Chemical and radiation mutagenesis: Induction and detection by whole genome sequencing

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon has emerged as an effective model system to address fundamental questions in grass biology. With its small sequenced genome, short generation time and rapidly expanding array of genetic tools B. distachyon is an ideal system to elucidate the molecular basis of important trai...

Characterization and complete genome sequence of a previously uncharacterized panicovirus from Bermuda grass detected by high throughput sequencing

USDA-ARS?s Scientific Manuscript database

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high throughput sequencing (HTS). The nearly full genome sequence of a previously uncharacterized Panicovirus was identified from...

[Association of phytoplasma with Bermuda grass white-leaf disease].

PubMed

Tan, Weijun; Chen, Yong; Zhang, Wu; Han, Chengchou; Tan, Zhiyuan; Zhang, Juming

2008-10-01

Bermuda grass white leaf is an important disease on Bermuda grass all over the world. The aim of this research is to identify the pathogen which leads to Bermuda grass white leaf occurring on the Chinese mainland. PCR amplification technique, sequence analysis and Southern hybridization were used. A 1.3 kb fragment was amplified by PCR phytoplasma universal primers and total DNA sample extracted from ill Bermuda grass as the amplified template. Sequence analysis of the amplified fragment indicated it clustered into Candidatus Phytoplasm Cynodontis. Southern hybridization analysis showed differential cingulums. The pathogen of Bermuda grass white leaf on the Chinese mainland contains phytoplasma, which provides a scientific basis for further identification, prevention and control of the disease.

Spatial methods for deriving crop rotation history

NASA Astrophysics Data System (ADS)

Mueller-Warrant, George W.; Trippe, Kristin M.; Whittaker, Gerald W.; Anderson, Nicole P.; Sullivan, Clare S.

2017-08-01

Benefits of converting 11 years of remote sensing classification data into cropping history of agricultural fields included measuring lengths of rotation cycles and identifying specific sequences of intervening crops grown between final years of old grass seed stands and establishment of new ones. Spatial and non-spatial methods were complementary. Individual-year classification errors were often correctable in spreadsheet-based non-spatial analysis, whereas their presence in spatial data generally led to exclusion of fields from further analysis. Markov-model testing of non-spatial data revealed that year-to-year cropping sequences did not match average frequencies for transitions among crops grown in western Oregon, implying that rotations into new grass seed stands were influenced by growers' desires to achieve specific objectives. Moran's I spatial analysis of length of time between consecutive grass seed stands revealed that clustering of fields was relatively uncommon, with high and low value clusters only accounting for 7.1 and 6.2% of fields.

Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.

PubMed

Chen, Sunlu; Zheng, Huizhen; Kishima, Yuji

2017-06-01

The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons.

PubMed

Qi, L L; Wu, J J; Friebe, B; Qian, C; Gu, Y Q; Fu, D L; Gill, B S

2013-08-01

Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species.

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

PubMed Central

Zhou, Yang; Zhu, Honghui; Fu, Shenglei; Yao, Qing

2017-01-01

Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important plant groups; however, their influences on the SMC structure are seldom compared, and the variation in the SMC structure among legume or grass species is largely unknown. In this study, we grew three legume species vs. three grass species in mesocosms, and monitored the soil chemical property, quantified the abundance of bacteria and fungi. The SMC structure was also characterized using PCR-DGGE and Miseq sequencing. Results showed that legume and grass differentially affected soil pH, dissolved organic C, total N content, and available P content, and that legume enriched fungi more greatly than grass. Both DGGE profiling and Miseq-sequencing indicated that the bacterial diversity associated with legume was higher than that associated with grass. When legume increased the abundance of Verrucomicrobia, grass decreased it, and furthermore, linear discriminant analysis identified some group-specific microbial taxa as potential biomarkers of legume or grass. These data suggest that legume and grass differentially select for the SMC. More importantly, clustering analysis based on both DGGE profiling and Miseq-sequencing demonstrated that the variation in the SMC structure associated with three legume species was greater than that associated with three grass species. PMID:28620371

Using the Model Perennial Grass Brachypodium sylvaticum to Engineer Resistance to Multiple Abiotic Stresses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gordon, Sean; Reguera, Maria; Sade, Nir

2015-03-20

We are using the perennial model grass Brachypodium sylvaticum to identify combinations of transgenes that enhance tolerance to multiple, simultaneous abiotic stresses. The most successful transgene combinations will ultimately be used to create improved switchgrass (Panicum virgatum L.) cultivars. To further develop B. sylvaticum as a perennial model grass, and facilitate our planned transcriptional profiling, we are sequencing and annotating the genome. We have generated ~40x genome coverage using PacBio sequencing of the largest possible size selected libraries (18, 22, 25 kb). Our initial assembly using only long-read sequence contained 320 Mb of sequence with an N50 contig length ofmore » 315 kb and an N95 contig length of 40 kb. This assembly consists of 2,430 contigs, the largest of which was 1.6 Mb. The estimated genome size based on c-values is 340 Mb indicating that about 20 Mb of presumably repetitive DNA remains yet unassembled. Significantly, this assembly is far superior to an assembly created from paired-end short-read sequence, ~100x genome coverage. The short-read-only assembly contained only 226 Mb of sequence in 19k contigs. To aid the assembly of the scaffolds into chromosome-scale assemblies we produced an F2 mapping population and have genotyped 480 individuals using a genotype by sequence approach. One of the reasons for using B. sylvaticum as a model system is to determine if the transgenes adversely affect perenniality and winter hardiness. Toward this goal, we examined the freezing tolerance of wild type B. sylvaticum lines to determine the optimal conditions for testing the freezing tolerance of the transgenics. A survey of seven accessions noted significant natural variation in freezing tolerance. Seedling or adult Ain-1 plants, the line used for transformation, survived an 8 hour challenge down to -6 oC and 50% survived a challenge down to -9 oC. Thus, we will be able to easily determine if the transgenes compromise freezing tolerance. In the effort to develop biotechnological tools for perennial grass improvement, we have completed the transformation of B. sylvaticum with constructs containing 20 genes shown to be associated with enhanced abiotic stress tolerance in monocots. In addition, we have transformed plants with constructs containing a combination of genes (i.e. SARK::IPT- Ubi::HSR1::Ubi::NHX1) in order to simultaneously overexpress genes associated with drought + heat tolerance + salt tolerance. We generated single copy insert T1 lines for all constructs and the generation and bulking of homozygous T2 lines is well underway. In addition to our B. sylvaticum transgenics, we transformed B. distachyon with many of the same genes. Some of the transgenic B. distachyon plants subjected to a combined stress of both drought and salinity were able to produced higher yields than wild type plants. Our results indicate a great potential for the development of grasses with improved performance and yield in water-limited areas.« less

Integrative analysis and expression profiling of secondary cell wall genes in C4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering

PubMed Central

Muthamilarasan, Mehanathan; Khan, Yusuf; Jaishankar, Jananee; Shweta, Shweta; Lata, Charu; Prasad, Manoj

2015-01-01

Several underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization. PMID:26583030

Integrative analysis and expression profiling of secondary cell wall genes in C4 biofuel model Setaria italica reveals targets for lignocellulose bioengineering.

PubMed

Muthamilarasan, Mehanathan; Khan, Yusuf; Jaishankar, Jananee; Shweta, Shweta; Lata, Charu; Prasad, Manoj

2015-01-01

Several underutilized grasses have excellent potential for use as bioenergy feedstock due to their lignocellulosic biomass. Genomic tools have enabled identification of lignocellulose biosynthesis genes in several sequenced plants. However, the non-availability of whole genome sequence of bioenergy grasses hinders the study on bioenergy genomics and their genomics-assisted crop improvement. Foxtail millet (Setaria italica L.; Si) is a model crop for studying systems biology of bioenergy grasses. In the present study, a systematic approach has been used for identification of gene families involved in cellulose (CesA/Csl), callose (Gsl) and monolignol biosynthesis (PAL, C4H, 4CL, HCT, C3H, CCoAOMT, F5H, COMT, CCR, CAD) and construction of physical map of foxtail millet. Sequence alignment and phylogenetic analysis of identified proteins showed that monolignol biosynthesis proteins were highly diverse, whereas CesA/Csl and Gsl proteins were homologous to rice and Arabidopsis. Comparative mapping of foxtail millet lignocellulose biosynthesis genes with other C4 panicoid genomes revealed maximum homology with switchgrass, followed by sorghum and maize. Expression profiling of candidate lignocellulose genes in response to different abiotic stresses and hormone treatments showed their differential expression pattern, with significant higher expression of SiGsl12, SiPAL2, SiHCT1, SiF5H2, and SiCAD6 genes. Further, due to the evolutionary conservation of grass genomes, the insights gained from the present study could be extrapolated for identifying genes involved in lignocellulose biosynthesis in other biofuel species for further characterization.

Expanding the Range of Plant Functional Diversity Represented in Global Vegetation Models: Towards Lineage-based Plant Functional Types

NASA Astrophysics Data System (ADS)

Still, C. J.; Griffith, D.; Edwards, E.; Forrestel, E.; Lehmann, C.; Anderson, M.; Craine, J.; Pau, S.; Osborne, C.

2014-12-01

Variation in plant species traits, such as photosynthetic and hydraulic properties, can indicate vulnerability or resilience to climate change, and feed back to broad-scale spatial and temporal patterns in biogeochemistry, demographics, and biogeography. Yet, predicting how vegetation will respond to future environmental changes is severely limited by the inability of our models to represent species-level trait variation in processes and properties, as current generation process-based models are mostly based on the generalized and abstracted concept of plant functional types (PFTs) which were originally developed for hydrological modeling. For example, there are close to 11,000 grass species, but most vegetation models have only a single C4 grass and one or two C3 grass PFTs. However, while species trait databases are expanding rapidly, they have been produced mostly from unstructured research, with a focus on easily researched traits that are not necessarily the most important for determining plant function. Additionally, implementing realistic species-level trait variation in models is challenging. Combining related and ecologically similar species in these models might ameliorate this limitation. Here we argue for an intermediate, lineage-based approach to PFTs, which draws upon recent advances in gene sequencing and phylogenetic modeling, and where trait complex variations and anatomical features are constrained by a shared evolutionary history. We provide an example of this approach with grass lineages that vary in photosynthetic pathway (C3 or C4) and other functional and structural traits. We use machine learning approaches and geospatial databases to infer the most important environmental controls and climate niche variation for the distribution of grass lineages, and utilize a rapidly expanding grass trait database to demonstrate examples of lineage-based grass PFTs. For example, grasses in the Andropogoneae are typically tall species that dominate wet and seasonally burned ecosystems, whereas Chloridoideae grasses are associated with semi-arid regions. These two C4 lineages are expected to respond quite differently to climate change, but are often modelled as a single PFT.

Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle

PubMed Central

Li, Yaokun; Carrillo, José A.; Ding, Yi; He, YangHua; Zhao, Chunping; Zan, Linsen; Song, Jiuzhou

2015-01-01

Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. PMID:26090810

Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

PubMed Central

Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

2013-01-01

Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses

PubMed Central

Dudnik, Alexey; Dudler, Robert

2014-01-01

The Pseudomonas syringae species complex has recently been named the number one plant pathogen, due to its economic and environmental impacts, as well as for its role in scientific research. The bacterium has been repeatedly reported to cause outbreaks on bean, cucumber, stone fruit, kiwi and olive tree, as well as on other crop and non-crop plants. It also serves as a model organism for research on the Type III secretion system (T3SS) and plant-pathogen interactions. While most of the current work on this pathogen is either carried out on one of three model strains found on dicot plants with completely sequenced genomes or on isolates obtained from recent outbreaks, not much is known about strains isolated from grasses (Poaceae). Here, we use comparative genomics in order to identify putative virulence-associated genes and other Poaceae-specific adaptations in several newly available genome sequences of strains isolated from grass species. All strains possess only a small number of known Type III effectors, therefore pointing to the importance of non-Type III secreted virulence factors. The implications of this finding are discussed. PMID:25437611

Molecular cloning and sequence analysis of stearoyl-CoA desaturase in milkfish, Chanos chanos.

PubMed

Hsieh, S L; Liao, W L; Kuo, C M

2001-12-01

Stearoyl-CoA desaturase (EC 1.14.99.5) is a key enzyme in the biosynthesis of polyunsaturated fatty acids and the maintenance of the homeoviscous fluidity of biological membranes. The stearoyl-CoA desaturase cDNA in milkfish (Chanos chanos) was cloned by RT-PCR and RACE, and it was compared with the stearoyl-CoA desaturase in cold-tolerant teleosts, common carp and grass carp. Nucleotide sequence analysis revealed that the cDNA clone has a 972-bp open reading frame encoding 323 amino acid residues. Alignments of the deduced amino acid sequence showed that the milkfish stearoyl-CoA desaturase shares 79% and 75% identity with common carp and grass carp, and 63%-64% with other vertebrates such as sheep, hamsters, rats, mice, and humans. Like common carp and grass carp, the deduced amino acid sequence in milkfish well conserves three histidine cluster motifs (one HXXXXH and two HXXHH) that are essential for catalysis of stearoyl-CoA desaturase activity. However, RT-PCR analysis showed that stearoyl-CoA desaturase expression in milkfish is detected in the tissues of liver, muscle, kidney, brain, and gill, and more expression sites were found in milkfish than in common carp and grass carp. Phylogenic relationships among the deduced stearoyl-CoA desaturase amino acid sequence in milkfish and those in other vertebrates showed that the milkfish stearoyl-CoA desaturase amino acid sequence is phylogenetically closer to those of common carp and grass carp than to other higher vertebrates.

Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Gupta, Sarika; Kumari, Kajal; Sahu, Pranav Pankaj; Vidapu, Sudhakar; Prasad, Manoj

2012-02-01

The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar 'Prasad', 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F(2) mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30-0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.

Brachypodium distachyon genomics for sustainable food and fuel production.

PubMed

Bevan, Michael W; Garvin, David F; Vogel, John P

2010-04-01

Grass crops are the most important sources of human nutrition, and their improvement is centrally important for meeting the challenges of sustainable agriculture, for feeding the world's population and for developing renewable supplies of fuel and industrial products. We describe the complete sequence of the compact genome of Brachypodium distachyon (Brachypodium) the first pooid grass to be sequenced. We demonstrate the many favorable characteristics of Brachypodium as an experimental system and show how it can be used to navigate the large and complex genomes of closely related grasses. The functional genomics and other experimental resources that are being developed will provide a key resource for improving food and forage crops, in particular wheat, barley and forage grasses, and for establishing new grass crops for sustainable energy production. Copyright 2010 Elsevier Ltd. All rights reserved.

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

PubMed

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects.

Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses

PubMed Central

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Background Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. Methodology/Principal Findings We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Conclusions/Significance Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects. PMID:22272330

Brachypodium distachyon genetic resources

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon is a well-established model species for the grass family Poaceae. It possesses an array of features that make it suited for this purpose, including a small sequenced genome, simple transformation methods, and additional functional genomics tools. However, the most critical to...

Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae.

PubMed

Guisinger, Mary M; Chumley, Timothy W; Kuehl, Jennifer V; Boore, Jeffrey L; Jansen, Robert K

2010-02-01

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.

Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyler, Ludmila; Lee, Scott J.; Young, Nelson D.

The small, annual grass Brachypodium distachyon (L.) Beauv., a close relative of wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in B. distachyon by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 B. distachyon, seven B. hybridum, and three B. stacei accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Overmore » 90,000 high-quality single-nucleotide polymorphisms (SNPs) distributed across the Bd21 reference genome were identified. Our results confirm the hybrid nature of the B. hybridum genome, which appears as a mosaic of B. distachyon-like and B. stacei-like sequences. Analysis of more than 50,000 SNPs for the B. distachyon accessions revealed three distinct, genetically defined populations. Surprisingly, these genomic profiles are associated with differences in flowering time rather than with broad geographic origin. High levels of differentiation in loci associated with floral development support the differences in flowering phenology between B. distachyon populations. Genome-wide association studies combining genotypic and phenotypic data also suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within B. distachyon populations. As a result, our characterization elucidates genes underlying population differences, expands the germplasm resources available for Brachypodium, and illustrates the feasibility and limitations of GWAS in this model grass.« less

Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas

DOE PAGES

Tyler, Ludmila; Lee, Scott J.; Young, Nelson D.; ...

2016-04-29

The small, annual grass Brachypodium distachyon (L.) Beauv., a close relative of wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in B. distachyon by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 B. distachyon, seven B. hybridum, and three B. stacei accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Overmore » 90,000 high-quality single-nucleotide polymorphisms (SNPs) distributed across the Bd21 reference genome were identified. Our results confirm the hybrid nature of the B. hybridum genome, which appears as a mosaic of B. distachyon-like and B. stacei-like sequences. Analysis of more than 50,000 SNPs for the B. distachyon accessions revealed three distinct, genetically defined populations. Surprisingly, these genomic profiles are associated with differences in flowering time rather than with broad geographic origin. High levels of differentiation in loci associated with floral development support the differences in flowering phenology between B. distachyon populations. Genome-wide association studies combining genotypic and phenotypic data also suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within B. distachyon populations. As a result, our characterization elucidates genes underlying population differences, expands the germplasm resources available for Brachypodium, and illustrates the feasibility and limitations of GWAS in this model grass.« less

Drought resilience across ecologically dominant species: An experiment-model integration approach

NASA Astrophysics Data System (ADS)

Felton, A. J.; Warren, J.; Ricciuto, D. M.; Smith, M. D.

2017-12-01

Poorly understood are the mechanisms contributing to variability in ecosystem recovery following drought. Grasslands of the central U.S. are ecologically and economically important ecosystems, yet are also highly sensitive to drought. Although characteristics of these ecosystems change across gradients of temperature and precipitation, a consistent feature among these systems is the presence of highly abundant, dominant grass species that control biomass production. As a result, the incorporation of these species' traits into terrestrial biosphere models may constrain predictions amid increases in climatic variability. Here we report the results of a modeling-experiment (MODEX) research approach. We investigated the physiological, morphological and growth responses of the dominant grass species from each of the four major grasslands of the central U.S. (ranging from tallgrass prairie to desert grassland) following severe drought. Despite significant differences in baseline values, full recovery in leaf physiological function was evident across species, of which was consistently driven by the production of new leaves. Further, recovery in whole-plant carbon uptake tended to be driven by shifts in allocation from belowground to aboveground structures. However, there was clear variability among species in the magnitude of this dynamic as well as the relative allocation to stem versus leaf production. As a result, all species harbored the physiological capacity to recover from drought, yet we posit that variability in the recovery of whole-plant carbon uptake to be more strongly driven by variability in the sensitivity of species' morphology to soil moisture increases. The next step of this project will be to incorporate these and other existing data on these species and ecosystems into the community land model in an effort to test the sensitivity of this model to these data.

Combining Livestock Production Information in a Process-Based Vegetation Model to Reconstruct the History of Grassland Management

NASA Technical Reports Server (NTRS)

Chang, Jinfeng; Ciais, Philippe; Herrero, Mario; Havlik, Petr; Campioli, Matteo; Zhang, Xianzhou; Bai, Yongfei; Viovy, Nicolas; Joiner, Joanna; Wang, Xuhui;

De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses.

PubMed

Meena, Seema; Kumar, Sarma R; Venkata Rao, D K; Dwivedi, Varun; Shilpashree, H B; Rastogi, Shubhra; Shasany, Ajit K; Nagegowda, Dinesh A

2016-01-01

Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition.

De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses

PubMed Central

Meena, Seema; Kumar, Sarma R.; Venkata Rao, D. K.; Dwivedi, Varun; Shilpashree, H. B.; Rastogi, Shubhra; Shasany, Ajit K.; Nagegowda, Dinesh A.

2016-01-01

Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition. PMID:27516768

Genotypic and phenotypic evaluation of off-type grasses in hybrid Bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] putting greens using genotyping-by-sequencing and morphological characterization.

PubMed

Reasor, Eric H; Brosnan, James T; Staton, Margaret E; Lane, Thomas; Trigiano, Robert N; Wadl, Phillip A; Conner, Joann A; Schwartz, Brian M

2018-01-01

Interspecific hybrid bermudagrass [ Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] is one of the most widely used grasses on golf courses, with cultivars derived from 'Tifgreen' or 'Tifdwarf' particularly used for putting greens. Many bermudagrass cultivars established for putting greens can be genetically unstable and lead to the occurrence of undesirable off-type grasses that vary in phenotype. The objective of this research was to genetically and phenotypically differentiate off-type grasses and hybrid cultivars. Beginning in 2013, off-type and desirable hybrid bermudagrass samples were collected from golf course putting greens in the southeastern United States and genetically and phenotypically characterized using genotyping-by-sequencing and morphology. Genotyping-by-sequencing determined that 11% (5) of off-type and desirable samples from putting greens were genetically divergent from standard cultivars such as Champion, MiniVerde, Tifdwarf, TifEagle, and Tifgreen. In addition, genotyping-by-sequencing was unable to genetically distinguish all standard cultivars from one another due to their similar origin and clonal propagation; however, over 90,000 potentially informative nucleotide variants were identified among the triploid hybrid cultivars. Although few genetic differences were found in this research, samples harvested from golf course putting greens had variable morphology and were clustered into three distinct phenotypic groups. The majority of off-type grasses in hybrid bermudagrass putting greens were genetically similar with variable morphological traits. Off-type grasses within golf course putting greens have the potential to compromise putting surface functionality and aesthetics.

Nucleotide sequence and genome organization of a novel Panicovirus from Bermuda grass

USDA-ARS?s Scientific Manuscript database

Bermuda grass, (Cynodon dactylon) is widely used in tropical and subtropical areas for golf greens, athletic fields, and landscapes. Samples of Bermuda grass associated with decline symptoms were tested at the University of Minnesota plant virology lab. Spherical virus particles (28-30 nm) were obse...

A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.

PubMed Central

Davis, G L; McMullen, M D; Baysdorfer, C; Musket, T; Grant, D; Staebell, M; Xu, G; Polacco, M; Koster, L; Melia-Hancock, S; Houchins, K; Chao, S; Coe, E H

1999-01-01

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits. PMID:10388831

Transcriptomic data of pre-meiotic stage of floret development in apomictic and sexual types of guinea grass (Panicum maximum Jacq.).

PubMed

Radhakrishna, Auji; Dwivedi, Krishna Kumar; Srivastava, Manoj Kumar; Roy, A K; Malaviya, D R; Kaushal, P

2018-06-01

Guinea grass ( Panicum maximum Jacq), an important fodder crop of humid and sub-humid tropical regions, reproduces through apomixis, a method of clonal propagation through seeds. Lack of knowledge of the genetic and molecular control of this phenomena has hindered the genetic improvement of this crop. The dataset provided here represents the first RNA-Seq based assembly and analysis of florets at pre-meiotic stage from the apomictic and sexual genotypes of guinea grass. The raw sequence files in FASTQ format were deposited in the NCBI SRA database with accession number SRP115883. A total of 24.8 Gb raw sequence data, corresponding to 17,96,65,827 raw reads was obtained by paired end sequencing. We used Trinity for de-novo assembly and identified 57,647 transcripts in sexual and 49,093 transcripts in apomictic type. This transcriptome data will be useful for identification and comparative analysis of genes regulating the mode of reproduction in grasses.

Sarocladium spinificis, a new endophytic species from the coastal grass Spinifex littoreus in Taiwan.

PubMed

Yeh, Yu-Hung; Kirschner, Roland

2014-12-01

Sarocladium species are frequently associated with grasses as saprobes, parasites, and mutualistic endophytes. A species of Sarocladium (anamorphic Hypocreales) was isolated as endophytic fungus from the coastal grass Spinifex littoreus (Poaceae). According to characterization by LSU and ITS rDNA sequences and culture morphology and micromorphology, the species differed from the species hitherto described in Sarocladium. A key to the known species of Sarocladium is given. Sarocladium spinificis is proposed as a new species. LSU rDNA sequences and conidiophore branching and conidium size are useful characters for distinguishing between species of Sarocladium.

BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeted expression to secondary cell-wall-forming cells of grasses

DOE PAGES

Petrik, Deborah L.; Cass, Cynthia L.; Padmakshan, Dharshana; ...

2016-02-04

Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels inmore » stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven expression was strongest in leaf veins, leaf margins, and trichomes; relatively weaker and patchy expression was observed in the epidermis. BdPMT promoter-driven expression was similar to the BdCESA promoters expression patterns, including strong expression in trichomes. The intensity and extent of GUS staining varied considerably between transgenic lines, suggesting that positional effects influenced promoter activity. Introducing the BdPMT and BdCESA8 Open Reading Frames into BdPMT and BdCESA8 utility promoter binary vectors, respectively, and transforming those constructs into Brachypodium pmt and cesa8 loss-of-function mutants resulted in rescue of the corresponding mutant phenotypes. This work therefore validates the functionality of these utility promoter binary vectors for use in Brachypodium and likely other grass species. Lastly, the identification, in Bdcesa8-1 T-DNA mutant stems, of an 80% reduction in crystalline cellulose levels confirms that the BdCESA8 gene is a secondary-cell-wall-forming cellulose synthase.« less

BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeted expression to secondary cell-wall-forming cells of grasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Deborah L.; Cass, Cynthia L.; Padmakshan, Dharshana

Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels inmore » stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven expression was strongest in leaf veins, leaf margins, and trichomes; relatively weaker and patchy expression was observed in the epidermis. BdPMT promoter-driven expression was similar to the BdCESA promoters expression patterns, including strong expression in trichomes. The intensity and extent of GUS staining varied considerably between transgenic lines, suggesting that positional effects influenced promoter activity. Introducing the BdPMT and BdCESA8 Open Reading Frames into BdPMT and BdCESA8 utility promoter binary vectors, respectively, and transforming those constructs into Brachypodium pmt and cesa8 loss-of-function mutants resulted in rescue of the corresponding mutant phenotypes. This work therefore validates the functionality of these utility promoter binary vectors for use in Brachypodium and likely other grass species. Lastly, the identification, in Bdcesa8-1 T-DNA mutant stems, of an 80% reduction in crystalline cellulose levels confirms that the BdCESA8 gene is a secondary-cell-wall-forming cellulose synthase.« less

Modelling the Impact of Climate Change on Soil Water Availability and Plant Community Shifts in the Colorado Plateau

NASA Astrophysics Data System (ADS)

Thomas, A.; Gill, R. A.

2016-12-01

Climate change with an accompanying decrease in soil moisture is expected to have a significant impact on the sensitive, water-limited ecosystems of America's southwestern deserts. Already, studies have documented shifts in the distributions of competing grasses and shrubs in this region, potentially altering ecosystem function. Of particular interest is the loss of desert grasses and the expansion of desert shrubs over the past three decades. The objective of this work is to use a process-based hydrological model to extrapolate site-level measurements to assess trends in soil moisture availability that may impact plant communities in the Colorado Plateau and surrounding regions. The model, SOILWAT, simulates the daily movement of water through plant and soil layers, incorporating precipitation, interception, evaporation, infiltration between soil layers, and absorption and transpiration by plants, as well as physical site characteristics. We applied SOILWAT to 50 sites that were stratified through the northern, central, and southern regions of Ephedra viridis. We focused on E. viridis because it has displaced desert grasses in plot-scale studies. The model was driven using spatially interpolated daily weather data from the PRISM climate model over a 34-year period. We found that across all years, average soil water content in the sandy soil of the region was higher in soil layers 40-60 cm deep than in the top 20 cm, and highest in the deepest layers down to 100 cm. The consistently higher margin of water in deeper layers may indicate the vulnerability of shallow-rooted grass to increasing evaporation and an advantage to deeply-rooted shrubs such as Ephedra.

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecul...

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines

USDA-ARS?s Scientific Manuscript database

Natural variation provides a powerful opportunity to study the genetic basis of biological traits. Brachypodium distachyon is a broadly distributed diploid model grass with a small genome and a large collection of diverse inbred lines. As a step towards understanding the genetic basis of the natura...

Gene expression in grass ovaries infected with seed born fungal endophyte Neotyphodium occultans analyzed by a next-generation sequencing system

USDA-ARS?s Scientific Manuscript database

Fungal endophytes of the genus Neotyphodium form symbiotic associations with many grass species of the subfamily Pooideae, including some important forage and turf species such as Lolium grasses. The endophytes are maintained in host plant communities by seed transmission from maternal plants to off...

Facilitation or Competition? Tree Effects on Grass Biomass across a Precipitation Gradient

PubMed Central

Moustakas, Aristides; Kunin, William E.; Cameron, Tom C.; Sankaran, Mahesh

2013-01-01

Savanna ecosystems are dominated by two distinct plant life forms, grasses and trees, but the interactions between them are poorly understood. Here, we quantified the effects of isolated savanna trees on grass biomass as a function of distance from the base of the tree and tree height, across a precipitation gradient in the Kruger National Park, South Africa. Our results suggest that mean annual precipitation (MAP) mediates the nature of tree-grass interactions in these ecosystems, with the impact of trees on grass biomass shifting qualitatively between 550 and 737 mm MAP. Tree effects on grass biomass were facilitative in drier sites (MAP≤550 mm), with higher grass biomass observed beneath tree canopies than outside. In contrast, at the wettest site (MAP = 737 mm), grass biomass did not differ significantly beneath and outside tree canopies. Within this overall precipitation-driven pattern, tree height had positive effect on sub-canopy grass biomass at some sites, but these effects were weak and not consistent across the rainfall gradient. For a more synthetic understanding of tree-grass interactions in savannas, future studies should focus on isolating the different mechanisms by which trees influence grass biomass, both positively and negatively, and elucidate how their relative strengths change over broad environmental gradients. PMID:23451137

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.

PubMed

VanBuren, Robert; Bryant, Doug; Edger, Patrick P; Tang, Haibao; Burgess, Diane; Challabathula, Dinakar; Spittle, Kristi; Hall, Richard; Gu, Jenny; Lyons, Eric; Freeling, Michael; Bartels, Dorothea; Ten Hallers, Boudewijn; Hastie, Alex; Michael, Todd P; Mockler, Todd C

2015-11-26

Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.

Genome sequence of the progenitor of wheat A subgenome Triticum urartu.

PubMed

Ling, Hong-Qing; Ma, Bin; Shi, Xiaoli; Liu, Hui; Dong, Lingli; Sun, Hua; Cao, Yinghao; Gao, Qiang; Zheng, Shusong; Li, Ye; Yu, Ying; Du, Huilong; Qi, Ming; Li, Yan; Lu, Hongwei; Yu, Hua; Cui, Yan; Wang, Ning; Chen, Chunlin; Wu, Huilan; Zhao, Yan; Zhang, Juncheng; Li, Yiwen; Zhou, Wenjuan; Zhang, Bairu; Hu, Weijuan; van Eijk, Michiel J T; Tang, Jifeng; Witsenboer, Hanneke M A; Zhao, Shancen; Li, Zhensheng; Zhang, Aimin; Wang, Daowen; Liang, Chengzhi

2018-05-09

Triticum urartu (diploid, AA) is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat 1,2 . Genomic studies of T. urartu have been useful for investigating the structure, function and evolution of polyploid wheat genomes. Here we report the generation of a high-quality genome sequence of T. urartu by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule real-time whole-genome shotgun sequencing 3 , linked reads and optical mapping 4,5 . We assembled seven chromosome-scale pseudomolecules and identified protein-coding genes, and we suggest a model for the evolution of T. urartu chromosomes. Comparative analyses with genomes of other grasses showed gene loss and amplification in the numbers of transposable elements in the T. urartu genome. Population genomics analysis of 147 T. urartu accessions from across the Fertile Crescent showed clustering of three groups, with differences in altitude and biostress, such as powdery mildew disease. The T. urartu genome assembly provides a valuable resource for studying genetic variation in wheat and related grasses, and promises to facilitate the discovery of genes that could be useful for wheat improvement.

Isolation and in silico analysis of a novel H+-pyrophosphatase gene orthologue from the halophytic grass Leptochloa fusca

NASA Astrophysics Data System (ADS)

Rauf, Muhammad; Saeed, Nasir A.; Habib, Imran; Ahmed, Moddassir; Shahzad, Khurram; Mansoor, Shahid; Ali, Rashid

2017-02-01

Structure prediction can provide information about function and active sites of protein which helps to design new functional proteins. H+-pyrophosphatase is transmembrane protein involved in establishing proton motive force for active transport of Na+ across membrane by Na+/H+ antiporters. A full length novel H+-pyrophosphatase gene was isolated from halophytic grass Leptochloa fusca using RT-PCR and RACE method. Full length LfVP1 gene sequence of 2292 nucleotides encodes protein of 764 amino acids. DNA and protein sequences were used for characterization using bioinformatics tools. Various important potential sites were predicted by PROSITE webserver. Primary structural analysis showed LfVP1 as stable protein and Grand average hydropathy (GRAVY) indicated that LfVP1 protein has good hydrosolubility. Secondary structure analysis showed that LfVP1 protein sequence contains significant proportion of alpha helix and random coil. Protein membrane topology suggested the presence of 14 transmembrane domains and presence of catalytic domain in TM3. Three dimensional structure from LfVP1 protein sequence also indicated the presence of 14 transmembrane domains and hydrophobicity surface model showed amino acid hydrophobicity. Ramachandran plot showed that 98% amino acid residues were predicted in the favored region.

Multigene analysis suggests ecological speciation in the fungal pathogen Claviceps purpurea

PubMed Central

DOUHAN, G. W.; SMITH, M. E.; HUYRN, K. L.; WESTBROOK, A.; Beerli, P.; FISHER, A. J.

2008-01-01

Claviceps purpurea is an important pathogen of grasses and source of novel chemical compounds. Three groups within this species (G1, G2, and G3) have been recognized based on habitat association, sclerotia and conidia morphology, and alkaloid production. These groups have further been supported by RAPD and AFLP markers, suggesting this species may be more accurately described as a species complex. However, all divergent ecotypes can coexist in sympatric populations with no obvious physical barriers to prevent gene flow. In this study, we used both phylogenetic and population genetic analyses to test for speciation within C. purpurea using DNA sequences from ITS, a RAS-like locus, and a portion of beta-tubulin. The G1 types are significantly divergent from the G2/G3 types based on each of the three loci and the combined dataset, whereas the G2/G3 types are more integrated with one another. Although the G2 and G3 lineages have not diverged as much as the G1 lineage based on DNA sequence data, the use of three DNA loci does reliably separate the G2 and G3 lineages. However, the population genetic analyses strongly suggest little to no gene flow occurring between the different ecotypes and we argue that this process is driven by adaptations to ecological habitats; G1 isolates are associated with terrestrial grasses, G2 isolates are found in wet and shady environments, and G3 isolates are found in salt marsh habitats. PMID:18373531

Various cross-reactivity of the grass pollen group 4 allergens: crystallographic study of the Bermuda grass isoallergen Cyn d 4.

PubMed

Huang, Tse-Hao; Peng, Ho-Jen; Su, Song-Nan; Liaw, Shwu-Huey

2012-10-01

The structure of Cyn d 4, the group 4 allergen from Bermuda grass, is reported at 2.15 Å resolution and is the first crystal structure of a naturally isolated pollen allergen. A conserved N-terminal segment that is only present in the large isoallergens forms extensive interactions with surrounding residues and hence greatly enhances the structural stability of the protein. Cyn d 4 contains an FAD cofactor that is covalently linked to His88 and Cys152. To date, all identified bicovalent flavoproteins are oxidases and their substrates are either sugars or secondary metabolites. A deep large hydrophobic substrate-binding cleft is present. Thus, Cyn d 4 may be an oxidase that is involved in the biosynthesis of a pollen-specific metabolite. Cyn d 4 shares ~70% sequence identity with the Pooideae group 4 allergens. Various cross-reactivities between grass pollen group 4 allergens have previously been demonstrated using sera from allergic patients. The protein surface displays an unusually large number of positively charged clusters, reflecting the high pI of ~10. 38 decapeptides that cover the solvent-accessible sequences did not show any significant IgE-binding activity using sera with high Cyn d 4 reactivity from four patients, suggesting that the IgE epitopes of Cyn d 4 are predominantly conformational in nature. Several group 4 structures were then modelled and their potential cross-reactive and species-specific IgE epitopes were proposed.

Sustainability Factors for E-Learning Initiatives

ERIC Educational Resources Information Center

Gunn, Cathy

2010-01-01

This paper examines the challenges that "grass roots" e-learning initiatives face in trying to become sustainable. A cross-institutional study focused on local, rather than centrally driven, initiatives. A number of successful e-learning innovations were identified that had been driven by capable teachers seeking solutions to real…

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.

PubMed

Zhang, Gengyun; Liu, Xin; Quan, Zhiwu; Cheng, Shifeng; Xu, Xun; Pan, Shengkai; Xie, Min; Zeng, Peng; Yue, Zhen; Wang, Wenliang; Tao, Ye; Bian, Chao; Han, Changlei; Xia, Qiuju; Peng, Xiaohua; Cao, Rui; Yang, Xinhua; Zhan, Dongliang; Hu, Jingchu; Zhang, Yinxin; Li, Henan; Li, Hua; Li, Ning; Wang, Junyi; Wang, Chanchan; Wang, Renyi; Guo, Tao; Cai, Yanjie; Liu, Chengzhang; Xiang, Haitao; Shi, Qiuxiang; Huang, Ping; Chen, Qingchun; Li, Yingrui; Wang, Jun; Zhao, Zhihai; Wang, Jian

2012-05-13

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C(4) photosynthesis pathway were also identified.

Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events.

PubMed

Wang, Xiyin; Wang, Jingpeng; Jin, Dianchuan; Guo, Hui; Lee, Tae-Ho; Liu, Tao; Paterson, Andrew H

2015-06-01

Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations. To date, the genome sequences of eight grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic-level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

DOE Office of Scientific and Technical Information (OSTI.GOV)

VanBuren, Robert; Bryant, Doug; Edger, Patrick P.

Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly1. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetiummore » genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a ‘near-complete’ draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. As a result, the Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.« less

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

DOE PAGES

VanBuren, Robert; Bryant, Doug; Edger, Patrick P.; ...

2015-11-11

Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly1. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetiummore » genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a ‘near-complete’ draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. As a result, the Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.« less

Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis.

PubMed

Ordóñez-Baquera, Perla Lucía; González-Rodríguez, Everardo; Aguado-Santacruz, Gerardo Armando; Rascón-Cruz, Quintín; Conesa, Ana; Moreno-Brito, Verónica; Echavarria, Raquel; Dominguez-Viveros, Joel

2017-02-01

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate signal transduction, development, metabolism, and stress responses in plants through post-transcriptional degradation and/or translational repression of target mRNAs. Several studies have addressed the role of miRNAs in model plant species, but miRNA expression and function in economically important forage crops, such as Bouteloua gracilis (Poaceae), a high-quality and drought-resistant grass distributed in semiarid regions of the United States and northern Mexico remain unknown. We applied high-throughput sequencing technology and bioinformatics analysis and identified 31 conserved miRNA families and 53 novel putative miRNAs with different abundance of reads in chlorophyllic cell cultures derived from B. gracilis. Some conserved miRNA families were highly abundant and possessed predicted targets involved in metabolism, plant growth and development, and stress responses. We also predicted additional identified novel miRNAs with specific targets, including B. gracilis ESTs, which were detected under drought stress conditions. Here we report 31 conserved miRNA families and 53 putative novel miRNAs in B. gracilis. Our results suggested the presence of regulatory miRNAs involved in modulating physiological and stress responses in this grass species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses.

PubMed

Chandra, Amaresh; Jain, Radha; Solomon, Sushil; Shrivastava, Shiksha; Roy, Ajoy K

2013-02-04

Sugarcane is an important cash crop, providing 70% of the global raw sugar as well as raw material for biofuel production. Genetic analysis is hindered in sugarcane because of its large and complex polyploid genome and lack of sufficiently informative gene-tagged markers. Modern genomics has produced large amount of ESTs, which can be exploited to develop molecular markers based on comparative analysis with EST datasets of related crops and whole rice genome sequence, and accentuate their cross-technical functionality in orphan crops like tropical grasses. Utilising 246,180 Saccharum officinarum EST sequences vis-à-vis its comparative analysis with ESTs of sorghum and barley and the whole rice genome sequence, we have developed 3425 novel gene-tagged markers - namely, conserved-intron scanning primers (CISP) - using the web program GeMprospector. Rice orthologue annotation results indicated homology of 1096 sequences with expressed proteins, 491 with hypothetical proteins. The remaining 1838 were miscellaneous in nature. A total of 367 primer-pairs were tested in diverse panel of samples. The data indicate amplification of 41% polymorphic bands leading to 0.52 PIC and 3.50 MI with a set of sugarcane varieties and Saccharum species. In addition, a moderate technical functionality of a set of such markers with orphan tropical grasses (22%) and fodder cum cereal oat (33%) is observed. Developed gene-tagged CISP markers exhibited considerable technical functionality with varieties of sugarcane and unexplored species of tropical grasses. These markers would thus be particularly useful in identifying the economical traits in sugarcane and developing conservation strategies for orphan tropical grasses.

Evaluation and comparison of gross primary production estimates for the Northern Great Plains grasslands

USGS Publications Warehouse

Zhang, Li; Wylie, Bruce K.; Loveland, Thomas R.; Fosnight, Eugene A.; Tieszen, Larry L.; Ji, Lei; Gilmanov, Tagir

2007-01-01

Two spatially-explicit estimates of gross primary production (GPP) are available for the Northern Great Plains. An empirical piecewise regression (PWR) GPP model was developed from flux tower measurements to map carbon flux across the region. The Moderate Resolution Imaging Spectrometer (MODIS) GPP model is a process-based model that uses flux tower data to calibrate its parameters. Verification and comparison of the regional PWR GPP and the global MODIS GPP are important for the modeling of grassland carbon flux. This study compared GPP estimates from PWR and MODIS models with five towers in the grasslands. Among them, PWR GPP and MODIS GPP showed a good agreement with tower-based GPP at three towers. The global MODIS GPP, however, did not agree well with tower-based GPP at two other towers, probably because of the insensitivity of MODIS model to regional ecosystem and climate change and extreme soil moisture conditions. Cross-validation indicated that the PWR model is relatively robust for predicting regional grassland GPP. However, the PWR model should include a wide variety of flux tower data as the training data sets to obtain more accurate results.In addition, GPP maps based on the PWR and MODIS models were compared for the entire region. In the northwest and south, PWR GPP was much higher than MODIS GPP. These areas were characterized by the higher water holding capacity with a lower proportion of C4 grasses in the northwest and a higher proportion of C4 grasses in the south. In the central and southeastern regions, PWR GPP was much lower than MODIS GPP under complicated conditions with generally mixed C3/C4 grasses. The analysis indicated that the global MODIS GPP model has some limitations on detecting moisture stress, which may have been caused by the facts that C3 and C4 grasses are not distinguished, water stress is driven by vapor pressure deficit (VPD) from coarse meteorological data, and MODIS land cover data are unable to differentiate the sub-pixel cropland components.

A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations.

PubMed

Ward, Jodie; Gilmore, Simon R; Robertson, James; Peakall, Rod

2009-11-01

Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

Molecular detection of genotype II grass carp reovirus based on nucleic acid sequence-based amplification combined with enzyme-linked immunosorbent assay (NASBA-ELISA).

PubMed

Zeng, Weiwei; Yao, Wei; Wang, Yingying; Li, Yingying; Bermann, Sven M; Ren, Yan; Shi, Cunbin; Song, Xinjian; Huang, Qiwen; Zheng, Shuchen; Wang, Qing

2017-05-01

Grass carp reovirus (GCRV) is the causative agent of the grass carp hemorrhagic disease that has resulted in severe economic losses in the grass carp (Ctenopharyngodon idella) farming industry in China. Early diagnosis and vaccine administration are important priorities for GCRV control. In this study, a nucleic acid sequence-based amplification with enzyme-linked immunosorbent assay (NASBA-ELISA) was developed for to detect genotype II GCRV (GCRV- II). Primers specifically targeting viral RNA genome segment 6 were utilized for amplification in an isothermal digoxigenin-labeling NASBA process, resulting in DIG-labeled RNA amplicons. The amplicons were hybridized to specific biotinylated DNA probes and the products were detected colorimetrically using horseradish peroxidase and a microplate reader. The new method is able to detect GCRV at 14 copies/μL within 5h and had a diagnostic sensitivity and a specificity of 100% when GCRV-II and non-target virus were tested. This NASBA-ELISA was evaluated using a panel of clinical samples (n=103) to demonstrate that it is a rapid, effective and sensitive method for GCRV detection in grass carp aquaculture. Copyright © 2017 Elsevier B.V. All rights reserved.

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes.

PubMed

Nussbaumer, Thomas; Kugler, Karl G; Schweiger, Wolfgang; Bader, Kai C; Gundlach, Heidrun; Spannagl, Manuel; Poursarebani, Naser; Pfeifer, Matthias; Mayer, Klaus F X

2014-12-10

Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner. We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering. This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat1[W][OA

PubMed Central

Akhunov, Eduard D.; Sehgal, Sunish; Liang, Hanquan; Wang, Shichen; Akhunova, Alina R.; Kaur, Gaganpreet; Li, Wanlong; Forrest, Kerrie L.; See, Deven; Šimková, Hana; Ma, Yaqin; Hayden, Matthew J.; Luo, Mingcheng; Faris, Justin D.; Doležel, Jaroslav; Gill, Bikram S.

2013-01-01

Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%–25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits. PMID:23124323

A ˜50 ka record of monsoonal variability in the Darjeeling foothill region, eastern Himalayas

NASA Astrophysics Data System (ADS)

Ghosh, Ruby; Bera, Subir; Sarkar, Anindya; Paruya, Dipak Kumar; Yao, Yi-Feng; Li, Cheng-Sen

2015-04-01

Pollen, phytoliths and δ 13C signatures of soil organic matter from two fluvial sedimentary sequences of the Darjeeling foothill region, eastern Himalayas are used to portray palaeoclimatic oscillations and their impact on regional plant communities over the last ˜50 ka. Quantitative palaeoclimate estimation using coexistence approach on pollen data and other proxies indicate significant oscillations in precipitation during the late part of MIS 3 (46.4-25.9 ka), early and middle part of MIS 2 (25.9-15.6 ka), and 5.4 to 3.5 ka. Middle to late MIS 3 (ca 46.4-31 ka.) was characterized by a comparatively low monsoonal activity and slightly higher temperature than that during ca 31 ka onwards. Simultaneous expansion of deciduous trees and chloridoid grasses also imply a drier and warmer phase. Between 31 and 22.3 ka (late MIS 3 to mid-MIS 2), higher precipitation and a slightly cooler temperature led to an increase in evergreen elements over deciduous taxa and wet-loving panicoid grasses over dry-loving chloridoid grasses than earlier. After ca 22.3 ka, shrinking of forest cover, expansion of C4 chloridoid grasses, Asteraceae and Cheno-ams in the vegetation with lowering of temperature and precipitation characterized the onset of the LGM which continued till 18.3 ka. End of the LGM is manifested by a restoration in the forest cover and in the temperature and precipitation regime. Later, during 5.4 to 4.3 ka, a strong monsoonal activity supported a dense moist evergreen forest cover that subsequently declined during 4.3 to 3.5 ka. A further increase in deciduous elements and non-arboreals might be a consequence of reduced precipitation and higher temperature during this phase. A comparison between monsoonal rainfall, MAT and palaeoatmospheric CO2 with floral dynamics since last ˜50 ka indicates that these fluctuations in plant succession were mainly driven by monsoonal variations.

Plant-soil feedbacks and the reversal of desertification with climate change

USDA-ARS?s Scientific Manuscript database

Our objective was to provide a conceptual framework for perennial grass recovery in a series of wet years, which includes both plant-soil feedbacks that increase available water to grasses and effects of precipitation on a sequence of recovery-related processes. We tested hypotheses based on this fr...

Characterisation of the genomes of four putative vesiculoviruses: tench rhabdovirus, grass carp rhabdovirus, perch rhabdovirus and eel rhabdovirus European X.

PubMed

Stone, David M; Kerr, Rose C; Hughes, Margaret; Radford, Alan D; Darby, Alistair C

2013-11-01

The complete coding sequences were determined for four putative vesiculoviruses isolated from fish. Sequence alignment and phylogenetic analysis based on the predicted amino acid sequences of the five main proteins assigned tench rhabdovirus and grass carp rhabdovirus together with spring viraemia of carp and pike fry rhabdovirus to a lineage that was distinct from the mammalian vesiculoviruses. Perch rhabdovirus, eel virus European X, lake trout rhabdovirus 903/87 and sea trout virus were placed in a second lineage that was also distinct from the recognised genera in the family Rhabdoviridae. Establishment of two new rhabdovirus genera, "Perhabdovirus" and "Sprivivirus", is discussed.

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

PubMed Central

Saski, Christopher; Lee, Seung-Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Clarke, Jihong Liu

2009-01-01

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae. PMID:17534593

GRASS GIS: a peer-reviewed scientific platform and future research repository

NASA Astrophysics Data System (ADS)

Chemin, Yann; Petras, Vaclav; Petrasova, Anna; Landa, Martin; Gebbert, Sören; Zambelli, Pietro; Neteler, Markus; Löwe, Peter; Di Leo, Margherita

2015-04-01

Geographical Information System (GIS) is known for its capacity to spatially enhance the management of natural resources. While being often used as an analytical tool, it also represents a collaborative scientific platform to develop new algorithms. Thus, it is critical that GIS software as well as the algorithms are open and accessible to anybody [18]. We present how GRASS GIS, a free and open source GIS, is used by many scientists to implement and perform geoprocessing tasks. We will show how integrating scientific algorithms into GRASS GIS helps to preserve reproducibility of scientific results over time [15]. Moreover, subsequent improvements are tracked in the source code version control system and are immediately available to the public. GRASS GIS therefore acts as a repository of scientific peer-reviewed code, algorithm library, and knowledge hub for future generation of scientists. In the field of hydrology, with the various types of actual evapotranspiration (ET) models being developed in the last 20 years, it becomes necessary to inter-compare methods. Most of already published ETa models comparisons address few number of models, and small to medium areas [3, 6, 7, 22, 23]. With the large amount of remote sensing data covering the Earth, and the daily information available for the past ten years (i.e. Aqua/Terra-MODIS) for each pixel location, it becomes paramount to have a more complete comparison, in space and time. To address this new experimental requirement, a distributed computing framework was designed, and created [3, 4]. The design architecture was built from original satellite datasets to various levels of processing until reaching the requirement of various ETa models input dataset. Each input product is computed once and reused in all ETa models requiring such input. This permits standardization of inputs as much as possible to zero-in variations of models to the models internals/specificities. All of the ET models are available in the new GRASS GIS version 7 as imagery modules and replicability is complete for future research. A set of modules for multiscale analysis of landscape structure was added in 1992 by [1], who developed the r.le model similar to FRAGSTATS ([10]). The modules were gradually improved to become r.li in 2006. Further development continued, with a significant speed up [9] and new interactive user interface. The development of spatial interpolation module v.surf.rst started in 1988 [11] and continued by introduction of new interpolation methods and finally full integration into GRASS GIS version 4 [13]. Since then it was improved several times [8]. The module is an important part of GRASS GIS and is taught at geospatial modeling courses, for example at North Carolina State University [14]. GRASS GIS entails several modules that constitute the result of active research on natural hazard. The r.sim.water simulation model [12] for overland flow under rainfall excess conditions was integrated into the Emergency Routing Decision Planning system as a WPS [17]. It was also utilized by [16] and is now part of Tangible Landscape, a tangible GIS system, which also incorporated the r.damflood, a dam break inundation simulation [2]. The wildfire simulation toolset, originally developed by [24], implementing Rothermel's model [21], available through the GRASS GIS modules r.ros and r.spread, is object of active research. It has been extensively tested and recently adapted to European fuel types ([5, 19, 20]). References [1] Baker, W.L., Cai, Y., 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. Landscape Ecology, 7(4):291-302. [2] Cannata M. and Marzocchi R., 2012. Two-dimensional dam break flooding simulation: a GIS embedded approach. - Natural Hazards 61(3):1143-1159. [3] Chemin, Y.H., 2012. A Distributed Benchmarking Framework for Actual ET Models. In Evapotranspiration - Remote Sensing and Modeling, Intech (Eds). [4] Chemin, Y. H. , 2014. Remote Sensing Raster Programming, 3rd Ed., Lulu (Eds). [5] Di Leo, M., de Rigo, D., Rodriguez-Aseretto, D., Bosco, C., Petroliagkis, T., Camia, A., San-Miguel-Ayanz, J., 2013. Dynamic data driven ensemble for wildfire behaviour assessment: A case study. IFIP Advances in Information and Communication Technology, vol. 413, pp. 11-22, 2013, ISSN:1868-4238. Special issue: "Environmental Software Systems. Fostering sharing information". [6] García, M., Villagarcía, L., Contreras, S., Domingo, F. & Puigdefábregas, J. (2007). Comparison of three operative models for estimating the surface water deficit using aster reflective and thermal data, Sensors 7(6): 860-883. [7] Gao, Y. & Long, D. ,2008. Intercomparison of remote sensing-based models for estimation of evapotranspiration and accuracy assessment based on swat, Hydrological Processes 22: 4850-4869. [8] GRASS GIS Trac, changelog for v.surf.rst, 2015. http://trac.osgeo.org/grass/ [9] GRASS GIS Trac, changelog for r.li, 2015. http://trac.osgeo.org/grass/ [10] McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern analysis program for quantifying landscape structure. USDA For. Serv. Gen. Tech. Rep. PNW-351 [11] Mitas, L., and Mitasova H., 1988, General variational approach to the approximation problem, Computers and Mathematics with Applications, v.16, p. 983-992. [12] Mitas, L., and Mitasova, H., 1998, Distributed soil erosion simulation for effective erosion prevention. Water Resources Research, 34(3), 505-516. [13] Mitasova, H. and Mitas, L., 1993: Interpolation by Regularized Spline with Tension: I. Theory and Implementation, Mathematical Geology, 25, 641-655. [14] North Carolina State University, Geospatial Modeling Course, GIS/MEA582, 2015. http://courses.ncsu.edu/ [15] Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. [16] Petrasova, A., Harmon, B., Petras, V., Mitasova, H., 2014. GIS-based environmental modeling with tangible interaction and dynamic visualization. In: Ames, D.P., Quinn, N.W.T., Rizzoli, A.E. (Eds.), Proceedings of the 7th International Congress on Environmental Modelling and Software, June 15-19, San Diego, California, USA. ISBN: 978-88-9035-744-2 [17] Raghavan, v., Choosumrong, S., Yoshida, D., Vinayaraj, P., 2014. Deploying Dynamic Routing Service for Emergency Scenarios using pgRouting, GRASS and ZOO. In Proc. of FOSS4G Europe, Jacobs University, Bremen, Germany, July 15-17, 2014. [18] Rocchini, D., Neteler, M. ,2012. Let the four freedoms paradigm apply to ecology. Trends in Ecology & Evolution, 27: 310-311. [19] Rodriguez-Aseretto, D., de Rigo, D., Di Leo, M., Cortés, A., and San-Miguel-Ayanz, J., 2013. A data-driven model for large wildfire behaviour prediction in europe. Procedia Computer Science, vol. 18, pp. 1861-1870. [20] de Rigo, D., Rodriguez-Aseretto, D., Bosco, C., Di Leo, M., and San-Miguel-Ayanz, J., 2013. An architecture for adaptive robust modelling of wildfire behaviour under deep uncertainty. in Environmental Software Systems. Fostering Information Sharing, ser. IFIP Advances in Information and Communication Technology, J. Ȟrebíˇ cek, G. Schimak, M. Kubásek, and A. Rizzoli, Eds. Springer Berlin Heidelberg, 2013, vol. 413, pp. 367-380. [21] Rothermel, R. C., 1983. How to predict the spread and intensity of forest and range fires. US Forest Service, Gen. Tech. Rep. INT-143. Ogden, Utah. [22] Suleiman, A., Al-Bakri, J., Duqqah, M. & Crago, R. ,2008. Intercomparison ofevapotranspiration estimates at the different ecological zones in jordan, Journal of Hydrometeorology 9(5): 903-919. [23] Timmermans, W. J., Kustas, W. P., Anderson, M. C. & French, A. N. ,2007. An intercomparison of the surface energy balance algorithm for land (sebal) and the two-source energy balance (tseb) modeling schemes, Remote Sensing of Environment 108(4): 369 - 384. [24] Xu, Jianping, 1994. Simulating the spread of wildfires using a geographic information system and remote sensing. Ph. D. Dissertation, Rutgers University, New Brunswick, New Jersey.

Growing C4 perennial grass for bioenergy using a new Agro-BGC ecosystem model

NASA Astrophysics Data System (ADS)

di Vittorio, A. V.; Anderson, R. S.; Miller, N. L.; Running, S. W.

2009-12-01

Accurate, spatially gridded estimates of bioenergy crop yields require 1) biophysically accurate crop growth models and 2) careful parameterization of unavailable inputs to these models. To meet the first requirement we have added the capacity to simulate C4 perennial grass as a bioenergy crop to the Biome-BGC ecosystem model. This new model, hereafter referred to as Agro-BGC, includes enzyme driven C4 photosynthesis, individual live and dead leaf, stem, and root carbon/nitrogen pools, separate senescence and litter fall processes, fruit growth, optional annual seeding, flood irrigation, a growing degree day phenology with a killing frost option, and a disturbance handler that effectively simulates fertilization, harvest, fire, and incremental irrigation. There are four Agro-BGC vegetation parameters that are unavailable for Panicum virgatum (switchgrass), and to meet the second requirement we have optimized the model across multiple calibration sites to obtain representative values for these parameters. We have verified simulated switchgrass yields against observations at three non-calibration sites in IL. Agro-BGC simulates switchgrass growth and yield at harvest very well at a single site. Our results suggest that a multi-site optimization scheme would be adequate for producing regional-scale estimates of bioenergy crop yields on high spatial resolution grids.

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

PubMed Central

McFadden, David G.; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K.; Song, Xiaoling; Pirun, Mono; Santiago, Philip M.; Kim-Kiselak, Caroline; Platt, James T.; Lee, Emily; Hodges, Emily; Rosebrock, Adam P.; Bronson, Roderick T.; Socci, Nicholas D.; Hannon, Gregory J.; Jacks, Tyler; Varmus, Harold

2016-01-01

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity. PMID:27702896

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma.

PubMed

McFadden, David G; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K; Song, Xiaoling; Pirun, Mono; Santiago, Philip M; Kim-Kiselak, Caroline; Platt, James T; Lee, Emily; Hodges, Emily; Rosebrock, Adam P; Bronson, Roderick T; Socci, Nicholas D; Hannon, Gregory J; Jacks, Tyler; Varmus, Harold

2016-10-18

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.

Genes and QTLs controlling inflorescence and stem branch architecture in Leymus (Poaceae: Triticeae) Wildrye.

PubMed

Larson, Steven R; Kellogg, Elizabeth A; Jensen, Kevin B

2013-01-01

Grass inflorescence and stem branches show recognizable architectural differences among species. The inflorescence branches of Triticeae cereals and grasses, including wheat, barley, and 400-500 wild species, are usually contracted into a spike formation, with the number of flowering branches (spikelets) per node conserved within species and genera. Perennial Triticeae grasses of genus Leymus are unusual in that the number of spikelets per node varies, inflorescences may have panicle branches, and vegetative stems may form subterranean rhizomes. Leymus cinereus and L. triticoides show discrete differences in inflorescence length, branching architecture, node number, and density; number of spikelets per node and florets per spikelet; culm length and width; and perimeter of rhizomatous spreading. Quantitative trait loci controlling these traits were detected in 2 pseudo-backcross populations derived from the interspecific hybrids using a linkage map with 360 expressed gene sequence markers from Leymus tiller and rhizome branch meristems. Alignments of genes, mutations, and quantitative trait loci controlling similar traits in other grass species were identified using the Brachypodium genome reference sequence. Evidence suggests that loci controlling inflorescence and stem branch architecture in Leymus are conserved among the grasses, are governed by natural selection, and can serve as possible gene targets for improving seed, forage, and grain production.

