Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl

Experience of Stereotactic Breast Biopsy Using the Vacuum-assisted Core Needle Biopsy Device and the Advanced Breast Biopsy Instrumentation System in Hong Kong Women

Stereotactic breast biopsy of non-palpable lesions using the vacuum-assisted core needle biopsy (CNB) device and the large core excision biopsy system is a reliable biopsy method when compared with open biopsy. Its use in Western countries is well accepted. This study aimed to assess the feasibility and results of using these systems to perform stereotactic biopsy in Asian women. Methods: A total of 114 patients with non-palpable mammographic lesions underwent stereotactic breast biopsy using the vacuum-assisted CNB device and the large core excision biopsy system between November 1999 and December 2002. The indications for biopsy were mammographic abnormalities considered indeterminate or suspicious that were not palpable or visible on ultrasound. The methods adopted for biopsy in Asian women were reviewed and the results including the final pathology, complications, scarring and acceptance by patients were recorded. Results: Stereotactic breast biopsy was performed using the vacuum-assisted CNB device in 107 patients and the large core excision biopsy system in seven patients. Of those who underwent biopsy using the vacuum-assisted CNB device, 15 (14%) had moderate to severe bleeding during the procedure and seven (6.5%) had severe bruising afterwards. Carcinoma was detected in 31 of the 114 patients (27.2%). Conclusion: Although Asian women in general have smaller and denser breasts than their Western counterparts, stereotactic breast biopsy using the vacuum-assisted CNB device and the large core excision biopsy system was feasible with modification of the individual steps during the procedure. Our results are comparable with those published previously and the procedure was well accepted by patients

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field