Sexual and asexual states of some endophytic Phialocephala species of Picea.

Unidentified DNA sequences in isolation-based or culture-free studies of conifer endophytes are a persistent problem that requires a field approach to resolve. An investigation of foliar endophytes of Picea glauca, P. mariana, P. rubens and Pinus strobus in eastern Canada, using a combined field, morphological, cultural and DNA sequencing approach, resulted in the frequent isolation of Phialocephala spp. and the first verified discovery of their mollisia-like sexual states in the field. Phialocephala scopiformis and Ph. piceae were the most frequent species isolated as endophytes from healthy conifer needles. Corresponding Mollisia or mollisioid sexual states for Ph. scopiformis, Ph. piceae and several undescribed species in a clade containing Ph. dimorphospora were collected in the sampling area and characterized by analysis of the nuc internal transcribed spacer rDNA (ITS) and gene for the largest subunit of RNA polymerase II (RPB1) loci. Four novel species and one new combination in a clade containing Ph. dimorphospora, the type of Phialocephala, are presented, accompanied by descriptions of apothecia and previously undocumented synanamorphs. An epitype culture and corresponding reference sequences for Phialocephala dimorphospora are proposed. The resulting ITS barcodes linked with robust taxonomic species concepts are an important resource for future research on forest ecosystems and endophytes.

Towards a unified paradigm for sequence-based identification of fungi.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

The genome sequence of the Fruity Milkcap, Lactarius evosmus (Kühner & Romagn., 1954).

We present a genome assembly from an individual Lactarius evosmus (Fruity Milkcap; Basidiomycota; Agaricomycetes; Russulales; Russulaceae). The genome sequence is 57.2 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 61.51 kilobases in length.

The genome sequence of the chicken of the woods fungus, Laetiporus sulphureus (Bull.) Murrill, 1920.

We present a genome assembly from an individual Laetiporus sulphureus (the chicken of the woods fungus; Basidiomycota; Agaricomycetes; Polyporales; Laetiporaceae). The genome sequence is 37.4 megabases in span. The complete assembly is scaffolded into 14 chromosomal pseudomolecules.

Italian validation of the Neck Dissection Impairment Index questionnaire.

Objective: The Neck Dissection Impairment Index (NDII) questionnaire is a useful and validated Quality of Life (QoL) evaluation instrument in patients undergoing major head-neck surgery. Its English version has been used in several studies in the last years. The aim of this work is to validate the NDII in Italian for both patient assessment and future studies. Materials and methods: Cross-cultural adaptation of the NDII was performed using standard techniques. Items of the original NDII were translated into Italian by a professional translator and two bilingual investigators. A final consensus version was obtained and given to two professional translators to produce a literal translation into English. The two translators and an expert committee synthesised the results of the translations in an English back-translated version that was compared with the original to check that they had the same semantic value. Results: Finally, a total of 42 patients completed both copies of the translated questionnaires. Internal consistency proved to be excellent, with Cronbach's alpha = 0.95. Conclusions: The NDII was successfully translated into Italian and its use was easy for patients. The translation of the NDII can represent a useful tool for individual patient assessment and future research.

Clinical characteristics of renal cell carcinoma in patients under the age of 40.

BACKGROUND: Renal cell carcinoma (RCC) most commonly afflicts older patients while those 40 years old or younger represent an uncommon population. We aim to describe the tumor characteristics and treatment patterns for young kidney cancer patients utilizing the National Cancer Database. METHODS: The National Cancer Database Participant User File for RCC was queried from 2004 to 2016. Demographics and treatment trends were analyzed and compared between a young cohort, those aged 40 and younger vs. a conventional cohort, those older than 40. Pathology analyzed included clear cell, papillary, chromophobe, RCC not otherwise specified, and miscellaneous uncategorized. Subanalysis was performed for patients with localized disease and treatment type. RESULTS: Amongst the 514,879 patients diagnosed with RCC, 4.7% were ≤40 years old. RCC for individuals ≤40 has a higher proportion of female gender, non-Caucasian race, and chromophobe pathology, relative to the conventional cohort. Younger patients more often presented with cT1 disease with decreased rates of metastasis. Risk of 30-day readmission after surgery was similar between cohorts. For patients with cT1-2N0M0 disease, there was a decreasing rate of radical nephrectomy and increasing rate of partial nephrectomy; however, the conventional cohort had an increasing rate of percutaneous ablation while this remained stable in the younger cohort. CONCLUSION: Young RCC patients had a higher proportion of female gender, chromophobe histology, and favorable tumor characteristics. Partial nephrectomy has seen a dramatic increase in application regardless of age while percutaneous ablation increased only in the conventional cohort.

beta-D-Xylosidase from Selenomonas ruminantium: role of glutamate 186 in catalysis revealed by site-directed mutagenesis, alternate substrates, and active-site inhibitor.

beta-D-Xylosidase/alpha-L-arabinofuranosidase from Selenomonas ruminantium is the most active enzyme known for catalyzing hydrolysis of 1,4-beta-D-xylooligosaccharides to D-xylose. Catalysis and inhibitor binding by the GH43 beta-xylosidase are governed by the protonation states of catalytic base (D14, pKa 5.0) and catalytic acid (E186, pKa 7.2). Biphasic inhibition by triethanolamine of E186A preparations reveals minor contamination by wild-type-like enzyme, the contaminant likely originating from translational misreading. Titration of E186A preparations with triethanolamine allows resolution of binding and kinetic parameters of the E186A mutant from those of the contaminant. The E186A mutation abolishes the pKa assigned to E186; mutant enzyme binds only the neutral aminoalcohol pH-independent K(triethanolamine)(i)=19 mM), whereas wild-type enzyme binds only the cationic aminoalcohol pH-independent K(triethanolamine)(i)=0.065 mM. At pH 7.0 and 25 degrees C, relative kinetic parameter, k(4NPX)(cat)=k(4NPA)(cat), for substrates 4-nitrophenyl-beta-D-xylopyranoside (4NPX) and 4-nitrophenyl-alpha-L-arabinofuranoside (4NPA) of E186A is 100-fold that of wild-type enzyme, consistent with the view that, on the enzyme, protonation is of greater importance to the transition state of 4NPA whereas ring deformation dominates the transition state of 4NPX.

Simultaneous orientation and cellular force measurements in adult cardiac myocytes using three-dimensional polymeric microstructures.

A number of techniques have been developed to monitor contractile function in isolated cardiac myocytes. While invaluable observations have been gained from these methodologies in understanding the contractile processes of the heart, they are invariably limited by their in vitro conditions. The present challenge is to develop innovative assays to mimic the in vivo milieu so as to allow a more physiological assessment of cardiac myocyte contractile forces. Here we demonstrate the use of a silicone elastomer, poly(dimethylsiloxane) (PDMS), to simultaneously orient adult cardiac myocytes in primary culture and measure the cellular forces in a three-dimensional substrate. The realignment of adult cardiac myocytes in long-term culture (7 days) was achieved due to directional reassembly of the myofibrils along the parallel polymeric sidewalls. The cellular mechanical forces were recorded in situ by observing the deformation of the micropillars embedded in the substrate. By coupling the cellular mechanical force measurements with on-chip cell orientation, this novel assay is expected to provide a means of a more physiological assessment of single cardiac myocyte contractile function and may facilitate the future development of in vitro assembled functional cardiac tissue.