Intracellular pH is a vital parameter that is maintained close to neutrality in all mammalian cells and tissues and acidic in most intracellular compartments. After presenting the main techniques used for intracellular an vesicular pH measurements we will briefly recall the main molecular mechanisms that affect and regulate intracellular pH. Following this we will discuss the large functional redundancy found in the transporters of H or acid-base equivalents. For this purpose, we will use mathematical modeling to simulate cellular response to persistent and/or transient acidification, in the presence of different transporters, single or in combination. We will also test the presence or absence of intracellular buffering. This latter section will highlight how modeling can yield fundamental insight into deep biological questions such as the utility of functional redundancy in natural selection.
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http://dx.doi.org/10.3389/fmolb.2022.825028 | DOI Listing |
Alzheimers Dement
December 2024
Department of Psychiatry, McGill University, Montréal, QC, Canada.
Background: The immune complement system is key to the elimination of redundant neural connections in the brain through a process called synaptic pruning. In neurodegenerative diseases such as Alzheimer's disease (AD), this system may result in excessive synapse loss, leading to brain atrophy and cognitive impairment. While increased cerebrospinal fluid (CSF) levels of complement proteins have been observed in patients with AD dementia, no studies have yet investigated the role of complement in the pre-symptomatic phase of AD, nor throughout its progression.
View Article and Find Full Text PDFBackground: Recent anti-amyloid mAb trial results demonstrate slowing of Alzheimer's disease progression, but to date do not fully halt or reverse this progression. Optimization of anti-amyloid therapy (timing and duration of intervention, modality, combinations, biomarker guidance) is limited by incomplete understanding of the disease, such as relationship between amyloid and tau pathways. Mechanistic Alzheimer's progression modeling investigated how amyloid and tau pathologies are connected in driving progression.
View Article and Find Full Text PDFSci Rep
January 2025
XtalPi Innovation Center, 706 Block B, Dongsheng Building, Haidian District, Beijing, China.
High-content analysis (HCA) holds enormous potential for drug discovery and research, but widely used methods can be cumbersome and yield inaccurate results. Noisy and redundant signals in cell images impede accurate deep learning-based image analysis. To address these issues, we introduce X-Profiler, a novel HCA method that combines cellular experiments, image processing, and deep learning modeling.
View Article and Find Full Text PDFPlant Mol Biol
January 2025
National Key Laboratory for Tropical Crop Breeding, Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Haikou, 572024/571101, Hainan, China.
Arabidopsis MYB transcription factor, AtDUO1 regulates generative cell body (GC) morphogenesis from round to semi and fully elongated forms before pollen mitosis-II (PM II). It was hypothesised that DUO1 might regulate morphogenesis through any of its direct target genes or components of the DUO1-DAZ1 network. The developmental analysis of plants harbouring T-DNA insertions in some DUO1 target genes using light and fluorescence microscopy revealed abnormal GC morphogenesis only in daz1 and daz2, but gcs1, trm16, mapkkk10, mapkkk20, tet11, and tip1 all undergo normal elongation indicating that these target genes have no important roles in morphogenesis or may be redundant.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, 36849, USA.
Identifying representative sequences for groups of functionally similar proteins and enzymes poses significant computational challenges. In this study, we applied submodular optimization, a method effective in data summarization, to select representative sequences for thioesterase enzyme families. We introduced and validated two algorithms, Greedy and Bidirectional Greedy, using curated protein sequence data from the ThYme (Thioester-active enzYmes) database.
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