The genus includes more than 200 epithets, but only the type species, and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 "" species are reassessed to clarify their identity and phylogenetic position. DNA sequences of four regions, ITS, LSU, and , are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, and are transferred to . The generic status of and is confirmed in . var. and . var. are treated synonyms of . is transferred to as , and to as . is reduced to synonymy with . , , , and are tentatively kept in until further phylogenetic analysis is carried out on verified specimens. The ordinal status of , , and cannot be determined, and tentatively accommodate these species in . The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.
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http://dx.doi.org/10.3389/fmicb.2021.737541 | DOI Listing |
ACS Appl Mater Interfaces
January 2025
Department of Chemistry, Yeungnam University, 280 Daehak-ro, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea.
Recent studies have reported that the cause and progression of many diseases are closely related to complex and diverse gene regulation involving multiple microRNAs (miRNAs). However, most existing methods for miRNA detection typically deal with one sample at a time, which limits the achievement of high diagnostic accuracy for diseases associated with multiple gene dysregulations. Herein, we develop a liquid flow-based microfluidic optical assay for the simple and reliable detection of two different target miRNAs simultaneously at room temperature without any enzymatic reactions.
View Article and Find Full Text PDFBiophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFJ Mol Diagn
January 2025
Labcorp Oncology (PGDx), Baltimore, MD 21224.
To help guide treatment decisions and clinical trial matching, tumor genomic profiling is an essential precision oncology tool. Liquid biopsy, a complementary approach to tissue testing, can assess tumor-specific DNA alterations circulating in the blood. Labcorp Plasma Complete is a next-generation sequencing, cell-free DNA comprehensive genomic profiling test that identifies clinically relevant somatic variants across 521 genes in advanced and metastatic solid cancers.
View Article and Find Full Text PDFSTAR Protoc
January 2025
Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. Electronic address:
Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of cell states but often lacks insights into tissue clonal structures. Here, we present a protocol to probe cell states and clonal information simultaneously by enriching mitochondrial DNA (mtDNA) variants from 3'-barcoded full-length cDNA. We describe steps for input library preparation, mtDNA enrichment, PCR product cleanup, and paired-end sequencing.
View Article and Find Full Text PDFOMICS
January 2025
Department of Biotechnology, Brainware University, Barasat, West Bengal, India.
Next-generation cancer phenomics by deployment of multiple molecular endophenotypes coupled with high-throughput analyses of gene expression offer veritable opportunities for triangulation of discovery findings in non-small cell lung cancer (NSCLC) research. This study reports differentially expressed genes in NSCLC using publicly available datasets (GSE18842 and GSE229253), uncovering 130 common genes that may potentially represent crucial molecular signatures of NSCLC. Additionally, network analyses by GeneMANIA and STRING revealed significant coexpression and interaction patterns among these genes, with four notable hub genes-, , and -identified as pivotal in NSCLC progression.
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