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Development of resident and migratory three-spined stickleback, Gasterosteus aculeatus (2024)
Journal Article
Barnes, M., Chakrabarti, L., & MacColl, A. D. C. (2024). Development of resident and migratory three-spined stickleback, Gasterosteus aculeatus. PLoS ONE, 19(7), Article e0295485. https://doi.org/10.1371/journal.pone.0295485

The three-spined stickleback (Gasterosteus aculeatus) is a teleost fish and a model organism in evolutionary ecology, useful for both laboratory and natural experiments. It is especially valued for the substantial intraspecific variation in morpholog... Read More about Development of resident and migratory three-spined stickleback, Gasterosteus aculeatus.

Development of resident and migratory three-spined stickleback,Gasterosteus aculeatus (2023)
Preprint / Working Paper
Barnes, M., Chakrabarti, L., & MacColl, A. (2023). Development of resident and migratory three-spined stickleback,Gasterosteus aculeatus

The three-spined stickleback (Gasterosteus aculeatus) is a teleost fish and a model organism in evolutionary ecology, useful for both laboratory and natural experiments. It is especially valued for the substantial intraspecific variation in morpholog... Read More about Development of resident and migratory three-spined stickleback,Gasterosteus aculeatus.

Second-generation antipsychotics and metabolic syndrome: a role for mitochondria (2023)
Journal Article
Mortimer, K. R. H., Katshu, M. Z. U. H., & Chakrabarti, L. (2023). Second-generation antipsychotics and metabolic syndrome: a role for mitochondria. Frontiers in Psychiatry, 14, Article 1257460. https://doi.org/10.3389/fpsyt.2023.1257460

Psychosis is a known risk factor for developing metabolic syndrome (MetS). The risk is even greater in patients who are taking second-generation antipsychotics (SGAs). SGAs exacerbate metabolic abnormalities and lead to a 3-fold increased risk of sev... Read More about Second-generation antipsychotics and metabolic syndrome: a role for mitochondria.

Author Correction: Universal DNA methylation age across mammalian tissues (2023)
Journal Article
Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Almunia, J., Aloysius, A., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., …Horvath, S. (2023). Author Correction: Universal DNA methylation age across mammalian tissues. Nature Aging, 3(11), 1462-1462. https://doi.org/10.1038/s43587-023-00499-7

Correction to: Nature Aging, published online 10 August 2023. In the version of Supplementary Data initially published with this article, data were missing from Table S1.13 (Updated AnAge version in Class Mammalia), which now appear in an updated Sup... Read More about Author Correction: Universal DNA methylation age across mammalian tissues.

DNA methylation networks underlying mammalian traits (2023)
Journal Article
Haghani, A., Li, C. Z., Robeck, T. R., Zhang, J., Lu, A. T., Ablaeva, J., Acosta-Rodríguez, V. A., Adams, D. M., Alagaili, A. N., Almunia, J., Aloysius, A., Amor, N. M., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., Bennett, N. C., Black, P., Blumstein, D. T., …Horvath, S. (2023). DNA methylation networks underlying mammalian traits. Science, 381(6658), https://doi.org/10.1126/science.abq5693

Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct c... Read More about DNA methylation networks underlying mammalian traits.

Universal DNA methylation age across mammalian tissues (2023)
Journal Article
Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., Ablaeva, J., Acosta-Rodriguez, V. A., Adams, D. M., Almunia, J., Aloysius, A., Ardehali, R., Arneson, A., Baker, C. S., Banks, G., Belov, K., …Horvath, S. (2023). Universal DNA methylation age across mammalian tissues. Nature Aging, 3(9), 1144-1166. https://doi.org/10.1038/s43587-023-00462-6

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,7... Read More about Universal DNA methylation age across mammalian tissues.

A method to assess the mitochondrial respiratory capacity of complexes I and II from frozen tissue using the Oroboros O2k-FluoRespirometer (2023)
Journal Article
Ebanks, B., Kwiecinska, P., Moisoi, N., & Chakrabarti, L. (2023). A method to assess the mitochondrial respiratory capacity of complexes I and II from frozen tissue using the Oroboros O2k-FluoRespirometer. PLoS ONE, 18(7), Article e0276147. https://doi.org/10.1371/journal.pone.0276147

High-resolution respirometry methods allow for the assessment of oxygen consumption by the electron transfer systems within cells, tissue samples, and isolated mitochondrial preparations. As mitochondrial integrity is compromised by the process of cr... Read More about A method to assess the mitochondrial respiratory capacity of complexes I and II from frozen tissue using the Oroboros O2k-FluoRespirometer.

