PeerJ:Biophysicshttps://peerj.com/articles/index.atom?journal=peerj&subject=600Biophysics articles published in PeerJA Cellular Potts Model of the interplay of synchronization and aggregationhttps://peerj.com/articles/169742024-02-292024-02-29Rose UnaTilmann Glimm
We investigate the behavior of systems of cells with intracellular molecular oscillators (“clocks”) where cell-cell adhesion is mediated by differences in clock phase between neighbors. This is motivated by phenomena in developmental biology and in aggregative multicellularity of unicellular organisms. In such systems, aggregation co-occurs with clock synchronization. To account for the effects of spatially extended cells, we use the Cellular Potts Model (CPM), a lattice agent-based model. We find four distinct possible phases: global synchronization, local synchronization, incoherence, and anti-synchronization (checkerboard patterns). We characterize these phases via order parameters. In the case of global synchrony, the speed of synchronization depends on the adhesive effects of the clocks. Synchronization happens fastest when cells in opposite phases adhere the strongest (“opposites attract”). When cells of the same clock phase adhere the strongest (“like attracts like”), synchronization is slower. Surprisingly, the slowest synchronization happens in the diffusive mixing case, where cell-cell adhesion is independent of clock phase. We briefly discuss potential applications of the model, such as pattern formation in the auditory sensory epithelium.
We investigate the behavior of systems of cells with intracellular molecular oscillators (“clocks”) where cell-cell adhesion is mediated by differences in clock phase between neighbors. This is motivated by phenomena in developmental biology and in aggregative multicellularity of unicellular organisms. In such systems, aggregation co-occurs with clock synchronization. To account for the effects of spatially extended cells, we use the Cellular Potts Model (CPM), a lattice agent-based model. We find four distinct possible phases: global synchronization, local synchronization, incoherence, and anti-synchronization (checkerboard patterns). We characterize these phases via order parameters. In the case of global synchrony, the speed of synchronization depends on the adhesive effects of the clocks. Synchronization happens fastest when cells in opposite phases adhere the strongest (“opposites attract”). When cells of the same clock phase adhere the strongest (“like attracts like”), synchronization is slower. Surprisingly, the slowest synchronization happens in the diffusive mixing case, where cell-cell adhesion is independent of clock phase. We briefly discuss potential applications of the model, such as pattern formation in the auditory sensory epithelium.Multiscale transport and 4D time-lapse imaging in precision-cut liver slices (PCLS)https://peerj.com/articles/169942024-02-262024-02-26Iqra AzamJames D. Benson
Background
Monitoring cellular processes across different levels of complexity, from the cellular to the tissue scale, is important for understanding tissue structure and function. However, it is challenging to monitor and estimate these structural and dynamic interactions within three-dimensional (3D) tissue models.
Objective
The aim of this study was to design a method for imaging, tracking, and quantifying 3D changes in cell morphology (shape and size) within liver tissue, specifically a precision-cut liver slice (PCLS). A PCLS is a 3D model of the liver that allows the study of the structure and function of liver cells in their native microenvironment.
Methods
Here, we present a method for imaging liver tissue during anisosmotic exposure in a multispectral four-dimensional manner. Three metrics of tissue morphology were measured to quantify the effects of osmotic stress on liver tissue. We estimated the changes in the volume of whole precision cut liver slices, quantified the changes in nuclei position, and calculated the changes in volumetric responses of tissue-embedded cells.
Results
During equilibration with cell-membrane-permeating and non-permeating solutes, the whole tissue experiences shrinkage and expansion. As nuclei showed a change in position and directional displacement under osmotic stress, we demonstrate that nuclei could be used as a probe to measure local osmotic and mechanical stress. Moreover, we demonstrate that cells change their volume within tissue slices as a result of osmotic perturbation and that this change in volume is dependent on the position of the cell within the tissue and the duration of the exposure.
Conclusion
The results of this study have implications for a better understanding of multiscale transport, mechanobiology, and triggered biological responses within complex biological structures.
Background
Monitoring cellular processes across different levels of complexity, from the cellular to the tissue scale, is important for understanding tissue structure and function. However, it is challenging to monitor and estimate these structural and dynamic interactions within three-dimensional (3D) tissue models.
Objective
The aim of this study was to design a method for imaging, tracking, and quantifying 3D changes in cell morphology (shape and size) within liver tissue, specifically a precision-cut liver slice (PCLS). A PCLS is a 3D model of the liver that allows the study of the structure and function of liver cells in their native microenvironment.
