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"McKenzie, Matthew"
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The Pathogenesis of Very Long-Chain Acyl-CoA Dehydrogenase Deficiency
Living systems require energy to maintain their existence and perform tasks such as cell division. This energy is stored in several molecular forms in nature, specifically lipids, carbohydrates, and amino acids. At a cellular level, energy is extracted from these complex molecules and transferred to adenosine triphosphate (ATP) in the cytoplasm and mitochondria. Within the mitochondria, fatty acid β-oxidation (FAO) and oxidative phosphorylation (OXPHOS) are crucial metabolic processes involved in generating ATP, with defects in these pathways causing mitochondrial disease. Very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) is a fatty acid β-oxidation disorder (FAOD) affecting 1 to 2 individuals per 100,000. Similar to other mitochondrial disorders, there is no cure for VLCADD, with symptomatic treatment comprising dietary management and supplementation with medium-chain fatty acids to bypass the enzyme deficiency. While this addresses the primary defect in VLCADD, there is growing evidence that other aspects of mitochondrial function are also affected in VLCADD, including secondary defects in OXPHOS function. Here, we review our current understanding of VLCADD with a focus on the associated biochemical and molecular defects that can disrupt multiple aspects of mitochondrial function. We describe the interactions between FAO proteins and the OXPHOS complexes and how these interactions are critical for maintaining the activity of both metabolic pathways. In particular, we describe what is now known about the protein–protein interactions between VLCAD and the OXPHOS supercomplex and how their disruption contributes to overall VLCADD pathogenesis.
Journal Article
Computational model of integrin adhesion elongation under an actin fiber
Cells create physical connections with the extracellular environment through adhesions. Nascent adhesions form at the leading edge of migrating cells and either undergo cycles of disassembly and reassembly, or elongate and stabilize at the end of actin fibers. How adhesions assemble has been addressed in several studies, but the exact role of actin fibers in the elongation and stabilization of nascent adhesions remains largely elusive. To address this question, here we extended our computational model of adhesion assembly by incorporating an actin fiber that locally promotes integrin activation. The model revealed that an actin fiber promotes adhesion stabilization and elongation. Actomyosin contractility from the fiber also promotes adhesion stabilization and elongation, by strengthening integrin-ligand interactions, but only up to a force threshold. Above this force threshold, most integrin-ligand bonds fail, and the adhesion disassembles. In the absence of contraction, actin fibers still support adhesions stabilization. Collectively, our results provide a picture in which myosin activity is dispensable for adhesion stabilization and elongation under an actin fiber, offering a framework for interpreting several previous experimental observations.
Journal Article
The Importance of Surprising Results and Best Practices in Historical Ecology
The growing field of historical ecology describes population abundances, biodiversity, spatial structure, and ecological functioning in the past, which are important to understanding ecological dynamics and recovery potential. However, because historical ecological analyses often incorporate nontraditional data sources (i.e., archival materials and oral histories) and may reveal unexpected changes to species and populations, the results are subject to critiques of objectivity and quality control, which may hamper their broad application. Here, we argue that surprising results revealed by historical sources are essential for ecology and conservation, providing new hypotheses that can be tested with additional data and new understandings of ecological dynamics that have immediate conservation implications. We outline four best practices in conducting conservation-relevant historical ecology research using nontraditional sources, and we argue that if these practices are considered in designing historical ecological analyses, the results can provide reliable insight into past change, current ecosystem structure, and future recovery targets.
Journal Article
Low-temperature nucleation anomaly in silicate glasses shown to be artifact in a 5BaO·8SiO2 glass
For over 40 years, measurements of the nucleation rates in a large number of silicate glasses have indicated a breakdown in the Classical Nucleation Theory at temperatures below that of the peak nucleation rate. The data show that instead of steadily decreasing with decreasing temperature, the work of critical cluster formation enters a plateau and even starts to increase. Many explanations have been offered to explain this anomaly, but none have provided a satisfactory answer. We present an experimental approach to demonstrate explicitly for the example of a 5BaO ∙ 8SiO
2
glass that the anomaly is not a real phenomenon, but instead an artifact arising from an insufficient heating time at low temperatures. Heating times much longer than previously used at a temperature 50 K below the peak nucleation rate temperature give results that are consistent with the predictions of the Classical Nucleation Theory. These results raise the question of whether the claimed anomaly is also an artifact in other glasses.
The breakdown of classical nucleation theory at low temperatures for silicate glasses has been a puzzle for decades. Here, Xia
et al
. show with a long-term experiment for the specific case of a barium-silicate glass that this anomaly is in fact an artifact arising from insufficient heating time.