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

PubMed Central

Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-01-01

Foxtail millet ( Setaria italica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02–0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species. PMID:23805325

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.

PubMed

Kumari, Kajal; Muthamilarasan, Mehanathan; Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-01-01

Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

Grass-specific CD4(+) T-cells exhibit varying degrees of cross-reactivity, implications for allergen-specific immunotherapy.

PubMed

Archila, L D; DeLong, J H; Wambre, E; James, E A; Robinson, D M; Kwok, W W

2014-07-01

Conceptually, allergic responses may involve cross-reactivity by antibodies or T-cells. While IgE cross-reactivity among grass-pollen allergens has been observed, cross-reactivity at the allergen-specific T-cell level has been less documented. Identification of the patterns of cross-reactivity may improve our understanding, allowing optimization of better immunotherapy strategies. We use Phleum pratense as model for the studying of cross-reactivity at the allergen-specific CD4(+) T cell level among DR04:01 restricted Pooideae grass-pollen T-cell epitopes. After in vitro culture of blood mono-nucleated cells from grass-pollen-allergic subjects with specific Pooideae antigenic epitopes, dual tetramer staining with APC-labelled DR04:01/Phleum pratense tetramers and PE-labelled DR04:01/Pooideae grass homolog tetramers was assessed to identify cross-reactivity among allergen-specific DR04:01-restricted T-cells in six subjects. Direct ex vivo staining enabled the comparison of frequency and phenotype of different Pooideae grass-pollen reactive T-cells. Intracellular cytokine staining (ICS) assays were also used to examine phenotypes of these T-cells. T-cells with various degrees of cross-reactive profiles could be detected. Poa p 1 97-116 , Lol p 1 221-240 , Lol p 5a 199-218 , and Poa p 5a 199-218 were identified as minimally cross-reactive T-cell epitopes that do not show cross-reactivity to Phl p 1 and Phl p 5a epitopes. Ex vivo tetramer staining assays demonstrated T-cells that recognized these minimally cross-reactive T-cell epitopes are present in Grass-pollen-allergic subjects. Our results suggest that not all Pooideae grass epitopes with sequence homology are cross-reactive. Non-cross-reactive T-cells with comparable frequency, phenotype and functionality to Phl p-specific T-cells suggest that a multiple allergen system should be considered for immunotherapy instead of a mono-allergen system. © 2014 John Wiley & Sons Ltd.

Occurrence of Bothriocephalus acheilognathi (Cestoda, Bothriocephallidea) in grass carp Ctenopharyngodon idella in the Changjiang River drainage

NASA Astrophysics Data System (ADS)

Xi, Bingwen; Wang, Guitang; Xie, Jun

2011-05-01

Bothriocephalus acheilognathi is a potentially serious pathogen in wild or cultured fish in worldwide distribution. We examined 58-farmed grass carp from Nanchang in the Changjiang (Yangtze) River drainage, from which 20.7% were found to harbor the parasite with an infection intensity of 36.9±54.7. The parasites were identified based on morphology and rDNA ITS sequence analysis. The present report represents the first record of the parasite in grass carp Ctenopharyngodon idella in the river drainage.

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

PubMed Central

2013-01-01

Background The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. Results Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere. Conclusions This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications. PMID:24359668

Regional and seasonal variation in airborne grass pollen levels between cities of Australia and New Zealand.

PubMed

Medek, Danielle E; Beggs, Paul J; Erbas, Bircan; Jaggard, Alison K; Campbell, Bradley C; Vicendese, Don; Johnston, Fay H; Godwin, Ian; Huete, Alfredo R; Green, Brett J; Burton, Pamela K; Bowman, David M J S; Newnham, Rewi M; Katelaris, Constance H; Haberle, Simon G; Newbigin, Ed; Davies, Janet M

2016-06-01

Although grass pollen is widely regarded as the major outdoor aeroallergen source in Australia and New Zealand (NZ), no assemblage of airborne pollen data for the region has been previously compiled. Grass pollen count data collected at 14 urban sites in Australia and NZ over periods ranging from 1 to 17 years were acquired, assembled and compared, revealing considerable spatiotemporal variability. Although direct comparison between these data is problematic due to methodological differences between monitoring sites, the following patterns are apparent. Grass pollen seasons tended to have more than one peak from tropics to latitudes of 37°S and single peaks at sites south of this latitude. A longer grass pollen season was therefore found at sites below 37°S, driven by later seasonal end dates for grass growth and flowering. Daily pollen counts increased with latitude; subtropical regions had seasons of both high intensity and long duration. At higher latitude sites, the single springtime grass pollen peak is potentially due to a cooler growing season and a predominance of pollen from C 3 grasses. The multiple peaks at lower latitude sites may be due to a warmer season and the predominance of pollen from C 4 grasses. Prevalence and duration of seasonal allergies may reflect the differing pollen seasons across Australia and NZ. It must be emphasized that these findings are tentative due to limitations in the available data, reinforcing the need to implement standardized pollen-monitoring methods across Australasia. Furthermore, spatiotemporal differences in grass pollen counts indicate that local, current, standardized pollen monitoring would assist with the management of pollen allergen exposure for patients at risk of allergic rhinitis and asthma.

Regional and seasonal variation in airborne grass pollen levels between cities of Australia and New Zealand

PubMed Central

Beggs, Paul J.; Erbas, Bircan; Jaggard, Alison K.; Campbell, Bradley C.; Vicendese, Don; Johnston, Fay H.; Godwin, Ian; Huete, Alfredo R.; Green, Brett J.; Burton, Pamela K.; Bowman, David M. J. S.; Newnham, Rewi M.; Katelaris, Constance H.; Haberle, Simon G.; Newbigin, Ed; Davies, Janet M.

2016-01-01

Although grass pollen is widely regarded as the major outdoor aeroallergen source in Australia and New Zealand (NZ), no assemblage of airborne pollen data for the region has been previously compiled. Grass pollen count data collected at 14 urban sites in Australia and NZ over periods ranging from 1 to 17 years were acquired, assembled and compared, revealing considerable spatiotemporal variability. Although direct comparison between these data is problematic due to methodological differences between monitoring sites, the following patterns are apparent. Grass pollen seasons tended to have more than one peak from tropics to latitudes of 37°S and single peaks at sites south of this latitude. A longer grass pollen season was therefore found at sites below 37°S, driven by later seasonal end dates for grass growth and flowering. Daily pollen counts increased with latitude; subtropical regions had seasons of both high intensity and long duration. At higher latitude sites, the single springtime grass pollen peak is potentially due to a cooler growing season and a predominance of pollen from C3 grasses. The multiple peaks at lower latitude sites may be due to a warmer season and the predominance of pollen from C4 grasses. Prevalence and duration of seasonal allergies may reflect the differing pollen seasons across Australia and NZ. It must be emphasized that these findings are tentative due to limitations in the available data, reinforcing the need to implement standardized pollen-monitoring methods across Australasia. Furthermore, spatiotemporal differences in grass pollen counts indicate that local, current, standardized pollen monitoring would assist with the management of pollen allergen exposure for patients at risk of allergic rhinitis and asthma. PMID:27069303

Alignment of the Genomes of Brachypodium distachyon and Temperate Cereals and Grasses Using Bacterial Artificial Chromosome Landing With Fluorescence in Situ Hybridization

PubMed Central

Hasterok, Robert; Marasek, Agnieszka; Donnison, Iain S.; Armstead, Ian; Thomas, Ann; King, Ian P.; Wolny, Elzbieta; Idziak, Dominika; Draper, John; Jenkins, Glyn

2006-01-01

As part of an initiative to develop Brachypodium distachyon as a genomic “bridge” species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice. PMID:16489232

Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.

PubMed

Hasterok, Robert; Marasek, Agnieszka; Donnison, Iain S; Armstead, Ian; Thomas, Ann; King, Ian P; Wolny, Elzbieta; Idziak, Dominika; Draper, John; Jenkins, Glyn

2006-05-01

As part of an initiative to develop Brachypodium distachyon as a genomic "bridge" species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice.

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes.

PubMed

Studer, Anthony J; Schnable, James C; Weissmann, Sarit; Kolbe, Allison R; McKain, Michael R; Shao, Ying; Cousins, Asaph B; Kellogg, Elizabeth A; Brutnell, Thomas P

2016-10-28

Comparisons between C 3 and C 4 grasses often utilize C 3 species from the subfamilies Ehrhartoideae or Pooideae and C 4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C 3 panicoid grass Dichanthelium oligosanthes from the independent C 4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C 3 and C 4 grasses. We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C 3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C 4 photosynthesis. The phylogenetic location of D. oligosanthes makes it an ideal C 3 plant for comparative analysis of C 4 evolution in the panicoid grasses. This genome will not only provide a better C 3 species for comparisons with C 4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.

The draft genome of the C 3 panicoid grass species Dichanthelium oligosanthes

DOE PAGES

Studer, Anthony J.; Schnable, James C.; Weissmann, Sarit; ...

2016-10-28

Comparisons between C 3 and C 4 grasses often utilize C 3 species from the subfamilies Ehrhartoideae or Pooideae and C 4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C 3 panicoid grass Dichanthelium oligosanthes from the independent C 4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C 3 and C 4 grasses. Here, wemore » report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C 3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C 4 photosynthesis. In conclusion, the phylogenetic location of D. oligosanthes makes it an ideal C 3 plant for comparative analysis of C 4 evolution in the panicoid grasses. This genome will not only provide a better C 3 species for comparisons with C 4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.« less

The draft genome of the C 3 panicoid grass species Dichanthelium oligosanthes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Studer, Anthony J.; Schnable, James C.; Weissmann, Sarit

Comparisons between C 3 and C 4 grasses often utilize C 3 species from the subfamilies Ehrhartoideae or Pooideae and C 4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C 3 panicoid grass Dichanthelium oligosanthes from the independent C 4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C 3 and C 4 grasses. Here, wemore » report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C 3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C 4 photosynthesis. In conclusion, the phylogenetic location of D. oligosanthes makes it an ideal C 3 plant for comparative analysis of C 4 evolution in the panicoid grasses. This genome will not only provide a better C 3 species for comparisons with C 4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.« less

Reference genome sequence of the model plant Setaria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species thatmore » demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).« less

Reference genome sequence of the model plant Setaria.

PubMed

Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela C; Panaud, Olivier; Kellogg, Elizabeth A; Brutnell, Thomas P; Doust, Andrew N; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

2012-05-13

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Coherent Microwave Scattering Model of Marsh Grass

NASA Astrophysics Data System (ADS)

Duan, Xueyang; Jones, Cathleen E.

2017-12-01

In this work, we developed an electromagnetic scattering model to analyze radar scattering from tall-grass-covered lands such as wetlands and marshes. The model adopts the generalized iterative extended boundary condition method (GIEBCM) algorithm, previously developed for buried cylindrical media such as vegetation roots, to simulate the scattering from the grass layer. The major challenge of applying GIEBCM to tall grass is the extremely time-consuming iteration among the large number of short subcylinders building up the grass. To overcome this issue, we extended the GIEBCM to multilevel GIEBCM, or M-GIEBCM, in which we first use GIEBCM to calculate a T matrix (transition matrix) database of "straws" with various lengths, thicknesses, orientations, curvatures, and dielectric properties; we then construct the grass with a group of straws from the database and apply GIEBCM again to calculate the T matrix of the overall grass scene. The grass T matrix is transferred to S matrix (scattering matrix) and combined with the ground S matrix, which is computed using the stabilized extended boundary condition method, to obtain the total scattering. In this article, we will demonstrate the capability of the model by simulating scattering from scenes with different grass densities, different grass structures, different grass water contents, and different ground moisture contents. This model will help with radar experiment design and image interpretation for marshland and wetland observations.

Evaluation of off-type grasses in hybrid bermudagrass (Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy) putting greens using genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Use of hybrid ultradwarf bermudagrasses (UDBG; Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy) on golf course putting greens is increasing in the southern United States. However, off-type grasses within many putting surfaces have been observed. To explore the genetic variation among UD...

Sequence Grazing of Perennial and Annual Cool-Season Grasses to Extend the Grazing Season for Stocker Calves

USDA-ARS?s Scientific Manuscript database

Grazing of cool-season grasses by beef calves before entry into the feedlot for finishing is an important component of the US beef production system. The length of time in the feedlot and the quantity of feed grain required to reach market BW would be reduced if more BW was gained during the grazing...

Homogenous stands of a wetland grass harbour diverse consortia of arbuscular mycorrhizal fungi.

PubMed

Wirsel, Stefan G R

2004-05-01

A molecular approach was applied to investigate the colonisation of arbuscular mycorrhizal fungi (AMF) on the wetland grass Phragmites australis. A PCR assay targeting the traditional families of the Glomeromycota yielded products that were used to construct libraries of 18S rDNA. Five hundred and forty six clones were typed by restriction analysis and 76 representatives were sequenced. The majority corresponded to a wide range of taxa within Glomus group A, a few belonged to the "Diversisporaceae" and none to the genera Scutellospora or Acaulospora. Among these sequences, some were very similar to those reported earlier, e.g. Glomus mosseae and G. fasciculatum, other pointed to various new taxa. Although this wetland habitat harboured just one single plant species, phylogenetic analysis exhibited 21 AMF phylotypes, which is in the same range as reported for other natural ecosystems composed of more diverse host communities. Diversity indices supported the perception that the AMF mycoflora associated with this natural grass "monoculture" is not depauperate as it had been described for grasses of crop monocultures. Soil conditions determined the mycorrhizal state of the host, since AMF were not detected at the lakeward front of the reed belt, which is permanently waterlogged.

A 30-day-ahead forecast model for grass pollen in north London, United Kingdom.

PubMed

Smith, Matt; Emberlin, Jean

2006-03-01

A 30-day-ahead forecast method has been developed for grass pollen in north London. The total period of the grass pollen season is covered by eight multiple regression models, each covering a 10-day period running consecutively from 21 May to 8 August. This means that three models were used for each 30-day forecast. The forecast models were produced using grass pollen and environmental data from 1961 to 1999 and tested on data from 2000 and 2002. Model accuracy was judged in two ways: the number of times the forecast model was able to successfully predict the severity (relative to the 1961-1999 dataset as a whole) of grass pollen counts in each of the eight forecast periods on a scale of 1 to 4; the number of times the forecast model was able to predict whether grass pollen counts were higher or lower than the mean. The models achieved 62.5% accuracy in both assessment years when predicting the relative severity of grass pollen counts on a scale of 1 to 4, which equates to six of the eight 10-day periods being forecast correctly. The models attained 87.5% and 100% accuracy in 2000 and 2002, respectively, when predicting whether grass pollen counts would be higher or lower than the mean. Attempting to predict pollen counts during distinct 10-day periods throughout the grass pollen season is a novel approach. The models also employed original methodology in the use of winter averages of the North Atlantic Oscillation to forecast 10-day means of allergenic pollen counts.

14 CFR Appendix G to Part 36 - Takeoff Noise Requirements for Propeller-Driven Small Airplane and Propeller-Driven, Commuter...

Code of Federal Regulations, 2011 CFR

2011-01-01

... excessive sound absorption characteristics such as those caused by thick, matted, or tall grass, by shrubs..., inclusively; (4) Wind speed may not exceed 10 knots (19 km/h) and cross wind may not exceed 5 knots (9 km/h... level atmospheric pressure of 1013.25 mb (013.25 hPa); (2) Ambient air temperature of 59 °F (15 °C); (3...

14 CFR Appendix G to Part 36 - Takeoff Noise Requirements for Propeller-Driven Small Airplane and Propeller-Driven, Commuter...

Code of Federal Regulations, 2010 CFR

2010-01-01

... excessive sound absorption characteristics such as those caused by thick, matted, or tall grass, by shrubs..., inclusively; (4) Wind speed may not exceed 10 knots (19 km/h) and cross wind may not exceed 5 knots (9 km/h... level atmospheric pressure of 1013.25 mb (013.25 hPa); (2) Ambient air temperature of 59 °F (15 °C); (3...

Genotypic and phenotypic evaluation of off-type grasses in hybrid bermudagrass (Cynodon dactylon (L.) Pers. x C. transvaalensis burtt-Davy) putting greens using genotyping-by-sequencing and morphological characterization

USDA-ARS?s Scientific Manuscript database

Interspecific hybrid bermudagrass (Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy) is one of the most widely used grasses on golf courses, with cultivars derived from ‘Tifgreen’ or ‘Tifdwarf’ particularly used for putting greens in the southern agronomic region. Many bermudagrass cultiv...

Successional trajectories of rhizosphere bacterial communities over consecutive seasons

DOE PAGES

Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; ...

2015-08-04

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable over two growing seasons. There are few studies assessing the reproducibility over multiple seasons. Through the growing season, the rhizosphere community became progressively less diverse, likely reflecting root homogenization of soil microniches. Phylogenetic clustering of the rhizosphere dynamic taxa suggests evolutionary adaptation to Avena roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.« less

Successional trajectories of rhizosphere bacterial communities over consecutive seasons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Shengjing; Nuccio, Erin; Herman, Donald J.

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable over two growing seasons. There are few studies assessing the reproducibility over multiple seasons. Through the growing season, the rhizosphere community became progressively less diverse, likely reflecting root homogenization of soil microniches. Phylogenetic clustering of the rhizosphere dynamic taxa suggests evolutionary adaptation to Avena roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.« less

Genetic resources for maize cell wall biology.

PubMed

Penning, Bryan W; Hunter, Charles T; Tayengwa, Reuben; Eveland, Andrea L; Dugard, Christopher K; Olek, Anna T; Vermerris, Wilfred; Koch, Karen E; McCarty, Donald R; Davis, Mark F; Thomas, Steven R; McCann, Maureen C; Carpita, Nicholas C

2009-12-01

Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions.

Surface-attached and suspended bacterial community structure as affected by C/N ratios: relationship between bacteria and fish production.

PubMed

Yu, Ermeng; Xie, Jun; Wang, Jinlin; Ako, Harry; Wang, Guangjun; Chen, Zhanghe; Liu, Yongfeng

2016-07-01

Bacteria play crucial roles in the combined system of substrate addition and C/N control, which has been demonstrated to improve aquaculture production. However, the complexity of surface-attached bacteria on substrates and suspended bacteria in the water column hamper further application of this system. This study firstly applied this combined system into the culture of grass carp, and then explored the relationship between microbial complexes from surface-attached and suspended bacteria in this system and the production of grass carp. In addition, this study investigated bacterial community structures as affected by four C/N ratios using Illumina sequencing technology. The results demonstrated that the weight gain rate and specific growth rate of grass carp in the CN20 group (C/N ratio 20:1) were the highest (P < 0.05), and dietary supplementation of the microbial complex had positive effects on the growth of grass carp (P < 0.05). Sequencing data revealed that, (1) the proportions of Verrucomicrobiae and Rhodobacter (surface-attached), sediminibacterium (suspended), and emticicia (surface-attached and suspended) were much higher in the CN20 group compared with those in the other groups (P < 0.05); (2) Rhodobacter, Flavobacterium, Acinetobacter, Pseudomonas, Planctomyces, and Cloacibacterium might be important for the microbial colonization on substrates; (3) as the C/N ratio increased, proportions of Hydrogenophaga (surface-attached and suspended), Zoogloea, and Flectobacillus (suspended) increased, but proportions of Bacillus, Clavibacter, and Cellvibro (surface-attached and suspended) decreased. In summary, a combined system of substrate addition and C/N control increased the production of grass carp, and Verrucomicrobiae and Rhodobacter in the surface-attached bacterial community were potential probiotic bacteria that contributed to the enhanced growth of grass carp.

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass.

PubMed

Hardegen, Justus; Latorre-Pérez, Adriel; Vilanova, Cristina; Günther, Thomas; Porcar, Manuel; Luschnig, Olaf; Simeonov, Claudia; Abendroth, Christian

2018-06-06

In this work, liquid and solid fractions of grass biomass were used as co-substrates for anaerobic co-digestion of sewage sludge. The input of grass biomass was increased gradually, and the underlying methanogenic microbiome was assessed by means of microscopy-based cell counting and full-length 16S rRNA gene high-throughput sequencing, proving for the first time the suitability of nanopore-based portable sequencers as a monitoring tool for anaerobic digestion systems. In both cases co-fermentation resulted in an increased number of bacteria and methanogenic archaea. Interestingly, the microbial communities were highly different between solid and liquid-fed batches. Liquid-fed batches developed a more stable microbiome, enriched in Methanosarcina spp., and resulted in higher methanogenic yield. In contrast, solid-fed batches were highly unstable at higher substrate concentrations, and kept Methanosaeta spp. - typically associated to sewage sludge - as the majoritary methanogenic archaea. Copyright © 2018 Elsevier Ltd. All rights reserved.

Stimulation of glycerol kinase in grass carp preadipocytes by EPA.

PubMed

Lei, Caixia; Tian, Jingjing; Ji, Hong

2017-06-01

This study was conducted to assess the effect of eicosapentaenoic acid (EPA) on grass carp preadipocyte glycerol kinase (GyK) expression, as well as to explore the mechanism. Here, we cloned partial sequence of grass carp GyK gene and analyzed its tissue distribution. The result showed that GyK gene expressed most in the liver, followed by adipose tissue and the kidney. Besides, 400 μM oleic acid (18:1n-9, OA) was used to establish a hypertrophic preadipocyte model. GyK gene expression and enzyme activity were significantly enhanced after model cells were treated with 100 μM eicosapentaenoic acid (20:5n-3, EPA) for 6, 12, and 24 h. Meanwhile, peroxisome proliferative-activated receptor (PPAR)γ, adipose triglyceride lipase (ATGL), and the two isoforms of grass carp HSL gene were first identified by Sun et al (2016), and they defined the two isoforms as HSLa and HSLb. Therefore, maybe HSLa and HSLb are appropriate.. The content of triglyceride was dramatically increased by EPA treatment for 24 h. Further, a competitive ATGL antagonist, HY-15859, attenuated the increase in GyK induced by EPA at 12 h. Surprisingly, the enhanced lipolysis and PPARγ gene expression induced by serum deprivation were paralleled by an increase in GyK gene expression, whereas a stabilization in GyK enzyme activity. Other fatty acids, including docosahexaenoic acid, alpha-linolenic acid, linoleic acid, and OA also promoted GyK gene expression. Moreover, an irreversible PPARγ antagonist, GW9662, was used to investigate the role of PPARγ in GyK induction. Data showed that GW9662 abolished the induction of GyK by EPA at 12 h. Together, these data suggested that EPA elevated grass carp preadipocytes GyK expression. ATGL and PPARγ contributed to the induction of GyK. PPARγ may be a key regulator in response to GyK expression induced by EPA.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogel, John P.

The goal of this project was to apply high-throughput, non-destructive phenotyping (phenomics) to collections of natural variants and induced mutants of the model grass Brachypodium distachyon and characterize a small subset of that material in detail. B. distachyon is well suited to this phenomic approach because its small size and rapid generation time allow researchers to grow many plants under carefully controlled conditions. In addition, the simple diploid genetics, high quality genome sequence and existence of numerous experimental tools available for B. distachyon allow us to rapidly identify genes affecting specific phenotypes. Our phenomic analysis revealed great diversity in biofuel-relevantmore » traits like growth rate, biomass and photosynthetic rate. This clearly demonstrated the feasibility of applying a phenomic approach to the model grass B. distachyon. We also demonstrated the utility of B. distachyon for studying mature root system, something that is virtually impossible to do with biomass crops. We showed tremendous natural variation in root architecture that can potentially be used to design crops with superior nutrient and water harvesting capability. Finally, we demonstrated the speed with which we can link specific genes to specific phenotypes by studying two mutants in detail. Importantly, in both cases, the specific biological lessons learned were grass-specific and could not have been learned from a dicot model system. Furthermore, one of the genes affects cell wall integrity and thus may be a useful target in the context of biomass crop improvement. Ultimately, all this information can be used to accelerate the creation of improved biomass crops.« less

Modeled hydraulic redistribution in tree-grass, CAM-grass, and tree-CAM associations: the implications of crassulacean acid metabolism (CAM).

PubMed

Yu, Kailiang; Foster, Adrianna

2016-04-01

Past studies have largely focused on hydraulic redistribution (HR) in trees, shrubs, and grasses, and recognized its role in interspecies interactions. HR in plants that conduct crassulacean acid metabolism (CAM), however, remains poorly investigated, as does the effect of HR on transpiration in different vegetation associations (i.e., tree-grass, CAM-grass, and tree-CAM associations). We have developed a mechanistic model to investigate the net direction and magnitude of HR at the patch scale for tree-grass, CAM-grass, and tree-CAM associations at the growing season to yearly timescale. The modeling results show that deep-rooted CAM plants in CAM-grass associations could perform hydraulic lift at a higher rate than trees in tree-grass associations in a relatively wet environment, as explained by a significant increase in grass transpiration rate in the shallow soil layer, balancing a lower transpiration rate by CAM plants. By comparison, trees in tree-CAM associations may perform hydraulic descent at a higher rate than those in tree-grass associations in a dry environment. Model simulations also show that hydraulic lift increases the transpiration of shallow-rooted plants, while hydraulic descent increases that of deep-rooted plants. CAM plants transpire during the night and thus perform HR during the day. Based on these model simulations, we suggest that the ability of CAM plants to perform HR at a higher rate may have different effects on the surrounding plant community than those of plants with C3 or C4 photosynthetic pathways (i.e., diurnal transpiration).

Phylogeny and photosynthesis of the grass tribe Paniceae.

PubMed

Washburn, Jacob D; Schnable, James C; Davidse, Gerrit; Pires, J Chris

2015-09-01

The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved. Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used to build a phylogenetic tree of the Paniceae based on 102 markers (78 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction analyses were also performed within the Paniceae using both the traditional and two subtype classification systems to test hypotheses of C4 subtype evolution. The phylogenetic tree resolves many areas of the Paniceae with high support and provides insight into the origin and number of C4 evolution events within the tribe. The recovered phylogeny and ancestral state reconstructions support between four and seven independent origins of C4 photosynthesis within the tribe and indicate which species are potentially the closest C3 sister taxa of each of these events. Although the sequence of evolutionary events that produced multiple C4 subtypes within the Paniceae remains undetermined, the results presented here are consistent with only a subset of currently proposed models. The species used in this study constitute a panel of C3 and C4 grasses that are suitable for further studies on C4 photosynthesis, bioenergy, food and forage crops, and various developmental features of the Paniceae. © 2015 Botanical Society of America.

Tissue distribution and early developmental expression patterns of aldolase A, B, and C in grass carp Ctenopharyngodon idellus.

PubMed

Fan, J J; Bai, J J; Ma, D M; Yu, L Y; Jiang, P

2017-09-27

Aldolase is a key enzyme involved in glycolysis, gluconeogenesis, and the pentose phosphate pathway. To establish the expression patterns of all three aldolase isozyme genes in different tissues and during early embryogenesis in lower vertebrates, as well as to explore the functional differences between these three isozymes, the grass carp was selected as a model owing to its relatively high glucose-metabolizing capability. Based on the cDNA sequences of the aldolase A, B, and C genes, the expression patterns of these three isozymes were analyzed in different tissues and during early embryogenesis using quantitative real-time polymerase chain reaction (qRT-PCR). Sequence analysis of cDNAs indicated that aldolase A, B, and C (GenBank accession numbers: KM192250, KM192251, and KM192252) consist of 364, 364, and 363 amino acids, respectively. The qRT-PCR results showed that the expression levels of aldolase A, B, and C were highest in the muscle, liver, and brain, respectively. Aldolase A and C exhibited similar expression patterns during embryogenesis, with high levels observed in unfertilized and fertilized eggs and at the blastocyst stage, followed by a decline and then increase after organogenesis. In contrast, aldolase B transcript was not detected during the unfertilized egg stage, and appeared only from gastrulation; the expression increased markedly during the feeding period (72 h after hatching), at which point the level was higher than those of aldolase A and C. These data suggest that the glucose content of grass carp starter feed should be adjusted according to the metabolic activity of aldolase B.

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

PubMed

He, Shui-Lian; Yang, Yang; Morrell, Peter L; Yi, Ting-Shuang

2015-01-01

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

Draft Genome Sequence of Geobacillus sp. LEMMY01, a Thermophilic Bacterium Isolated from the Site of a Burning Grass Pile

PubMed Central

de Souza, Yuri Pinheiro Alves; da Mota, Fábio Faria

2017-01-01

ABSTRACT We report here the 3,586,065-bp draft genome of Geobacillus sp. LEMMY01, which was isolated (axenic culture) from a thermophilic chemolitoautotrophic consortium obtained from the site of a burning grass pile. The genome contains biosynthetic gene clusters coding for secondary metabolites, such as terpene and lantipeptide, confirming the biotechnological potential of this strain. PMID:28495764

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment

PubMed Central

Gould, Billie; McCouch, Susan; Geber, Monica

2015-01-01

Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE. PMID:26148203

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

PubMed

Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

PubMed

Gould, Billie; McCouch, Susan; Geber, Monica

2015-01-01

Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.

The use of multi-temporal Landsat Normalized Difference Vegetation Index (NDVI) data for mapping fuels in Yosemite National Park, USA

USGS Publications Warehouse

Van Wagtendonk, Jan W.; Root, Ralph R.

2003-01-01

The objective of this study was to test the applicability of using Normalized Difference Vegetation Index (NDVI) values derived from a temporal sequence of six Landsat Thematic Mapper (TM) scenes to map fuel models for Yosemite National Park, USA. An unsupervised classification algorithm was used to define 30 unique spectral-temporal classes of NDVI values. A combination of graphical, statistical and visual techniques was used to characterize the 30 classes and identify those that responded similarly and could be combined into fuel models. The final classification of fuel models included six different types: short annual and perennial grasses, tall perennial grasses, medium brush and evergreen hardwoods, short-needled conifers with no heavy fuels, long-needled conifers and deciduous hardwoods, and short-needled conifers with a component of heavy fuels. The NDVI, when analysed over a season of phenologically distinct periods along with ancillary data, can elicit information necessary to distinguish fuel model types. Fuels information derived from remote sensors has proven to be useful for initial classification of fuels and has been applied to fire management situations on the ground.

[Canopy interception of sub-alpine dark coniferous communities in western Sichuan, China].

PubMed

Lü, Yu-liang; Liu, Shi-rong; Sun, Peng-sen; Liu, Xing-liang; Zhang, Rui-pu

2007-11-01

Based on field measurements of throughfall and stemflow in combination with climatic data collected from the meteorological station adjacent to the studied sub-alpine dark coniferous forest in Wolong, Sichuan Province, canopy interception of sub-alpine dark coniferous forests was analyzed and modeled at both stand scale and catchment scale. The results showed that monthly interception rate of Fargesia nitida, Bashania fangiana--Abies faxoniana old-growth ranged from 33% Grass to 72%, with the average of 48%. In growing season, there was a linear or powerful or exponential relationship between rainfall and interception an. a negative exponential relationship between rainfall and interception rate. The mean maximum canopy interception by the vegetation in the catchment of in.44 km was 1.74 ment and the significant differences among the five communities occurred in the following sequence: Moss-Fargesia nitida, Bashan afanglana-A. faxoniana stand > Grass-F. nitida, B. fangiana-A. faxoniana stand > Moss-Rhododendron spp.-A. faxoniana stand > Grass-Rh. spp.-A. faxoniana stand > Rh. spp. shrub. In addition, a close linear relationship existed between leaf area index (LAI) and maximum canopy interception. The simulated value of canopy interception rate, maximum canopy interception rate and addition interception rate of the vegetation in the catchment were 39%, 25% and 14%, respectively. Simulation of the canopy interception model was better at the overall growing season scale, that the mean relative error was 9%-14%.

Greenhouse studies on the phyto-extraction capacity of Cynodon nlemfuensis for lead and cadmium under irrigation with treated wastewater

NASA Astrophysics Data System (ADS)

Madyiwa, S.; Chimbari, M. J.; Schutte, C. F.; Nyamangara, J.

For over 30 years, discharge of sewage effluent and sludge on pasturelands has been used in Zimbabwe as a cheap method for secondary treatment of wastewater without any monitoring of accumulation of heavy metals in soils and grasses, let alone in animals grazing on the pastures. Cynodon nlemfuensis (star grass) has been the main grass planted on the wastewater irrigated pasturelands. This study was conducted to assess the capacity of star grass to accumulate lead (Pb) and cadmium (Cd) and develop models incorporating grass yield, metal uptake and soil bio-available (EDTA extractable) metal content, that could be used to determine critical grass and soil concentrations at which grass productivity declines. Star grass was planted in 30 fertilized pots containing sandy soil within a greenhouse. The pots consisted of nine treatments of varying levels of added inorganic Pb and Cd subjected to treated wastewater application and one control that had no added metals and received water application only. The elements were applied to the soils once just after planting the grass. Chemical analyses showed that star grass had a relatively high phyto-extraction capacity of Pb and Cd, comparable to that of hyper-accumulating grasses such as Lolium perenne (rye grass). It accumulated Pb and Cd to levels far beyond the recommended maximum limits for pasture grass. Analysis of variance on log-normal transformed data showed that bio-available soil metal concentrations correlated strongly with grass metal content and grass metal content correlated strongly with the yield. There was however a weak correlation between the yield and bio-available soil levels. The yield versus grass metal content models that were developed for the first crop and re-growth predicted similar critical metal concentrations and yields. Using the critical grass metal concentrations in the soil bio-available metal concentration versus grass metal concentration models allowed for the prediction of the corresponding critical soil concentrations.

Harnessing the sorghum genome sequence:development of a genome-wide microsattelite (SSR) resource for swift genetic mapping and map based cloning in sorghum

USDA-ARS?s Scientific Manuscript database

Sorghum is the second cereal crop to have a full genome completely sequenced (Nature (2009), 457:551). This achievement is widely recognized as a scientific milestone for grass genetics and genomics in general. However, the true worth of genetic information lies in translating the sequence informa...

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

PubMed Central

Burke, Sean V.; Wysocki, William P.; Clark, Lynn G.

2018-01-01

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity. PMID:29416954

The Prospect of Market-Driven Improvements in Animal Welfare: Lessons from the Case of Grass Milk in Denmark

PubMed Central

Heerwagen, Lennart R.; Christensen, Tove; Sandøe, Peter

2013-01-01

Simple Summary Increased consumption of animal welfare-friendly products is suggested as one way of addressing public worries about the welfare of farm animals. However, the factors that drive and limit markets for animal welfare-friendly products are poorly understood. Based on an analysis of market for grass milk in Denmark, we conclude that successful cases of market-driven improvements in animal welfare require the joint presence of a number of positive drivers as well as low consumption barriers. Abstract Citizens in many European countries urge that the welfare of farm animals should be improved. Policy-makers propose that this could, at least to some extent, be achieved through increased consumption of animal products produced under labeling schemes guaranteeing higher standards of animal welfare. Yet considerable uncertainties exist about the ability of the market to promote animal welfare. So far the consumption of most welfare-friendly products has been limited, and the impact of driving and limiting factors is poorly understood. Reviewing market studies, we identify the factors that have shaped the relatively successful market for grass milk in Denmark. We conclude that the positive drivers such as an appealing animal welfare attribute and animal welfare being bundled with other qualities are essentially the same as those operating in connection with less successful animal welfare-friendly products. It is therefore to be expected that other animal welfare-friendly food products marketed via “natural behaviors” in the farm animals will catch the interest of consumers. However, grass milk consumption has been supported by proper labeling, ready availability and low price premiums as well as multifaceted public support. This suggests that successful cases require the joint presence of a number of positive drivers as well as low consumption barriers. PMID:26487414

Brachypodium as a model for the grasses: today and the future

USDA-ARS?s Scientific Manuscript database

Over the past several years, Brachypodium distachyon (Brachypodium) has emerged as a tractable model system to study biological questions relevant to the grasses. To place its relevance in the larger context of plant biology, we outline here the expanding adoption of Brachypodium as a model grass an...

Development and validation of a 5-day-ahead hay fever forecast for patients with grass-pollen-induced allergic rhinitis

NASA Astrophysics Data System (ADS)

de Weger, Letty A.; Beerthuizen, Thijs; Hiemstra, Pieter S.; Sont, Jacob K.

2014-08-01

One-third of the Dutch population suffers from allergic rhinitis, including hay fever. In this study, a 5-day-ahead hay fever forecast was developed and validated for grass pollen allergic patients in the Netherlands. Using multiple regression analysis, a two-step pollen and hay fever symptom prediction model was developed using actual and forecasted weather parameters, grass pollen data and patient symptom diaries. Therefore, 80 patients with a grass pollen allergy rated the severity of their hay fever symptoms during the grass pollen season in 2007 and 2008. First, a grass pollen forecast model was developed using the following predictors: (1) daily means of grass pollen counts of the previous 10 years; (2) grass pollen counts of the previous 2-week period of the current year; and (3) maximum, minimum and mean temperature ( R 2 = 0.76). The second modeling step concerned the forecasting of hay fever symptom severity and included the following predictors: (1) forecasted grass pollen counts; (2) day number of the year; (3) moving average of the grass pollen counts of the previous 2 week-periods; and (4) maximum and mean temperatures ( R 2 = 0.81). Since the daily hay fever forecast is reported in three categories (low-, medium- and high symptom risk), we assessed the agreement between the observed and the 1- to 5-day-ahead predicted risk categories by kappa, which ranged from 65 % to 77 %. These results indicate that a model based on forecasted temperature and grass pollen counts performs well in predicting symptoms of hay fever up to 5 days ahead.

Development and validation of a 5-day-ahead hay fever forecast for patients with grass-pollen-induced allergic rhinitis.

PubMed

de Weger, Letty A; Beerthuizen, Thijs; Hiemstra, Pieter S; Sont, Jacob K

2014-08-01

One-third of the Dutch population suffers from allergic rhinitis, including hay fever. In this study, a 5-day-ahead hay fever forecast was developed and validated for grass pollen allergic patients in the Netherlands. Using multiple regression analysis, a two-step pollen and hay fever symptom prediction model was developed using actual and forecasted weather parameters, grass pollen data and patient symptom diaries. Therefore, 80 patients with a grass pollen allergy rated the severity of their hay fever symptoms during the grass pollen season in 2007 and 2008. First, a grass pollen forecast model was developed using the following predictors: (1) daily means of grass pollen counts of the previous 10 years; (2) grass pollen counts of the previous 2-week period of the current year; and (3) maximum, minimum and mean temperature (R (2)=0.76). The second modeling step concerned the forecasting of hay fever symptom severity and included the following predictors: (1) forecasted grass pollen counts; (2) day number of the year; (3) moving average of the grass pollen counts of the previous 2 week-periods; and (4) maximum and mean temperatures (R (2)=0.81). Since the daily hay fever forecast is reported in three categories (low-, medium- and high symptom risk), we assessed the agreement between the observed and the 1- to 5-day-ahead predicted risk categories by kappa, which ranged from 65 % to 77 %. These results indicate that a model based on forecasted temperature and grass pollen counts performs well in predicting symptoms of hay fever up to 5 days ahead.

Draft Genome Sequence of Geobacillus sp. LEMMY01, a Thermophilic Bacterium Isolated from the Site of a Burning Grass Pile.

PubMed

de Souza, Yuri Pinheiro Alves; da Mota, Fábio Faria; Rosado, Alexandre Soares

2017-05-11

We report here the 3,586,065-bp draft genome of Geobacillus sp. LEMMY01, which was isolated (axenic culture) from a thermophilic chemolitoautotrophic consortium obtained from the site of a burning grass pile. The genome contains biosynthetic gene clusters coding for secondary metabolites, such as terpene and lantipeptide, confirming the biotechnological potential of this strain. Copyright © 2017 de Souza et al.

Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches.

PubMed

Kanokratana, Pattanop; Wongwilaiwalin, Sarunyou; Mhuantong, Wuttichai; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Champreda, Verawat

2018-04-01

Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Genetic Resources for Maize Cell Wall Biology1[C][W][OA

PubMed Central

Penning, Bryan W.; Hunter, Charles T.; Tayengwa, Reuben; Eveland, Andrea L.; Dugard, Christopher K.; Olek, Anna T.; Vermerris, Wilfred; Koch, Karen E.; McCarty, Donald R.; Davis, Mark F.; Thomas, Steven R.; McCann, Maureen C.; Carpita, Nicholas C.

2009-01-01

Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions. PMID:19926802

A novel soil manganese mechanism drives plant species loss with increased nitrogen deposition in a temperate steppe.

PubMed

Tian, Qiuying; Liu, Nana; Bai, Wenming; Li, Linghao; Chen, Jiquan; Reich, Peter B; Yu, Qiang; Guo, Dali; Smith, Melinda D; Knapp, Alan K; Cheng, Weixin; Lu, Peng; Gao, Yan; Yang, An; Wang, Tianzuo; Li, Xin; Wang, Zhengwen; Ma, Yibing; Han, Xingguo; Zhang, Wen-Hao

2016-01-01

Loss of plant diversity with increased anthropogenic nitrogen (N) deposition in grasslands has occurred globally. In most cases, competitive exclusion driven by preemption of light or space is invoked as a key mechanism. Here, we provide evidence from a 9-yr N-addition experiment for an alternative mechanism: differential sensitivity of forbs and grasses to increased soil manganese (Mn) levels. In Inner Mongolia steppes, increasing the N supply shifted plant community composition from grass-forb codominance (primarily Stipa krylovii and Artemisia frigida, respectively) to exclusive dominance by grass, with associated declines in overall species richness. Reduced abundance of forbs was linked to soil acidification that increased mobilization of soil Mn, with a 10-fold greater accumulation of Mn in forbs than in grasses. The enhanced accumulation of Mn in forbs was correlated with reduced photosynthetic rates and growth, and is consistent with the loss of forb species. Differential accumulation of Mn between forbs and grasses can be linked to fundamental differences between dicots and monocots in the biochemical pathways regulating metal transport. These findings provide a mechanistic explanation for N-induced species loss in temperate grasslands by linking metal mobilization in soil to differential metal acquisition and impacts on key functional groups in these ecosystems.

Draft genome sequences of seven 4-Formylaminooxyvinylglycine producers belonging to the Pseudomonas fluorescens species complex

USDA-ARS?s Scientific Manuscript database

Vinylglycines are non-proteinogenic amino acids that inhibit amino acid metabolism and ethylene production. In this report, we describe the draft genome sequences of seven isolates of Pseudomonas that produce 4-formylaminooxyvinylglycine, a compound known to inhibit the germination of grasses and t...

Bipolaris microstegii Minnis, Rossman, Kleczewki & S.L. Flory, sp. nov.

USDA-ARS?s Scientific Manuscript database

Many species of Bipolaris are significant pathogens of grasses. A new species of Bipolaris was isolated from Microstegium vimineum, an invasive plant in the USA. The fungus causes disease on Microstegium, but it also infects a wider range of hosts. Comparison of ITS and gpd sequence data to sequence...

Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models

PubMed Central

2017-01-01

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder–decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis. PMID:29104927

Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays

USDA-ARS?s Scientific Manuscript database

Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another in...

Thermodynamics-based models of transcriptional regulation with gene sequence.

PubMed

Wang, Shuqiang; Shen, Yanyan; Hu, Jinxing

2015-12-01

Quantitative models of gene regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled or heuristic approximations of the underlying regulatory mechanisms. In this work, we have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence. The proposed model relies on a continuous time, differential equation description of transcriptional dynamics. The sequence features of the promoter are exploited to derive the binding affinity which is derived based on statistical molecular thermodynamics. Experimental results show that the proposed model can effectively identify the activity levels of transcription factors and the regulatory parameters. Comparing with the previous models, the proposed model can reveal more biological sense.

Grass competition suppresses savanna tree growth across multiple demographic stages.

PubMed

Riginos, Corinna

2009-02-01

Savanna ecosystems, defined by the codominance of trees and grasses, cover one-fifth of the world's land surface and are of great socioeconomic and biological importance. Yet, the fundamental question of how trees and grasses coexist to maintain the savanna state remains poorly understood. Many models have been put forward to explain tree-grass coexistence, but nearly all have assumed that grasses do not limit tree growth and demography beyond the sapling stage. This assumption, however, has rarely been tested. Here I show that grass can strongly suppress the growth of trees. I removed grass around trees of three size classes in an Acacia drepanolobium savanna in Laikipia, Kenya. For even the largest trees, grass removal led to a doubling in growth and a doubling in the probability of transitioning to the next size class over two years. These results suggest that grass competition in productive (nutrient-rich) savannas may limit tree growth as much as herbivory and fire (the main factors thought to determine tree demography within a rainfall region) and should be incorporated into savanna models if tree-grass coexistence and savanna dynamics are to be understood.

Forage quality declines with rising temperatures, with implications for livestock production and methane emissions

NASA Astrophysics Data System (ADS)

Lee, Mark A.; Davis, Aaron P.; Chagunda, Mizeck G. G.; Manning, Pete

2017-03-01

Livestock numbers are increasing to supply the growing demand for meat-rich diets. The sustainability of this trend has been questioned, and future environmental changes, such as climate change, may cause some regions to become less suitable for livestock. Livestock and wild herbivores are strongly dependent on the nutritional chemistry of forage plants. Nutrition is positively linked to weight gains, milk production and reproductive success, and nutrition is also a key determinant of enteric methane production. In this meta-analysis, we assessed the effects of growing conditions on forage quality by compiling published measurements of grass nutritive value and combining these data with climatic, edaphic and management information. We found that forage nutritive value was reduced at higher temperatures and increased by nitrogen fertiliser addition, likely driven by a combination of changes to species identity and changes to physiology and phenology. These relationships were combined with multiple published empirical models to estimate forage- and temperature-driven changes to cattle enteric methane production. This suggested a previously undescribed positive climate change feedback, where elevated temperatures reduce grass nutritive value and correspondingly may increase methane production by 0.9 % with a 1 °C temperature rise and 4.5 % with a 5 °C rise (model average), thus creating an additional climate forcing effect. Future methane production increases are expected to be largest in parts of North America, central and eastern Europe and Asia, with the geographical extent of hotspots increasing under a high emissions scenario. These estimates require refinement and a greater knowledge of the abundance, size, feeding regime and location of cattle, and the representation of heat stress should be included in future modelling work. However, our results indicate that the cultivation of more nutritious forage plants and reduced livestock farming in warming regions may reduce this additional source of pastoral greenhouse gas emissions.

Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs).

PubMed

Mao, Hongliang; Wang, Hao

2017-08-01

Instances of highly conserved plant short interspersed nuclear element (SINE) families and their enrichment near genes have been well documented, but little is known about the general patterns of such conservation and enrichment and underlying mechanisms. Here, we perform a comprehensive investigation of the structure, distribution, and evolution of SINEs in the grass family by analyzing 14 grass and 5 other flowering plant genomes using comparative genomics methods. We identify 61 SINE families composed of 29,572 copies, in which 46 families are first described. We find that comparing with other grass TEs, grass SINEs show much higher level of conservation in terms of genomic retention: The origin of at least 26% families can be traced to early grass diversification and these families are among most abundant SINE families in 86% species. We find that these families show much higher level of enrichment near protein coding genes than families of relatively recent origin (51%:28%), and that 40% of all grass SINEs are near gene and the percentage is higher than other types of grass TEs. The pattern of enrichment suggests that differential removal of SINE copies in gene-poor regions plays an important role in shaping the genomic distribution of these elements. We also identify a sequence motif located at 3' SINE end which is shared in 17 families. In short, this study provides insights into structure and evolution of SINEs in the grass family. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Molecular Evolution of Hypoallergenic Hybrid Proteins for Vaccination against Grass Pollen Allergy

PubMed Central

Linhart, Birgit; Focke-Tejkl, Margarete; Weber, Milena; Narayanan, Meena; Neubauer, Angela; Mayrhofer, Hannes; Blatt, Katharina; Lupinek, Christian; Valent, Peter

2015-01-01

More than 10% of the population in Europe and North America suffer from IgE-associated allergy to grass pollen. In this article, we describe the development of a vaccine for grass pollen allergen-specific immunotherapy based on two recombinant hypoallergenic mosaic molecules, designated P and Q, which were constructed out of elements derived from the four major timothy grass pollen allergens: Phl p 1, Phl p 2, Phl p 5, and Phl p 6. Seventeen recombinant mosaic molecules were expressed and purified in Escherichia coli using synthetic genes, characterized regarding biochemical properties, structural fold, and IgE reactivity. We found that depending on the arrangement of allergen fragments, mosaic molecules with strongly varying IgE reactivity were obtained. Based on an extensive screening with sera and basophils from allergic patients, two hypoallergenic mosaic molecules, P and Q, incorporating the primary sequence elements of the four grass pollen allergens were identified. As shown by lymphoproliferation experiments, they contained allergen-specific T cell epitopes required for tolerance induction, and upon immunization of animals induced higher allergen-specific IgG Abs than the wild-type allergens and a registered monophosphoryl lipid A–adjuvanted vaccine based on natural grass pollen allergen extract. Moreover, IgG Abs induced by immunization with P and Q inhibited the binding of patients’ IgE to natural allergens from five grasses better than IgG induced with the wild-type allergens or an extract-based vaccine. Our results suggest that vaccines based on the hypoallergenic grass pollen mosaics can be used for immunotherapy of grass pollen allergy. PMID:25786690

Characteristics of spondylotic myelopathy on 3D driven-equilibrium fast spin echo and 2D fast spin echo magnetic resonance imaging: a retrospective cross-sectional study.

PubMed

Abdulhadi, Mike A; Perno, Joseph R; Melhem, Elias R; Nucifora, Paolo G P

2014-01-01

In patients with spinal stenosis, magnetic resonance imaging of the cervical spine can be improved by using 3D driven-equilibrium fast spin echo sequences to provide a high-resolution assessment of osseous and ligamentous structures. However, it is not yet clear whether 3D driven-equilibrium fast spin echo sequences adequately evaluate the spinal cord itself. As a result, they are generally supplemented by additional 2D fast spin echo sequences, adding time to the examination and potential discomfort to the patient. Here we investigate the hypothesis that in patients with spinal stenosis and spondylotic myelopathy, 3D driven-equilibrium fast spin echo sequences can characterize cord lesions equally well as 2D fast spin echo sequences. We performed a retrospective analysis of 30 adult patients with spondylotic myelopathy who had been examined with both 3D driven-equilibrium fast spin echo sequences and 2D fast spin echo sequences at the same scanning session. The two sequences were inspected separately for each patient, and visible cord lesions were manually traced. We found no significant differences between 3D driven-equilibrium fast spin echo and 2D fast spin echo sequences in the mean number, mean area, or mean transverse dimensions of spondylotic cord lesions. Nevertheless, the mean contrast-to-noise ratio of cord lesions was decreased on 3D driven-equilibrium fast spin echo sequences compared to 2D fast spin echo sequences. These findings suggest that 3D driven-equilibrium fast spin echo sequences do not need supplemental 2D fast spin echo sequences for the diagnosis of spondylotic myelopathy, but they may be less well suited for quantitative signal measurements in the spinal cord.

Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

PubMed

Budak, Hikmet; Kantar, Melda

2015-07-01

MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

General practices as emergent research organizations: a qualitative study into organizational development.

PubMed

Macfarlane, Fraser; Shaw, Sara; Greenhalgh, Trisha; Carter, Yvonne H

2005-06-01

An increasing proportion of research in primary care is locally undertaken in designated research practices. Capacity building to support high quality research at these grass roots is urgently needed and is a government priority. There is little previously published research on the process by which GP practices develop as research organizations or on their specific support needs at organizational level. Using in-depth qualitative interviews with 28 key informants in 11 research practices across the UK, we explored their historical accounts of the development of research activity. We analysed the data with reference to contemporary theories of organizational development. Participants identified a number of key events and processes, which allowed us to produce a five-phase model of practice development in relation to research activity (creative energy, concrete planning, transformation/differentiation, consolidation and collaboration). Movement between these phases was not linear or continuous, but showed emergent and adaptive properties in which specific triggers and set-backs were often critical. This developmental model challenges previous categorical taxonomies of research practices. It forms a theory-driven framework for providing appropriate support at the grass roots of primary care research, based on the practice's phase of development and the nature of external triggers and potential setbacks. Our findings have important implications for the strategic development of practice-based research in the UK, and could serve as a model for the wider international community.

Increasing atmospheric CO2 overrides the historical legacy of multiple stable biome states in Africa.

PubMed

Moncrieff, Glenn R; Scheiter, Simon; Bond, William J; Higgins, Steven I

2014-02-01

The dominant vegetation over much of the global land surface is not predetermined by contemporary climate, but also influenced by past environmental conditions. This confounds attempts to predict current and future biome distributions, because even a perfect model would project multiple possible biomes without knowledge of the historical vegetation state. Here we compare the distribution of tree- and grass-dominated biomes across Africa simulated using a dynamic global vegetation model (DGVM). We explicitly evaluate where and under what conditions multiple stable biome states are possible for current and projected future climates. Our simulation results show that multiple stable biomes states are possible for vast areas of tropical and subtropical Africa under current conditions. Widespread loss of the potential for multiple stable biomes states is projected in the 21st Century, driven by increasing atmospheric CO2 . Many sites where currently both tree-dominated and grass-dominated biomes are possible become deterministically tree-dominated. Regions with multiple stable biome states are widespread and require consideration when attempting to predict future vegetation changes. Testing for behaviour characteristic of systems with multiple stable equilibria, such as hysteresis and dependence on historical conditions, and the resulting uncertainty in simulated vegetation, will lead to improved projections of global change impacts. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Associative diazotrophic bacteria in grass roots and soils from heavy metal contaminated sites.

PubMed

Moreira, Fátima M S; Lange, Anderson; Klauberg-Filho, Osmar; Siqueira, José O; Nóbrega, Rafaela S A; Lima, Adriana S

2008-12-01

This work aimed to evaluate density of associative diazotrophic bacteria populations in soil and grass root samples from heavy metal contaminated sites, and to characterize isolates from these populations, both, phenotypically (Zinc, Cadmium and NaCl tolerance in vitro, and protein profiles) and genotypically (16S rDNA sequencing), as compared to type strains of known diazotrophic species. Densities were evaluated by using NFb, Fam and JNFb media, commonly used for enrichment cultures of diazotrophic bacteria. Bacterial densities found in soil and grass root samples from contaminated sites were similar to those reported for agricultural soils. Azospirillum spp. isolates from contaminated sites and type strains from non-contaminated sites varied substantially in their in vitro tolerance to Zn+2 and Cd+2, being Cd+2 more toxic than Zn+2. Among the most tolerant isolates (UFLA 1S, 1R, S181, S34 and S22), some (1R, S34 and S22) were more tolerant to heavy metals than rhizobia from tropical and temperate soils. The majority of the isolates tolerant to heavy metals were also tolerant to salt stress as indicated by their ability to grow in solid medium supplemented with 30 g L(-1) NaCl. Five isolates exhibited high dissimilarity in protein profiles, and the 16S rDNA sequence analysis of two of them revealed new sequences for Azospirillum.

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

PubMed Central

2013-01-01

Background The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon. Results B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. Conclusions B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants. PMID:24367943

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

PubMed Central

Saarela, Jeffery M.; Wysocki, William P.; Barrett, Craig F.; Soreng, Robert J.; Davis, Jerrold I.; Clark, Lynn G.; Kelchner, Scot A.; Pires, J. Chris; Edger, Patrick P.; Mayfield, Dustin R.; Duvall, Melvin R.

2015-01-01

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some ‘early-diverging’ tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae–Meliceae and Ampelodesmeae–Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae–Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae–Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae–Loliinae clade. PMID:25940204

ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass).

PubMed

Gardin, Jeanne Aude Christiane; Gouzy, Jérôme; Carrère, Sébastien; Délye, Christophe

2015-08-12

Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available. RNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74% GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein. Our data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides.

Plant assemblage composition and soil P concentration differentially affect communities of AM and total fungi in a semi-arid grassland.

PubMed

Klabi, Rim; Bell, Terrence H; Hamel, Chantal; Iwaasa, Alan; Schellenberg, Mike; Raies, Aly; St-Arnaud, Marc

2015-01-01

Adding inorganic P- and N-fixing legumes to semi-arid grasslands can increase forage yield, but soil nutrient concentrations and plant cover may also interact to modify soil fungal populations, impacting short- and long-term forage production. We tested the effect of plant assemblage (seven native grasses, seven native grasses + the domesticated N-fixing legume Medicago sativa, seven native grasses + the native N-fixing legume Dalea purpurea or the introduced grass Bromus biebersteinii + M. sativa) and soil P concentration (addition of 0 or 200 P2O5 kg ha(-1) at sowing) on the diversity and community structure of arbuscular mycorrhizal (AM) fungi and total fungi over two consecutive years, using 454-pyrosequencing of 18S rDNA and ITS amplicons. Treatment effects were stronger in the wet year (2008) than the dry year (2009). The presence of an N-fixing legume with native grasses generally increased AM fungal diversity, while the interaction between soil P concentration and plant assemblage modified total fungal community structure in 2008. Excluding interannual variations, which are likely driven by moisture and plant productivity, AM fungal communities in semi-arid grasslands appear to be primarily affected by plant assemblage composition, while the composition of other fungi is more closely linked to soil P. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events.

PubMed

Clayton, William; Eaton, Carla Jane; Dupont, Pierre-Yves; Gillanders, Tim; Cameron, Nick; Saikia, Sanjay; Scott, Barry

2017-01-01

Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

Using a prescribed fire to test custom and standard fuel models for fire behaviour prediction in a non-native, grass-invaded tropical dry shrubland

Treesearch

Andrew D. Pierce; Sierra McDaniel; Mark Wasser; Alison Ainsworth; Creighton M. Litton; Christian P. Giardina; Susan Cordell; Ralf Ohlemuller

2014-01-01

Questions: Do fuel models developed for North American fuel types accurately represent fuel beds found in grass-invaded tropical shrublands? Do standard or custom fuel models for firebehavior models with in situ or RAWS measured fuel moistures affect the accuracy of predicted fire behavior in grass-invaded tropical shrublands? Location: Hawai’i Volcanoes National...

Effects of high-sugar ryegrass silage and mixtures with red clover silage on ruminant digestion. 2. Lipids.

PubMed

Lee, M R F; Connelly, P L; Tweed, J K S; Dewhurst, R J; Merry, R J; Scollan, N D

2006-11-01

The experiment investigated the digestion of lipids from different forage silages in beef steers. Six Hereford x Friesian steers prepared with rumen and duodenal cannulas were given ad libitum access to a high-sugar grass silage, control grass silage, red clover silage, or mixtures of the red clover and each of the grass silages (50:50, DM basis). The experiment was conducted as an incomplete 5 x 5 Latin square, with an additional randomly repeated sequence. Total fatty acid and C18:3n-3 concentrations were greater (P < 0.05) for the high-sugar grass silage than the control grass silage or the red clover silage. Dry matter and total fatty acid intake were less (P < 0.05) for steers fed the control grass silage than for steers fed the other diets. Duodenal flow of C18:3n-3 was greater (P < 0.05), and flows of C18:0 and total C18:1 trans were less (P < 0.05), for the red clover silage compared with the 2 grass silage diets, with the mixtures intermediate. These results were supported by a reduction (P < 0.05) in biohydrogenation of C18:3n-3 for the red clover silage, with the mixtures again being intermediate. Flows of total branched- and odd-chain fatty acids were greater (P < 0.05) for the high-sugar grass silage diet, possibly as a result of greater microbial flow, because these fatty acids are associated with bacterial lipid. Duodenal flows of the chlorophyll metabolite, phytanic acid, were greater (P < 0.05) for animals fed the high-sugar grass silage treatments compared with the other treatments. These results confirm the potential for modifying the fatty acid composition of ruminant products by feeding red clover silage.

Molecular evolution of hypoallergenic hybrid proteins for vaccination against grass pollen allergy.

