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is a fungal order of within the subphylum Pucciniomycotina. This order encompasses significant yeasts, such as the oleaginous species and the opportunistic pathogen . We present the sequencing and comparative analysis of 35 strains from 27 species, alongside a strain (), and incorporating publicly available genomic data for related fungi. Based on the phylogenomics data, we found that the topologies obtained were relatively similar and in line with previous reports. A comparison between genomic makeup and previously described phenotypes revealed that the ability to utilize nitrate, raffinose, rhamnose, or sucrose clearly correlated with the existence of key enzymes involved in the corresponding metabolic pathways. However, similar associations could not be established for other carbon sources, such as maltose, galactose, or xylose. We further identified orthologs that are specifically present or absent in each taxon. These results and the genomic sequencing data will help in gaining a better understanding of these non-model yeast species.
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http://dx.doi.org/10.3897/imafungus.16.141626 | DOI Listing |
Arch Microbiol
September 2025
Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India.
Salmonella enterica serovar Typhi, the etiological agent of Typhoid fever, remains a critical public health concern associated with high morbidity in many developing countries. The widespread emergence of multidrug-resistant (MDR) Salmonella Typhi strains against the fluoroquinolone group of antibiotics, particularly ciprofloxacin, poses a significant global therapeutic challenge with underlying resistance due to mutations in quinolone-resistance determining region (QRDR) of gyrA gene, encoding DNA gyrase subunit A (GyrA). In pursuit of alternative therapeutic candidates, the present study was designed to evaluate ciprofloxacin analogues against prevalent GyrA mutations (S83F, D87G, and D87N) to overcome fluoroquinolone resistance through machine learning (ML)-based approach.
View Article and Find Full Text PDFInt J Cancer
September 2025
Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Cervical cancer remains a significant public health issue, ranking as the fourth most common cancer in women globally. In the Netherlands, cervical cancer incidence declined steadily from 1989 to 2001 but increased between 2001 and 2007. This study updates trends in cervical cancer incidence from 1989 to 2023 in the Netherlands and evaluates the impact of screening practices and participation rates in the national population-based screening program.
View Article and Find Full Text PDFJ Chem Phys
September 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, 5735 S. Ellis Ave., SCL 123, Chicago, Illinois 60637, USA.
Molecular dynamics simulations are essential for studying complex molecular systems, but their high computational cost limits scalability. Coarse-grained (CG) models reduce this cost by simplifying the system, yet traditional approaches often fail to maintain dynamic consistency, compromising their reliability in kinetics-driven processes. Here, we introduce an adversarial training framework that aligns CG trajectory ensembles with all-atom (AA) reference dynamics, ensuring both thermodynamic and kinetic fidelity.
View Article and Find Full Text PDFmBio
September 2025
Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA.
infection is a frequent cause of sepsis in humans, a disease associated with high mortality and without specific intervention. Clumping factor A (ClfA) displayed on the bacterial surface plays a key role in promoting replication during invasive disease. Decades of research have pointed to a wide array of ligands engaged by ClfA.
View Article and Find Full Text PDFLiver Int
October 2025
Division of Gastroenterology and Hepatology, Department of Medicine, The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Northwell Health, Manhasset, New York, USA.
Background: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths, primarily due to late-stage diagnosis. In this multicenter study, our goal is to identify functional biomarkers that stratify the risk of HCC in patients with cirrhosis (CP) for early diagnosis.
Methods: Five thousand and eight serum proteins (Somascan) were analysed in Cohort A (477 CP, including 125 HCC).