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Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures.

Manzano AI, van Loon JJ, Christianen PC, Gonzalez-Rubio JM, Medina FJ, Herranz R - BMC Genomics (2012)

Bottom Line: A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself.Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies.A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Investigaciones Biológicas (CSIC), C/Ramiro de Maeztu 9, E-28040 Madrid, Spain.

ABSTRACT

Background: Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself.

Results: Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T), intermediate g* (0.1 g* at B = 14.7 T) and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T) plus an internal 1 g* control (B = 16.5 T). The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg) and a Large Diameter Centrifuge (2 g).Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies.

Conclusions: A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR). A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment.

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Magnetic levitation experiment set up. A) Photo of the water-cooled duplex-Bitter magnet located at HFML with our samples placed inside (not visible). The samples are positioned inside the magnet bore. The temperature is controlled by a double-walled metal tube connected to a 22°C water bath. A PVC spacer is used to place the stack of samples in the correct position. B) The samples are contained in 40.8 mm high tubes placed on top of each other at five effective g* levels. The spacing between the samples was 40.8 mm and all samples were in the dark before and during the experiment (no light reached the magnet bore). C) Closer view of a sample tube. Callus cell culture is grown in a 1-2 mm layer to ensure a similar force throughout the whole biological sample. D) Profile of the magnetic field strength (B) and the effective gravity (g*) as a function of position inside the magnet. The samples were placed symmetrically in relation to the centre of the bore (195 mm above the top) indicated in the graph by vertical lines (straight lines for μg*, 1 g* and 2 g* and dotted lines for intermediate 0.1 g* and 1.9 g*). The red curve shows the magnetic field strength as a function of the vertical position (z) in the magnet. The blue curve indicates the product of the field strength B(z) and the field gradient (B' (z) = dB/dz), which is the derivative of the field strength with respect to the vertical position. The corresponding value of the effective gravity is equal to g(1 + B(z) B' (z)/1360), so a magnetic force of -1360 T2/m is able to levitate water.
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Figure 1: Magnetic levitation experiment set up. A) Photo of the water-cooled duplex-Bitter magnet located at HFML with our samples placed inside (not visible). The samples are positioned inside the magnet bore. The temperature is controlled by a double-walled metal tube connected to a 22°C water bath. A PVC spacer is used to place the stack of samples in the correct position. B) The samples are contained in 40.8 mm high tubes placed on top of each other at five effective g* levels. The spacing between the samples was 40.8 mm and all samples were in the dark before and during the experiment (no light reached the magnet bore). C) Closer view of a sample tube. Callus cell culture is grown in a 1-2 mm layer to ensure a similar force throughout the whole biological sample. D) Profile of the magnetic field strength (B) and the effective gravity (g*) as a function of position inside the magnet. The samples were placed symmetrically in relation to the centre of the bore (195 mm above the top) indicated in the graph by vertical lines (straight lines for μg*, 1 g* and 2 g* and dotted lines for intermediate 0.1 g* and 1.9 g*). The red curve shows the magnetic field strength as a function of the vertical position (z) in the magnet. The blue curve indicates the product of the field strength B(z) and the field gradient (B' (z) = dB/dz), which is the derivative of the field strength with respect to the vertical position. The corresponding value of the effective gravity is equal to g(1 + B(z) B' (z)/1360), so a magnetic force of -1360 T2/m is able to levitate water.

Mentions: We exposed samples to five different conditions (g* and B fields) within a magnet located in the High Field Magnet Laboratory (HFML) at the Radboud University Nijmegen, The Netherlands [30,31]. The asterisk in g* indicates the presence of the background magnetic field, whose spatial profile is shown in Figure 1. In the centre of the magnet bore (positioned 195 mm from the top of the magnet) the magnetic field strength is maximal (16.5 T in our case). Here the magnetic field gradient is zero and, therefore, the magnetic force is also zero, leaving gravity unaffected; this is the 1 g* point (Figure 1). At a distance of 81.6 mm above the centre position within the solenoid (113 mm from the top), the diamagnetic force on water balances the force of gravity (at B = 10.1 T and BB' = 1360 T2/m), leading to stable levitation; this is the μg* point (zero gravity 0 g* is only reached in a single point). An intermediate sample was placed at 40.8 mm above the centre, where the calculated residual g force is 0.1 g* and the magnetic field 14.7 T. Below the centre of the magnet the magnetic force acts in the same direction as gravity, leading to enhanced gravity levels. Two samples were placed in positions with 1.9 g* (B = 14.7 T) and 2 g* (B = 10.1 T) forces (Figure 1 and Additional file 1: Figure S1). In order to discriminate between the effects due to the high magnetic field and field gradients and those due to the altered gravity, we carried out five 200 min simultaneous experiments exposing the samples at these 5 positions at 22°C. External controls, at 1 g, were kept at RT (22°C ± 0.1°C, 1 g ground gravity) away from the magnet (the magnetic field is negligible beyond the 4 metre security radius). The temperature in the magnet was controlled using a double-walled metallic holder tube with a thermostated water bath. The availability of the magnet and the cost of the experiments restricted the experimental time to 200 min.


Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures.