PubMed

Linhart, Birgit; Focke-Tejkl, Margarete; Weber, Milena; Narayanan, Meena; Neubauer, Angela; Mayrhofer, Hannes; Blatt, Katharina; Lupinek, Christian; Valent, Peter; Valenta, Rudolf

2015-04-15

More than 10% of the population in Europe and North America suffer from IgE-associated allergy to grass pollen. In this article, we describe the development of a vaccine for grass pollen allergen-specific immunotherapy based on two recombinant hypoallergenic mosaic molecules, designated P and Q, which were constructed out of elements derived from the four major timothy grass pollen allergens: Phl p 1, Phl p 2, Phl p 5, and Phl p 6. Seventeen recombinant mosaic molecules were expressed and purified in Escherichia coli using synthetic genes, characterized regarding biochemical properties, structural fold, and IgE reactivity. We found that depending on the arrangement of allergen fragments, mosaic molecules with strongly varying IgE reactivity were obtained. Based on an extensive screening with sera and basophils from allergic patients, two hypoallergenic mosaic molecules, P and Q, incorporating the primary sequence elements of the four grass pollen allergens were identified. As shown by lymphoproliferation experiments, they contained allergen-specific T cell epitopes required for tolerance induction, and upon immunization of animals induced higher allergen-specific IgG Abs than the wild-type allergens and a registered monophosphoryl lipid A-adjuvanted vaccine based on natural grass pollen allergen extract. Moreover, IgG Abs induced by immunization with P and Q inhibited the binding of patients' IgE to natural allergens from five grasses better than IgG induced with the wild-type allergens or an extract-based vaccine. Our results suggest that vaccines based on the hypoallergenic grass pollen mosaics can be used for immunotherapy of grass pollen allergy. Copyright © 2015 by The American Association of Immunologists, Inc.

A molecular identification system for grasses: a novel technology for forensic botany.

PubMed

Ward, J; Peakall, R; Gilmore, S R; Robertson, J

2005-09-10

Our present inability to rapidly, accurately and cost-effectively identify trace botanical evidence remains the major impediment to the routine application of forensic botany. Grasses are amongst the most likely plant species encountered as forensic trace evidence and have the potential to provide links between crime scenes and individuals or other vital crime scene information. We are designing a molecular DNA-based identification system for grasses consisting of several PCR assays that, like a traditional morphological taxonomic key, provide criteria that progressively identify an unknown grass sample to a given taxonomic rank. In a prior study of DNA sequences across 20 phylogenetically representative grass species, we identified a series of potentially informative indels in the grass mitochondrial genome. In this study we designed and tested five PCR assays spanning these indels and assessed the feasibility of these assays to aid identification of unknown grass samples. We confirmed that for our control set of 20 samples, on which the design of the PCR assays was based, the five primer combinations produced the expected results. Using these PCR assays in a 'blind test', we were able to identify 25 unknown grass samples with some restrictions. Species belonging to genera represented in our control set were all correctly identified to genus with one exception. Similarly, genera belonging to tribes in the control set were correctly identified to the tribal level. Finally, for those samples for which neither the tribal or genus specific PCR assays were designed, we could confidently exclude these samples from belonging to certain tribes and genera. The results confirmed the utility of the PCR assays and the feasibility of developing a robust full-scale usable grass identification system for forensic purposes.

Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

USDA-ARS?s Scientific Manuscript database

Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS)approach to identify the reproductive system, gene...

Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphism was employed in the construction of a high-resolution, expressed sequence tag (EST) map of Aegilops tauschii, the diploid source of the wheat D genome. Comparison of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and...

Data-Driven Sequence of Changes to Anatomical Brain Connectivity in Sporadic Alzheimer's Disease.

PubMed

Oxtoby, Neil P; Garbarino, Sara; Firth, Nicholas C; Warren, Jason D; Schott, Jonathan M; Alexander, Daniel C

2017-01-01

Model-based investigations of transneuronal spreading mechanisms in neurodegenerative diseases relate the pattern of pathology severity to the brain's connectivity matrix, which reveals information about how pathology propagates through the connectivity network. Such network models typically use networks based on functional or structural connectivity in young and healthy individuals, and only end-stage patterns of pathology, thereby ignoring/excluding the effects of normal aging and disease progression. Here, we examine the sequence of changes in the elderly brain's anatomical connectivity over the course of a neurodegenerative disease. We do this in a data-driven manner that is not dependent upon clinical disease stage, by using event-based disease progression modeling. Using data from the Alzheimer's Disease Neuroimaging Initiative dataset, we sequence the progressive decline of anatomical connectivity, as quantified by graph-theory metrics, in the Alzheimer's disease brain. Ours is the first single model to contribute to understanding all three of the nature, the location, and the sequence of changes to anatomical connectivity in the human brain due to Alzheimer's disease. Our experimental results reveal new insights into Alzheimer's disease: that degeneration of anatomical connectivity in the brain may be a viable, even early, biomarker and should be considered when studying such neurodegenerative diseases.

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

USDA-ARS?s Scientific Manuscript database

The wild grass Brachypodium distachyon (Brachypodium) is a new model system for temperate cereals, but its potential for studying interactions between grasses and their pathogens remains underexploited. Leaf rust caused by members of the fungal genus Puccinia is a major disease affecting temperate c...

Abiotic stresses activate a MAPkinase in the model grass species Lolium temulentum L.

USDA-ARS?s Scientific Manuscript database

Forage and turf grasses are utilized in diverse environments which exposes them to a variety of abiotic stresses, however very little is known concerning the perception or molecular responses to these various stresses. In the model grass species Lolium temulentum (Lt), a 46 kDa mitogen-activated pro...

Grass flower development.

PubMed

Hirano, Hiro-Yuki; Tanaka, Wakana; Toriba, Taiyo

2014-01-01

Grasses bear unique flowers lacking obvious petals and sepals in special inflorescence units, the florets and the spikelet. Despite this, grass floral organs such as stamens and lodicules (petal homologs) are specified by ABC homeotic genes encoding MADS domain transcription factors, suggesting that the ABC model of eudicot flower development is largely applicable to grass flowers. However, some modifications need to be made for the model to fit grasses well: for example, a YABBY gene plays an important role in carpel specification. In addition, a number of genes are involved in the development of the lateral organs that constitute the spikelet. In this review, we discuss recent progress in elucidating the genes required for flower and spikelet development in grasses, together with those involved in fate determination of the spikelet and flower meristems.

Animation control of surface motion capture.

PubMed

Tejera, Margara; Casas, Dan; Hilton, Adrian

2013-12-01

Surface motion capture (SurfCap) of actor performance from multiple view video provides reconstruction of the natural nonrigid deformation of skin and clothing. This paper introduces techniques for interactive animation control of SurfCap sequences which allow the flexibility in editing and interactive manipulation associated with existing tools for animation from skeletal motion capture (MoCap). Laplacian mesh editing is extended using a basis model learned from SurfCap sequences to constrain the surface shape to reproduce natural deformation. Three novel approaches for animation control of SurfCap sequences, which exploit the constrained Laplacian mesh editing, are introduced: 1) space–time editing for interactive sequence manipulation; 2) skeleton-driven animation to achieve natural nonrigid surface deformation; and 3) hybrid combination of skeletal MoCap driven and SurfCap sequence to extend the range of movement. These approaches are combined with high-level parametric control of SurfCap sequences in a hybrid surface and skeleton-driven animation control framework to achieve natural surface deformation with an extended range of movement by exploiting existing MoCap archives. Evaluation of each approach and the integrated animation framework are presented on real SurfCap sequences for actors performing multiple motions with a variety of clothing styles. Results demonstrate that these techniques enable flexible control for interactive animation with the natural nonrigid surface dynamics of the captured performance and provide a powerful tool to extend current SurfCap databases by incorporating new motions from MoCap sequences.

Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements.

PubMed

Hudson, William H; Vera, Ian Mitchelle S de; Nwachukwu, Jerome C; Weikum, Emily R; Herbst, Austin G; Yang, Qin; Bain, David L; Nettles, Kendall W; Kojetin, Douglas J; Ortlund, Eric A

2018-04-06

Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the glucocorticoid receptor (GR) within this critical signaling pathway. GR binding directly to NF-κB itself-tethering in a DNA binding-independent manner-represents the standing model of how GCs inhibit NF-κB-driven transcription. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. We report five crystal structures and solution NMR data of GR DBD-κBRE complexes, which reveal that GR recognizes a cryptic response element between the binding footprints of NF-κB subunits within κBREs. These cryptic sequences exhibit high sequence and functional conservation, suggesting that GR binding to κBREs is an evolutionarily conserved mechanism of controlling the inflammatory response.

Investigation of mircroorganisms colonising activated zeolites during anaerobic biogas production from grass silage.

PubMed

Weiss, S; Zankel, A; Lebuhn, M; Petrak, S; Somitsch, W; Guebitz, G M

2011-03-01

The colonisation of activated zeolites (i.e. clinoptilolites) as carriers for microorganisms involved in the biogas process was investigated. Zeolite particle sizes of 1.0-2.5mm were introduced to anaerobic laboratory batch-cultures and to continuously operated bioreactors during biogas production from grass silage. Incubation over 5-84 days led to the colonisation of zeolite surfaces in small batch-cultures (500 ml) and even in larger scaled and flow-through disturbed bioreactors (28 l). Morphological insights were obtained by using scanning electron microscopy (SEM). Single strand conformation polymorphism (SSCP) analysis based on amplification of bacterial and archaeal 16S rRNA fragments demonstrated structurally distinct populations preferring zeolite as operational environment. via sequence analysis conspicuous bands from SSCP patterns were identified. Populations immobilised on zeolite (e.g. Ruminofilibacter xylanolyticum) showed pronounced hydrolytic enzyme activity (xylanase) shortly after re-incubation in sterilised sludge on model substrate. In addition, the presence of methanogenic archaea on zeolite particles was demonstrated. Copyright © 2010 Elsevier Ltd. All rights reserved.

Direct and indirect effects of climate change on projected future fire regimes in the western United States.

PubMed

Liu, Zhihua; Wimberly, Michael C

2016-01-15

We asked two research questions: (1) What are the relative effects of climate change and climate-driven vegetation shifts on different components of future fire regimes? (2) How does incorporating climate-driven vegetation change into future fire regime projections alter the results compared to projections based only on direct climate effects? We used the western United States (US) as study area to answer these questions. Future (2071-2100) fire regimes were projected using statistical models to predict spatial patterns of occurrence, size and spread for large fires (>400 ha) and a simulation experiment was conducted to compare the direct climatic effects and the indirect effects of climate-driven vegetation change on fire regimes. Results showed that vegetation change amplified climate-driven increases in fire frequency and size and had a larger overall effect on future total burned area in the western US than direct climate effects. Vegetation shifts, which were highly sensitive to precipitation pattern changes, were also a strong determinant of the future spatial pattern of burn rates and had different effects on fire in currently forested and grass/shrub areas. Our results showed that climate-driven vegetation change can exert strong localized effects on fire occurrence and size, which in turn drive regional changes in fire regimes. The effects of vegetation change for projections of the geographic patterns of future fire regimes may be at least as important as the direct effects of climate change, emphasizing that accounting for changing vegetation patterns in models of future climate-fire relationships is necessary to provide accurate projections at continental to global scales. Copyright © 2015 Elsevier B.V. All rights reserved.

Fuel model selection for BEHAVE in midwestern oak savannas

USGS Publications Warehouse

Grabner, K.W.; Dwyer, J.P.; Cutter, B.E.

2001-01-01

BEHAVE, a fire behavior prediction system, can be a useful tool for managing areas with prescribed fire. However, the proper choice of fuel models can be critical in developing management scenarios. BEHAVE predictions were evaluated using four standardized fuel models that partially described oak savanna fuel conditions: Fuel Model 1 (Short Grass), 2 (Timber and Grass), 3 (Tall Grass), and 9 (Hardwood Litter). Although all four models yielded regressions with R2 in excess of 0.8, Fuel Model 2 produced the most reliable fire behavior predictions.

Coexistence of Trees and Grass: Importance of climate and fire within the tropics

NASA Astrophysics Data System (ADS)

Shuman, J. K.; Fisher, R.; Koven, C.; Knox, R. G.; Andre, B.; Kluzek, E. B.

2017-12-01

Tropical forests are characterized by transition zones where dominance shifts between trees and grasses with some areas exhibiting bistability of the two. The cause of this transition and bistability has been linked to the interacting effects of climate, vegetation structure and fire behavior. Utilizing the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a demographic vegetation model, and the CESM ESM, we explore the coexistence of trees and grass across the tropics with an active fire regime. FATES has been updated to use a fire module based on Spitfire. FATES-Spitfire tracks fire ignition, spread and impact based on fuel state and combustion. Fire occurs within the model with variable intensity that kills trees according to the combined effects of cambial damage and crown scorch due to flame height and fire intensity. As a size-structured model, FATES allows for variable mortality based on the size of tree cohorts, where larger trees experience lower morality compared to small trees. Results for simulation scenarios where vegetation is represented by all trees, all grass, or a combination of competing trees and grass are compared to assess changes in biomass, fire regime and tree-grass coexistence. Within the forest-grass transition area there is a critical time during which grass fuels fire spread and prevents the establishment of trees. If trees are able to escape mortality a tree-grass bistable area is successful. The ability to simulate the bistability and transition of trees and grass throughout the tropics is critical to representing vegetation dynamics in response to changing climate and CO2.

Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses.

PubMed

Kögler, Anja; Schmidt, Thomas; Wenke, Torsten

2017-11-01

Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7

NASA Astrophysics Data System (ADS)

Petras, Vaclav; Petrasova, Anna; Chemin, Yann; Zambelli, Pietro; Landa, Martin; Gebbert, Sören; Neteler, Markus; Löwe, Peter

2015-04-01

GRASS GIS 7 is a free and open source GIS software developed and used by many scientists (Neteler et al., 2012). While some users of GRASS GIS prefer its graphical user interface, significant part of the scientific community takes advantage of various scripting and programing interfaces offered by GRASS GIS to develop new models and algorithms. Here we will present different interfaces added to GRASS GIS 7 and available in Python, a popular programming language and environment in geosciences. These Python interfaces are designed to satisfy the needs of scientists and programmers under various circumstances. PyGRASS (Zambelli et al., 2013) is a new object-oriented interface to GRASS GIS modules and libraries. The GRASS GIS libraries are implemented in C to ensure maximum performance and the PyGRASS interface provides an intuitive, pythonic access to their functionality. GRASS GIS Python scripting library is another way of accessing GRASS GIS modules. It combines the simplicity of Bash and the efficiency of the Python syntax. When full access to all low-level and advanced functions and structures from GRASS GIS library is required, Python programmers can use an interface based on the Python ctypes package. Ctypes interface provides complete, direct access to all functionality as it would be available to C programmers. GRASS GIS provides specialized Python library for managing and analyzing spatio-temporal data (Gebbert and Pebesma, 2014). The temporal library introduces space time datasets representing time series of raster, 3D raster or vector maps and allows users to combine various spatio-temporal operations including queries, aggregation, sampling or the analysis of spatio-temporal topology. We will also discuss the advantages of implementing scientific algorithm as a GRASS GIS module and we will show how to write such module in Python. To facilitate the development of the module, GRASS GIS provides a Python library for testing (Petras and Gebbert, 2014) which helps researchers to ensure the robustness of the algorithm, correctness of the results in edge cases as well as the detection of changes in results due to new development. For all modules GRASS GIS automatically creates standardized command line and graphical user interfaces and documentation. Finally, we will show how GRASS GIS can be used together with powerful Python tools such as the NumPy package and the IPython Notebook. References: Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environmental Modelling & Software 53, 1-12. Neteler, M., Bowman, M.H., Landa, M. and Metz, M., 2012. GRASS GIS: a multi-purpose Open Source GIS. Environmental Modelling & Software 31: 124-130. Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS International Journal of Geo-Information 2, 201-219.

Molecular features of grass allergens and development of biotechnological approaches for allergy prevention.

PubMed

Devis, Deborah L; Davies, Janet M; Zhang, Dabing

2017-09-01

Allergic diseases are characterized by elevated allergen-specific IgE and excessive inflammatory cell responses. Among the reported plant allergens, grass pollen and grain allergens, derived from agriculturally important members of the Poaceae family such as rice, wheat and barley, are the most dominant and difficult to prevent. Although many allergen homologs have been predicted from species such as wheat and timothy grass, fundamental aspects such as the evolution and function of plant pollen allergens remain largely unclear. With the development of genetic engineering and genomics, more primary sequences, functions and structures of plant allergens have been uncovered, and molecular component-based allergen-specific immunotherapies are being developed. In this review, we aim to provide an update on (i) the distribution and importance of pollen and grain allergens of the Poaceae family, (ii) the origin and evolution, and functional aspects of plant pollen allergens, (iii) developments of allergen-specific immunotherapy for pollen allergy using biotechnology and (iv) development of less allergenic plants using gene engineering techniques. We also discuss future trends in revealing fundamental aspects of grass pollen allergens and possible biotechnological approaches to reduce the amount of pollen allergens in grasses. Copyright © 2017. Published by Elsevier Inc.

Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform

PubMed Central

Sun, Sangrong; Wang, Jinpeng; Yu, Jigao; Meng, Fanbo; Xia, Ruiyan; Wang, Li; Wang, Zhenyi; Ge, Weina; Liu, Xiaojian; Li, Yuxian; Liu, Yinzhe; Yang, Nanshan; Wang, Xiyin

2017-01-01

Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material. PMID:28912789

Streptococcus caviae sp. nov., isolated from guinea pig faecal samples.

PubMed

Palakawong Na Ayudthaya, Susakul; Hilderink, Loes J; Oost, John van der; Vos, Willem M de; Plugge, Caroline M

2017-05-01

A novel cellobiose-degrading and lactate-producing bacterium, strain Cavy grass 6T, was isolated from faecal samples of guinea pigs (Cavia porcellus). Cells of the strain were ovalshaped, non-motile, non-spore-forming, Gram-stain-positive and facultatively anaerobic. The strain gr at 25-40 °C (optimum 37 °C) and pH 4.5-9.5 (optimum 8.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Cavy grass 6T belongs to the genus Streptococcus with its closest relative being Streptococcus devriesei CCUG 47155T with only 96.5 % similarity. Comparing strain Cavy grass 6T and Streptococcus devriesei CCUG 47155T, average nucleotide identity and level of digital DNA-DNA hybridization dDDH were only 86.9 and 33.3 %, respectively. Housekeeping genes groEL and gyrA were different between strain Cavy grass 6T and other streptococci. The G+C content of strain Cavy grass 6T was 42.6±0.3 mol%. The major (>10 %) cellular fatty acids of strain Cavy grass 6T were C16:0, C20 : 1ω9c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain Cavy grass 6T ferment a range of plant mono- and disaccharides as well as polymeric carbohydrates, including cellobiose, dulcitol, d-glucose, maltose, raffinose, sucrose, l-sorbose, trehalose, inulin and dried grass extract, to lactate, formate, acetate and ethanol. Based on phylogenetic and physiological characteristics, Cavy grass 6T can be distinguished from other members of the genus Streptococcus. Therefore, a novel species of the genus Streptococcus, family Streptococcaceae, order Lactobacillales is proposed, Streptococcuscaviae sp. nov. (type strain Cavy grass 6T=TISTR 2371T=DSM 102819T).

Molecular characterization and expression of the M6 gene of grass carp hemorrhage virus (GCHV), an aquareovirus.

PubMed

Qiu, T; Lu, R H; Zhang, J; Zhu, Z Y

2001-07-01

The complete nucleotide sequence of M6 gene of grass carp hemorrhage virus (GCHV) was determined. It is 2039 nucleotides in length and contains a single large open reading frame that could encode a protein of 648 amino acids with predicted molecular mass of 68.7 kDa. Amino acid sequence comparison revealed that the protein encoded by GCHV M6 is closely related to the protein mu1 of mammalian reovirus. The M6 gene, encoding the major outer-capsid protein, was expressed using the pET fusion protein vector in Escherichia coli and detected by Western blotting using chicken anti-GCHV immunoglobulin (IgY). The result indicates that the protein encoded by M6 may share a putative Asn-42-Pro-43 proteolytic cleavage site with mu1.

Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar

PubMed Central

Silva, Christian; Besnard, Guillaume; Piot, Anthony; Razanatsoa, Jacqueline; Oliveira, Reyjane P.; Vorontsova, Maria S.

2017-01-01

Background and Aims Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS. Methods Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages. Key Results Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory. Conclusions Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups. PMID:28028020

Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Hahnke, Sarah; Abendroth, Christian; Langer, Thomas; Codoñer, Francisco M; Ramm, Patrice; Porcar, Manuel; Luschnig, Olaf; Klocke, Michael

2018-04-05

A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera. Copyright © 2018 Hahnke et al.

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN

PubMed Central

Law, MeiYee; Childs, Kevin L.; Campbell, Michael S.; Stein, Joshua C.; Olson, Andrew J.; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M.; Lawrence, Carolyn J.; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

2015-01-01

The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. PMID:25384563

Embryonic development of the grass pufferfish (Takifugu niphobles): From egg to larvae.

PubMed

Gallego, V; Yoshida, M; Kurokawa, D; Asturiano, J F; Fraser, G J

2017-03-01

Tetraodontidae (pufferfish) family members carry the smallest genomes among vertebrates, and these pocket-sized genomes have directly contributed to our understanding of the structure and evolution of higher animals. The grass pufferfish (Takifugu niphobles) could be considered a potential new model organism for comparative genomics and development due to the potential access to embryos, and availability of sequence data for two similar genomes: that of spotted green pufferfish (Tetraodon nigroviridis) and Fugu (Takifugu rubripes). In this study, we provide the first description of the normal embryonic development of T. niphobles, by drawing comparisons with the closely related species cited above. Embryos were obtained by in vitro fertilization of eggs, and subsequent development was monitored at a constant temperature consistent with natural conditions. T. niphobles development was divided into seven periods of embryogenesis: the zygote, cleavage, blastula, gastrula, segmentation, pharyngula, and hatching periods; and stages subdividing these periods are defined based on morphological characteristics. The developmental stage series described in this study aims to provide the utilization of T. niphobles as an experimental model organism for comparative developmental studies. Copyright © 2016 Elsevier Inc. All rights reserved.

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species

PubMed Central

Diekmann, Kerstin; Hodkinson, Trevor R.; Barth, Susanne

2012-01-01

Background and Aims Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Methods Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. Key Results All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A8 mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. Conclusions The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species. PMID:22419761

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

PubMed

Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

2012-11-01

Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species.

The impact of invasive grasses on the population growth of Anemone patens, a long-lived native forb.

PubMed

Williams, Jennifer L; Crone, Elizabeth E

2006-12-01

Negative impacts of invasive plants on natives have been well documented, but much less is known about whether invasive plants can cause population level declines. We used demographic models to investigate the effects of two invasive grasses on the demography and population growth of Anemone patens, a long-lived native perennial of North American grasslands. Demographic data of A. patens growing in patches characterized by Bromus inermis, Poa pratensis, or native grasses were used to parameterize integral projection models. Models based on both average conditions and those allowing for environmental stochasticity indicate that A. patens is slowly increasing in patches of native grass (lambda = 1.02) and declining in patches of invasive grasses, particularly those dominated by B. inermis (lambda = 0.93). Extinction probabilities indicate that A. patens should persist in native grass patches, but has a much higher probability of extinction in Bromus patches compared to Poa patches. While sensitivity analyses showed that survival had the biggest effect on population growth rates in all habitats, results of a Life Table Response Experiment (LTRE) revealed that slower individual growth rates in patches of invasive grasses contributed the most to the observed reduction in population growth. These results suggest that invasive grasses may cause slow declines in A. patens, despite short-term coexistence, and that controlling B. inermis only would not be sufficient to ensure A. patens persistence.

Endo-(1,4)-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1

PubMed Central

2012-01-01

Background Endo-(1,4)-β-glucanase (cellulase) glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4)-β-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4)-β-glucanase gene families from barley (Hordeum vulgare), maize (Zea mays), sorghum (Sorghum bicolor), rice (Oryza sativa) and Brachypodium (Brachypodium distachyon) range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4)-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4)-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4)-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re-modelling and degradation, together with their potential role in lignocellulose conversion during biofuel production from grasses and cereal crop residues. PMID:23231659

Spectral and spatial variability of undisturbed and disturbed grass under different view and illumination directions

NASA Astrophysics Data System (ADS)

Borel-Donohue, Christoph C.; Shivers, Sarah Wells; Conover, Damon

2017-05-01

It is well known that disturbed grass covered surfaces show variability with view and illumination conditions. A good example is a grass field in a soccer stadium that shows stripes indicating in which direction the grass was mowed. These spatial variations are due to a complex interplay of spectral characteristics of grass blades, density, their length and orientations. Viewing a grass surface from nadir or near horizontal directions results in observing different components. Views from a vertical direction show more variations due to reflections from the randomly oriented grass blades and their shadows. Views from near horizontal show a mixture of reflected and transmitted light from grass blades. An experiment was performed on a mowed grass surface which had paths of simulated heavy foot traffic laid down in different directions. High spatial resolution hyperspectral data cubes were taken by an imaging spectrometer covering the visible through near infrared over a period of time covering several hours. Ground truth grass reflectance spectra with a hand held spectrometer were obtained of undisturbed and disturbed areas. Close range images were taken of selected areas with a hand held camera which were then used to reconstruct the 3D geometry of the grass using structure-from-motion algorithms. Computer graphics rendering using raytracing of reconstructed and procedurally created grass surfaces were used to compute BRDF models. In this paper, we discuss differences between observed and simulated spectral and spatial variability. Based on the measurements and/or simulations, we derive simple spectral index methods to detect spatial disturbances and apply scattering models.

Alternative pathways to landscape transformation: Invasive grasses, burn severity and fire frequency in arid ecosystems

USGS Publications Warehouse

Klinger, Robert C.; Brooks, Matthew L.

2017-01-01

Arid ecosystems are often vulnerable to transformation to invasive-dominated states following fire, but data on persistence of these states are sparse. The grass/fire cycle is a feedback process between invasive annual grasses and fire frequency that often leads to the formation of alternative vegetation states dominated by the invasive grasses. However, other components of fire regimes, such as burn severity, also have the potential to produce long-term vegetation transformations. Our goal was to evaluate the influence of both fire frequency and burn severity on the transformation of woody-dominated communities to communities dominated by invasive grasses in major elevation zones of the Mojave Desert of western North America.We used a chronosequence design to collect data on herbaceous and woody cover at 229 unburned reference plots and 578 plots that burned between 1972 and 2010. We stratified the plots by elevation zone (low, mid, high), fire frequency (1–3 times) and years post-fire (YPF; 1–5, 6–10, 11–20 and 21–40 YPF). Burn severity for each plot was estimated by the difference normalized burn ratio.We identified two broad post-fire successional pathways. One was an outcome of fire frequency, resulting in a strong potential transformation via the grass/fire cycle. The second pathway was driven by burn severity, the critical aspect being that long-term transformation of a community could occur from just one fire in areas that burned at high or sometimes moderate severity. Dominance by invasive grasses was most likely to occur in low-and high-elevation communities; cover of native herbaceous species was often greater than that of invasive grasses in the mid-elevation zone.Synthesis. Invasive grasses can dominate a site that burned only one time in many decades at high severity, or a site that burned at low severity but multiple times in the same time period. However, high burn severity may predispose areas to more frequent fire because they have relatively high cover of invasive annual grass, suggesting burn severity and fire frequency have both independent and synergistic effects. Resilience in vegetation structure following fire in many arid communities may be limited to a narrow window of low burn severity in areas that have not burned in many decades.

The role of teosinte glume architecture (tga1) in coordinated regulation and evolution of grass glumes and inflorescence axes.

PubMed

Preston, Jill C; Wang, Huai; Kursel, Lisa; Doebley, John; Kellogg, Elizabeth A

2012-01-01

• Hardened floral bracts and modifications to the inflorescence axis of grasses have been hypothesized to protect seeds from predation and/or aid seed dispersal, and have evolved multiple times independently within the family. Previous studies have demonstrated that mutations in the maize (Zea mays ssp. mays) gene teosinte glume architecture (tga1) underlie a reduction in hardened structures, yielding free fruits that are easy to harvest. It remains unclear whether the causative mutation(s) occurred in the cis-regulatory or protein-coding regions of tga1, and whether similar mutations in TGA1-like genes can explain variation in the dispersal unit in related grasses. • To address these questions TGA1-like genes were cloned and sequenced from a number of grasses and analyzed phylogenetically in relation to morphology; protein expression was investigated by immunolocalization. • TGA1-like proteins were expressed throughout the spikelet in the early development of all grasses, and throughout the flower of the grass relative Joinvillea. Later in development, expression patterns differed between Tripsacum dactyloides, maize and teosinte (Z. mays ssp. parviglumis). • These results suggest an ancestral role for TGA1-like genes in early spikelet development, but do not support the hypothesis that TGA1-like genes have been repeatedly modified to affect glume and inflorescence axis diversification. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Modeled Changes in Potential Grassland Productivity and in Grass-Fed Ruminant Livestock Density in Europe over 1961-2010.

PubMed

Chang, Jinfeng; Viovy, Nicolas; Vuichard, Nicolas; Ciais, Philippe; Campioli, Matteo; Klumpp, Katja; Martin, Raphaël; Leip, Adrian; Soussana, Jean-François

2015-01-01

About 25% of European livestock intake is based on permanent and sown grasslands. To fulfill rising demand for animal products, an intensification of livestock production may lead to an increased consumption of crop and compound feeds. In order to preserve an economically and environmentally sustainable agriculture, a more forage based livestock alimentation may be an advantage. However, besides management, grassland productivity is highly vulnerable to climate (i.e., temperature, precipitation, CO2 concentration), and spatial information about European grassland productivity in response to climate change is scarce. The process-based vegetation model ORCHIDEE-GM, containing an explicit representation of grassland management (i.e., herbage mowing and grazing), is used here to estimate changes in potential productivity and potential grass-fed ruminant livestock density across European grasslands over the period 1961-2010. Here "potential grass-fed ruminant livestock density" denotes the maximum density of livestock that can be supported by grassland productivity in each 25 km × 25 km grid cell. In reality, livestock density could be higher than potential (e.g., if additional feed is supplied to animals) or lower (e.g., in response to economic factors, pedo-climatic and biotic conditions ignored by the model, or policy decisions that can for instance reduce livestock numbers). When compared to agricultural statistics (Eurostat and FAOstat), ORCHIDEE-GM gave a good reproduction of the regional gradients of annual grassland productivity and ruminant livestock density. The model however tends to systematically overestimate the absolute values of productivity in most regions, suggesting that most grid cells remain below their potential grassland productivity due to possible nutrient and biotic limitations on plant growth. When ORCHIDEE-GM was run for the period 1961-2010 with variable climate and rising CO2, an increase of potential annual production (over 3%) per decade was found: 97% of this increase was attributed to the rise in CO2, -3% to climate trends and 15% to trends in nitrogen fertilization and deposition. When compared with statistical data, ORCHIDEE-GM captures well the observed phase of climate-driven interannual variability in grassland production well, whereas the magnitude of the interannual variability in modeled productivity is larger than the statistical data. Regional grass-fed livestock numbers can be reproduced by ORCHIDEE-GM based on its simple assumptions and parameterization about productivity being the only limiting factor to define the sustainable number of animals per unit area. Causes for regional model-data misfits are discussed, including uncertainties in farming practices (e.g., nitrogen fertilizer application, and mowing and grazing intensity) and in ruminant diet composition, as well as uncertainties in the statistical data and in model parameter values.

Modeled Changes in Potential Grassland Productivity and in Grass-Fed Ruminant Livestock Density in Europe over 1961–2010

PubMed Central

Chang, Jinfeng; Viovy, Nicolas; Vuichard, Nicolas; Ciais, Philippe; Campioli, Matteo; Klumpp, Katja; Martin, Raphaël; Leip, Adrian; Soussana, Jean-François

2015-01-01

About 25% of European livestock intake is based on permanent and sown grasslands. To fulfill rising demand for animal products, an intensification of livestock production may lead to an increased consumption of crop and compound feeds. In order to preserve an economically and environmentally sustainable agriculture, a more forage based livestock alimentation may be an advantage. However, besides management, grassland productivity is highly vulnerable to climate (i.e., temperature, precipitation, CO2 concentration), and spatial information about European grassland productivity in response to climate change is scarce. The process-based vegetation model ORCHIDEE-GM, containing an explicit representation of grassland management (i.e., herbage mowing and grazing), is used here to estimate changes in potential productivity and potential grass-fed ruminant livestock density across European grasslands over the period 1961–2010. Here “potential grass-fed ruminant livestock density” denotes the maximum density of livestock that can be supported by grassland productivity in each 25 km × 25 km grid cell. In reality, livestock density could be higher than potential (e.g., if additional feed is supplied to animals) or lower (e.g., in response to economic factors, pedo-climatic and biotic conditions ignored by the model, or policy decisions that can for instance reduce livestock numbers). When compared to agricultural statistics (Eurostat and FAOstat), ORCHIDEE-GM gave a good reproduction of the regional gradients of annual grassland productivity and ruminant livestock density. The model however tends to systematically overestimate the absolute values of productivity in most regions, suggesting that most grid cells remain below their potential grassland productivity due to possible nutrient and biotic limitations on plant growth. When ORCHIDEE-GM was run for the period 1961–2010 with variable climate and rising CO2, an increase of potential annual production (over 3%) per decade was found: 97% of this increase was attributed to the rise in CO2, -3% to climate trends and 15% to trends in nitrogen fertilization and deposition. When compared with statistical data, ORCHIDEE-GM captures well the observed phase of climate-driven interannual variability in grassland production well, whereas the magnitude of the interannual variability in modeled productivity is larger than the statistical data. Regional grass-fed livestock numbers can be reproduced by ORCHIDEE-GM based on its simple assumptions and parameterization about productivity being the only limiting factor to define the sustainable number of animals per unit area. Causes for regional model-data misfits are discussed, including uncertainties in farming practices (e.g., nitrogen fertilizer application, and mowing and grazing intensity) and in ruminant diet composition, as well as uncertainties in the statistical data and in model parameter values. PMID:26018186

Foraminifera and the ecology of sea grass communities since the late Cretaceous

NASA Astrophysics Data System (ADS)

Hart, Malcolm; Smart, Christopher; Jagt, John

2016-04-01

Sea grasses are marine angiosperms (plants) that, in the late Cretaceous, migrated from the land into shallow-water marine environments. They represent a distinct, but fragile, marine habitat and sea grass meadows are often regarded as biodiversity hot-spots with a range of species (including fish, sea horses and cuttlefish) using them as nurseries for their young. Foraminifera are often found associated with sea grass meadows, with the associated taxa reflecting both the environment and palaeolatitude. In the tropics and sub-tropics, miliolid foraminifera dominate (e.g., Peneroplis spp.) as do large discoidal taxa such as Marginopora and Calcarina. In temperate to cool latitudes the assemblage changes to one dominated by smaller benthic taxa, including Elphidium spp. One taxon, Elphidium crispum, is geotropic and is often found - in the summer months - to crowd the fronds of the sea grass. In the Gulpen and Maastricht formations of the Maastricht area (The Netherlands and Belgium) sea grass fossils (both fronds and rhizomes) have been recorded in association with assemblages of both larger and smaller benthic foraminifera (Hart et al., 2016). Some of the large discoidal forms (e.g., Omphalocyclus and Orbitoides/Lepidorbitoides) and the distinctive Siderolites are associated with these sea grass fossils and are suggestive of the modern sea grass communities of sub-tropical areas. While earlier records were of relatively isolated sea grasses, in September/October 2015 surfaces with abundant sea grasses were found that are suggestive of complete 'meadows'. Preservation of some silicified rhizomes indicates that silicification must have been very rapid, before any degradation or compaction of the delicate tissues. The presence of sea grass fossils and their associated benthic foraminifera is indicative of a clear, shallow-water seaway, with a maximum depth of 15-20 m. The reported variations in sea level during the latest Cretaceous cannot, therefore, have been very large as such a change in water depth would have been disastrous to such a fragile ecosystem. The fossil record of sea grasses in the Cenozoic is relatively limited, though there are some assemblages of benthic foraminifera that are suggestive of their presence, despite the lack of plant fossils. Hart, M.B., FitzPatrick, M.E.J. & Smart, C.W. 2016. The Cretaceous/Paleogene boundary: Foraminifera, sea grasses, sea level change and sequence stratigraphy. Palaeogeography, Palaeoclimatology, Palaeoecology, 441, 420-429.

Noise characteristics of grass-trimming machine engines and their effect on operators.

PubMed

Mallick, Zulquernain; Badruddin, Irfan Anjum; Khaleed Hussain, M T; Salman Ahmed, N J; Kanesan, Jeevan

2009-01-01

Over the last few years, interaction of humans with noisy power-driven agricultural tools and its possible adverse after effects have been realized. Grass-trimmer engine is the primary source of noise and the use of motorized cutter, spinning at high speed, is the secondary source of noise to which operators are exposed. In the present study, investigation was carried out to determine the effect of two types of grass-trimming machine engines (SUM 328 SE and BG 328) noise on the operators in real working environment. It was found that BG-328 and SUM-328 SE produced high levels of noise, of the order of 100 and 105 dB(A), respectively, to which operators are exposed while working. It was also observed that situation aggravates when a number of operators simultaneously operate resulting in still higher levels of noise. Operators should be separated 15 meters from each other in order to avoid the combined level of noise exposure while working with these machines. It was found that SPL, of the grass-trimmer machine engines (BG-328 and SUM-328 SE), were higher than the limit of noise recommended by ISO, NIOSH, and OSHA for an 8-hour workday. Such a high level of noise exposure may cause physiological and psychological problems to the operators in long run.

Shallow cumulus rooted in photosynthesis

NASA Astrophysics Data System (ADS)

Vila-Guerau Arellano, J.; Ouwersloot, H.; Horn, G.; Sikma, M.; Jacobs, C. M.; Baldocchi, D.

2014-12-01

We investigate the interaction between plant evapotranspiration, controlled by photosynthesis (for a low vegetation cover by C3 and C4 grasses), and the moist thermals that are responsible for the formation and development of shallow cumulus clouds (SCu). We perform systematic numerical experiments at fine spatial scales using large-eddy simulations explicitly coupled to a plant-physiology model. To break down the complexity of the vegetation-atmospheric system at the diurnal scales, we design the following experiments with increasing complexity: (a) clouds that are transparent to radiation, (b) clouds that shade the surface from the incoming shortwave radiation and (c) plant stomata whose apertures react with an adjustment in time to cloud perturbations. The shading by SCu leads to a strong spatial variability in photosynthesis and the surface energy balance. As a result, experiment (b) simulates SCu that are characterized by less extreme and less skewed values of the liquid water path and cloud-base height. These findings are corroborated by the calculation of characteristics lengths scales of the thermals and clouds using autocorrelation and spectral analysis methods. We find that experiments (a) and (b) are characterized by similar cloud cover evolution, but different cloud population characteristics. Experiment (b), including cloud shading, is characterized by smaller clouds, but closer to each other. By performing a sensitivity analysis on the exchange of water vapor and carbon dioxide at the canopy level, we show that the larger water-use efficiency of C4 grass leads to two opposing effects that directly influence boundary-layer clouds: the thermals below the clouds are more vigorous and deeper driven by a larger buoyancy surface flux (positive effect), but are characterized by less moisture content (negative effect). We conclude that under the investigated mid-latitude atmospheric and well-watered soil conditions, SCu over C4 grass fields is characterized by larger cloud cover and an enhanced liquid water path compared to C3 grass fields.

Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses.

PubMed

Muthamilarasan, Mehanathan; Prasad, Manoj

2015-01-01

Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.

Influence factors and prediction of stormwater runoff of urban green space in Tianjin, China: laboratory experiment and quantitative theory model.

PubMed

Yang, Xu; You, Xue-Yi; Ji, Min; Nima, Ciren

2013-01-01

The effects of limiting factors such as rainfall intensity, rainfall duration, grass type and vegetation coverage on the stormwater runoff of urban green space was investigated in Tianjin. The prediction equation of stormwater runoff was established by the quantitative theory with the lab experimental data of soil columns. It was validated by three field experiments and the relative errors between predicted and measured stormwater runoff are 1.41, 1.52 and 7.35%, respectively. The results implied that the prediction equation could be used to forecast the stormwater runoff of urban green space. The results of range and variance analysis indicated the sequence order of limiting factors is rainfall intensity > grass type > rainfall duration > vegetation coverage. The least runoff of green land in the present study is the combination of rainfall intensity 60.0 mm/h, duration 60.0 min, grass Festuca arundinacea and vegetation coverage 90.0%. When the intensity and duration of rainfall are 60.0 mm/h and 90.0 min, the predicted volumetric runoff coefficient is 0.23 with Festuca arundinacea of 90.0% vegetation coverage. The present approach indicated that green space is an effective method to reduce stormwater runoff and the conclusions are mainly applicable to Tianjin and the semi-arid areas with main summer precipitation and long-time interval rainfalls.

Effects of field-grown genetically modified Zoysia grass on bacterial community structure.

PubMed

Lee, Yong-Eok; Yang, Sang-Hwan; Bae, Tae-Woong; Kang, Hong-Gyu; Lim, Pyung-Ok; Lee, Hyo-Yeon

2011-04-01

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P〈0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

PubMed Central

Mochida, Keiichi; Uehara-Yamaguchi, Yukiko; Takahashi, Fuminori; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo

2013-01-01

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops. PMID:24130698

Transgenic Tobacco Plants Overexpressing a Grass PpEXP1 Gene Exhibit Enhanced Tolerance to Heat Stress

PubMed Central

Xu, Qian; Xu, Xiao; Shi, Yang; Xu, Jichen; Huang, Bingru

2014-01-01

Heat stress is a detrimental abiotic stress limiting the growth of many plant species and is associated with various cellular and physiological damages. Expansins are a family of proteins which are known to play roles in regulating cell wall elongation and expansion, as well as other growth and developmental processes. The in vitro roles of expansins regulating plant heat tolerance are not well understood. The objectives of this study were to isolate and clone an expansin gene in a perennial grass species (Poa pratensis) and to determine whether over-expression of expansin may improve plant heat tolerance. Tobacco (Nicotiana tabacum) was used as the model plant for gene transformation and an expansin gene PpEXP1 from Poa pratensis was cloned. Sequence analysis showed PpEXP1 belonged to α-expansins and was closely related to two expansin genes in other perennial grass species (Festuca pratensis and Agrostis stolonifera) as well as Triticum aestivum, Oryza sativa, and Brachypodium distachyon. Transgenic tobacco plants over-expressing PpEXP1 were generated through Agrobacterium-mediated transformation. Under heat stress (42°C) in growth chambers, transgenic tobacco plants over-expressing the PpEXP1 gene exhibited a less structural damage to cells, lower electrolyte leakage, lower levels of membrane lipid peroxidation, and lower content of hydrogen peroxide, as well as higher chlorophyll content, net photosynthetic rate, relative water content, activity of antioxidant enzyme, and seed germination rates, compared to the wild-type plants. These results demonstrated the positive roles of PpEXP1 in enhancing plant tolerance to heat stress and the possibility of using expansins for genetic modification of cool-season perennial grasses in the development of heat-tolerant germplasm and cultivars. PMID:25003197

Characterization of a filamentous virus from Bermuda grass and its molecular, serological and biological comparison with Spartina mottle virus.

PubMed

Hosseini, A; Koohi Habibi, M; Izadpanah, K; Mosahebi, G H; Rubies-Autonell, C; Ratti, C

2010-10-01

Bermuda grass with mosaic symptoms have been found in many parts of Iran. No serological correlation was observed between two isolates of this filamentous virus and any of the members of the family Potyviridae that were tested. Aphid transmission was demonstrated at low efficiency for isolates of this virus, whereas no transmission through seed was observed. A DNA fragment corresponding to the 3' end of the viral genome of these two isolates from Iran and one isolate from Italy was amplified and sequenced. A BLAST search showed that these isolates are more closely related to Spartina mottle virus (SpMV) than to any other virus in the family Potyviridae. Specific serological assays confirmed the phylogenetic analysis. Sequence and phylogenetic analysis suggested that these isolates could be considered as divergent strains of SpMV in the proposed genus Sparmovirus.

Modeling leaf phenology variation by groupings of species within and across ecosystems in northern Alaska

NASA Astrophysics Data System (ADS)

Euskirchen, E. S.; Carman, T. B.; McGuire, A. D.

2012-12-01

The phenology of arctic ecosystems is driven primarily by abiotic forces, with temperature acting as the main determinant of growing season onset and leaf budburst and in the spring. However, while the plant species in arctic ecosystems require differing amounts of accumulated heat for leaf-out, dynamic vegetation models simulated over a regional to global scale typically assume some average leaf-out for all of the species within an ecosystem. Here, we make use of air temperature records and observational data of spring leaf phenology collected across dominant groupings of species (dwarf birch shrubs, willow shrubs, other deciduous shrubs, grasses, sedges, and forbs) in arctic and ecotonal boreal ecosystems in Alaska. We then parameterize a dynamic vegetation model based on these data for four types of tundra ecosystems (heath tundra, shrub tundra, wet sedge tundra, and tussock tundra), as well as ecotonal boreal white spruce forest. This implementation improves the timing of the onset of carbon uptake in the spring, permitting a more accurate assessment of the contribution of each grouping of species to ecosystem performance. Furthermore, this implementation provides a more nuanced perspective on light competition among species and across ecosystems. For example, in the shrub tundra, the sedges and grasses leaf-out before the shade-inducing willow and dwarf birch, thereby providing the sedges and grasses time to accumulate biomass before shading effects arise. Also in the shrub tundra, the forbs leaf-out last, and are therefore, more prone to shading impacts by the taller willow and dwarf birch shrubs. However, in the wet sedge and heath tundra ecosystems, the forbs leaf-out before the shrubs, and are therefore less prone to shading impacts early in the growing season. These findings indicate the importance of leaf phenology data collection by species and across the various ecosystem types within the highly heterogeneous Arctic landscape. These findings also demonstrate that high-latitude dynamic vegetation models should consider variation in leaf-out by groupings of species within and across ecosystems in order to provide more accurate projections of future plant distributions in Arctic regions.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

PubMed

Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

2015-05-04

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade. Published by Oxford University Press on behalf of the Annals of Botany Company.

Mechanistic prediction of fission-gas behavior during in-cell transient heating tests on LWR fuel using the GRASS-SST and FASTGRASS computer codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rest, J; Gehl, S M

1979-01-01

GRASS-SST and FASTGRASS are mechanistic computer codes for predicting fission-gas behavior in UO/sub 2/-base fuels during steady-state and transient conditions. FASTGRASS was developed in order to satisfy the need for a fast-running alternative to GRASS-SST. Althrough based on GRASS-SST, FASTGRASS is approximately an order of magnitude quicker in execution. The GRASS-SST transient analysis has evolved through comparisons of code predictions with the fission-gas release and physical phenomena that occur during reactor operation and transient direct-electrical-heating (DEH) testing of irradiated light-water reactor fuel. The FASTGRASS calculational procedure is described in this paper, along with models of key physical processes included inmore » both FASTGRASS and GRASS-SST. Predictions of fission-gas release obtained from GRASS-SST and FASTGRASS analyses are compared with experimental observations from a series of DEH tests. The major conclusions is that the computer codes should include an improved model for the evolution of the grain-edge porosity.« less

Recurrent sequence exchange between homeologous grass chromosomes.

PubMed

Wicker, Thomas; Wing, Rod A; Schubert, Ingo

2015-11-01

All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently 'younger' age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced transmission and subsequent lineage sorting of the involved chromosomes to offspring. Molecular dating of these translocation events also allowed us to date major chromosome 'fusions' in the evolutionary lineages that led to Brachypodium and Triticeae. Furthermore, we provide evidence that rice is exceptional regarding the evolution of chromosomes 11 and 12, inasmuch as in other species the process of sequence exchange between homeologous chromosomes ceased much earlier than in rice. We presume that random events rather than selective forces are responsible for the observed high similarity between the short arm ends of rice chromosomes 11 and 12. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host.

PubMed

Shinozuka, Hiroshi; Hettiarachchige, Inoka K; Shinozuka, Maiko; Cogan, Noel O I; Spangenberg, German C; Cocks, Benjamin G; Forster, John W; Sawbridge, Timothy I

2017-08-22

Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time. The gene was identified from de novo sequencing and assembly of the genome and transcriptome of perennial ryegrass, a cool-season grass species. Molecular analysis confirmed the presence of the complete gene in the genome of perennial ryegrass. No corresponding sequence was found in other plant species, apart from members of the Poeae sub-tribes Loliinae and Dactylidinae. Evidence suggests that a common ancestor of the two sub-tribes acquired the gene from a species ancestral to contemporary grass-associated fungal endophytes around 9-13 million years ago. This first report of horizontal transfer of a nuclear gene from a taxonomically distant eukaryote to modern flowering plants provides evidence for a novel adaptation mechanism in angiosperms.

Colletotrichum caudatum s.l. is a species complex.

PubMed

Crouch, Jo Anne

2014-06-01

Colletotrichum caudatum sensu lato is a widespread fungal pathogen of warm-season grasses. The fungus is easily differentiated from other Colletotrichum species through the presence of a unique filiform appendage at the apex of the conidium. Multi-locus phylogenetic analysis of four DNA sequence markers from 21 isolates of C. caudatum s.l. from six grass hosts recovered the morphospecies as a well-supported monophyletic group. Although closely related to other Colletotrichum species pathogenic to warm-season grasses (e.g. C. sublineola, C. falcatum, C. navitas, C. graminicola), the sister taxon placement of C. caudatum remained unclear. Four major subgroups and three monotypic lineages were identified from the C. caudatum s.l. isolates. Despite the presence of localized, taxon-specific incongruence between gene trees and evidence for recombination in the dataset, application of genealogical concordance species recognition criteria diagnosed the four subgroups as phylogenetic species. Traditional morphology-based species concept defines C. caudatum as one species with a broad host range; however, multi-locus phylogenetic analyses refuted this model. Instead, isolates from different hosts were mainly segregated into different lineages. In particular, isolates from the type locale and host (USA, Sorghastrum nutans) collected within a 400 km radius were divided into three distinct species that corresponded with the three sampling sites. These data established that traditional morphological and ecological features are not informative for recognition of taxa within C. caudatum s.l., although there is some evidence that some species may be host specific. To stabilize the application of the name C. caudatum, DNA sequence data from the lectotype was generated, an epitype strain consistent with the type was designated and illustrated, and an emended description of C. caudatum sensu stricto is provided. Colletotrichum alcornii, C. baltimorense, C. somersetense, and C. zoysiae are described as new morphologically cryptic species related to C. caudatum s.s.

Unlocking Triticeae genomics to sustainably feed the future

PubMed Central

Mochida, Keiichi; Shinozaki, Kazuo

2013-01-01

The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species—barley, wheat, Tausch’s goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)—have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae. PMID:24204022

Complete chloroplast genome sequence of green foxtail (Setaria viridis), a promising model system for C4 photosynthesis.

PubMed

Wang, Shuo; Gao, Li-Zhi

2016-09-01

The complete chloroplast genome of green foxtail (Setaria viridis), a promising model system for C4 photosynthesis, is first reported in this study. The genome harbors a large single copy (LSC) region of 81 016 bp and a small single copy (SSC) region of 12 456  bp separated by a pair of inverted repeat (IRa and IRb) regions of 22 315 bp. GC content is 38.92%. The proportion of coding sequence is 57.97%, comprising of 111 (19 duplicated in IR regions) unique genes, 71 of which are protein-coding genes, four are rRNA genes, and 36 are tRNA genes. Phylogenetic analysis indicated that S. viridis was clustered with its cultivated species S. italica in the tribe Paniceae of the family Poaceae. This newly determined chloroplast genome will provide valuable genetic resources to assist future studies on C4 photosynthesis in grasses.

Natural lactic acid bacteria population of tropical grasses and their fermentation factor analysis of silage prepared with cellulase and inoculant.

PubMed

Khota, Waroon; Pholsen, Suradej; Higgs, David; Cai, Yimin

2016-12-01

Natural lactic acid bacteria (LAB) populations in tropical grasses and their fermentation characteristics on silage prepared with cellulase enzyme and LAB inoculants were studied. A commercial inoculant Lactobacillus plantarum Chikuso 1 (CH), a local selected strain Lactobacillus casei TH14 (TH14), and 2 cellulases, Acremonium cellulase (AC) and Maicelase (MC; Meiji Seika Pharma Co. Ltd., Tokyo, Japan), were used as additives to silage preparation with fresh and wilted (6 h) Guinea grass and Napier grass. Silage was prepared using a laboratory-scale fermentation system. Treatments were CH, TH14, AC at 0.01% fresh matter, AC 0.1%, MC 0.01%, MC 0.1%, CH+AC 0.01%, CH+AC 0.1%, CH+MC 0.01%, CH+MC 0.1%, TH14+AC 0.1%, TH14+AC 0.01%, TH14+MC 0.1%, and TH14+MC 0.01%. Microorganism counts of Guinea grass and Napier grass before ensiling were 10 2 LAB and 10 6 aerobic bacteria; these increased during wilting. Based on morphological and biochemical characteristics, and 16S rRNA gene sequence analysis, natural strains from both grasses were identified as L. plantarum, L. casei, Lactobacillus acidipiscis, Leuconostoc pseudomesenteroides, Leuconostoc garlicum, Weissella confusa, and Lactococcus lactis. Lactobacillus plantarum and L. casei are the dominant species and could grow at lower pH and produce more lactic acid than the other isolates. Crude protein and neutral detergent fiber were 5.8 and 83.7% of dry matter (DM) for Guinea grass, and 7.5 and 77.1% of DM for Napier grass. Guinea grass had a low level of water-soluble carbohydrates (0.39% of DM). Guinea grass silage treated with cellulase had a lower pH and higher lactic acid content than control and LAB treatments. The 0.1% AC and MC treatments had the best result for fermentation quality. All high water-soluble carbohydrate (2.38% DM) Napier grass silages showed good fermentation quality. Compared with control and LAB-inoculated silage, the cellulase-treated silages had significantly higher crude protein content and lower neutral detergent fiber and acid detergent fiber contents. The results confirmed that cellulase could improve tropical silage quality, inhibiting protein degradation and promoting fiber degradation. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Climatic, landform, microtopographic, and overstory canopy controls of tree invasion in a subalpine meadow landscape, Oregon Cascades, USA

Treesearch

Harold S.J. Zald; Thomas A. Spies; Manuela Huso; Demetrios Gatziolis

2012-01-01

Tree invasions have been documented throughout Northern Hemisphere high elevation meadows, as well as globally in many grass and forb-dominated ecosystems. Tree invasions are often associated with large-scale changes in climate or disturbance regimes, but are fundamentally driven by regeneration processes influenced by interactions between climatic, topographic, and...

Socio-Technical Relations in the Creation of an Interest-Driven Open Course

ERIC Educational Resources Information Center

Ponti, Marisa

2011-01-01

The aim of this article is to present the findings from a small exploratory case study of an open course on cyberpunk literature conducted at the Peer 2 Peer University (P2PU), an online grass-roots organisation that runs non-accredited courses. Employing actor network theory to inform an ethnographic-inductive approach, the case study sought to…

A proposed model for the flowering signaling pathway of sugarcane under photoperiodic control.

PubMed

Coelho, C P; Costa Netto, A P; Colasanti, J; Chalfun-Júnior, A

2013-04-25

Molecular analysis of floral induction in Arabidopsis has identified several flowering time genes related to 4 response networks defined by the autonomous, gibberellin, photoperiod, and vernalization pathways. Although grass flowering processes include ancestral functions shared by both mono- and dicots, they have developed their own mechanisms to transmit floral induction signals. Despite its high production capacity and its important role in biofuel production, almost no information is available about the flowering process in sugarcane. We searched the Sugarcane Expressed Sequence Tags database to look for elements of the flowering signaling pathway under photoperiodic control. Sequences showing significant similarity to flowering time genes of other species were clustered, annotated, and analyzed for conserved domains. Multiple alignments comparing the sequences found in the sugarcane database and those from other species were performed and their phylogenetic relationship assessed using the MEGA 4.0 software. Electronic Northerns were run with Cluster and TreeView programs, allowing us to identify putative members of the photoperiod-controlled flowering pathway of sugarcane.

Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar.

PubMed

Silva, Christian; Besnard, Guillaume; Piot, Anthony; Razanatsoa, Jacqueline; Oliveira, Reyjane P; Vorontsova, Maria S

2017-02-01

Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS. Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages. Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory. Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Small mammal use of native warm-season and non-native cool-season grass forage fields

USGS Publications Warehouse

Ryan L Klimstra,; Christopher E Moorman,; Converse, Sarah J.; Royle, J. Andrew; Craig A Harper,

2015-01-01

Recent emphasis has been put on establishing native warm-season grasses for forage production because it is thought native warm-season grasses provide higher quality wildlife habitat than do non-native cool-season grasses. However, it is not clear whether native warm-season grass fields provide better resources for small mammals than currently are available in non-native cool-season grass forage production fields. We developed a hierarchical spatially explicit capture-recapture model to compare abundance of hispid cotton rats (Sigmodon hispidus), white-footed mice (Peromyscus leucopus), and house mice (Mus musculus) among 4 hayed non-native cool-season grass fields, 4 hayed native warm-season grass fields, and 4 native warm-season grass-forb ("wildlife") fields managed for wildlife during 2 summer trapping periods in 2009 and 2010 of the western piedmont of North Carolina, USA. Cotton rat abundance estimates were greater in wildlife fields than in native warm-season grass and non-native cool-season grass fields and greater in native warm-season grass fields than in non-native cool-season grass fields. Abundances of white-footed mouse and house mouse populations were lower in wildlife fields than in native warm-season grass and non-native cool-season grass fields, but the abundances were not different between the native warm-season grass and non-native cool-season grass fields. Lack of cover following haying in non-native cool-season grass and native warm-season grass fields likely was the key factor limiting small mammal abundance, especially cotton rats, in forage fields. Retention of vegetation structure in managed forage production systems, either by alternately resting cool-season and warm-season grass forage fields or by leaving unharvested field borders, should provide refugia for small mammals during haying events.

Investigation of the Acoustics of Marine Sediments using an Impedance Tube

DTIC Science & Technology

2007-09-30

Thalassia testudinum (turtle grass), Syringodium filiforme (manatee grass), and Halodule wrightii (shoal grass). The work led to an invited paper and...equation could be used to model sound propagation in seagrass beds as an effective medium. A typical result for the species Thalassia testudinum (turtle...analysis (Fig. 13), was found to be χleaf = 0.23. Similar results were found the Thalassia testudinum (turtle grass) rhizomes (underground root

Enhanced precipitation variability decreases grass- and increases shrub-productivity

PubMed Central

Gherardi, Laureano A.; Sala, Osvaldo E.

2015-01-01

Although projections of precipitation change indicate increases in variability, most studies of impacts of climate change on ecosystems focused on effects of changes in amount of precipitation, overlooking precipitation variability effects, especially at the interannual scale. Here, we present results from a 6-y field experiment, where we applied sequences of wet and dry years, increasing interannual precipitation coefficient of variation while maintaining a precipitation amount constant. Increased precipitation variability significantly reduced ecosystem primary production. Dominant plant-functional types showed opposite responses: perennial-grass productivity decreased by 81%, whereas shrub productivity increased by 67%. This pattern was explained by different nonlinear responses to precipitation. Grass productivity presented a saturating response to precipitation where dry years had a larger negative effect than the positive effects of wet years. In contrast, shrubs showed an increasing response to precipitation that resulted in an increase in average productivity with increasing precipitation variability. In addition, the effects of precipitation variation increased through time. We argue that the differential responses of grasses and shrubs to precipitation variability and the amplification of this phenomenon through time result from contrasting root distributions of grasses and shrubs and competitive interactions among plant types, confirmed by structural equation analysis. Under drought conditions, grasses reduce their abundance and their ability to absorb water that then is transferred to deep soil layers that are exclusively explored by shrubs. Our work addresses an understudied dimension of climate change that might lead to widespread shrub encroachment reducing the provisioning of ecosystem services to society. PMID:26417095

Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Abendroth, Christian; Hahnke, Sarah; Codoñer, Francisco M; Klocke, Michael; Luschnig, Olaf; Porcar, Manuel

2017-10-05

A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism. Copyright © 2017 Abendroth et al.

