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DeHaan LR, Anderson JA, Bajgain P, Basche A, Cattani DJ, Crain J, Crews TE, David C, Duchene O, Gutknecht J, Hayes RC, Hu F, Jungers JM, Knudsen S, Kong W, Larson S, Lundquist PO, Luo G, Miller AJ, Nabukalu P, Newell MT, Olsson L, Palmgren M, Paterson AH, Picasso VD, Poland JA, Sacks EJ, Wang S, Westerbergh A. Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits. Sci Total Environ 2023; 895:164975. [PMID: 37336402 DOI: 10.1016/j.scitotenv.2023.164975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.
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Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA.
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Andrea Basche
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 1875 N. 38th St, 279 PLSH, Lincoln, NE 68583-0915, USA
| | - Douglas J Cattani
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB R3T 2N2, Canada
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, 1712 Claflin Rd, 4024 Throckmorton PSC, Manhattan, KS 66506, USA
| | - Timothy E Crews
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA
| | - Christophe David
- ISARA, Agroecology and Environment Research Unit, 23 rue Jean Baldassini, 69364 Lyon, France
| | - Olivier Duchene
- ISARA, Agroecology and Environment Research Unit, 23 rue Jean Baldassini, 69364 Lyon, France
| | - Jessica Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Richard C Hayes
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Rd, NSW 2650, Australia
| | - Fengyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, 2 Cuihu N Rd, Wuhua District, Kunming 650106, China
| | - Jacob M Jungers
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Søren Knudsen
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen, Denmark
| | | | - Steve Larson
- USDA-ARS, Forage and Range Research, 696 North 1100 East, Logan, UT 84321, USA
| | - Per-Olof Lundquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Allison J Miller
- Saint Louis University, Donald Danforth Plant Science Center, 975 N Warson Rd, Olivette, MO 63132, USA
| | - Pheonah Nabukalu
- NESPAL, University of Georgia, 2356 Rainwater Rd, Tifton, GA 31793, USA
| | - Matthew T Newell
- NSW Department of Primary Industries, Cowra Agricultural Research Station, 296 Binni Creek Rd, Cowra, NSW 2794, Australia
| | - Lennart Olsson
- Lund University Centre for Sustainability Studies, P.O. Box 170, SE-221 Lund, Sweden
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | | | | | - Jesse A Poland
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Shuwen Wang
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
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Wagoner P, Crain J, Larson S, DeHaan L. Origin of current intermediate wheatgrass germplasm being developed for Kernza grain production. Res Sq 2023:rs.3.rs-3399539. [PMID: 37886550 PMCID: PMC10602115 DOI: 10.21203/rs.3.rs-3399539/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Intermediate wheatgrass (IWG, Thinopyrum intermedium [Host] Barkworth & D. R. Dewey) has been developed as a perennial grain crop to provide ecosystem services, environmental benefits, and human food. Grain and products derived from IWG varieties improved for food production have been marketed under the registered trademark, Kernza. In the 1980s, a joint breeding effort between the Rodale Institute (RI) and the Big Flats Plant Material Center used IWG plant introductions (PI) from the National Plant Germplasm System (NPGS) and recurrent phenotypic selection to improve populations of IWG with the goal of developing a perennial grain. Initial selections were provided to The Land Institute where they were subsequently improved for grain production, yet the identity of the founder material of improved, food-grade IWG has not been publicly documented. Recently recovered original documents have been used to reconstruct the early breeding program to identify the most likely 20 PIs that form the founders of modern food-grade IWG. Molecular data using genotyping-by-sequencing in current elite breeding material, remnant seed from the initial RI selections, and preserved sample material have provided supporting evidence for the historical records. The genetic origin for food-grade IWG is focused between the Black Sea and Caspian Sea in the Stavropol region of Russia, with smaller contributions likely from collections as distant as Kazakhstan in the east to Turkey in the west. This work connects the flow of germplasm and utility of NPGS PIs to present day IWG grain cultivars being developed in multiple breeding programs around the world.
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Crain J, Larson S, Dorn K, DeHaan L, Poland J. Genetic architecture and QTL selection response for Kernza perennial grain domestication traits. Theor Appl Genet 2022; 135:2769-2784. [PMID: 35763029 PMCID: PMC9243872 DOI: 10.1007/s00122-022-04148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication. Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8-5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an FST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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Silva P, Evers B, Kieffaber A, Wang X, Brown R, Gao L, Fritz A, Crain J, Poland J. Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat. G3 Genes|Genomes|Genetics 2022; 12:6556002. [PMID: 35353191 PMCID: PMC9258586 DOI: 10.1093/g3journal/jkac064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/12/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Barley yellow dwarf is one of the major viral diseases of cereals. Phenotyping barley yellow dwarf in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to (1) evaluate the use of high-throughput phenotyping to improve barley yellow dwarf assessment; (2) identify genomic regions associated with barley yellow dwarf resistance; and (3) evaluate the ability of genomic selection models to predict barley yellow dwarf resistance. Up to 107 wheat lines were phenotyped during each of 5 field seasons under both insecticide treated and untreated plots. Across all seasons, barley yellow dwarf severity was lower within the insecticide treatment along with increased plant height and grain yield compared with untreated entries. Only 9.2% of the lines were positive for the presence of the translocated segment carrying the resistance gene Bdv2. Despite the low frequency, this region was identified through association mapping. Furthermore, we mapped a potentially novel genomic region for barley yellow dwarf resistance on chromosome 5AS. Given the variable heritability of the trait (0.211–0.806), we obtained a predictive ability for barley yellow dwarf severity ranging between 0.06 and 0.26. Including the presence or absence of Bdv2 as a covariate in the genomic selection models had a large effect for predicting barley yellow dwarf but almost no effect for other observed traits. This study was the first attempt to characterize barley yellow dwarf using field-high-throughput phenotyping and apply genomic selection to predict disease severity. These methods have the potential to improve barley yellow dwarf characterization, additionally identifying new sources of resistance will be crucial for delivering barley yellow dwarf resistant germplasm.