Methods
Here, we present a method for imaging liver tissue during anisosmotic exposure in a multispectral four-dimensional manner. Three metrics of tissue morphology were measured to quantify the effects of osmotic stress on liver tissue. We estimated the changes in the volume of whole precision cut liver slices, quantified the changes in nuclei position, and calculated the changes in volumetric responses of tissue-embedded cells.
Results
During equilibration with cell-membrane-permeating and non-permeating solutes, the whole tissue experiences shrinkage and expansion. As nuclei showed a change in position and directional displacement under osmotic stress, we demonstrate that nuclei could be used as a probe to measure local osmotic and mechanical stress. Moreover, we demonstrate that cells change their volume within tissue slices as a result of osmotic perturbation and that this change in volume is dependent on the position of the cell within the tissue and the duration of the exposure.
Conclusion
The results of this study have implications for a better understanding of multiscale transport, mechanobiology, and triggered biological responses within complex biological structures.Arthrological reconstructions of the pterosaur neck and their implications for the cervical position at resthttps://peerj.com/articles/168842024-02-212024-02-21Richard BuchmannTaissa Rodrigues
The lack of any pterosaur living descendants creates gaps in the knowledge of the biology of this group, including its cervical biomechanics, which makes it difficult to understand their posture and life habits. To mitigate part of this issue, we reconstructed the cervical osteology and arthrology of three pterosaurs, allowing us to make inferences about the position of the neck of these animals at rest. We used scans of three-dimensionally preserved cervical series of Anhanguera piscator, Azhdarcho lancicollis and Rhamphorhynchus muensteri for the reconstructions, thus representing different lineages. For the recognition of ligaments, joint cartilages, and levels of overlapping of the zygapophyses, we applied the Extant Phylogenetic Bracket method, based on various extant birds and on Caiman latirostris. We inferred that pterosaur intervertebral joints were probably covered by a thin layer of synovial cartilage whose thickness varied along the neck, being thicker in the posterior region. Ignoring this cartilage can affect reconstructions. According to the vertebral angulation, their neck was slightly sinuous when in rest position. Our analyses also indicate that pterosaurs had segmented and supra-segmented articular cervical ligaments, which could confer stabilization, execute passive forces on the neck and store elastic energy.
The lack of any pterosaur living descendants creates gaps in the knowledge of the biology of this group, including its cervical biomechanics, which makes it difficult to understand their posture and life habits. To mitigate part of this issue, we reconstructed the cervical osteology and arthrology of three pterosaurs, allowing us to make inferences about the position of the neck of these animals at rest. We used scans of three-dimensionally preserved cervical series of Anhanguera piscator, Azhdarcho lancicollis and Rhamphorhynchus muensteri for the reconstructions, thus representing different lineages. For the recognition of ligaments, joint cartilages, and levels of overlapping of the zygapophyses, we applied the Extant Phylogenetic Bracket method, based on various extant birds and on Caiman latirostris. We inferred that pterosaur intervertebral joints were probably covered by a thin layer of synovial cartilage whose thickness varied along the neck, being thicker in the posterior region. Ignoring this cartilage can affect reconstructions. According to the vertebral angulation, their neck was slightly sinuous when in rest position. Our analyses also indicate that pterosaurs had segmented and supra-segmented articular cervical ligaments, which could confer stabilization, execute passive forces on the neck and store elastic energy.Nitrogen addition enhances seed yield by improving soil enzyme activity and nutrientshttps://peerj.com/articles/167912024-01-192024-01-19Wenbo MiFeng LuoWenhui LiuYan QinYongchao ZhangKaiqiang LiuWen Li
Nitrogen (N) addition is a simple and effective field management approach to enhancing plant productivity. Nonetheless, the regulatory mechanisms governing nitrogen concentrations and their effect on soil enzyme activity, nutrient levels, and seed yield in the Festuca kirilowii seed field have yet to be elucidated. Therefore, this study sought to investigate the effect of N fertilizer application on soil enzyme activities, soil nutrients, and seed yield of F. kirilowii Steud cv. Huanhu, the only domesticated variety in the Festuca genus of the Poaceae family, was investigated based on two-year field experiments in the Qinghai–Tibet Plateau (QTP). Results showed that N input significantly affected soil nutrients (potential of hydrogen, total nitrogen, organic matter, and total phosphorus). In addition, soil enzyme activities (urease, catalase, sucrase, and nitrate reductase) significantly increased in response to varying N concentrations, inducing changes in soil nutrient contents. Introducing N improved both seed yield and yield components (number of tillers and number of fertile tillers). These findings suggest that the introduction of different concentrations of N fertilizers can stimulate soil enzyme activity, thus hastening nutrient conversion and increasing seed yield. The exhaustive evaluation of the membership function showed that the optimal N fertilizer treatment was N4 (75 kg·hm−2) for both 2022 and 2023. This finding provides a practical recommendation for improving the seed production of F. kirilowii in QTP.
