Limits...
A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8.

Fengler S, Spirer I, Neef M, Ecke M, Nieselt K, Hampp R - Biomed Res Int (2015)

Bottom Line: The results show a major impact of nonmicrogravity related spaceflight conditions.In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity.These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

View Article: PubMed Central - PubMed

Affiliation: Physiological Ecology of Plants, University of Tübingen, Auf der Morgenstelle 1, 72076 Tübingen, Germany.

ABSTRACT
The Simbox mission was the first joint space project between Germany and China in November 2011. Eleven-day-old Arabidopsis thaliana wild type semisolid callus cultures were integrated into fully automated plant cultivation containers and exposed to spaceflight conditions within the Simbox hardware on board of the spacecraft Shenzhou 8. The related ground experiment was conducted under similar conditions. The use of an in-flight centrifuge provided a 1 g gravitational field in space. The cells were metabolically quenched after 5 days via RNAlater injection. The impact on the Arabidopsis transcriptome was investigated by means of whole-genome gene expression analysis. The results show a major impact of nonmicrogravity related spaceflight conditions. Genes that were significantly altered in transcript abundance are mainly involved in protein phosphorylation and MAPK cascade-related signaling processes, as well as in the cellular defense and stress responses. In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity. These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

Show MeSH

Related in: MedlinePlus

Pearson correlation heat map shows high degree of similarity between front and rear culture chamber of each sample within each sample group. Flight space (FS), in-flight centrifugation (FC), and ground static (GS).
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4309294&req=5

fig9: Pearson correlation heat map shows high degree of similarity between front and rear culture chamber of each sample within each sample group. Flight space (FS), in-flight centrifugation (FC), and ground static (GS).

Mentions: The quality of the extracted total ribonucleic acid was satisfying for GeneChip hybridization (for RNA quality, see Supplementary Material S2) with clear bands representing the 28S and 18S rRNA. Whole-genome microarray screening was performed for each sample. Due to the limited amount of total RNA, the confirmation of expression data by quantitative real-time PCR was not possible. The data analysis revealed experiment-specific properties of biological replicates which were visualized by hierarchical clustering on the basis of the calculation of the Pearson Correlation coefficient (Figure 8). In this graph, a relatively short distance implies a high correlation between the samples. As obvious from Figure 8, the flight and ground experiment showed group-based clustering. The short distance between FS and FC (FS and FC boxes) in contrast to GS (GS boxes) indicates that nonmicrogravity related spaceflight conditions have major impact. The transcriptome of the biological replicates within the experiment groups (front and rear chamber of FS, FC, GS; n = 2) showed a high degree of similarity (Figure 8). This fact was confirmed by heat map generation based on calculated correlations (Figure 9). The Pearson Correlation was about 0.99 between front and rear CC for all three modules (FS, FC, and GS, n = 2, Figure 9). Statistical (Student's t-test, P < 0.1, and FDR correction) and comparative analysis showed a relatively low response of semisolid callus cultures (Figure 10). Interestingly, microgravity conditions did not induce statistically significant changes (P < 0.1) at the gene expression level, although 298 genes were at least 2-fold differentially expressed (275 up- and 23 downregulated) within flight space (FS) samples. In contrast, nonmicrogravity related spaceflight conditions interfered with gene expression, considerably. Eight hundred ninety-seven genes were significantly and differentially expressed (at least 2-fold, P < 0.1) when 1 g ground and μg exposed flight samples were compared. Among them, 463 were upregulated and 434 genes were downregulated within FS (Figure 10). Comparison between both 1 g controls (in-flight, ground) resulted in 826 significantly (P < 0.1) differentially altered genes (543 up and 283 downregulated, Figure 10). Thereby, 573 significant DEGs (P < 0.1) were identical in both comparisons (Figure 10).


A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8.

Fengler S, Spirer I, Neef M, Ecke M, Nieselt K, Hampp R - Biomed Res Int (2015)

Pearson correlation heat map shows high degree of similarity between front and rear culture chamber of each sample within each sample group. Flight space (FS), in-flight centrifugation (FC), and ground static (GS).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4309294&req=5

fig9: Pearson correlation heat map shows high degree of similarity between front and rear culture chamber of each sample within each sample group. Flight space (FS), in-flight centrifugation (FC), and ground static (GS).
Mentions: The quality of the extracted total ribonucleic acid was satisfying for GeneChip hybridization (for RNA quality, see Supplementary Material S2) with clear bands representing the 28S and 18S rRNA. Whole-genome microarray screening was performed for each sample. Due to the limited amount of total RNA, the confirmation of expression data by quantitative real-time PCR was not possible. The data analysis revealed experiment-specific properties of biological replicates which were visualized by hierarchical clustering on the basis of the calculation of the Pearson Correlation coefficient (Figure 8). In this graph, a relatively short distance implies a high correlation between the samples. As obvious from Figure 8, the flight and ground experiment showed group-based clustering. The short distance between FS and FC (FS and FC boxes) in contrast to GS (GS boxes) indicates that nonmicrogravity related spaceflight conditions have major impact. The transcriptome of the biological replicates within the experiment groups (front and rear chamber of FS, FC, GS; n = 2) showed a high degree of similarity (Figure 8). This fact was confirmed by heat map generation based on calculated correlations (Figure 9). The Pearson Correlation was about 0.99 between front and rear CC for all three modules (FS, FC, and GS, n = 2, Figure 9). Statistical (Student's t-test, P < 0.1, and FDR correction) and comparative analysis showed a relatively low response of semisolid callus cultures (Figure 10). Interestingly, microgravity conditions did not induce statistically significant changes (P < 0.1) at the gene expression level, although 298 genes were at least 2-fold differentially expressed (275 up- and 23 downregulated) within flight space (FS) samples. In contrast, nonmicrogravity related spaceflight conditions interfered with gene expression, considerably. Eight hundred ninety-seven genes were significantly and differentially expressed (at least 2-fold, P < 0.1) when 1 g ground and μg exposed flight samples were compared. Among them, 463 were upregulated and 434 genes were downregulated within FS (Figure 10). Comparison between both 1 g controls (in-flight, ground) resulted in 826 significantly (P < 0.1) differentially altered genes (543 up and 283 downregulated, Figure 10). Thereby, 573 significant DEGs (P < 0.1) were identical in both comparisons (Figure 10).

Bottom Line: The results show a major impact of nonmicrogravity related spaceflight conditions.In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity.These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

View Article: PubMed Central - PubMed

Affiliation: Physiological Ecology of Plants, University of Tübingen, Auf der Morgenstelle 1, 72076 Tübingen, Germany.

ABSTRACT
The Simbox mission was the first joint space project between Germany and China in November 2011. Eleven-day-old Arabidopsis thaliana wild type semisolid callus cultures were integrated into fully automated plant cultivation containers and exposed to spaceflight conditions within the Simbox hardware on board of the spacecraft Shenzhou 8. The related ground experiment was conducted under similar conditions. The use of an in-flight centrifuge provided a 1 g gravitational field in space. The cells were metabolically quenched after 5 days via RNAlater injection. The impact on the Arabidopsis transcriptome was investigated by means of whole-genome gene expression analysis. The results show a major impact of nonmicrogravity related spaceflight conditions. Genes that were significantly altered in transcript abundance are mainly involved in protein phosphorylation and MAPK cascade-related signaling processes, as well as in the cellular defense and stress responses. In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity. These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

Show MeSH
Related in: MedlinePlus