Manzano AI, van Loon JJ, Christianen PC, Gonzalez-Rubio JM, Medina FJ, Herranz R - BMC Genomics (2012)

Magnetic levitation experiment set up. A) Photo of the water-cooled duplex-Bitter magnet located at HFML with our samples placed inside (not visible). The samples are positioned inside the magnet bore. The temperature is controlled by a double-walled metal tube connected to a 22°C water bath. A PVC spacer is used to place the stack of samples in the correct position. B) The samples are contained in 40.8 mm high tubes placed on top of each other at five effective g* levels. The spacing between the samples was 40.8 mm and all samples were in the dark before and during the experiment (no light reached the magnet bore). C) Closer view of a sample tube. Callus cell culture is grown in a 1-2 mm layer to ensure a similar force throughout the whole biological sample. D) Profile of the magnetic field strength (B) and the effective gravity (g*) as a function of position inside the magnet. The samples were placed symmetrically in relation to the centre of the bore (195 mm above the top) indicated in the graph by vertical lines (straight lines for μg*, 1 g* and 2 g* and dotted lines for intermediate 0.1 g* and 1.9 g*). The red curve shows the magnetic field strength as a function of the vertical position (z) in the magnet. The blue curve indicates the product of the field strength B(z) and the field gradient (B' (z) = dB/dz), which is the derivative of the field strength with respect to the vertical position. The corresponding value of the effective gravity is equal to g(1 + B(z) B' (z)/1360), so a magnetic force of -1360 T2/m is able to levitate water.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368779&req=5

Figure 1: Magnetic levitation experiment set up. A) Photo of the water-cooled duplex-Bitter magnet located at HFML with our samples placed inside (not visible). The samples are positioned inside the magnet bore. The temperature is controlled by a double-walled metal tube connected to a 22°C water bath. A PVC spacer is used to place the stack of samples in the correct position. B) The samples are contained in 40.8 mm high tubes placed on top of each other at five effective g* levels. The spacing between the samples was 40.8 mm and all samples were in the dark before and during the experiment (no light reached the magnet bore). C) Closer view of a sample tube. Callus cell culture is grown in a 1-2 mm layer to ensure a similar force throughout the whole biological sample. D) Profile of the magnetic field strength (B) and the effective gravity (g*) as a function of position inside the magnet. The samples were placed symmetrically in relation to the centre of the bore (195 mm above the top) indicated in the graph by vertical lines (straight lines for μg*, 1 g* and 2 g* and dotted lines for intermediate 0.1 g* and 1.9 g*). The red curve shows the magnetic field strength as a function of the vertical position (z) in the magnet. The blue curve indicates the product of the field strength B(z) and the field gradient (B' (z) = dB/dz), which is the derivative of the field strength with respect to the vertical position. The corresponding value of the effective gravity is equal to g(1 + B(z) B' (z)/1360), so a magnetic force of -1360 T2/m is able to levitate water.
Mentions: We exposed samples to five different conditions (g* and B fields) within a magnet located in the High Field Magnet Laboratory (HFML) at the Radboud University Nijmegen, The Netherlands [30,31]. The asterisk in g* indicates the presence of the background magnetic field, whose spatial profile is shown in Figure 1. In the centre of the magnet bore (positioned 195 mm from the top of the magnet) the magnetic field strength is maximal (16.5 T in our case). Here the magnetic field gradient is zero and, therefore, the magnetic force is also zero, leaving gravity unaffected; this is the 1 g* point (Figure 1). At a distance of 81.6 mm above the centre position within the solenoid (113 mm from the top), the diamagnetic force on water balances the force of gravity (at B = 10.1 T and BB' = 1360 T2/m), leading to stable levitation; this is the μg* point (zero gravity 0 g* is only reached in a single point). An intermediate sample was placed at 40.8 mm above the centre, where the calculated residual g force is 0.1 g* and the magnetic field 14.7 T. Below the centre of the magnet the magnetic force acts in the same direction as gravity, leading to enhanced gravity levels. Two samples were placed in positions with 1.9 g* (B = 14.7 T) and 2 g* (B = 10.1 T) forces (Figure 1 and Additional file 1: Figure S1). In order to discriminate between the effects due to the high magnetic field and field gradients and those due to the altered gravity, we carried out five 200 min simultaneous experiments exposing the samples at these 5 positions at 22°C. External controls, at 1 g, were kept at RT (22°C ± 0.1°C, 1 g ground gravity) away from the magnet (the magnetic field is negligible beyond the 4 metre security radius). The temperature in the magnet was controlled using a double-walled metallic holder tube with a thermostated water bath. The availability of the magnet and the cost of the experiments restricted the experimental time to 200 min.

Bottom Line: A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself.Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies.A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Investigaciones Biológicas (CSIC), C/Ramiro de Maeztu 9, E-28040 Madrid, Spain.

ABSTRACT

Background: Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself.

Results: Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T), intermediate g* (0.1 g* at B = 14.7 T) and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T) plus an internal 1 g* control (B = 16.5 T). The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg) and a Large Diameter Centrifuge (2 g).Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies.

Conclusions: A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR). A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment.

Show MeSH
Related in: MedlinePlus