Invasive C4 Perennial Grass Alters Net Ecosystem Exchange in Mixed C3/C4 Savanna Grassland

NASA Astrophysics Data System (ADS)

Basham, T. S.; Litvak, M.

2006-12-01

The invasion of ecosystems by non-native plants that differ from native plants in physiological characteristics and phenology has the potential to alter ecosystem function. In Texas and other regions of the southern central plains of the United States, the introduced C4 perennial grass, Bothriochloa ischaemum, invades C3/C4 mixed grasslands and savannas, resulting in decreased plant community diversity (Gabbard 2003; Harmoney et al 2004). The objective of this study was to quantify how the conversion of these mixed grass communities to C4 dominated, B. ischaemum monocultures impacts carbon cycling and sequestration. Seasonal measurements of Net Ecosystem Exchange (NEE) of CO2, leaf level gas exchange and soil respiration were compared between savanna grassland plots composed of either naturally occurring B. ischaemum monocultures or native mixed grasses (n=16). NEE was measured using a closed system chamber that attached to permanently installed stainless steel bases. Temperature, soil moisture, aerial percent species cover and leaf area index were also monitored in plots to explain variability in measured responses. Results showed that NEE differed seasonally between invaded and native plots due to 1) greater leaf surface area per unit ground area in invaded plots, 2) differences in phenological patterns of plant activity and 3) differences in responses to water limitation between invaded and native plots. Cold season and summer drought NEE were driven primarily by belowground respiration in both plot types, however spring uptake activity commenced two months later in invaded plots. This later start in invaded plots was compensated for by greater uptake throughout the growing season and in particular during the drier summer months. Differences in NEE between plot types were not due to differences in soil respiration nor were they due to greater leaf level photosynthetic capabilities of B. ischaemum relative to the dominant native grasses. NEE, soil respiration and biomass accumulation were limited by temperature and soil moisture in both native and invaded plots; however, invaded areas were less sensitive to both higher temperatures and lower soil moisture. Preliminary modeling results suggest that from January-August 2006, invaded grasslands stored approximately one third more carbon than native grasslands, making them 20% less of a carbon source than native plots during this year of record high temperatures and drought. Gabbard, BL. 2003. The Population Dynamics and Distribution of the Exotic Grass,Bothriochloa ischaemum, PhD Dissertation, University of Texas, Austin, TX Harmoney et al. 2004. Herbicide Effects on Established Yellow Old World Bluestem (Bothriochloa ischaemum). Weed Technology 18:545 550

Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses

PubMed Central

2012-01-01

Background Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3) that have been widely characterized in rice, maize and sorghum. Results In wheat, for which yellow pigment content is extremely important for flour colour, only PSY1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY2 has been partially characterized. Here, we report the isolation of bread wheat PSY3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing. Wheat PSY3 homoeologous genes were sequenced and annotated, unravelling their novel structure associated with intron-loss events and consequent exonic fusions. A wheat PSY3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid (ABA), since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses. Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY3 during abiotic stress. Conclusions We investigated the structural and functional determinisms of PSY genes in wheat. More generally, among eudicots and monocots, the PSY gene family was found to be associated with differences in gene copy numbers, allowing us to propose an evolutionary model for the entire PSY gene family in Grasses. PMID:22672222

Allergen-specific IgG and IgA in serum and bronchoalveolar lavage fluid in a model of experimental feline asthma.

PubMed

Norris, C R; Byerly, J R; Decile, K C; Berghaus, R D; Walby, W F; Schelegle, E S; Hyde, D M; Gershwin, L J

2003-12-15

Allergic asthma, a Th2 cell driven response to inhaled allergens, has classically been thought of as predominantly mediated by IgE antibodies. To investigate the role of other immunoglobulin classes (e.g., IgG and IgA) in the immunopathogenesis of allergic asthma, levels of these allergen-specific immunoglobulins were measured in serum and mucosal fluids. Bermuda grass allergen (BGA)-specific IgG and IgA ELISAs in serum and bronchoalveolar lavage fluid (BALF) were developed and optimized in an experimental model of BGA-induced feline asthma. Levels of BGA-specific IgG and IgA significantly increased over time in serum and BALF after allergen sensitization. Additionally, these elevated levels of BGA-specific IgG and IgA were seen in conjunction with the development of an asthmatic phenotype indicated by positive intradermal skin tests, enhanced airways hyperreactivity, and increased eosinophil percentages in the BALF.

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

PubMed

Law, MeiYee; Childs, Kevin L; Campbell, Michael S; Stein, Joshua C; Olson, Andrew J; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M; Lawrence, Carolyn J; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

2015-01-01

The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. © 2015 American Society of Plant Biologists. All Rights Reserved.

Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses.

PubMed

Zhang, Wei; Xu, Jianhong; Bennetzen, Jeffrey L; Messing, Joachim

2016-06-13

Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragrostis tef) has been sequenced. We find gene duplications, deletions, and rapid mutations in protein-coding sequences. The main SSPs in teff, like other grasses, are prolamins, here called eragrostins. Teff has γ- and δ-prolamins, but has no β-prolamins. One δ-type prolamin (δ1) in teff has higher methionine (33%) levels than in maize (23-25%). The other δ-type prolamin (δ2) has reduced methionine residues (<10%) and is phylogenetically closer to α prolamins. Prolamin δ2 in teff represents an intermediate between δ and α types that appears to have been lost in maize and other Panicoideae, and was replaced by the expansion of α-prolamins. Teff also has considerably larger numbers of α-prolamin genes, which we further divide into five sub-groups, where α2 and α5 represent the most abundant α-prolamins both in number and in expression. In addition, indolines that determine kernel softness are present in teff and the panicoid cereal called foxtail millet (Setaria italica) but not in sorghum or maize, indicating that these genes were only recently lost in some members of the Panicoideae Moreover, this study provides not only information on the evolution of SSPs in the grass family but also the importance of α-globulins in protein aggregation and germplasm divergence. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Effector cell signature in peripheral blood following nasal allergen challenge in grass pollen allergic individuals.

PubMed

Shamji, M H; Bellido, V; Scadding, G W; Layhadi, J A; Cheung, D K M; Calderon, M A; Asare, A; Gao, Z; Turka, L A; Tchao, N; Togias, A; Phippard, D; Durham, S R

2015-02-01

Several studies have demonstrated the time course of inflammatory mediators in nasal fluids following nasal allergen challenge (NAC), whereas the effects of NAC on cells in the periphery are unknown. We examined the time course of effector cell markers (for basophils, dendritic cells and T cells) in peripheral blood after nasal grass pollen allergen challenge. Twelve participants with seasonal allergic rhinitis underwent a control (diluent) challenge followed by NAC after an interval of 14 days. Nasal symptoms and peak nasal inspiratory flow (PNIF) were recorded along with peripheral basophil, T-cell and dendritic cell responses (flow cytometry), T-cell proliferative responses (thymidine incorporation), and cytokine expression (FluoroSpot assay). Robust increases in nasal symptoms and decreases in PNIF were observed during the early (0-1 h) response and modest significant changes during the late (1-24 h) response. Sequential peaks in peripheral blood basophil activation markers were observed (CD107a at 3 h, CD63 at 6 h, and CD203c(bright) at 24 h). T effector/memory cells (CD4(+) CD25(lo) ) were increased at 6 h and accompanied by increases in CD80(+) and CD86(+) plasmacytoid dendritic cells (pDCs). Ex vivo grass antigen-driven T-cell proliferative responses and the frequency of IL-4(+) CD4(+) T cells were significantly increased at 6 h after NAC when compared to the control day. Basophil, T-cell, and dendritic cell activation increased the frequency of allergen-driven IL-4(+) CD4(+) T cells, and T-cell proliferative responses are detectable in the periphery after NAC. These data confirm systemic cellular activation following a local nasal provocation. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

NASA Astrophysics Data System (ADS)

Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

2013-12-01

Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

PubMed Central

Li, De-Zhu

2011-01-01

Background Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. Methodology/Principal Findings Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. Conclusions/Significance The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly. PMID:21655229

Exserohilum rostratum: characterization of a cross-kingdom pathogen of plants and humans.

PubMed

Sharma, Kalpana; Goss, Erica M; Dickstein, Ellen R; Smith, Matthew E; Johnson, Judith A; Southwick, Frederick S; van Bruggen, Ariena H C

2014-01-01

Pathogen host shifts represent a major source of new infectious diseases. There are several examples of cross-genus host jumps that have caused catastrophic epidemics in animal and plant species worldwide. Cross-kingdom jumps are rare, and are often associated with nosocomial infections. Here we provide an example of human-mediated cross-kingdom jumping of Exserohilum rostratum isolated from a patient who had received a corticosteroid injection and died of fungal meningitis in a Florida hospital in 2012. The clinical isolate of E. rostratum was compared with two plant pathogenic isolates of E. rostratum and an isolate of the closely related genus Bipolaris in terms of morphology, phylogeny, and pathogenicity on one C3 grass, Gulf annual rye grass (Lolium multiflorum), and two C4 grasses, Japanese stilt grass (Microstegium vimineum) and bahia grass (Paspalum notatum). Colony growth and color, as well as conidia shape and size were the same for the clinical and plant isolates of E. rostratum, while these characteristics differed slightly for the Bipolaris sp. isolate. The plant pathogenic and clinical isolates of E. rostratum were indistinguishable based on morphology and ITS and 28S rDNA sequence analysis. The clinical isolate was as pathogenic to all grass species tested as the plant pathogenic strains that were originally isolated from plant hosts. The clinical isolate induced more severe symptoms on stilt grass than on rye grass, while this was the reverse for the plant isolates of E. rostratum. The phylogenetic similarity between the clinical and plant-associated E. rostratum isolates and the ability of the clinical isolate to infect plants suggests that a plant pathogenic strain of E. rostratum contaminated the corticosteroid injection fluid and was able to cause systemic disease in the affected patient. This is the first proof that a clinical isolate of E. rostratum is also an effective plant pathogen.

Exserohilum rostratum: Characterization of a Cross-Kingdom Pathogen of Plants and Humans

PubMed Central

Sharma, Kalpana; Goss, Erica M.; Dickstein, Ellen R.; Smith, Matthew E.; Johnson, Judith A.; Southwick, Frederick S.; van Bruggen, Ariena H. C.

2014-01-01

Pathogen host shifts represent a major source of new infectious diseases. There are several examples of cross-genus host jumps that have caused catastrophic epidemics in animal and plant species worldwide. Cross-kingdom jumps are rare, and are often associated with nosocomial infections. Here we provide an example of human-mediated cross-kingdom jumping of Exserohilum rostratum isolated from a patient who had received a corticosteroid injection and died of fungal meningitis in a Florida hospital in 2012. The clinical isolate of E. rostratum was compared with two plant pathogenic isolates of E. rostratum and an isolate of the closely related genus Bipolaris in terms of morphology, phylogeny, and pathogenicity on one C3 grass, Gulf annual rye grass (Lolium multiflorum), and two C4 grasses, Japanese stilt grass (Microstegium vimineum) and bahia grass (Paspalum notatum). Colony growth and color, as well as conidia shape and size were the same for the clinical and plant isolates of E. rostratum, while these characteristics differed slightly for the Bipolaris sp. isolate. The plant pathogenic and clinical isolates of E. rostratum were indistinguishable based on morphology and ITS and 28S rDNA sequence analysis. The clinical isolate was as pathogenic to all grass species tested as the plant pathogenic strains that were originally isolated from plant hosts. The clinical isolate induced more severe symptoms on stilt grass than on rye grass, while this was the reverse for the plant isolates of E. rostratum. The phylogenetic similarity between the clinical and plant-associated E. rostratum isolates and the ability of the clinical isolate to infect plants suggests that a plant pathogenic strain of E. rostratum contaminated the corticosteroid injection fluid and was able to cause systemic disease in the affected patient. This is the first proof that a clinical isolate of E. rostratum is also an effective plant pathogen. PMID:25285444

Viral pathogen production in a wild grass host driven by host growth and soil nitrogen.

PubMed

Whitaker, Briana K; Rúa, Megan A; Mitchell, Charles E

2015-08-01

Nutrient limitation is a basic ecological constraint that has received little attention in studies on virus production and disease dynamics. Nutrient availability could directly limit the production of viral nucleic acids and proteins, or alternatively limit host growth and thus indirectly limit metabolic pathways necessary for viral replication. In order to compare direct and indirect effects of nutrient limitation on virus production within hosts, we manipulated soil nitrogen (N) and phosphorus (P) availability in a glasshouse for the wild grass host Bromus hordeaceus and the viral pathogen Barley yellow dwarf virus-PAV. We found that soil N additions increased viral concentrations within host tissues, and the effect was mediated by host growth. Specifically, in statistical models evaluating the roles of host biomass production, leaf N and leaf P, viral production depended most strongly on host biomass, rather than the concentration of either nutrient. Furthermore, at low soil N, larger plants supported greater viral concentrations than smaller ones, whereas at high N, smaller plants supported greater viral concentrations. Our results suggest that enhanced viral productivity under N enrichment is an indirect consequence of nutrient stimulation to host growth rate. Heightened pathogen production in plants has important implications for a world facing increasing rates of nutrient deposition. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Revisiting the two-layer hypothesis: coexistence of alternative functional rooting strategies in savannas.

PubMed

Holdo, Ricardo M

2013-01-01

The two-layer hypothesis of tree-grass coexistence posits that trees and grasses differ in rooting depth, with grasses exploiting soil moisture in shallow layers while trees have exclusive access to deep water. The lack of clear differences in maximum rooting depth between these two functional groups, however, has caused this model to fall out of favor. The alternative model, the demographic bottleneck hypothesis, suggests that trees and grasses occupy overlapping rooting niches, and that stochastic events such as fires and droughts result in episodic tree mortality at various life stages, thus preventing trees from otherwise displacing grasses, at least in mesic savannas. Two potential problems with this view are: 1) we lack data on functional rooting profiles in trees and grasses, and these profiles are not necessarily reflected by differences in maximum or physical rooting depth, and 2) subtle, difficult-to-detect differences in rooting profiles between the two functional groups may be sufficient to result in coexistence in many situations. To tackle this question, I coupled a plant uptake model with a soil moisture dynamics model to explore the environmental conditions under which functional rooting profiles with equal rooting depth but different depth distributions (i.e., shapes) can coexist when competing for water. I show that, as long as rainfall inputs are stochastic, coexistence based on rooting differences is viable under a wide range of conditions, even when these differences are subtle. The results also indicate that coexistence mechanisms based on rooting niche differentiation are more viable under some climatic and edaphic conditions than others. This suggests that the two-layer model is both viable and stochastic in nature, and that a full understanding of tree-grass coexistence and dynamics may require incorporating fine-scale rooting differences between these functional groups and realistic stochastic climate drivers into future models.

Revisiting the Two-Layer Hypothesis: Coexistence of Alternative Functional Rooting Strategies in Savannas

PubMed Central

Holdo, Ricardo M.

2013-01-01

The two-layer hypothesis of tree-grass coexistence posits that trees and grasses differ in rooting depth, with grasses exploiting soil moisture in shallow layers while trees have exclusive access to deep water. The lack of clear differences in maximum rooting depth between these two functional groups, however, has caused this model to fall out of favor. The alternative model, the demographic bottleneck hypothesis, suggests that trees and grasses occupy overlapping rooting niches, and that stochastic events such as fires and droughts result in episodic tree mortality at various life stages, thus preventing trees from otherwise displacing grasses, at least in mesic savannas. Two potential problems with this view are: 1) we lack data on functional rooting profiles in trees and grasses, and these profiles are not necessarily reflected by differences in maximum or physical rooting depth, and 2) subtle, difficult-to-detect differences in rooting profiles between the two functional groups may be sufficient to result in coexistence in many situations. To tackle this question, I coupled a plant uptake model with a soil moisture dynamics model to explore the environmental conditions under which functional rooting profiles with equal rooting depth but different depth distributions (i.e., shapes) can coexist when competing for water. I show that, as long as rainfall inputs are stochastic, coexistence based on rooting differences is viable under a wide range of conditions, even when these differences are subtle. The results also indicate that coexistence mechanisms based on rooting niche differentiation are more viable under some climatic and edaphic conditions than others. This suggests that the two-layer model is both viable and stochastic in nature, and that a full understanding of tree-grass coexistence and dynamics may require incorporating fine-scale rooting differences between these functional groups and realistic stochastic climate drivers into future models. PMID:23950900

Complete genome sequence of Pseudomonas rhizosphaerae IH5T (=DSM 16299T), a phosphate-solubilizing rhizobacterium for bacterial biofertilizer.

PubMed

Kwak, Yunyoung; Jung, Byung Kwon; Shin, Jae-Ho

2015-01-10

Pseudomonas rhizosphaerae IH5(T) (=DSM 16299(T)), isolated from the rhizospheric soil of grass growing in Spain, has been reported as a novel species of the genus Pseudomonas harboring insoluble phosphorus solubilizing activity. To understanding the multifunctional biofertilizer better, we report the complete genome sequence of P. rhizosphaerae IH5(T). Copyright © 2014 Elsevier B.V. All rights reserved.

Data-driven Modeling of Metal-oxide Sensors with Dynamic Bayesian Networks

NASA Astrophysics Data System (ADS)

Gosangi, Rakesh; Gutierrez-Osuna, Ricardo

2011-09-01

We present a data-driven probabilistic framework to model the transient response of MOX sensors modulated with a sequence of voltage steps. Analytical models of MOX sensors are usually built based on the physico-chemical properties of the sensing materials. Although building these models provides an insight into the sensor behavior, they also require a thorough understanding of the underlying operating principles. Here we propose a data-driven approach to characterize the dynamical relationship between sensor inputs and outputs. Namely, we use dynamic Bayesian networks (DBNs), probabilistic models that represent temporal relations between a set of random variables. We identify a set of control variables that influence the sensor responses, create a graphical representation that captures the causal relations between these variables, and finally train the model with experimental data. We validated the approach on experimental data in terms of predictive accuracy and classification performance. Our results show that DBNs can accurately predict the dynamic response of MOX sensors, as well as capture the discriminatory information present in the sensor transients.

Characterizing differential gene expression in polyploid grasses lacking a reference transcriptome

USDA-ARS?s Scientific Manuscript database

Basal transcriptome characterization and differential gene expression in response to varying conditions are often addressed through next generation sequencing (NGS) and data analysis techniques. While these strategies are commonly used, there are countless tools, pipelines, data analysis methods an...

Climate, CO2, and the history of North American grasses since the Last Glacial Maximum

PubMed Central

Cotton, Jennifer M.; Cerling, Thure E.; Hoppe, Kathryn A.; Mosier, Thomas M.; Still, Christopher J.

2016-01-01

The spread of C4 grasses in the late Neogene is one of the most important ecological transitions of the Cenozoic, but the primary driver of this global expansion is widely debated. We use the stable carbon isotopic composition (δ13C) of bison and mammoth tissues as a proxy for the relative abundance of C3 and C4 vegetation in their grazing habitat to determine climatic and atmospheric CO2 controls on C4 grass distributions from the Last Glacial Maximum (LGM) to the present. We predict the spatial variability of grass δ13C in North America using a mean of three different methods of classification and regression tree (CART) machine learning techniques and nine climatic variables. We show that growing season precipitation and temperature are the strongest predictors of all single climate variables. We apply this CART analysis to high-resolution gridded climate data and Coupled Model Intercomparison Project (CMIP5) mean paleoclimate model outputs to produce predictive isotope landscape models (“isoscapes”) for the current, mid-Holocene, and LGM average δ13C of grass-dominated areas across North America. From the LGM to the present, C4 grass abundances substantially increased in the Great Plains despite concurrent increases in atmospheric CO2. These results suggest that changes in growing season precipitation rather than atmospheric CO2 were critically important in the Neogene expansion of C4 grasses. PMID:27051865

Modelling the effectiveness of grass buffer strips in managing muddy floods under a changing climate

NASA Astrophysics Data System (ADS)

Mullan, Donal; Vandaele, Karel; Boardman, John; Meneely, John; Crossley, Laura H.

2016-10-01

Muddy floods occur when rainfall generates runoff on agricultural land, detaching and transporting sediment into the surrounding natural and built environment. In the Belgian Loess Belt, muddy floods occur regularly and lead to considerable economic costs associated with damage to property and infrastructure. Mitigation measures designed to manage the problem have been tested in a pilot area within Flanders and were found to be cost-effective within three years. This study assesses whether these mitigation measures will remain effective under a changing climate. To test this, the Water Erosion Prediction Project (WEPP) model was used to examine muddy flooding diagnostics (precipitation, runoff, soil loss and sediment yield) for a case study hillslope in Flanders where grass buffer strips are currently used as a mitigation measure. The model was run for present day conditions and then under 33 future site-specific climate scenarios. These future scenarios were generated from three earth system models driven by four representative concentration pathways and downscaled using quantile mapping and the weather generator CLIGEN. Results reveal that under the majority of future scenarios, muddy flooding diagnostics are projected to increase, mostly as a consequence of large scale precipitation events rather than mean changes. The magnitude of muddy flood events for a given return period is also generally projected to increase. These findings indicate that present day mitigation measures may have a reduced capacity to manage muddy flooding given the changes imposed by a warming climate with an enhanced hydrological cycle. Revisions to the design of existing mitigation measures within existing policy frameworks are considered the most effective way to account for the impacts of climate change in future mitigation planning.

Periodic regulation of expression of genes for kisspeptin, gonadotropin-inhibitory hormone and their receptors in the grass puffer: Implications in seasonal, daily and lunar rhythms of reproduction.

PubMed

Ando, Hironori; Shahjahan, Md; Kitahashi, Takashi

2018-04-03

The seasonal, daily and lunar control of reproduction involves photoperiodic, circadian and lunar changes in the activity of kisspeptin, gonadotropin-inhibitory hormone (GnIH) and gonadotropin-releasing hormone (GnRH) neurons. These changes are brought through complex networks of light-, time- and non-photic signal-dependent control mechanisms, which are mostly unknown at present. The grass puffer, Takifugu alboplumbeus, a semilunar spawner, provides a unique and excellent animal model to assess this question because its spawning is synchronized with seasonal, daily and lunar cycles. In the diencephalon, the genes for kisspeptin, GnIH and their receptors showed similar expression patterns with clear seasonal and daily oscillations, suggesting that they are regulated by common mechanisms involving melatonin, circadian clock and water temperature. For implications in semilunar-synchronized spawning rhythm, melatonin receptor genes showed ultradian oscillations in expression with the period of 14.0-15.4 h in the pineal gland. This unique ultradian rhythm might be driven by circatidal clock. The possible circatidal clock and circadian clock in the pineal gland may cooperate to drive circasemilunar rhythm to regulate the expression of the kisspeptin, GnIH and their receptor genes. On the other hand, high temperature (over 28 °C) conditions, under which the expression of the kisspeptin and its receptor genes is markedly suppressed, may provide an environmental signal that terminates reproduction at the end of breeding period. Taken together, the periodic regulation of the kisspeptin, GnIH and their receptor genes by melatonin, circadian clock and water temperature may be important in the precisely-timed spawning of the grass puffer. Copyright © 2018 Elsevier Inc. All rights reserved.

EBIPM | Finding the Tools to Manage Invasive Annual Grasses

Science.gov Websites

Grass Management How much could prevention save you? Guidelines to Implement EBIPM Weed Prevention Areas Grass Facts/ID The EBIPM Model Crooked River Weed Management Area Guide Tools for Educators EBIPM High Agricultural Research Center for more information on invasive plant research. Eastern Oregon Agricultural

Modelling Water Uptake Provides a New Perspective on Grass and Tree Coexistence

PubMed Central

2015-01-01

Root biomass distributions have long been used to infer patterns of resource uptake. These patterns are used to understand plant growth, plant coexistence and water budgets. Root biomass, however, may be a poor indicator of resource uptake because large roots typically do not absorb water, fine roots do not absorb water from dry soils and roots of different species can be difficult to differentiate. In a sub-tropical savanna, Kruger Park, South Africa, we used a hydrologic tracer experiment to describe the abundance of active grass and tree roots across the soil profile. We then used this tracer data to parameterize a water movement model (Hydrus 1D). The model accounted for water availability and estimated grass and tree water uptake by depth over a growing season. Most root biomass was found in shallow soils (0–20 cm) and tracer data revealed that, within these shallow depths, half of active grass roots were in the top 12 cm while half of active tree roots were in the top 21 cm. However, because shallow soils provided roots with less water than deep soils (20–90 cm), the water movement model indicated that grass and tree water uptake was twice as deep as would be predicted from root biomass or tracer data alone: half of grass and tree water uptake occurred in the top 23 and 43 cm, respectively. Niche partitioning was also greater when estimated from water uptake rather than tracer uptake. Contrary to long-standing assumptions, shallow grass root distributions absorbed 32% less water than slightly deeper tree root distributions when grasses and trees were assumed to have equal water demands. Quantifying water uptake revealed deeper soil water uptake, greater niche partitioning and greater benefits of deep roots than would be estimated from root biomass or tracer uptake data alone. PMID:26633177

A standardized evaluation of artefacts from metallic compounds during fast MR imaging

PubMed Central

Murakami, Shumei; Kataoka, Miyoshi; Kakimoto, Naoya; Shimamoto, Hiroaki; Kreiborg, Sven

2016-01-01

Objectives: Metallic compounds present in the oral and maxillofacial regions (OMRs) cause large artefacts during MR scanning. We quantitatively assessed these artefacts embedded within a phantom according to standards set by the American Society for Testing and Materials (ASTM). Methods: Seven metallic dental materials (each of which was a 10-mm3 cube embedded within a phantom) were scanned [i.e. aluminium (Al), silver alloy (Ag), type IV gold alloy (Au), gold–palladium–silver alloy (Au-Pd-Ag), titanium (Ti), nickel–chromium alloy (NC) and cobalt–chromium alloy (CC)] and compared with a reference image. Sequences included gradient echo (GRE), fast spin echo (FSE), gradient recalled acquisition in steady state (GRASS), a spoiled GRASS (SPGR), a fast SPGR (FSPGR), fast imaging employing steady state (FIESTA) and echo planar imaging (EPI; axial/sagittal planes). Artefact areas were determined according to the ASTM-F2119 standard, and artefact volumes were assessed using OsiriX MD software (Pixmeo, Geneva, Switzerland). Results: Tukey–Kramer post hoc tests were used for statistical comparisons. For most materials, scanning sequences eliciting artefact volumes in the following (ascending) order FSE-T1/FSE-T2 < FSPGR/SPGR < GRASS/GRE < FIESTA < EPI. For all scanning sequences, artefact volumes containing Au, Al, Ag and Au-Pd-Ag were significantly smaller than other materials (in which artefact volume size increased, respectively, from Ti < NC < CC). The artefact-specific shape (elicited by the cubic sample) depended on the scanning plane (i.e. a circular pattern for the axial plane and a “clover-like” pattern for the sagittal plane). Conclusions: The availability of standardized information on artefact size and configuration during MRI will enhance diagnosis when faced with metallic compounds in the OMR. PMID:27459058

Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes

PubMed Central

Vitte, C.; Estep, M. C.; Leebens-Mack, J.; Bennetzen, J. L.

2013-01-01

Background and Aims Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. Methods To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. Key Results The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. Conclusions Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae. PMID:23887091

Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae.

PubMed

Wang, Yi; Yang, Chao; Jin, Qiaojun; Zhou, Dongjie; Wang, Shuangshuang; Yu, Yuanjie; Yang, Long

2015-02-15

The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability. In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/). Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.

A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA.

PubMed

Hochbach, Anne; Schneider, Julia; Röser, Martin

2015-06-01

To investigate phylogenetic relationships within the grass subfamily Pooideae we studied about 50 taxa covering all recognized tribes, using one plastid DNA (cpDNA) marker (matK gene-3'trnK exon) and for the first time four nuclear single copy gene loci. DNA sequence information from two parts of the nuclear genes topoisomerase 6 (Topo6) spanning the exons 8-13 and 17-19, the exons 9-13 encoding plastid acetyl-CoA-carboxylase (Acc1) and the partial exon 1 of phytochrome B (PhyB) were generated. Individual and nuclear combined data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All of the phylogenetic results show Brachyelytrum and the tribe Nardeae as earliest diverging lineages within the subfamily. The 'core' Pooideae (Hordeeae and the Aveneae/Poeae tribe complex) are also strongly supported, as well as the monophyly of the tribes Brachypodieae, Meliceae and Stipeae (except PhyB). The beak grass tribe Diarrheneae and the tribe Duthieeae are not monophyletic in some of the analyses. However, the combined nuclear DNA (nDNA) tree yields the highest resolution and the best delimitation of the tribes, and provides the following evolutionary hypothesis for the tribes: Brachyelytrum, Nardeae, Duthieeae, Meliceae, Stipeae, Diarrheneae, Brachypodieae and the 'core' Pooideae. Within the individual datasets, the phylogenetic trees obtained from Topo6 exon 8-13 shows the most interesting results. The divergent positions of some clone sequences of Ampelodesmos mauritanicus and Trikeraia pappiformis, for instance, may indicate a hybrid origin of these stipoid taxa. Copyright © 2015 Elsevier Inc. All rights reserved.

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus).

PubMed

Tran, Ngoc Tuan; Zhang, Jing; Xiong, Fan; Wang, Gui-Tang; Li, Wen-Xiang; Wu, Shan-Gong

2018-05-18

Gut microbiota plays a crucial importance in their host. Disturbance of the microbial structure and function is known to be associated with inflammatory intestinal disorders. Enteritis is a significant cause of high mortality in fish species, including grass carp (Ctenopharyngodon idellus). Study regarding the association between microbial alternations and enteritis in grass carp is still absent. In this study, changes in the gut microbiota of grass carp suffering from enteritis were investigated using NGS-based 16S rRNA sequencing. Six healthy and ten abnormal fish (showing reddening anus, red odiferous fluid accumulating in the abdominal capacity, and flatulence and haemorrhage in the intestine) were collected from a fish farm in Huanggang Fisheries Institute (Hubei, China). Our results revealed that the diversity, structure, and function of gut microbiota were significantly different between diseased and healthy fish (P < 0.05). Particularly, members of the genera Dechloromonas, Methylocaldum, Planctomyces, Rhodobacter, Caulobacter, Flavobacterium, and Pseudomonas were significantly increased in diseased fish compared with that in healthy fish (P < 0.05). Predicted function indicated that microbiota significantly changed the specific metabolic pathways (related to amino acid metabolism, xenobiotics biodegradation and metabolism, and carbohydrate metabolism) in diseased fish (P < 0.05). Taken together, our findings point out the association between changes of the gut microbiota and enteritis in grass carp, which provide basic information useful for diagnoses, prevention, and treatment of intestinal diseases occurring in cultured fish.

Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses.

PubMed

Schnable, James C; Pedersen, Brent S; Subramaniam, Sabarinath; Freeling, Michael

2011-01-01

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein-protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This has been explained as a consequence of protein-protein interactions, just as for other highly retained classes of genes. We show that the quantity of conserved noncoding sequences (CNSs) associated with genes predicts the likelihood of their retention as duplicate pairs following whole genome duplication. As many CNSs likely represent binding sites for transcriptional regulators, we propose that the likelihood of gene retention following tetraploidy may also be influenced by dose-sensitive protein-DNA interactions between the regulatory regions of CNS-rich genes - nicknamed bigfoot genes - and the proteins that bind to them. Using grass genomes, we show that differential loss of CNSs from one member of a pair following the pre-grass tetraploidy reduces its chance of retention in the subsequent maize lineage tetraploidy.

DNA analysis of herbarium Specimens of the grass weed Alopecurus myosuroides reveals herbicide resistance pre-dated herbicides.

PubMed

Délye, Christophe; Deulvot, Chrystel; Chauvel, Bruno

2013-01-01

Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic variation in weed populations, we used herbarium specimens of the grass weed Alopecurus myosuroides to seek mutant ACCase alleles carrying an isoleucine-to-leucine substitution at codon 1781 that endows herbicide resistance. These specimens had been collected between 1788 and 1975, i.e., prior to the commercial release of herbicides inhibiting ACCase. Among the 734 specimens investigated, 685 yielded DNA suitable for PCR. Genotyping the ACCase locus using the derived Cleaved Amplified Polymorphic Sequence (dCAPS) technique identified one heterozygous mutant specimen that had been collected in 1888. Occurrence of a mutant codon encoding a leucine residue at codon 1781 at the heterozygous state was confirmed in this specimen by sequencing, clearly demonstrating that resistance to herbicides can pre-date herbicides in weeds. We conclude that point mutations endowing resistance to herbicides without having associated deleterious pleiotropic effects can be present in weed populations as part of their standing genetic variation, in frequencies higher than the mutation frequency, thereby facilitating their subsequent selection by herbicide applications.

Dose–Sensitivity, Conserved Non-Coding Sequences, and Duplicate Gene Retention Through Multiple Tetraploidies in the Grasses

PubMed Central

Schnable, James C.; Pedersen, Brent S.; Subramaniam, Sabarinath; Freeling, Michael

2011-01-01

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This has been explained as a consequence of protein–protein interactions, just as for other highly retained classes of genes. We show that the quantity of conserved noncoding sequences (CNSs) associated with genes predicts the likelihood of their retention as duplicate pairs following whole genome duplication. As many CNSs likely represent binding sites for transcriptional regulators, we propose that the likelihood of gene retention following tetraploidy may also be influenced by dose–sensitive protein–DNA interactions between the regulatory regions of CNS-rich genes – nicknamed bigfoot genes – and the proteins that bind to them. Using grass genomes, we show that differential loss of CNSs from one member of a pair following the pre-grass tetraploidy reduces its chance of retention in the subsequent maize lineage tetraploidy. PMID:22645525

Methods for performing crosses in Setaria viridis, a new model system for the grasses.

PubMed

Jiang, Hui; Barbier, Hugues; Brutnell, Thomas

2013-10-01

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced (1,2) and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production (3) and developed systems for both transient and stable transformation (4). However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses. The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 °C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.

Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress.

PubMed

Lee, Jungeun; Noh, Eun Kyeung; Choi, Hyung-Seok; Shin, Seung Chul; Park, Hyun; Lee, Hyoungseok

2013-03-01

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been studied as an extremophile that has successfully adapted to marginal land with the harshest environment for terrestrial plants. However, limited genetic research has focused on this species due to the lack of genomic resources. Here, we present the first de novo assembly of its transcriptome by massive parallel sequencing and its expression profile using D. antarctica grown under various stress conditions. Total sequence reads generated by pyrosequencing were assembled into 60,765 unigenes (28,177 contigs and 32,588 singletons). A total of 29,173 unique protein-coding genes were identified based on sequence similarities to known proteins. The combined results from all three stress conditions indicated differential expression of 3,110 genes. Quantitative reverse transcription polymerase chain reaction showed that several well-known stress-responsive genes encoding late embryogenesis abundant protein, dehydrin 1, and ice recrystallization inhibition protein were induced dramatically and that genes encoding U-box-domain-containing protein, electron transfer flavoprotein-ubiquinone, and F-box-containing protein were induced by abiotic stressors in a manner conserved with other plant species. We identified more than 2,000 simple sequence repeats that can be developed as functional molecular markers. This dataset is the most comprehensive transcriptome resource currently available for D. antarctica and is therefore expected to be an important foundation for future genetic studies of grasses and extremophiles.

Ecophysiological responses of native and invasive grasses to simulated warming and drought

NASA Astrophysics Data System (ADS)

Ravi, S.; Law, D. J.; Wiede, A.; Barron-Gafford, G. A.; Breshears, D. D.; Dontsova, K.; Huxman, T. E.

2011-12-01

Climate models predict that many arid regions around the world - including the North American deserts - may become affected more frequently by recurrent droughts. At the same time, these regions are experiencing rapid vegetation transformations such as invasion by exotic grasses. Thus, understanding the ecophysiological processes accompanying exotic grass invasion in the context of rising temperatures and recurrent droughts is fundamental to global change research. Under ambient and warmer (+ 4° C) conditions inside the Biosphere 2 facility, we compared the ecophysiological responses (e.g. photosynthesis, stomatal conductance, pre-dawn leaf water potential, light & CO2 response functions, biomass) of a native grass - Heteropogan contortus (Tangle head) and an invasive grass - Pennisetum ciliare (Buffel grass) growing in single and mixed communities. Further, we monitored the physiological responses and mortality of these plant communities under moisture stress conditions, simulating a global change-type-drought. The results indicate that the predicted warming scenarios may enhance the invasibility of desert landscapes by exotic grasses. In this study, buffel grass assimilated more CO2 per unit leaf area and out-competed native grasses more efficiently in a warmer environment. However, scenarios involving a combination of drought and warming proved disastrous to both the native and invasive grasses, with drought-induced grass mortality occurring at much shorter time scales under warmer conditions.

Mapping and modeling the biogeochemical cycling of turf grasses in the United States.

PubMed

Milesi, Cristina; Running, Steven W; Elvidge, Christopher D; Dietz, John B; Tuttle, Benjamin T; Nemani, Ramakrishna R

2005-09-01

Turf grasses are ubiquitous in the urban landscape of the United States and are often associated with various types of environmental impacts, especially on water resources, yet there have been limited efforts to quantify their total surface and ecosystem functioning, such as their total impact on the continental water budget and potential net ecosystem exchange (NEE). In this study, relating turf grass area to an estimate of fractional impervious surface area, it was calculated that potentially 163,800 km2 (+/- 35,850 km2) of land are cultivated with turf grasses in the continental United States, an area three times larger than that of any irrigated crop. Using the Biome-BGC ecosystem process model, the growth of warm-season and cool-season turf grasses was modeled at a number of sites across the 48 conterminous states under different management scenarios, simulating potential carbon and water fluxes as if the entire turf surface was to be managed like a well-maintained lawn. The results indicate that well-watered and fertilized turf grasses act as a carbon sink. The potential NEE that could derive from the total surface potentially under turf (up to 17 Tg C/yr with the simulated scenarios) would require up to 695 to 900 liters of water per person per day, depending on the modeled water irrigation practices, suggesting that outdoor water conservation practices such as xeriscaping and irrigation with recycled waste-water may need to be extended as many municipalities continue to face increasing pressures on freshwater.

Climate change drives a northward expansion of C4 grasses in North America by the end of the century

NASA Astrophysics Data System (ADS)

Cotton, J. M.; Mosier, T. M.; Cerling, T. E.; Ehleringer, J. R.; Hoppe, K. A.; Still, C. J.

2016-12-01

C4 grasses currently cover 18% of the earth's surface and are critically important as food sources, and account for roughly 25% of terrestrial productivity. Yet in the future these patterns will change as a result of the opposing impacts of atmospheric CO2 and climate on C3 and C4 physiologies. Here, we use the carbon isotope ratio (d13C) of modern and fossil bison and mammoth tissues as a proxy for the abundance of C3 and C4 vegetation across North American habitats. We then combine stable isotope data with CMIP5 climate model simulations, and used eight different climatic predictor variables and advanced statistical techniques to model the spatial distributions of C3 and C4 grasses from today through the year 2100 for two fossil-fuel emissions scenarios. For both scenarios, our vegetation model predicts increases in C4 grass abundance of up to 50% in the northern Great Plains and moderate decreases in C4 grass abundance in the central and southern Great Plains. The overall effect of these C3/C4 distribution changes will be a decreases in the magnitude of the north-south grass gradient in the Great Plains ecoregion with the loss of the highest abundance of C4 ecosystems in the panhandles of Texas, Oklahoma and western Kansas. These results have important implications for future changes in animal and plant biodiversity, agricultural productivity, and C4 grass invasions in North America. Our study suggests that changing climates will likely start to favor C4 crops over C3 crops in the northern Great Plains, potentially influencing the nature of different grain food supplies. Additionally, changes in C3 and C4 grass distributions, including decreases in the abundance of C3 grasses in native grasslands in the northern Great Plains, could have negative effects on the fauna that feed preferentially on those C3 grasses, and may also reduce also the number of unique habitats that currently maintain high biodiversity.

DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses

PubMed Central

Wicker, Thomas; Yu, Yeisoo; Haberer, Georg; Mayer, Klaus F. X.; Marri, Pradeep Reddy; Rounsley, Steve; Chen, Mingsheng; Zuccolo, Andrea; Panaud, Olivier; Wing, Rod A.; Roffler, Stefan

2016-01-01

DNA (class 2) transposons are mobile genetic elements which move within their ‘host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind. PMID:27599761

Native Grasses as a Management Alternative on Vegetated Closure Caps

NASA Astrophysics Data System (ADS)

Kwit, Charles; Collins, Beverly

2008-06-01

Capped waste sites often are vegetated with commercial turf grasses to increase evapotranspiration and prevent erosion and possible exposure of the barrier. Fertilizer, frequent watering, and mowing may be required to establish the turf grass and prevent invasion by trees and shrubs. Oldfield vegetation of grasses and forbs is a possible sustainable alternative to turf grass communities. To determine if oldfield vegetation can establish on caps, we (1) compared establishment of a dominant oldfield grass and a commercial turf grass under different combinations of new closure cap management: spring or summer planting and presence or absence of amendments to alleviate drought (watering, mulch) or increase soil fertility (fertilizer, lime, a nitrogen-fixing legume); (2) surveyed existing caps to determine if oldfield species establish naturally; and (3) performed a greenhouse experiment to compare growth of two native grasses under low and amended (added water, soil nutrients) conditions. Both the commercial grass and oldfield species established under new cap conditions; fertilizer, water, and mulch improved vegetation establishment in spring or summer, but legumes decreased grass cover. In the greenhouse, both native grasses grew best with amendments; however, substantial stem and root length were obtained with no fertilizer and only once-weekly watering. Existing vegetated caps supported planted grasses and naturally established oldfield species. Overall, the results indicate native grasses can establish on new caps and oldfields can serve as a management model; further work is needed to determine the management strategy to maintain herbaceous vegetation and slow woody species invasion.

Dynamic ecological observations from satellites inform aerobiology of allergenic grass pollen.

PubMed

Devadas, Rakhesh; Huete, Alfredo R; Vicendese, Don; Erbas, Bircan; Beggs, Paul J; Medek, Danielle; Haberle, Simon G; Newnham, Rewi M; Johnston, Fay H; Jaggard, Alison K; Campbell, Bradley; Burton, Pamela K; Katelaris, Constance H; Newbigin, Ed; Thibaudon, Michel; Davies, Janet M

2018-08-15

Allergic diseases, including respiratory conditions of allergic rhinitis (hay fever) and asthma, affect up to 500 million people worldwide. Grass pollen are one major source of aeroallergens globally. Pollen forecast methods are generally site-based and rely on empirical meteorological relationships and/or the use of labour-intensive pollen collection traps that are restricted to sparse sampling locations. The spatial and temporal dynamics of the grass pollen sources themselves, however, have received less attention. Here we utilised a consistent set of MODIS satellite measures of grass cover and seasonal greenness (EVI) over five contrasting urban environments, located in Northern (France) and Southern Hemispheres (Australia), to evaluate their utility for predicting airborne grass pollen concentrations. Strongly seasonal and pronounced pollinating periods, synchronous with satellite measures of grass cover greenness, were found at the higher latitude temperate sites in France (46-50° N. Lat.), with peak pollen activity lagging peak greenness, on average by 2-3weeks. In contrast, the Australian sites (34-38° S. Lat.) displayed pollinating periods that were less synchronous with satellite greenness measures as peak pollen concentrations lagged peak greenness by as much as 4 to 7weeks. The Australian sites exhibited much higher spatial and inter-annual variations compared to the French sites and at the Sydney site, broader and multiple peaks in both pollen concentrations and greenness data coincided with flowering of more diverse grasses including subtropical species. Utilising generalised additive models (GAMs) we found the satellite greenness data of grass cover areas explained 80-90% of airborne grass pollen concentrations across the three French sites (p<0.001) and accounted for 34 to 76% of grass pollen variations over the two sites in Australia (p<0.05). Our results demonstrate the potential of satellite sensing to augment forecast models of grass pollen aerobiology as a tool to reduce the health and socioeconomic burden of pollen-sensitive allergic diseases. Copyright © 2018 Elsevier B.V. All rights reserved.

Novel application of ALMANAC: Modelling a functional group, exotic warm-season perennial grasses

USDA-ARS?s Scientific Manuscript database

Introduced perennial C4 grasses such buffelgrass (Pennisetum ciliare [(L.) Link]) and old world bluestems (OWB), including genera such as Bothriochloa Kuntze, Capillipedium Stapf, and Dichanthium Willemet have the potential to dominate landscapes. A process-based model that realistically simulates ...

Improving dynamic global vegetation model (DGVM) simulation of western U.S. rangelands vegetation seasonal phenology and productivity

NASA Astrophysics Data System (ADS)

Kerns, B. K.; Kim, J. B.; Day, M. A.; Pitts, B.; Drapek, R. J.

2017-12-01

Ecosystem process models are increasingly being used in regional assessments to explore potential changes in future vegetation and NPP due to climate change. We use the dynamic global vegetation model MAPSS-Century 2 (MC2) as one line of evidence for regional climate change vulnerability assessments for the US Forest Service, focusing our fine tuning model calibration from observational sources related to forest vegetation. However, there is much interest in understanding projected changes for arid rangelands in the western US such as grasslands, shrublands, and woodlands. Rangelands provide many ecosystem service benefits and local rural human community sustainability, habitat for threatened and endangered species, and are threatened by annual grass invasion. Past work suggested MC2 performance related to arid rangeland plant functional types (PFT's) was poor, and the model has difficulty distinguishing annual versus perennial grasslands. Our objectives are to increase the model performance for rangeland simulations and explore the potential for splitting the grass plant functional type into annual and perennial. We used the tri-state Blue Mountain Ecoregion as our study area and maps of potential vegetation from interpolated ground data, the National Land Cover Data Database, and ancillary NPP data derived from the MODIS satellite. MC2 historical simulations for the area overestimated woodland occurrence and underestimated shrubland and grassland PFT's. The spatial location of the rangeland PFT's also often did not align well with observational data. While some disagreement may be due to differences in the respective classification rules, the errors are largely linked to MC2's tree and grass biogeography and physiology algorithms. Presently, only grass and forest productivity measures and carbon stocks are used to distinguish PFT's. MC2 grass and tree productivity simulation is problematic, in particular grass seasonal phenology in relation to seasonal patterns of temperature and precipitation. The algorithm also does not accurately translate simulated carbon stocks into the canopy allometry of woodland tree species that dominate the BME, thereby inaccurately shading out the grasses in the understory. We are devising improvements to these shortcomings in the model architecture.

Cumulative Weighing of Time in Intertemporal Tradeoffs

PubMed Central

2016-01-01

We examine preferences for sequences of delayed monetary gains. In the experimental literature, two prominent models have been advanced as psychological descriptions of preferences for sequences. In one model, the instantaneous utilities of the outcomes in a sequence are discounted as a function of their delays, and assembled into a discounted utility of the sequence. In the other model, the accumulated utility of the outcomes in a sequence is considered along with utility or disutility from improvement in outcome utilities and utility or disutility from the spreading of outcome utilities. Drawing on three threads of evidence concerning preferences for sequences of monetary gains, we propose that the accumulated utility of the outcomes in a sequence is traded off against the duration of utility accumulation. In our first experiment, aggregate choice behavior provides qualitative support for the tradeoff model. In three subsequent experiments, one of which incentivized, disaggregate choice behavior provides quantitative support for the tradeoff model in Bayesian model contests. One thread of evidence motivating the tradeoff model is that, when, in the choice between two single dated outcomes, it is conveyed that receiving less sooner means receiving nothing later, preference for receiving more later increases, but when it is conveyed that receiving more later means receiving nothing sooner, preference is left unchanged. Our results show that this asymmetric hidden-zero effect is indeed driven by those supporting the tradeoff model. The tradeoff model also accommodates all remaining evidence on preferences for sequences of monetary gains. PMID:27560853

Future of African terrestrial biodiversity and ecosystems under anthropogenic climate change

NASA Astrophysics Data System (ADS)

Midgley, Guy F.; Bond, William J.

2015-09-01

Projections of ecosystem and biodiversity change for Africa under climate change diverge widely. More than other continents, Africa has disturbance-driven ecosystems that diversified under low Neogene CO2 levels, in which flammable fire-dependent C4 grasses suppress trees, and mega-herbivore action alters vegetation significantly. An important consequence is metastability of vegetation state, with rapid vegetation switches occurring, some driven by anthropogenic CO2-stimulated release of trees from disturbance control. These have conflicting implications for biodiversity and carbon sequestration relevant for policymakers and land managers. Biodiversity and ecosystem change projections need to account for both disturbance control and direct climate control of vegetation structure and function.

Cell wall composition throughout development for the model grass Brachypodium distachyon

PubMed Central

Rancour, David M.; Marita, Jane M.; Hatfield, Ronald D.

2012-01-01

Temperate perennial grasses are important worldwide as a livestock nutritive energy source and a potential feedstock for lignocellulosic biofuel production. The annual temperate grass Brachypodium distachyon has been championed as a useful model system to facilitate biological research in agriculturally important temperate forage grasses based on phylogenetic relationships. To physically corroborate genetic predictions, we determined the chemical composition profiles of organ-specific cell walls throughout the development of two common diploid accessions of Brachypodium distachyon, Bd21-3 and Bd21. Chemical analysis was performed on cell walls isolated from distinct organs (i.e., leaves, sheaths, stems, and roots) at three developmental stages of (1) 12-day seedling, (2) vegetative-to-reproductive transition, and (3) mature seed fill. In addition, we have included cell wall analysis of embryonic callus used for genetic transformations. Composition of cell walls based on components lignin, hydroxycinnamates, uronosyls, neutral sugars, and protein suggests that Brachypodium distachyon is similar chemically to agriculturally important forage grasses. There were modest compositional differences in hydroxycinnamate profiles between accessions Bd21-3 and Bd21. In addition, when compared to agronomical important C3 grasses, more mature Brachypodium stem cell walls have a relative increase in glucose of 48% and a decrease in lignin of 36%. Though differences exist between Brachypodium and agronomical important C3 grasses, Brachypodium distachyon should be still a useful model system for genetic manipulation of cell wall composition to determine the impact upon functional characteristics such as rumen digestibility or energy conversion efficiency for bioenergy production. PMID:23227028

Comparison of Interglacial fire dynamics in Southern Africa

NASA Astrophysics Data System (ADS)

Brücher, Tim; Daniau, Anne-Laure

2016-04-01

Responses of fire activity to a change in climate are still uncertain and biases exist by integrating this non-linear process into global modeling of the Earth system. Warming and regional drying can force fire activity in two opposite directions: an increase in fire in fuel supported ecosystems or a fire reduction in fuel-limited ecosystems. Therefore, climate variables alone can not be used to estimate the fire risk because vegetation variability is an important determinant of fire dynamics and responds itself to change in climate. Southern Africa (south of 20°S) paleofire history reconstruction obtained from the analysis of microcharcoal preserved in a deep-sea core located off Namibia reveals changes of fire activity on orbital timescales in the precession band. In particular, increase in fire is observed during glacial periods, and reduction of fire during interglacials such as the Eemian and the Holocene. The Holocene was characterized by even lower level of fire activity than Eemian. Those results suggest the alternance of grass-fueled fires during glacials driven by increase in moisture and the development of limited fueled ecosystems during interglacials characterized by dryness. Those results question the simulated increase in the fire risk probability projected for this region under a warming and drying climate obtained by Pechony and Schindell (2010). To explore the validity of the hypotheses we conducted a data-model comparison for both interglacials from 126.000 to 115.000 BP for the Eemian and from 8.000 to 2.000 BP for the Holocene. Data out of a transient, global modeling study with a Vegetation-Fire model of full complexity (JSBACH) is used, driven by a Climate model of intermediate complexity (CLIMBER). Climate data like precipitation and temperature as well as vegetation data like soil moisture, productivity (NPP) on plant functional type level are used to explain trends in fire activity. The comparison of trends in fire activity during the Eemian (126.000 to 120.000 BP) and the Holocene (8.000 to 200 BP) shows an increase in fire data and in simulated fire. Lower level of fire during the Holocene than Eemian can be explained by differences due to unequal trends in vegetation as a result of climate forcing due to orbital changes: while woody type vegetation plays a major role during the Eemian, the Holocene is influenced by grass land. From the modelling perspective changes in the seasonal precipitation drives the vegetation pattern.

Influence of Cleats-Surface Interaction on the Performance and Risk of Injury in Soccer: A Systematic Review

PubMed Central

Macedo, Rui; Montes, António Mesquita

2017-01-01

Objective To review the influence of cleats-surface interaction on the performance and risk of injury in soccer athletes. Design Systematic review. Data Sources Scopus, Web of science, PubMed, and B-on. Eligibility Criteria Full experimental and original papers, written in English that studied the influence of soccer cleats on sports performance and injury risk in artificial or natural grass. Results Twenty-three articles were included in this review: nine related to performance and fourteen to injury risk. On artificial grass, the soft ground model on dry and wet conditions and the turf model in wet conditions are related to worse performance. Compared to rounded studs, bladed ones improve performance during changes of directions in both natural and synthetic grass. Cleat models presenting better traction on the stance leg improve ball velocity while those presenting a homogeneous pressure across the foot promote better kicking accuracy. Bladed studs can be considered less secure by increasing plantar pressure on lateral border. The turf model decrease peak plantar pressure compared to other studded models. Conclusion The soft ground model provides lower performance especially on artificial grass, while the turf model provides a high protective effect in both fields. PMID:28684897

Influence of Cleats-Surface Interaction on the Performance and Risk of Injury in Soccer: A Systematic Review.

PubMed

Silva, Diogo C F; Santos, Rubim; Vilas-Boas, João Paulo; Macedo, Rui; Montes, António Mesquita; Sousa, Andreia S P

2017-01-01

To review the influence of cleats-surface interaction on the performance and risk of injury in soccer athletes. Systematic review. Scopus, Web of science, PubMed, and B-on. Full experimental and original papers, written in English that studied the influence of soccer cleats on sports performance and injury risk in artificial or natural grass. Twenty-three articles were included in this review: nine related to performance and fourteen to injury risk. On artificial grass, the soft ground model on dry and wet conditions and the turf model in wet conditions are related to worse performance. Compared to rounded studs, bladed ones improve performance during changes of directions in both natural and synthetic grass. Cleat models presenting better traction on the stance leg improve ball velocity while those presenting a homogeneous pressure across the foot promote better kicking accuracy. Bladed studs can be considered less secure by increasing plantar pressure on lateral border. The turf model decrease peak plantar pressure compared to other studded models. The soft ground model provides lower performance especially on artificial grass, while the turf model provides a high protective effect in both fields.

A Recommendation for Naming Transcription Factor Proteins in the Grasses

USDA-ARS?s Scientific Manuscript database

Transcription factors are central for the exquisite temporal and spatial expression patterns of many genes. These proteins are characterized by their ability to be tethered to particular regulatory sequences in the genes that they control. While many other proteins participate in the regulation of g...

Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi

USDA-ARS?s Scientific Manuscript database

Magnaporthaceae is a family of ascomycetes that includes three fungi of great economic importance: Magnaporthe oryzae, Gaeumannomyces graminis var. tritici, and Magnaporthe poae. These three fungi cause widespread disease and loss in cereal and grass crops, including rice blast disease (M. oryzae), ...

Simple sequence repeat markers for interspecific hybrid detections in Agrostis

USDA-ARS?s Scientific Manuscript database

Agrostis stolonifera L. (creeping bentgrass) and Agrostis capillaris (colonial bentgrass) are turfgrass species that are well adapted for golf course use in regions of the world where cool-season grasses are grown. Interspecific hybrids between the species do form and have the potential to incorpora...

Detection and characterization of the first North American mastrevirus in Switchgrass

USDA-ARS?s Scientific Manuscript database

Virus infections have the potential to reduce biomass yields in energy crops, including Panicum virgatum (switchgrass). As a first step towards managing virus-induced biomass reductions, deep sequencing was used to identify viruses associated with mosaic symptoms in switch grass, which detected thre...

Spatial methods for deriving crop rotation history

USDA-ARS?s Scientific Manuscript database

Converting multi-year remote sensing classification data into crop rotations is beneficial by defining length of crop rotation cycles and the specific sequences of intervening crops grown between the final year of a grass seed stand and establishment of a new perennial ryegrass seed crop. Markov mod...

Confronting species distribution model predictions with species functional traits.

PubMed

Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

2016-02-01

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

A Main Sequence For Quasars

NASA Astrophysics Data System (ADS)

Marziani, Paola; Sulentic, J. W.; Dultzin, D.; Negrete, A.; del Olmo, A.; Martínez-Carballo, M. A.; Stirpe, G. M.; D'Onofrio, M.; Perea, J.

2016-10-01

The 4D eigenvector 1 parameter space defined by Sulentic et al. may be seen as a surrogate H-R diagram for quasars. As in the stellar H-R diagram, a source sequence can be easily identified. In the case of quasars, the main sequence appears to be mainly driven by Eddington ratio. A transition Eddington ratio may in part explain the striking observational differences between quasars at opposite ends of the main sequence. The eigenvector-1 approach opens the door towards properly contextualized models of quasar physics, geometry and kinematics. We review some of the progress that has been made over the past 15 years, and point out still unsolved issues.

Seasonal, inter-annual and decadal drivers of tree and grass productivity in an Australian tropical savanna.

NASA Astrophysics Data System (ADS)

Moore, C.; Beringer, J.; Hutley, L. B.; Evans, B. J.; Tapper, N. J.; Donohue, R. J.; Exbrayat, J. F.

2016-12-01

Tree-grass savannas are a widespread biome and are highly valued for their ecosystem services. Natural or anthropogenic shifts in the savanna tree-grass ratio have wide-reaching implications for food production, timber harvesting, biodiversity, the water cycle and carbon sequestration. It is important to understand the long-term dynamics and drivers of both tree and grass productivity separately, in order to successfully manage savannas in the future. This study investigates the inter-annual variability (IAV) of tree (overstory) and grass (understory) productivity at the Howard Springs OzFlux/Fluxnet site by combining a long-term (15 year) eddy covariance flux record and DIFFUSE model estimates of tree and grass productivity inferred from satellite remote sensing. On a seasonal basis, the primary drivers of overstory and understory productivity were solar radiation in the wet season and soil moisture in the dry season, with deeper soil layers becoming more important as the dry season progressed. On an inter-annual basis, variability in the amount of annual rainfall and length of the rainy season determined soil water availability, which had a positive effect on overstory productivity and a negative effect on understory productivity. No linear trend in the tree-grass ratio was observed over the 15-year study period, indicating that woody encroachment was not occurring to a significant degree at the study site. However, the tree-grass ratio was well correlated with modes of climate variability, namely the Southern Oscillation Index. This study has provided important insight into the long-term contributions of trees and grasses to savanna productivity, along with the respective drivers of IAV. The results will contribute towards model development and building better links with remote sensing techniques in order to more comprehensively monitor savanna structure and function across space and time.

Further Development of a Computational Vision Model for the Generation and Analysis of Photo-Realistic Scenes for Military and Civilian Virtual Reality Applications

DTIC Science & Technology

1996-02-01

rectangle in the center of the image straddling the boundary between the foreground grass and background treeline . The synthetic content of the target region...the square in the middle of the grass, the square in the middle of the tree leaves, and the square on the treeline are all synthetic textures. The...target rectangle on the treeline boundary. What was suprising was that the synthetic grass texture was not well matched in the rectangle in the grass

Grassland plant composition alters vehicular disturbance effects in Kansas, USA.

