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The evolution, evolvability and engineering of gene regulatory DNA. Nature 2022; 603:455-463. [PMID: 35264797 DOI: 10.1038/s41586-022-04506-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Abstract
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness1-3. Constructing complete fitness landscapes, in which DNA sequences are mapped to fitness, is a long-standing goal in biology, but has remained elusive because it is challenging to generalize reliably to vast sequence spaces4-6. Here we build sequence-to-expression models that capture fitness landscapes and use them to decipher principles of regulatory evolution. Using millions of randomly sampled promoter DNA sequences and their measured expression levels in the yeast Saccharomyces cerevisiae, we learn deep neural network models that generalize with excellent prediction performance, and enable sequence design for expression engineering. Using our models, we study expression divergence under genetic drift and strong-selection weak-mutation regimes to find that regulatory evolution is rapid and subject to diminishing returns epistasis; that conflicting expression objectives in different environments constrain expression adaptation; and that stabilizing selection on gene expression leads to the moderation of regulatory complexity. We present an approach for using such models to detect signatures of selection on expression from natural variation in regulatory sequences and use it to discover an instance of convergent regulatory evolution. We assess mutational robustness, finding that regulatory mutation effect sizes follow a power law, characterize regulatory evolvability, visualize promoter fitness landscapes, discover evolvability archetypes and illustrate the mutational robustness of natural regulatory sequence populations. Our work provides a general framework for designing regulatory sequences and addressing fundamental questions in regulatory evolution.
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Araújo ASL, Verna C, Araújo Júnior OP, Soares Júnior JM, Simões RS, Baracat EC, Simões MDJ, Gomes RCT. Imbalance between the cellular proliferation and death in harderian gland of female mice with hyperprolactinemia. ACTA ACUST UNITED AC 2021; 67:650-655. [PMID: 34550251 DOI: 10.1590/1806-9282.20200737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/20/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To assess the impact of the metoclopramide-induced hyperprolactinemia in cellular death and proliferation in the harderian gland of female mice. METHODS Twenty female mice were divided into two groups of 10 animals each and treated: 0.2 mL of saline solution (controls, Ctr) and 200 µg of metoclopramide (experimental, hyperprolactinemia), both for 50 consecutive days and at 12:00 a.m. On the 50th day, the female were euthanized, and the harderian glands were removed and processed for immunohistochemistry for detected ki67 and TUNEL method. Data were statistically analyzed by unpaired Student's t test (p<0.05). RESULTS The harderian gland of the hyperprolactinemia group showed increase in the immunoexpression of Ki67 and TUNEL compared to the Ctr group (p<0.05), and there was no significant difference in the amount of porphyrin in the HPrl group compared to the Ctr group. CONCLUSION The hyperprolactinemia led to increased cell death in the acini the harderian gland and cell proliferation in the stroma glandular, fact that suggesting a reduction process of cellular activity and fibrosis, which suggests impairment in the functioning of the lacrimal harderian.
