Supplementary figure 3. The comparison of cfDNA fragment size distribution pattern between two te... more Supplementary figure 3. The comparison of cfDNA fragment size distribution pattern between two techniques analysis; automated capillary electrophoresis and genome wide sequencing of sample (A) OS07 (B) OS08, and (C) OS10. For automated capillary electrophoresis, the distribution of cfDNA fragment was analyzed and presented as electropherogram by QIAxcel screengel software. While all read of insert size obtained from whole-genome sequencing was plotted as histogram using Picard software.
Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms ill... more Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms illustrated the identification of cfDNA fragments using cutoff of ≤150 bp, samples with at least one detected cfDNA peak shorter than or equal to 150 bp are considered positive, whereas samples with all cfDNA peaks longer than 150 bp are considered negative. (B) The electropherograms represented the distribution of all detectable peak of cfDNA found in plasma samples from osteosarcoma patients. The table demonstrated the detectable sub-peaks and main peaks in each sample.
Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size i... more Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size in plasma from (A) healthy donors (n=15) and (B) osteosarcoma (n=50). (C) Comparison of cfDNA fragment size distribution pattern between healthy control, patient with osteosarcoma stage IIb, and osteosarcoma stage III. All results were analyzed by QIAxcel screengel software.
Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size i... more Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size in plasma from (A) healthy donors (n=15) and (B) osteosarcoma (n=50). (C) Comparison of cfDNA fragment size distribution pattern between healthy control, patient with osteosarcoma stage IIb, and osteosarcoma stage III. All results were analyzed by QIAxcel screengel software.
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them ... more Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment...
Purpose:Cell-free DNA (cfDNA) analysis is a powerful tool for noninvasively predicting patient ou... more Purpose:Cell-free DNA (cfDNA) analysis is a powerful tool for noninvasively predicting patient outcomes. We analyzed the size distribution of cfDNA and assessed its prognostic and diagnostic values in an osteosarcoma cohort.Experimental Design:The fragment size distribution and level of cfDNA were analyzed in 15 healthy donors and 50 patients with osteosarcoma using automated capillary electrophoresis. The prognostic performance of cfDNA size analysis was assessed using univariate and multivariable analyses. By performing whole-genome sequencing of matched cfDNA and osteosarcoma tissue samples, we investigated the correlation between the size and mutation profiles of cfDNA and the mutation concordance between cfDNA and paired tissue tumors.Results:The size of cfDNA fragments in patients with osteosarcoma was significantly shorter than in healthy donors, with the integrative analysis of size distribution and level of cfDNA achieving a high specificity and sensitivity of 100%. The sho...
This study was aimed to investigate relevant aspects of effect from nano-ranged low-energy plasma... more This study was aimed to investigate relevant aspects of effect from nano-ranged low-energy plasma ion bombardment of DNA on mutation induction for fundamental understanding of low-energy ion effect on life. Samples of extracellular plasmid DNA pUC19 and DNA fragment containing lacZ gene (encoding β-galactosidase) were directly bombarded using the nitrogen plasma immersion ion implantation (PIII) method with varied bias in an order of kV and varied fluences in an order of 1015 ions/cm2. The PIII-treated DNA and DNA fragment were transferred using the electroporation into bacteria Escherichia coli (E. coli) to observe mutation induction. Mutant DNA was sequenced. The mutation frequencies as a function of the bias voltage at a fixed fluence and as a function of the fluence at a fixed bias were found to increase linearly as increasing of the bias or the fluence. Damage in the lacZ gene was thereafter identified as being responsible for the bacterial mutation induced by PIII of DNA. DNA ...
Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms ill... more Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms illustrated the identification of cfDNA fragments using cutoff of ≤150 bp, samples with at least one detected cfDNA peak shorter than or equal to 150 bp are considered positive, whereas samples with all cfDNA peaks longer than 150 bp are considered negative. (B) The electropherograms represented the distribution of all detectable peak of cfDNA found in plasma samples from osteosarcoma patients. The table demonstrated the detectable sub-peaks and main peaks in each sample.