PubMed

Dickson, Timothy L; Wilsey, Brian J; Busby, Ryan R; Gebhart, Dick L

2008-05-01

Many "natural" areas are exposed to military or recreational off-road vehicles. The interactive effects of different types of vehicular disturbance on vegetation have rarely been examined, and it has been proposed that some vegetation types are less susceptible to vehicular disturbance than others. At Fort Riley, Kansas, we experimentally tested how different plant community types changed after disturbance from an M1A1 Abrams tank driven at different speeds and turning angles during different seasons. The greatest vegetation change was observed because of driving in the spring in wet soils and the interaction of turning while driving fast (vegetation change was measured with Bray-Curtis dissimilarity). We found that less vegetation change occurred in communities with high amounts of native prairie vegetation than in communities with high amounts of introduced C(3) grasses, which is the first experimental evidence we are aware of that suggests plant communities dominated by introduced C(3) grasses changed more because of vehicular disturbance than communities dominated by native prairie grasses. We also found that vegetation changed linearly with vehicular disturbance intensity, suggesting that at least initially there was no catastrophic shift in vegetation beyond a certain disturbance intensity threshold. Overall, the intensity of vehicular disturbance appeared to play the greatest role in vegetation change, but the plant community type also played a strong role and this should be considered in land use planning. The reasons for greater vegetation change in introduced C(3) grass dominated areas deserve further study.

Diversification of C(4) grasses (Poaceae) does not coincide with their ecological dominance.

PubMed

Bouchenak-Khelladi, Yanis; Slingsby, Jasper A; Verboom, G Anthony; Bond, William J

2014-02-01

The radiation of a lineage and its rise to ecological dominance are distinct phenomena and driven by different processes. For example, paleoecological data has been used to show that the Cretaceous angiosperm radiation did not coincide with their rise to dominance. Using a phylogenetic approach, we here explored the evolution of C4 grasses and evaluated whether the diversification of this group and its rise to ecological dominance in the late Miocene were decoupled. We assembled a matrix including 675 grass species of the PACMAD clade and 2784 characters (ITS and ndhF) to run a molecular dating analysis using three fossils as reference calibrations. We coded species as C3 vs. C4 and reconstructed ancestral states under maximum likelihood. We used the program BiSSE to test whether rates of diversification are correlated with photosynthetic pathway and whether the radiation of C4 lineages preceded or coincided with their rise to ecological dominance from ∼10 Ma. C4 grass lineages first originated around 35 Ma at the time of the Eocene-Oligocene transition. Accelerated diversification of C4 lineages did not coincide with their rise to ecological dominance. C4-dominated grasslands have expanded only since the Late Miocene and Pliocene. The initial diversification of their biotic elements can be tracked back as far as the Eocene-Oligocene transition. We suggest that shifts in taxonomic diversification and ecological dominance were stimulated by different factors, as in the case of the early angiosperms in the Cretaceous.

Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences.

PubMed

Galson, Jacob D; Trück, Johannes; Fowler, Anna; Clutterbuck, Elizabeth A; Münz, Márton; Cerundolo, Vincenzo; Reinhard, Claudia; van der Most, Robbert; Pollard, Andrew J; Lunter, Gerton; Kelly, Dominic F

2015-12-01

Generating a diverse B cell immunoglobulin repertoire is essential for protection against infection. The repertoire in humans can now be comprehensively measured by high-throughput sequencing. Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. Clonal sequence expansions were seen 7 days after vaccination, which correlated with vaccine-specific plasma cell numbers. These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. We also saw an increase in sequence convergence between participants 14 and 21 days after vaccination, coinciding with an increase of vaccine-specific memory cells. These features allowed development of a model for in silico enrichment of vaccine-specific sequences from the total repertoire. Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation.

Automatic Parameterization Strategy for Cardiac Electrophysiology Simulations.

PubMed

Costa, Caroline Mendonca; Hoetzl, Elena; Rocha, Bernardo Martins; Prassl, Anton J; Plank, Gernot

2013-10-01

Driven by recent advances in medical imaging, image segmentation and numerical techniques, computer models of ventricular electrophysiology account for increasingly finer levels of anatomical and biophysical detail. However, considering the large number of model parameters involved parameterization poses a major challenge. A minimum requirement in combined experimental and modeling studies is to achieve good agreement in activation and repolarization sequences between model and experiment or patient data. In this study, we propose basic techniques which aid in determining bidomain parameters to match activation sequences. An iterative parameterization algorithm is implemented which determines appropriate bulk conductivities which yield prescribed velocities. In addition, a method is proposed for splitting the computed bulk conductivities into individual bidomain conductivities by prescribing anisotropy ratios.

Statistical analysis of life history calendar data.

PubMed

Eerola, Mervi; Helske, Satu

2016-04-01

The life history calendar is a data-collection tool for obtaining reliable retrospective data about life events. To illustrate the analysis of such data, we compare the model-based probabilistic event history analysis and the model-free data mining method, sequence analysis. In event history analysis, we estimate instead of transition hazards the cumulative prediction probabilities of life events in the entire trajectory. In sequence analysis, we compare several dissimilarity metrics and contrast data-driven and user-defined substitution costs. As an example, we study young adults' transition to adulthood as a sequence of events in three life domains. The events define the multistate event history model and the parallel life domains in multidimensional sequence analysis. The relationship between life trajectories and excess depressive symptoms in middle age is further studied by their joint prediction in the multistate model and by regressing the symptom scores on individual-specific cluster indices. The two approaches complement each other in life course analysis; sequence analysis can effectively find typical and atypical life patterns while event history analysis is needed for causal inquiries. © The Author(s) 2012.

A New Method for Setting Calculation Sequence of Directional Relay Protection in Multi-Loop Networks

NASA Astrophysics Data System (ADS)

Haijun, Xiong; Qi, Zhang

2016-08-01

Workload of relay protection setting calculation in multi-loop networks may be reduced effectively by optimization setting calculation sequences. A new method of setting calculation sequences of directional distance relay protection in multi-loop networks based on minimum broken nodes cost vector (MBNCV) was proposed to solve the problem experienced in current methods. Existing methods based on minimum breakpoint set (MBPS) lead to more break edges when untying the loops in dependent relationships of relays leading to possibly more iterative calculation workloads in setting calculations. A model driven approach based on behavior trees (BT) was presented to improve adaptability of similar problems. After extending the BT model by adding real-time system characters, timed BT was derived and the dependency relationship in multi-loop networks was then modeled. The model was translated into communication sequence process (CSP) models and an optimization setting calculation sequence in multi-loop networks was finally calculated by tools. A 5-nodes multi-loop network was applied as an example to demonstrate effectiveness of the modeling and calculation method. Several examples were then calculated with results indicating the method effectively reduces the number of forced broken edges for protection setting calculation in multi-loop networks.

The Sorghum bicolor genome and the diversification of grasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paterson, Andrew H.; Bowers, John E.; Bruggmann, Remy

2008-08-20

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approx730-megabase Sorghum bicolor (L.) Moench genome, placing approx98percent of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approx75percent larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidizationmore » approx70 million years ago, most duplicated gene sets lost one member before the sorghum rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24percent of genes are grass-specific and 7percent are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.« less

The Sorghum bicolor genome and the diversification of grasses.

PubMed

Paterson, Andrew H; Bowers, John E; Bruggmann, Rémy; Dubchak, Inna; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hellsten, Uffe; Mitros, Therese; Poliakov, Alexander; Schmutz, Jeremy; Spannagl, Manuel; Tang, Haibao; Wang, Xiyin; Wicker, Thomas; Bharti, Arvind K; Chapman, Jarrod; Feltus, F Alex; Gowik, Udo; Grigoriev, Igor V; Lyons, Eric; Maher, Christopher A; Martis, Mihaela; Narechania, Apurva; Otillar, Robert P; Penning, Bryan W; Salamov, Asaf A; Wang, Yu; Zhang, Lifang; Carpita, Nicholas C; Freeling, Michael; Gingle, Alan R; Hash, C Thomas; Keller, Beat; Klein, Patricia; Kresovich, Stephen; McCann, Maureen C; Ming, Ray; Peterson, Daniel G; Mehboob-ur-Rahman; Ware, Doreen; Westhoff, Peter; Mayer, Klaus F X; Messing, Joachim; Rokhsar, Daniel S

2009-01-29

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Bacterial abundance and diversity in pond water supplied with different feeds

NASA Astrophysics Data System (ADS)

Qin, Ya; Hou, Jie; Deng, Ming; Liu, Quansheng; Wu, Chongwei; Ji, Yingjie; He, Xugang

2016-10-01

The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.

The interplay between the effectiveness of the grass-endophyte mutualism and the genetic variability of the host plant

PubMed Central

Gundel, Pedro E; Omacini, Marina; Sadras, Victor O; Ghersa, Claudio M

2010-01-01

Neotyphodium endophytic fungi, the asexual state of Epichloë species, protect cool-season grasses against stresses. The outcomes of Neotyphodium-grass symbioses are agronomically relevant as they may affect the productivity of pastures. It has been suggested that the mutualism is characteristic of agronomic grasses and that differential rates of gene flow between both partners’ populations are expected to disrupt the specificity of the association and, thus, the mutualism in wild grasses. We propose that compatibility is necessary but not sufficient to explain the outcomes of Neotyphodium-grass symbiosis, and advance a model that links genetic compatibility, mutualism effectiveness, and endophyte transmission efficiency. For endophytes that reproduce clonally and depend on allogamous hosts for reproduction and dissemination, we propose that this symbiosis works as an integrated entity where gene flow promotes its fitness and evolution. Compatibility between the host plant and the fungal endophyte would be high in genetically close parents; however, mutualism effectiveness and transmission efficiency would be low in fitness depressed host plants. Increasing the genetic distance of mating parents would increase mutualism effectiveness and transmission efficiency. This tendency would be broken when the genetic distance between parents is high (out-breeding depression). Our model allows for testable hypotheses that would contribute to understand the coevolutionary origin and future of the endophyte-grass mutualism. PMID:25567945

Differentiation of plant age in grasses using remote sensing

NASA Astrophysics Data System (ADS)

Knox, Nichola M.; Skidmore, Andrew K.; van der Werff, Harald M. A.; Groen, Thomas A.; de Boer, Willem F.; Prins, Herbert H. T.; Kohi, Edward; Peel, Mike

2013-10-01

Phenological or plant age classification across a landscape allows for examination of micro-topographical effects on plant growth, improvement in the accuracy of species discrimination, and will improve our understanding of the spatial variation in plant growth. In this paper six vegetation indices used in phenological studies (including the newly proposed PhIX index) were analysed for their ability to statistically differentiate grasses of different ages in the sequence of their development. Spectra of grasses of different ages were collected from a greenhouse study. These were used to determine if NDVI, NDWI, CAI, EVI, EVI2 and the newly proposed PhIX index could sequentially discriminate grasses of different ages, and subsequently classify grasses into their respective age category. The PhIX index was defined as: (AVNIRn+log(ASWIR2n))/(AVNIRn-log(ASWIR2n)), where AVNIRn and ASWIR2n are the respective normalised areas under the continuum removed reflectance curve within the VNIR (500-800 nm) and SWIR2 (2000-2210 nm) regions. The PhIX index was found to produce the highest phenological classification accuracy (Overall Accuracy: 79%, and Kappa Accuracy: 75%) and similar to the NDVI, EVI and EVI2 indices it statistically sequentially separates out the developmental age classes. Discrimination between seedling and dormant age classes and the adult and flowering classes was problematic for most of the tested indices. Combining information from the visible near infrared (VNIR) and shortwave infrared region (SWIR) region into a single phenological index captures the phenological changes associated with plant pigments and the ligno-cellulose absorption feature, providing a robust method to discriminate the age classes of grasses. This work provides a valuable contribution into mapping spatial variation and monitoring plant growth across savanna and grassland ecosystems.

A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)

PubMed Central

López-Alvarez, Diana; López-Herranz, Maria Luisa; Betekhtin, Alexander; Catalán, Pilar

2012-01-01

Background Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). Methodology/Principal Findings We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. Conclusion/Significance Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents. PMID:23240000

Diversity and population structure of northern switchgrass as revealed though exome capture sequencing

USDA-ARS?s Scientific Manuscript database

Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a so...

Complete genome sequence of the Rathayibacter toxicus phage NCPPB3778

USDA-ARS?s Scientific Manuscript database

Rathayibacter toxicus is a select agent plant pathogen largely due to the fact that it generates a toxin (tunicamycin) in forage grasses that causes death in livestock, a disease called annual ryegrass toxicity (ARGT). The majority of previous literature suggested that toxin production and ARGT was ...

Comparative study of switchgrass cultivars using RNA sequencing technology

USDA-ARS?s Scientific Manuscript database

Switchgrass (Panicum virgatum L.) is a C4 perennial grass, identified as a promising bioenergy crop. Switchgrass exists in two ecotypes, upland and lowland, which are heterotic, or genetically complementary to each other. The objectives of this study are to assess the potential of SNP markers as a b...

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

PubMed Central

Jin, Xiaoli; Ren, Jing; Nevo, Eviatar; Yin, Xuegui; Sun, Dongfa; Peng, Junhua

2017-01-01

NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses. PMID:28713414

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores.

PubMed

Kartzinel, Tyler R; Chen, Patricia A; Coverdale, Tyler C; Erickson, David L; Kress, W John; Kuzmina, Maria L; Rubenstein, Daniel I; Wang, Wei; Pringle, Robert M

2015-06-30

Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species-even pairs of grazers matched in size, digestive physiology, and location-and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized.

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

PubMed Central

Kartzinel, Tyler R.; Chen, Patricia A.; Coverdale, Tyler C.; Erickson, David L.; Kress, W. John; Kuzmina, Maria L.; Rubenstein, Daniel I.; Wang, Wei; Pringle, Robert M.

2015-01-01

Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species—even pairs of grazers matched in size, digestive physiology, and location—and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized. PMID:26034267

Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn.

PubMed

Teisher, J K; McKain, M R; Schaal, B A; Kellogg, E A

2017-11-10

Subfamily Arundinoideae represents one of the last unsolved taxonomic mysteries in the grass family (Poaceae) due to the narrow and remote distributions of many of its 19 morphologically and ecologically heterogeneous genera. Resolving the phylogenetic relationships of these genera could have substantial implications for understanding character evolution in the grasses, for example the twisted geniculate awn - a hygroscopic awn that has been shown to be important in seed germination for some grass species. In this study, the phylogenetic positions of most arundinoid genera were determined using DNA from herbarium specimens, and their placement affects interpretation of this ecologically important trait. A phylogenetic analysis was conducted on a matrix of full-plastome sequences from 123 species in 107 genera representing all grass subfamilies, with 15 of the 19 genera in subfamily Arundinoideae. Parsimony and maximum likelihood mapping approaches were used to estimate ancestral states for presence of a geniculate lemma awn with a twisted column across Poaceae. Lastly, anatomical characters were examined for former arundinoid taxa using light microscopy and scanning electron microscopy. Four genera traditionally included in Arundinoideae fell outside the subfamily in the plastome phylogeny, with the remaining 11 genera forming Arundinoideae sensu stricto . The twisted geniculate awn has originated independently at least five times in the PACMAD grasses, in the subfamilies Panicoideae, Danthonioideae/Chloridoideae and Arundinoideae. Morphological and anatomical characters support the new positions of the misplaced arundinoid genera in the phylogeny, but also highlight convergent and parallel evolution in the grasses. In placing the majority of arundinoid genera in a phylogenetic framework, our study answers one of the last remaining big questions in grass taxonomy while highlighting examples of convergent evolution in an ecologically important trait, the hygroscopic, twisted geniculate awn. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

PubMed Central

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz-Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

2017-01-01

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX). PMID:28448065

Towards a High Temporal Frequency Grass Canopy Thermal IR Model for Background Signatures

NASA Technical Reports Server (NTRS)

Ballard, Jerrell R., Jr.; Smith, James A.; Koenig, George G.

2004-01-01

In this paper, we present our first results towards understanding high temporal frequency thermal infrared response from a dense plant canopy and compare the application of our model, driven both by slowly varying, time-averaged meteorological conditions and by high frequency measurements of local and within canopy profiles of relative humidity and wind speed, to high frequency thermal infrared observations. Previously, we have employed three-dimensional ray tracing to compute the intercepted and scattered radiation fluxes and for final scene rendering. For the turbulent fluxes, we employed simple resistance models for latent and sensible heat with one-dimensional profiles of relative humidity and wind speed. Our modeling approach has proven successful in capturing the directional and diurnal variation in background thermal infrared signatures. We hypothesize that at these scales, where the model is typically driven by time-averaged, local meteorological conditions, the primary source of thermal variance arises from the spatial distribution of sunlit and shaded foliage elements within the canopy and the associated radiative interactions. In recent experiments, we have begun to focus on the high temporal frequency response of plant canopies in the thermal infrared at 1 second to 5 minute intervals. At these scales, we hypothesize turbulent mixing plays a more dominant role. Our results indicate that in the high frequency domain, the vertical profile of temperature change is tightly coupled to the within canopy wind speed In the results reported here, the canopy cools from the top down with increased wind velocities and heats from the bottom up at low wind velocities. .

The dot{M}-M_* relation of pre-main-sequence stars: a consequence of X-ray driven disc evolution

NASA Astrophysics Data System (ADS)

Ercolano, B.; Mayr, D.; Owen, J. E.; Rosotti, G.; Manara, C. F.

2014-03-01

We analyse current measurements of accretion rates on to pre-main-sequence stars as a function of stellar mass, and conclude that the steep dependence of accretion rates on stellar mass is real and not driven by selection/detection threshold, as has been previously feared. These conclusions are reached by means of statistical tests including a survival analysis which can account for upper limits. The power-law slope of the dot{M}-M_* relation is found to be in the range of 1.6-1.9 for young stars with masses lower than 1 M⊙. The measured slopes and distributions can be easily reproduced by means of a simple disc model which includes viscous accretion and X-ray photoevaporation. We conclude that the dot{M}-M_* relation in pre-main-sequence stars bears the signature of disc dispersal by X-ray photoevaporation, suggesting that the relation is a straightforward consequence of disc physics rather than an imprint of initial conditions.

Regression Model for MODTRAN with Applications to Inactivation of Microbes Suspended in the Atmosphere by Solar Ultraviolet Radiation

DTIC Science & Technology

2012-05-01

mixed vegetation): 0.007 (0.017) For materials tested, • The albedo levels of old grass, dead grass, burnt grass, and maple leaf at 300 nm were...as 0.016-0.017 over vegetation, 0.04-0.05 over bare fertile soil, and 0.07-0.10 over concrete (autobahn, Germany). The albedo over dry bright sand

Competition between trees and grasses for both soil water and mineral nitrogen in dry savannas.

PubMed

Donzelli, D; De Michele, C; Scholes, R J

2013-09-07

The co-existence of trees and grasses in savannas in general can be the result of processes involving competition for resources (e.g. water and nutrients) or differential response to disturbances such as fire, animals and human activities; or a combination of both broad mechanisms. In moist savannas, the tree-grass coexistence is mainly attributed to of disturbances, while in dry savannas, limiting resources are considered the principal mechanism of co-existence. Virtually all theoretical explorations of tree-grass dynamics in dry savannas consider only competition for soil water. Here we investigate whether coexistence could result from a balanced competition for two resources, namely soil water and mineral nitrogen. We introduce a simple dynamical resource-competition model for trees and grasses. We consider two alternative hypotheses: (1) trees are the superior competitors for nitrogen while grasses are superior competitors for water, and (2) vice-versa. We study the model properties under the two hypotheses and test each hypothesis against data from 132 dry savannas in Africa using Kendall's test of independence. We find that Hypothesis 1 gets much more support than Hypothesis 2, and more support than the null hypothesis that neither is operative. We further consider gradients of rainfall and nitrogen availability and find that the Hypothesis 1 model reproduces the observed patterns in nature. We do not consider our results to definitively show that tree-grass coexistence in dry savannas is due to balanced competition for water and nitrogen, but show that this mechanism is a possibility, which cannot be a priori excluded and should thus be considered along with the more traditional explanations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mass loss from pre-main-sequence accretion disks. I - The accelerating wind of FU Orionis

NASA Technical Reports Server (NTRS)

Calvet, Nuria; Hartmann, Lee; Kenyon, Scott J.

1993-01-01

We present evidence that the wind of the pre-main-sequence object FU Orionis arises from the surface of the luminous accretion disk. A disk wind model calculated assuming radiative equilibrium explains the differential behavior of the observed asymmetric absorption-line profiles. The model predicts that strong lines should be asymmetric and blueshifted, while weak lines should be symmetric and double-peaked due to disk rotation, in agreement with observations. We propose that many blueshifted 'shell' absorption features are not produced in a true shell of material, but rather form in a differentially expanding wind that is rapidly rotating. The inference of rapid rotation supports the proposal that pre-main-sequence disk winds are rotationally driven.

Does vapor pressure deficit drive the seasonality of δ 13 C of the net land-atmosphere CO 2 exchange across the United States?: The Influence of VPD on δ 13 C of NEE

DOE PAGES

Raczka, B.; Biraud, S. C.; Ehleringer, J. R.; ...

2017-08-10

The seasonal pattern of the carbon isotope content (δ 13C) of atmospheric CO 2 depends on local and nonlocal land-atmosphere exchange and atmospheric transport. Previous studies suggested that the δ13C of the net land-atmosphere CO 2 flux (δsource) varies seasonally as stomatal conductance of plants responds to vapor pressure deficit of air (VPD). We studied the variation of δ source at seven sites across the United States representing forests, grasslands, and an urban center. Using a two-part mixing model, we calculated the seasonal δsource for each site after removing background influence and, when possible, removing δ 13C variation of nonlocalmore » sources. Compared to previous analyses, we found a reduced seasonal (March–September) variation in δ source at the forest sites (0.5‰variation). We did not find a consistent seasonal relationship between VPD and δ source across forest (or other) sites, providing evidence that stomatal response to VPD was not the cause of the global, coherent seasonal pattern in δsource. In contrast to the forest sites, grassland and urban sites had a larger seasonal variation in δ source (5‰) dominated by seasonal transitions in C 3/C 4 grass productivity and in fossil fuel emissions, respectively. Our findings were sensitive to the location used to account for atmospheric background variation within the mixing model method that determined δsource. Special consideration should be given to background location depending on whether the intent is to understand site level dynamics or regional scale impacts of land-atmosphere exchange. The seasonal amplitude in δ 13C of land-atmosphere CO 2 exchange (δ source) varied across land cover types and was not driven by seasonal changes in vapor pressure deficit. The largest seasonal amplitudes of δsource were at grassland and urban sites, driven by changes in C 3/C 4 grass productivity and fossil fuel emissions, respectively. Mixing model approaches may incorrectly calculate δs ource when background atmospheric observations are remote and/or prone to anthropogenic influence.« less

Does vapor pressure deficit drive the seasonality of δ 13 C of the net land-atmosphere CO 2 exchange across the United States?: The Influence of VPD on δ 13 C of NEE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raczka, B.; Biraud, S. C.; Ehleringer, J. R.

The seasonal pattern of the carbon isotope content (δ 13C) of atmospheric CO 2 depends on local and nonlocal land-atmosphere exchange and atmospheric transport. Previous studies suggested that the δ13C of the net land-atmosphere CO 2 flux (δsource) varies seasonally as stomatal conductance of plants responds to vapor pressure deficit of air (VPD). We studied the variation of δ source at seven sites across the United States representing forests, grasslands, and an urban center. Using a two-part mixing model, we calculated the seasonal δsource for each site after removing background influence and, when possible, removing δ 13C variation of nonlocalmore » sources. Compared to previous analyses, we found a reduced seasonal (March–September) variation in δ source at the forest sites (0.5‰variation). We did not find a consistent seasonal relationship between VPD and δ source across forest (or other) sites, providing evidence that stomatal response to VPD was not the cause of the global, coherent seasonal pattern in δsource. In contrast to the forest sites, grassland and urban sites had a larger seasonal variation in δ source (5‰) dominated by seasonal transitions in C 3/C 4 grass productivity and in fossil fuel emissions, respectively. Our findings were sensitive to the location used to account for atmospheric background variation within the mixing model method that determined δsource. Special consideration should be given to background location depending on whether the intent is to understand site level dynamics or regional scale impacts of land-atmosphere exchange. The seasonal amplitude in δ 13C of land-atmosphere CO 2 exchange (δ source) varied across land cover types and was not driven by seasonal changes in vapor pressure deficit. The largest seasonal amplitudes of δsource were at grassland and urban sites, driven by changes in C 3/C 4 grass productivity and fossil fuel emissions, respectively. Mixing model approaches may incorrectly calculate δs ource when background atmospheric observations are remote and/or prone to anthropogenic influence.« less

QTLs for resistance to the leaf rust Puccinia brachypodii in the model grass Brachypodium distachyon

USDA-ARS?s Scientific Manuscript database

The wild grass Brachypodium distachyon is a useful new model for temperate cereals, but its potential to study the interactions with pathogens remains underexploited. Leaf rust is one of the major fungal diseases affecting cereals, and recently the host status of Brachypodium to Puccinia rusts was i...

Green leaf volatiles, fire and nonanoic acid activate MAPkinases in the model grass species Lolium temulentum

USDA-ARS?s Scientific Manuscript database

Forage and turf related grasses are utilized in diverse environments where they are routinely subjected to herbicides and exposed to fire and volatiles after cutting, however very little is known concerning the perception or molecular responses to these different stresses or compounds. In the model ...

Elevation Control on Vegetation Organization in a Semiarid Ecosystem in Central New Mexico

NASA Astrophysics Data System (ADS)

Nudurupati, S. S.; Istanbulluoglu, E.; Adams, J. M.; Hobley, D. E. J.; Gasparini, N. M.; Tucker, G. E.; Hutton, E. W. H.

2015-12-01

Many semiarid and desert ecosystems are characterized by patchy and dynamic vegetation. Topography plays a commanding role on vegetation patterns. It is observed that plant biomes and biodiversity vary systematically with slope and aspect, from shrublands in low desert elevations, to mixed grass/shrublands in mid elevations, and forests at high elevations. In this study, we investigate the role of elevation dependent climatology on vegetation organization in a semiarid New Mexico catchment where elevation and hillslope aspect play a defining role on plant types. An ecohydrologic cellular automaton model developed within Landlab (component based modeling framework) is used. The model couples local vegetation dynamics (that simulate biomass production based on local soil moisture and potential evapotranspiration) and plant establishment and mortality based on competition for resources and space. This model is driven by elevation dependent rainfall pulses and solar radiation. The domain is initialized with randomly assigned plant types and the model parameters that couple plant response with soil moisture are systematically changed. Climate perturbation experiments are conducted to examine spatial vegetation organization and associated timescales. Model results reproduce elevation and aspect controls on observed vegetation patterns indicating that this model captures necessary and sufficient conditions that explain these observed ecohydrological patterns.

Molecular fingerprinting of complex grass allergoids: size assessments reveal new insights in epitope repertoires and functional capacities.

PubMed

Starchenka, S; Bell, A J; Mwange, J; Skinner, M A; Heath, M D

2017-01-01

Subcutaneous allergen immunotherapy (SCIT) is a well-documented treatment for allergic disease which involves injections of native allergen or modified (allergoid) extracts. The use of allergoid vaccines is a growing sector of the allergy immunotherapy market, associated with shorter-course therapy. The aim of this study was the structural and immunological characterisation of group 1 (Lol p 1) IgG-binding epitopes within a complex mix grass allergoid formulation containing rye grass. HP-SEC was used to resolve a mix grass allergoid preparation of high molecular weight into several distinct fractions with defined molecular weight and elution profiles. Allergen verification of the HP-SEC allergoid fractions was confirmed by mass spectrometry analysis. IgE and IgG immunoreactivity of the allergoid preparations was explored and Lol p 1 specific IgG-binding epitopes mapped by SPOT synthesis technology (PepSpot™) with structural analysis based on a Lol p 1 homology model. Grass specific IgE reactivity of the mix grass modified extract (allergoid) was diminished in comparison with the mix grass native extract. A difference in IgG profiles was observed between an intact mix grass allergoid preparation and HP-SEC allergoid fractions, which indicated enhancement of accessible reactive IgG epitopes across size distribution profiles of the mix grass allergoid formulation. Detailed analysis of the epitope specificity showed retention of six Lol p 1 IgG-binding epitopes in the mix grass modified extract. The structural and immunological changes which take place following the grass allergen modification process was further unravelled revealing distinct IgG immunological profiles. All epitopes were mapped on the solvent exposed area of Lol p 1 homology model accessible for IgG binding. One of the epitopes was identified as an 'immunodominant' Lol p 1 IgG-binding epitope (62-IFKDGRGCGSCFEIK-76) and classified as a novel epitope. The results from this study support the concept that modification allows shorter-course therapy options as a result of providing an IgG epitope repertoire important for efficacy. Additionally, the work paves the way to help further develop methods for standardising allergoid platforms.

Improving our understanding of environmental controls on the distribution of C3 and C4 grasses.

PubMed

Pau, Stephanie; Edwards, Erika J; Still, Christopher J

2013-01-01

A number of studies have demonstrated the ecological sorting of C3 and C4 grasses along temperature and moisture gradients. However, previous studies of C3 and C4 grass biogeography have often inadvertently compared species in different and relatively unrelated lineages, which are associated with different environmental settings and distinct adaptive traits. Such confounded comparisons of C3 and C4 grasses may bias our understanding of ecological sorting imposed strictly by photosynthetic pathway. Here, we used MaxEnt species distribution modeling in combination with satellite data to understand the functional diversity of C3 and C4 grasses by comparing both large clades and closely related sister taxa. Similar to previous work, we found that C4 grasses showed a preference for regions with higher temperatures and lower precipitation compared with grasses using the C3 pathway. However, air temperature differences were smaller (2 °C vs. 4 °C) and precipitation and % tree cover differences were larger (1783 mm vs. 755 mm, 21.3% vs. 7.7%, respectively) when comparing C3 and C4 grasses within the same clade vs. comparing all C4 and all C3 grasses (i.e., ignoring phylogenetic structure). These results were due to important differences in the environmental preferences of C3 BEP and PACMAD clades (the two main grass clades). Winter precipitation was found to be more important for understanding the distribution and environmental niche of C3 PACMADs in comparison with both C3 BEPs and C4 taxa, for which temperature was much more important. Results comparing closely related C3 -C4 sister taxa supported the patterns derived from our modeling of the larger clade groupings. Our findings, which are novel in comparing the distribution and niches of clades, demonstrate that the evolutionary history of taxa is important for understanding the functional diversity of C3 and C4 grasses, and should have implications for how grasslands will respond to global change. © 2012 Blackwell Publishing Ltd.

Validation of behave fire behavior predictions in oak savannas

USGS Publications Warehouse

Grabner, Keith W.; Dwyer, John; Cutter, Bruce E.

1997-01-01

Prescribed fire is a valuable tool in the restoration and management of oak savannas. BEHAVE, a fire behavior prediction system developed by the United States Forest Service, can be a useful tool when managing oak savannas with prescribed fire. BEHAVE predictions of fire rate-of-spread and flame length were validated using four standardized fuel models: Fuel Model 1 (short grass), Fuel Model 2 (timber and grass), Fuel Model 3 (tall grass), and Fuel Model 9 (hardwood litter). Also, a customized oak savanna fuel model (COSFM) was created and validated. Results indicate that standardized fuel model 2 and the COSFM reliably estimate mean rate-of-spread (MROS). The COSFM did not appreciably reduce MROS variation when compared to fuel model 2. Fuel models 1, 3, and 9 did not reliably predict MROS. Neither the standardized fuel models nor the COSFM adequately predicted flame lengths. We concluded that standardized fuel model 2 should be used with BEHAVE when predicting fire rates-of-spread in established oak savannas.

HMM-based lexicon-driven and lexicon-free word recognition for online handwritten Indic scripts.

PubMed

Bharath, A; Madhvanath, Sriganesh

2012-04-01

Research for recognizing online handwritten words in Indic scripts is at its early stages when compared to Latin and Oriental scripts. In this paper, we address this problem specifically for two major Indic scripts--Devanagari and Tamil. In contrast to previous approaches, the techniques we propose are largely data driven and script independent. We propose two different techniques for word recognition based on Hidden Markov Models (HMM): lexicon driven and lexicon free. The lexicon-driven technique models each word in the lexicon as a sequence of symbol HMMs according to a standard symbol writing order derived from the phonetic representation. The lexicon-free technique uses a novel Bag-of-Symbols representation of the handwritten word that is independent of symbol order and allows rapid pruning of the lexicon. On handwritten Devanagari word samples featuring both standard and nonstandard symbol writing orders, a combination of lexicon-driven and lexicon-free recognizers significantly outperforms either of them used in isolation. In contrast, most Tamil word samples feature the standard symbol order, and the lexicon-driven recognizer outperforms the lexicon free one as well as their combination. The best recognition accuracies obtained for 20,000 word lexicons are 87.13 percent for Devanagari when the two recognizers are combined, and 91.8 percent for Tamil using the lexicon-driven technique.

Insects traversing grass-like vertical compliant beams

NASA Astrophysics Data System (ADS)

Li, Chen; Fearing, Ronald; Full, Robert

2014-03-01

Small running animals encounter many challenging terrains. These terrains can be filled with 3D, multi-component obstacles. Here, we study cockroaches (Blaberus discoidalis) moving through grass-like vertical compliant beams during escape. We created an apparatus to control and vary geometric parameters and mechanical properties of model grass including height, width, thickness, lateral and fore-aft spacings, angle, number of layers, stiffness, and damping. We observed a suite of novel locomotor behaviors not previously described on simpler 2D ground. When model grass height was >2 × body length and lateral spacing was <0.5 × body width, the animal primarily (probability P = 50%) rolled its body onto its side to rapidly (time t = 2.1 s) maneuver through the gaps between model grass. We developed a simple energy minimization model, and found that body roll reduces the energy barriers that the animal must overcome during traversal. We hypothesized that the animal's ellipsoidal body shape facilitated traversal. To test our hypothesis, we modified body shape by adding either a rectangular or an oval plate onto its dorsal surface, and found that P dropped by an order of magnitude and t more than doubled. Upon removal of either plate, both P and t recovered. Locomotor kinematics and geometry effectively coupled to terrain properties enables negotiation of 3D, multi-component obstacles, and provides inspiration for small robots to navigate such terrain with minimal sensing and control.

Modeling the integration of bacterial rRNA fragments into the human cancer genome.

PubMed

Sieber, Karsten B; Gajer, Pawel; Dunning Hotopp, Julie C

2016-03-21

Cancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. We previously identified in silico evidence of DNA fragments from a Pseudomonas-like bacteria integrating into the 5'-UTR of four proto-oncogenes in stomach cancer sequencing data. The functional and biological consequences of these bacterial DNA integrations remain unknown. Modeling of these integrations suggests that the previously identified sequences cover most of the sequence flanking the junction between the bacterial and human DNA. Further examination of these reads reveals that these integrations are rich in guanine nucleotides and the integrated bacterial DNA may have complex transcript secondary structures. The models presented here lay the foundation for future experiments to test if bacterial DNA integrations alter the transcription of the human genes.

Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E. Desv.

PubMed

John, Ulrik P; Polotnianka, Renatam M; Sivakumaran, Kailayapillai A; Chew, Orinda; Mackin, Leanne; Kuiper, Micheal J; Talbot, Jonathan P; Nugent, Gregory D; Mautord, Julie; Schrauf, Gustavo E; Spangenberg, German C

2009-04-01

Antarctic hair grass (Deschampsia antarctica E. Desv.), the only grass indigenous to Antarctica, has well-developed freezing tolerance, strongly induced by cold acclimation. Here, we show that in response to low temperatures, D. antarctica expresses potent recrystallization inhibition (RI) activity that, inhibits the growth of small ice crystals into potentially damaging large ones, is proteinaceous and localized to the apoplasm. A gene family from D. antarctica encoding putative homologs of an ice recrystallization inhibition protein (IRIP) has been isolated and characterized. IRIPs are apoplastically targeted proteins with two potential ice-binding motifs: 1-9 leucine-rich repeats (LRRs) and c. 16 'IRIP' repeats. IRIP genes appear to be confined to the grass subfamily Pooideae and their products, exhibit sequence similarity to phytosulphokine receptors and are predicted to adopt conformations with two ice-binding surfaces. D. antarctica IRIP (DaIRIP) transcript levels are greatly enhanced in leaf tissue following cold acclimation. Transgenic Arabidopsis thaliana expressing a DaIRIP has novel RI activity, and purified DaIRIP, when added back to extracts of leaves from non-acclimated D. antarctica, can reconstitute the activity found in acclimated plants. We propose that IRIP-mediated RI activity may contribute to the cryotolerance of D. antarctica, and thus to its unique ability to have colonized Antarctica.

Data driven CAN node reliability assessment for manufacturing system

NASA Astrophysics Data System (ADS)

Zhang, Leiming; Yuan, Yong; Lei, Yong

2017-01-01

The reliability of the Controller Area Network(CAN) is critical to the performance and safety of the system. However, direct bus-off time assessment tools are lacking in practice due to inaccessibility of the node information and the complexity of the node interactions upon errors. In order to measure the mean time to bus-off(MTTB) of all the nodes, a novel data driven node bus-off time assessment method for CAN network is proposed by directly using network error information. First, the corresponding network error event sequence for each node is constructed using multiple-layer network error information. Then, the generalized zero inflated Poisson process(GZIP) model is established for each node based on the error event sequence. Finally, the stochastic model is constructed to predict the MTTB of the node. The accelerated case studies with different error injection rates are conducted on a laboratory network to demonstrate the proposed method, where the network errors are generated by a computer controlled error injection system. Experiment results show that the MTTB of nodes predicted by the proposed method agree well with observations in the case studies. The proposed data driven node time to bus-off assessment method for CAN networks can successfully predict the MTTB of nodes by directly using network error event data.

Molecular cloning and functional characterization of peptidoglycan recognition protein 6 in grass carp Ctenopharyngodon idella.

PubMed

Li, Jun Hua; Yu, Zhang Long; Xue, Na Na; Zou, Peng Fei; Hu, Jing Yu; Nie, P; Chang, Ming Xian

2014-02-01

Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules of innate immunity. In this study, a long-form PGRP, designated as gcPGRP6, was identified from grass carp Ctenopharyngodon idella. The deduced amino acid sequence of gcPGRP6 is composed of 464 residues with a conserved PGRP domain at the C-terminus. The gcPGRP6 gene consists of four exons and three introns, spacing approximately 2.7 kb of genomic sequence. Phylogenetic analysis demonstrated that gcPGRP6 is clustered closely with zebrafish PGLYRP6, and formed a long-type PGRP subfamily together with PGLYRP2 members identified in teleosts and mammals. Real-time PCR and Western blotting analyses revealed that gcPGRP6 is constitutively expressed in organs/tissues examined, and its expression was significantly induced in liver and intestine of grass carp in response to PGN stimulation and in CIK cells treated with lipoteichoic acid (LTA), polyinosinic polycytidylic acid (Poly I:C) and peptidoglycan (PGN). Immunofluorescence microscopy and Western blotting analyses revealed that gcPGRP6 is effectively secreted to the exterior of CIK cells. The over-expression of gcPGRP6 in CIK cells leads to the activation of NF-κB and the inhibition of intracellular bacterial growth. Moreover, cell lysates from CIK cells transfected with pTurbo-gcPGRP6-GFP plasmid display the binding activity towards Lys-type PGN from Staphylococcus aureus and DAP-type PGN from Bacillus subtilis. Furthermore, proinflammatory cytokine IL-2 and intracellular PGN receptor NOD2 had a significantly increased expression in CIK cells overexpressed with gcPGRP6. It is demonstrated that the PGRP6 in grass carp has a role in binding PGN, in inhibiting the growth of intracellular bacteria, and in activating NF-κB, as well as in regulating innate immune genes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sequence-Mandated, Distinct Assembly of Giant Molecules

DOE PAGES

Zhang, Wei; Lu, Xinlin; Mao, Jialin; ...

2017-10-24

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collectivemore » hydrogen bonding and the sequence-mandated topology of the molecules. Lastly, these results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.« less

Sequence-Mandated, Distinct Assembly of Giant Molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Wei; Lu, Xinlin; Mao, Jialin

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collectivemore » hydrogen bonding and the sequence-mandated topology of the molecules. Lastly, these results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.« less

Diversity among elephant grass genotypes using Bayesian multi-trait model.

PubMed

Rossi, D A; Daher, R F; Barbé, T C; Lima, R S N; Costa, A F; Ribeiro, L P; Teodoro, P E; Bhering, L L

2017-09-27

Elephant grass is a perennial tropical grass with great potential for energy generation from biomass. The objective of this study was to estimate the genetic diversity among elephant grass accessions based on morpho-agronomic and biomass quality traits and to identify promising genotypes for obtaining hybrids with high energetic biomass production capacity. The experiment was installed at experimental area of the State Agricultural College Antônio Sarlo, in Campos dos Goytacazes. Fifty-two elephant grass genotypes were evaluated in a randomized block design with two replicates. Components of variance and the genotypic means were obtained using a Bayesian multi-trait model. We considered 350,000 iterations in the Gibbs sampler algorithm for each parameter adopted, with a warm-up period (burn-in) of 50,000 Iterations. For obtaining an uncorrelated sample, we considered five iterations (thinning) as a spacing between sampled points, which resulted in a final sample size 60,000. Subsequently, the Mahalanobis distance between each pair of genotypes was estimated. Estimates of genotypic variance indicated a favorable condition for gains in all traits. Elephant grass accessions presented greater variability for biomass quality traits, for which three groups were formed, while for the agronomic traits, two groups were formed. Crosses between Mercker Pinda México x Mercker 86-México, Mercker Pinda México x Turrialba, and Mercker 86-México x Taiwan A-25 can be carried out for obtaining elephant grass hybrids for energy purposes.

Basket Studies: Redefining Clinical Trials in the Era of Genome-Driven Oncology.

PubMed

Tao, Jessica J; Schram, Alison M; Hyman, David M

2018-01-29

Understanding a tumor's detailed molecular profile has become increasingly necessary to deliver the standard of care for patients with advanced cancer. Innovations in both tumor genomic sequencing technology and the development of drugs that target molecular alterations have fueled recent gains in genome-driven oncology care. "Basket studies," or histology-agnostic clinical trials in genomically selected patients, represent one important research tool to continue making progress in this field. We review key aspects of genome-driven oncology care, including the purpose and utility of basket studies, biostatistical considerations in trial design, genomic knowledgebase development, and patient matching and enrollment models, which are critical for translating our genomic knowledge into clinically meaningful outcomes.

Long-term Effects of Shrub Encroachment and Grazing on Soil Microbial Composition and Function

NASA Astrophysics Data System (ADS)

Gallery, R. E.; O'Shea, C.; Kwiecien, A.; Predick, K.; Archer, S. R.

2014-12-01

Drylands account for ca. 35% of terrestrial net primary productivity and thus play a significant role in global water and biogeochemical cycles. Replacement of grasses by shrubs has been widespread in these systems and has altered rates of erosion and native plant biodiversity and productivity. The net effect of these changes on biogeochemical cycling is not well understood. Projected warmer and drier conditions may further alter the function and stability of these ecosystems and soil resources through direct effects on soil microbiota and plant-microbe interactions. We quantified microbial community responses to long-term livestock grazing and shrub encroachment in a Sonoran Desert grassland. We sought to characterize tipping points where biotic controls over ecosystem processes shift from being 'grass-driven' to 'shrub-driven.' We asked: How do livestock grazing (the predominant land use in dryland ecosystems) and shrub invasion (a predominant land cover change) interact to influence microbial biomass and the relative abundance of bacteria, archaea, and fungi and their extracellular enzyme activities? Surface soil from bare-ground patches, native and invasive grass rhizospheres, and bole and canopy dripline locations in patches of mature mesquite trees in long-term grazed and long-term (70+ y) protected pastures were collected and analyzed for microbial community composition, biomass, potential exoenzyme activities, and a suite of biogeochemical characteristics. We found no differences in microbial communities or the soils associated with native vs. exotic grasses. Overall, mesquite bole patches differed from other patches in all soil characteristics except potential enzyme activity: soil temperature was significantly lower, and total carbon (C) and soil moisture were significantly higher. Potential activities were lowest for bare ground and highest at shrub dripline patches for all seven exoenzymes tested. Mean potential activities for C and phosphorous (P) hydrolyzing enzymes in long-term protected pastures (C: 21.4 ug activity g-1 h-1 ± 2.3; P: 29.8 ug activity g-1 h-1 ± 3.5) were significantly higher than those in grazed pastures (C: 16.6 ug activity g-1 h-1 ± 2.1; P: 15.8 ug activity g-1 h-1 ± 2.5), suggesting long-term effects of past land use on current soil microbial populations.

C4 expansion in the central Inner Mongolia during the latest Miocene and early Pliocene

NASA Astrophysics Data System (ADS)

Zhang, Chunfu; Wang, Yang; Deng, Tao; Wang, Xiaoming; Biasatti, Dana; Xu, Yingfeng; Li, Qiang

2009-10-01

The emergence of C4 photosynthesis in plants as a significant component of terrestrial ecosystems is thought to be an adaptive response to changes in atmospheric CO 2 concentration and/or climate during Neogene times and has had a profound effect on the global terrestrial biosphere. Although expansion of C4 grasses in the latest Miocene and Pliocene has been widely documented around the world, the spatial and temporal variations in the C4 expansion are still not well understood and its driving mechanisms remain a contentious issue. Here we present the results of carbon and oxygen isotope analyses of fossil and modern mammalian tooth enamel samples from the central Inner Mongolia. Our samples represent a diverse group of herbivorous mammals including deer, elephants, rhinos, horses and giraffes, ranging in age from the late Oligocene to modern. The δ13C values of 91 tooth enamel samples of early late-Miocene age or older, with the exception of two 13 Ma rhino samples (- 7.8 and - 7.6‰) and one 8.5 Ma suspected rhino sample (- 7.6‰), were all less than - 8.0‰ (VPDB), indicating that there were no C4 grasses present in their diets and thus probably few or no C4 grasses in the ecosystems of the central Inner Mongolia prior to ~ 8 Ma. However, 12 out of 26 tooth enamel samples of younger ages (~ 7.5 Ma to ~ 3.9 Ma) have δ13C values higher than - 8.0‰ (up to - 2.4‰), indicating that herbivores in the area had variable diets ranging from pure C3 to mixed C3-C4 vegetation during that time interval. The presence of C4 grasses in herbivores' diets (up to ~ 76% C4) suggests that C4 grasses were a significant component of the local ecosystems in the latest Miocene and early Pliocene, consistent with the hypothesis of a global factor as the driving mechanism of the late Miocene C4 expansion. Today, C3 grasses dominate grasslands in the central Inner Mongolia area. The retreat of C4 grasses from this area after the early Pliocene may have been driven by regional climate change associated with tectonic processes in central Asia as well as global climate change.

Dynamic modeling of the cesium, strontium, and ruthenium transfer to grass and vegetables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renaud, P.; Real, J.; Maubert, H.

1999-05-01

From 1988 to 1993, the Nuclear Safety and Protection Institute (Institut de Protection et de Surete Nucleaire -- IPSN) conducted experimental programs focused on transfers to vegetation following accidental localized deposits of radioactive aerosols. In relation to vegetable crops (fruit, leaves, and root vegetables) and meadow grass these experiments have enabled a determination of the factors involved in the transfer of cesium, strontium, and ruthenium at successive harvests, or cuttings, in respect of various time lags after contamination. The dynamic modeling given by these results allows an evaluation of changes in the mass activity of vegetables and grass during themore » months following deposit. It constitutes part of the ASTRAL post-accident radioecology model.« less

Automatic Parameterization Strategy for Cardiac Electrophysiology Simulations

PubMed Central

Costa, Caroline Mendonca; Hoetzl, Elena; Rocha, Bernardo Martins; Prassl, Anton J; Plank, Gernot

2014-01-01

Driven by recent advances in medical imaging, image segmentation and numerical techniques, computer models of ventricular electrophysiology account for increasingly finer levels of anatomical and biophysical detail. However, considering the large number of model parameters involved parameterization poses a major challenge. A minimum requirement in combined experimental and modeling studies is to achieve good agreement in activation and repolarization sequences between model and experiment or patient data. In this study, we propose basic techniques which aid in determining bidomain parameters to match activation sequences. An iterative parameterization algorithm is implemented which determines appropriate bulk conductivities which yield prescribed velocities. In addition, a method is proposed for splitting the computed bulk conductivities into individual bidomain conductivities by prescribing anisotropy ratios. PMID:24729986

Bar Mode Instability in Relativistic Rotating Stars: A Post-Newtonian Treatment

NASA Astrophysics Data System (ADS)

Shapiro, Stuart L.; Zane, Silvia

1998-08-01

We construct analytic models of incompressible, uniformly rotating stars in post-Newtonian (PN) gravity and evaluate their stability against nonaxisymmetric bar modes. We model the PN configurations by homogeneous triaxial ellipsoids and employ an energy variational principle to determine their equilibrium shape and stability. The spacetime metric is obtained by solving Einstein's equations of general relativity in 3 + 1 ADM form. We use an approximate subset of these equations well suited to numerical integration in the case of strong-field, three-dimensional configurations in quasi equilibrium. However, the adopted equations are exact at PN order, where they admit an analytic solution for homogeneous ellipsoids. We obtain this solution for the metric, as well as analytic functionals for the conserved global quantities, M, M0, and J. We present sequences of axisymmetric, rotating equilibria of constant density and rest mass parametrized by their eccentricity. These configurations represent the PN generalization of Newtonian Maclaurin spheroids, which we compare to other PN and full relativistic incompressible equilibrium sequences constructed by previous investigators. We employ the variational principle to consider nonaxisymmetric ellipsoidal deformations of the configurations, holding the angular momentum constant and the rotation uniform. We locate the point along each sequence at which these Jacobi-like bar modes will be driven secularly unstable by the presence of a dissipative agent such as viscosity. We find that the value of the eccentricity, as well as related ratios such as Ω2/(πρ0) and T/|W| (=rotational kinetic energy/gravitational potential energy), defined invariantly, all increase at the onset of instability as the stars become more relativistic. Since higher degrees of rotation are required to trigger a viscosity-driven bar mode instability as the stars become more compact, the effect of general relativity is to weaken the instability, at least to PN order. This behavior is in stark contrast to that found recently for secular instability via nonaxisymmetric, Dedekind-like modes driven by gravitational radiation. These findings support the suggestion that in general relativity nonaxisymmetric modes driven unstable by viscosity no longer coincide with those driven unstable by gravitational radiation.

Biodegradation of atrazine by three transgenic grasses and alfalfa expressing a modified bacterial atrazine chlorohydrolase gene

USDA-ARS?s Scientific Manuscript database

The widespread use of atrazine and other s-triazine herbicides to control weeds in agricultural production fields has impacted surface and ground water in the United States and elsewhere. We previously reported the cloning, sequencing, and expression of six genes involved in the atrazine biodegradat...

An 11-year history of crop rotation into new perennial ryegrass and tall fescue

USDA-ARS?s Scientific Manuscript database

Converting multi-year remote sensing classification data into crop rotations is beneficial by defining the length of crop rotation cycles and the specific sequences of intervening crops grown between the final year of a grass seed stand and establishment of new perennial ryegrass and tall fescue see...

Genetic diversity of Danthonia spicata (L.) Beauv. Based on genomic simple sequence repeat markers

USDA-ARS?s Scientific Manuscript database

Danthonia spicata, commonly known as poverty oatgrass, is a perennial bunch-type grass native to North America. D. spicata has dimorphic seed heads; the hypothesis is that terminal seed heads allow some level of outcrossing and axial seed heads are only self-fertilized. However, there is no genetic ...

Spatiotemporal Variation in the Environmental Controls of C4-Grass Origin and Ecology: Insights from Grass-Pollen δ13C Data

NASA Astrophysics Data System (ADS)

Nelson, D. M.; Urban, M.; Hu, F.

2014-12-01

Understanding the environmental factors controlling the origin and shifting abundance of C4 grasses in Earth's history is useful for projecting the response of C4-grass dominated grasslands to future environmental change. Unfortunately, grass pollen is typically morphologically indistinct, making palynological analysis a blunt tool for studying C4-grasses in the paleorecord. δ13C of individual grass-pollen grains using a spooling wire microcombustion device interfaced with an isotope ratio mass spectrometer (Single Pollen Isotope Ratio AnaLysis, SPIRAL) overcomes this challenge and the potential biases of δ13C data from other substrates (e.g. leaf waxes). To assess the presence and relative abundance of C3- and C4-grass pollen in samples of unknown composition, we developed a hierarchical Bayesian model, trained with ~1,900 δ13C values from pollen grains of 31 grass species. Surface-sediment data from Africa, Australia, and North America demonstrate the reliability of this technique for quantifying C4-grass abundance on the landscape. To investigate the timing and control of the origin of C4-grasses we analyzed samples from the Oligocene-Miocene from Europe and from the Eocene from North America. Results indicate that C4 grasses appeared on the landscape of southwest Europe no later than the early Oligocene, implying that low atmospheric pCO2 may not have been the main driver and/or precondition for the development of C4 photosynthesis in the grass family. In contrast, we found no evidence for C4 grasses in the southeast United States before pCO2 fell. In application of SPIRAL to the late Quaternary, we found that shifts in pCO2 and moisture balance exerted key controls on the relative abundance of C3 and C4 grasses in Africa and Australia. Overall, our results imply that as in the past, future changes in the C3/C4 composition of grass-dominated ecosystems will likely exhibit striking spatiotemporal variability as a result of differing combinations of environmental controls.

Experimental Investigation of the Deepening of the Combustion Front into Peat Layers Different in Botanical Composition

NASA Astrophysics Data System (ADS)

Kasymov, D. P.

2017-01-01

The deepening of the center of combustion into peat layers of different botanical compositions (pine-cotton grass and grass-sphagnum peats), typical for the Tomsk region, was investigated experimentally. Peats were ignited from a model ground forest fire initiated by firing of a needle-litter layer. As a result of laboratory investigations, the change in the temperature in the bulk of peat samples with time was determined and analyzed, and the rates of their combustion in the horizontal and vertical directions were estimated. It was established that a fire penetrates deep into a layer of grass-sphagnum peat, containing more than 70% of combustion conductors in its composition, more rapidly as compared to that of pine-cotton grass peat. The rates of combustion of grass-sphagnum peat in the vertical and horizontal directions are larger by 20 and 22%, respectively, than those of pine-cotton grass peat, which is evidently due to the botanical composition of grass-sphagnum peat and the random arrangement of components in its layers.

A grass-fire cycle eliminates an obligate-seeding tree in a tropical savanna.

PubMed

Bowman, David M J S; MacDermott, Harry J; Nichols, Scott C; Murphy, Brett P

2014-11-01

A grass-fire cycle in Australian tropical savannas has been postulated as driving the regional decline of the obligate-seeding conifer Callitris intratropica and other fire-sensitive components of the regional flora and fauna, due to proliferation of flammable native grasses. We tested the hypothesis that a high-biomass invasive savanna grass drives a positive feedback process where intense fires destroy fire-sensitive trees, and the reduction in canopy cover facilitates further invasion by grass. We undertook an observational and experimental study using, as a model system, a plantation of C. intratropica that has been invaded by an African grass, gamba (Andropogon gayanus) in the Northern Territory, Australia. We found that high grass biomass was associated with reduced canopy cover and restriction of foliage to the upper canopy of surviving stems, and mortality of adult trees was very high (>50%) even in areas with low fuel loads (1 t·ha(-1)). Experimental fires, with fuel loads >10 t·ha(-1), typical of the grass-invasion front, caused significant mortality due to complete crown scorch. Lower fuel loads cause reduced canopy cover through defoliation of the lower canopy. These results help explain how increases in grass biomass are coupled with the decline of C. intratropica throughout northern Australia by causing a switch from litter and sparse perennial grass fuels, and hence low-intensity surface fires, to heavy annual grass fuel loads that sustain fires that burn into the midstorey. This study demonstrates that changes in fuel type can alter fire regimes with substantial knock-on effects on the biota.

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

Mechanisms controlling the complete accretionary beach state sequence

NASA Astrophysics Data System (ADS)

Dubarbier, Benjamin; Castelle, Bruno; Ruessink, Gerben; Marieu, Vincent

2017-06-01

Accretionary downstate beach sequence is a key element of observed nearshore morphological variability along sandy coasts. We present and analyze the first numerical simulation of such a sequence using a process-based morphodynamic model that solves the coupling between waves, depth-integrated currents, and sediment transport. The simulation evolves from an alongshore uniform barred beach (storm profile) to an almost featureless shore-welded terrace (summer profile) through the highly alongshore variable detached crescentic bar and transverse bar/rip system states. A global analysis of the full sequence allows determining the varying contributions of the different hydro-sedimentary processes. Sediment transport driven by orbital velocity skewness is critical to the overall onshore sandbar migration, while gravitational downslope sediment transport acts as a damping term inhibiting further channel growth enforced by rip flow circulation. Accurate morphological diffusivity and inclusion of orbital velocity skewness opens new perspectives in terms of morphodynamic modeling of real beaches.

Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates

PubMed Central

Chitsazzadeh, Vida; Coarfa, Cristian; Drummond, Jennifer A.; Nguyen, Tri; Joseph, Aaron; Chilukuri, Suneel; Charpiot, Elizabeth; Adelmann, Charles H.; Ching, Grace; Nguyen, Tran N.; Nicholas, Courtney; Thomas, Valencia D.; Migden, Michael; MacFarlane, Deborah; Thompson, Erika; Shen, Jianjun; Takata, Yoko; McNiece, Kayla; Polansky, Maxim A.; Abbas, Hussein A.; Rajapakshe, Kimal; Gower, Adam; Spira, Avrum; Covington, Kyle R.; Xiao, Weimin; Gunaratne, Preethi; Pickering, Curtis; Frederick, Mitchell; Myers, Jeffrey N.; Shen, Li; Yao, Hui; Su, Xiaoping; Rapini, Ronald P.; Wheeler, David A.; Hawk, Ernest T.; Flores, Elsa R.; Tsai, Kenneth Y.

2016-01-01

Cutaneous squamous cell carcinoma (cuSCC) comprises 15–20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible. PMID:27574101

Loss of a large grazer impacts savanna grassland plant communities similarly in North America and South Africa.

PubMed

Eby, Stephanie; Burkepile, Deron E; Fynn, Richard W S; Burns, Catherine E; Govender, Navashni; Hagenah, Nicole; Koerner, Sally E; Matchett, Katherine J; Thompson, Dave I; Wilcox, Kevin R; Collins, Scott L; Kirkman, Kevin P; Knapp, Alan K; Smith, Melinda D

2014-05-01

Large herbivore grazing is a widespread disturbance in mesic savanna grasslands which increases herbaceous plant community richness and diversity. However, humans are modifying the impacts of grazing on these ecosystems by removing grazers. A more general understanding of how grazer loss will impact these ecosystems is hampered by differences in the diversity of large herbivore assemblages among savanna grasslands, which can affect the way that grazing influences plant communities. To avoid this we used two unique enclosures each containing a single, functionally similar large herbivore species. Specifically, we studied a bison (Bos bison) enclosure at Konza Prairie Biological Station, USA and an African buffalo (Syncerus caffer) enclosure in Kruger National Park, South Africa. Within these enclosures we erected exclosures in annually burned and unburned sites to determine how grazer loss would impact herbaceous plant communities, while controlling for potential fire-grazing interactions. At both sites, removal of the only grazer decreased grass and forb richness, evenness and diversity, over time. However, in Kruger these changes only occurred with burning. At both sites, changes in plant communities were driven by increased dominance with herbivore exclusion. At Konza, this was caused by increased abundance of one grass species, Andropogon gerardii, while at Kruger, three grasses, Themeda triandra, Panicum coloratum, and Digitaria eriantha increased in abundance.

Infrared laser driven double proton transfer. An optimal control theory study

NASA Astrophysics Data System (ADS)

Abdel-Latif, Mahmoud K.; Kühn, Oliver

2010-02-01

Laser control of ultrafast double proton transfer is investigated for a two-dimensional model system describing stepwise and concerted transfer pathways. The pulse design has been done by employing optimal control theory in combination with the multiconfiguration time-dependent Hartree wave packet propagation. The obtained laser fields correspond to multiple pump-dump pulse sequences. Special emphasis is paid to the relative importance of stepwise and concerted transfer pathways for the driven wave packet and its dependence on the parameters of the model Hamiltonian as well as on the propagation time. While stepwise transfer is dominating in all cases considered, for high barrier systems concerted transfer proceeding via tunneling can make a contribution.