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Affiliation(s)
| | - Carina Verna
- Universidade Federal de São Paulo, Morphology and Genetics Department - São Paulo (SP), Brazil
| | | | - José Maria Soares Júnior
- Universidade de São Paulo, Faculty of Medicine Obstetrics and Gynecology Department - São Paulo (SP), Brazil
| | - Ricardo Santos Simões
- Universidade de São Paulo, Faculty of Medicine Obstetrics and Gynecology Department - São Paulo (SP), Brazil
| | - Edmund Chada Baracat
- Universidade de São Paulo, Faculty of Medicine Obstetrics and Gynecology Department - São Paulo (SP), Brazil
| | - Manuel de Jesus Simões
- Universidade Federal de São Paulo, Morphology and Genetics Department - São Paulo (SP), Brazil
| | - Regina Célia Teixeira Gomes
- Universidade Federal de São Paulo, Morphology and Genetics Department - São Paulo (SP), Brazil.,Universidade de São Paulo, Faculty of Medicine Obstetrics and Gynecology Department - São Paulo (SP), Brazil
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García-Macia M, Rubio-Gonzalez A, de Luxán-Delgado B, Potes Y, Rodríguez-González S, de Gonzalo-Calvo D, Boga JA, Coto-Montes A. Autophagic and proteolytic processes in the Harderian gland are modulated during the estrous cycle. Histochem Cell Biol 2013; 141:519-29. [PMID: 24310659 DOI: 10.1007/s00418-013-1170-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2013] [Indexed: 11/25/2022]
Abstract
The Syrian hamster Harderian gland (HG) is an organ that undergoes physiological autophagy in response to oxidative stress induced by porphyrin production. Porphyrin production in the HG has marked sex differences and is closely linked to reproductive function. In the present study, we observed that the estrous cycle and associated estrogen variations may affect oxidative-stress-induced proteolytic processes. In particular, significant changes in autophagic activity were detected during the estrous cycle. Notably, increased activation of macroautophagy as well as chaperone-mediated autophagy in the estrus phase coincided with a minimal antioxidant capability and the highest protein damage levels. By contrast, autophagic machinery was found to be blocked in the diestrus phase, likely due to mammalian target of rapamycin activation, which could be corroborated by the subsequent pS6K activation. Analogous results were observed regarding proteasome activity, which also showed maximal activity in the estrus phase. Interestingly, all these mechanisms were associated with important morphological changes in the HG during the estrous cycle. We observed statistically significant increases in Type II cells, which may be related to extensive autophagy in the estrus phase. Physiologically, this would result in a significant release of porphyrins specifically when females are more receptive. These data support the role of porphyrins as pheromones, as other authors have previously suggested, thus making the HG a scent organ. In addition, these results suggest a porphyrin-based approach to the treatment of porphyria during pregnancy, a condition for which no treatment is currently known.
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Affiliation(s)
- M García-Macia
- Department of Morphology and Cellular Biology, Cellular Biology Area, Faculty of Medicine, University of Oviedo, Julián Clavería s/n, 33006, Oviedo, Spain,
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Vega-Naredo I, Coto-Montes A. Physiological autophagy in the Syrian hamster Harderian gland. Methods Enzymol 2009; 452:457-76. [PMID: 19200898 DOI: 10.1016/s0076-6879(08)03627-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Syrian hamster Harderian gland (HG) displays a huge porphyrins metabolism with sexual dimorphism. Even in male Syrian hamsters with much lower porphyrins concentration than female HG, this activity is higher than in the liver. The damage derived from constant porphyrin production, displayed by reactive oxygen species, forces the gland to develop mechanisms that allow it to continue with its normal physiology. The survival strategy of the Harderian gland is mainly based on autophagic processes that are considered as a constant renovation system. Our results show different autophagy mechanisms in Syrian hamster HG, macroautophagy and other lysosomal-like processes such as chaperone-mediated autophagy, depending on sex and probably related to oxidative stress status. This chapter describes the methods used by us to characterize the autophagic processes that are being physiologically developed by this organ under normal conditions.
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Affiliation(s)
- Ignacio Vega-Naredo
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
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Tomás-Zapico C, Caballero B, Sierra V, Vega-Naredo I, Alvarez-García O, Tolivia D, Rodríguez-Colunga MJ, Coto-Montes A. Survival mechanisms in a physiological oxidative stress model. FASEB J 2005; 19:2066-8. [PMID: 16186173 DOI: 10.1096/fj.04-3595fje] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Syrian hamster Harderian gland has as the remarkable feature of an extraordinary rate of porphyrin production, even higher than the liver. The low activity of the last enzyme of the route gives rise to the accumulation of the uncomplex porphyrins in the female glands. Moreover, due to the localization of the Harderian gland, porphyrins exposed to light produce reactive oxygen species and, thus, the gland presents a physiological oxidative stress, with a great number of sings of degeneration, but without compromising the gland integrity. The appearance of abnormal features in this gland was largely described in the past, but the significance is interpreted for the first time in this study. We have found that autophagic processes are the first result of an elevated porphyrin metabolism, as it is observed in both sexes. This mechanism is considered, in this case, as a constant renovation system that allows the normal gland activity to be sustained. Furthermore, there is a second procedure, invasive processes toward connective tissue, which even occasionally reach blood vessels with intravasation of damaged gland components into the bloodstream. This effect is a consequence of a strong oxidative stress environment that is mainly observed in the female gland, resembling to tumoral progression. Both mechanisms, autophagy and invasive processes, have to be implied in the maintenance of the gland integrity.
