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Oleaginous fungi natively accumulate large amounts of triacylglycerides (TAG), widely used as precursors for sustainable biodiesel production. However, little attention has been paid to the diversity and roles of fungal mixed microbial cultures (MMCs) in sequencing batch reactors (SBR). In this study, a lipid-rich stream produced in the fish-canning industry was used as a substrate in two laboratory-scale SBRs operated under the feast/famine (F/F) regime to enrich microorganisms with high TAG-storage ability, under two different concentrations of NaCl (SBR-N: 0.5 g/L; SBR-S: 10 g/L). The size of the fungal community in the enriched activated sludge (EAS) was analyzed using 18S rRNA-based qPCR, and the fungal community structure was determined by Illumina sequencing. The different selective pressures (feeding strategy and control of pH) implemented in the enrichment SBRs throughout operation increased the abundance of total fungi. In general, there was an enrichment of genera previously identified as TAG-accumulating fungi (Apiotrichum, Candida, Cutaneotrichosporon, Geotrichum, Haglerozyma, Metarhizium, Mortierella, Saccharomycopsis, and Yarrowia) in both SBRs. However, the observed increase of their relative abundances throughout operation was not significantly linked to a higher TAG accumulation.
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http://dx.doi.org/10.1016/j.nbt.2022.08.001 | DOI Listing |
Int J Biol Macromol
September 2025
Department of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), Okhla Phase III, New Delhi, 110020, India; Infosys Centre for Artificial Intelligence, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), Okhla Phase III, New Delhi, 110020, In
Understanding the structural and functional diversity of toxin proteins is critical for elucidating macromolecular behavior, mechanistic variability, and structure-driven bioactivity. Traditional approaches have primarily focused on binary toxicity prediction, offering limited resolution into distinct modes of action of toxins. Here, we present MultiTox, an ensemble stacking framework for the classification of toxin proteins based on their molecular mode of action: neurotoxins, cytotoxins, hemotoxins, and enterotoxins.
View Article and Find Full Text PDFMediators Inflamm
September 2025
Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, Fujian, China.
Osteoporosis is a prevalent metabolic bone disorder with complex molecular underpinnings. Emerging evidence implicates endoplasmic reticulum stress (ERS) in its pathogenesis; however, systematic exploration of ERS-related genes (ERSRGs) remains limited. This study aimed to identify ERS-related differentially expressed genes (ERSRDEGs) in osteoporosis, construct a diagnostic model, and elucidate associated molecular mechanisms.
View Article and Find Full Text PDFiScience
September 2025
Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, School of Computing and Information Technology, Great Bay University, Dongguan, China.
Distinguishing similar cancer subtypes and predicting responses to immune checkpoint blockade (ICB) are critical for improving clinical outcomes. However, existing gene expression signatures often suffer from batch effects and poor generalizability across cohorts. To address these limitations, we propose adaptive individualized gene pair signatures (AIGPS), a robust method that adaptively quantifies gene pair reversals and selects informative features using machine learning.
View Article and Find Full Text PDFAdv Sci (Weinh)
September 2025
School of Artificial Intelligence, Jilin University, Changchun, 130012, China.
Single-cell multi-omics technologies are pivotal for deciphering the complexities of biological systems, with Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) emerging as a particularly valuable approach. The dual-modality capability makes CITE-seq particularly advantageous for dissecting cellular heterogeneity and understanding the dynamic interplay between transcriptomic and proteomic landscapes. However, existing computational models for integrating these two modalities often struggle to capture the complex, non-linear interactions between RNA and antibody-derived tags (ADTs), and are computationally intensive.
View Article and Find Full Text PDFMed
August 2025
Joint Academic Rheumatology Program, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; Centre of New Biotechnologies and Precision Medicine (CNBPM), School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece. Electronic address: p
Background: Pathogenic responses against self and foreign antigens in systemic autoimmunity and infection, respectively, engage similar immunologic components, thus lacking distinguishing diagnostic biomarkers. Herein, we tested whether whole-blood transcriptome analysis discriminates autoimmune from infectious diseases.
Methods: We applied nested cross-validation methodology to tune and validate random forests, k-nearest neighbors, and support vector machines, using a new preprocessing method on 22 publicly available datasets, including 594 patients with a broad spectrum of systemic autoimmune diseases and 615 patients with diverse viral, bacterial, and parasitic infections.