Journal Article
Mitochondrial Fatty Acid Oxidation Disorders Associated with Short-Chain Enoyl-CoA Hydratase (ECHS1) Deficiency
Mitochondrial fatty acid β-oxidation (FAO) is the primary pathway for fatty acid metabolism in humans, performing a key role in liver, heart and skeletal muscle energy homeostasis. FAO is particularly important during times of fasting when glucose supply is limited, providing energy for many organs and tissues, including the heart, liver and brain. Deficiencies in FAO can cause life-threatening metabolic disorders in early childhood that present with liver dysfunction, hypoglycemia, dilated hypertrophic cardiomyopathy and Reye-like Syndrome. Alternatively, FAO defects can also cause ‘milder’ adult-onset disease with exercise-induced myopathy and rhabdomyolysis. Short-chain enoyl-CoA hydratase (ECHS1) is a key FAO enzyme involved in the metabolism of fatty acyl-CoA esters. ECHS1 deficiency (ECHS1D) also causes human disease; however, the clinical manifestation is unlike most other FAO disorders. ECHS1D patients commonly present with Leigh syndrome, a lethal form of subacute necrotizing encephalomyelopathy traditionally associated with defects in oxidative phosphorylation (OXPHOS). In this article, we review the clinical, biochemical and genetic features of the ESHS1D patients described to date, and discuss the significance of the secondary OXPHOS defects associated with ECHS1D and their contribution to overall disease pathogenesis.
Journal Article
Laser-induced structural modification in calcium aluminosilicate glasses using molecular dynamic simulations
Glass structures of multicomponent oxide systems (CaO–Al
2
O
3
–SiO
2
) are studied using a simulated pulsed laser with molecular dynamics. The short- and intermediate-range order structures revealed a direct correlation between the transformation of Al
(IV)
to Al
(V)
, regions of increased density following laser processing, inherent reduction in the average T–O–T (T = Al, Si) angle, and associated elongation of the T–O bonding distance. Variable laser pulse energies were simulated across calcium aluminosilicate glasses with high silica content (50–80%) to identify densification trends attributed to composition and laser energy. High-intensity pulsed laser effects on fictive temperature and shockwave promotion are discussed in detail for their role in glass densification. Laser-induced structural changes are found to be highly dependent on pulse energy and glass chemistry.
Journal Article
Impaired Cellular Bioenergetics Causes Mitochondrial Calcium Handling Defects in MT-ND5 Mutant Cybrids
Mutations in mitochondrial DNA (mtDNA) can cause mitochondrial disease, a group of metabolic disorders that affect both children and adults. Interestingly, individual mtDNA mutations can cause very different clinical symptoms, however the factors that determine these phenotypes remain obscure. Defects in mitochondrial oxidative phosphorylation can disrupt cell signaling pathways, which may shape these disease phenotypes. In particular, mitochondria participate closely in cellular calcium signaling, with profound impact on cell function. Here, we examined the effects of a homoplasmic m.13565C>T mutation in MT-ND5 on cellular calcium handling using transmitochondrial cybrids (ND5 mutant cybrids). We found that the oxidation of NADH and mitochondrial membrane potential (Δψm) were significantly reduced in ND5 mutant cybrids. These metabolic defects were associated with a significant decrease in calcium uptake by ND5 mutant mitochondria in response to a calcium transient. Inhibition of glycolysis with 2-deoxy-D-glucose did not affect cytosolic calcium levels in control cybrids, but caused an increase in cytosolic calcium in ND5 mutant cybrids. This suggests that glycolytically-generated ATP is required not only to maintain Δψm in ND5 mutant mitochondria but is also critical for regulating cellular calcium homeostasis. We conclude that the m.13565C>T mutation in MT-ND5 causes defects in both mitochondrial oxidative metabolism and mitochondrial calcium sequestration. This disruption of mitochondrial calcium handling, which leads to defects in cellular calcium homeostasis, may be an important contributor to mitochondrial disease pathogenesis.
Journal Article
Nucleation pathways in barium silicate glasses
Nucleation is generally viewed as a structural fluctuation that passes a critical size to eventually become a stable emerging new phase. However, this concept leaves out many details, such as changes in cluster composition and competing pathways to the new phase. In this work, both experimental and computer modeling studies are used to understand the cluster composition and pathways. Monte Carlo and molecular dynamics approaches are used to analyze the thermodynamic and kinetic contributions to the nucleation landscape in barium silicate glasses. Experimental techniques examine the resulting polycrystals that form. Both the modeling and experimental data indicate that a silica rich core plays a dominant role in the nucleation process.
Journal Article