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Affiliation(s)
- Cristina Tomás-Zapico
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
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Coto-Montes A, Tomás-Zapico C, Escames G, León J, Tolivia D, JosefaRodríguez-Colunga M, Acuña-Castroviejo D. Characterization of melatonin high-affinity binding sites in purified cell nuclei of the hamster (Mesocricetus auratus) harderian gland. J Pineal Res 2003; 34:202-7. [PMID: 12614480 DOI: 10.1034/j.1600-079x.2003.00029.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present paper, binding of melatonin to purified cell nuclei from harderian glands of male and female hamsters was assessed. Binding of 125I-melatonin to cell nuclei fulfills the criteria for binding to a receptor site. Binding kinetics exhibit properties such as dependence on time and temperature as well as reversibility, saturability, high affinity and specificity. The dissociation constants (K(D)) and the number of binding sites (B(max)) for the binding of 125I-melatonin to harderian gland nuclei were 260 +/- 56 pm and 12.2 +/- 0.8 fmol/mg protein in male glands, and 280 +/- 43 pm and 9.8 +/- 0.6 fmol/mg protein in female glands, respectively. Competition experiments showed IC50 values for melatonin of 250 +/- 45 pm and 290 +/- 68 pm in male and female glands, respectively. Other indoleamines such as N-acetylserotonine and 5-metoxytryptamine showed IC50 values in the micromolar range, suggesting that the binding sites are specific for melatonin. Hill analyses of the data show nH values of 0.96-0.98, suggesting the existence of a single class of binding sites. These data indicate that specific 125I-melatonin binding sites exist in the cell nuclei of Harderian glands in male as well as in female hamsters, without significant differences between them. The K(D) and B(max) values obtained from the binding in both sexes correlates well with the concentration of melatonin described in these respective Harderian glands. It is hypothesized that the nuclear binding sites of melatonin here described could be a physiological melatonin receptor, which may be involved in the genomic-dependent antioxidant effects of melatonin on hamster Harderian glands elsewhere reported.
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Affiliation(s)
- Ana Coto-Montes
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Spain
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Tomás-Zapico C, Coto-Montes A, Martínez-Fraga J, Rodríguez-Colunga MJ, Tolivia D. Effects of continuous light exposure on antioxidant enzymes, porphyric enzymes and cellular damage in the Harderian gland of the Syrian hamster. J Pineal Res 2003; 34:60-8. [PMID: 12485373 DOI: 10.1034/j.1600-079x.2003.02951.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Syrian hamster Harderian gland (HG), an organ present in the male two secretory cell types (type-I and type-II cells), is physiologically exposed to high oxidative stress because of high concentrations of porphyrins and their precursor, 5-aminolevulinic acid. Because of its juxtaorbital location, the HG is accessible to light, and subject to phototoxic effects of these substances. After having previously demonstrated circadian rhythms in antioxidant enzymes, porphyric enzymes and oxidative damage of proteins and lipids, as well as influences of melatonin on these parameters, we have now studied the effects of continuous light (LL), which suppresses melatonin secretion by the pineal gland. Measurements were performed in two different circadian phases, in order to detect the presence or absence of day/night differences. In LL, no differences between circadian phases of subjective day and subjective night were demonstrable for 5-aminolevulinate synthase, 5-aminolevulinate dehydratase, porphobilinogen deaminase, or superoxide dismutase; temporal differences in glutathione reductase and catalase were markedly diminished, whereas all these parameters showed marked day/night differences in the rats exposed to a light/dark cycle of 14:10. In LL, oxidative damage to lipids was minimally effected, while protein damage was enhanced. LL also caused a reduction in the percentage of type-II cells. Therefore, cell differentiation in the HG does not seem to be controlled only by the androgen, but, unexpectedly, also by melatonin.