Gramene database in 2010: updates and extensions.

PubMed

Youens-Clark, Ken; Buckler, Ed; Casstevens, Terry; Chen, Charles; Declerck, Genevieve; Derwent, Paul; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul; Karthikeyan, A S; Lu, Jerry; McCouch, Susan R; Ren, Liya; Spooner, William; Stein, Joshua C; Thomason, Jim; Wei, Sharon; Ware, Doreen

2011-01-01

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

PubMed

Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

2016-11-23

The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

Arbuscular mycorrhizal assemblages in native plant roots change in the presence of invasive exotic grasses

USGS Publications Warehouse

Hawkes, C.V.; Belnap, J.; D'Antonio, C.; Firestone, M.K.

2006-01-01

Plant invasions have the potential to significantly alter soil microbial communities, given their often considerable aboveground effects. We examined how plant invasions altered the arbuscular mycorrhizal fungi of native plant roots in a grassland site in California and one in Utah. In the California site, we used experimentally created plant communities composed of exotic (Avena barbata, Bromus hordeaceus) and native (Nassella pulchra, Lupinus bicolor) monocultures and mixtures. In the Utah semi-arid grassland, we took advantage of invasion by Bromus tectorum into long-term plots dominated by either of two native grasses, Hilaria jamesii or Stipa hymenoides. Arbuscular mycorrhizal fungi colonizing roots were characterized with PCR amplification of the ITS region, cloning, and sequencing. We saw a significant effect of the presence of exotic grasses on the diversity of mycorrhizal fungi colonizing native plant roots. In the three native grasses, richness of mycorrhizal fungi decreased; in the native forb at the California site, the number of fungal RFLP patterns increased in the presence of exotics. The exotic grasses also caused the composition of the mycorrhizal community in native roots to shift dramatically both in California, with turnover of Glomus spp., and Utah, with replacement of Glomus spp. by apparently non-mycorrhizal fungi. Invading plants may be able to influence the network of mycorrhizal fungi in soil that is available to natives through either earlier root activity or differential carbon provision compared to natives. Alteration of the soil microbial community by plant invasion can provide a mechanism for both successful invasion and the resulting effects of invaders on the ecosystem. ?? Springer 2006.

Induction of lead-binding phytochelatins in vetiver grass [Vetiveria zizanioides (L.)].

PubMed

Andra, Syam S; Datta, Rupali; Sarkar, Dibyendu; Makris, Konstantinos C; Mullens, Conor P; Sahi, Shivendra V; Bach, Stephan B H

2009-01-01

Elevated lead (Pb) concentrations in residential houseyards around house walls painted with Pb-based pigments pose serious human health risks, especially to children. Vetiver grass (Vetiveria zizanioides L.) has shown promise for use in in situ Pb phytoremediation efforts. However, little is known about the biochemical mechanisms responsible for the observed high Pb tolerance by vetiver. We hypothesized that vetiver exposure to Pb induced the synthesis of phytochelatins (PC(n)) and the formation of Pb-PC(n) complexes, alleviating the phytotoxic effects of free Pb ions. Our main objective was to identify PC(n) and Pb-PC(n) complexes in root and shoot compartments of vetiver grass using high-performance liquid chromatography coupled to electrospray mass spectrometry (HPLC-ES-MS). After 7 d of exposure to Pb, vetiver accumulated up to 3000 mg Pb kg(-1) in shoot tissues, but much higher Pb concentrations were measured in root ( approximately 20,000 mg kg(-1)), without phytotoxic symptoms. Scanning electron micrographs showed Pb deposition in the vascular tissues of root and shoot, suggesting Pb translocation to shoot. Collision-induced dissociation analyses in MS/ MS mode during HPLC-ES-MS analysis allowed for the confirmation of four unique PC(n) (n = 1-4) based on their respective amino acid sequence. The high tolerance of vetiver grass to Pb was attributed to the formation of PC(n) and Pb-PC(n) complexes within the plant tissues, using ES-MS and Pb mass isotopic patterns. These data illustrate the mechanism of high Pb tolerance by vetiver grass, suggesting its potential usefulness for the remediation of Pb-contaminated residential sites.

Complexity in African savannas: Direct, indirect, and cascading effects of animal densities, rainfall and vegetation availability

PubMed Central

Leeuwis, Tim; Peel, Mike

2018-01-01

Savanna ecosystems are popular subjects for interaction studies. Multiple studies have been done on the impact of elephants on vegetation, the impact of grass and browse availability on animal densities or on competition between herbivore species. Previous studies showed that elephant densities are frequently negatively correlated with densities of tall trees, and that browse and grass availability are correlated with browser and grazer density respectively. Additionally, a competition effect between browse and grass availability has been reported. These relationships are usually analysed by testing direct relationships between e.g., herbivore densities and food availability, without addressing competition effects or other indirect effects. In this study, multiple interactions in a savanna system have been analysed simultaneously using Partial Least Square-Path Modelling (PLS-PM) using mammal and vegetation data from three different wildlife reserves in southern KwaZulu-Natal. The results showed that the processes that three separate models for the three areas provided the best understanding of the importance of the different interactions. These models suggest that elephants had a negative impact on trees, but also on grass availability. The impact is stronger when elephants are not able to migrate during the dry season. Browsers and grazers were correlated with browse and grass availability, but competition between browse and grass was not detected. This study shows that due to the complexity of the interactions in an ecosystem and differences in environmental factors, these interactions are best studied per area. PLS-PM can be a useful tool for estimating direct, indirect, and cascading effects of changing animal densities in conservation areas. PMID:29768481

CONFOLD2: improved contact-driven ab initio protein structure modeling.

PubMed

Adhikari, Badri; Cheng, Jianlin

2018-01-25

Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted contacts need to be developed. We develop an improved contact-driven protein modelling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input. It builds models using various subsets of input contacts to explore the fold space under the guidance of a soft square energy function, and then clusters the models to obtain the top five models. CONFOLD2 obtains an average reconstruction accuracy of 0.57 TM-score for the 150 proteins in the PSICOV contact prediction dataset. When benchmarked on the CASP11 contacts predicted using CONSIP2 and CASP12 contacts predicted using Raptor-X, CONFOLD2 achieves a mean TM-score of 0.41 on both datasets. CONFOLD2 allows to quickly generate top five structural models for a protein sequence when its secondary structures and contacts predictions at hand. The source code of CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/ .

Estimates of spatial and temporal variation of energy crops biomass yields in the US

NASA Astrophysics Data System (ADS)

Song, Y.; Jain, A. K.; Landuyt, W.; Kheshgi, H. S.

2013-12-01

Perennial grasses, such as switchgrass (Panicum viragatum) and Miscanthus (Miscanthus x giganteus) have been identified for potential use as biomass feedstocks in the US. Current research on perennial grass biomass production has been evaluated on small-scale plots. However, the extent to which this potential can be realized at a landscape-scale will depend on the biophysical potential to grow these grasses with minimum possible amount of land that needs to be diverted from food to fuel production. To assess this potential three questions about the biomass yield for these grasses need to be answered: (1) how the yields for different grasses are varied spatially and temporally across the US; (2) whether the yields are temporally stable or not; and (3) how the spatial and temporal trends in yields of these perennial grasses are controlled by limiting factors, including soil type, water availability, climate, and crop varieties. To answer these questions, the growth processes of the perennial grasses are implemented into a coupled biophysical, physiological and biogeochemical model (ISAM). The model has been applied to quantitatively investigate the spatial and temporal trends in biomass yields for over the period 1980 -2010 in the US. The bioenergy grasses considered in this study include Miscanthus, Cave-in-Rock switchgrass and Alamo switchgrass. The effects of climate, soil and topography on the spatial and temporal trends of biomass yields are quantitatively analyzed using principal component analysis and GIS based geographically weighted regression. The spatial temporal trend results are evaluated further to classify each part of the US into four homogeneous potential yield zones: high and stable yield zone (HS), high but unstable yield zone (HU), low and stable yield zone (LS) and low but unstable yield zone (LU). Our preliminary results indicate that the yields for perennial grasses among different zones are strongly related to the different controlling factors. For example, the yield in HS zone is depended on soil and topography factors. However, the yields in HU zone are more controlled by climate factors, leading to a large uncertainty in yield potential of bioenergy grasses under future climate change.

SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

PubMed Central

Pouyet, Fanny; Bailly-Bechet, Marc; Mouchiroud, Dominique; Guéguen, Laurent

2016-01-01

Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences. PMID:27401173

Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses.

PubMed

Li, Pinghua; Brutnell, Thomas P

2011-05-01

Setaria italica and its wild ancestor Setaria viridis are diploid C(4) grasses with small genomes of ∼515 Mb. Both species have attributes that make them attractive as model systems. Setaria italica is a grain crop widely grown in Northern China and India that is closely related to the major food and feed crops maize and sorghum. A large collection of S. italica accessions are available and thus opportunities exist for association mapping and allele mining for novel variants that will have direct application in agriculture. Setaria viridis is the weedy relative of S. italica with many attributes suitable for genetic analyses including a small stature, rapid life cycle, and prolific seed production. Setaria sp. are morphologically similar to most of the Panicoideae grasses, including major biofuel feedstocks, switchgrass (Panicum virgatum) and Miscanthus (Miscanthus giganteus). They are broadly distributed geographically and occupy diverse ecological niches. The cross-compatibility of S. italica and S. viridis also suggests that gene flow is likely between wild and domesticated accessions. In addition to serving as excellent models for C(4) photosynthesis, these grasses provide novel opportunities to study abiotic stress tolerance and as models for bioenergy feedstocks.

Bottom-up driven involuntary auditory evoked field change: constant sound sequencing amplifies but does not sharpen neural activity.

PubMed

Okamoto, Hidehiko; Stracke, Henning; Lagemann, Lothar; Pantev, Christo

2010-01-01

The capability of involuntarily tracking certain sound signals during the simultaneous presence of noise is essential in human daily life. Previous studies have demonstrated that top-down auditory focused attention can enhance excitatory and inhibitory neural activity, resulting in sharpening of frequency tuning of auditory neurons. In the present study, we investigated bottom-up driven involuntary neural processing of sound signals in noisy environments by means of magnetoencephalography. We contrasted two sound signal sequencing conditions: "constant sequencing" versus "random sequencing." Based on a pool of 16 different frequencies, either identical (constant sequencing) or pseudorandomly chosen (random sequencing) test frequencies were presented blockwise together with band-eliminated noises to nonattending subjects. The results demonstrated that the auditory evoked fields elicited in the constant sequencing condition were significantly enhanced compared with the random sequencing condition. However, the enhancement was not significantly different between different band-eliminated noise conditions. Thus the present study confirms that by constant sound signal sequencing under nonattentive listening the neural activity in human auditory cortex can be enhanced, but not sharpened. Our results indicate that bottom-up driven involuntary neural processing may mainly amplify excitatory neural networks, but may not effectively enhance inhibitory neural circuits.

[Mechanisms of grass in slope erosion control in Loess sandy soil region of Northwest China].

PubMed

Zhao, Chun-Hong; Gao, Jian-En; Xu, Zhen

2013-01-01

By adopting the method of simulated precipitation and from the viewpoint of slope hydrodynamics, in combining with the analysis of soil resistance to erosion, a quantitative study was made on the mechanisms of grass in controlling the slope erosion in the cross area of wind-water erosion in Loess Plateau of Northwest China under different combinations of rainfall intensity and slope gradient, aimed to provide basis to reveal the mechanisms of vegetation in controlling soil erosion and to select appropriate vegetation for the soil and water conservation in Loess Plateau. The grass Astragalus adsurgens with the coverage about 40% could effectively control the slope erosion. This grass had an efficiency of more than 70% in reducing sediment, and the grass root had a greater effect than grass canopy. On bare slope and on the slopes with the grass plant or only the grass root playing effect, there existed a functional relation between the flow velocity on the slopes and the rainfall intensity and slope gradient (V = DJ(0.33 i 0.5), where V is flow velocity, D is the comprehensive coefficient which varies with different underlying surfaces, i is rainfall intensity, and J is slope gradient). Both the grass root and the grass canopy could markedly decrease the flow velocity on the slopes, and increase the slope resistance, but the effect of grass root in decreasing flow velocity was greater while the effect in increasing resistance was smaller than that of grass canopy. The effect of grass root in increasing slope resistance was mainly achieved by increasing the sediment grain resistance, while the effect of canopy was mainly achieved by increasing the slope form resistance and wave resistance. The evaluation of the soil resistance to erosion by using a conceptual model of sediment generation by overland flow indicated that the critical shear stress value of bare slope and of the slopes with the grass plant or only the grass root playing effect was 0.533, 1.672 and 0.925 Pa, respectively.

Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar

PubMed Central

Besnard, Guillaume; Christin, Pascal-Antoine; Malé, Pierre-Jean G.; Coissac, Eric; Ralimanana, Hélène; Vorontsova, Maria S.

2013-01-01

Background and Aims An accurate characterization of biodiversity requires analyses of DNA sequences in addition to classical morphological descriptions. New methods based on high-throughput sequencing may allow investigation of specimens with a large set of genetic markers to infer their evolutionary history. In the grass family, the phylogenetic position of the monotypic genus Lecomtella, a rare bamboo-like endemic from Madagascar, has never been appropriately evaluated. Until now its taxonomic treatment has remained controversial, indicating the need for re-evaluation based on a combination of molecular and morphological data. Methods The phylogenetic position of Lecomtella in Poaceae was evaluated based on sequences from the nuclear and plastid genomes generated by next-generation sequencing (NGS). In addition, a detailed morphological description of L. madagascariensis was produced, and its distribution and habit were investigated in order to assess its conservation status. Key Results The complete plastid sequence, a ribosomal DNA unit and fragments of low-copy nuclear genes (phyB and ppc) were obtained. All phylogenetic analyses place Lecomtella as an isolated member of the core panicoids, which last shared a common ancestor with other species >20 million years ago. Although Lecomtella exhibits morphological characters typical of Panicoideae, an unusual combination of traits supports its treatment as a separate group. Conclusions The study showed that NGS can be used to generate abundant phylogenetic information rapidly, opening new avenues for grass phylogenetics. These data clearly showed that Lecomtella forms an isolated lineage, which, in combination with its morphological peculiarities, justifies its treatment as a separate tribe: Lecomtelleae. New descriptions of the tribe, genus and species are presented with a typification, a distribution map and an IUCN conservation assessment. PMID:23985988

Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar.

PubMed

Besnard, Guillaume; Christin, Pascal-Antoine; Malé, Pierre-Jean G; Coissac, Eric; Ralimanana, Hélène; Vorontsova, Maria S

2013-10-01

An accurate characterization of biodiversity requires analyses of DNA sequences in addition to classical morphological descriptions. New methods based on high-throughput sequencing may allow investigation of specimens with a large set of genetic markers to infer their evolutionary history. In the grass family, the phylogenetic position of the monotypic genus Lecomtella, a rare bamboo-like endemic from Madagascar, has never been appropriately evaluated. Until now its taxonomic treatment has remained controversial, indicating the need for re-evaluation based on a combination of molecular and morphological data. The phylogenetic position of Lecomtella in Poaceae was evaluated based on sequences from the nuclear and plastid genomes generated by next-generation sequencing (NGS). In addition, a detailed morphological description of L. madagascariensis was produced, and its distribution and habit were investigated in order to assess its conservation status. The complete plastid sequence, a ribosomal DNA unit and fragments of low-copy nuclear genes (phyB and ppc) were obtained. All phylogenetic analyses place Lecomtella as an isolated member of the core panicoids, which last shared a common ancestor with other species >20 million years ago. Although Lecomtella exhibits morphological characters typical of Panicoideae, an unusual combination of traits supports its treatment as a separate group. The study showed that NGS can be used to generate abundant phylogenetic information rapidly, opening new avenues for grass phylogenetics. These data clearly showed that Lecomtella forms an isolated lineage, which, in combination with its morphological peculiarities, justifies its treatment as a separate tribe: Lecomtelleae. New descriptions of the tribe, genus and species are presented with a typification, a distribution map and an IUCN conservation assessment.

Prediction of genetic gains by selection indices using mixed models in elephant grass for energy purposes.

PubMed

Silva, V B; Daher, R F; Araújo, M S B; Souza, Y P; Cassaro, S; Menezes, B R S; Gravina, L M; Novo, A A C; Tardin, F D; Júnior, A T Amaral

2017-09-27

Genetically improved cultivars of elephant grass need to be adapted to different ecosystems with a faster growth speed and lower seasonality of biomass production over the year. This study aimed to use selection indices using mixed models (REML/BLUP) for selecting families and progenies within full-sib families of elephant grass (Pennisetum purpureum) for biomass production. One hundred and twenty full-sib progenies were assessed from 2014 to 2015 in a randomized block design with three replications. During this period, the traits dry matter production, the number of tillers, plant height, stem diameter, and neutral detergent fiber were assessed. Families 3 and 1 were the best classified, being the most indicated for selection effect. Progenies 40, 45, 46, and 49 got the first positions in the three indices assessed in the first cut. The gain for individual 40 was 161.76% using Mulamba and Mock index. The use of selection indices using mixed models is advantageous in elephant grass since they provide high gains with the selection, which are distributed among all the assessed traits in the most appropriate situation to breeding programs.

Health economic comparison of SLIT allergen and SCIT allergoid immunotherapy in patients with seasonal grass-allergic rhinoconjunctivitis in Germany.

PubMed

Verheggen, Bram G; Westerhout, Kirsten Y; Schreder, Carl H; Augustin, Matthias

2015-01-01

Allergoids are chemically modified allergen extracts administered to reduce allergenicity and to maintain immunogenicity. Oralair® (the 5-grass tablet) is a sublingual native grass allergen tablet for pre- and co-seasonal treatment. Based on a literature review, meta-analysis, and cost-effectiveness analysis the relative effects and costs of the 5-grass tablet versus a mix of subcutaneous allergoid compounds for grass pollen allergic rhinoconjunctivitis were assessed. A Markov model with a time horizon of nine years was used to assess the costs and effects of three-year immunotherapy treatment. Relative efficacy expressed as standardized mean differences was estimated using an indirect comparison on symptom scores extracted from available clinical trials. The Rhinitis Symptom Utility Index (RSUI) was applied as a proxy to estimate utility values for symptom scores. Drug acquisition and other medical costs were derived from published sources as well as estimates for resource use, immunotherapy persistence, and occurrence of asthma. The analysis was executed from the German payer's perspective, which includes payments of the Statutory Health Insurance (SHI) and additional payments by insurants. Comprehensive deterministic and probabilistic sensitivity analyses and different scenarios were performed to test the uncertainty concerning the incremental model outcomes. The applied model predicted a cost-utility ratio of the 5-grass tablet versus a market mix of injectable allergoid products of € 12,593 per QALY in the base case analysis. Predicted incremental costs and QALYs were € 458 (95% confidence interval, CI: € 220; € 739) and 0.036 (95% CI: 0.002; 0.078), respectively. Compared to the allergoid mix the probability of the 5-grass tablet being the most cost-effective treatment option was predicted to be 76% at a willingness-to-pay threshold of € 20,000. The results were most sensitive to changes in efficacy estimates, duration of the pollen season, and immunotherapy persistence rates. This analysis suggests the sublingual native 5-grass tablet to be cost-effective relative to a mix of subcutaneous allergoid compounds. The robustness of these statements has been confirmed in extensive sensitivity and scenario analyses.

Tree-grass phenology information improves light use efficiency modelling of gross primary productivity for an Australian tropical savanna

NASA Astrophysics Data System (ADS)

Moore, Caitlin E.; Beringer, Jason; Evans, Bradley; Hutley, Lindsay B.; Tapper, Nigel J.

2017-01-01

The coexistence of trees and grasses in savanna ecosystems results in marked phenological dynamics that vary spatially and temporally with climate. Australian savannas comprise a complex variety of life forms and phenologies, from evergreen trees to annual/perennial grasses, producing a boom-bust seasonal pattern of productivity that follows the wet-dry seasonal rainfall cycle. As the climate changes into the 21st century, modification to rainfall and temperature regimes in savannas is highly likely. There is a need to link phenology cycles of different species with productivity to understand how the tree-grass relationship may shift in response to climate change. This study investigated the relationship between productivity and phenology for trees and grasses in an Australian tropical savanna. Productivity, estimated from overstory (tree) and understory (grass) eddy covariance flux tower estimates of gross primary productivity (GPP), was compared against 2 years of repeat time-lapse digital photography (phenocams). We explored the phenology-productivity relationship at the ecosystem scale using Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices and flux tower GPP. These data were obtained from the Howard Springs OzFlux/Fluxnet site (AU-How) in northern Australia. Two greenness indices were calculated from the phenocam images: the green chromatic coordinate (GCC) and excess green index (ExG). These indices captured the temporal dynamics of the understory (grass) and overstory (trees) phenology and were correlated well with tower GPP for understory (r2 = 0.65 to 0.72) but less so for the overstory (r2 = 0.14 to 0.23). The MODIS enhanced vegetation index (EVI) correlated well with GPP at the ecosystem scale (r2 = 0.70). Lastly, we used GCC and EVI to parameterise a light use efficiency (LUE) model and found it to improve the estimates of GPP for the overstory, understory and ecosystem. We conclude that phenology is an important parameter to consider in estimating GPP from LUE models in savannas and that phenocams can provide important insights into the phenological variability of trees and grasses.

Systems Level Engineering of Plant Cell Wall Biosynthesis to Improve Biofuel Feedstock Quality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazen, Samuel

2013-09-27

Our new regulatory model of cell wall biosynthesis proposes original network architecture with several newly incorporated components. The mapped set of protein-DNA interactions will serve as a foundation for 1) understanding the regulation of a complex and integral plant component and 2) the manipulation of crop species for biofuel and biotechnology purposes. This study revealed interesting and novel aspects of grass growth and development and further enforce the importance of a grass model system. By functionally characterizing a suite of genes, we have begun to improve the sparse model for transcription regulation of biomass accumulation in grasses. In the process,more » we have advanced methodology and brachy molecular genetic tools that will serve as valuable community resource.« less

Identification of a locus characteristic of male individuals of buffalo grass [Buchloe dactyloides (Nutt.) Engelm.] by using an RAPD marker.

PubMed

Li, Y X; Wang, X G; Yang, C H; Cong, L L; Wu, F F; Xue, J G; Han, Y H

2013-09-27

Buffalo grass [Buchloe dactyloides (Nutt.) Engelm.] plants can be either male, female, or hermaphrodite (monoecious). As there is no morphological difference in the early vegetative growth of these three classes of plants, it is worthwhile to use molecular biological methods to attempt to identify the sex of a plant at this early growth period. In this study, we identified 23 plants that had a stable sex for over at least 3 years. Of these, 9 were male plants, 10 were female plants, and 4 were hermaphrodites. Screening of 300 RAPD primers identified a primer, namely S211 (5'-ttccccgcga-3'), which is capable of identifying male plants. The specific fragment was cloned, sequenced, and submitted to the GenBank database (accession No. JN982469). When used to identify the sex of 188 plants during their first growing season, the S211 primer correctly identified 85.8% of all male plants. Our results showed that the S211 primer can identify the male, and in doing so, it facilitates buffalo grass breeding work.

An Improved Brome mosaic virus Silencing Vector: Greater Insert Stability and More Extensive VIGS1[OPEN

PubMed Central

2018-01-01

Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus-silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is the instability of the foreign gene fragment (insert) in the vector during VIGS. Here, we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence. Modification of the BMV RNA3 sequence yielded a vector, BMVCP5, that better maintained phytoene desaturase and heat shock protein70-1 (HSP70-1) inserts in Nicotiana benthamiana and maize (Zea mays). Longer maintenance of inserts was correlated with greater target gene silencing and more extensive visible silencing phenotypes displaying greater tissue penetration and involving more leaves. The modified vector accumulated similarly to the original vector in N. benthamiana after agroinfiltration, thus maintaining a high titer of virus in this intermediate host used to produce virus inoculum for grass hosts. For HSP70, silencing one family member led to a large increase in the expression of another family member, an increase likely related to the target gene knockdown and not a general effect of virus infection. The cause of the increased insert stability in the modified vector is discussed in relationship to its recombination and accumulation potential. The modified vector will improve functional genomic studies in grasses, and the conceptual methods used to improve the vector may be applied to other VIGS vectors. PMID:29127260

Magnitude of efficacy measurements in grass allergy immunotherapy trials is highly dependent on pollen exposure.

PubMed

Durham, S R; Nelson, H S; Nolte, H; Bernstein, D I; Creticos, P S; Li, Z; Andersen, J S

2014-05-01

The objective was to evaluate the association between grass pollen exposure, allergy symptoms and impact on measured treatment effect after grass sublingual immunotherapy (SLIT)-tablet treatment. The association between grass pollen counts and total combined rhinoconjunctivitis symptom and medication score (TCS) was based on a post hoc analysis of data collected over six trials and seven grass pollen seasons across North America and Europe, including 2363 subjects treated with grass SLIT-tablet or placebo. Daily pollen counts were obtained from centralized pollen databases. The effect of treatment on the relationship between the TCS and pollen counts was investigated, and the relative difference between grass SLIT-tablet and placebo as a function of average grass pollen counts was modelled by linear regression. The magnitude of treatment effect based on TCS was greater with higher pollen exposure (P < 0.001). The relative treatment effect in terms of TCS for each trial was correlated with the average grass pollen exposure during the first period of the season, with predicted reduction in TCS = 12% + 0.35% × pollen count (slope significantly different from 0, P = 0.003; R(2)  = 0.66). Corresponding correlations to the entire grass pollen season and to the peak season were equally good, whereas there was a poor correlation between difference in measured efficacy and pollen exposure during the last part of the season. In seasonal allergy trials with grass SLIT-tablet, the observed treatment effect is highly dependent on pollen exposure with the magnitude being greater with higher pollen exposure. This is an important relationship to consider when interpreting individual clinical trial results. © 2014 The Authors. Allergy Published by John Wiley & Sons Ltd.

Magnitude of efficacy measurements in grass allergy immunotherapy trials is highly dependent on pollen exposure

PubMed Central

Durham, S R; Nelson, H S; Nolte, H; Bernstein, D I; Creticos, P S; Li, Z; Andersen, J S

2014-01-01

Background The objective was to evaluate the association between grass pollen exposure, allergy symptoms and impact on measured treatment effect after grass sublingual immunotherapy (SLIT)-tablet treatment. Methods The association between grass pollen counts and total combined rhinoconjunctivitis symptom and medication score (TCS) was based on a post hoc analysis of data collected over six trials and seven grass pollen seasons across North America and Europe, including 2363 subjects treated with grass SLIT-tablet or placebo. Daily pollen counts were obtained from centralized pollen databases. The effect of treatment on the relationship between the TCS and pollen counts was investigated, and the relative difference between grass SLIT-tablet and placebo as a function of average grass pollen counts was modelled by linear regression. Results The magnitude of treatment effect based on TCS was greater with higher pollen exposure (P < 0.001). The relative treatment effect in terms of TCS for each trial was correlated with the average grass pollen exposure during the first period of the season, with predicted reduction in TCS = 12% + 0.35% × pollen count (slope significantly different from 0, P = 0.003; R2 = 0.66). Corresponding correlations to the entire grass pollen season and to the peak season were equally good, whereas there was a poor correlation between difference in measured efficacy and pollen exposure during the last part of the season. Conclusions In seasonal allergy trials with grass SLIT-tablet, the observed treatment effect is highly dependent on pollen exposure with the magnitude being greater with higher pollen exposure. This is an important relationship to consider when interpreting individual clinical trial results. PMID:24605984

The role of seasonal grass pollen on childhood asthma emergency department presentations.

PubMed

Erbas, B; Akram, M; Dharmage, S C; Tham, R; Dennekamp, M; Newbigin, E; Taylor, P; Tang, M L K; Abramson, M J

2012-05-01

Few studies have focused on the role of grass pollen on asthma emergency department (ED) presentations among children. None have examined whether a dose-response effect exists between grass pollen levels and these asthma exacerbations. To examine the association between increasing ambient levels of grass pollen and asthma ED presentations in children. To determine whether these associations are seen only after a thunderstorm, or whether grass pollen levels have a consistent influence on childhood asthma ED visits during the season. A short time series ecological study was conducted for asthma presentations to ED among children in Melbourne, Victoria, and grass pollen, meteorological and air quality measurements recorded during the selected 2003 period. A semi-parametric Poisson regression model was used to examine dose-response associations between daily grass pollen levels and mean daily ED attendance for asthma. A smoothed plot suggested a dose-response association. As ambient grass pollen increased to about 19 grains/m(3) , the same day risk of childhood ED presentations also increased linearly (P < 0.001). Grass pollen levels were also associated with an increased risk in asthma ED presentations on the following day (lag 1, P < 0.001). This is the first study to establish a clear relationship between increased risk of childhood asthma ED attendance and levels of ambient grass pollen below 20 grains/m(3) , independent of any impact of thunderstorm-associated asthma. These findings have important implications for patient care, such as asthma management programs that notify the general public regarding periods of high grass pollen exposure, as well as defining the timing of initiation of pollen immunotherapy. © 2012 Blackwell Publishing Ltd.

[Analysis of structural characteristics of alpha-tubulins in plants with enhanced cold tolerance].

PubMed

Nyporko, A Iu; Demchuk, O N; Blium, Ia B

2003-01-01

The uniqueness of the point substitutions in the sequences of two alpha-tubulin isotypes from psychrophilic alga Chloromonas that can determine the increased cold tolerance of this alga was analyzed. The comparison of all known amino acid sequences of plant alpha-tubulins enabled to ascertain that only M268-->V replacement is unique and may have a significant influence on spatial structure of plant alpha-tubulins. Modeling of molecular surfaces of alpha-tubulins from Chloromonas, Chalmydomonas reinhardtii and goose grass Eleusine indica showed that insertion of the amino acid replacement M268-->V into the sequence of goose grace tubulin led to the likening of this protein surface to the surface of native alpha-tubulin from Chloromonas. Alteration of local hydrophobic properties of alpha-tubulin molecular surface in interdimeric contact zone as a result of the mentioned replacement was shown that may play important role in increasing the level of cold resistance of microtubules. The crucial role of amino acid residue in 268 position for forming the interdimeric contact surface of alpha-tubulin molecule was revealed. The assumption is made about the importance of replacements at this position for plant tolerance to abiotic factors of different nature (cold, herbicides).

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

USDA-ARS?s Scientific Manuscript database

Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

USDA-ARS?s Scientific Manuscript database

Basidiomycete fungi in the genus Limonomyces are important pathogens of turfgrasses, causing pink patch and cream leaf blight diseases on numerous grass hosts worldwide. Much is unknown about the biology and taxonomy of these fungi, and molecular resources are extremely rare. Here, we report draft...

BAC Library Development for Allotetraploid Leymus (Triticeae) Wildryes Enable Comparative Genetic Analysis of Lax-Barrenstalk1 Orthogene Sequences and Growth Habit QTLs

USDA-ARS?s Scientific Manuscript database

Tall caespitose basin wildrye (Leymus cinereus) and rhizomatous creeping wildrye (Leymus triticoides) are two of the largest native grasses in western North America and the interspecific hybrids display a heterotic combination of traits. The rice lax panicle and maize barrenstalk1 orthogenes are tr...

Whole genome sequence of two Rathayibacter toxicus strains reveals a tunicamycin biosynthetic cluster similar to Streptomyces chartreusis

USDA-ARS?s Scientific Manuscript database

Rathayibacter toxicus is a forage grass associated Gram-positive bacterium of major concern to food safety and agriculture. The species is listed by USDA-APHIS as a plant pathogen select agent due to the fact that it produces a tunicamycin-like toxin that is lethal to livestock. The complete genomes...

Origin of a Fungal Symbiont of Perennial Ryegrass by Interspecific Hybridization of a Mutualist with the Ryegrass Choke Pathogen, Epichloe Typhina

PubMed Central

Schardl, C. L.; Leuchtmann, A.; Tsai, H. F.; Collett, M. A.; Watt, D. M.; Scott, D. B.

1994-01-01

Seed-borne fungal symbionts (endophytes) provide many cool-season grass species with biological protection from biotic and abiotic stresses. The endophytes are asexual, whereas closely related sexual species of genus Epichloe (Clavicipitales) cause grass choke disease. Perennial ryegrass (Lolium perenne) is a host of two endophyte taxa, LpTG-1 (L. perenne endophyte taxonomic grouping one = Acremonium lolii) and LpTG-2, as well as the choke pathogen, Epichloe typhina (represented by isolate E8). Relationships among these fungi and other Epichloe species were investigated by analysis of gene sequences, DNA polymorphisms and allozymes. The results indicate that LpTG-2 is a heteroploid derived from an interspecific hybrid. The LpTG-2 isolates had two copies each of nine out of ten genes analyzed (the exception being the rRNA gene locus), and the profiles for seven of these were composites of those from E. typhina E8 and A. lolii isolate Lp5. Molecular phylogenetic analysis grouped the two β-tubulin genes of LpTG-2 into separate clades. One (tub2-1) was related to that of E. typhina E8, and the other (tub2-2) to that of A. lolii. The mitochondrial DNA profile of LpTG-2 was similar to that of A. lolii, but its rRNA gene sequence grouped it with E. typhina E8. A proposed model for the evolution of LpTG-2 involves infection of a L. perenne-A. lolii symbiotum by E. typhina, followed by hybridization of the two fungi. Such interspecific hybridization may be a common and important mechanism for genetic variation in Epichloe endophytes. PMID:8013907

A mathematical model of cancer stem cell driven tumor initiation: implications of niche size and loss of homeostatic regulatory mechanisms.

PubMed

Gentry, Sara N; Jackson, Trachette L

2013-01-01

Hierarchical organized tissue structures, with stem cell driven cell differentiation, are critical to the homeostatic maintenance of most tissues, and this underlying cellular architecture is potentially a critical player in the development of a many cancers. Here, we develop a mathematical model of mutation acquisition to investigate how deregulation of the mechanisms preserving stem cell homeostasis contributes to tumor initiation. A novel feature of the model is the inclusion of both extrinsic and intrinsic chemical signaling and interaction with the niche to control stem cell self-renewal. We use the model to simulate the effects of a variety of types and sequences of mutations and then compare and contrast all mutation pathways in order to determine which ones generate cancer cells fastest. The model predicts that the sequence in which mutations occur significantly affects the pace of tumorigenesis. In addition, tumor composition varies for different mutation pathways, so that some sequences generate tumors that are dominated by cancerous cells with all possible mutations, while others are primarily comprised of cells that more closely resemble normal cells with only one or two mutations. We are also able to show that, under certain circumstances, healthy stem cells diminish due to the displacement by mutated cells that have a competitive advantage in the niche. Finally, in the event that all homeostatic regulation is lost, exponential growth of the cancer population occurs in addition to the depletion of normal cells. This model helps to advance our understanding of how mutation acquisition affects mechanisms that influence cell-fate decisions and leads to the initiation of cancers.

Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences

PubMed Central

Imashimizu, Masahiko; Afek, Ariel; Takahashi, Hiroki; Lubkowska, Lucyna; Lukatsky, David B.

2016-01-01

In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations. PMID:27830653

Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

PubMed Central

Preston, Jill C.; Kellogg, Elizabeth A.

2006-01-01

Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

The effect of essential oils on microbial composition and quality of grass carp (Ctenopharyngodon idellus) fillets during chilled storage.

PubMed

Huang, Zhan; Liu, Xiaochang; Jia, Shiliang; Zhang, Longteng; Luo, Yongkang

2018-02-02

Antimicrobial and antioxidant effects of essential oils (oregano, thyme, and star anise) on microbial composition and quality of grass carp fillets were investigated. Essential oils treatment was found to be effective in inhibiting microbial growth, delaying lipid oxidation, and retarding the increase of TVB-N, putrescine, hypoxanthine, and K-value. Based on sensory analysis, shelf-life of grass carp fillets was 6days for control and 8days for treatment groups. Among the essential oils, oregano essential oil exhibited the highest antimicrobial and antioxidant activities. GC-MS analysis of essential oils components revealed that carvacrol (88.64%) was the major component of oregano essential oil. According to the results of high-throughput sequencing, Aeromonas, Glutamicibacter, and Aequorivita were the predominant microbiota in fresh control samples. However, oregano essential oil decreased the relative abundance of Aeromonas, while thyme and star anise essential oils decreased the relative abundance of Glutamicibacter and Aequorivita in fresh treated samples. The microbial composition of both control and treatment groups became less diverse as storage time increased. Aeromonas and Pseudomonas were dominant in spoiled samples and contributed to fish spoilage. Compared to the control, essential oils effectively inhibited the growth of Aeromonas and Shewanella in grass carp fillets during chilled storage. Copyright © 2017 Elsevier B.V. All rights reserved.

Temperate pine barrens and tropical rain forests are both rich in undescribed fungi.

PubMed

Luo, Jing; Walsh, Emily; Naik, Abhishek; Zhuang, Wenying; Zhang, Keqin; Cai, Lei; Zhang, Ning

2014-01-01

Most of fungal biodiversity on Earth remains unknown especially in the unexplored habitats. In this study, we compared fungi associated with grass (Poaceae) roots from two ecosystems: the temperate pine barrens in New Jersey, USA and tropical rain forests in Yunnan, China, using the same sampling, isolation and species identification methods. A total of 426 fungal isolates were obtained from 1600 root segments from 80 grass samples. Based on the internal transcribed spacer (ITS) sequences and morphological characteristics, a total of 85 fungal species (OTUs) belonging in 45 genera, 23 families, 16 orders, and 6 classes were identified, among which the pine barrens had 38 and Yunnan had 56 species, with only 9 species in common. The finding that grass roots in the tropical forests harbor higher fungal species diversity supports that tropical forests are fungal biodiversity hotspots. Sordariomycetes was dominant in both places but more Leotiomycetes were found in the pine barrens than Yunnan, which may play a role in the acidic and oligotrophic pine barrens ecosystem. Equal number of undescribed fungal species were discovered from the two sampled ecosystems, although the tropical Yunnan had more known fungal species. Pine barrens is a unique, unexplored ecosystem. Our finding suggests that sampling plants in such unexplored habitats will uncover novel fungi and that grass roots in pine barrens are one of the major reservoirs of novel fungi with about 47% being undescribed species.

PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

PubMed

Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

2016-01-01

PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

PubMed Central

Joyce, Aoife; Ijaz, Umer Z.; Nzeteu, Corine; Vaughan, Aoife; Shirran, Sally L.; Botting, Catherine H.; Quince, Christopher; O’Flaherty, Vincent; Abram, Florence

2018-01-01

Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored. PMID:29619022

Grass carp in the Great Lakes region: establishment potential, expert perceptions, and re-evaluation of experimental evidence of ecological impact

USGS Publications Warehouse

Wittmann, Marion E.; Jerde, Christopher L.; Howeth, Jennifer G.; Maher, Sean P.; Deines, Andrew M.; Jenkins, Jill A.; Whitledge, Gregory W.; Burbank, Sarah B.; Chadderton, William L.; Mahon, Andrew R.; Tyson, Jeffrey T.; Gantz, Crysta A.; Keller, Reuben P.; Drake, John M.; Lodge, David M.

2014-01-01

Intentional introductions of nonindigenous fishes are increasing globally. While benefits of these introductions are easily quantified, assessments to understand the negative impacts to ecosystems are often difficult, incomplete, or absent. Grass carp (Ctenopharyngodon idella) was originally introduced to the United States as a biocontrol agent, and recent observations of wild, diploid individuals in the Great Lakes basin have spurred interest in re-evaluating its ecological risk. Here, we evaluate the ecological impact of grass carp using expert opinion and a suite of the most up-to-date analytical tools and data (ploidy assessment, eDNA surveillance, species distribution models (SDMs), and meta-analysis). The perceived ecological impact of grass carp by fisheries experts was variable, ranging from unknown to very high. Wild-caught triploid and diploid individuals occurred in multiple Great Lakes waterways, and eDNA surveillance suggests that grass carp are abundant in a major tributary of Lake Michigan. SDMs predicted suitable grass carp climate occurs in all Great Lakes. Meta-analysis showed that grass carp introductions impact both water quality and biota. Novel findings based on updated ecological impact assessment tools indicate that iterative risk assessment of introduced fishes may be warranted.

Distinguishing thrust sequences in gravity-driven fold and thrust belts

NASA Astrophysics Data System (ADS)

Alsop, G. I.; Weinberger, R.; Marco, S.

2018-04-01

Piggyback or foreland-propagating thrust sequences, where younger thrusts develop in the footwalls of existing thrusts, are generally assumed to be the typical order of thrust development in most orogenic settings. However, overstep or 'break-back' sequences, where later thrusts develop above and in the hangingwalls of earlier thrusts, may potentially form during cessation of movement in gravity-driven mass transport deposits (MTDs). In this study, we provide a detailed outcrop-based analysis of such an overstep thrust sequence developed in an MTD in the southern Dead Sea Basin. Evidence that may be used to discriminate overstep thrusting from piggyback thrust sequences within the gravity-driven fold and thrust belt includes upright folds and forethrusts that are cut by younger overlying thrusts. Backthrusts form ideal markers that are also clearly offset and cut by overlying younger forethrusts. Portions of the basal detachment to the thrust system are folded and locally imbricated in footwall synclines below forethrust ramps, and these geometries also support an overstep sequence. However, new 'short-cut' basal detachments develop below these synclines, indicating that movement continued on the basal detachment rather than it being abandoned as in classic overstep sequences. Further evidence for 'synchronous thrusting', where movement on more than one thrust occurs at the same time, is provided by displacement patterns on sequences of thrust ramp imbricates that systematically increases downslope towards the toe of the MTD. Older thrusts that initiate downslope in the broadly overstep sequence continue to move and therefore accrue greater displacements during synchronous thrusting. Our study provides a template to help distinguish different thrust sequences in both orogenic settings and gravity-driven surficial systems, with displacement patterns potentially being imaged in seismic sections across offshore MTDs.

Devil's staircase and the absence of chaos in the dc- and ac-driven overdamped Frenkel-Kontorova model

NASA Astrophysics Data System (ADS)

Sokolović, I.; Mali, P.; Odavić, J.; Radošević, S.; Medvedeva, S. Yu.; Botha, A. E.; Shukrinov, Yu. M.; Tekić, J.

2017-08-01

The devil's staircase structure arising from the complete mode locking of an entirely nonchaotic system, the overdamped dc+ac driven Frenkel-Kontorova model with deformable substrate potential, was observed. Even though no chaos was found, a hierarchical ordering of the Shapiro steps was made possible through the use of a previously introduced continued fraction formula. The absence of chaos, deduced here from Lyapunov exponent analyses, can be attributed to the overdamped character and the Middleton no-passing rule. A comparative analysis of a one-dimensional stack of Josephson junctions confirmed the disappearance of chaos with increasing dissipation. Other common dynamic features were also identified through this comparison. A detailed analysis of the amplitude dependence of the Shapiro steps revealed that only for the case of a purely sinusoidal substrate potential did the relative sizes of the steps follow a Farey sequence. For nonsinusoidal (deformed) potentials, the symmetry of the Stern-Brocot tree, depicting all members of particular Farey sequence, was seen to be increasingly broken, with certain steps being more prominent and their relative sizes not following the Farey rule.

Accuracy of Genomic Prediction in a Commercial Perennial Ryegrass Breeding Program.

PubMed

Fè, Dario; Ashraf, Bilal H; Pedersen, Morten G; Janss, Luc; Byrne, Stephen; Roulund, Niels; Lenk, Ingo; Didion, Thomas; Asp, Torben; Jensen, Christian S; Jensen, Just

2016-11-01

The implementation of genomic selection (GS) in plant breeding, so far, has been mainly evaluated in crops farmed as homogeneous varieties, and the results have been generally positive. Fewer results are available for species, such as forage grasses, that are grown as heterogenous families (developed from multiparent crosses) in which the control of the genetic variation is far more complex. Here we test the potential for implementing GS in the breeding of perennial ryegrass ( L.) using empirical data from a commercial forage breeding program. Biparental F and multiparental synthetic (SYN) families of diploid perennial ryegrass were genotyped using genotyping-by-sequencing, and phenotypes for five different traits were analyzed. Genotypes were expressed as family allele frequencies, and phenotypes were recorded as family means. Different models for genomic prediction were compared by using practically relevant cross-validation strategies. All traits showed a highly significant level of genetic variance, which could be traced using the genotyping assay. While there was significant genotype × environment (G × E) interaction for some traits, accuracies were high among F families and between biparental F and multiparental SYN families. We have demonstrated that the implementation of GS in grass breeding is now possible and presents an opportunity to make significant gains for various traits. Copyright © 2016 Crop Science Society of America.

Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum.

PubMed

VanBuren, Robert; Wai, Ching Man; Zhang, Qingwei; Song, Xiaomin; Edger, Patrick P; Bryant, Doug; Michael, Todd P; Mockler, Todd C; Bartels, Dorothea

2017-10-01

Resurrection plants desiccate during periods of prolonged drought stress, then resume normal cellular metabolism upon water availability. Desiccation tolerance has multiple origins in flowering plants, and it likely evolved through rewiring seed desiccation pathways. Oropetium thomaeum is an emerging model for extreme drought tolerance, and its genome, which is the smallest among surveyed grasses, was recently sequenced. Combining RNA-seq, targeted metabolite analysis and comparative genomics, we show evidence for co-option of seed-specific pathways during vegetative desiccation. Desiccation-related gene co-expression clusters are enriched in functions related to seed development including several seed-specific transcription factors. Across the metabolic network, pathways involved in programmed cell death inhibition, ABA signalling and others are activated during dehydration. Oleosins and oil bodies that typically function in seed storage are highly abundant in desiccated leaves and may function for membrane stability and storage. Orthologs to seed-specific LEA proteins from rice and maize have neofunctionalized in Oropetium with high expression during desiccation. Accumulation of sucrose, raffinose and stachyose in drying leaves mirrors sugar accumulation patterns in maturing seeds. Together, these results connect vegetative desiccation with existing seed desiccation and drought responsive pathways and provide some key candidate genes for engineering improved drought tolerance in crop plants. © 2017 John Wiley & Sons Ltd.

Thermal and Hydraulic Conditions Supporting the Recruitment of Asian Carp in Seiche Affected Rivers of Lake Erie Basin - A Case Study of the Lower Sandusky River in Ohio

NASA Astrophysics Data System (ADS)

Soong, D. T.; Santacruz, S.; Jones, L.; Garcia, T.; Kočovský, P. M.; Embke, H.

2017-12-01

Grass Carp Ctenopharyngodon idella (Cyprinidae) is an invasive fish species that spawns in rivers during high-flow events. In their native range, it is believed eggs must hatch within the riverine environment in order to eventually result in production of adult fish. The lower Sandusky River is approximately 26 km long extending from its confluence with Sandusky Bay upstream to the Ballville Dam, which is impassible for Grass Carp. Grass Carp are known to have spawned in the Sandusky River, a tributary to Lake Erie, in 2011, 2013, 2015, and 2017. This study characterizes the thermal and hydraulic conditions under which these eggs could hatch in the lower Sandusky River, a relatively short river reach for egg hatching. Grass Carp eggs collected in 2015 were previously analyzed for hatching locations using a one-dimensional steady-state HEC-RAS hydraulic model. In this study we refine estimates of hatching locations by incorporating the influence of fluctuating water levels downstream due to seiches in Lake Erie and overland and tributary inflows using an unsteady 1D/2D HEC-RAS hydraulic model. Additionally, conditions conducive to successful hatching, which occurs when eggs reach the hatching stage within the river, were analyzed from nine high-flow events between 2011 and 2015. Simulated hydraulic and water temperature data were used as inputs to the Fluvial Egg Drift Simulator (FluEgg) model, which was used to analyze the transport and dispersal of Grass carp eggs until hatching. We will describe the differences in steady- and unsteady-state hydraulic modeling in predicting hatching locations of Grass Carp eggs for the 2015 spawning events. Results will also include hydraulic and temperature variables that contribute to the successful/unsuccessful in-river hatching for the nine flow events simulated.

Natural and anthropogenic land cover change and its impact on the regional climate and hydrological extremes over Sanjiangyuan region

NASA Astrophysics Data System (ADS)

Ji, P.; Yuan, X.

2017-12-01

Located in the northern Tibetan Plateau, Sanjiangyuan is the headwater region of the Yellow River, Yangtze River and Mekong River. Besides climate change, natural and human-induced land cover change (e.g., Graze for Grass Project) is also influencing the regional hydro-climate and hydrological extremes significantly. To quantify their impacts, a land surface model (LSM) with consideration of soil moisture-lateral surface flow interaction and quasi-three-dimensional subsurface flow, is used to conduct long-term high resolution simulations driven by China Meteorological Administration Land Data Assimilation System forcing data and different land cover scenarios. In particular, the role of surface and subsurface lateral flows is also analyzed by comparing with typical one-dimensional models. Lateral flows help to simulate soil moisture variability caused by topography at hyper-resolution (e.g., 100m), which is also essential for simulating hydrological extremes including soil moisture dryness/wetness and high/low flows. The LSM will also be coupled with a regional climate model to simulate the effect of natural and anthropogenic land cover change on regional climate, with particular focus on the land-atmosphere coupling at different resolutions with different configurations in modeling land surface hydrology.

Quantitative trait loci associated with drought tolerance in brachypodium distachyon

USDA-ARS?s Scientific Manuscript database

The temperate wild grass Brachypodium distachyon (Brachypodium) serves as model system for studying turf and forage grasses. Brachypodium collections show diverse responses to drought stress, but little is known about the genetic mechanisms of drought tolerance of this species. The objective of this...

Switchgrass for forage and bioenergy

USDA-ARS?s Scientific Manuscript database

Switchgrass is a native warm-season grass that has been used for hay, forage, and conservation purposes for decades and switchgrass research in Nebraska has been ongoing since 1936. Recently, switchgrass has been identified as a model perennial grass for bioenergy in the Great Plains and Midwest. Si...

When does ecological sustainability ensure economic sustainability? An integrated analysis of thresholds in semi-arid western rangelands

NASA Astrophysics Data System (ADS)

Cobourn, K. M.; Peckham, S. D.

2011-12-01

The vulnerability of agri-environmental systems to ecological threshold events depends on the combined influence of economic factors and natural drivers, such as climate and disturbance. This analysis builds an integrated ecologic-economic model to evaluate the behavioral response of agricultural producers to changing and uncertain natural conditions. The model explicitly reflects the effect of producer behavior on the likelihood of a threshold event that threatens the ecological and/or economic sustainability of the agri-environmental system. The foundation of the analysis is a threshold indicator that incorporates the population dynamics of a species that supports economic production and an episodic disturbance regime-in this case rangeland grass that is grazed by livestock and is subject to wildfire. This ecological indicator is integrated into an economic model in which producers choose grazing intensity given the state of the grass population and a set of economic parameters. We examine two model variants that characterize differing economic circumstances. The first characterizes the optimal grazing regime assuming that the system is managed by a single planner whose objective is to maximize the aggregate long-run returns of producers in the system. The second examines the case in which individual producers choose their own stocking rates in order to maximize their private economic benefit. The results from the first model variant illustrate the difference between an ecologic and an economic threshold. Failure to cross an ecological threshold does not necessarily ensure that the system remains economically viable: Economic sustainability, defined as the ability of the system to support optimal production into the infinite future, requires that the net growth rate of the supporting population exceeds the level required for ecological sustainability by an amount that depends on the market price of livestock and grazing efficiency. The results from the second model variant define the circumstances under which a system that is otherwise ecologically sustainable is driven over a threshold by the actions of economic agents. The difference between the two model solutions identifies bounds between which the viability of livestock production over the long-run is uncertain and depends upon the policy setting in which the agri-environmental system operates.

Floral gene resources from basal angiosperms for comparative genomics research

PubMed Central

Albert, Victor A; Soltis, Douglas E; Carlson, John E; Farmerie, William G; Wall, P Kerr; Ilut, Daniel C; Solow, Teri M; Mueller, Lukas A; Landherr, Lena L; Hu, Yi; Buzgo, Matyas; Kim, Sangtae; Yoo, Mi-Jeong; Frohlich, Michael W; Perl-Treves, Rafael; Schlarbaum, Scott E; Bliss, Barbara J; Zhang, Xiaohong; Tanksley, Steven D; Oppenheimer, David G; Soltis, Pamela S; Ma, Hong; dePamphilis, Claude W; Leebens-Mack, James H

2005-01-01

Background The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. Results Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. Conclusion Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways. PMID:15799777

A multiscale assessment of tree avoidance by prairie birds

USGS Publications Warehouse

Thompson, Sarah J.; Arnold, Todd W.; Amundson, Courtney L.

2014-01-01

In North America, grassland bird abundances have declined, likely as a result of loss and degradation of prairie habitat. Given the expense and limited opportunity to procure new grasslands, managers are increasingly focusing on ways to improve existing habitat for grassland birds, using techniques such as tree removal. To examine the potential for tree removal to benefit grassland birds, we conducted 446 point counts on 35 grassland habitat patches in the highly fragmented landscape of west-central Minnesota during 2009–2011. We modeled density of four grassland bird species in relation to habitat composition at multiple scales, focusing on covariates that described grass, woody vegetation (trees and large shrubs), or combinations of grass and woody vegetation. The best-supported models for all four grassland bird species incorporated variables measured at multiple scales, including local features such as grass height, litter depth, and local tree abundance, as well as landscape-level measures of grass and tree cover. Savannah Sparrows (Passerculus sandwichensis), Sedge Wrens (Cistothorus platensis), and Bobolinks (Dolichonyx oryzivorus) responded consistently and negatively to woody vegetation, but response to litter depth, grass height, and grassland extent were mixed among species. Our results suggest that reducing shrub and tree cover is more likely to increase the density of grassland birds than are attempts to improve grass quality or quantity. In particular, tree removal is more likely to increase density of Savannah Sparrows and Sedge Wrens than any reasonable changes in grass quality or quantity. Yet tree removal may not result in increased abundance of grassland birds if habitat composition is not considered at multiple scales. Managers will need to either manage at large scales (80–300 ha) or focus their efforts on removing trees in landscapes that contain some grasslands but few nearby wooded areas.

Changes of the Shrub/Grass balance under Climate Change: Mechanisms and Consequences

NASA Astrophysics Data System (ADS)

Sala, O.; Gherardi, L.; Anadon, J.

2016-12-01

Most arid and semiarid ecosystems are made up of grasses and shrubs; and their balance could be altered by changes in climate, fire and grazing among others. Here, we focus on the effects of climate change on the shrub/grass balance and the mechanisms mediating alterations of the balance. We assess hypotheses that state that climate change affects shrub/grass balance by affecting the distribution of soil water in the profile. We report on studies that range from the plot to the sub-continental scale using manipulative experiments, simulation modelling and remote sensing tools. Specifically, we evaluate the effect of amount of precipitation on the shrub/grass balance. In Chihuahuan desert ecosystems, prolonged drought drove shrub encroachment as a result of a-symmetric competition between shrubs and grasses. Demise of shallow-rooted grasses after prolonged drought resulted in an increase in soil-water resources for deep-rooted shrubs. We also quantitatively assessed the effect of changes in shrub/grass balance on the provisioning of ecosystem services in North and South America. In both regions, woody-plant encroachment reduced livestock production, which is the main ecosystem service provided by drylands. However, the effect of woody-plant encroachment had a larger impact in South than North America. The differential effect of changes in the shrub/balance was mediated by differences in the demand of ecosystem services.

Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus

PubMed Central

Yamamoto, Naoki; Takano, Tomoyuki; Tanaka, Keisuke; Ishige, Taichiro; Terashima, Shin; Endo, Chisato; Kurusu, Takamitsu; Yajima, Shunsuke; Yano, Kentaro; Tada, Yuichi

2015-01-01

The turf grass Sporobolus virginicus is halophyte and has high salinity tolerance. To investigate the molecular basis of its remarkable tolerance, we performed Illumina high-throughput RNA sequencing on roots and shoots of a S. virginicus genotype under normal and saline conditions. The 130 million short reads were assembled into 444,242 unigenes. A comparative analysis of the transcriptome with rice and Arabidopsis transcriptome revealed six turf grass-specific unigenes encoding transcription factors. Interestingly, all of them showed root specific expression and five of them encode bZIP type transcription factors. Another remarkable transcriptional feature of S. virginicus was activation of specific pathways under salinity stress. Pathway enrichment analysis suggested transcriptional activation of amino acid, pyruvate, and phospholipid metabolism. Up-regulation of several unigenes, previously shown to respond to salt stress in other halophytes was also observed. Gene Ontology enrichment analysis revealed that unigenes assigned as proteins in response to water stress, such as dehydrin and aquaporin, and transporters such as cation, amino acid, and citrate transporters, and H+-ATPase, were up-regulated in both shoots and roots under salinity. A correspondence analysis of the enriched pathways in turf grass cells, but not in rice cells, revealed two groups of unigenes similarly up-regulated in the turf grass in response to salt stress; one of the groups, showing excessive up-regulation under salinity, included unigenes homologos to salinity responsive genes in other halophytes. Thus, the present study identified candidate genes involved in salt tolerance of S. virginicus. This genetic resource should be valuable for understanding the mechanisms underlying high salt tolerance in S. virginicus. This information can also provide insight into salt tolerance in other halophytes. PMID:25954282

Recilia banda Kramer (Hemiptera: Cicadellidae), a vector of Napier stunt phytoplasma in Kenya

NASA Astrophysics Data System (ADS)

Obura, Evans; Midega, Charles A. O.; Masiga, Daniel; Pickett, John A.; Hassan, Mohamed; Koji, Shinsaku; Khan, Zeyaur R.

2009-10-01

Napier grass ( Pennisetum purpureum) is the most important fodder crop in smallholder dairy production systems in East Africa, characterized by small zero-grazing units. It is also an important trap crop used in the management of cereal stemborers in maize in the region. However, production of Napier grass in the region is severely constrained by Napier stunt disease. The etiology of the disease is known to be a phytoplasma, 16SrXI strain. However, the putative insect vector was yet unknown. We sampled and identified five leafhopper and three planthopper species associated with Napier grass and used them as candidates in pathogen transmission experiments. Polymerase chain reaction (PCR), based on the highly conserved 16S gene, primed by P1/P6-R16F2n/R16R2 nested primer sets was used to diagnose phytoplasma on test plants and insects, before and after transmission experiments. Healthy plants were exposed for 60 days to insects that had fed on diseased plants and acquired phytoplasma. The plants were then incubated for another 30 days. Nested PCR analyses showed that 58.3% of plants exposed to Recilia banda Kramer (Hemiptera: Cicadellidae) were positive for phytoplasma and developed characteristic stunt disease symptoms while 60% of R. banda insect samples were similarly phytoplasma positive. We compared the nucleotide sequences of the phytoplasma isolated from R. banda, Napier grass on which these insects were fed, and Napier grass infected by R. banda, and found them to be virtually identical. The results confirm that R. banda transmits Napier stunt phytoplasma in western Kenya, and may be the key vector of Napier stunt disease in this region.

C3–C4 intermediacy in grasses: organelle enrichment and distribution, glycine decarboxylase expression, and the rise of C2 photosynthesis

PubMed Central

Khoshravesh, Roxana; Stinson, Corey R.; Stata, Matt; Busch, Florian A.; Sage, Rowan F.; Ludwig, Martha; Sage, Tammy L.

2016-01-01

Photorespiratory glycine shuttling and decarboxylation in bundle sheath (BS) cells exhibited by C2 species is proposed to be the evolutionary bridge to C4 photosynthesis in eudicots. To evaluate this in grasses, we compare anatomy, cellular localization of glycine decarboxylase (GDC), and photosynthetic physiology of a suspected C2 grass, Homolepis aturensis, with these traits in known C2 grasses, Neurachne minor and Steinchisma hians, and C3 S. laxum that is sister to S. hians. We also use publicly available genome and RNA-sequencing data to examine the evolution of GDC subunits and enhance our understanding of the evolution of BS-specific GDC expression in C2 and C4 grasses. Our results confirm the identity of H. aturensis as a C2 species; GDC is confined predominantly to the organelle-enriched BS cells in H. aturensis and S. hians and to mestome sheath cells of N. minor. Phylogenetic analyses and data obtained from immunodetection of the P-subunit of GDC are consistent with the hypothesis that the BS dominant levels of GDC in C2 and C4 species are due to changes in expression of a single GLDP gene in M and BS cells. All BS mitochondria and peroxisomes and most chloroplasts in H. aturensis and S. hians are situated centripetally in a pattern identical to C2 eudicots. In S. laxum, which has C3-like gas exchange patterns, mitochondria and peroxisomes are positioned centripetally as they are in S. hians. This subcellular phenotype, also present in eudicots, is posited to initiate a facilitation cascade leading to C2 and C4 photosynthesis. PMID:27073202

C3-C4 intermediacy in grasses: organelle enrichment and distribution, glycine decarboxylase expression, and the rise of C2 photosynthesis.

PubMed

Khoshravesh, Roxana; Stinson, Corey R; Stata, Matt; Busch, Florian A; Sage, Rowan F; Ludwig, Martha; Sage, Tammy L

2016-05-01

Photorespiratory glycine shuttling and decarboxylation in bundle sheath (BS) cells exhibited by C2 species is proposed to be the evolutionary bridge to C4 photosynthesis in eudicots. To evaluate this in grasses, we compare anatomy, cellular localization of glycine decarboxylase (GDC), and photosynthetic physiology of a suspected C2 grass, Homolepis aturensis, with these traits in known C2 grasses, Neurachne minor and Steinchisma hians, and C3 S laxum that is sister to S hians We also use publicly available genome and RNA-sequencing data to examine the evolution of GDC subunits and enhance our understanding of the evolution of BS-specific GDC expression in C2 and C4 grasses. Our results confirm the identity of H aturensis as a C2 species; GDC is confined predominantly to the organelle-enriched BS cells in H aturensis and S hians and to mestome sheath cells of N minor Phylogenetic analyses and data obtained from immunodetection of the P-subunit of GDC are consistent with the hypothesis that the BS dominant levels of GDC in C2 and C4 species are due to changes in expression of a single GLDP gene in M and BS cells. All BS mitochondria and peroxisomes and most chloroplasts in H aturensis and S hians are situated centripetally in a pattern identical to C2 eudicots. In S laxum, which has C3-like gas exchange patterns, mitochondria and peroxisomes are positioned centripetally as they are in S hians This subcellular phenotype, also present in eudicots, is posited to initiate a facilitation cascade leading to C2 and C4 photosynthesis. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses.

PubMed

Wu, Zhiqiang; Sloan, Daniel B; Brown, Colin W; Rosenblueth, Mónica; Palmer, Jeffrey D; Ong, Han Chuan

2017-09-01

Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Isolating and evaluating lactic acid bacteria strains for effectiveness of Leymus chinensis silage fermentation.

PubMed

Zhang, Q; Li, X J; Zhao, M M; Yu, Z

2014-10-01

Five LAB strains were evaluated using the acid production ability test, morphological observation, Gram staining, physiological, biochemical and acid tolerance tests. All five strains (LP1, LP2, LP3, LC1 and LC2) grew at pH 4·0, and LP1 grew at 15°C. Strains LP1, LP2 and LP3 were identified as Lactobacillus plantarum, whereas LC1 and LC2 were classified as Lactobacillus casei by sequencing 16S rDNA. The five isolated strains and two commercial inoculants (PS and CL) were added to native grass and Leymus chinensis (Trin.) Tzvel. for ensiling. All five isolated strains decreased the pH and ammonia nitrogen content, increased the lactic acid content and LP1, LP2 and LP3 increased the acetic content and lactic/acetic acid ratio of L. chinensis silage significantly. The five isolated strains and two commercial inoculants decreased the butyric acid content of the native grass silage. LP2 treatment had lower butyric acid content and ammonia nitrogen content than the other treatments. The five isolated strains improved the quality of L. chinensis silage. The five isolated strains and the two commercial inoculants were not effective in improving the fermentation quality of the native grass silage, but LP2 performed better comparatively. Significance and impact of the study: Leymus chinensis is an important grass in China and Russia, being the primary grass of the short grassland 'steppe' regions of central Asia. However, it has been difficult to make high-quality silage of this species because of low concentration of water-soluble carbohydrates (WSC). Isolating and evaluating lactic acid bacteria strains will be helpful for improving the silage quality of this extensively grown species. © 2014 The Society for Applied Microbiology.

The palaeoecological context of the Oldowan-Acheulean in southern Africa.

PubMed

Ecker, Michaela; Brink, James S; Rossouw, Lloyd; Chazan, Michael; Horwitz, Liora K; Lee-Thorp, Julia A

2018-05-21

The influence of climatic and environmental change on human evolution in the Pleistocene epoch is understood largely from extensive East African stable isotope records. These records show increasing proportions of C 4 plants in the Early Pleistocene. We know far less about the expansion of C 4 grasses at higher latitudes, which were also occupied by early Homo but are more marginal for C 4 plants. Here we show that both C 3 and C 4 grasses and prolonged wetlands remained major components of Early Pleistocene environments in the central interior of southern Africa, based on enamel stable carbon and oxygen isotope data and associated faunal abundance and phytolith evidence from the site of Wonderwerk Cave. Vegetation contexts associated with Oldowan and early Acheulean lithic industries, in which climate is driven by an interplay of regional rainfall seasonality together with global CO 2 levels, develop along a regional distinct trajectory compared to eastern South Africa and East Africa.

Landscape management of fire and grazing regimes alters the fine-scale habitat utilisation by feral cats.

PubMed

McGregor, Hugh W; Legge, Sarah; Jones, Menna E; Johnson, Christopher N

2014-01-01

Intensification of fires and grazing by large herbivores has caused population declines in small vertebrates in many ecosystems worldwide. Impacts are rarely direct, and usually appear driven via indirect pathways, such as changes to predator-prey dynamics. Fire events and grazing may improve habitat and/or hunting success for the predators of small mammals, however, such impacts have not been documented. To test for such an interaction, we investigated fine-scale habitat selection by feral cats in relation to fire, grazing and small-mammal abundance. Our study was conducted in north-western Australia, where small mammal populations are sensitive to changes in fire and grazing management. We deployed GPS collars on 32 cats in landscapes with contrasting fire and grazing treatments. Fine-scale habitat selection was determined using discrete choice modelling of cat movements. We found that cats selected areas with open grass cover, including heavily-grazed areas. They strongly selected for areas recently burnt by intense fires, but only in habitats that typically support high abundance of small mammals. Intense fires and grazing by introduced herbivores created conditions that are favoured by cats, probably because their hunting success is improved. This mechanism could explain why, in northern Australia, impacts of feral cats on small mammals might have increased. Our results suggest the impact of feral cats could be reduced in most ecosystems by maximising grass cover, minimising the incidence of intense fires, and reducing grazing by large herbivores.

Development Policy in Thailand: From Top-down to Grass Roots.

PubMed

Kelly, Matthew; Yutthaphonphinit, Phattaraphon; Seubsman, Sam-Ang; Sleigh, Adrian

2012-11-01

Top-down industrial development strategies initially dominated the developing world after the second World War but were eventually found to produce inequitable economic growth. For a decade or more, governments and international development agencies have embraced the idea of participatory grass roots development as a potential solution. Here we review Thailand's experience with development strategies and we examine the current focus on participatory approaches. Thai government planning agencies have adopted "people centred development" and a "sufficiency economy", particularly emphasised since the disruptions caused by the 1997 Asian financial crisis. They aim to address the inequitable sharing of the benefits of decades of rapid growth that was particularly unfair for the rural poor. Thai policies aim to decentralise power to the local level, allowing civil society and Non-Governmental Organisations (NGOs) more of a voice in national decision making and promoting sustainable farming practices aimed at enriching rural communities. An example of this change in Thai government policy is the Community Worker Accreditation Scheme which is aiming to develop human resources at the local level by training community based leaders and supporting networks of community organisations. This enables autonomous local development projects led by trained and accredited individuals and groups. The political tensions notable in Thailand at present are part of this modern transition driven by conflicting models of top-down (industrial) development and the bottom-up (participatory) development ideals described above. Once resolved, Thailand will have few obstacles to moving to a new economic level.

Landscape Management of Fire and Grazing Regimes Alters the Fine-Scale Habitat Utilisation by Feral Cats

PubMed Central

McGregor, Hugh W.; Legge, Sarah; Jones, Menna E.; Johnson, Christopher N.

2014-01-01

Intensification of fires and grazing by large herbivores has caused population declines in small vertebrates in many ecosystems worldwide. Impacts are rarely direct, and usually appear driven via indirect pathways, such as changes to predator-prey dynamics. Fire events and grazing may improve habitat and/or hunting success for the predators of small mammals, however, such impacts have not been documented. To test for such an interaction, we investigated fine-scale habitat selection by feral cats in relation to fire, grazing and small-mammal abundance. Our study was conducted in north-western Australia, where small mammal populations are sensitive to changes in fire and grazing management. We deployed GPS collars on 32 cats in landscapes with contrasting fire and grazing treatments. Fine-scale habitat selection was determined using discrete choice modelling of cat movements. We found that cats selected areas with open grass cover, including heavily-grazed areas. They strongly selected for areas recently burnt by intense fires, but only in habitats that typically support high abundance of small mammals. Intense fires and grazing by introduced herbivores created conditions that are favoured by cats, probably because their hunting success is improved. This mechanism could explain why, in northern Australia, impacts of feral cats on small mammals might have increased. Our results suggest the impact of feral cats could be reduced in most ecosystems by maximising grass cover, minimising the incidence of intense fires, and reducing grazing by large herbivores. PMID:25329902

Carbon dioxide and the uneasy interactions of trees and savannah grasses

PubMed Central

Bond, William J.; Midgley, Guy F.

2012-01-01

Savannahs are a mixture of trees and grasses often occurring as alternate states to closed forests. Savannah fires are frequent where grass productivity is high in the wet season. Fires help maintain grassy vegetation where the climate is suitable for woodlands or forests. Saplings in savannahs are particularly vulnerable to topkill of above-ground biomass. Larger trees are more fire-resistant and suffer little damage when burnt. Recruitment to large mature tree size classes depends on sapling growth rates to fire-resistant sizes and the time between fires. Carbon dioxide (CO2) can influence the growth rate of juvenile plants, thereby affecting tree recruitment and the conversion of open savannahs to woodlands. Trees have increased in many savannahs throughout the world, whereas some humid savannahs are being invaded by forests. CO2 has been implicated in this woody increase but attribution to global drivers has been controversial where changes in grazing and fire have also occurred. We report on diverse tests of the magnitude of CO2 effects on both ancient and modern ecosystems with a particular focus on African savannahs. Large increases in trees of mesic savannahs in the region cannot easily be explained by land use change but are consistent with experimental and simulation studies of CO2 effects. Changes in arid savannahs seem less obviously linked to CO2 effects and may be driven more by overgrazing. Large-scale shifts in the tree–grass balance in the past and the future need to be better understood. They not only have major impacts on the ecology of grassy ecosystems but also on Earth–atmosphere linkages and the global carbon cycle in ways that are still being discovered. PMID:22232770

Carbon dioxide and the uneasy interactions of trees and savannah grasses.

PubMed

Bond, William J; Midgley, Guy F

2012-02-19

Savannahs are a mixture of trees and grasses often occurring as alternate states to closed forests. Savannah fires are frequent where grass productivity is high in the wet season. Fires help maintain grassy vegetation where the climate is suitable for woodlands or forests. Saplings in savannahs are particularly vulnerable to topkill of above-ground biomass. Larger trees are more fire-resistant and suffer little damage when burnt. Recruitment to large mature tree size classes depends on sapling growth rates to fire-resistant sizes and the time between fires. Carbon dioxide (CO(2)) can influence the growth rate of juvenile plants, thereby affecting tree recruitment and the conversion of open savannahs to woodlands. Trees have increased in many savannahs throughout the world, whereas some humid savannahs are being invaded by forests. CO(2) has been implicated in this woody increase but attribution to global drivers has been controversial where changes in grazing and fire have also occurred. We report on diverse tests of the magnitude of CO(2) effects on both ancient and modern ecosystems with a particular focus on African savannahs. Large increases in trees of mesic savannahs in the region cannot easily be explained by land use change but are consistent with experimental and simulation studies of CO(2) effects. Changes in arid savannahs seem less obviously linked to CO(2) effects and may be driven more by overgrazing. Large-scale shifts in the tree-grass balance in the past and the future need to be better understood. They not only have major impacts on the ecology of grassy ecosystems but also on Earth-atmosphere linkages and the global carbon cycle in ways that are still being discovered.

Prediction of enteric methane emissions from sheep offered fresh perennial ryegrass () using data measured in indirect open-circuit respiration chambers.

PubMed

Zhao, Y G; O'Connell, N E; Yan, T

2016-06-01

Development of effective methane (CH) mitigation strategies for grazing sheep requires accurate prediction tools. The present study aimed to identify key parameters influencing enteric CH emissions and develop prediction equations for enteric CH emissions from sheep offered fresh grass. The data used were collected from 82 sheep offered fresh perennial ryegrass () as sole diets in 6 metabolism experiments (data from non-grass-only diets were not used). Sheep were from breeds of Highlander, Texel, Scottish Blackface, and Swaledale at the age of 5 to 18 mo and weighing from 24.5 to 62.7 kg. Grass was harvested daily from 6 swards on contrasting harvest dates (May to December). Before the commencement of each study, the experimental sward was harvested at a residual height of 4 cm and allowed to grow for 2 to 4 wk. The feeding trials commenced when the grass sward was suitable to zero grazing (average grass height = 15 cm), thus offering grass of a quality similar to what grazing animals would receive under routine grazing management. Sheep were housed in individual pens for 14 d and then moved to individual calorimeter chambers for 4 d. Feed intake, fecal and urine outputs, and CH emissions were measured during the final 4 d. Data were analyzed using the REML procedure to develop prediction equations for CH emissions. Linear and multiple prediction equations were developed using BW, DMI, GE intake (GEI), and grass chemical concentrations (DM, OM, water-soluble carbohydrates [WSC], NDF, ADF, nitrogen [N], GE, DE, and ME) as explanatory variables. The mean CH production was 21.1 g/kg DMI or 0.062 MJ/MJ GEI. Dry matter intake and GEI were much more accurate predictors for CH emissions than BW ( < 0.001, = 0.86 and = 0.87 vs. = 0.09, respectively). Adding grass DE and ME concentrations and grass nutrient concentrations (e.g., OM, N, GE, NDF, and WSC) to the relationships between DMI or GEI and CH emissions improved prediction accuracy with values increased to 0.93. Models based on farm-level data, for example, BW and grass nutrient (i.e., DM, GE, OM, and N) concentrations, were also developed and performed satisfactorily ( < 0.001, = 0.63). These models can contribute to improve prediction accuracy for enteric CH emissions from sheep grazing on ryegrass pasture.

Composition and design of vegetative filter strips instrumental in improving water quality by mass reduction of suspended sediment, nutrients and Escherichia coli in overland flows in eastern escarpment of Mau Forest, Njoro River Watershed, Kenya

PubMed Central

Olilo, C. O.; Onyando, J. O.; Moturi, W. N.; Muia, A. W.; Roegner, Amber F.; Ogari, Z.; Ombui, P. N.; Shivoga, W. A.

2016-01-01

This study assessed the effect of vegetative filter strip (VFS) in removal of suspended sediment (SS), total nitrogen, total phosphorus and Escherichia coli (E. coli) in overland flow to improve receiving water quality standards. Four and half kilograms of cowpat manure was applied to the model pasture 14 m beyond the edge of vegetated filter strip (VFS) comprising 10-m Napier grass draining into 20-m Kikuyu grass (VFS II), 10-m Kikuyu grass draining into 20-m Napier grass (VFS III) and native grass mixture of Couch–Buffel (VFS I-control). Overland flow water samples were collected from the sites at positions 0, 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 and 30 m along the length of VFSs. E. coli removal by Napier grass VFS was on the order of log unit, which provided an important level of protection and reduced surface-flow concentrations of E. coli to below the 200 (CFU 100 mL−1) recommended water quality standards, but not for nutrients and SS. The Napier grass showed highest efficiency (99.6 %), thus outperforming both Kikuyu grass (85.8 %) and Couch–Buffel grasses VFS (67.9 ± 4.2 %) in removing E. coli from overland flow. The low-level efficiency of native Couch–Buffel grasses in reducing E. coli in overland flow was because of preferential flow. Composition and design of VFS was instrumental and could be applied with a high potential of contracting the uncertainty in improving water quality standards through mass reduction of SS, nutrients and E. coli load in watersheds. PMID:28133624

Belowground impacts of perennial grass cultivation for sustainable biofuel feedstock production in the tropics

DOE PAGES

Sumiyoshi, Yudai; Crow, Susan E.; Litton, Creighton M.; ...

2016-07-08

Perennial grasses can sequester soil organic carbon (SOC) in sustainably managed biofuel systems, directly mitigating atmospheric CO 2 concentrations while simultaneously generating biomass for renewable energy. Our objective was to quantify SOC accumulation and identify the primary drivers of belowground C dynamics in a zero-tillage production system of tropical perennial C4 grasses grown for biofuel feedstock in Hawaii. Specifically, the quantity, quality, and fate of soil C inputs were determined for eight grass accessions – four varieties each of napier grass and guinea grass. Carbon fluxes (soil CO 2 efflux, aboveground net primary productivity, litterfall, total belowground carbon flux, rootmore » decay constant), C pools (SOC pool and root biomass), and C quality (root chemistry, C and nitrogen concentrations, and ratios) were measured through three harvest cycles following conversion of a fallow field to cultivated perennial grasses. A wide range of SOC accumulation occurred, with both significant species and accession effects. Aboveground biomass yield was greater, and root lignin concentration was lower for napier grass than guinea grass. Structural equation modeling revealed that root lignin concentration was the most important driver of SOC pool: varieties with low root lignin concentration, which was significantly related to rapid root decomposition, accumulated the greatest amount of SOC. Roots with low lignin concentration decomposed rapidly, but the residue and associated microbial biomass/by-products accumulated as SOC. In general, napier grass was better suited for promoting soil C sequestration in this system. Further, high-yielding varieties with low root lignin concentration provided the greatest climate change mitigation potential in a ratoon system. By understanding the factors affecting SOC accumulation and the net greenhouse gas trade-offs within a biofuel production system will aid in crop selection to meet multiple goals toward environmental and economic sustainability.« less

Immunochemical Analysis of Paxilline and Ergot Alkaloid Mycotoxins in Grass Seeds and Plants.

PubMed

Bauer, Julia I; Gross, Madeleine; Cramer, Benedikt; Humpf, Hans-Ulrich; Hamscher, Gerd; Usleber, Ewald

2018-01-10

Limited availability of toxin standards for lolitrem B and ergovaline impedes routine control of grasses for endophyte toxins. This study aimed at assessing the applicability of an enzyme immunoassay (EIA) for the indole-diterpene mycotoxin paxilline, in combination with a generic EIA for ergot alkaloids, as alternative parameters for screening purposes. Analysis of grass seeds and model pastures of four different grass species showed that both EIAs yielded highly positive results for paxilline and ergot alkaloids in perennial ryegrass seeds. Furthermore, evidence for natural occurrence of paxilline in grass in Germany was obtained. High performance liquid chromatography-tandem mass spectrometry analysis qualitatively confirmed the paxilline EIA results but showed that paxilline analogues 1'-O-acetylpaxilline and 13-desoxypaxilline were the predominant compounds in seeds and grass. In the absence of easily accessible reference standards for specific analysis of some major endophyte toxins, analysis of paxilline and ergot alkaloids by EIA may be suitable substitute parameters. The major advantage of this approach is its ease of use and speed, providing an analytical tool which could enhance routine screening for endophyte toxins in pasture.

Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography.

PubMed

Gussakovsky, Daniel; Neustaeter, Haley; Spicer, Victor; Krokhin, Oleg V

2017-11-07

The development of a peptide retention prediction model for strong cation exchange (SCX) separation on a Polysulfoethyl A column is reported. Off-line 2D LC-MS/MS analysis (SCX-RPLC) of S. cerevisiae whole cell lysate was used to generate a retention dataset of ∼30 000 peptides, sufficient for identifying the major sequence-specific features of peptide retention mechanisms in SCX. In contrast to RPLC/hydrophilic interaction liquid chromatography (HILIC) separation modes, where retention is driven by hydrophobic/hydrophilic contributions of all individual residues, SCX interactions depend mainly on peptide charge (number of basic residues at acidic pH) and size. An additive model (incorporating the contributions of all 20 residues into the peptide retention) combined with a peptide length correction produces a 0.976 R 2 value prediction accuracy, significantly higher than the additive models for either HILIC or RPLC. Position-dependent effects on peptide retention for different residues were driven by the spatial orientation of tryptic peptides upon interaction with the negatively charged surface functional groups. The positively charged N-termini serve as a primary point of interaction. For example, basic residues (Arg, His, Lys) increase peptide retention when located closer to the N-terminus. We also found that hydrophobic interactions, which could lead to a mixed-mode separation mechanism, are largely suppressed at 20-30% of acetonitrile in the eluent. The accuracy of the final Sequence-Specific Retention Calculator (SSRCalc) SCX model (∼0.99 R 2 value) exceeds all previously reported predictors for peptide LC separations. This also provides a solid platform for method development in 2D LC-MS protocols in proteomics and peptide retention prediction filtering of false positive identifications.

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas.

PubMed

Vigna, Bianca Baccili Zanotto; de Oliveira, Fernanda Ancelmo; de Toledo-Silva, Guilherme; da Silva, Carla Cristina; do Valle, Cacilda Borges; de Souza, Anete Pereira

2016-11-11

Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi. We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated. The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.

Task Demands in OSCEs Influence Learning Strategies.

PubMed

Lafleur, Alexandre; Laflamme, Jonathan; Leppink, Jimmie; Côté, Luc

2017-01-01

Models on pre-assessment learning effects confirmed that task demands stand out among the factors assessors can modify in an assessment to influence learning. However, little is known about which tasks in objective structured clinical examinations (OSCEs) improve students' cognitive and metacognitive processes. Research is needed to support OSCE designs that benefit students' metacognitive strategies when they are studying, reinforcing a hypothesis-driven approach. With that intent, hypothesis-driven physical examination (HDPE) assessments ask students to elicit and interpret findings of the physical exam to reach a diagnosis ("Examine this patient with a painful shoulder to reach a diagnosis"). When studying for HDPE, students will dedicate more time to hypothesis-driven discussions and practice than when studying for a part-task OSCE ("Perform the shoulder exam"). It is expected that the whole-task nature of HDPE will lead to a hypothesis-oriented use of the learning resources, a frequent use of adjustment strategies, and persistence with learning. In a mixed-methods study, 40 medical students were randomly paired and filmed while studying together for two hypothetical OSCE stations. Each 25-min study period began with video cues asking to study for either a part-task OSCE or an HDPE. In a crossover design, sequences were randomized for OSCEs and contents (shoulder or spine). Time-on-task for discussions or practice were categorized as "hypothesis-driven" or "sequence of signs and maneuvers." Content analysis of focus group interviews summarized students' perception of learning resources, adjustment strategies, and persistence with learning. When studying for HDPE, students allocate significantly more time for hypothesis-driven discussions and practice. Students use resources contrasting diagnoses and report persistence with learning. When studying for part-task OSCEs, time-on-task is reversed, spent on rehearsing a sequence of signs and maneuvers. OSCEs with similar contents but different task demands lead to opposite learning strategies regarding how students manage their study time. Measuring pre-assessment effects from a metacognitive perspective provides empirical evidence to redesign assessments for learning.

Grass invasion into switchgrass managed for biomass energy

USDA-ARS?s Scientific Manuscript database

Switchgrass (Panicum virgatum) is a warm-season perennial grass and is the model herbaceous perennial bioenergy feedstock. Although it is indigenous to North American grasslands east of the Rocky Mountains and has been planted for forage and conservation purposes for more than 75 years, there is con...

Predicting As, Cd, Cu, Pb and Zn levels in grasses (Agrostis sp. and Poa sp.) and stinging nettle (Urtica dioica) applying soil-plant transfer models.

PubMed

Boshoff, Magdalena; De Jonge, Maarten; Scheifler, Renaud; Bervoets, Lieven

2014-09-15

The aim of this study was to derive regression-based soil-plant models to predict and compare metal(loid) (i.e. As, Cd, Cu, Pb and Zn) concentrations in plants (grass Agrostis sp./Poa sp. and nettle Urtica dioica L.) among sites with a wide range of metal pollution and a wide variation in soil properties. Regression models were based on the pseudo total (aqua-regia) and exchangeable (0.01 M CaCl2) soil metal concentrations. Plant metal concentrations were best explained by the pseudo total soil metal concentrations in combination with soil properties. The most important soil property that influenced U. dioica metal concentrations was the clay content, while for grass organic matter (OM) and pH affected the As (OM) and Cu and Zn (pH). In this study multiple linear regression models proved functional in predicting metal accumulation in plants on a regional scale. With the proposed models based on the pseudo total metal concentration, the percentage of variation explained for the metals As, Cd, Cu, Pb and Zn were 0.56%, 0.47%, 0.59%, 0.61%, 0.30% in nettle and 0.46%, 0.38%, 0.27%, 0.50%, 0.28% in grass. Copyright © 2014 Elsevier B.V. All rights reserved.

Stable Carbon Isotope Ratios of Individual Pollen Grains as a Proxy for C3- Versus C4-Grass Abundance in Paleorecords: A Validation Study

NASA Astrophysics Data System (ADS)

Nelson, D. M.; Hu, F.; Pearson, A.

2007-12-01

C3 and C4 grasses have distinct influences on major biogeochemical processes and unique responses to important environmental controls. Difficulties in distinguishing between these two functional groups of grasses have hindered paleoecological studies of grass-dominated ecosystems. We recently developed a technique to analyze the stable carbon isotope composition of individual grass-pollen grains using a spooling- wire microcombustion device interfaced with an isotope-ratio mass spectrometer (Nelson et al. 2007). This technique holds promise for improving C3 and C4 grass reconstructions. It requires ~90% fewer grains than typical methods and avoids assumptions associated with mixing models. However, our previous work was based on known C3 and C4 grasses from herbarium specimens and field collections and the technique had not been test using geological samples. To test the ability of this technique to reproduce the abundance of C3 and C4 grasses on the landscape, we measured δ13C values of >1500 individual grains of grass pollen isolated from the surface sediments of 10 North American lakes that span a large gradient of C3 and C4 grass abundance. Results indicate a strong positive correlation (r=0.94) between % C4-grass pollen (derived from classifying δ13C values from single grains as C3 and C4) and the literature-reported abundance of C4 grasses on the landscape. However, the measured % C4-grass pollen shows some deviation from the actual abundance at sites with high proportions of C4 grasses. This is likely caused by uncertainty in the magnitude, composition, and variability of the analytical blank associated with these measurements. Correcting for this deviation using regression analysis improves the estimation of the abundance of C4 grasses on the landscape. Comparison of the % C4-grass pollen with C/N and δ13C measurements of total organic matter in the same lake-sediment samples illustrates the distinct advantage of grass-pollen δ13C as a proxy for distinguishing C3 and C4 shifts. At 9 of the 10 sites C/N values indicate that surface-sediment organic matter was derived primarily from aquatic production. At the one site where organic matter was produced primarily by vascular plants the δ13C value (-29.3°) suggests organic matter derived exclusively from C3 plants. However, ~80% of the grasses on the landscape at this site are C4 grasses. The C3- like bulk-sediment δ13C value likely represents woody species, which comprise >90% of the pollen spectra. Thus δ13C analysis of single grains of grass pollen offers a new tool to classify grass pollen into two major functional groups and promises to advance our understanding of grassland ecology and evolution. Reference Nelson, D.M., Hu, F.S., Mikucki, J., Tian, J., and Pearson, A., 2007, Carbon isotopic analysis of individual pollen grains from C3 and C4 grasses using a spooling wire microcombustion interface: Geochimica et Cosmochimica Acta, v. 71, p. 4005-4014.

Natural forest succession and fire history

Treesearch

G. E. Gruell; W. C. Schmidt; S. F. Arno; W. J. Reich

1999-01-01

“Succession” is the term applied to a change or sequence of vegetation on a given site through time following disturbance. For example, a succession of plant communities that follows clearcutting with broadcast burning of slash might be (1) grass-forb, (2) shrubfield, (3) saplings and shrubs, (4) pole-size trees, (5) mature forest, and (6) old-growth forest. Succession...

Population genetic structure of the seed pathogen Pyrenophora semeniperda on Bromus tectorum in western North America

Treesearch

David Boose; Steven Harrison; Suzette Clement; Susan E. Meyer

2011-01-01

We examined genetic variation in the ascomycete pathogen Pyrenophora semeniperda cultured from seeds of the invasive grass Bromus tectorum in the Intermountain West of North America. We sequenced the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA genome in 417 monoconidial cultures collected from 20 sites in Washington, Idaho, Utah and Colorado,...

A Japanese Encephalitis Virus Peptide Present on Johnson Grass Mosaic Virus-Like Particles Induces Virus-Neutralizing Antibodies and Protects Mice against Lethal Challenge

PubMed Central

Saini, Manisha; Vrati, Sudhanshu

2003-01-01

Protection against Japanese encephalitis virus (JEV) is antibody dependent, and neutralizing antibodies alone are sufficient to impart protection. Thus, we are aiming to develop a peptide-based vaccine against JEV by identifying JEV peptide sequences that could induce virus-neutralizing antibodies. Previously, we have synthesized large amounts of Johnson grass mosaic virus (JGMV) coat protein (CP) in Escherichia coli and have shown that it autoassembled to form virus-like particles (VLPs). The envelope (E) protein of JEV contains the virus-neutralization epitopes. Four peptides from different locations within JEV E protein were chosen, and these were fused to JGMV CP by recombinant DNA methods. The fusion protein autoassembled to form VLPs that could be purified by sucrose gradient centrifugation. Immunization of mice with the recombinant VLPs containing JEV peptide sequences induced anti-peptide and anti-JEV antibodies. A 27-amino-acid peptide containing amino acids 373 to 399 from JEV E protein, present on JGMV VLPs, induced virus-neutralizing antibodies. Importantly, these antibodies were obtained without the use of an adjuvant. The immunized mice showed significant protection against a lethal JEV challenge. PMID:12610124

Grass pollen counts, air pollution levels and allergic rhinitis severity.

PubMed

Annesi-Maesano, Isabella; Rouve, Sarah; Desqueyroux, Hélène; Jankovski, Roger; Klossek, Jean-Michel; Thibaudon, Michel; Demoly, Pascal; Didier, Alain

2012-01-01

Little is known about the relation between allergic rhinitis severity and airborne pollen in combination with air pollutants. To model the risk of suffering from severe seasonal allergic rhinitis (SAR) as a function of both pollen count and air pollution levels in a large nationwide sample of patients whose SAR was diagnosed by a physician and confirmed by skin prick test positivity or specific immunolglobulin E to common aeroallergens. The severity of SAR symptoms was estimated with the Symptomatic Global Score (SGS) among 36,397 patients suffering from an untreated and uncomplicated SAR between May and August 2004 in metropolitan France. Patients who had an SGS in the upper third quartile were classified as suffering from severe SAR. A multilevel model relating SAR severity, pollen and air pollution was used to take into account the hierarchical data structure. 18.9% of the 17,567 urban patients retained for the analysis suffered from severe rhinitis. At the Lag0 (day of the visit), a rise of 60 grass pollen grains/m(3) increased the risk of suffering from a severe SAR form by 8% in the multileveled model after adjusting for potential confounders and air pollution levels. Results were also confirmed in the subsample of individuals with documented sensitization to grass pollen. Grass pollen count aggravated SAR in terms of symptoms in our nationwide sample. These findings confirm the need for proper treatment and preventive measures in SAR patients sensitized to grass pollen. Copyright © 2012 S. Karger AG, Basel.

Distribution modelling of pre-Columbian California grasslands with soil phytoliths: New insights for prehistoric grassland ecology and restoration

PubMed Central

2018-01-01

Historical reconstructions of plant community distributions are useful for biogeographic studies and restoration planning, but the quality of insights gained depends on the depth and reliability of historical information available. For the Central Valley of California, one of the most altered terrestrial ecosystems on the planet, this task is particularly difficult given poor historical documentation and sparse relict assemblages of pre-invasion plant species. Coastal and interior prairies were long assumed to have been dominated by perennial bunchgrasses, but this hypothesis has recently been challenged. We evaluated this hypothesis by creating species distribution models (SDMs) using a novel approach based on the abundance of soil phytoliths (microscopic particles of biogenic silica used as a proxy for long-term grass presence) extracted from soil samples at locations statewide. Modeled historical grass abundance was consistently high along the coast and to a lesser extent in higher elevation foothills surrounding the Central Valley. SDMs found strong associations with mean temperature, temperature variability, and precipitation variability, with higher predicted abundance in regions with cooler, equable temperatures and moderated rainfall, mirroring the pattern for modern perennial grass distribution across the state. The results of this study strongly suggest that the pre-Columbian Central Valley of California was not dominated by grasses. Using soil phytolith data as input for SDMs is a promising new method for predicting the extent of prehistoric grass distributions where alternative historical datasets are lacking. PMID:29617400

Distribution modelling of pre-Columbian California grasslands with soil phytoliths: New insights for prehistoric grassland ecology and restoration.

PubMed

Fick, Stephen E; Evett, Rand R

2018-01-01

Historical reconstructions of plant community distributions are useful for biogeographic studies and restoration planning, but the quality of insights gained depends on the depth and reliability of historical information available. For the Central Valley of California, one of the most altered terrestrial ecosystems on the planet, this task is particularly difficult given poor historical documentation and sparse relict assemblages of pre-invasion plant species. Coastal and interior prairies were long assumed to have been dominated by perennial bunchgrasses, but this hypothesis has recently been challenged. We evaluated this hypothesis by creating species distribution models (SDMs) using a novel approach based on the abundance of soil phytoliths (microscopic particles of biogenic silica used as a proxy for long-term grass presence) extracted from soil samples at locations statewide. Modeled historical grass abundance was consistently high along the coast and to a lesser extent in higher elevation foothills surrounding the Central Valley. SDMs found strong associations with mean temperature, temperature variability, and precipitation variability, with higher predicted abundance in regions with cooler, equable temperatures and moderated rainfall, mirroring the pattern for modern perennial grass distribution across the state. The results of this study strongly suggest that the pre-Columbian Central Valley of California was not dominated by grasses. Using soil phytolith data as input for SDMs is a promising new method for predicting the extent of prehistoric grass distributions where alternative historical datasets are lacking.

Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

PubMed Central

2010-01-01

Background Physical maps employing libraries of bacterial artificial chromosome (BAC) clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum), Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete Triticeae genome. This study demonstrates that global fingerprinting of the large plant genomes is a viable strategy for generating physical maps. Physical maps allow the description of the co-linearity between wheat and grass genomes and provide a powerful tool for positional cloning of new genes. PMID:20553621

Severe plant invasions can increase mycorrhizal fungal abundance and diversity.

PubMed

Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

2013-07-01

Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)--but not cheatgrass (Bromus tectorum)--support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance.

Severe plant invasions can increase mycorrhizal fungal abundance and diversity

PubMed Central

Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

2013-01-01

Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)—but not cheatgrass (Bromus tectorum)—support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance. PMID:23486251

Relationship between Heavy Metal Concentrations in Soils and Grasses of Roadside Farmland in Nepal

PubMed Central

Yan, Xuedong; Zhang, Fan; Zeng, Chen; Zhang, Man; Devkota, Lochan Prasad; Yao, Tandong

2012-01-01

Transportation activities can contribute to accumulation of heavy metals in roadside soil and grass, which could potentially compromise public health and the environment if the roadways cross farmland areas. Particularly, heavy metals may enter the food chain as a result of their uptake by roadside edible grasses. This research was conducted to investigate heavy metal (Cu, Zn, Cd, and Pb) concentrations in roadside farmland soils and corresponding grasses around Kathmandu, Nepal. Four factors were considered for the experimental design, including sample type, sampling location, roadside distance, and tree protection. A total of 60 grass samples and 60 topsoil samples were collected under dry weather conditions. The Multivariate Analysis of Variance (MANOVA) results indicate that the concentrations of Cu, Zn, and Pb in the soil samples are significantly higher than those in the grass samples; the concentrations of Cu and Pb in the suburban roadside farmland are higher than those in the rural mountainous roadside farmland; and the concentrations of Cu and Zn at the sampling locations with roadside trees are significantly lower than those without tree protection. The analysis of transfer factor, which is calculated as the ratio of heavy-metal concentrations in grass to those in the corresponding soil, indicates that the uptake capabilities of heavy metals from soil to grass is in the order of Zn > Cu > Pb. Additionally, it is found that as the soils’ heavy-metal concentrations increase, the capability of heavy-metal transfer to the grass decreases, and this relationship can be characterized by an exponential regression model. PMID:23202679

A grass–fire cycle eliminates an obligate-seeding tree in a tropical savanna

PubMed Central

Bowman, David M J S; MacDermott, Harry J; Nichols, Scott C; Murphy, Brett P

2014-01-01

A grass–fire cycle in Australian tropical savannas has been postulated as driving the regional decline of the obligate-seeding conifer Callitris intratropica and other fire-sensitive components of the regional flora and fauna, due to proliferation of flammable native grasses. We tested the hypothesis that a high-biomass invasive savanna grass drives a positive feedback process where intense fires destroy fire-sensitive trees, and the reduction in canopy cover facilitates further invasion by grass. We undertook an observational and experimental study using, as a model system, a plantation of C. intratropica that has been invaded by an African grass, gamba (Andropogon gayanus) in the Northern Territory, Australia. We found that high grass biomass was associated with reduced canopy cover and restriction of foliage to the upper canopy of surviving stems, and mortality of adult trees was very high (>50%) even in areas with low fuel loads (1 t·ha−1). Experimental fires, with fuel loads >10 t·ha−1, typical of the grass-invasion front, caused significant mortality due to complete crown scorch. Lower fuel loads cause reduced canopy cover through defoliation of the lower canopy. These results help explain how increases in grass biomass are coupled with the decline of C. intratropica throughout northern Australia by causing a switch from litter and sparse perennial grass fuels, and hence low-intensity surface fires, to heavy annual grass fuel loads that sustain fires that burn into the midstorey. This study demonstrates that changes in fuel type can alter fire regimes with substantial knock-on effects on the biota. PMID:25505543

On the relative role of fire and rainfall in determining vegetation patterns in tropical savannas: a simulation study

NASA Astrophysics Data System (ADS)

Spessa, Allan; Fisher, Rosie

2010-05-01

Tropical savannas cover 18% of the world's land surface and are amongst the most productive terrestrial systems in the world. They comprise 15% of the total terrestrial carbon stock, with an estimated mean net primary productivity (NPP) of 7.2 tCha-1yr-1 or two thirds of NPP in tropical forests. Tropical savannas are the most frequently burnt biome, with fire return intervals in highly productive areas being typically 1-2 years. Fires shape vegetation species composition, tree to grass ratios and nutrient redistribution, as well as the biosphere-atmosphere exchange of trace gases, momentum and radiative energy. Tropical savannas are a major source of emissions, contributing 38 % of total annual CO2 from biomass burning, 30% CO, 19 % CH4 and 59 % NOx. Climatically, they occur in regions subject to a strongly seasonal ‘wet-dry' regime, usually under monsoonal control from the movement of the inter-tropical convergence zone. In general, rainfall during the prior wet season(s) determines the amount of grass fuel available for burning while the length of the dry season influences fuel moisture content. Rainfall in tropical savannas exhibits high inter-annual variability, and under future climate change, is projected to change significantly in much of Africa, South America and northern Australia. Process-based simulation models of fire-vegetation dynamics and feedbacks are critical for determining the impacts of wildfires under projected future climate change on i) ecosystem structure and function, and ii) emissions of trace gases and aerosols from biomass burning. A new mechanistic global fire model SPITFIRE (SPread and InTensity of FIRE) has been designed to overcome many of the limitations in existing fire models set within Dynamic Global Vegetation Models (DGVMs). SPITFIRE has been applied in coupled mode globally and southern Africa, both as part of the LPJ DGVM. It has also been driven with MODIS burnt area data applied to sub-Saharan Africa, while coupled to the LPJ-GUESS vegetation model. Recently, SPIFTIRE has been coupled to the Ecosystem Demography (ED) model, which simulates global vegetation dynamics as part of the new land surface scheme JULES (Joint UK Environment Simulator) within the QUEST Earth System Model (http://www.quest-esm.ac.uk/). This study forms part of on-going work to further improve and test the ability of JULES to accurately simulate the terrestrial carbon cycle and land-atmosphere exchanges under different climates. Using the JULES (ED-SPITFIRE) model driven by observed climate (1901-2002), and focusing on large-scale rainfall gradients in the tropical savannas of west Africa, the Northern Territory (Australia) and central-southern Brazil, this study assesses: i) simulated versus observed vegetation dynamics and distributions, and ii) the relative importance of fire versus rainfall in determining vegetation patterns. A sensitivity analysis approach was used.

Functional language and data flow architectures

NASA Technical Reports Server (NTRS)

Ercegovac, M. D.; Patel, D. R.; Lang, T.

1983-01-01

This is a tutorial article about language and architecture approaches for highly concurrent computer systems based on the functional style of programming. The discussion concentrates on the basic aspects of functional languages, and sequencing models such as data-flow, demand-driven and reduction which are essential at the machine organization level. Several examples of highly concurrent machines are described.

Hydraulic lift as a determinant of tree-grass coexistence on savannas.

PubMed

Yu, Kailiang; D'Odorico, Paolo

2015-09-01

The coexistence of woody plants and grasses in savannas is determined by a complex set of interacting factors that determine access to resources and demographic dynamics, under the control of external drivers and vegetation feedbacks with the physical environment. Existing theories explain coexistence mainly as an effect of competitive relations and/or disturbances. However, theoretical studies on the way facilitative interactions resulting from hydraulic lift affect tree-grass coexistence and the range of environmental conditions in which savannas are stable are still lacking. We investigated the role of hydraulic lift in the stability of tree-grass coexistence in savannas. To that end, we developed a new mechanistic model that accounts for both competition for soil water in the shallow soil and fire-induced disturbance. We found that hydraulic lift favors grasses, which scavenge the water lifted by woody plants. Thus, hydraulic lift expands (at the expenses of woodlands) the range of environmental conditions in which savannas are stable. These results indicate that hydraulic lift can be an important mechanism responsible for the coexistence of woody plants and grasses in savannas. Grass facilitation by trees through the process of hydraulic lift could allow savannas to persist stably in mesic regions that would otherwise exhibit a forest cover. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

High-biomass C4 grasses-Filling the yield gap.

PubMed

Mullet, John E

2017-08-01

A significant increase in agricultural productivity will be required by 2050 to meet the needs of an expanding and rapidly developing world population, without allocating more land and water resources to agriculture, and despite slowing rates of grain yield improvement. This review examines the proposition that high-biomass C 4 grasses could help fill the yield gap. High-biomass C 4 grasses exhibit high yield due to C 4 photosynthesis, long growth duration, and efficient capture and utilization of light, water, and nutrients. These C 4 grasses exhibit high levels of drought tolerance during their long vegetative growth phase ideal for crops grown in water-limited regions of agricultural production. The stems of some high-biomass C 4 grasses can accumulate high levels of non-structural carbohydrates that could be engineered to enhance biomass yield and utility as feedstocks for animals and biofuels production. The regulatory pathway that delays flowering of high-biomass C 4 grasses in long days has been elucidated enabling production and deployment of hybrids. Crop and landscape-scale modeling predict that utilization of high-biomass C 4 grass crops on land and in regions where water resources limit grain crop yield could increase agricultural productivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Environmental assessment of a representative grass-finishing beef operation in southern Pennsylvania

USDA-ARS?s Scientific Manuscript database

The objective of this study was to quantify environmental impacts of a representative grass-finished beef operation in southeastern Pennsylvania. A farm-gate life cycle assessment was conducted using the Integrated Farm System Model to estimate greenhouse gas emissions, reactive nitrogen loss, and w...

On the causes of variability in amounts of airborne grass pollen in Melbourne, Australia

NASA Astrophysics Data System (ADS)

de Morton, Julian; Bye, John; Pezza, Alexandre; Newbigin, Edward

2011-07-01

In Melbourne, Australia, airborne grass pollen is the predominant cause of hay fever (seasonal rhinitis) during late spring and early summer, with levels of airborne grass pollen also influencing hospital admissions for asthma. In order to improve predictions of conditions that are potentially hazardous to susceptible individuals, we have sought to better understand the causes of diurnal, intra-seasonal and inter-seasonal variability of atmospheric grass pollen concentrations (APC) by analysing grass pollen count data for Melbourne for 16 grass pollen seasons from 1991 to 2008 (except 1994 and 1995). Some of notable features identified in this analysis were that on days when either extreme (>100 pollen grains m-3) or high (50-100 pollen grains m-3) levels of grass pollen were recorded the winds were of continental origin. In contrast, on days with a low (<20 pollen grains m-3) concentration of grass pollen, winds were of maritime origin. On extreme and high grass pollen days, a peak in APC occurred on average around 1730 hours, probably due to a reduction in surface boundary layer turbulence. The sum of daily APC for each grass pollen season was highly correlated ( r = 0.79) with spring rainfall in Melbourne for that year, with about 60% of a declining linear trend across the study period being attributable to a reduction of meat cattle and sheep (and hence grazing land) in rural areas around Melbourne. Finally, all of the ten extreme pollen events (3 days or more with APC > 100 pollen grains m-3) during the study period were characterised by an average downward vertical wind anomaly in the surface boundary layer over Melbourne. Together these findings form a basis for a fine resolution atmospheric general circulation model for grass pollen in Melbourne's air that can be used to predict daily (and hourly) APC. This information will be useful to those sectors of Melbourne's population that suffer from allergic problems.

On the causes of variability in amounts of airborne grass pollen in Melbourne, Australia.

PubMed

de Morton, Julian; Bye, John; Pezza, Alexandre; Newbigin, Edward

2011-07-01

In Melbourne, Australia, airborne grass pollen is the predominant cause of hay fever (seasonal rhinitis) during late spring and early summer, with levels of airborne grass pollen also influencing hospital admissions for asthma. In order to improve predictions of conditions that are potentially hazardous to susceptible individuals, we have sought to better understand the causes of diurnal, intra-seasonal and inter-seasonal variability of atmospheric grass pollen concentrations (APC) by analysing grass pollen count data for Melbourne for 16 grass pollen seasons from 1991 to 2008 (except 1994 and 1995). Some of notable features identified in this analysis were that on days when either extreme (>100 pollen grains m(-3)) or high (50-100 pollen grains m(-3)) levels of grass pollen were recorded the winds were of continental origin. In contrast, on days with a low (<20 pollen grains m(-3)) concentration of grass pollen, winds were of maritime origin. On extreme and high grass pollen days, a peak in APC occurred on average around 1730 hours, probably due to a reduction in surface boundary layer turbulence. The sum of daily APC for each grass pollen season was highly correlated (r = 0.79) with spring rainfall in Melbourne for that year, with about 60% of a declining linear trend across the study period being attributable to a reduction of meat cattle and sheep (and hence grazing land) in rural areas around Melbourne. Finally, all of the ten extreme pollen events (3 days or more with APC > 100 pollen grains m(-3)) during the study period were characterised by an average downward vertical wind anomaly in the surface boundary layer over Melbourne. Together these findings form a basis for a fine resolution atmospheric general circulation model for grass pollen in Melbourne's air that can be used to predict daily (and hourly) APC. This information will be useful to those sectors of Melbourne's population that suffer from allergic problems.

Germination sensitivities to water potential among co-existing C3 and C4 grasses of cool semi-arid prairie grasslands.

PubMed

Mollard, F P O; Naeth, M A

2015-03-01

An untested theory states that C4 grass seeds could germinate under lower water potentials (Ψ) than C3 grass seeds. We used hydrotime modelling to study seed water relations of C4 and C3 Canadian prairie grasses to address Ψ divergent sensitivities and germination strategies along a risk-spreading continuum of responses to limited water. C4 grasses were Bouteloua gracilis, Calamovilfa longifolia and Schizachyrium scoparium; C3 grasses were Bromus carinatus, Elymus trachycaulus, Festuca hallii and Koeleria macrantha. Hydrotime parameters were obtained after incubation of non-dormant seeds under different Ψ PEG 6000 solutions. A t-test between C3 and C4 grasses did not find statistical differences in population mean base Ψ (Ψb (50)). We found idiosyncratic responses of C4 grasses along the risk-spreading continuum. B. gracilis showed a risk-taker strategy of a species able to quickly germinate in a dry soil due to its low Ψb (50) and hydrotime (θH ). The high Ψb (50) of S. scoparium indicates it follows the risk-averse strategy so it can only germinate in wet soils. C. longifolia showed an intermediate strategy: the lowest Ψb (50) yet the highest θH . K. macrantha, a C3 grass which thrives in dry habitats, had the highest Ψb (50), suggesting a risk-averse strategy for a C3 species. Other C3 species showed intermediate germination patterns in response to Ψ relative to C4 species. Our results indicate that grasses display germination sensitivities to Ψ across the risk-spreading continuum of responses. Thus seed water relations may be poor predictors to explain differential recruitment and distribution of C3 and C4 grasses in the Canadian prairies. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Characterizing phenological vegetation dynamics amidst extreme climate variability in Australia with MODIS VI data

NASA Astrophysics Data System (ADS)

Broich, M.; Huete, A. R.; Xuanlon, M.; Davies, K.; Restrepo-Coupe, N.; Ratana, P.

2012-12-01

Australia's climate is extremely variable with inter-annual rainfall at any given site varying by 5- or 6-fold or more, across the continent. In addition to such inter-annual variability, there can be significant intra-annual variability, especially in monsoonal Australia (e.g. the wet tropical savannas) and Mediterranean climates in SW Australia where prolonged dry seasons occur each year. This presents unique challenges to the characterization of seasonal dynamics with satellite datasets. In contrast to annual reoccurring temperature-driven phenology of northern hemisphere mid-latitudes, vegetation dynamics of the vast and dry Australian interior are poorly quantified by existing remote sensing products. For example, in the current global-based MODIS phenology product, central Australia is covered by ~30% fill values for any given year. Two challenges are specific to Australian landscapes: first, the difficulty of characterizing seasonality of rainfall-driven ecosystems in interior Australia where duration and magnitude of green-up and brown down cycles show high inter annual variability; second, modeling two phenologic layers, the trees and the grass in savannas were the trees are evergreen but the herbaceous understory varies with rainfall. Savannas cover >50% of Australia. Australia's vegetation and climate are different from other continents. A MODIS phenology product capable of characterizing vegetation dynamics across the continent is being developed in this research as part of the AusCover national expert network aiming to provide Australian biophysical remote sensing data time-series and continental-scale map products. These products aim to support the Terrestrial Ecosystem Research Network (TERN) serving ecosystem research in Australia. The MODIS land surface product for Australia first searches the entire time series of each Climate Modeling Grid pixel for low-high-low extreme point sequences. A double logistic function is then fit to each of these sequences allowing identification of growth periods with different magnitudes and durations anywhere in the time series. Results show that the highest absolute variability in peak greenness occurred in cropped areas while the highest relative variability (coefficient of variation) occurred in interior Australia particularly around Lake Eyre, the center of a closed drainage basin in the dry interior of the continent. Across the desert interior, the timing of the green-up onset and the peak greenness was correlated with the landfall of cyclones and the inland penetration and strength of the north Australian summer monsoon (represented by TRMM data). The variability of Australian land surface phenology magnitude and timing was found to be strongly correlated with the swings between La Nina and El Nino events. The information on vegetation dynamics represented here is critical for land surface, fuel accumulation, agricultural production, and permanent ecosystem change modeling in relation to climate trends. A unique research opportunity is provided by recent climate variability: in 2010 a persistent El Nino has given way to a strong two-year La Nina breaking a decade long drought that was followed by record-breaking rainfall across most of the continent and extensive flooding followed by sustained greening.

Grass plastomes reveal unexpected paraphyly with endemic species of Micrairoideae from India and new haplotype markers in Arundinoideae.

PubMed

Duvall, Melvin R; Yadav, Shrirang R; Burke, Sean V; Wysocki, William P

2017-02-01

We investigated the little-studied Arundinoideae/Micrairoideae clade of grasses with an innovative plastome phylogenomic approach. This method gives robust results for taxa of uncertain phylogenetic placement. Arundinoideae comprise ∼45 species, although historically was much larger. Arundinoideae is notable for the widely invasive Phragmites australis . Micrairoideae comprise nine genera and ∼200 species. Some are threatened with extinction, including Hubbardia , some Isachne spp., and Limnopoa . Two micrairoid genera, Eriachne and Pheidochloa , exhibit C 4 photosynthesis in this otherwise C 3 subfamily and represent an independent origin of the C 4 pathway among grasses. Five new plastomes were sequenced with next-generation sequencing-by-synthesis methods. Plastomes were assembled by de novo methods and phylogenetically analyzed with eight other recently published arundinoid or micrairoid plastomes and 11 outgroup species. Stable carbon isotope ratios were determined for micrairoid and arundinoid species to investigate ambiguities in the proxy evidence for C 4 photosynthesis. Phylogenomic analyses showed strong support for ingroup nodes in the Arundinoideae/Micrairoideae subtree, including a paraphyletic clade of Hubbardieae with Isachneae. Anatomical, biochemical, and positively selected sites data are ambiguous with regard to the photosynthetic pathways in Micrairoideae. Species of Hubbardia , Isachne , and Limnopoa were definitively shown by δ 13 C measurements to be C 3 and Eriachne to be C 4 . Our plastome phylogenomic analyses for Micrairoideae are the first phylogenetic results to indicate paraphyly between Isachneae and Hubbardieae. The definitive δ 13 C data for four genera of Micrairoideae indicates the breadth of variation possible in the proxy evidence for photosynthetic pathways of both C 3 and C 4 taxa. © 2017 Duvall et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY-NC).

An Improved Brome mosaic virus Silencing Vector: Greater Insert Stability and More Extensive VIGS.

PubMed

Ding, Xin Shun; Mannas, Stephen W; Bishop, Bethany A; Rao, Xiaolan; Lecoultre, Mitchell; Kwon, Soonil; Nelson, Richard S

2018-01-01

Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus-silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is the instability of the foreign gene fragment (insert) in the vector during VIGS. Here, we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence. Modification of the BMV RNA3 sequence yielded a vector, BMVCP5, that better maintained phytoene desaturase and heat shock protein70-1 ( HSP70-1 ) inserts in Nicotiana benthamiana and maize ( Zea mays ). Longer maintenance of inserts was correlated with greater target gene silencing and more extensive visible silencing phenotypes displaying greater tissue penetration and involving more leaves. The modified vector accumulated similarly to the original vector in N. benthamiana after agroinfiltration, thus maintaining a high titer of virus in this intermediate host used to produce virus inoculum for grass hosts. For HSP70 , silencing one family member led to a large increase in the expression of another family member, an increase likely related to the target gene knockdown and not a general effect of virus infection. The cause of the increased insert stability in the modified vector is discussed in relationship to its recombination and accumulation potential. The modified vector will improve functional genomic studies in grasses, and the conceptual methods used to improve the vector may be applied to other VIGS vectors. © 2018 American Society of Plant Biologists. All Rights Reserved.

The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses.

PubMed

Jouet, Agathe; McMullan, Mark; van Oosterhout, Cock

2015-06-01

Plant immune genes, or resistance genes, are involved in a co-evolutionary arms race with a diverse range of pathogens. In agronomically important grasses, such R genes have been extensively studied because of their role in pathogen resistance and in the breeding of resistant cultivars. In this study, we evaluate the importance of recombination, mutation and selection on the evolution of the R gene complex Rp1 of Sorghum, Triticum, Brachypodium, Oryza and Zea. Analyses show that recombination is widespread, and we detected 73 independent instances of sequence exchange, involving on average 1567 of 4692 nucleotides analysed (33.4%). We were able to date 24 interspecific recombination events and found that four occurred postspeciation, which suggests that genetic introgression took place between different grass species. Other interspecific events seemed to have been maintained over long evolutionary time, suggesting the presence of balancing selection. Significant positive selection (i.e. a relative excess of nonsynonymous substitutions (dN /dS >1)) was detected in 17-95 codons (0.42-2.02%). Recombination was significantly associated with areas with high levels of polymorphism but not with an elevated dN /dS ratio. Finally, phylogenetic analyses show that recombination results in a general overestimation of the divergence time (mean = 14.3%) and an alteration of the gene tree topology if the tree is not calibrated. Given that the statistical power to detect recombination is determined by the level of polymorphism of the amplicon as well as the number of sequences analysed, it is likely that many studies have underestimated the importance of recombination relative to the mutation rate. © 2015 John Wiley & Sons Ltd.

The pineapple genome and the evolution of CAM photosynthesis

PubMed Central

Ming, Ray; VanBuren, Robert; Wai, Ching Man; Tang, Haibao; Schatz, Michael C.; Bowers, John E.; Lyons, Eric; Wang, Ming-Li; Chen, Jung; Biggers, Eric; Zhang, Jisen; Huang, Lixian; Zhang, Lingmao; Miao, Wenjing; Zhang, Jian; Ye, Zhangyao; Miao, Chenyong; Lin, Zhicong; Wang, Hao; Zhou, Hongye; Yim, Won C.; Priest, Henry D.; Zheng, Chunfang; Woodhouse, Margaret; Edger, Patrick P.; Guyot, Romain; Guo, Hao-Bo; Guo, Hong; Zheng, Guangyong; Singh, Ratnesh; Sharma, Anupma; Min, Xiangjia; Zheng, Yun; Lee, Hayan; Gurtowski, James; Sedlazeck, Fritz J.; Harkess, Alex; McKain, Michael R.; Liao, Zhenyang; Fang, Jingping; Liu, Juan; Zhang, Xiaodan; Zhang, Qing; Hu, Weichang; Qin, Yuan; Wang, Kai; Chen, Li-Yu; Shirley, Neil; Lin, Yann-Rong; Liu, Li-Yu; Hernandez, Alvaro G.; Wright, Chris L.; Bulone, Vincent; Tuskan, Gerald A.; Heath, Katy; Zee, Francis; Moore, Paul H.; Sunkar, Ramanjulu; Leebens-Mack, James H.; Mockler, Todd; Bennetzen, Jeffrey L.; Freeling, Michael; Sankoff, David; Paterson, Andrew H.; Zhu, Xinguang; Yang, Xiaohan; Smith, J. Andrew C.; Cushman, John C.; Paull, Robert E.; Yu, Qingyi

2016-01-01

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water use efficiency, and the second most important tropical fruit after banana in terms of international trade. We sequenced the genomes of pineapple varieties ‘F153’ and ‘MD2’, and a wild pineapple relative A. bracteatus accession CB5. The pineapple genome has one fewer ancient whole genome duplications than sequenced grass genomes and, therefore, provides an important reference for elucidating gene content and structure in the last common ancestor of extant members of the grass family (Poaceae). Pineapple has a conserved karyotype with seven pre rho duplication chromosomes that are ancestral to extant grass karyotypes. The pineapple lineage has transitioned from C3 photosynthesis to CAM with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues using beta-carbonic anhydrase (βCA) for initial capture of CO2. Promoter regions of all three βCA genes contain a CCA1 binding site that can bind circadian core oscillators. CAM pathway genes were enriched with cis-regulatory elements including the morning (CCACAC) and evening (AAAATATC) elements associated with regulation of circadian-clock genes, providing the first link between CAM and the circadian clock regulation. Gene-interaction network analysis revealed both activation and repression of regulatory elements that control key enzymes in CAM photosynthesis, indicating that CAM evolved by reconfiguration of pathways preexisting in C3 plants. Pineapple CAM photosynthesis is the result of regulatory neofunctionalization of preexisting gene copies and not acquisition of neofunctionalized genes via whole genome or tandem gene duplication. PMID:26523774

Mathematical modelling of digesta passage rate, mean retention time and in vivo apparent digestibility of two different lengths of hay and big-bale grass silage in ponies.