Purpose: Cell-free DNA analysis is a powerful tool for non-invasively predicting patient outcomes... more Purpose: Cell-free DNA analysis is a powerful tool for non-invasively predicting patient outcomes. We analyzed the size distribution of cfDNA and assessed its prognostic and diagnostic values in an osteosarcoma cohort. Experimental Design: The fragment size distribution and level of cfDNA were analyzed in 15 healthy donors and 50 osteosarcoma patients using automated capillary electrophoresis. The prognostic performance of cfDNA size analysis was assessed using univariate and multivariable analyses. By performing whole-genome sequencing of matched cfDNA and osteosarcoma tissue samples, we investigated the correlation between the size and mutation profiles of cfDNA and the mutation concordance between cfDNA and paired tissue tumors. Results: The size of cfDNA fragments in osteosarcoma patients was significantly shorter than in healthy donors, with the integrative analysis of size distribution and level of cfDNA achieving a high specificity and sensitivity of 100%. The short cfDNA fra...
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2012
ABSTRACT DNA conformation change or damage induced by low-energy ion irradiation has been of grea... more ABSTRACT DNA conformation change or damage induced by low-energy ion irradiation has been of great interest owing to research developments in ion beam biotechnology and ion beam application in biomedicine. Mechanisms involved in the induction of DNA damage may account for effect from implanting ion charge. In order to check this effect, we used both ion beam and neutralized beam at keV energy to bombard naked DNA. Argon or nitrogen ion beam was generated and extracted from a radiofrequency (RF) ion source and neutralized by microwave-driven plasma in the beam path. Plasmid DNA pGFP samples were irradiated with the ion or neutralized beam in vacuum, followed by gel electrophoresis to observe changes in the DNA conformations. It was revealed that the ion charge played a certain role in inducing DNA conformation change. The subsequent DNA transfer into bacteria Escherichia coli (E. coli) for mutation analysis indicated that the charged ion beam induced DNA change had high potential in mutation induction while neutralized beam did not. The intrinsic reason was attributed to additional DNA deformation and contortion caused by ion charge exchange effect so that the ion beam induced DNA damage could hardly be completely repaired, whereas the neutralized beam induced DNA change could be more easily recoverable owing to absence of the additional DNA deformation and contortion.
ABSTRACT Low-energy ion beams at a few tens of keV were demonstrated to be able to induce exogeno... more ABSTRACT Low-energy ion beams at a few tens of keV were demonstrated to be able to induce exogenous macromolecules to transfer into plant and bacterial cells. In the process, the ion beam with well controlled energy and fluence bombarded living cells to cause certain degree damage in the cell envelope in nanoscales to facilitate the macromolecules such as DNA to pass through the cell envelope and enter the cell. Consequently, the technique was applied for manipulating positive improvements in the biological species. This physical DNA transfer method was highly efficient and had less risk of side-effects compared with chemical and biological methods. For better understanding of mechanisms involved in the process, a systematic study on the mechanisms was carried out. Applications of the technique were also expanded from DNA transfer in plant and bacterial cells to DNA transfection in human cancer cells potentially for the stem cell therapy purpose. Low-energy nitrogen and argon ion beams that were applied in our experiments had ranges of 100 nm or less in the cell envelope membrane which was majorly composed of polymeric cellulose. The ion beam bombardment caused chain-scission dominant damage in the polymer and electrical property changes such as increase in the impedance in the envelope membrane. These nano-modifications of the cell envelope eventually enhanced the permeability of the envelope membrane to favor the DNA transfer. The paper reports details of our research in this direction.
Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to ... more Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our r...
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2014
ABSTRACT This work is on a novel application of ion beam effect on biological mutation. Bacillus ... more ABSTRACT This work is on a novel application of ion beam effect on biological mutation. Bacillus licheniformis (B. licheniformis) is a common soil bacterium with an antagonistic effect on Curcuma alismatifolia Gagnep. and Chrysanthemum indicum Linn. In an attempt to control fungal diseases of local crops by utilizing B. licheniformis, we carried out gene analysis of the bacterium to understand the bacterial antagonistic mechanism. The bacterial cells were bombarded to induce mutations using nitrogen ion beam. After ion bombardment, DNA analysis revealed that the modified polymorphism fragment present in the wild type was missing in a bacterial mutant which lost the antifungal activity. The fragments conserved in the wild type but lost in the mutant bacteria was identified to code for the thioredoxin reductase (TrxR) gene. The gene analysis showed that the TrxR gene from B. licheniformis had the expression of the antagonism to fungi in a synchronous time evolution with the fungus inhibition when the bacteria were co-cultivated with the fungi. The collective results indicate the TrxR gene responsible for the antagonism of bacteria B. licheniformis to fungal infection.
Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy ra... more Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy range, it is very interesting to know effects from ultra-low-energy ion interaction with DNA for understanding ion-beam-induced genetic mutation. Tens-keV Ar- and N-ion beams were decelerated to ultra-low energy ranging from 20 to 100 eV, or only a few to 10 eV/u, to bombard naked plasmid DNA. The bombarded DNA was analyzed using gel electrophoresis for DNA form changes. The original DNA supercoiled form was found to change to relaxed and linear forms, indicating single or double strand breaks after bombarded by tens-eV ion beam. N-ion beam was found more effective in inducing DNA change and mutation than Ar-ion beam. The study demonstrated that the ion bombardment with energy as low as several-tens eV was able to break DNA strands and thus potentially to cause genetic modification of biological cells. The experimental results were discussed in terms of direct atomic collision between the ...
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2013
ABSTRACT Low-energy ion beam biotechnology has achieved tremendous successes in inducing crop mut... more ABSTRACT Low-energy ion beam biotechnology has achieved tremendous successes in inducing crop mutation and gene transfer. However, mechanisms involved in the related processes are not yet well understood. In ion-beam-induced mutation, ion-bombardment-produced X-ray has been proposed to be one of the secondary mutation sources, but the speculation has not yet been experimentally tested. We carried out this investigation to test whether the low-energy ion-beam-produced X-ray was a source of ion-beam-induced mutation. In the investigation, X-ray emission from 29-keV nitrogen- or argon- ion beam bombarded bacterial Escherichia coli (E. coli) cells held in a metal or plastic sample holder was in situ detected using a highly sensitive X-ray detector. The ion beam bombarded bacterial cells held in different material holders were observed for mutation induction. The results led to a conclusion that secondary X-ray emitted from ion-beam-bombarded biological living materials themselves was not a, or at least a negligible, mutational source, but the ion-beam-induced X-ray emission from the metal that made the sample holder could be a source of mutation.
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2014
ABSTRACT As a useful ion beam biotechnology, ion-bombardment-induced DNA transfer into bacterial ... more ABSTRACT As a useful ion beam biotechnology, ion-bombardment-induced DNA transfer into bacterial Escherichia coli (E. coli) cells has been successfully operated using argon ions. In the process ion bombardment of the bacterial cells modifies the cell envelope materials to favor the exogenous DNA molecules to pass through the envelope to enter the cell. The occurrence of the DNA transfer induction was found ion energy and fluence dependent in a complex manner. At ion energy of a few keV and a few tens of keV to moderate fluences the DNA transfer could be induced by ion bombardment of the bacterial cells, while at the same ion energy but to high fluences DNA transfer could not be induced. On the other hand, when the ion energy was medium, about 10–20 keV, the DNA transfer could not be induced by ion bombardment of the cells. The complexity of the experimental results indicated a complex mechanism which should be related to the complex structure of the bacterial E. coli cell envelope. A phase diagram was proposed to interpret different mechanisms involved as functions of the ion energy and fluence.
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2014
ABSTRACT Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-... more ABSTRACT Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy range, it is very interesting to know effects from ultra-low-energy ion interaction with DNA for understanding ion-beam-induced genetic mutation. Tens-keV Ar- and N-ion beams were decelerated to ultra-low energy ranging from 20 to 100 eV, or only a few to 10 eV/u, to bombard naked plasmid DNA. The bombarded DNA was analyzed using gel electrophoresis for DNA form changes. The original DNA supercoiled form was found to change to relaxed and linear forms, indicating single or double strand breaks after bombarded by tens-eV ion beam. N-ion beam was found more effective in inducing DNA change and mutation than Ar-ion beam. The study demonstrated that the ion bombardment with energy as low as several-tens eV was able to break DNA strands and thus potentially to cause genetic modification of biological cells. The experimental results were discussed in terms of direct atomic collision between the ions and DNA atoms.