Nitrogen (N) addition is a simple and effective field management approach to enhancing plant productivity. Nonetheless, the regulatory mechanisms governing nitrogen concentrations and their effect on soil enzyme activity, nutrient levels, and seed yield in the Festuca kirilowii seed field have yet to be elucidated. Therefore, this study sought to investigate the effect of N fertilizer application on soil enzyme activities, soil nutrients, and seed yield of F. kirilowii Steud cv. Huanhu, the only domesticated variety in the Festuca genus of the Poaceae family, was investigated based on two-year field experiments in the Qinghai–Tibet Plateau (QTP). Results showed that N input significantly affected soil nutrients (potential of hydrogen, total nitrogen, organic matter, and total phosphorus). In addition, soil enzyme activities (urease, catalase, sucrase, and nitrate reductase) significantly increased in response to varying N concentrations, inducing changes in soil nutrient contents. Introducing N improved both seed yield and yield components (number of tillers and number of fertile tillers). These findings suggest that the introduction of different concentrations of N fertilizers can stimulate soil enzyme activity, thus hastening nutrient conversion and increasing seed yield. The exhaustive evaluation of the membership function showed that the optimal N fertilizer treatment was N4 (75 kg·hm−2) for both 2022 and 2023. This finding provides a practical recommendation for improving the seed production of F. kirilowii in QTP.Carotenoid-dependent singlet oxygen photogeneration in light-harvesting complex 2 of Ectothiorhodospira haloalkaliphila leads to the formation of organic hydroperoxides and damage to both pigments and protein matrixhttps://peerj.com/articles/166152024-01-162024-01-16Denis YanykinMark PaskhinAleksandr Aleksandrovich AshikhminMaxim Alexandrovich Bolshakov
Earlier, it was suggested that carotenoids in light-harvesting complexes 2 (LH2) can generate singlet oxygen, further oxidizing bacteriochlorophyll to 3-acetyl-chlorophyll. In the present work, it was found that illumination of isolated LH2 preparations of purple sulfur bacterium Ectothiorhodospira haloalkaliphila with light in the carotenoid absorption region leads to the photoconsumption of molecular oxygen, which is accompanied by the formation of hydroperoxides of organic molecules in the complexes. Photoformation of two types of organic hydroperoxides were revealed: highly lipophilic (12 molecules per one LH2) and relatively hydrophobic (68 per one LH2). It has been shown that illumination leads to damage to light-harvesting complexes. On the one hand, photobleaching of bacteriochlorophyll and a decrease in its fluorescence intensity are observed. On the other hand, the photoinduced increase in the hydrodynamic radius of the complexes, the reduction in their thermal stability, and the change in fluorescence intensity indicate conformational changes occurring in the protein molecules of the LH2 preparations. Inhibition of the processes described above upon the addition of singlet oxygen quenchers (L-histidine, Trolox, sodium L-ascorbate) may support the hypothesis that carotenoids in LH2 preparations are capable of generating singlet oxygen, which, in turn, damage to protein molecules.