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Affiliation(s)
- Paula Silva
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
- Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Colonia 70006, Uruguay
| | - Byron Evers
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
| | - Alexandria Kieffaber
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
| | - Xu Wang
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
- Department of Agricultural and Biological Engineering, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33598, USA
| | - Richard Brown
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
| | - Liangliang Gao
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
| | - Allan Fritz
- Department of Agronomy, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
| | - Jared Crain
- Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA
| | - Jesse Poland
- Corresponding author: Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia. ,
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Rahman MM, Crain J, Haghighattalab A, Singh RP, Poland J. Improving Wheat Yield Prediction Using Secondary Traits and High-Density Phenotyping Under Heat-Stressed Environments. Front Plant Sci 2021; 12:633651. [PMID: 34646280 PMCID: PMC8502926 DOI: 10.3389/fpls.2021.633651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/19/2021] [Indexed: 06/08/2023]
Abstract
A primary selection target for wheat (Triticum aestivum) improvement is grain yield. However, the selection for yield is limited by the extent of field trials, fluctuating environments, and the time needed to obtain multiyear assessments. Secondary traits such as spectral reflectance and canopy temperature (CT), which can be rapidly measured many times throughout the growing season, are frequently correlated with grain yield and could be used for indirect selection in large populations particularly in earlier generations in the breeding cycle prior to replicated yield testing. While proximal sensing data collection is increasingly implemented with high-throughput platforms that provide powerful and affordable information, efficient and effective use of these data is challenging. The objective of this study was to monitor wheat growth and predict grain yield in wheat breeding trials using high-density proximal sensing measurements under extreme terminal heat stress that is common in Bangladesh. Over five growing seasons, we analyzed normalized difference vegetation index (NDVI) and CT measurements collected in elite breeding lines from the International Maize and Wheat Improvement Center at the Regional Agricultural Research Station, Jamalpur, Bangladesh. We explored several variable reduction and regularization techniques followed by using the combined secondary traits to predict grain yield. Across years, grain yield heritability ranged from 0.30 to 0.72, with variable secondary trait heritability (0.0-0.6), while the correlation between grain yield and secondary traits ranged from -0.5 to 0.5. The prediction accuracy was calculated by a cross-fold validation approach as the correlation between observed and predicted grain yield using univariate and multivariate models. We found that the multivariate models resulted in higher prediction accuracies for grain yield than the univariate models. Stepwise regression performed equal to, or better than, other models in predicting grain yield. When incorporating all secondary traits into the models, we obtained high prediction accuracies (0.58-0.68) across the five growing seasons. Our results show that the optimized phenotypic prediction models can leverage secondary traits to deliver accurate predictions of wheat grain yield, allowing breeding programs to make more robust and rapid selections.
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Affiliation(s)
- Mohammad Mokhlesur Rahman
- Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, United States
| | - Jared Crain
- Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, United States
| | - Atena Haghighattalab
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St Paul, MN, United States
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, United States
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Altendorf KR, Larson SR, DeHaan LR, Crain J, Neyhart J, Dorn KM, Anderson JA. Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass. G3 (Bethesda) 2021; 11:6124305. [PMID: 33890617 PMCID: PMC8063084 DOI: 10.1093/g3journal/jkab025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 11/16/2022]
Abstract
Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop. Though many traits are selection targets, understanding the genetic architecture of those important for local adaptation may accelerate the domestication process. Nested association mapping (NAM) has proven useful in dissecting the genetic control of agronomic traits many crop species, but its utility in primarily outcrossing, perennial species has yet to be demonstrated. Here, we introduce an intermediate wheatgrass NAM population developed by crossing ten phenotypically divergent donor parents to an adapted common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genomewide association mapping and linkage mapping combined across and within families, we characterized the genetic control of flowering time. In the analysis of two measures of maturity across four separate environments, we detected as many as 75 significant QTL, many of which correspond to the same regions in both analysis methods across 11 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, traits, and within families. The methods were effective at detecting previously identified QTL, as well as new QTL that align closely to the well-characterized flowering time orthologs from barley, including Ppd-H1 and Constans. Our results demonstrate the utility of the NAM population for understanding the genetic control of flowering time and its potential for application to other traits of interest.
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Affiliation(s)
- Kayla R Altendorf
- USDA-ARS, Forage Seed and Cereal Research Unit, Irrigated Agriculture Research and Extension Center, Prosser, WA 99350, USA
| | | | - Lee R DeHaan
- USDA-ARS, Forage Range and Research Lab, Utah State University, Logan, UT 84322, USA
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Jeff Neyhart
- GEMS Informatics Initiative, University of Minnesota, St. Paul, MN 55108, USA
| | - Kevin M Dorn
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO 80526, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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Crain J, DeHaan L, Poland J. Genomic prediction enables rapid selection of high-performing genets in an intermediate wheatgrass breeding program. Plant Genome 2021; 14:e20080. [PMID: 33660427 DOI: 10.1002/tpg2.20080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
In an era of constrained and depleted natural resources, perennial grains could provide sustainable food production along with beneficial ecosystem services like reduced erosion and increased atmospheric carbon capture. Intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey subsp. intermedium] has been undergoing continuous breeding for domestication to develop a perennial grain crop since the 1980s. As a perennial, IWG has required 2-5 yr per selection generation, but starting in 2017, genomic selection (GS) was initiated in the breeding program at The Land Institute, Salina, KS (TLI), enabling one complete cycle per year. For each cycle, ∼4,000 seedlings were profiled using genotyping-by-sequencing (GBS) and genomic estimated breeding values (GEBVs) were calculated. Selection based on GEBVs identified ∼100 individuals to advance as parents each generation, while validation populations of 1,000-1,200 genets for GS model training were also selected using the genomic relationship matrix to represent genetic diversity in each cycle. The selected parents were randomly intermated in a greenhouse crossing block to form the subsequent cycle, while the validation populations were transplanted to irrigated and nonirrigated field sites for phenotypic evaluations in the following years. For priority breeding traits of seed mass, free threshing, and nonshattering, correlations between predicted values and observed data were >.5. The realized selection differential ranged from 11-23% for selected traits, and the expected genetic gains for these traits, including spike yield, ranged from 6 to 14% per year. Genomic selection is a powerful tool to speed the domestication and development of IWG and other perennial crops with extended breeding timelines.
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Affiliation(s)
- Jared Crain
- Dep. Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, USA, 66506
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, USA, 67401
| | - Jesse Poland
- Wheat Genetics Resource Center, Dep. Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, USA, 66506
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Crain J, Haghighattalab A, DeHaan L, Poland J. Development of whole-genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding. Plant Genome 2021; 14:e20089. [PMID: 33900690 DOI: 10.1002/tpg2.20089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG)[Thinopyrum intermedium (Host) Barkworth & D.R Dewey] have low seed yield and other detrimental traits. Next-generation sequencing has made genomic selection (GS) a tractable and viable breeding method. To investigate how an IWG breeding program may use GS, we evaluated 3,658 genets over 2 yr for 46 traits to build a training population. Six statistical models were used to evaluate the non-replicated data, and a model using autoregressive order 1 (AR1) spatial correction for rows and columns combined with the genomic relationship matrix provided the highest estimates of heritability. Genomic selection models were built from 18,357 single nucleotide polymorphism markers via genotyping-by-sequencing, and a 20-fold cross-validation showed high predictive ability for all traits (r > .80). Predictive abilities improved with increased training population size and marker numbers, even with larger amounts of missing data per marker. On the basis of these results, we propose a GS breeding method that is capable of completing one cycle per year compared with a minimum of 2 yr per cycle with phenotypic selection. We estimate that this breeding approach can increase the rate of genetic gain up to 2.6× above phenotypic selection for spike yield in IWG, allowing GS to enable rapid domestication and improvement of this crop. These breeding methods should be transferable to other species with similar long breeding cycles or limited capacity for replicated observations.