Supplementary figure 3. The comparison of cfDNA fragment size distribution pattern between two te... more Supplementary figure 3. The comparison of cfDNA fragment size distribution pattern between two techniques analysis; automated capillary electrophoresis and genome wide sequencing of sample (A) OS07 (B) OS08, and (C) OS10. For automated capillary electrophoresis, the distribution of cfDNA fragment was analyzed and presented as electropherogram by QIAxcel screengel software. While all read of insert size obtained from whole-genome sequencing was plotted as histogram using Picard software.
Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms ill... more Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms illustrated the identification of cfDNA fragments using cutoff of ≤150 bp, samples with at least one detected cfDNA peak shorter than or equal to 150 bp are considered positive, whereas samples with all cfDNA peaks longer than 150 bp are considered negative. (B) The electropherograms represented the distribution of all detectable peak of cfDNA found in plasma samples from osteosarcoma patients. The table demonstrated the detectable sub-peaks and main peaks in each sample.
Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size i... more Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size in plasma from (A) healthy donors (n=15) and (B) osteosarcoma (n=50). (C) Comparison of cfDNA fragment size distribution pattern between healthy control, patient with osteosarcoma stage IIb, and osteosarcoma stage III. All results were analyzed by QIAxcel screengel software.
Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size i... more Supplementary figure 2. Gel image analysis demonstrated the distribution of cfDNA fragment size in plasma from (A) healthy donors (n=15) and (B) osteosarcoma (n=50). (C) Comparison of cfDNA fragment size distribution pattern between healthy control, patient with osteosarcoma stage IIb, and osteosarcoma stage III. All results were analyzed by QIAxcel screengel software.
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them ... more Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment...
Purpose:Cell-free DNA (cfDNA) analysis is a powerful tool for noninvasively predicting patient ou... more Purpose:Cell-free DNA (cfDNA) analysis is a powerful tool for noninvasively predicting patient outcomes. We analyzed the size distribution of cfDNA and assessed its prognostic and diagnostic values in an osteosarcoma cohort.Experimental Design:The fragment size distribution and level of cfDNA were analyzed in 15 healthy donors and 50 patients with osteosarcoma using automated capillary electrophoresis. The prognostic performance of cfDNA size analysis was assessed using univariate and multivariable analyses. By performing whole-genome sequencing of matched cfDNA and osteosarcoma tissue samples, we investigated the correlation between the size and mutation profiles of cfDNA and the mutation concordance between cfDNA and paired tissue tumors.Results:The size of cfDNA fragments in patients with osteosarcoma was significantly shorter than in healthy donors, with the integrative analysis of size distribution and level of cfDNA achieving a high specificity and sensitivity of 100%. The sho...
This study was aimed to investigate relevant aspects of effect from nano-ranged low-energy plasma... more This study was aimed to investigate relevant aspects of effect from nano-ranged low-energy plasma ion bombardment of DNA on mutation induction for fundamental understanding of low-energy ion effect on life. Samples of extracellular plasmid DNA pUC19 and DNA fragment containing lacZ gene (encoding β-galactosidase) were directly bombarded using the nitrogen plasma immersion ion implantation (PIII) method with varied bias in an order of kV and varied fluences in an order of 1015 ions/cm2. The PIII-treated DNA and DNA fragment were transferred using the electroporation into bacteria Escherichia coli (E. coli) to observe mutation induction. Mutant DNA was sequenced. The mutation frequencies as a function of the bias voltage at a fixed fluence and as a function of the fluence at a fixed bias were found to increase linearly as increasing of the bias or the fluence. Damage in the lacZ gene was thereafter identified as being responsible for the bacterial mutation induced by PIII of DNA. DNA ...
Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms ill... more Supplementary figure 1. To identify peak of cfDNA fragments, (A) the scheme electropherograms illustrated the identification of cfDNA fragments using cutoff of ≤150 bp, samples with at least one detected cfDNA peak shorter than or equal to 150 bp are considered positive, whereas samples with all cfDNA peaks longer than 150 bp are considered negative. (B) The electropherograms represented the distribution of all detectable peak of cfDNA found in plasma samples from osteosarcoma patients. The table demonstrated the detectable sub-peaks and main peaks in each sample.