Earlier, it was suggested that carotenoids in light-harvesting complexes 2 (LH2) can generate singlet oxygen, further oxidizing bacteriochlorophyll to 3-acetyl-chlorophyll. In the present work, it was found that illumination of isolated LH2 preparations of purple sulfur bacterium Ectothiorhodospira haloalkaliphila with light in the carotenoid absorption region leads to the photoconsumption of molecular oxygen, which is accompanied by the formation of hydroperoxides of organic molecules in the complexes. Photoformation of two types of organic hydroperoxides were revealed: highly lipophilic (12 molecules per one LH2) and relatively hydrophobic (68 per one LH2). It has been shown that illumination leads to damage to light-harvesting complexes. On the one hand, photobleaching of bacteriochlorophyll and a decrease in its fluorescence intensity are observed. On the other hand, the photoinduced increase in the hydrodynamic radius of the complexes, the reduction in their thermal stability, and the change in fluorescence intensity indicate conformational changes occurring in the protein molecules of the LH2 preparations. Inhibition of the processes described above upon the addition of singlet oxygen quenchers (L-histidine, Trolox, sodium L-ascorbate) may support the hypothesis that carotenoids in LH2 preparations are capable of generating singlet oxygen, which, in turn, damage to protein molecules.Pharmacoscreening, molecular dynamics, and quantum mechanics of inermin from Panax ginseng: a crucial molecule inhibiting exosomal protein target associated with coronary artery disease progressionhttps://peerj.com/articles/164812023-12-062023-12-06Janakiraman VSudhan MAbubakar WaniSheikh F. AhmadAhmed NadeemAshutosh SharmaShiek S. S. J. Ahmed
Background
Exosomes, microvesicles, carry and release several vital molecules across cells, tissues, and organs. Epicardial adipose tissue exosomes are critical in the development and progression of coronary artery disease (CAD). It is hypothesized that exosomes may transport causative molecules from inflamed tissue and deliver to the target tissue and progress CAD. Thus, identifying and inhibiting the CAD-associated proteins that are being transported to other cells via exosomes will help slow the progression of CAD.
Methods
This study uses a systems biological approach that integrates differential gene expression in the CAD, exosomal cargo assessment, protein network construction, and functional enrichment to identify the crucial exosomal cargo protein target. Meanwhile, absorption, distribution, metabolism, and excretion (ADME) screening of Panax ginseng-derived compounds was conducted and then docked against the protein target to identify potential inhibitors and then subjected to molecular dynamics simulation (MDS) to understand the behavior of the protein-ligand complex till 100 nanoseconds. Finally, density functional theory (DFT) calculation was performed on the ligand with the highest affinity with the target.
Results
Through the systems biological approach, Mothers against decapentaplegic homolog 2 protein (SMAD2) was determined as a potential target that linked with PI3K-Akt signaling, Ubiquitin mediated proteolysis, and the focal adhesion pathway. Further, screening of 190 Panax ginseng compounds, 27 showed drug-likeness properties. Inermin, a phytochemical showed good docking with −5.02 kcal/mol and achieved stability confirmation with SMAD2 based on MDS when compared to the known CAD drugs. Additionally, DFT analysis of inermin showed high chemical activity that significantly contributes to effective target binding. Overall, our computational study suggests that inermin could act against SMAD2 and may aid in the management of CAD.
Background
Exosomes, microvesicles, carry and release several vital molecules across cells, tissues, and organs. Epicardial adipose tissue exosomes are critical in the development and progression of coronary artery disease (CAD). It is hypothesized that exosomes may transport causative molecules from inflamed tissue and deliver to the target tissue and progress CAD. Thus, identifying and inhibiting the CAD-associated proteins that are being transported to other cells via exosomes will help slow the progression of CAD.
Methods
This study uses a systems biological approach that integrates differential gene expression in the CAD, exosomal cargo assessment, protein network construction, and functional enrichment to identify the crucial exosomal cargo protein target. Meanwhile, absorption, distribution, metabolism, and excretion (ADME) screening of Panax ginseng-derived compounds was conducted and then docked against the protein target to identify potential inhibitors and then subjected to molecular dynamics simulation (MDS) to understand the behavior of the protein-ligand complex till 100 nanoseconds. Finally, density functional theory (DFT) calculation was performed on the ligand with the highest affinity with the target.
