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SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.
Virus Evol
January 2025
Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
A consistent area of interest since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been the sequence composition of the virus and how it has changed over time. Many resources have been developed for the storage and analysis of SARS-CoV-2 data, such as GISAID (Global Initiative on Sharing All Influenza Data), NCBI, Nextstrain, and outbreak.info.
View Article and Find Full Text PDFEarly life adverse environmental, nutrition and infection factors are associated with lower developmental scores in Pakistani children at 5 years: a cohort study.
BMJ Nutr Prev Health
November 2024
Centre for Global Child Health, The Hospital for Sick Children, Toronto, Ontario, Canada.
Background: The effects of multiple early adverse psychosocial and biological factors on child development at preschool age in deprived settings are not fully understood.
Methods: The 'Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development' (MAL-ED) project followed children from eight countries, recording sociodemographic, nutritional, illness, enteroinfection biomarkers and scores for quality of home environment (Home Observation for Measurement of the Environment (HOME)), development (Bayley) and maternal depression during the first year of life. In the Pakistan cohort, we investigated associations of these early factors with Z-scores (derived from the eight participating countries) of three developmental outcomes at 5 years: Executive Functions (Z-EF), the Wechsler Preschool and Primary Scale for Intelligence (Z-WPPSI) and the externalising behaviours component of the Strength and Difficulties test (Z-externalising behaviours).
ADSL promotes autophagy and tumor growth through fumarate-mediated Beclin1 dimethylation.
Nat Chem Biol
January 2025
Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.
As an enzyme with a critical role in de novo purine synthesis, adenylosuccinate lyase (ADSL) expression is upregulated in various malignancies. However, whether ADSL possesses noncanonical functions that contribute to cancer progression remains poorly understood. Here, we demonstrate that protein kinase R-like endoplasmic reticulum kinase (PERK) activated by lipid deprivation or ER stress phosphorylates ADSL at S140, leading to an enhanced association between ADSL and Beclin1.
View Article and Find Full Text PDFGemistocytic tumor cells programmed for glial scarring characterize T cell confinement in IDH-mutant astrocytoma.
Nat Commun
January 2025
Department of Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
Isocitrate dehydrogenase 1/2 mutant (IDHmt) astrocytoma is considered a T cell-deprived tumor, yet little is known regarding the phenotypes underlying T cell exclusion. Using bulk, single nucleus and spatial RNA and protein profiling, we demonstrate that a distinct spatial organization underlies T cell confinement to the perivascular space (T cell cuff) in IDHmt astrocytoma. T cell cuffs are uniquely characterized by a high abundance of gemistocytic tumor cells (GTC) in the surrounding stroma.
View Article and Find Full Text PDFfos genes in mainly invertebrate model systems: A review of commonalities and some diversities.
Cells Dev
January 2025
Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus UNAM Juriquilla, Querétaro, Querétaro, Mexico. Electronic address:
fos genes, transcription factors with a common basic region and leucine zipper domains binding to a consensus DNA sequence (TGA{}TCA), are evolutionarily conserved in eukaryotes. Homologs can be found in many different species from yeast to vertebrates. In yeast, the homologous GCN4 gene is required to mediate "emergency" situations like nutrient deprivation and the unfolded protein response.
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