Purpose: Cell-free DNA analysis is a powerful tool for non-invasively predicting patient outcomes... more Purpose: Cell-free DNA analysis is a powerful tool for non-invasively predicting patient outcomes. We analyzed the size distribution of cfDNA and assessed its prognostic and diagnostic values in an osteosarcoma cohort. Experimental Design: The fragment size distribution and level of cfDNA were analyzed in 15 healthy donors and 50 osteosarcoma patients using automated capillary electrophoresis. The prognostic performance of cfDNA size analysis was assessed using univariate and multivariable analyses. By performing whole-genome sequencing of matched cfDNA and osteosarcoma tissue samples, we investigated the correlation between the size and mutation profiles of cfDNA and the mutation concordance between cfDNA and paired tissue tumors. Results: The size of cfDNA fragments in osteosarcoma patients was significantly shorter than in healthy donors, with the integrative analysis of size distribution and level of cfDNA achieving a high specificity and sensitivity of 100%. The short cfDNA fra...
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2012
ABSTRACT DNA conformation change or damage induced by low-energy ion irradiation has been of grea... more ABSTRACT DNA conformation change or damage induced by low-energy ion irradiation has been of great interest owing to research developments in ion beam biotechnology and ion beam application in biomedicine. Mechanisms involved in the induction of DNA damage may account for effect from implanting ion charge. In order to check this effect, we used both ion beam and neutralized beam at keV energy to bombard naked DNA. Argon or nitrogen ion beam was generated and extracted from a radiofrequency (RF) ion source and neutralized by microwave-driven plasma in the beam path. Plasmid DNA pGFP samples were irradiated with the ion or neutralized beam in vacuum, followed by gel electrophoresis to observe changes in the DNA conformations. It was revealed that the ion charge played a certain role in inducing DNA conformation change. The subsequent DNA transfer into bacteria Escherichia coli (E. coli) for mutation analysis indicated that the charged ion beam induced DNA change had high potential in mutation induction while neutralized beam did not. The intrinsic reason was attributed to additional DNA deformation and contortion caused by ion charge exchange effect so that the ion beam induced DNA damage could hardly be completely repaired, whereas the neutralized beam induced DNA change could be more easily recoverable owing to absence of the additional DNA deformation and contortion.
ABSTRACT Low-energy ion beams at a few tens of keV were demonstrated to be able to induce exogeno... more ABSTRACT Low-energy ion beams at a few tens of keV were demonstrated to be able to induce exogenous macromolecules to transfer into plant and bacterial cells. In the process, the ion beam with well controlled energy and fluence bombarded living cells to cause certain degree damage in the cell envelope in nanoscales to facilitate the macromolecules such as DNA to pass through the cell envelope and enter the cell. Consequently, the technique was applied for manipulating positive improvements in the biological species. This physical DNA transfer method was highly efficient and had less risk of side-effects compared with chemical and biological methods. For better understanding of mechanisms involved in the process, a systematic study on the mechanisms was carried out. Applications of the technique were also expanded from DNA transfer in plant and bacterial cells to DNA transfection in human cancer cells potentially for the stem cell therapy purpose. Low-energy nitrogen and argon ion beams that were applied in our experiments had ranges of 100 nm or less in the cell envelope membrane which was majorly composed of polymeric cellulose. The ion beam bombardment caused chain-scission dominant damage in the polymer and electrical property changes such as increase in the impedance in the envelope membrane. These nano-modifications of the cell envelope eventually enhanced the permeability of the envelope membrane to favor the DNA transfer. The paper reports details of our research in this direction.
Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to ... more Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our r...
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2014
ABSTRACT This work is on a novel application of ion beam effect on biological mutation. Bacillus ... more ABSTRACT This work is on a novel application of ion beam effect on biological mutation. Bacillus licheniformis (B. licheniformis) is a common soil bacterium with an antagonistic effect on Curcuma alismatifolia Gagnep. and Chrysanthemum indicum Linn. In an attempt to control fungal diseases of local crops by utilizing B. licheniformis, we carried out gene analysis of the bacterium to understand the bacterial antagonistic mechanism. The bacterial cells were bombarded to induce mutations using nitrogen ion beam. After ion bombardment, DNA analysis revealed that the modified polymorphism fragment present in the wild type was missing in a bacterial mutant which lost the antifungal activity. The fragments conserved in the wild type but lost in the mutant bacteria was identified to code for the thioredoxin reductase (TrxR) gene. The gene analysis showed that the TrxR gene from B. licheniformis had the expression of the antagonism to fungi in a synchronous time evolution with the fungus inhibition when the bacteria were co-cultivated with the fungi. The collective results indicate the TrxR gene responsible for the antagonism of bacteria B. licheniformis to fungal infection.
Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy ra... more Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy range, it is very interesting to know effects from ultra-low-energy ion interaction with DNA for understanding ion-beam-induced genetic mutation. Tens-keV Ar- and N-ion beams were decelerated to ultra-low energy ranging from 20 to 100 eV, or only a few to 10 eV/u, to bombard naked plasmid DNA. The bombarded DNA was analyzed using gel electrophoresis for DNA form changes. The original DNA supercoiled form was found to change to relaxed and linear forms, indicating single or double strand breaks after bombarded by tens-eV ion beam. N-ion beam was found more effective in inducing DNA change and mutation than Ar-ion beam. The study demonstrated that the ion bombardment with energy as low as several-tens eV was able to break DNA strands and thus potentially to cause genetic modification of biological cells. The experimental results were discussed in terms of direct atomic collision between the ...
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2013
ABSTRACT Low-energy ion beam biotechnology has achieved tremendous successes in inducing crop mut... more ABSTRACT Low-energy ion beam biotechnology has achieved tremendous successes in inducing crop mutation and gene transfer. However, mechanisms involved in the related processes are not yet well understood. In ion-beam-induced mutation, ion-bombardment-produced X-ray has been proposed to be one of the secondary mutation sources, but the speculation has not yet been experimentally tested. We carried out this investigation to test whether the low-energy ion-beam-produced X-ray was a source of ion-beam-induced mutation. In the investigation, X-ray emission from 29-keV nitrogen- or argon- ion beam bombarded bacterial Escherichia coli (E. coli) cells held in a metal or plastic sample holder was in situ detected using a highly sensitive X-ray detector. The ion beam bombarded bacterial cells held in different material holders were observed for mutation induction. The results led to a conclusion that secondary X-ray emitted from ion-beam-bombarded biological living materials themselves was not a, or at least a negligible, mutational source, but the ion-beam-induced X-ray emission from the metal that made the sample holder could be a source of mutation.
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2014
ABSTRACT As a useful ion beam biotechnology, ion-bombardment-induced DNA transfer into bacterial ... more ABSTRACT As a useful ion beam biotechnology, ion-bombardment-induced DNA transfer into bacterial Escherichia coli (E. coli) cells has been successfully operated using argon ions. In the process ion bombardment of the bacterial cells modifies the cell envelope materials to favor the exogenous DNA molecules to pass through the envelope to enter the cell. The occurrence of the DNA transfer induction was found ion energy and fluence dependent in a complex manner. At ion energy of a few keV and a few tens of keV to moderate fluences the DNA transfer could be induced by ion bombardment of the bacterial cells, while at the same ion energy but to high fluences DNA transfer could not be induced. On the other hand, when the ion energy was medium, about 10–20 keV, the DNA transfer could not be induced by ion bombardment of the cells. The complexity of the experimental results indicated a complex mechanism which should be related to the complex structure of the bacterial E. coli cell envelope. A phase diagram was proposed to interpret different mechanisms involved as functions of the ion energy and fluence.
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2014
ABSTRACT Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-... more ABSTRACT Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy range, it is very interesting to know effects from ultra-low-energy ion interaction with DNA for understanding ion-beam-induced genetic mutation. Tens-keV Ar- and N-ion beams were decelerated to ultra-low energy ranging from 20 to 100 eV, or only a few to 10 eV/u, to bombard naked plasmid DNA. The bombarded DNA was analyzed using gel electrophoresis for DNA form changes. The original DNA supercoiled form was found to change to relaxed and linear forms, indicating single or double strand breaks after bombarded by tens-eV ion beam. N-ion beam was found more effective in inducing DNA change and mutation than Ar-ion beam. The study demonstrated that the ion bombardment with energy as low as several-tens eV was able to break DNA strands and thus potentially to cause genetic modification of biological cells. The experimental results were discussed in terms of direct atomic collision between the ions and DNA atoms.
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