Mitochondrial Haemoglobin Is Upregulated with Hypoxia in Skeletal Muscle and Has a Conserved Interaction with ATP Synthase and Inhibitory Factor 1 (2023)
Journal Article
Ebanks, B., Katyal, G., Taylor, C., Dowle, A., Papetti, C., Lucassen, M., Moisoi, N., & Chakrabarti, L. (2023). Mitochondrial Haemoglobin Is Upregulated with Hypoxia in Skeletal Muscle and Has a Conserved Interaction with ATP Synthase and Inhibitory Factor 1. Cells, 12(6), Article 912. https://doi.org/10.3390/cells12060912

The globin protein superfamily has diverse functions. Haemoglobin has been found in non-erythroid locations, including within the mitochondria. Using co-immunoprecipitation and in silico methods, we investigated the interaction of mitochondrial haemo... Read More about Mitochondrial Haemoglobin Is Upregulated with Hypoxia in Skeletal Muscle and Has a Conserved Interaction with ATP Synthase and Inhibitory Factor 1.

A Common Anaesthetic, MS-222, Alters Measurements Made Using High-Resolution Respirometry in the Three-Spined Stickleback (Gasterosteus aculeatus) (2023)
Journal Article
Barnes, M., Ebanks, B., MacColl, A., & Chakrabarti, L. (2023). A Common Anaesthetic, MS-222, Alters Measurements Made Using High-Resolution Respirometry in the Three-Spined Stickleback (Gasterosteus aculeatus). Fishes, 8(1), Article 42. https://doi.org/10.3390/fishes8010042

Submersion in the anaesthetic MS-222 is a well-established and effective method used during the euthanasia of fish, but the consequences of treatment with this anaesthetic for mitochondrial respiration are yet to be established. This is important to... Read More about A Common Anaesthetic, MS-222, Alters Measurements Made Using High-Resolution Respirometry in the Three-Spined Stickleback (Gasterosteus aculeatus).

The large numbers of minicolumns in the primary visual cortex of humans, chimpanzees and gorillas are related to high visual acuity (2022)
Journal Article
Wallace, M. N., Zobay, O., Hardman, E., Thompson, Z., Dobbs, P., Chakrabarti, L., & Palmer, A. R. (2022). The large numbers of minicolumns in the primary visual cortex of humans, chimpanzees and gorillas are related to high visual acuity. Frontiers in Neuroanatomy, 16, Article 1034264. https://doi.org/10.3389/fnana.2022.1034264

Minicolumns are thought to be a fundamental neural unit in the neocortex and their replication may have formed the basis of the rapid cortical expansion that occurred during primate evolution. We sought evidence of minicolumns in the primary visual c... Read More about The large numbers of minicolumns in the primary visual cortex of humans, chimpanzees and gorillas are related to high visual acuity.

Quantitative Proteomics and Network Analysis of Differentially Expressed Proteins in Proteomes of Icefish Muscle Mitochondria Compared with Closely Related Red-Blooded Species (2022)
Journal Article
Katyal, G., Ebanks, B., Dowle, A., Shephard, F., Papetti, C., Lucassen, M., & Chakrabarti, L. (2022). Quantitative Proteomics and Network Analysis of Differentially Expressed Proteins in Proteomes of Icefish Muscle Mitochondria Compared with Closely Related Red-Blooded Species. Biology, 11(8), Article 1118. https://doi.org/10.3390/biology11081118

Antarctic icefish are extraordinary in their ability to thrive without haemoglobin. We wanted to understand how the mitochondrial proteome has adapted to the loss of this protein. Metabolic pathways that utilise oxygen are most likely to be rearrange... Read More about Quantitative Proteomics and Network Analysis of Differentially Expressed Proteins in Proteomes of Icefish Muscle Mitochondria Compared with Closely Related Red-Blooded Species.

Proteomic analysis of the ATP synthase interactome in notothenioids highlights a pathway that inhibits ceruloplasmin production. (2022)
Journal Article
Ebanks, B., Katyal, G., Lucassen, M., Papetti, C., & Chakrabarti, L. (2022). Proteomic analysis of the ATP synthase interactome in notothenioids highlights a pathway that inhibits ceruloplasmin production. American Journal of Physiology, 323(2), R181-R192. https://doi.org/10.1152/ajpregu.00069.2022

Antarctic notothenioids have unique adaptations that allow them to thrive in subzero Antarctic waters. Within the suborder Notothenioidei, species of the family Channichthyidae (icefish) lack hemoglobin and in some instances myoglobin too. In studies... Read More about Proteomic analysis of the ATP synthase interactome in notothenioids highlights a pathway that inhibits ceruloplasmin production..