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Affiliation(s)
- Jared Crain
- Dep. of Plant Pathology, Kansas State Univ., 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
| | - Atena Haghighattalab
- Stakman-Borlaug Center for Sustainable Plant Health, Center for Applied Phenomics, Univ. of Minnesota, 1519 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Wheat Genetics Resource Center, Dep. of Plant Pathology, Kansas State Univ., 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
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Crain J, Larson S, Dorn K, Hagedorn T, DeHaan L, Poland J. Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium). Theor Appl Genet 2020; 133:3217-3233. [PMID: 32785739 PMCID: PMC7547974 DOI: 10.1007/s00122-020-03666-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE Paternity assignment and genome-wide association analyses for fertility were applied to a Thinopyrum intermedium breeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon's diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Traci Hagedorn
- AAAS Science and Technology Policy Fellow, USDA-APHIS, 4700 River Road, Riverdale, MD, 20737, USA
- Quantitative Scientific Solutions LLC, Arlington, VA, 22203, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA.
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, 66506, USA.
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Crain J, Bajgain P, Anderson J, Zhang X, DeHaan L, Poland J. Enhancing Crop Domestication Through Genomic Selection, a Case Study of Intermediate Wheatgrass. Front Plant Sci 2020; 11:319. [PMID: 32265968 PMCID: PMC7105684 DOI: 10.3389/fpls.2020.00319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/04/2020] [Indexed: 05/14/2023]
Abstract
Perennial grains could simultaneously provide food for humans and a host of ecosystem services, including reduced erosion, minimized nitrate leaching, and increased carbon capture. Yet most of the world's food and feed is supplied by annual grains. Efforts to domesticate intermediate wheatgrass (Thinopyrumn intermedium, IWG) as a perennial grain crop have been ongoing since the 1980's. Currently, there are several breeding programs within North America and Europe working toward developing IWG into a viable crop. As new breeding efforts are established to provide a widely adapted crop, questions of how genomic and phenotypic data can be used among sites and breeding programs have emerged. Utilizing five cycles of breeding data that span 8 years and two breeding programs, University of Minnesota, St. Paul, MN, and The Land Institute, Salina, KS, we developed genomic selection (GS) models to predict IWG traits. Seven traits were evaluated with free-threshing seed, seed mass, and non-shattering being considered domestication traits while agronomic traits included spike yield, spikelets per inflorescence, plant height, and spike length. We used 6,199 genets - unique, heterozygous, individual plants - that had been profiled with genotyping-by-sequencing, resulting in 23,495 SNP markers to develop GS models. Within cycles, the predictive ability of GS was high, ranging from 0.11 to 0.97. Across-cycle predictions were generally much lower, ranging from -0.22 to 0.76. The prediction ability for domestication traits was higher than agronomic traits, with non-shattering and free threshing prediction abilities ranging from 0.27 to 0.75 whereas spike yield had prediction abilities ranging from -0.22 to 0.26. These results suggest that progress to reduce shattering and increase the percent free-threshing grain can be made irrespective of the location and breeding program. While site-specific programs may be required for agronomic traits, synergies can be achieved in rapidly improving key domestication traits for IWG. As other species are targeted for domestication, these results will aid in rapidly domesticating new crops.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - James Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Xiaofei Zhang
- The Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, Colombia
| | - Lee DeHaan
- The Land Institute, Salina, KS, United States
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
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Larson S, DeHaan L, Poland J, Zhang X, Dorn K, Kantarski T, Anderson J, Schmutz J, Grimwood J, Jenkins J, Shu S, Crain J, Robbins M, Jensen K. Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium). Theor Appl Genet 2019; 132:2325-2351. [PMID: 31172227 DOI: 10.1007/s00122-019-03357-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/02/2019] [Indexed: 05/14/2023]
Abstract
Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.
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Affiliation(s)
- Steve Larson
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA.
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Xiaofei Zhang
- Department of Horticultural Science, North Carolina State University, 212 Kilgore Hall, 2721 Founders Drive, PO Box 7609, Raleigh, NC, 27607, USA
| | - Kevin Dorn
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Traci Kantarski
- American Association for the Advancement of Science, Science and Technology Policy Fellow at the United States Department of Agriculture, Animal and Plant Health Inspection Service, 4700 River Road, Riverdale, MD, 20737, USA
| | - James Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Buford Circle, St. Paul, MN, 55108, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Matthew Robbins
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Jensen
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
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Taylor T, Das D, Patrick J, Katz S, Johnson L, Crain J. Embryo euploidy rates from advanced maternal age (AMA) patients with and without coenzyme Q10 (COQ10) supplemntation: a pilot study and randomized control trial. Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.1165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Crain J, Mondal S, Rutkoski J, Singh RP, Poland J. Combining High-Throughput Phenotyping and Genomic Information to Increase Prediction and Selection Accuracy in Wheat Breeding. Plant Genome 2018; 11:170043. [PMID: 29505641 DOI: 10.3835/plantgenome2017.05.0043] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS), we evaluated 1170 of these advanced lines in two environments, drought (2014, 2015) and heat (2015). A portable phenotyping system called 'Phenocart' was used to measure normalized difference vegetation index and canopy temperature simultaneously while tagging each data point with precise GPS coordinates. For genomic profiling, genotyping-by-sequencing (GBS) was used for marker discovery and genotyping. Several GS models were evaluated utilizing the 2254 GBS markers along with over 1.1 million phenotypic observations. The physiological measurements collected by HTP, whether used as a response in multivariate models or as a covariate in univariate models, resulted in a range of 33% below to 7% above the standard univariate model. Continued advances in yield prediction models as well as increasing data generating capabilities for both genomic and phenomic data will make these selection strategies tractable for plant breeders to implement increasing the rate of genetic gain.
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Buzzacott P, Schiller D, Crain J, Denoble PJ. Epidemiology of morbidity and mortality in US and Canadian recreational scuba diving. Public Health 2018; 155:62-68. [PMID: 29306625 DOI: 10.1016/j.puhe.2017.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/30/2017] [Accepted: 11/12/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVES This study investigates morbidity and mortality suffered by divers in the USA and Canada. STUDY DESIGN Prospectively recruited probability-weighted sample for estimating the national burden of injury and a weighted retrospective survey for estimating exposure. METHODS The National Electronic Surveillance System and Canadian Hospitals Injury Reporting and Prevention Program (CHIRPP) were searched for scuba diving injuries. The Divers Alert Network diving fatality database was searched for deaths, and Sports and Fitness Industry Association estimates for diving were obtained from annual surveys. RESULTS In the USA, there were an estimated 1394 emergency department (ED) presentations annually for scuba-related injuries. The majority (80%) were treated and/or released. There were an estimated 306 million dives made by the US residents 2006-2015 and concurrently 563 recreational diving deaths, a fatality rate of 0.18 per 105 dives and 1.8 per 105 diver-years. There were 658 diving deaths in the US 2006-2015 and 13,943 ED presentations for scuba injuries, giving a ratio of 47 diving deaths in the USA for every 1000 ED presentations. There were 98 cases of scuba-related injuries identified in the CHIRPP data. The prevalence of scuba-related injuries for patients aged 3-17 years was 1.5 per 105 cases, and the prevalence of scuba-related injuries to patients 18-62 years was 16.5 per 105 cases. DISCUSSION In Canada and the USA, only one out of every 10,000 ED presentations is due to a scuba-related injury. That there are 47 deaths for every 1000 ED presentations for scuba injuries speaks to the relatively unforgiving environment in which scuba diving takes place. For 1.8 deaths per million recreational dives, mortality in scuba diving is nonetheless relatively low.
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Affiliation(s)
- P Buzzacott
- Divers Alert Network, 6 Est Colony Place, Durham, NC, 27705, USA; School of Sport Science, Exercise and Health, The University of Western Australia, 35 Stirling Highway, Perth, 6009, Australia.
| | - D Schiller
- Sports Marketing Surveys, 6650 W Indiantown Road, Jupiter, FL, 33458, USA.
| | - J Crain
- Injury and Healthy Living Section, Public Health Agency of Canada, 785 Carling Avenue, 7th Floor, Ottawa, ON, K1A 0K9, Canada.
| | - P J Denoble
- Divers Alert Network, 6 Est Colony Place, Durham, NC, 27705, USA.
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Crain J, McFaull S, Rao DP, Do MT, Thompson W. At-a-glance, Emergency department surveillance of thermal burns and scalds, electronic Canadian Hospitals Injury Reporting and Prevention Program, 2013. Health Promot Chronic Dis Prev Can 2017; 37:30-31. [PMID: 28102994 DOI: 10.24095/hpcdp.37.1.03] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Although fatality and hospitalization rates for burns in Canada have declined over time, less serious cases still commonly present to the emergency department (ED). METHODS The Canadian Hospitals Injury Reporting and Prevention Program (CHIRPP) is an injury and poisoning surveillance system administered by the Public Health Agency of Canada, operating in emergency departments of 17 hospitals. RESULTS Overall, cases reported in 2013 were scalds and contact burns from hot objects. The leading direct causes of scalds were hot beverages and hot water. The leading causes of contact burns were stoves/ovens and fireplaces/accessories. While the overall proportion of burns was highest among females, males comprised a higher proportion of burns from all mechanisms except scalds.
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Affiliation(s)
- J Crain
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - S McFaull
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - D P Rao
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - M T Do
- Public Health Agency of Canada, Ottawa, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - W Thompson
- Public Health Agency of Canada, Ottawa, Ontario, Canada
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Do MT, McFaull S, Cheesman J, Mersereau T, Rao DP, Crain J, Thompson W. Emergency department presentations for hoverboard-related injuries: the electronic Canadian Hospitals Injury Reporting and Prevention Program, 2015 to 2016. Health Promot Chronic Dis Prev Can 2016; 36:316-317. [PMID: 27977087 DOI: 10.24095/hpcdp.36.12.06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- M T Do
- Public Health Agency of Canada, Ottawa, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - S McFaull
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - J Cheesman
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - T Mersereau
- Consumer Product Safety Directorate, Health Canada, Ottawa, Ontario, Canada
| | - D P Rao
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - J Crain
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - W Thompson
- Public Health Agency of Canada, Ottawa, Ontario, Canada
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Crain J, McFaull S, Thompson W, Skinner R, Do MT, Fréchette M, Mukhi S. Status report - The Canadian Hospitals Injury Reporting and Prevention Program: a dynamic and innovative injury surveillance system. Health Promot Chronic Dis Prev Can 2016; 36:112-117. [PMID: 27284703 PMCID: PMC4910447 DOI: 10.24095/hpcdp.36.6.02] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
This status report on the Canadian Hospitals Injury Reporting and Prevention Program (CHIRPP), an emergency department-based injury and poisoning surveillance system, describes the result of migrating from a centralized data entry and coding process to a decentralized process, the web-based eCHIRPP system, in 2011. This secure system is improving the CHIRPP's overall flexibility and timeliness, which are key attributes of an effective surveillance system. The integrated eCHIRPP platform enables near real-time data entry and access, has user-friendly data management and analysis tools, and allows for easier communication and connectivity across the CHIRPP network through an online collaboration centre. Current pilot testing of automated data monitoring and trend analysis tools-designed to monitor and flag incoming data according to predefined criteria (for example, a new consumer product)-is revealing eCHIRPP's potential for providing early warnings of new hazards, issues and trends.
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Affiliation(s)
- J Crain
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - S McFaull
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - W Thompson
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - R Skinner
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - M T Do
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - M Fréchette
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - S Mukhi
- Canadian Network for Public Health Intelligence, Public Health Agency of Canada, Ottawa, Ontario, Canada
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Sokhan VP, Jones A, Cipcigan FS, Crain J, Martyna GJ. Molecular-scale remnants of the liquid-gas transition in supercritical polar fluids. Phys Rev Lett 2015; 115:117801. [PMID: 26406855 DOI: 10.1103/physrevlett.115.117801] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Indexed: 06/05/2023]
Abstract
An electronically coarse-grained model for water reveals a persistent vestige of the liquid-gas transition deep into the supercritical region. A crossover in the density dependence of the molecular dipole arises from the onset of nonpercolating hydrogen bonds. The crossover points coincide with the Widom line in the scaling region but extend farther, tracking the heat capacity maxima, offering evidence for liquidlike and gaslike state points in a "one-phase" fluid. The effect is present even in dipole-limit models, suggesting that it is common for all molecular liquids exhibiting dipole enhancement in the liquid phase.
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Affiliation(s)
- V P Sokhan
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - A Jones
- School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - F S Cipcigan
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
- School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - J Crain
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
- School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - G J Martyna
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
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Corrigan DK, Schulze H, Henihan G, Hardie A, Ciani I, Giraud G, Terry JG, Walton AJ, Pethig R, Ghazal P, Crain J, Campbell CJ, Templeton KE, Mount AR, Bachmann TT. Development of a PCR-free electrochemical point of care test for clinical detection of methicillin resistant Staphylococcus aureus (MRSA). Analyst 2014; 138:6997-7005. [PMID: 24093127 DOI: 10.1039/c3an01319g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An MRSA assay requiring neither labeling nor amplification of target DNA has been developed. Sequence specific binding of fragments of bacterial genomic DNA is detected at femtomolar concentrations using electrochemical impedance spectroscopy (EIS). This has been achieved using systematic optimisation of probe chemistry (PNA self-assembled monolayer film on gold electrode), electrode film structure (the size and nature of the chemical spacer) and DNA fragmentation, as these are found to play an important role in assay performance. These sensitivity improvements allow the elimination of the PCR step and DNA labeling and facilitate the development of a simple and rapid point of care test for MRSA. Assay performance is then evaluated and specific direct detection of the MRSA diagnostic mecA gene from genomic DNA, extracted directly from bacteria without further treatment is demonstrated for bacteria spiked into saline (10(6) cells per mL) on gold macrodisc electrodes and into human wound fluid (10(4) cells per mL) on screen printed gold electrodes. The latter detection level is particularly relevant to clinical requirements and point of care testing where the general threshold for considering a wound to be infected is 10(5) cells per mL. By eliminating the PCR step typically employed in nucleic acid assays, using screen printed electrodes and achieving sequence specific discrimination under ambient conditions, the test is extremely simple to design and engineer. In combination with a time to result of a few minutes this means the assay is well placed for use in point of care testing.
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Affiliation(s)
- D K Corrigan
- Division of Pathway Medicine, Medical School, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK.
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McVey A, Crain J. Nonlinear optical methods for cellular imaging and localization. Methods 2014; 68:371-7. [PMID: 24704357 DOI: 10.1016/j.ymeth.2014.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/28/2014] [Accepted: 03/02/2014] [Indexed: 10/25/2022] Open
Abstract
Of all the ways in which complex materials (including many biological systems) can be explored, imaging is perhaps the most powerful because delivering high information content directly. This is particular relevant in aspects of cellular localization where the physical proximity of molecules is crucial in biochemical processes. A great deal of effort in imaging has been spent on enabling chemically selective imaging so that only specific features are revealed. This is almost always achieved by adding fluorescent chemical labels to specific molecules. Under appropriate illumination conditions only the molecules (via their labels) will be visible. The technique is simple and elegant but does suffer from fundamental limitations: (1) the fluorescent labels may fade when illuminated (a phenomenon called photobleaching) thereby constantly decreasing signal contrast over the course of image acquisition. To combat photobleaching one must reduce observation times or apply unfavourably low excitation levels all of which reduce the information content of images; (2) the fluorescent species may be deactivated by various environmental factors (the general term is fluorescence quenching); (3) the presence of fluorescent labels may introduce unexpected complications or may interfere with processes of interest (4) Some molecules of interest cannot be labelled. In these circumstances we require a fundamentally different strategy. One of the most promising alternative is based on a technique called Coherent Anti-Stokes Raman scattering (CARS). CARS is a fundamentally more complex process than is fluorescence and the experimental procedures and optical systems required to deliver high quality CARS images are intricate. However, the rewards are correspondingly very high: CARS probes the chemically distinct vibrations of the constituent molecules in a complex system and is therefore also chemically selective as are fluorescence-based methods. Moreover,the potentially severe problems of fluorescence bleaching and quenching are circumvented and high-resolution three dimensional images can be obtained on completely unlabelled specimens. We review here aspects of CARS and Multiphoton fluorescence techniques to cellular localization and measurement.
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Affiliation(s)
- A McVey
- School of Physics, The University of Edinburgh, EH9 3JZ Scotland, United Kingdom
| | - J Crain
- School of Physics, The University of Edinburgh, EH9 3JZ Scotland, United Kingdom; National Physical Laboratory Teddington, TW11 0LW, United Kingdom.
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Jones A, Crain J, Cipcigan F, Sokhan V, Modani M, Martyna G. Electronically coarse-grained molecular dynamics using quantum Drude oscillators. Mol Phys 2013. [DOI: 10.1080/00268976.2013.843032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Patrick J, Welch L, Teaff N, Whelan J, Crain J, Wilson M. Comparative assessment of blastocyst conversion rates in sequential vs continuous culture systems. Fertil Steril 2013. [DOI: 10.1016/j.fertnstert.2013.07.1748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
We introduce an electronically coarse-grained description of water representing all long range, many-body electronic responses via an embedded quantum oscillator. Leading-order response coefficients and gas phase electrostatic moments are exactly reproduced. Molecular dynamics, using electronic path integral sampling, shows that this framework is sufficient for a realistic liquid to emerge naturally with transferability extending further to nonambient state points and to the free water surface. The model allows the strength of many-body dispersion and polarization to be adjusted independently and these are found to have significant effects on the condensed phase.
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Affiliation(s)
- A Jones
- School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Cardinal M, Crain J, Do MT, Fréchette M, McFaull S, Skinner R, Thompson W. Report summary - Injury in Review, 2012 Edition: Spotlight on Road and Transport Safety. ACTA ACUST UNITED AC 2012. [DOI: 10.24095/hpcdp.32.4.08] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Injury in Review, 2012 Edition: Spotlight on Road and Transport Safety, the first national public health report of its kind, synthesizes road- and transport-related injury statistics from a variety of sources. It profiles injury patterns among Canadians aged up to 24 years, explains risks and protective factors, and makes recommendations for action. The findings inform the development of targeted injury prevention efforts.
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Affiliation(s)
- M Cardinal
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
| | - J Crain
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
| | - MT Do
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
| | - M Fréchette
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
| | - S McFaull
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
| | - R Skinner
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
| | - W Thompson
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
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Cardinal M, Crain J, Do MT, Fréchette M, McFaull S, Skinner R, Thompson W. Report summary - injury in review, 2012 edition: spotlight on road and transport safety. Chronic Dis Inj Can 2012; 32:229-230. [PMID: 23046806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Injury in Review, 2012 Edition: Spotlight on Road and Transport Safety, the first national public health report of its kind, synthesizes road- and transport-related injury statistics from a variety of sources. It profiles injury patterns among Canadians aged up to 24 years, explains risks and protective factors, and makes recommendations for action. The findings inform the development of targeted injury prevention efforts.
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Affiliation(s)
- M Cardinal
- Injury Section, Health Surveillance and Epidemiology Division, Centre for Chronic Disease Prevention and Control, Ottawa, Ontario, Canada
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Tulip PR, Gregor CR, Troitzsch RZ, Martyna GJ, Cerasoli E, Tranter G, Crain J. Conformational Plasticity in an HIV-1 Antibody Epitope. J Phys Chem B 2010; 114:7942-50. [DOI: 10.1021/jp100929n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. R. Tulip
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - C. R. Gregor
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - R. Z. Troitzsch
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - G. J. Martyna
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - E. Cerasoli
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - G. Tranter
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - J. Crain
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, U.K., IBM T.J. Watson Research Center, Yorktown Heights, New York, 10598, and National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
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Troitzsch RZ, Vass H, Hossack WJ, Martyna GJ, Crain J. Molecular Mechanisms of Cryoprotection in Aqueous Proline: Light Scattering and Molecular Dynamics Simulations. J Phys Chem B 2008; 112:4290-7. [DOI: 10.1021/jp076713m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Z. Troitzsch
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, and National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - H. Vass
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, and National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - W. J. Hossack
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, and National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - G. J. Martyna
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, and National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - J. Crain
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, and National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
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Mountford CP, Buck AH, Campbell CJ, Dickinson P, Ferapontova EE, Terry JG, Beattie JS, Walton AJ, Ghazal P, Mount AR, Crain J. Molecular Recognition with DNA Nanoswitches: Effects of Single Base Mutations on Structure. J Phys Chem B 2008; 112:2439-44. [DOI: 10.1021/jp073817o] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- C. P. Mountford
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. H. Buck
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - C. J. Campbell
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - P. Dickinson
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - E. E. Ferapontova
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. G. Terry
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. S. Beattie
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. J. Walton
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - P. Ghazal
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - A. R. Mount
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
| | - J. Crain
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom, The Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB Scotland, United Kingdom, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Institute of Integrated Systems, Scottish Microelectronics Centre, School of Engineering and Electronics, University of Edinburgh, Edinburgh, EH9
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Whitfield TW, Crain J, Martyna GJ. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics. J Chem Phys 2007; 124:94503. [PMID: 16526863 DOI: 10.1063/1.2150432] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
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Affiliation(s)
- T W Whitfield
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
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Whitfield TW, Martyna GJ, Allison S, Bates SP, Vass H, Crain J. Structure and hydrogen bonding in neat N-methylacetamide: classical molecular dynamics and Raman spectroscopy studies of a liquid of peptidic fragments. J Phys Chem B 2007; 110:3624-37. [PMID: 16494418 DOI: 10.1021/jp053140+] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The results of classical molecular dynamics (MD) simulations and Raman spectroscopy studies of neat liquid N-methylacetamide (NMA), the simplest model system relevant to the peptides, are reported as a function of temperature and pressure. The MD simulations predict that near ambient conditions, the molecules form a hydrogen bond network consisting primarily of linear chains. Both the links between molecules within the hydrogen-bonded chains and the associations between chains are stabilized by weak methyl-donated "improper" hydrogen bonds. The three-dimensional structural motifs observed in the liquid show some similarity to protein beta-sheets. The temperature and pressure dependence of the hydrogen bond network, as probed by the mode frequency of the experimentally determined amide-I Raman band, blue shifts on heating and red shifts under compression, respectively, suggesting weakened and enhanced hydrogen bonding in response to temperature and pressure increases. Disruption of the hydrogen-bonding network is clearly observed in the simulation data as temperature is increased, whereas the improper hydrogen bonding is enhanced under compression to reduce the energetic cost of increasing the packing fraction. Because of the neglect of polarizability in the molecular model, the computed dielectric constant is underestimated compared to the experimental value, indicating that the simulation may underestimate dipolar coupling in the liquid.
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Affiliation(s)
- T W Whitfield
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
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Troitzsch RZ, Martyna GJ, McLain SE, Soper AK, Crain J. Structure of Aqueous Proline via Parallel Tempering Molecular Dynamics and Neutron Diffraction. J Phys Chem B 2007; 111:8210-22. [PMID: 17592868 DOI: 10.1021/jp0714973] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of aqueous L-proline amino acid has been the subject of much debate centering on the validity of various proposed models, differing widely in the extent to which local and long-range correlations are present. Here, aqueous proline is investigated by atomistic, replica exchange molecular dynamics simulations, and the results are compared to neutron diffraction and small angle neutron scattering (SANS) data, which have been reported recently (McLain, S.; Soper, A.; Terry, A.; Watts, A. J. Phys. Chem. B 2007, 111, 4568). Comparisons between neutron experiments and simulation are made via the static structure factor S(Q) which is measured and computed from several systems with different H/D isotopic compositions at a concentration of 1:20 molar ratio. Several different empirical water models (TIP3P, TIP4P, and SPC/E) in conjunction with the CHARMM22 force field are investigated. Agreement between experiment and simulation is reasonably good across the entire Q range although there are significant model-dependent variations in some cases. In general, agreement is improved slightly upon application of approximate quantum corrections obtained from gas-phase path integral simulations. Dimers and short oligomeric chains formed by hydrogen bonds (frequently bifurcated) coexist with apolar (hydrophobic) contacts. These emerge as the dominant local motifs in the mixture. Evidence for long-range association is more equivocal: No long-range structures form spontaneously in the MD simulations, and no obvious low-Q signature is seen in the SANS data. Moreover, associations introduced artificially to replicate a long-standing proposed mesoscale structure for proline correlations as an initial condition are annealed out by parallel tempering MD simulations. However, some small residual aggregates do remain, implying a greater degree of long-range order than is apparent in the SANS data.
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Affiliation(s)
- R Z Troitzsch
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Mount AR, Mountford CP, Evans SAG, Su TJ, Buck AH, Dickinson P, Campbell CJ, Keane LM, Terry JG, Beattie JS, Walton AJ, Ghazal P, Crain J. The stability and characteristics of a DNA Holliday junction switch. Biophys Chem 2006; 124:214-21. [PMID: 16716492 DOI: 10.1016/j.bpc.2006.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 03/25/2006] [Indexed: 11/17/2022]
Abstract
A Holliday junction (HJ) consists of four DNA double helices, with a branch point discontinuity at the intersection of the component strands. At low ionic strength, the HJ adopts an open conformation, with four widely spaced arms, primarily due to strong electrostatic repulsion between the phosphate groups on the backbones. At high ionic strength, screening of this repulsion induces a switch to a more compact (closed) junction conformation. Fluorescent labelling with dyes placed on the HJ arms allows this conformational switch to be detected optically using fluorescence resonance energy transfer (FRET), producing a sensitive fluorescent output of the switch state. This paper presents a systematic and quantitative survey of the switch characteristics of such a labelled HJ. A short HJ (arm length 8 bp) is shown to be prone to dissociation at low switching ion concentration, whereas an HJ of arm length 12 bp is shown to be stable over all switching ion concentrations studied. The switching characteristics of this HJ have been systematically and quantitatively studied for a variety of switching ions, by measuring the required ion concentration, the sharpness of the switching transition and the fluorescent output intensity of the open and closed states. This stable HJ is shown to have favourable switch characteristics for a number of inorganic switching ions, making it a promising candidate for use in nanoscale biomolecular switch devices.
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Affiliation(s)
- A R Mount
- School of Chemistry, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JJ, UK.
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Affiliation(s)
- S. J. Clark
- a Department of Physics and Astronomy , The University of Edinburgh , Mayfield Road, EH9 352 , Scotland
| | - C. J. Adam
- a Department of Physics and Astronomy , The University of Edinburgh , Mayfield Road, EH9 352 , Scotland
| | - H. C. Hsueh
- a Department of Physics and Astronomy , The University of Edinburgh , Mayfield Road, EH9 352 , Scotland
| | - F. Pu
- a Department of Physics and Astronomy , The University of Edinburgh , Mayfield Road, EH9 352 , Scotland
- b Institute of High Temperature and Pressure Physics, Chengdu University of Science and Technology , P. R. China
| | - J. Crain
- a Department of Physics and Astronomy , The University of Edinburgh , Mayfield Road, EH9 352 , Scotland
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Mountford CP, Mount AR, Evans SAG, Su TJ, Dickinson P, Buck AH, Campbell CJ, Terry JG, Beattie JS, Walton AJ, Ghazal P, Crain J. Time-Resolved FRET and FLIM of Four-way DNA Junctions. J Fluoresc 2006; 16:839-45. [PMID: 17031573 DOI: 10.1007/s10895-006-0125-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Accepted: 08/28/2006] [Indexed: 10/24/2022]
Abstract
Conformational transitions in a 4-way DNA junction when titrated with ionic solutions are studied using time-resolved fluorescence resonance energy transfer. Parameters characterising the transition in terms of critical ion concentration (c1/2) and the Hill coefficient for ion binding are obtained by fitting a simple two-state model using steady-state spectra. Data obtained from a fluorescence lifetime plate reader and analysed by fitting a single exponential to donor fluorescence lifetime decays are shown to be in good agreement with the parameters obtained from steady-state measurements. Fluorescence lifetimes, however, offer advantages, particularly in being independent of fluorophore concentration, output intensity, inhomogeneity in the excitation source and output wavelength. We demonstrate preliminary FRET-FLIM images of DNA junction solutions obtained using a picosecond gated CCD which are in agreement with results from a fluorescence lifetime plate reader. The results suggest that time-resolved FRET-FLIM is sensitive to subtle structural changes and may be useful in assays based on 4-way DNA junctions.
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Affiliation(s)
- C P Mountford
- School of Physics, The University of Edinburgh, Room 4606 James Clerk Maxwell Building, Mayfield Road, Edinburgh, EH9 3JZ, UK
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Anderson A, Graff K, Distefano J, Whelan J, Crain J. Early Syngamy; A Case Study Report. Fertil Steril 2005. [DOI: 10.1016/j.fertnstert.2005.07.991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Anderson A, Whelan J, Crain J. Age-Matched Comparison of Preimplantation Genetic Diagnosis and Conventional Blastocyst Transfers. Fertil Steril 2005. [DOI: 10.1016/j.fertnstert.2005.07.965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dougan L, Hargreaves R, Bates SP, Finney JL, Réat V, Soper AK, Crain J. Segregation in aqueous methanol enhanced by cooling and compression. J Chem Phys 2005; 122:174514. [PMID: 15910052 DOI: 10.1063/1.1888405] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular segregation in methanol-water mixtures is studied across a wide concentration range as a function of temperature and pressure. Cluster distributions obtained from both neutron diffraction and molecular dynamics simulations point to significantly enhanced segregation as the mixtures are cooled or compressed. This evolution toward greater molecular heterogenity in the mixture accounts for the observed changes in the water-water radial distribution function and there are indications also of a change in the topology of the water clusters. The observed behavior is consistent with an approach to an upper critical solution point. Such a point would appear to be "hidden" below the freezing line, thereby precluding observation of the two-fluid region.
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Affiliation(s)
- L Dougan
- School of Physics, The University of Edinburgh, UK
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Dougan L, Bates SP, Hargreaves R, Fox JP, Crain J, Finney JL, Reat V, Soper AK. Methanol-water solutions: A bi-percolating liquid mixture. J Chem Phys 2004; 121:6456-62. [PMID: 15446945 DOI: 10.1063/1.1789951] [Citation(s) in RCA: 261] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An extensive series of neutron diffraction experiments and molecular dynamics simulations has shown that mixtures of methanol and water exhibit extended structures in solution despite the components being fully miscible in all proportions. Of particular interest is a concentration region (methanol mole fraction between 0.27 and 0.54) where both methanol and water appear to form separate, percolating networks. This is the concentration range where many transport properties and thermodynamic excess functions reach extremal values. The observed concentration dependence of several of these material properties of the solution may therefore have a structural origin.
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Affiliation(s)
- L Dougan
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Abstract
Single molecule fluorescence imaging incorporated with optical tweezers and a laminar flow cell has been used to monitor the kinetic process of DNA condensation induced by spermidine. It was found that at least two steps were involved in the condensation process of the hydrodynamically-stretched linear DNA; a lag period followed by a rapid collapse of DNA. The lag time increased with the flow speed and the collapse time remained short within the range of the flow speed studied. The effect of salt concentration on the condensation process was examined, and the results suggest that the longer lag time observed in the higher salt buffer probably results from the displacement of bound cations and rearrangement of spermidine on the DNA. The flow-speed dependence of the lag time suggests that a nucleation event at the free end of the DNA, i.e. formation of a loop, may play a vital role in the kinetic process of condensation.
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Affiliation(s)
- T J Su
- School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, United Kingdom
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Abstract
When a simple alcohol such as methanol or ethanol is mixed with water, the entropy of the system increases far less than expected for an ideal solution of randomly mixed molecules. This well-known effect has been attributed to hydrophobic headgroups creating ice-like or clathrate-like structures in the surrounding water, although experimental support for this hypothesis is scarce. In fact, an increasing amount of experimental and theoretical work suggests that the hydrophobic headgroups of alcohol molecules in aqueous solution cluster together. However, a consistent description of the details of this self-association is lacking. Here we use neutron diffraction with isotope substitution to probe the molecular-scale structure of a concentrated alcohol water mixture (7:3 molar ratio). Our data indicate that most of the water molecules exist as small hydrogen-bonded strings and clusters in a 'fluid' of close-packed methyl groups, with water clusters bridging neighbouring methanol hydroxyl groups through hydrogen bonding. This behaviour suggests that the anomalous thermodynamics of water alcohol systems arises from incomplete mixing at the molecular level and from retention of remnants of the three-dimensional hydrogen-bonded network structure of bulk water.
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Affiliation(s)
- S Dixit
- Department of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK
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Meeker SP, Poon WC, Crain J, Terentjev EM. Colloid-liquid-crystal composites: An unusual soft solid. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 61:R6083-R6086. [PMID: 11088356 DOI: 10.1103/physreve.61.r6083] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2000] [Indexed: 05/23/2023]
Abstract
Mixing model colloidal particles with a thermotropic nematic liquid crystal results in a soft solid with significant storage modulus (G' approximately 10(3)-10(5) Pa). The soft solid comprises a network of particle aggregates, formed by the exclusion of particles from emergent nematic domains as the mixture is cooled below the isotropic-nematic transition. The unusually high storage modulus of the colloid-liquid-crystal composites may be due to the local frustration of nematic order within the particle aggregates. The birefringent soft solid is potentially important as a switchable electro-optical material that can be readily handled and processed.
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Affiliation(s)
- SP Meeker
- Department of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Twidale N, Manda V, Holliday R, Boler S, Sparks L, Crain J, Carrier S. Mitral regurgitation after atrioventricular node catheter ablation for atrial fibrillation and heart failure: acute hemodynamic features. Am Heart J 1999; 138:1166-75. [PMID: 10577449 DOI: 10.1016/s0002-8703(99)70084-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Radiofrequency catheter ablation of the atrioventricular node and pacemaker insertion have been associated with occasional development of mitral regurgitation (MR). Ventricular pacing might result in MR if (1) left ventricular (LV) compliance is decreased and/or (2) mitral valve leaflet apposition is disturbed. We studied acute hemodynamic changes resulting from initiation of ventricular pacing in patients undergoing ablation. METHODS AND RESULTS Thirteen patients (10 men and 3 women) with a mean age of 73.4 +/- 8. 6 years, with chronic atrial fibrillation and congestive heart failure, had permanent ventricular pacemaker insertion with lead placement at the right ventricular (RV) apex. The following hemodynamic recordings were obtained before ablation (during atrial fibrillation) and then immediately after ablation (during RV pacing): heart rate, mean arterial pressure, LV end-diastolic pressure (LVEDP), mean pulmonary capillary wedge pressure, V-wave amplitude, and cardiac index. Presence of MR was assessed by V-wave amplitude and the results of LV angiography. In patients who had MR, recordings were also obtained during temporary ventricular pacing from the RV outflow tract (RVOT). As a group there were no significant changes in any hemodynamic measurement. Before ablation, mild MR by LV angiogram was present in 5 patients, but none had large V-wave amplitude. After ablation, mild MR was present by LV angiogram in 6 patients, and in 3 of these patients large V-wave amplitude developed (mean amplitude 42.7 +/- 2.2 mm Hg; assigned to group 1). This was associated with a rise in LVEDP in 1 patient (consistent with reduced LV compliance), but LVEDP was unchanged in the other 2 patients (suggesting abnormal mitral valve leaflet apposition). All patients in group 1 exhibited a fall in V-wave amplitude when the pacing site was moved to the RVOT. CONCLUSIONS Both reduced LV compliance and disturbed mitral valve leaflet apposition contribute to MR after ablation. MR is reduced by pacing from the RVOT.
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Affiliation(s)
- N Twidale
- Bass Baptist Hospital, Enid, OK, USA
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Kutteh WH, Yetman DL, Chantilis SJ, Crain J. Effect of antiphospholipid antibodies in women undergoing in-vitro fertilization: role of heparin and aspirin. Hum Reprod 1997; 12:1171-5. [PMID: 9221995 DOI: 10.1093/humrep/12.6.1171] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
To describe the prevalence of antiphospholipid antibodies in women undergoing in-vitro fertilization (IVF) and to determine if heparin and aspirin affect implantation rates, 191 women with a history of infertility undergoing IVF were prospectively tested for antiphospholipid antibodies. This was a two-centre, non-randomized comparison of women with positive antiphospholipid antibodies receiving heparin and aspirin versus standard treatment. An enzyme-linked immunosorbent assay, with referenced standards and known positive and negative sera on each plate, was utilized to measure antibodies to cardiolipin, phosphatidylinositol, phosphatidylglycerol, phosphatidylserine and phosphatidylethanolamine. Statistical analyses of results included analysis of variance and Fisher's two-tailed exact test. Antiphospholipid antibodies were detected in 18.8% of patients undergoing IVF compared with only 5.5% in the 200 normal controls, 26% in 200 women with recurrent pregnancy loss, and 32% in 200 women with systemic lupus erythematosus. In conclusion, antiphospholipid antibodies were found more frequently in women undergoing IVF than in the normal control population. Although implantation rates appeared higher in the group of women treated with heparin and aspirin, no statistically significant differences were detected in implantation, pregnancy and ongoing pregnancy rates between those who received standard therapy and those treated with heparin and aspirin.
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Affiliation(s)
- W H Kutteh
- The University of Tennessee, Memphis Health Science Center, USA
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Maclean J, Hatton PD, Crain J, Harris KDM, Kariuki BM, Wu F, Cernik RJ. High-pressure structures of group V elements and group IV–VI compounds. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396078439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hsueh HC, Warren MC, Vass H, Ackland GJ, Clark SJ, Crain J. Vibrational properties of the layered semiconductor germanium sulfide under hydrostatic pressure: Theory and experiment. Phys Rev B Condens Matter 1996; 53:14806-14817. [PMID: 9983275 DOI: 10.1103/physrevb.53.14806] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Crain J, Piltz RO, Ackland GJ, Clark SJ, Payne MC, Milman V, Lin JS, Hatton PD, Nam YH. Erratum: Tetrahedral structures and phase transitions in III-V semiconductors. Phys Rev B Condens Matter 1995; 52:16936. [PMID: 9981104 DOI: 10.1103/physrevb.52.16936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Clark SJ, Ackland GJ, Crain J. Theoretical stability limit of diamond at ultrahigh pressure. Phys Rev B Condens Matter 1995; 52:15035-15038. [PMID: 9980844 DOI: 10.1103/physrevb.52.15035] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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