Results
Through the systems biological approach, Mothers against decapentaplegic homolog 2 protein (SMAD2) was determined as a potential target that linked with PI3K-Akt signaling, Ubiquitin mediated proteolysis, and the focal adhesion pathway. Further, screening of 190 Panax ginseng compounds, 27 showed drug-likeness properties. Inermin, a phytochemical showed good docking with −5.02 kcal/mol and achieved stability confirmation with SMAD2 based on MDS when compared to the known CAD drugs. Additionally, DFT analysis of inermin showed high chemical activity that significantly contributes to effective target binding. Overall, our computational study suggests that inermin could act against SMAD2 and may aid in the management of CAD.Metabolomic analyses uncover an inhibitory effect of niclosamide on mitochondrial membrane potential in cholangiocarcinoma cellshttps://peerj.com/articles/165122023-11-222023-11-22Thanaporn KulthawatsiriYingpinyapat KittiratJutarop PhetcharaburaninJittima TomachaBundit PromraksaArporn WangwiwatsinPoramate KlanritAttapol TitapunWatcharin LoilomeNisana Namwat
Background
Niclosamide is an oral anthelminthic drug that has been used for treating tapeworm infections. Its mechanism involves the disturbance of mitochondrial membrane potential that in turn inhibits oxidative phosphorylation leading to ATP depletion. To date, niclosamide has been validated as the potent anti-cancer agent against several cancers. However, the molecular mechanisms underlying the effects of niclosamide on the liver fluke Opisthorchis viverrini (Ov)-associated cholangiocarcinoma (CCA) cell functions remain to be elucidated. The aims of this study were to investigate the effects of niclosamide on CCA cell proliferation and on metabolic phenoconversion through the alteration of metabolites associated with mitochondrial function in CCA cell lines.
Materials and Methods
The inhibitory effect of niclosamide on CCA cells was determined using SRB assay. A mitochondrial membrane potential using tetramethylrhodamine, ethyl ester-mitochondrial membrane potential (TMRE-MMP) assay was conducted. Liquid chromatography-mass spectrometry-based metabolomics was employed to investigate the global metabolic changes upon niclosamide treatment. ATP levels were measured using CellTiter-Glo® luminescent cell viability assay. NAD metabolism was examined by the NAD+/NADH ratio.
Results
Niclosamide strongly inhibited CCA cell growth and reduced the MMP of CCA cells. An orthogonal partial-least square regression analysis revealed that the effects of niclosamide on suppressing cell viability and MMP of CCA cells were significantly associated with an increase in niacinamide, a precursor in NAD synthesis that may disrupt the electron transport system leading to suppression of NAD+/NADH ratio and ATP depletion.
Conclusion
Our findings unravel the mode of action of niclosamide in the energy depletion that could potentially serve as the promising therapeutic strategy for CCA treatment.
Background
Niclosamide is an oral anthelminthic drug that has been used for treating tapeworm infections. Its mechanism involves the disturbance of mitochondrial membrane potential that in turn inhibits oxidative phosphorylation leading to ATP depletion. To date, niclosamide has been validated as the potent anti-cancer agent against several cancers. However, the molecular mechanisms underlying the effects of niclosamide on the liver fluke Opisthorchis viverrini (Ov)-associated cholangiocarcinoma (CCA) cell functions remain to be elucidated. The aims of this study were to investigate the effects of niclosamide on CCA cell proliferation and on metabolic phenoconversion through the alteration of metabolites associated with mitochondrial function in CCA cell lines.
Materials and Methods
The inhibitory effect of niclosamide on CCA cells was determined using SRB assay. A mitochondrial membrane potential using tetramethylrhodamine, ethyl ester-mitochondrial membrane potential (TMRE-MMP) assay was conducted. Liquid chromatography-mass spectrometry-based metabolomics was employed to investigate the global metabolic changes upon niclosamide treatment. ATP levels were measured using CellTiter-Glo® luminescent cell viability assay. NAD metabolism was examined by the NAD+/NADH ratio.
Results
Niclosamide strongly inhibited CCA cell growth and reduced the MMP of CCA cells. An orthogonal partial-least square regression analysis revealed that the effects of niclosamide on suppressing cell viability and MMP of CCA cells were significantly associated with an increase in niacinamide, a precursor in NAD synthesis that may disrupt the electron transport system leading to suppression of NAD+/NADH ratio and ATP depletion.
