Though tremendous advances have been made in the field of in vitro fertilization (IVF), a portion of patients are still affected by embryo implantation failure issues. One of the most significant factors contributing to implantation failure is a uterine condition called displaced window of implantation (WOI), which refers to an unsynchronized endometrium and embryo transfer time for IVF patients. Previous studies have shown that microRNAs (miRNAs) can be important biomarkers in the reproductive process. In this study, we aim to develop a miRNA-based classifier to identify the WOI for optimal time for embryo transfer. A reproductive-related PanelChip® was used to obtain the miRNA expression profiles from the 200 patients who underwent IVF treatment. In total, 143 out of the 167 miRNAs with amplification signals across 90% of the expression profiles were utilized to build a miRNA-based classifier. The microRNA-based classifier identified the optimal timing for embryo transfer with an accuracy of 93.9%, a sensitivity of 85.3%, and a specificity of 92.4% in the training set, and an accuracy of 88.5% in the testing set, showing high promise in accurately identifying the WOI for the optimal timing for embryo transfer.

The Cancer Genome Atlas (TCGA) and analogous projects have yielded invaluable tumor-associated genomic data. Despite several web-based platforms designed to enhance accessibility, certain analyses require prior bioinformatic expertise. To address this need, we developed Gene ENrichment Identifier (GENI, https://www.shaullab.com/geni), which is designed to promptly compute correlations for genes of interest against the entire transcriptome and rank them against well-established biological gene sets. Additionally, it generates comprehensive tables containing genes of interest and their corresponding correlation coefficients, presented in publication-quality graphs. Furthermore, GENI has the capability to analyze multiple genes simultaneously within a given gene set, elucidating their significance within a specific biological context. Overall, GENI\'s user-friendly interface simplifies the biological interpretation and analysis of cancer patient-associated data, advancing the understanding of cancer biology and accelerating scientific discoveries.

Auricularia has a worldwide distribution and is very important due to its edibility and medicinal properties. Morphological examinations and multi-gene phylogenetic analyses of 277 samples from 35 countries in Asia, Europe, North and South America, Africa, and Oceania were carried out. Phylogenetic analyses were based on ITS, nLSU, rpb1, and rpb2 sequences using methods of Maximum Likelihood and Bayesian Inference analyses. According to the morphological and/or molecular characters, 37 Auricularia species were identified. Ten new species, A. camposii and A. novozealandica in the A. cornea complex, A. australiana, A. conferta, A. lateralis, A. pilosa and A. sinodelicata in the A. delicata complex, A. africana, A. srilankensis, and A. submesenterica in the A. mesenterica complex, are described. The two known species A. pusio and A. tremellosa, respectively belonging to the A. mesenterica complex and the A. delicata complex, are redefined, while A. angiospermarum, belonging to the A. auricula-judae complex, is validated. The morphological characters, photos, ecological traits, hosts and geographical distributions of those 37 species are outlined and discussed. Morphological differences and phylogenetic relations of species in five Auricularia morphological complexes (the A. auricula-judae, the A. cornea, the A. delicata, the A. fuscosuccinea and the A. mesenterica complexes) are elaborated. Synopsis data on comparisons of species in the five complexes are provided. An identification key for the accepted 37 species is proposed.

Many Isaria-like species have recently been moved into more appropriate genera. However, more robust molecular phylogenetic analyses are still required for Isaria-like fungi to ensure accurate taxonomic identification. We analyzed these Isaria-like strains using multi-gene phylogenetics. Cryptic diversity was discovered in several Isaria farinosa strains, and two new species, Samsoniella pseudogunnii and S. pupicola, are proposed. Our results reveal that more attention needs to be paid to cryptic intraspecific diversity across different isolates and genotypes of the Isaria-like species, some of which will need to be transferred to Samsoniella. Interestingly, S. hepiali, with a very broad host distribution, has been widely used as a medicinal and edible cordycipitoid fungus.

The order Pleosporales comprises a miscellaneous group of fungi and is considered to be the largest order of the class Dothideomycetes. The circumscription of Pleosporales has undergone numerous changes in recent years due to the addition of large numbers of families reported from various habitats and with a large amount of morphological variation. Many asexual genera have been reported in Pleosporales and can be either hyphomycetes or coelomycetes. Phoma-like taxa are common and have been shown to be polyphyletic within the order and allied with several sexual genera. During the exploration of biodiversity of pleosporalean fungi in Taiwan, a fungal strain was isolated from mycelium growing on the fruiting body of an Ophiocordyceps species. Fruiting structures that developed on PDA were morphologically similar to Phoma and its relatives in having pycnidial conidiomata with hyaline conidia. The fungus is characterised by holoblastic, cylindrical, aseptate conidiogenous cells and cylindrical, hyaline, aseptate, guttulated, thin-walled conidia. Phylogenetic analysis based on six genes, ITS, LSU, rpb2, SSU, tef1 and tub2, produced a phylogenetic tree with the newly generated sequences grouping in a distinct clade separate from all of the known families. Therefore, a new pleosporalean family Tzeananiaceae is established to accommodate the monotypic genus Tzeanania and the species T.taiwanensis in Pleosporales, Dothideomycetes. The Ophiocordyceps species was identified as O.macroacicularis and this is a new record in Taiwan.

Anthracnose caused by Colletotrichum species is a serious disease of more than 30 plant genera. Several Colletotrichum species have been reported to infect chili in different countries. Although China is the largest chili-producing country, little is known about the species that have been infecting chili locally. Therefore, we collected samples of diseased chili from 29 provinces of China, from which 1285 strains were isolated. The morphological characters of all strains were observed and compared, and multi-locus phylogenetic analyses (ITS, ACT, CAL, CHS-1, GAPDH, TUB2, and HIS3) were performed on selected representative strains. Fifteen Colletotrichum species were identified, with C. fioriniae, C. fructicola, C. gloeosporioides, C. scovillei, and C. truncatum being prevalent. Three new species, C. conoides, C. grossum, and C. liaoningense, were recognised and described in this paper. Colletotrichum aenigma, C. cliviae, C. endophytica, C. hymenocallidis, C. incanum, C. karstii, and C. viniferum were reported for the first time from chili. Pathogenicity of all species isolated from chili was confirmed, except for C. endophytica. The current study improves the understanding of species causing anthracnose on chili and provides useful information for the effective control of the disease in China.

During a study of saprobic fungi from Bagno di Cetica Province, Italy, we collected a pleosporoid ascomycete on stems of Cytisus sp. In morphology, our collection is similar to Cucurbitaria species, but molecular analysis of SSU, LSU and ITS genes reveals it can be referred to Camarosporium. In this study we compare all other Cucurbitaria species from Cytisus sp. and based on both morphology and molecular data, we introduce our collection as a new species in Camarosporium viz. C. arezzoensis.

Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.