines against the persistently circulating very virulent IBDV (vvIBDV), but its mechanism is still unknown. This study proved that the neutralizing titer of vvIBDV antiserum to the epizootic varIBDV reduced by 7.0 log2, and the neutralizing titer of the epizootic varIBDV antiserum to vvIBDV reduced by 3.2 log2. In addition, one monoclonal antibody (MAb) 2-5C-6F had good neutralizing activity against vvIBDV but could not well recognize the epizootic varIBDV. The epitope of the MAb 2-5C-6F was identified, and two mutations of G318D and D323Q of capsid protein VP2 occurred in the epizootic varIBDV compared to vvIBDV. Subsequently, the indirect immunofluorescence assay based on serial mutants of VP2 protein verified that residue mutations 318 and 323 influenced the recognition of the epizootic varIBDV and vvIBDV by the MAb 2-5C-6F, which was further confirmed by the serial rescued mutated virus. The following cross-neutralizing assay directed by MAb showed residue mutations 318 and 323 also affected the neutralization of the virus. Further data also showed that the mutations of residues 318 and 323 of VP2 significantly affected the neutralization of the IBDV by antiserum, which might be deeply involved in the immune circumvention of the epizootic varIBDV in the vaccinated flock. This study is significant for the comprehensive prevention and control of the emerging varIBDV

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold