Connectivity affects species demography, (meta)population dynamics, evolution, phylogeny and biogeography. Various methodological approaches are applied to measure connectivity. Biophysical modelling can explore systematically the influence of atmospheric, oceanic and ecological forcing, while genetics measures connectivity patterns within the sampling strategy limit. In the Pacific Ocean pearl farming lagoons, the activity relies on spat collecting of the black lipped pearl oyster Pinctada margaritifera occurring after the larval dispersal phase, which follows spawning from wild or farmed populations. Biophysical 3D modelling and genomic studies have both separately brought insights on within-lagoon connectivity and on the origin of spats. Here, we combined previous genetics results with new realistic biophysical modelling scenarios to elucidate connectivity in Ahe Atoll lagoon. When combined, we identified the weather sequence likely explaining the realized connectivity observations. We discuss the strengths, weaknesses, opportunities and threats of combining these two approaches considering specific pearl farming demographic connectivity questions.
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http://dx.doi.org/10.1016/j.marpolbul.2021.112324 | DOI Listing |
Cell
January 2025
Program in Bioinformatics, Boston University, Boston, MA 02215, USA; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Center for Network Systems Biology, Boston University, Boston, MA 02218, USA; Department of Chemistry, Boston University, Boston, MA 02215, USA; Department of Chemical Physiology and Biochemistry, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA. Electronic address:
Knowledge of protein-metabolite interactions can enhance mechanistic understanding and chemical probing of biochemical processes, but the discovery of endogenous ligands remains challenging. Here, we combined rapid affinity purification with precision mass spectrometry and high-resolution molecular docking to precisely map the physical associations of 296 chemically diverse small-molecule metabolite ligands with 69 distinct essential enzymes and 45 transcription factors in the gram-negative bacterium Escherichia coli. We then conducted systematic metabolic pathway integration, pan-microbial evolutionary projections, and independent in-depth biophysical characterization experiments to define the functional significance of ligand interfaces.
View Article and Find Full Text PDFPathogens
January 2025
Biomedical Sciences Laboratory (CBMU), School of Medicine, Universidad de Los Andes, Bogotá D.C 111711, Colombia.
, the etiological agent of Chagas disease, is a parasite known for its diverse genotypic variants, or Discrete Typing Units (DTUs), which have been associated with varying degrees of tissue involvement. However, aspects such as parasite attachment remain unclear. It has been suggested that the TcI genotype is associated with cardiac infection, the most common involved site in chronic human infection, while TcII is associated with digestive tract involvement.
View Article and Find Full Text PDFLife (Basel)
January 2025
The Laboratory of Personalized Chemo-Radiation Therapy, Institute of Future Biophysics, Moscow 141700, Russia.
Cancer-related deaths primarily occur due to metastasis, a process involving the migration and invasion of cancer cells. In most solid tumors, metastasis occurs through collective cell migration (CCM), guided by "cellular leaders". These leader cells generate forces through actomyosin-mediated protrusion and contractility.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
Hepatocellular carcinoma (HCC) cells critically depend on PARP1 and CHK1 activation for survival. Combining the PARP inhibitor (PARPi) olaparib with a CHK1 inhibitor (MK-8776, CHK1i) produced a synergistic effect, reducing cell viability and inducing marked oxidative stress and DNA damage, particularly in the HepG2 cells. This dual treatment significantly increased apoptosis markers, including γH2AX and caspase-3/7 activity.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, 41013 Seville, Spain.
The ubiquitin proteasome system (UPS) is implicated in protein homeostasis. One of the proteins involved in this system is HERC1 E3 ubiquitin ligase, which was associated with several processes including the normal development and neurotransmission at the neuromuscular junction (NMJ), autophagy in projection neurons, myelination of the peripheral nervous system, among others. The tambaleante (tbl) mouse model carries the spontaneous mutation Gly483Glu substitution in the HERC1 E3 protein.
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