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Affiliation(s)
- Cristina Tomás-Zapico
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
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Sbarbati A, Calderan L, Nicolato E, Marzola P, Lunati E, Donatella B, Bernardi P, Osculati F. Magnetic resonance imaging of the rat Harderian gland. J Anat 2002; 201:231-8. [PMID: 12363274 PMCID: PMC1570910 DOI: 10.1046/j.1469-7580.2002.00086.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The intra-orbital lacrimal gland (Harderian gland, or HG) of the female rat was studied by magnetic resonance imaging (MRI) to evaluate whether MRI can be used to visualize the gland in vivo and localized-1H-spectroscopy detect its lipid content. The results were correlated with post-mortem anatomical sections, and with light and electron microscopy. On MRI, HG presented as a mass located between the ocular bulb and the orbit. In strongly T2W sequences the secretory structures had a reduced signal while intraparenchymal connective tissue was visible. T2-quantitative maps values of HG (60.12 +/- 8.15 ms, mean +/- SD) were different from other tissues (i.e. muscular tissue, T2 = 44.79 +/- 3.43 ms and olfactory bulb, T2 = 79.26 +/- 4.25 ms). In contrast-enhanced-MRI, HG had a signal-intensity-drop of 0.074 +/- 0.072 (mean +/- SD), after injection of AMI-25, significantly different from the muscle (0.17 +/- 0.10). Localized MRI spectra gave a large part of the signal originating from fat protons, but with a significant percentage from water protons. At light and electron microscopy the lipid deposition appeared to be composed of low-density material filling a large part of the cytoplasm, and the porphyrin aggregates were easily recognizable. The data demonstrate that an in vivo study of the HG was feasible and that high-field MRI allowed analysis of the gross anatomy detecting the lipid content of the gland.
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Affiliation(s)
- Andrea Sbarbati
- Department of Morphological and Biomedical Sciences, Medical Faculty, University of Verona, Italy.
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Coto-Montes A, Tomás-Zapico C, Rodríguez-Colunga MJ, Tolivia-Cadrecha D, Martínez-Fraga J, Hardeland R, Tolivia D. Effects of the circadian mutation 'tau' on the Harderian glands of Syrian hamsters. J Cell Biochem 2001; 83:426-34. [PMID: 11596111 DOI: 10.1002/jcb.1240] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Syrian hamster Harderian gland (HG) is an organ continually exposed to oxidative stress caused by high concentrations of porphyric metabolites. According to previous studies, melatonin, which is rhythmically secreted by the pineal gland and tonically produced by the HG, antagonizes the oxidative damage. HGs exhibit a strong gender-dependent correlation between porphyrins, melatonin, and histological appearance. In HGs of both sexes, we have investigated effects of a single gene defect in the circadian clock system (tau mutation) causing a shortened free-running period and an advanced maximum of circulating melatonin. Comparisons were made with wild-type animals, one group of which received daily pharmacological injections of melatonin in late photophase. Changes were observed in histological characteristics, porphyrin content, antioxidant enzyme activities, and damage of proteins and lipids. HGs of tau hamsters showed morphological changes which can be partially interpreted in terms of increased damage. Additionally, tau females exhibited a many-fold augmentation in the percentage of so-called type II cells, which are otherwise typical for the male glands. In tau hamsters of both sexes, major antioxidative enzyme activities (superoxide dismutase, glutathione reductase, and catalase) were markedly enhanced, a presumably compensatory response to increased oxidative stress. Higher oxidative damage in tau HGs was directly demonstrable by a many-fold increase in protein carbonyl. Rises in antioxidative enzymes were also observed upon injections of melatonin; this was, however, not accompanied by changes in protein carbonyl, so that enzyme inductions by the hormone should be understood as protective actions. Our data are not only in accordance with findings on protective effects by melatonin, but also with our earlier observation made in Drosophila that perturbations in the circadian system lead to increased oxidative stress.
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Affiliation(s)
- A Coto-Montes
- Departamento de Morfología y Biología Celular, Universidad de Oviedo, E-33006 Oviedo, Asturias, Spain.
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Coto-Montes A, Boga JA, Tomás-Zapico C, Rodríguez-Colunga MJ, Martínez-Fraga J, Tolivia-Cadrecha D, Menéndez G, Hardeland R, Tolivia D. Porphyric enzymes in hamster Harderian gland, a model of damage by porphyrins and their precursors. A chronobiological study on the role of sex differences. Chem Biol Interact 2001; 134:135-49. [PMID: 11311210 DOI: 10.1016/s0009-2797(00)00320-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Syrian hamster Harderian gland (HG), representing a highly porphyrogenic organ, was used as a model system for studying physiologically occurring damage of biomolecules by porphyrins and their precursors, phenomena associated with from the pathological situation of porphyrias. The species used exhibits the peculiarity of much higher porphyrogenesis in females than in males, offering possibilities for comparison of effects by different porphyrin levels in one species. Since concentrations of free, and therefore, radical-generating porphyric metabolites are difficult to determine in the presence of high amounts of secreted and crystallizing porphyrins, which are, moreover, mainly surface-reactive, and since indications existed for temporal changes in the oxidative stress caused by these molecules, the following approach was chosen: in HGs of both females and males, activities of the relevant porphyric enzymes, delta-aminolevulinate synthase (ALA-S), delta-aminolevulinate dehydratase (ALA-D) and porphobilinogen deaminase (PBG-D), were determined throughout the circadian cycle. Results were compared with the temporal patterns of lipid peroxidation and protein damage in the same glands. In females, a strong correspondence was observed between protein carbonyl and lipid peroxidation, peaking at the end of both photophase and scotophase; maximal activities of the three porphyric enzymes ALA-S, ALA-D, and PBG-D either coincided or slightly preceded the peaks of oxidative damage. In males, lower enzyme activities, especially in PBG-D, were associated with weakly expressed rhythmicity. Correspondingly, lipid peroxidation was lower and exhibited a smaller rhythm amplitude; protein carbonyl of males showed a temporal pattern differing from that of females, with regard to amplitude and phasing. These data are in agreement with morphological observations demonstrating particularly severe cell damage in the female HG under normal conditions.
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Affiliation(s)
- A Coto-Montes
- Departamento de Moifología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, C/ Julián Clavería s/n, E-33006 Oviedo, Asturias, Spain.
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Coto-Montes A, Boga JA, Tomás-Zapico C, Rodríguez-Colunga MJ, Martínez-Fraga J, Tolivia-Cadrecha D, Menéndez G, Hardeland R, Tolivia D. Physiological oxidative stress model: Syrian hamster Harderian gland-sex differences in antioxidant enzymes. Free Radic Biol Med 2001; 30:785-92. [PMID: 11275478 DOI: 10.1016/s0891-5849(01)00468-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Syrian hamster Harderian gland, a juxtaorbital organ exhibiting marked gender-associated differences in contents of porphyrins and melatonin, was used as a model system for comparing strong (in females) and moderate (in males) physiological oxidative stress. Histological differences showing much higher cell damage in females were studied in conjunction with lipid peroxidation and activities of superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase. Lipid peroxidation and enzyme activities were measured throughout the circadian cycle, revealing the importance of dynamical processes in oxidative stress. Especially in lipid peroxidation and in catalase, short-lasting rises exhibited strongest gender differences. Peaks of lipid peroxidation were about three times higher in females, compared to males. Catalase peaks of females exceeded those in males by several hundred-fold. Average levels of superoxide dismutase and glutathione peroxidase were about three or two times higher in females, respectively. A clear-cut diurnally peaking rhythm was found in glutathione peroxidase of females, which was not apparent in males. Glutathione reductase showed differences in time patterns, but less in average activities. The time courses of lipid peroxidation and of protective enzymes are not explained by circulating melatonin, whereas melatonin formed in the Harderian gland should contribute to differences in average levels. Neither damage nor antioxidative defense simply reflect the illumination cycle and are, therefore, not only a consequence of photoreactions.
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Affiliation(s)
- A Coto-Montes
- Department of Morphology and Cellular Biology, University of Oviedo, Oviedo, Asturias, Spain.
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