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Additional file 7: Table S7. Regulated genes involved in cytoskeleton and extracellular matrix dynamics in all experimental groups classified by gene ontology. Abbreviations: D—dobutamine; LPS—lipopolysaccharide; OGD—oxygen–glucose-deprivation

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Additional file 5: Table S5. Regulated genes involved in growth and cell cycle related mechanisms in all experimental groups classified by gene ontology. Abbreviations: D—dobutamine; LPS—lipopolysaccharide; OGD—oxygen–glucose-deprivation

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Additional file 6: Table S6. Regulated genes involved in development in all experimental groups classified by gene ontology. Abbreviations: D—dobutamine; LPS—lipopolysaccharide; OGD—oxygen–glucose-deprivation

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Additional file 3: Table S3. Regulated genes involved in mechanisms of cell death and cell survival in all experimental groups classified by gene ontology. Abbreviations: D—dobutamine; LPS—lipopolysaccharide; OGD—oxygen–glucose-deprivation

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Additional file 2: Table S2. Regulated genes involved in transcription in all experimental groups classified by gene ontology. Abbreviations: D—dobutamine; LPS—lipopolysaccharide; OGD—oxygen–glucose-deprivation

Neuroscore.

<p>The normal neuroscore before stroke is 28. Values at different times after PT in rats subsequently housed in standard (STD) and enriched environment (EE) are presented in box plot: median; 1^st quartile to 3^rd quartile, minimum and maximum value. (n = 7 for each housing condition) (*: p<0.05 when STD compared to EE; #: p<0.05 when STD and EE where compared to the respective values before stroke).</p

Skilled reaching test.

<p>Skilled reaching test at different times of recovery after PT stroke for animals housed in standard (STD) and enriched environment (EE). (A) The total number of pasta pieces reached during 20 minutes prior to PT (pre) and at different time points after PT. (#: p<0.05 when compared to the respective group before stroke (pre). (B) Map of the reaching area presenting the number of animals (as indicated by colors) that reached the pasta pieces (n = 7 for each housing condition).</p

Experimental design.

<p>Rats were trained, and baseline values set for the different functional tests. Rats were then subjected to PT and the functional deficits assessed 2 days later. Subsequently, rats were placed either in standard (STD) or enriched environment (EE). Functional tests were regularly performed during 9 weeks following the onset of the stroke (the time of the different tests are represented by color dots). At 9 weeks, rats were perfusion fixed and brains were analyzed by immunohistochemistry.</p

Environmental stimulation decreases the number of AB1031⁺ PV/GABA neurons in the rat cerebral cortex after PT.

<p>(A) Confocal images of parvalbumin expressing cells (green) enwrapped by AB1031⁺ PNNs (red) in the somatosensory cortex of a representative STD animal, scale bar 20 μm. (B and C) Representative bright-field micrographs of AB1031⁺ PNNs in the rat cerebral cortex ipsilateral to the lesion, scale bar 100 μm; (B1 and C1) higher magnification, scale bar 20 μm. AB1031 immunoreactivity in (B) STD and (C) EE conditions. Quantification of cortical neurons bearing AB1031⁺ PNNs in the peri-infarct cortex (D), the corresponding area contralateral to the lesion (E), the ipsilateral somatosensory cortex (F) and the contralateral somatosensory cortex (G). (n = 7 for each housing condition; 9 weeks after stroke; D with *p = 0.04; E with p = 0.3613; F with *p = 0.007; G with p = 0.0963; STD: standard environment, EE: enriched environment, PI: peri-infarct cortex, SS: somatosensory cortex, IPSI: ipsilateral, CONTRA: contralateral).</p

Enriched housing decreases the number of Cat-315⁺ PV/GABA neurons in the rat cerebral cortex after PT.

<p>(A) Confocal images of a parvalbumin (PV) expressing cell (green) enwrapped by a Cat-315⁺ PNN (red) in the somatosensory cortex of a representative STD animal; Z-stack demonstrates close proximity of the Cat-315 aggrecan antibody and PV, scale bar 20 μm. (B and C) Representative bright-field micrographs of Cat-315⁺ PNNs in the rat cerebral cortex ipsilateral to the lesion, scale bar 100 μm; (B1 and C1) higher magnification, scale bar 20 μm. Cat-315 immunoreactivity denotes a critical difference between (B) STD and (C) EE conditions. Quantification of cortical neurons bearing Cat-315⁺ PNNs in the peri-infarct cortex (D), the corresponding area contralateral to the lesion (E), the ipsilateral somatosensory cortex (F) and the contralateral somatosensory cortex (G). (n = 7 for each housing condition; 9 weeks after stroke; D with *p = 0.04; E with p = 0.06; F with *p = 0.0007; G with p = 0.1; STD: standard environment, EE: enriched environment, PI: peri-infarct cortex, SS: somatosensory cortex, IPSI: ipsilateral, CONTRA: contralateral).</p