Oxysterols and Oxysterol Sulfates in Alzheimer's Disease Brain and Cerebrospinal Fluid (2022)
Journal Article
Dias, I. H., Shokr, H., Shephard, F., & Chakrabarti, L. (2022). Oxysterols and Oxysterol Sulfates in Alzheimer's Disease Brain and Cerebrospinal Fluid. Journal of Alzheimer's Disease, 87(4), 1527-1536. https://doi.org/10.3233/JAD-220083

Background: Brain cholesterol levels are tightly regulated but increasing evidence indicates that cholesterol metabolism may drive Alzheimer's disease (AD)-associated pathological changes. Recent advances in understanding of mitochondrial dysfunction... Read More about Oxysterols and Oxysterol Sulfates in Alzheimer's Disease Brain and Cerebrospinal Fluid.

Mitochondrial ATP Synthase is a Target of Oxidative Stress in Neurodegenerative Diseases (2022)
Journal Article
Ebanks, B., & Chakrabarti, L. (2022). Mitochondrial ATP Synthase is a Target of Oxidative Stress in Neurodegenerative Diseases. Frontiers in Molecular Biosciences, 9, Article 854321. https://doi.org/10.3389/fmolb.2022.854321

The mitochondrial ATP synthase is responsible for the production of cellular ATP, and it does so by harnessing the membrane potential of the mitochondria that is produced by the sequential oxidation of select cellular metabolites. Since the structura... Read More about Mitochondrial ATP Synthase is a Target of Oxidative Stress in Neurodegenerative Diseases.

Sox-positive cell population in the adult cerebellum increases upon tissue degeneration (2021)
Journal Article
Salih, S., Nizamudeen, Z. A., De Melo, N., Chakrabarti, L., & Sottile, V. (2022). Sox-positive cell population in the adult cerebellum increases upon tissue degeneration. Experimental Neurology, 348, Article 113950. https://doi.org/10.1016/j.expneurol.2021.113950

Adult neurogenesis is well-described in the subventricular and subgranular zones of the mammalian brain. Recent observations that resident glia express stem cell markers in some areas of the brain not traditionally associated with neurogenesis hint t... Read More about Sox-positive cell population in the adult cerebellum increases upon tissue degeneration.

Acute Imidacloprid Exposure Alters Mitochondrial Function in Bumblebee Flight Muscle and Brain (2021)
Journal Article
Sargent, C., Ebanks, B., Hardy, I. C., Davies, T. G. E., Chakrabarti, L., & Stöger, R. (2021). Acute Imidacloprid Exposure Alters Mitochondrial Function in Bumblebee Flight Muscle and Brain. Frontiers in Insect Science, 1, Article 765179. https://doi.org/10.3389/finsc.2021.765179

Mitochondria are intracellular organelles responsible for cellular respiration with one of their major roles in the production of energy in the form of ATP. Activities with increased energetic demand are especially dependent on efficient ATP producti... Read More about Acute Imidacloprid Exposure Alters Mitochondrial Function in Bumblebee Flight Muscle and Brain.

Exercising D. melanogaster Modulates the Mitochondrial Proteome and Physiology. The Effect on Lifespan Depends upon Age and Sex (2021)
Journal Article
Ebanks, B., Wang, Y., Katyal, G., Sargent, C., Ingram, T. L., Bowman, A., Moisoi, N., & Chakrabarti, L. (2021). Exercising D. melanogaster Modulates the Mitochondrial Proteome and Physiology. The Effect on Lifespan Depends upon Age and Sex. International Journal of Molecular Sciences, 22(21), Article 11606. https://doi.org/10.3390/ijms222111606

Ageing is a major risk factor for many of the most prevalent diseases, including neurode-generative diseases, cancer, and heart disease. As the global population continues to age, behavioural interventions that can promote healthy ageing will improve... Read More about Exercising D. melanogaster Modulates the Mitochondrial Proteome and Physiology. The Effect on Lifespan Depends upon Age and Sex.

Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish (2021)
Journal Article
Katyal, G., Ebanks, B., Lucassen, M., Papetti, C., & Chakrabarti, L. (2021). Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish. PLoS ONE, 16(10), 1-18. https://doi.org/10.1371/journal.pone.0245822

Mitochondrial changes such as tight coupling of the mitochondria have facilitated sustained oxygen and respiratory activity in haemoglobin-less icefish of the Channichthyidae family. We aimed to characterise features in the sequence and structure of... Read More about Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish.