Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world’s population. Research into when, where, and how ...rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica . These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated ...approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches “mark” the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen–deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Structural proteomics refers to large‐scale mapping of protein structures in order to understand the relationship between protein sequence, structure, and function. Chemical labeling, in combination ...with mass‐spectrometry (MS) analysis, have emerged as powerful tools to enable a broad range of biological applications in structural proteomics. The key to success is a biocompatible reagent that modifies a protein without affecting its high‐order structure. Fluorine, well‐known to exert profound effects on the physical and chemical properties of reagents, should have an impact on structural proteomics. In this Minireview, we describe several fluorine‐containing reagents that can be applied in structural proteomics. We organize their applications around four MS‐based techniques: a) affinity labeling, b) activity‐based protein profiling (ABPP), c) protein footprinting, and d) protein cross‐linking. Our aim is to provide an overview of the research, development, and application of fluorine‐containing reagents in protein structural studies.
The combination of mass spectrometry and chemical labeling has become a powerful approach in structural proteomics. Fluorine substitution enables the development of a wide range of biocompatible reagents for interrogating the high‐order structure and functions of proteins. This Minireview focuses on the application of fluorine‐containing reagents in structural proteomics.
Premise of the study: Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known ...about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits. Key results: We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops. Conclusions: Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction.Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.
Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands—farmland suboptimal for food crops—could help ...meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks—primarily annual grain crops—on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, and bird diversity than maize. Although biomass production was greater in maize, all other ecosystem services, including methane consumption, pest suppression, pollination, and conservation of grassland birds, were higher in perennial grasslands. Moreover, we found that the linkage between biodiversity and ecosystem services is dependent not only on the choice of bioenergy crop but also on its location relative to other habitats, with local landscape context as important as crop choice in determining provision of some services. Our study suggests that bioenergy policy that supports coordinated land use can diversify agricultural landscapes and sustain multiple critical ecosystem services.
Climate gradients shape spatial variation in the richness and composition of plant communities. Given future predicted changes in climate means and variability, and likely regional variation in the ...magnitudes of these changes, it is important to determine how temporal variation in climate influences temporal variation in plant community structure. Here, we evaluated how species richness, turnover, and composition of grassland plant communities responded to interannual variation in precipitation by synthesizing long-term data from grasslands across the United States. We found that mean annual precipitation (MAP) was a positive predictor of species richness across sites, but a positive temporal relationship between annual precipitation and richness was only evident within two sites with low MAP. We also found higher average rates of species turnover in dry sites that in turn had a high proportion of annual species, although interannual rates of species turnover were surprisingly high across all locations. Annual species were less abundant than perennial species at nearly all sites, and our analysis showed that the probability of a species being lost or gained from one year to the next increased with decreasing species abundance. Bray-Curtis dissimilarity from one year to the next, a measure of species composition change that is influenced mainly by abundant species, was insensitive to precipitation at all sites. These results suggest that the richness and turnover patterns we observed were driven primarily by rare species, which comprise the majority of the local species pools at these grassland sites. These findings are consistent with the idea that short-lived and less abundant species are more sensitive to interannual climate variability than longer-lived and more abundant species. We conclude that, among grassland ecosystems, xeric grasslands are likely to exhibit the greatest responsiveness of community composition (richness and turnover) to predicted future increases in interannual precipitation variability. Over the long term, species composition may shift to reflect spatial patterns of mean precipitation; however, perennial-dominated systems will be buffered against rising interannual variation, while systems that have a large number of rare, annual species will show the greatest temporal variability in species composition in response to rising interannual variability in precipitation.
Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific ...to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have implications for bacterial community resilience and the restoration of oral health.
SUMMARY
We present an inversion algorithm tailored for point gravity data. As the data are from multiple surveys, it is inconsistent with regards to spacing and accuracy. An algorithm design ...objective is the exact placement of gravity observations to ensure no interpolation of the data is needed prior to any inversion. This is accommodated by discretization using an unstructured tetrahedral finite-element mesh for both gravity and density with mesh nodes located at all observation points and a first-order system least-squares (FOSLS) formulation for the gravity modelling equations. Regularization follows the Bayesian framework where we use a differential operator approximation of an exponential covariance kernel, avoiding the usual requirement of inverting large dense covariance matrices. Rather than using higher order basis functions with continuous derivatives across element faces, regularization is also implemented with a FOSLS formulation using vector-valued property function (density and its gradient). Minimization of the cost function, comprised of data misfit and regularization, is achieved via a Lagrange multiplier method with the minimum of the gravity FOSLS functional as a constraint. The Lagrange variations are combined into a single equation for the property function and solved using an integral form of the pre-conditioned conjugate gradient method (I-PCG). The diagonal entries of the regularization operator are used as the pre-conditioner to minimize computational costs and memory requirements. Discretization of the differential operators with the finite-element method (FEM) results in matrix systems that are solved with smoothed aggregation algebraic multigrid pre-conditioned conjugate gradient (AMG-PCG). After their initial setup, the AMG-PCG operators and coarse grid solvers are reused in each iteration step, further reducing computation time. The algorithm is tested on data from 23 surveys with a total of 6519 observation points in the Mt Isa–Cloncurry region in north–west Queensland, Australia. The mesh had about 2.5 million vertices and 16.5 million cells. A synthetic case was also tested using the same mesh and error measures for localized concentrations of high and low densities. The inversion results for different parameters are compared to each other as well as to lower order smoothing. Final inversion results are shown with and without depth weighting and compared to previous geological studies for the Mt Isa–Cloncurry region.
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