Conclusion
Our findings unravel the mode of action of niclosamide in the energy depletion that could potentially serve as the promising therapeutic strategy for CCA treatment.Osmotic response during kidney perfusion with cryoprotectant in isotonic or hypotonic vehicle solutionhttps://peerj.com/articles/163232023-11-212023-11-21Ross M. WarnerJun YangAndrew DrakeYoungjoo LeeSarah NemanicDavid ScottAdam Z. Higgins
Organ cryopreservation would revolutionize transplantation by overcoming the shelf-life limitations of conventional organ storage. To prepare an organ for cryopreservation, it is first perfused with cryoprotectants (CPAs). These chemicals can enable vitrification during cooling, preventing ice damage. However, CPAs can also cause toxicity and osmotic damage. It is a major challenge to find the optimal balance between protecting the cells from ice and avoiding CPA-induced damage. In this study, we examined the organ perfusion process to shed light on phenomena relevant to cryopreservation protocol design, including changes in organ size and vascular resistance. In particular, we compared perfusion of kidneys (porcine and human) with CPA in either hypotonic or isotonic vehicle solution. Our results demonstrate that CPA perfusion causes kidney mass changes consistent with the shrink-swell response observed in cells. This response was observed when the kidneys were relatively fresh, but disappeared after prolonged warm and/or cold ischemia. Perfusion with CPA in a hypotonic vehicle solution led to a significant increase in vascular resistance, suggesting reduced capillary diameter due to cell swelling. This could be reversed by switching to perfusion with CPA in isotonic vehicle solution. Hypotonic vehicle solution did not cause notable osmotic damage, as evidenced by low levels of lactate dehydrogenase (LDH) in the effluent, and it did not have a statistically significant effect on the delivery of CPA into the kidney, as assessed by computed tomography (CT). Overall, our results show that CPA vehicle solution tonicity affects organ size and vascular resistance, which may have important implications for cryopreservation protocol design.
Organ cryopreservation would revolutionize transplantation by overcoming the shelf-life limitations of conventional organ storage. To prepare an organ for cryopreservation, it is first perfused with cryoprotectants (CPAs). These chemicals can enable vitrification during cooling, preventing ice damage. However, CPAs can also cause toxicity and osmotic damage. It is a major challenge to find the optimal balance between protecting the cells from ice and avoiding CPA-induced damage. In this study, we examined the organ perfusion process to shed light on phenomena relevant to cryopreservation protocol design, including changes in organ size and vascular resistance. In particular, we compared perfusion of kidneys (porcine and human) with CPA in either hypotonic or isotonic vehicle solution. Our results demonstrate that CPA perfusion causes kidney mass changes consistent with the shrink-swell response observed in cells. This response was observed when the kidneys were relatively fresh, but disappeared after prolonged warm and/or cold ischemia. Perfusion with CPA in a hypotonic vehicle solution led to a significant increase in vascular resistance, suggesting reduced capillary diameter due to cell swelling. This could be reversed by switching to perfusion with CPA in isotonic vehicle solution. Hypotonic vehicle solution did not cause notable osmotic damage, as evidenced by low levels of lactate dehydrogenase (LDH) in the effluent, and it did not have a statistically significant effect on the delivery of CPA into the kidney, as assessed by computed tomography (CT). Overall, our results show that CPA vehicle solution tonicity affects organ size and vascular resistance, which may have important implications for cryopreservation protocol design.A systematic review on physical mutagens in rice breeding in Southeast Asiahttps://peerj.com/articles/156822023-10-182023-10-18Rosina BaaduKhim Phin ChongJualang Azlan GansauMuhammad Rawi Mohamed ZinJedol Dayou
In the 1920s, Lewis Stadler initiated the introduction of permanent improvements to the genetic makeup of irradiated plants. Since then, studies related to breeding mutations have grown, as efforts have been made to expand and improve crop productivity and quality. Stadler’s discovery began with x-rays on corn and barley and later extended to the use of gamma-rays, thermal, and fast neutrons in crops. Radiation has since been shown to be an effective and unique method for increasing the genetic variability of species, including rice. Numerous systematic reviews have been conducted on the impact of physical mutagens on the production and grain quality of rice in Southeast Asia. However, the existing literature still lacks information on the type of radiation used, the rice planting materials used, the dosage of physical mutagens, and the differences in mutated characteristics. Therefore, this article aims to review existing literature on the use of physical mutagens in rice crops in Southeast Asian countries. Guided by the PRISMA Statement review method, 28 primary studies were identified through a systematic review of the Scopus, Science Direct, Emerald Insight, Multidisciplinary Digital Publishing, and MDPI journal databases published between 2016 and 2020. The results show that 96% of the articles used seeds as planting materials, and 80% of the articles focused on gamma-rays as a source of physical mutagens. The optimal dosage of gamma-rays applied was around 100 to 250 Gy to improve plant development, abiotic stress, biochemical properties, and nutritional and industrial quality of rice.
In the 1920s, Lewis Stadler initiated the introduction of permanent improvements to the genetic makeup of irradiated plants. Since then, studies related to breeding mutations have grown, as efforts have been made to expand and improve crop productivity and quality. Stadler’s discovery began with x-rays on corn and barley and later extended to the use of gamma-rays, thermal, and fast neutrons in crops. Radiation has since been shown to be an effective and unique method for increasing the genetic variability of species, including rice. Numerous systematic reviews have been conducted on the impact of physical mutagens on the production and grain quality of rice in Southeast Asia. However, the existing literature still lacks information on the type of radiation used, the rice planting materials used, the dosage of physical mutagens, and the differences in mutated characteristics. Therefore, this article aims to review existing literature on the use of physical mutagens in rice crops in Southeast Asian countries. Guided by the PRISMA Statement review method, 28 primary studies were identified through a systematic review of the Scopus, Science Direct, Emerald Insight, Multidisciplinary Digital Publishing, and MDPI journal databases published between 2016 and 2020. The results show that 96% of the articles used seeds as planting materials, and 80% of the articles focused on gamma-rays as a source of physical mutagens. The optimal dosage of gamma-rays applied was around 100 to 250 Gy to improve plant development, abiotic stress, biochemical properties, and nutritional and industrial quality of rice.Rational synthesis of total damage during cryoprotectant equilibration: modelling and experimental validation of osmomechanical, temperature, and cytotoxic damage in sea urchin (Paracentrotus lividus) oocyteshttps://peerj.com/articles/155392023-09-012023-09-01Dominic J. OlverPablo HeresEstefania ParedesJames D. Benson
Sea urchins (e.g., Paracentrotus lividus) are important for both aquaculture and as model species. Despite their importance, biobanking of urchin oocytes by cryopreservation is currently not possible. Optimized cryoprotectant loading may enable novel vitrification methods and thus successful cryopreservation of oocytes. One method for determining an optimized loading protocol uses membrane characteristics and models of damage, namely osmomechanical damage, temperature damage (e.g., chill injury) and cytotoxicity. Here we present and experimentally evaluate existing and novel models of these damage modalities as a function of time and temperature. In osmomechanical damage experiments, oocytes were exposed for 2 to 30 minutes in hypertonic NaCl or sucrose supplemented seawater or in hypotonic diluted seawater. In temperature damage experiments, oocytes were exposed to 1.7 °C, 10 °C, or 20 °C for 2 to 90 minutes. Cytotoxicity was investigated by exposing oocytes to solutions of Me2SO for 2 to 30 minutes. We identified a time-dependent osmotic damage model, a temperature-dependent damage model, and a temperature and time-dependent cytotoxicity model. We combined these models to estimate total damage during a cryoprotectant loading protocol and determined the optimal loading protocol for any given goal intracellular cryoprotectant concentration. Given our fitted models, we find sea urchin oocytes can only be loaded to 13% Me2SO v/v with about 50% survival. This synthesis of multiple damage modalities is the first of its kind and enables a novel approach to modelling cryoprotectant equilibration survival for cells in general.
Sea urchins (e.g., Paracentrotus lividus) are important for both aquaculture and as model species. Despite their importance, biobanking of urchin oocytes by cryopreservation is currently not possible. Optimized cryoprotectant loading may enable novel vitrification methods and thus successful cryopreservation of oocytes. One method for determining an optimized loading protocol uses membrane characteristics and models of damage, namely osmomechanical damage, temperature damage (e.g., chill injury) and cytotoxicity. Here we present and experimentally evaluate existing and novel models of these damage modalities as a function of time and temperature. In osmomechanical damage experiments, oocytes were exposed for 2 to 30 minutes in hypertonic NaCl or sucrose supplemented seawater or in hypotonic diluted seawater. In temperature damage experiments, oocytes were exposed to 1.7 °C, 10 °C, or 20 °C for 2 to 90 minutes. Cytotoxicity was investigated by exposing oocytes to solutions of Me2SO for 2 to 30 minutes. We identified a time-dependent osmotic damage model, a temperature-dependent damage model, and a temperature and time-dependent cytotoxicity model. We combined these models to estimate total damage during a cryoprotectant loading protocol and determined the optimal loading protocol for any given goal intracellular cryoprotectant concentration. Given our fitted models, we find sea urchin oocytes can only be loaded to 13% Me2SO v/v with about 50% survival. This synthesis of multiple damage modalities is the first of its kind and enables a novel approach to modelling cryoprotectant equilibration survival for cells in general.