PubMed

Moore-Colyer, M J S; Morrow, H J; Longland, A C

2003-07-01

Welsh-cross pony geldings (about 300 kg live weight) were used in a 4x4 Latin square experiment to determine the rate of passage and apparent digestibility of unchopped big-bale grass silage (BBL), chopped big-bale grass silage (BBS), unchopped grass hay (HL) and chopped grass hay (HS) offered at approximately 15 g/kg live weight per d. On day 1 of collection weeks, ponies were fed 85 g ytterbium chloride hexahydrate-marked feed 1.5 h after the morning meal. Total faecal collections commenced 8 h later and continued for 168 h. Apparent digestibilities of feed DM, organic matter (OM), crude protein (CP, Nx6.25), acid-detergent fibre (ADF) and neutral-detergent fibre (NDF) were also determined. Faecal excretion data were subjected to the models of Pond et al. (1988) and digesta mean retention time (MRT) calculated from these models and using the algebraic method of Thielmans et al. (1978). Silage had significantly (P<0.05) higher digestibilities of DM, OM, CP, ADF and NDF than hay; however, chop length had no effect. All the models of Pond et al. (1988) accurately described (R(2)>0.8) the pattern of faecal marker excretion. MRT of BBL (29.0 h)>BBS(27 h)>HS and HL (26 h). Compartmental analysis using the G3 model of Pond et al. (1988) showed BBL and HS diets had longer MRT in the time-dependent compartment, whereas BBS and HL had longer MRT in the time-independent compartment. Results from this experiment indicate that BBL and BBS are readily accepted and digested by ponies. While Yb is a successful external marker for determining total tract MRT and for modelling faecal excretion curves in horses, the results did not allow any definite conclusions to be drawn on digesta MRT within the different compartments of the equid gut.

Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae.

PubMed

Zhao, Lei; Zhang, Ning; Ma, Peng-Fei; Liu, Qi; Li, De-Zhu; Guo, Zhen-Hua

2013-01-01

BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.

Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

PubMed Central

Zhao, Lei; Zhang, Ning; Ma, Peng-Fei; Liu, Qi; Li, De-Zhu; Guo, Zhen-Hua

2013-01-01

BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family. PMID:23734211

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

PubMed

Pimentel, Manuel; Escudero, Marcial; Sahuquillo, Elvira; Minaya, Miguel Ángel; Catalán, Pilar

2017-01-01

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding ( ndhF , matk ) and three non-coding ( trnH-psbA , trnT-L and trnL-F ), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n  = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

PubMed Central

Escudero, Marcial; Sahuquillo, Elvira; Minaya, Miguel Ángel; Catalán, Pilar

2017-01-01

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae. PMID:28951814

Temperate Pine Barrens and Tropical Rain Forests Are Both Rich in Undescribed Fungi

PubMed Central

Luo, Jing; Walsh, Emily; Naik, Abhishek; Zhuang, Wenying; Zhang, Keqin; Cai, Lei; Zhang, Ning

2014-01-01

Most of fungal biodiversity on Earth remains unknown especially in the unexplored habitats. In this study, we compared fungi associated with grass (Poaceae) roots from two ecosystems: the temperate pine barrens in New Jersey, USA and tropical rain forests in Yunnan, China, using the same sampling, isolation and species identification methods. A total of 426 fungal isolates were obtained from 1600 root segments from 80 grass samples. Based on the internal transcribed spacer (ITS) sequences and morphological characteristics, a total of 85 fungal species (OTUs) belonging in 45 genera, 23 families, 16 orders, and 6 classes were identified, among which the pine barrens had 38 and Yunnan had 56 species, with only 9 species in common. The finding that grass roots in the tropical forests harbor higher fungal species diversity supports that tropical forests are fungal biodiversity hotspots. Sordariomycetes was dominant in both places but more Leotiomycetes were found in the pine barrens than Yunnan, which may play a role in the acidic and oligotrophic pine barrens ecosystem. Equal number of undescribed fungal species were discovered from the two sampled ecosystems, although the tropical Yunnan had more known fungal species. Pine barrens is a unique, unexplored ecosystem. Our finding suggests that sampling plants in such unexplored habitats will uncover novel fungi and that grass roots in pine barrens are one of the major reservoirs of novel fungi with about 47% being undescribed species. PMID:25072783

Factors influencing the grass carp gut microbiome and its effect on metabolism.

PubMed

Ni, Jiajia; Yan, Qingyun; Yu, Yuhe; Zhang, Tanglin

2014-03-01

Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redundancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness and feeding (i.e. ryegrass vs. commercial feed, and pond-cultured vs. wild) were significantly related to the gut microbiome. Moreover, many biosynthesis and metabolism pathways of carbohydrates, amino acids and lipids were significantly enhanced by the gut microbiome in ryegrass-fed grass carp. These findings suggest that the metabolic role played by the gut microbiome in grass carp can be affected by feeding. These findings contribute to the field of fish gut microbial ecology and also provide a basis for follow-up functional studies. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

GRASS GIS: The first Open Source Temporal GIS

NASA Astrophysics Data System (ADS)

Gebbert, Sören; Leppelt, Thomas

2015-04-01

GRASS GIS is a full featured, general purpose Open Source geographic information system (GIS) with raster, 3D raster and vector processing support[1]. Recently, time was introduced as a new dimension that transformed GRASS GIS into the first Open Source temporal GIS with comprehensive spatio-temporal analysis, processing and visualization capabilities[2]. New spatio-temporal data types were introduced in GRASS GIS version 7, to manage raster, 3D raster and vector time series. These new data types are called space time datasets. They are designed to efficiently handle hundreds of thousands of time stamped raster, 3D raster and vector map layers of any size. Time stamps can be defined as time intervals or time instances in Gregorian calendar time or relative time. Space time datasets are simplifying the processing and analysis of large time series in GRASS GIS, since these new data types are used as input and output parameter in temporal modules. The handling of space time datasets is therefore equal to the handling of raster, 3D raster and vector map layers in GRASS GIS. A new dedicated Python library, the GRASS GIS Temporal Framework, was designed to implement the spatio-temporal data types and their management. The framework provides the functionality to efficiently handle hundreds of thousands of time stamped map layers and their spatio-temporal topological relations. The framework supports reasoning based on the temporal granularity of space time datasets as well as their temporal topology. It was designed in conjunction with the PyGRASS [3] library to support parallel processing of large datasets, that has a long tradition in GRASS GIS [4,5]. We will present a subset of more than 40 temporal modules that were implemented based on the GRASS GIS Temporal Framework, PyGRASS and the GRASS GIS Python scripting library. These modules provide a comprehensive temporal GIS tool set. The functionality range from space time dataset and time stamped map layer management over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

Nitrogen deposition and sensitive ecosystems: a case study from the San Francisco Bay Area

NASA Astrophysics Data System (ADS)

Weiss, S. B.

2001-12-01

Nitrogen deposition from urban smog can greatly affect local ecosystems. This paper examines a complex situation in the Santa Clara Valley, CA where N-deposition from existing, new, and proposed developments threatens an ecosystem supporting numerous rare, threatened, and endangered species. Grasslands on nutrient-poor serpentinitic soils are being invaded by nutrient-demanding introduced annual grasses, driven by dry N-deposition of about 10 kg ha-1 yr-1. These grass invasions threaten the native biodiversity of the serpentinitic grasslands, including the federally-protected Bay checkerspot butterfly. Additional NOx and NH3 sources planned for the region include a 600 MW natural gas fired power plant, industrial parks that may eventually draw 20,000 to 50,000 additional cars per day, 25,000 housing units, and associated highway improvements. Ongoing mitigation proposals include purchase and long-term management of hundreds of hectares of habitat. The situation is a model for understanding N-deposition from a scientific and policy viewpoint. Fundamental biogeochemical questions include: 1) What are the relative contributions of NOx and NH3 to increased N-deposition? NH3 slip from power plant NOx scrubbers can release more reactive nitrogen than is removed as NOx, and modern automobiles release NH3 in addition to NOx. 2) How are N-emissions transported, chemically modified, and deposited on the local ecosystems, and are these processes adequately captured in regulatory models? How do point sources differ from line sources such as a heavily traveled freeway? 3) What are the effects of chronic N-deposition on the ecosystem, and is there a critical load or a steady cumulative effect? 4) What are the effects of management such as fire, grazing, mowing on N-cycling and plant composition? Policy issues include: 1) What are the incremental impacts of individual projects relative to high background deposition, 2) What margin of safety should be built into modeling and impact assessment? and 3) What are the most effective mitigation options?

Mechanisms control the soil organic carbon loss with grassland degradation in the Qinghai-Tibet Plateau

NASA Astrophysics Data System (ADS)

Peng, Fei; Xian, Xue; You, Quangang; Huang, Cuihua; Dong, Siyang; Liao, Jie; Duan, Hanchen; Wang, Tao

2017-04-01

Grassland in the Qinghai-Tibet Plateau (QTP) provides tremendous carbon (C) sinks and is the important ground for grazing. Grassland degradation, the loss of plant coverage and the emergence of sand activities, results in substantial reduction in soil organic carbon (SOC). To demonstrate the specific degradation pattern of SOC and elucidate underlying mechanisms, a sequence of five degradation stages over the whole grassland in the QTP were investigated. The survey and laboratory data were analyzed by three structural equation modeling (SEM) analysis. One of the analysis focused on the biological processes while the other two included both the biological and physical processes. Soil temperature had no significant change but soil moisture decreased in all layers. The above and the below-ground plant production decreased and the dominant plant functional group shifted from sedge and grass to forbs. The SOC concentration declined about 40-50% in the very severely degraded comparing with intact alpine grassland.All the three models were successfully fitted with R2 about 0.50. Three biological processes can explain the SOC change. The decrease in soil moisture suppressed C output through soil respiration (Rs) thus lower the SOC loss with land degradation. Decline in the plant production due to a decrease in coverage or to the change in relative abundance of sedge, forbs and grass directly or indirectly reduce the C input and finally lead to the 40-50% loss in SOC. The significant pathways from soil microclimate and soil properties to SOC in the black box model, only one significant pathway from soil properties to SOC indicate that physical processes like the wind and water erosion might control the SOC loss with land degradation in the alpine grassland in the QTP.

Neutrino-heated stars and broad-line emission from active galactic nuclei

NASA Technical Reports Server (NTRS)

Macdonald, James; Stanev, Todor; Biermann, Peter L.

1991-01-01

Nonthermal radiation from active galactic nuclei indicates the presence of highly relativistic particles. The interaction of these high-energy particles with matter and photons gives rise to a flux of high-energy neutrinos. In this paper, the influence of the expected high neutrino fluxes on the structure and evolution of single, main-sequence stars is investigated. Sequences of models of neutrino-heated stars in thermal equilibrium are presented for masses 0.25, 0.5, 0.8, and 1.0 solar mass. In addition, a set of evolutionary sequences for mass 0.5 solar mass have been computed for different assumed values for the incident neutrino energy flux. It is found that winds driven by the heating due to high-energy particles and hard electromagnetic radiation of the outer layers of neutrino-bloated stars may satisfy the requirements of the model of Kazanas (1989) for the broad-line emission clouds in active galactic nuclei.

Assessment of soil water, carbon and nitrogen cycling in reseeded grassland on the North Wyke Farm Platform using a process-based model.

PubMed

Li, Yuefen; Liu, Yi; Harris, Paul; Sint, Hadewij; Murray, Phil J; Lee, Michael R F; Wu, Lianhai

2017-12-15

The North Wyke Farm Platform (NWFP) generates large volumes of temporally-indexed data that provides a valuable test-bed for agricultural mathematical models in temperate grasslands. In our study, we used the primary datasets generated from the NWFP (https://nwfp.rothamsted.ac.uk/) to validate the SPACSYS model in terms of the dynamics of water loss and forage dry matter yield estimated through cutting. The SPACSYS model is capable of simulating soil water, carbon (C) and nitrogen (N) balance in the soil-plant-atmosphere system. The validated model was then used to simulate the responses of soil water, C and N to reseeding grass cultivars with either high sugar (Lolium perenne L. cv. AberMagic) or deep rooting (Festulolium cv. Prior) traits. Simulation results demonstrated that the SPACSYS model could predict reliably soil water, C and N cycling in reseeded grassland. Compared to AberMagic, the Prior grass could fix more C in the second year following reseeding, whereas less C was lost through soil respiration in the first transition year. In comparison to the grass cultivar of the permanent pasture that existed before reseeding, both grasses reduced N losses through runoff and contributed to reducing water loss, especially Prior in relation to the latter. The SPACSYS model could predict these differences as supported by the rich dataset from the NWFP, providing a tool for future predictions on less characterized pasture. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Systematics of Simplicia Kirk (Poaceae, Agrostidinae) – an endemic, threatened New Zealand grass genus

PubMed Central

de Lange, Peter J.; Smissen, Rob D.; Rolfe, Jeremy R.; Ogle, Colin C.

2016-01-01

Abstract A new species of the New Zealand endemic grass Simplicia, Simplicia felix is described. The new species is segregated from and compared with Simplicia buchananii and Simplicia laxa. Simplicia felix occurs mostly in lightly shaded areas of seasonally dry alluvial forest. A distribution map and an assessment of the conservation status of the new species are presented. Genetic variation in the genus was examined, building on previously published work but including additional sampling. Analysis of nrDNA ITS and ETS and plastid trnL intron and trnL–F intergenic spacer sequences show Simplicia felix to be more closely related to Simplicia laxa than to Simplicia buchananii. NeighborNet analyses of AFLP profiles for the three species of Simplicia show each to consist of distinct clusters of genotypes well separated from each other. PMID:28127249

Utilization of grasses for potential biofuel production and phytoremediation of heavy metal contaminated soils.

PubMed

Balsamo, Ronald A; Kelly, William J; Satrio, Justinus A; Ruiz-Felix, M Nydia; Fetterman, Marisa; Wynn, Rodd; Hagel, Kristen

2015-01-01

This research focuses on investigating the use of common biofuel grasses to assess their potential as agents of long-term remediation of contaminated soils using lead as a model heavy metal ion. We present evidence demonstrating that switch grass and Timothy grass may be potentially useful for long-term phytoremediation of heavy metal contaminated soils and describe novel techniques to track and remove contaminants from inception to useful product. Enzymatic digestion and thermochemical approaches are being used to convert this lignocellulosic feedstock into useful product (sugars, ethanol, biocrude oil+biochar). Preliminary studies on enzymatic hydrolysis and fast pyrolysis of the Switchgrass materials that were grown in heavy metal contaminated soil and non-contaminated soils show that the presence of lead in the Switchgrass material feedstock does not adversely affect the outcomes of the conversion processes. These results indicate that the modest levels of contaminant uptake allow these grass species to serve as phytoremediation agents as well as feedstocks for biofuel production in areas degraded by industrial pollution.

Two distinct Epichloë species symbiotic with Achnatherum inebrians, drunken horse grass.

PubMed

Chen, Li; Li, Xiuzhang; Li, Chunjie; Swoboda, Ginger A; Young, Carolyn A; Sugawara, Koya; Leuchtmann, Adrian; Schardl, Christopher L

2015-01-01

Achnatherum inebrians, colloquially known as drunken horse grass, is associated with livestock toxicity in northern China. Epichloë gansuensis (Eg) was described from endophyte isolates from A. inebrians in Sunan County, Gansu Province, whereas a morphologically distinct variety, E. gansuensis var. inebrians (Ei), was described based on two isolates from A. inebrians seeds collected in Urumqi County, Xinjiang Province. Genome sequencing and alkaloid analyses also distinguish these taxa; the Ei isolates produce neurotropic lysergic acid amides (ergot alkaloids), and an Eg isolate produces paxilline (an indole-diterpene alkaloid). To better elucidate the taxonomic diversity of Epichloë spp. symbiotic with A. inebrians, we surveyed eight populations in Xinjiang, Gansu and Inner Mongolia provinces of China and analyzed their genotypes by multiplex PCR for alkaloid biosynthesis genes and mating-type genes. Genotypes consistent with Ei were present in all eight populations, of which they dominated seven. The Ei isolates were all mating type A and tested positive for the ergot alkaloid gene, dmaW. In contrast Eg isolates were all mating type B and had the indole-diterpene gene, idtG. The genome was sequenced from an Ei isolate from seeds collected in Xiahe County, Gansu, and compared to that of the varietal ex type isolate from Urumqi. Alkaloid genes and four different housekeeping genes were nearly identical between the two sequenced Ei isolates and were distinct from a sequenced Eg isolate. Phylogenetic analysis placed Ei, Eg and Epichloë sibirica into respective subclades of a clade that emanated from the base of the Epichloë phylogeny. Given its chemotypic, genotypic, morphological and phylogenetic distinctiveness, its widespread occurrence in rangelands of northern China, and its importance in livestock toxicity, we propose raising Ei to species rank as Epichloë inebrians. © 2015 by The Mycological Society of America.

Defining Common Ground: A Grass Roots Model for University-Public School Collaboration.

ERIC Educational Resources Information Center

Starlings, Cable; Dybdahl, Claudia S.

1994-01-01

A collaborative, grass-roots partnership focusing on students at risk for educational failure has been developed by the University of Alaska Anchorage and the Anchorage (Alaska) School District. The effort is distinguished by a perception of common ground, a minimal administrative and financial structure, and a high degree of commitment from…

Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection

USDA-ARS?s Scientific Manuscript database

The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optim...

A diurnal reflectance model using grass: Surface-substrate interaction and inverse solution - October 16, 2011

EPA Science Inventory

We report an analysis of canopy reflectance (ρ) experiment, using hand-held radiometer to measure distribution of biomass in a grass field. The analysis: 1) separates the green-fraction from thatch and soil background, 2) accounts for the changing diurnal ρ with the sun elevation...

Interactions among resource partitioning, sampling effect, and facilitation on the biodiversity effect: a modeling approach.

PubMed

Flombaum, Pedro; Sala, Osvaldo E; Rastetter, Edward B

2014-02-01

Resource partitioning, facilitation, and sampling effect are the three mechanisms behind the biodiversity effect, which is depicted usually as the effect of plant-species richness on aboveground net primary production. These mechanisms operate simultaneously but their relative importance and interactions are difficult to unravel experimentally. Thus, niche differentiation and facilitation have been lumped together and separated from the sampling effect. Here, we propose three hypotheses about interactions among the three mechanisms and test them using a simulation model. The model simulated water movement through soil and vegetation, and net primary production mimicking the Patagonian steppe. Using the model, we created grass and shrub monocultures and mixtures, controlled root overlap and grass water-use efficiency (WUE) to simulate gradients of biodiversity, resource partitioning and facilitation. The presence of shrubs facilitated grass growth by increasing its WUE and in turn increased the sampling effect, whereas root overlap (resource partitioning) had, on average, no effect on sampling effect. Interestingly, resource partitioning and facilitation interacted so the effect of facilitation on sampling effect decreased as resource partitioning increased. Sampling effect was enhanced by the difference between the two functional groups in their efficiency in using resources. Morphological and physiological differences make one group outperform the other; once these differences were established further differences did not enhance the sampling effect. In addition, grass WUE and root overlap positively influence the biodiversity effect but showed no interactions.

Development of single-nucleotide polymorphism markers for Bromus tectorum (Poaceae) from a partially sequenced transcriptome

Treesearch

Keith R. Merrill; Craig E. Coleman; Susan E. Meyer; Elizabeth A. Leger; Katherine A. Collins

2016-01-01

Premise of the study: Bromus tectorum (Poaceae) is an annual grass species that is invasive in many areas of the world but most especially in the U.S. Intermountain West. Single-nucleotide polymorphism (SNP) markers were developed for use in investigating the geospatial and ecological diversity of B. tectorum in the Intermountain West to better understand the...

Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives

PubMed Central

Caignard, Grégory; Eva, Megan M.; van Bruggen, Rebekah; Eveleigh, Robert; Bourque, Guillaume; Malo, Danielle; Gros, Philippe; Vidal, Silvia M.

2014-01-01

Infectious diseases are responsible for over 25% of deaths globally, but many more individuals are exposed to deadly pathogens. The outcome of infection results from a set of diverse factors including pathogen virulence factors, the environment, and the genetic make-up of the host. The completion of the human reference genome sequence in 2004 along with technological advances have tremendously accelerated and renovated the tools to study the genetic etiology of infectious diseases in humans and its best characterized mammalian model, the mouse. Advancements in mouse genomic resources have accelerated genome-wide functional approaches, such as gene-driven and phenotype-driven mutagenesis, bringing to the fore the use of mouse models that reproduce accurately many aspects of the pathogenesis of human infectious diseases. Treatment with the mutagen N-ethyl-N-nitrosourea (ENU) has become the most popular phenotype-driven approach. Our team and others have employed mouse ENU mutagenesis to identify host genes that directly impact susceptibility to pathogens of global significance. In this review, we first describe the strategies and tools used in mouse genetics to understand immunity to infection with special emphasis on chemical mutagenesis of the mouse germ-line together with current strategies to efficiently identify functional mutations using next generation sequencing. Then, we highlight illustrative examples of genes, proteins, and cellular signatures that have been revealed by ENU screens and have been shown to be involved in susceptibility or resistance to infectious diseases caused by parasites, bacteria, and viruses. PMID:25268389

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq.

PubMed

Wang, Jun; Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

PubMed Central

Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet. PMID:28644843

DNA Methylation of T1R1 Gene in the Vegetarian Adaptation of Grass Carp Ctenopharyngodon idella.

PubMed

Cai, Wenjing; He, Shan; Liang, Xu-Fang; Yuan, Xiaochen

2018-05-02

Although previous studies have indicated importance of taste receptors in food habits formation in mammals, little is known about those in fish. Grass carp is an excellent model for studying vegetarian adaptation, as it shows food habit transition from carnivore to herbivore. In the present study, pseudogenization or frameshift mutations of the umami receptors that hypothesized related to dietary switch in vertebrates, were not found in grass carp, suggesting other mechanisms for vegetarian adaptation in grass carp. T1R1 and T1R3 strongly responded to L-Arg and L-Lys, differing from those of zebrafish and medaka, contributing to high species specificity in amino acid preferences and diet selection of grass carp. After food habit transition of grass carp, DNA methylation levels were higher in CPG1 and CPG3 islands of upstream control region of T1R1 gene. Luciferase activity assay of upstream regulatory region of T1R1 (-2500-0 bp) without CPG1 or CPG3 indicated that CPG1 and CPG3 might be involved in transcriptional regulation of T1R1 gene. Subsequently, high DNA methylation decreased expression of T1R1 in intestinal tract. It could be a new mechanism to explain, at least partially, the vegetarian adaptation of grass carp by regulation of expression of umami receptor via epigenetic modification.

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

PubMed Central

Jia, Baofeng; Raphenya, Amogelang R.; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara K.; Lago, Briony A.; Dave, Biren M.; Pereira, Sheldon; Sharma, Arjun N.; Doshi, Sachin; Courtot, Mélanie; Lo, Raymond; Williams, Laura E.; Frye, Jonathan G.; Elsayegh, Tariq; Sardar, Daim; Westman, Erin L.; Pawlowski, Andrew C.; Johnson, Timothy A.; Brinkman, Fiona S.L.; Wright, Gerard D.; McArthur, Andrew G.

2017-01-01

The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis. PMID:27789705

Effects of the heterogeneous landscape on a predator-prey system

NASA Astrophysics Data System (ADS)

Lee, Sang-Hee

2010-01-01

In order to understand how a heterogeneous landscape affects a predator-prey system, a spatially explicit lattice model consisting of predators, prey, grass, and landscape was constructed. The predators and preys randomly move on the lattice space and the grass grows in its neighboring site according to its growth probability. When predators and preys meet at the same site at the same time, a number of prey, equal to the number of predators are eaten. This rule was also applied to the relationship between the prey and grass. The predator (prey) could give birth to an offspring when it ate prey (grass), with a birth probability. When a predator or prey animal was initially introduced, or newly born, its health state was set at a given high value. This health state decreased by one with every time step. When the state of an animal decreased to less than zero, the animal died and was removed from the system. The heterogeneous landscape was characterized by parameter H, which controlled the heterogeneity according to the neutral model. The simulation results showed that H positively or negatively affected a predator’s survival, while its effect on prey and grass was less pronounced. The results can be understood by the disturbance of the balance between the prey and predator densities in the areas where the animals aggregated.

Assessing the biophysical naturalness of grassland in eastern North Dakota with hyperspectral imagery

NASA Astrophysics Data System (ADS)

Zhou, Qiang

Over the past two decades, non-native species within grassland communities have quickly developed due to human migration and commerce. Invasive species like Smooth Brome grass (Bromus inermis) and Kentucky Blue Grass (Poa pratensis), seriously threaten conservation of native grasslands. This study aims to discriminate between native grasslands and planted hayfields and conservation areas dominated by introduced grasses using hyperspectral imagery. Hyperspectral imageries from the Hyperion sensor on EO-1 were acquired in late spring and late summer on 2009 and 2010. Field spectra for widely distributed species as well as smooth brome grass and Kentucky blue grass were collected from the study sites throughout the growing season. Imagery was processed with an unmixing algorithm to estimate fractional cover of green and dry vegetation and bare soil. As the spectrum is significantly different through growing season, spectral libraries for the most common species are then built for both the early growing season and late growing season. After testing multiple methods, the Adaptive Coherence Estimator (ACE) was used for spectral matching analysis between the imagery and spectral libraries. Due in part to spectral similarity among key species, the results of spectral matching analysis were not definitive. Additional indexes, "Level of Dominance" and "Band variance", were calculated to measure the predominance of spectral signatures in any area. A Texture co-occurrence analysis was also performed on both "Level of Dominance" and "Band variance" indexes to extract spatial characteristics. The results suggest that compared with disturbed area, native prairie tend to have generally lower "Level of Dominance" and "Band variance" as well as lower spatial dissimilarity. A final decision tree model was created to predict presence of native or introduced grassland. The model was more effective for identification of Mixed Native Grassland than for grassland dominated by a single species. The discrimination of native and introduced grassland was limited by the similarity of spectral signatures between forb-dominated native grasslands and brome-grass stands. However, saline native grasslands were distinguishable from brome grass.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennetzen, Jeffrey L; Yang, Xiaohan; Ye, Chuyu

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The {approx}400-Mb assembly covers {approx}80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species thatmore » demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).« less

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.

PubMed

Akpinar, Bala Ani; Biyiklioglu, Sezgi; Alptekin, Burcu; Havránková, Miroslava; Vrána, Jan; Doležel, Jaroslav; Distelfeld, Assaf; Hernandez, Pilar; Budak, Hikmet

2018-05-04

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Identification and characterization of Bacillus subtilis from grass carp (Ctenopharynodon idellus) for use as probiotic additives in aquatic feed.

PubMed

Guo, Xia; Chen, Dan-Dan; Peng, Kai-Song; Cui, Zheng-Wei; Zhang, Xu-Jie; Li, Shun; Zhang, Yong-An

2016-05-01

Bacillus subtilis is widely used as probiotic species in aquaculture for water quality control, growth promoting, or immunity enhancing. The aim of this study is to find novel B. subtilis strains from fish as potential probiotics for aquaculture. Eleven B. subtilis isolates derived from the intestinal tract of grass carp were identified by gene sequencing and biochemical tests. These isolates were classified into 4 groups, and the representatives (GC-5, GC-6, GC-21 and GC-22) of each group were further investigated for antibiotic susceptibility, sporulation rate, biofilm formation, activity against pathogenic bacteria, resistance to stress conditions of intestinal tract (high percentage of bile and low pH) and high temperature, which are important for probiotics to be used as feed additives. Additionally, the adhesion properties of the 4 characterized strains were assessed using Caco-2 cell and gut mucus models. The results showed that the 4 strains differed in their capacities to adhere to intestinal epithelial cells and mucus. Furthermore, the strains GC-21 and GC-22 up-regulated the expression levels of IL-10 and TGF-β but down-regulated IL-1β, suggesting their potential anti-inflammatory abilities. Based on physiological properties of the 4 characterized B. subtilis strains, one or more strains may have potential to be used as probiotics in aquaculture. Copyright © 2016 Elsevier Ltd. All rights reserved.

Current quantization and fractal hierarchy in a driven repulsive lattice gas.

PubMed

Rotondo, Pietro; Sellerio, Alessandro Luigi; Glorioso, Pietro; Caracciolo, Sergio; Cosentino Lagomarsino, Marco; Gherardi, Marco

2017-11-01

Driven lattice gases are widely regarded as the paradigm of collective phenomena out of equilibrium. While such models are usually studied with nearest-neighbor interactions, many empirical driven systems are dominated by slowly decaying interactions such as dipole-dipole and Van der Waals forces. Motivated by this gap, we study the nonequilibrium stationary state of a driven lattice gas with slow-decayed repulsive interactions at zero temperature. By numerical and analytical calculations of the particle current as a function of the density and of the driving field, we identify (i) an abrupt breakdown transition between insulating and conducting states, (ii) current quantization into discrete phases where a finite current flows with infinite differential resistivity, and (iii) a fractal hierarchy of excitations, related to the Farey sequences of number theory. We argue that the origin of these effects is the competition between scales, which also causes the counterintuitive phenomenon that crystalline states can melt by increasing the density.

Current quantization and fractal hierarchy in a driven repulsive lattice gas

NASA Astrophysics Data System (ADS)

Rotondo, Pietro; Sellerio, Alessandro Luigi; Glorioso, Pietro; Caracciolo, Sergio; Cosentino Lagomarsino, Marco; Gherardi, Marco

2017-11-01

Driven lattice gases are widely regarded as the paradigm of collective phenomena out of equilibrium. While such models are usually studied with nearest-neighbor interactions, many empirical driven systems are dominated by slowly decaying interactions such as dipole-dipole and Van der Waals forces. Motivated by this gap, we study the nonequilibrium stationary state of a driven lattice gas with slow-decayed repulsive interactions at zero temperature. By numerical and analytical calculations of the particle current as a function of the density and of the driving field, we identify (i) an abrupt breakdown transition between insulating and conducting states, (ii) current quantization into discrete phases where a finite current flows with infinite differential resistivity, and (iii) a fractal hierarchy of excitations, related to the Farey sequences of number theory. We argue that the origin of these effects is the competition between scales, which also causes the counterintuitive phenomenon that crystalline states can melt by increasing the density.

Sequence-of-events-driven automation of the deep space network

NASA Technical Reports Server (NTRS)

Hill, R., Jr.; Fayyad, K.; Smyth, C.; Santos, T.; Chen, R.; Chien, S.; Bevan, R.

1996-01-01

In February 1995, sequence-of-events (SOE)-driven automation technology was demonstrated for a Voyager telemetry downlink track at DSS 13. This demonstration entailed automated generation of an operations procedure (in the form of a temporal dependency network) from project SOE information using artificial intelligence planning technology and automated execution of the temporal dependency network using the link monitor and control operator assistant system. This article describes the overall approach to SOE-driven automation that was demonstrated, identifies gaps in SOE definitions and project profiles that hamper automation, and provides detailed measurements of the knowledge engineering effort required for automation.

Sequence-of-Events-Driven Automation of the Deep Space Network

NASA Technical Reports Server (NTRS)

Hill, R., Jr.; Fayyad, K.; Smyth, C.; Santos, T.; Chen, R.; Chien, S.; Bevan, R.

1996-01-01

In February 1995, sequence-of-events (SOE)-driven automation technology was demonstrated for a Voyager telemetry downlink track at DSS 13. This demonstration entailed automated generation of an operations procedure (in the form of a temporal dependency network) from project SOE information using artificial intelligence planning technology and automated execution of the temporal dependency network using the link monitor and control operator assistant system. This article describes the overall approach to SOE-driven automation that was demonstrated, identifies gaps in SOE definitions and project profiles that hamper automation, and provides detailed measurements of the knowledge engineering effort required for automation.

Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress

USDA-ARS?s Scientific Manuscript database

Lolium temulentum is a valuable model grass species for the study of stress in forage and turf grasses. Gene expression analysis by quantitative real time RT-PCR relies on the use of proper internal standards. The aim of this study was to identify and evaluate reference genes for use in real-time q...

The Weighting Is The Hardest Part: On The Behavior of the Likelihood Ratio Test and the Score Test Under a Data-Driven Weighting Scheme in Sequenced Samples

PubMed Central

Minică, Camelia C.; Genovese, Giulio; Hultman, Christina M.; Pool, René; Vink, Jacqueline M.; Neale, Michael C.; Dolan, Conor V.; Neale, Benjamin M.

2017-01-01

Sequence-based association studies are at a critical inflexion point with the increasing availability of exome-sequencing data. A popular test of association is the sequence kernel association test (SKAT). Weights are embedded within SKAT to reflect the hypothesized contribution of the variants to the trait variance. Because the true weights are generally unknown, and so are subject to misspecification, we examined the efficiency of a data-driven weighting scheme. We propose the use of a set of theoretically defensible weighting schemes, of which, we assume, the one that gives the largest test statistic is likely to capture best the allele frequency-functional effect relationship. We show that the use of alternative weights obviates the need to impose arbitrary frequency thresholds in sequence data association analyses. As both the score test and the likelihood ratio test (LRT) may be used in this context, and may differ in power, we characterize the behavior of both tests. We found that the two tests have equal power if the set of weights resembled the correct ones. However, if the weights are badly specified, the LRT shows superior power (due to its robustness to misspecification). With this data-driven weighting procedure the LRT detected significant signal in genes located in regions already confirmed as associated with schizophrenia – the PRRC2A (P=1.020E-06) and the VARS2 (P=2.383E-06) – in the Swedish schizophrenia case-control cohort of 11,040 individuals with exome-sequencing data. The score test is currently preferred for its computational efficiency and power. Indeed, assuming correct specification, in some circumstances the score test is the most powerful. However, LRT has the advantageous properties of being generally more robust and more powerful under weight misspecification. This is an important result given that, arguably, misspecified models are likely to be the rule rather than the exception in weighting-based approaches. PMID:28238293

Energy-balance climate models

NASA Technical Reports Server (NTRS)

North, G. R.; Cahalan, R. F.; Coakley, J. A., Jr.

1980-01-01

An introductory survey of the global energy balance climate models is presented with an emphasis on analytical results. A sequence of increasingly complicated models involving ice cap and radiative feedback processes are solved and the solutions and parameter sensitivities are studied. The model parameterizations are examined critically in light of many current uncertainties. A simple seasonal model is used to study the effects of changes in orbital elements on the temperature field. A linear stability theorem and a complete nonlinear stability analysis for the models are developed. Analytical solutions are also obtained for the linearized models driven by stochastic forcing elements. In this context the relation between natural fluctuation statistics and climate sensitivity is stressed.

Energy balance climate models

NASA Technical Reports Server (NTRS)

North, G. R.; Cahalan, R. F.; Coakley, J. A., Jr.

1981-01-01

An introductory survey of the global energy balance climate models is presented with an emphasis on analytical results. A sequence of increasingly complicated models involving ice cap and radiative feedback processes are solved, and the solutions and parameter sensitivities are studied. The model parameterizations are examined critically in light of many current uncertainties. A simple seasonal model is used to study the effects of changes in orbital elements on the temperature field. A linear stability theorem and a complete nonlinear stability analysis for the models are developed. Analytical solutions are also obtained for the linearized models driven by stochastic forcing elements. In this context the relation between natural fluctuation statistics and climate sensitivity is stressed.

RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity.

PubMed

Anderson, David A; Walz, Marcus E; Weil, Ernesto; Tonellato, Peter; Smith, Matthew C

2016-01-01

Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.

RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity

PubMed Central

Walz, Marcus E.; Weil, Ernesto; Smith, Matthew C.

2016-01-01

Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system. PMID:26925311

Belowground competition drives invasive plant impact on native species regardless of nitrogen availability.

PubMed

Broadbent, Arthur; Stevens, Carly J; Peltzer, Duane A; Ostle, Nicholas J; Orwin, Kate H

2018-02-01

Plant invasions and eutrophication are pervasive drivers of global change that cause biodiversity loss. Yet, how invasive plant impacts on native species, and the mechanisms underpinning these impacts, vary in relation to increasing nitrogen (N) availability remains unclear. Competition is often invoked as a likely mechanism, but the relative importance of the above and belowground components of this is poorly understood, particularly under differing levels of N availability. To help resolve these issues, we quantified the impact of a globally invasive grass species, Agrostis capillaris, on two co-occurring native New Zealand grasses, and vice versa. We explicitly separated above- and belowground interactions amongst these species experimentally and incorporated an N addition treatment. We found that competition with the invader had large negative impacts on native species growth (biomass decreased by half), resource capture (total N content decreased by up to 75%) and even nutrient stoichiometry (native species tissue C:N ratios increased). Surprisingly, these impacts were driven directly and indirectly by belowground competition, regardless of N availability. Higher root biomass likely enhanced the invasive grass's competitive superiority belowground, indicating that root traits may be useful tools for understanding invasive plant impacts. Our study shows that belowground competition can be more important in driving invasive plant impacts than aboveground competition in both low and high fertility ecosystems, including those experiencing N enrichment due to global change. This can help to improve predictions of how two key drivers of global change, plant species invasions and eutrophication, impact native species diversity.

Functional Traits Differ between Cereal Crop Progenitors and Other Wild Grasses Gathered in the Neolithic Fertile Crescent

PubMed Central

Cunniff, Jennifer; Wilkinson, Sarah; Charles, Michael; Jones, Glynis; Rees, Mark; Osborne, Colin P.

2014-01-01

The reasons why some plant species were selected as crops and others were abandoned during the Neolithic emergence of agriculture are poorly understood. We tested the hypothesis that the traits of Fertile Crescent crop progenitors were advantageous in the fertile, disturbed habitats surrounding early settlements and in cultivated fields. We screened functional traits related to competition and disturbance in a group of grass species that were increasingly exploited by early plant gatherers, and that were later domesticated (crop progenitors); and in a set of grass species for which there is archaeological evidence of gathering, but which were never domesticated (wild species). We hypothesised that crop progenitors would have greater seed mass, growth rate, height and yield than wild species, as these traits are indicative of greater competitive ability, and that crop progenitors would be more resilient to defoliation. Our results show that crop progenitors have larger seed mass than wild species, germinate faster and have greater seedling size. Increased seed size is weakly but positively correlated with a higher growth rate, which is primarily driven by greater biomass assimilation per unit leaf area. Crop progenitors also tend to have a taller stature, greater grain yield and higher resilience to defoliation. Collectively, the data are consistent with the hypothesis that adaptations to competition and disturbance gave crop progenitors a selective advantage in the areas surrounding early human settlements and in cultivated environments, leading to their adoption as crops through processes of unconscious selection. PMID:24489941

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis.

PubMed

Ofek-Lalzar, Maya; Gur, Yonatan; Ben-Moshe, Sapir; Sharon, Or; Kosman, Evsey; Mochli, Elad; Sharon, Amir

2016-10-01

Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation-independent analysis identified a larger number of OTUs than the cultivation method, half of which were singletons or doubletons. For OTUs with a relative abundance >0.5%, similar numbers were obtained by both methods. Collectively, our data show that wild grass relatives of wheat contain a wealth of taxonomically diverse fungal endophytes that are not found in modern wheat, some of which belong to taxa with known beneficial effects. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Development of a regional-scale pollen emission and transport modeling framework for investigating the impact of climate change on allergic airway disease

PubMed Central

Zhang, Rui; Duhl, Tiffany; Salam, Muhammad T.; House, James M.; Flagan, Richard C.; Avol, Edward L.; Gilliland, Frank D.; Guenther, Alex; Chung, Serena H.; Lamb, Brian K.; VanReken, Timothy M.

2014-01-01

Exposure to bioaerosol allergens such as pollen can cause exacerbations of allergenic airway disease (AAD) in sensitive populations, and thus cause serious public health problems. Assessing these health impacts by linking the airborne pollen levels, concentrations of respirable allergenic material, and human allergenic response under current and future climate conditions is a key step toward developing preventive and adaptive actions. To that end, a regional-scale pollen emission and transport modeling framework was developed that treats allergenic pollens as non-reactive tracers within the WRF/CMAQ air-quality modeling system. The Simulator of the Timing and Magnitude of Pollen Season (STaMPS) model was used to generate a daily pollen pool that can then be emitted into the atmosphere by wind. The STaMPS is driven by species-specific meteorological (temperature and/or precipitation) threshold conditions and is designed to be flexible with respect to its representation of vegetation species and plant functional types (PFTs). The hourly pollen emission flux was parameterized by considering the pollen pool, friction velocity, and wind threshold values. The dry deposition velocity of each species of pollen was estimated based on pollen grain size and density. An evaluation of the pollen modeling framework was conducted for southern California for the period from March to June 2010. This period coincided with observations by the University of Southern California's Children's Health Study (CHS), which included O3, PM2.5, and pollen count, as well as measurements of exhaled nitric oxide in study participants. Two nesting domains with horizontal resolutions of 12 km and 4 km were constructed, and six representative allergenic pollen genera were included: birch tree, walnut tree, mulberry tree, olive tree, oak tree, and brome grasses. Under the current parameterization scheme, the modeling framework tends to underestimate walnut and peak oak pollen concentrations, and tends to overestimate grass pollen concentrations. The model shows reasonable agreement with observed birch, olive, and mulberry tree pollen concentrations. Sensitivity studies suggest that the estimation of the pollen pool is a major source of uncertainty for simulated pollen concentrations. Achieving agreement between emission modeling and observed pattern of pollen releases is the key for successful pollen concentration simulations. PMID:24839448

Development of a regional-scale pollen emission and transport modeling framework for investigating the impact of climate change on allergic airway disease

NASA Astrophysics Data System (ADS)

Zhang, R.; Duhl, T.; Salam, M. T.; House, J. M.; Flagan, R. C.; Avol, E. L.; Gilliland, F. D.; Guenther, A.; Chung, S. H.; Lamb, B. K.; VanReken, T. M.

2013-03-01

Exposure to bioaerosol allergens such as pollen can cause exacerbations of allergenic airway disease (AAD) in sensitive populations, and thus cause serious public health problems. Assessing these health impacts by linking the airborne pollen levels, concentrations of respirable allergenic material, and human allergenic response under current and future climate conditions is a key step toward developing preventive and adaptive actions. To that end, a regional-scale pollen emission and transport modeling framework was developed that treats allergenic pollens as non-reactive tracers within the WRF/CMAQ air-quality modeling system. The Simulator of the Timing and Magnitude of Pollen Season (STaMPS) model was used to generate a daily pollen pool that can then be emitted into the atmosphere by wind. The STaMPS is driven by species-specific meteorological (temperature and/or precipitation) threshold conditions and is designed to be flexible with respect to its representation vegetation species and plant functional types (PFTs). The hourly pollen emission flux was parameterized by considering the pollen pool, friction velocity, and wind threshold values. The dry deposition velocity of each species of pollen was estimated based on pollen grain size and density. An evaluation of the pollen modeling framework was conducted for southern California for the period from March to June 2010. This period coincided with observations by the University of Southern California's Children's Health Study (CHS), which included O3, PM2.5, and pollen count, as well as measurements of exhaled nitric oxide in study participants. Two nesting domains with horizontal resolutions of 12 km and 4 km were constructed, and six representative allergenic pollen genera were included: birch tree, walnut tree, mulberry tree, olive tree, oak tree, and brome grasses. Under the current parameterization scheme, the modeling framework tends to underestimate walnut and peak oak pollen concentrations, and tends to overestimate grass pollen concentrations. The model shows reasonable agreement with observed birch, olive, and mulberry tree pollen concentrations. Sensitivity studies suggest that the estimation of the pollen pool is a major source of uncertainty for simulated pollen concentrations. Achieving agreement between emission modeling and observed pattern of pollen releases is the key for successful pollen concentration simulations.

Development of a regional-scale pollen emission and transport modeling framework for investigating the impact of climate change on allergic airway disease

NASA Astrophysics Data System (ADS)

Zhang, R.; Duhl, T.; Salam, M. T.; House, J. M.; Flagan, R. C.; Avol, E. L.; Gilliland, F. D.; Guenther, A.; Chung, S. H.; Lamb, B. K.; VanReken, T. M.

2014-03-01

Exposure to bioaerosol allergens such as pollen can cause exacerbations of allergenic airway disease (AAD) in sensitive populations, and thus cause serious public health problems. Assessing these health impacts by linking the airborne pollen levels, concentrations of respirable allergenic material, and human allergenic response under current and future climate conditions is a key step toward developing preventive and adaptive actions. To that end, a regional-scale pollen emission and transport modeling framework was developed that treats allergenic pollens as non-reactive tracers within the coupled Weather Research and Forecasting Community Multiscale Air Quality (WRF/CMAQ) modeling system. The Simulator of the Timing and Magnitude of Pollen Season (STaMPS) model was used to generate a daily pollen pool that can then be emitted into the atmosphere by wind. The STaMPS is driven by species-specific meteorological (temperature and/or precipitation) threshold conditions and is designed to be flexible with respect to its representation of vegetation species and plant functional types (PFTs). The hourly pollen emission flux was parameterized by considering the pollen pool, friction velocity, and wind threshold values. The dry deposition velocity of each species of pollen was estimated based on pollen grain size and density. An evaluation of the pollen modeling framework was conducted for southern California (USA) for the period from March to June 2010. This period coincided with observations by the University of Southern California's Children's Health Study (CHS), which included O3, PM2.5, and pollen count, as well as measurements of exhaled nitric oxide in study participants. Two nesting domains with horizontal resolutions of 12 and 4 km were constructed, and six representative allergenic pollen genera were included: birch tree, walnut tree, mulberry tree, olive tree, oak tree, and brome grasses. Under the current parameterization scheme, the modeling framework tends to underestimate walnut and peak oak pollen concentrations, and tends to overestimate grass pollen concentrations. The model shows reasonable agreement with observed birch, olive, and mulberry tree pollen concentrations. Sensitivity studies suggest that the estimation of the pollen pool is a major source of uncertainty for simulated pollen concentrations. Achieving agreement between emission modeling and observed pattern of pollen releases is the key for successful pollen concentration simulations.

Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource.

PubMed

Shim, Hongseok; Kim, Ji Hyun; Kim, Chan Yeong; Hwang, Sohyun; Kim, Hyojin; Yang, Sunmo; Lee, Ji Eun; Lee, Insuk

2016-11-16

Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www.inetbio.org/danionet), which was constructed by Bayesian integration of genomics big data. Rigorous statistical assessment confirmed the high prediction capacity of DanioNet for a wide variety of human diseases. To demonstrate the feasibility of the function-driven disease gene discovery using DanioNet, we predicted genes for ciliopathies and performed experimental validation for eight candidate genes. We also validated the existence of heterozygous rare variants in the candidate genes of individuals with ciliopathies yet not in controls derived from the UK10K consortium, suggesting that these variants are potentially involved in enhancing the risk of ciliopathies. These results showed that an integrated genomics big data for a model animal of diseases can expand our opportunity for harnessing WES data in disease gene discovery. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Soil slip/debris flow localized by site attributes and wind-driven rain in the San Francisco Bay region storm of January 1982

USGS Publications Warehouse

Pike, R.J.; Sobieszczyk, S.

2008-01-01

GIS analysis at 30-m resolution reveals that effectiveness of slope-destabilizing processes in the San Francisco Bay area varies with compass direction. Nearly half the soil slip/debris flows mapped after the catastrophic rainstorm of 3-5 January 1982 occurred on slopes that face S to WSW, whereas fewer than one-quarter have a northerly aspect. Azimuthal analysis of hillside properties for susceptible terrain near the city of Oakland suggests that the skewed aspect of these landslides primarily reflects vegetation type, ridge and valley alignment, and storm-wind direction. Bedrock geology, soil expansivity, and terrain height and gradient also were influential but less so; the role of surface curvature is not wholly resolved. Normalising soil-slip aspect by that of the region's NNW-striking topography shifts the modal azimuth of soil-slip aspect from SW to SE, the direction of origin of winds during the 1982 storm-but opposite that of the prevailing WNW winds. Wind from a constant direction increases rainfall on windward slopes while diminishing it on leeward slopes, generating a modelled difference in hydrologically effective rainfall of up to 2:1 on steep hillsides in the Oakland area. This contrast is consistent with numerical simulations of wind-driven rain and with rainfall thresholds for debris-flow activity. We conclude that storm winds from the SE in January 1982 raised the vulnerability of the Bay region's many S-facing hillsides, most of which are covered in shallow-rooted shrub and grass that offer minimal resistance to soil slip. Wind-driven rainfall also appears to have controlled debris-flow location in a major 1998 storm and probably others. Incorporating this overlooked influence into GIS models of debris-flow likelihood would improve predictions of the hazard in central California and elsewhere.

Systematic features of axisymmetric neutrino-driven core-collapse supernova models in multiple progenitors

NASA Astrophysics Data System (ADS)

Nakamura, Ko; Takiwaki, Tomoya; Kuroda, Takami; Kotake, Kei

2015-12-01

We present an overview of two-dimensional (2D) core-collapse supernova simulations employing a neutrino transport scheme by the isotropic diffusion source approximation. We study 101 solar-metallicity, 247 ultra metal-poor, and 30 zero-metal progenitors covering zero-age main sequence mass from 10.8 M⊙ to 75.0 M⊙. Using the 378 progenitors in total, we systematically investigate how the differences in the structures of these multiple progenitors impact the hydrodynamics evolution. By following a long-term evolution over 1.0 s after bounce, most of the computed models exhibit neutrino-driven revival of the stalled bounce shock at ˜200-800 ms postbounce, leading to the possibility of explosion. Pushing the boundaries of expectations in previous one-dimensional studies, our results confirm that the compactness parameter ξ that characterizes the structure of the progenitors is also a key in 2D to diagnosing the properties of neutrino-driven explosions. Models with high ξ undergo high ram pressure from the accreting matter onto the stalled shock, which affects the subsequent evolution of the shock expansion and the mass of the protoneutron star under the influence of neutrino-driven convection and the standing accretion-shock instability. We show that the accretion luminosity becomes higher for models with high ξ, which makes the growth rate of the diagnostic explosion energy higher and the synthesized nickel mass bigger. We find that these explosion characteristics tend to show a monotonic increase as a function of the compactness parameter ξ.

Spatially explicit integrated modeling and economic valuation of climate driven land use change and its indirect effects.

PubMed

Bateman, Ian; Agarwala, Matthew; Binner, Amy; Coombes, Emma; Day, Brett; Ferrini, Silvia; Fezzi, Carlo; Hutchins, Michael; Lovett, Andrew; Posen, Paulette

2016-10-01

We present an integrated model of the direct consequences of climate change on land use, and the indirect effects of induced land use change upon the natural environment. The model predicts climate-driven shifts in the profitability of alternative uses of agricultural land. Both the direct impact of climate change and the induced shift in land use patterns will cause secondary effects on the water environment, for which agriculture is the major source of diffuse pollution. We model the impact of changes in such pollution on riverine ecosystems showing that these will be spatially heterogeneous. Moreover, we consider further knock-on effects upon the recreational benefits derived from water environments, which we assess using revealed preference methods. This analysis permits a multi-layered examination of the economic consequences of climate change, assessing the sequence of impacts from climate change through farm gross margins, land use, water quality and recreation, both at the individual and catchment scale. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae).

PubMed

Barth, Susanne; Jankowska, Marta Jolanta; Hodkinson, Trevor Roland; Vellani, Tia; Klaas, Manfred

2016-03-22

Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3% Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.

Assessment of Robinia pseudoacacia cultivations as a restoration strategy for reclaimed mine spoil heaps.

PubMed

Vlachodimos, Kostas; Papatheodorou, Efimia M; Diamantopoulos, John; Monokrousos, Nikolaos

2013-08-01

Reforestation with black locust (Robinia pseudoacacia) is considered a successful technique that is often used for the reclamation of open-cast mine areas. An alternative reclamation technique could be the natural regeneration of vegetation with spontaneous grass species. In this study, we compared the concentrations of chemical and biochemical variables in soil samples taken under black locust canopy to those from sites covered by spontaneous grass vegetation (control samples) in a time sequence of spoil deposition (0-10 years), in order to assess which of the two reclamation techniques yields higher soil quality. Soil quality refers here to the ability of soils to function ecologically. This has a special interest since the main question for the restored soils is their capacity to perform a range of ecological functions under stress or disturbance. Furthermore, we aimed at identifying the effect of vegetation type on soil ecological succession. The effect of vegetation type on primary succession becomes apparent after 2 years of reclamation. R. pseudoacacia as a nitrogen-fixing plant enriched soil with organic and inorganic nitrogen and organic matter to a greater extent than the natural grasses. It also increased the amount of soil microbial biomass and the activity of alkaline phosphatase. However, the fact that black locust failed to enhance dehydrogenase activity and actually decreased the activity of urease, activities that represent specialized niche functions and therefore, are more vulnerable to stress or disturbance, suggests that the development of an indigenous grass community in combination with organic supplements might often be more appropriate for the reclamation of similar kinds of mine areas.

Divergent evapotranspiration partition dynamics between shrubs and grasses in a shrub-encroached steppe ecosystem.

PubMed

Wang, Pei; Li, Xiao-Yan; Wang, Lixin; Wu, Xiuchen; Hu, Xia; Fan, Ying; Tong, Yaqin

2018-06-04

Previous evapotranspiration (ET) partitioning studies have usually neglected competitions and interactions between antagonistic plant functional types. This study investigated whether shrubs and grasses have divergent ET partition dynamics impacted by different water-use patterns, canopy structures, and physiological properties in a shrub-encroached steppe ecosystem in Inner Mongolia, China. The soil water-use patterns of shrubs and grasses have been quantified by an isotopic tracing approach and coupled into an improved multisource energy balance model to partition ET fluxes into soil evaporation, grass transpiration, and shrub transpiration. The mean fractional contributions to total ET were 24 ± 13%, 20 ± 4%, and 56 ± 16% for shrub transpiration, grass transpiration, and soil evaporation respectively during the growing season. Difference in ecohydrological connectivity and leaf development both contributed to divergent transpiration partitioning between shrubs and grasses. Shrub-encroachment processes result in larger changes in the ET components than in total ET flux, which could be well explained by changes in canopy resistance, an ecosystem function dominated by the interaction of soil water-use patterns and ecosystem structure. The analyses presented here highlight the crucial effects of vegetation structural changes on the processes of land-atmosphere interaction and climate feedback. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Industrial robot

NASA Astrophysics Data System (ADS)

Prakashan, A.; Mukunda, H. S.; Samuel, S. D.; Colaco, J. C.

1992-11-01

This paper addresses the design and development of a four degree of freedom industrial manipulator, with three liner axes in the positioning mechanism and one rotary axis in the orientation mechanism. The positioning mechanism joints are driven with dc servo motors fitted with incremental shaft encoders. The rotary joint of the orientation mechanism is driven by a stepping motor. The manipulator is controlled by an IBM 386 PC/AT. Microcomputer based interface cards have been developed for independent joint control. PID controllers for dc motors have been designed. Kinematic modeling, dynamic modeling, and path planning have been carried out to generate the control sequence to accomplish a given task with reference to source and destination state constraints. This project has been sponsored by the Department of Science and Technology, Government of India, New Delhi, and has been executed in collaboration with M/s Larsen & Toubro Ltd, Mysore, India.

Convergence of macroscopic tongue anatomy in ruminants and scaling relationships with body mass or tongue length.

PubMed

Meier, Andrea R; Schmuck, Ute; Meloro, Carlo; Clauss, Marcus; Hofmann, Reinhold R

2016-03-01

Various morphological measures demonstrate convergent evolution in ruminants with their natural diet, in particular with respect to the browser/grazer dichotomy. Here, we report quantitative macroanatomical measures of the tongue (length and width of specific parts) of 65 ruminant species and relate them to either body mass (BM) or total tongue length, and to the percentage of grass in the natural diet (%grass). Models without and with accounting for the phylogenetic structures of the dataset were used, and models were ranked using Akaike's Information Criterion. Scaling relationships followed geometric principles, that is, length measures scaled with BM to the power of 0.33. Models that used tongue length rather than BM as a body size proxy were consistently ranked better, indicating that using size proxies that are less susceptible to a wider variety of factors (such as BM that fluctuates with body condition) should be attempted whenever possible. The proportion of the freely mobile tongue tip of the total tongue (and hence also the corpus length) was negatively correlated to %grass, in accordance with concepts that the feeding mechanism of browsers requires more mobile tongues. It should be noted that some nonbrowsers, such as cattle, use a peculiar mechanism for grazing that also requires long, mobile tongues, but they appear to be exceptions. A larger corpus width with increasing %grass corresponds to differences in snout shape with broader snouts in grazers. The Torus linguae is longer with increasing %grass, a finding that still warrants functional interpretation. This study shows that tongue measures covary with diet in ruminants. In contrast, the shape of the tongue (straight or "hourglass-shaped" as measured by the ratio of the widest and smallest corpus width) is unrelated to diet and is influenced strongly by phylogeny. © 2015 Wiley Periodicals, Inc.

A Picture is Worth a Thousand Words: Art and Medicine.

PubMed

Dahan, Shani; Shoenfeld, Yehuda

2017-12-01

Medical practice is a form of art, with each complex detail essential to the welfare of the individuals in the care of the physician. Art and medicine have shared a close relationship in a variety of ways for centuries, as demonstrated by anatomical drawings and textbooks from the 16th century. Leonardo da Vinci, driven by his fascination with the details of the human body and how it functioned, succeeded in creating an anatomical model of the cerebral ventricles and the aorta using molten wax and a glass structure, respectively (Heart and Its Blood Vessels). By using water that contained grass seeds, this experiment enabled him to study blood flow. da Vinci's engrossment with the complexity of the human body is reflected in many of his drawings, including the famous depiction of the human physique in his drawing of the Vitruvian Man. This drawing, which defines the ideal proportions of the human body and their correlation with geometry, is an example of how artistic and scientific objectives integrate with each other.

Characteristics of lactic acid bacteria isolates and their effect on the fermentation quality of Napier grass silage at three high temperatures.

PubMed

Gulfam, Ali; Guo, Gang; Tajebe, Seare; Chen, Lei; Liu, Qinhua; Yuan, Xianjun; Bai, Yunfeng; Saho, Tao

2017-04-01

The poor fermentation quality of silage is an important issue for silage production during the high temperatures of summer. Pediococcus acidilactici GG13 (GG13) and Lactobacillus rhamnosus GG26 (GG26) isolated from Italian ryegrass (Lolium multiflorum Lam.) silage were characterised by morphological and physiological tests and 16S rRNA sequencing analysis, and their effects, along with those of a commercial lactic acid bacteria (LAB) inoculant (CB), on the fermentation quality of facultative halophyte Napier grass (Pennisetum purpureum Schumach) ensiled at 30 °C, 40 °C and 50 °C were studied, respectively. The strains GG13 and GG26 grew well at 50 °C and pH 3.5, and were tolerant to 6.5% NaCl. After ensiling for 50 days, the strains GG13 and GG26 and the CB decreased (P < 0.001) the pH and acetic acid and ammonia-N contents and increased (P < 0.001) the lactic acid contents at 30 °C, and decreased (P < 0.001) the ammonia-N contents at 40 °C in Napier grass. CB did not affect the fermentation quality at 50 °C, whereas both isolated strains improved the fermentation quality of Napier grass silage as indicated by the lower (P < 0.001) pH, butyric acid and ammonia-N contents and higher (P < 0.001) lactic acid contents. The strain GG13 is better than GG26 with regard to improvement in fermentation quality of Napier grass silage. The results of this study suggested that strain GG13 is a good LAB inoculant for producing well-fermented silages during the high temperatures of summer times. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Processing Motion Signals in Complex Environments

NASA Technical Reports Server (NTRS)

Verghese, Preeti

2000-01-01

Motion information is critical for human locomotion and scene segmentation. Currently we have excellent neurophysiological models that are able to predict human detection and discrimination of local signals. Local motion signals are insufficient by themselves to guide human locomotion and to provide information about depth, object boundaries and surface structure. My research is aimed at understanding the mechanisms underlying the combination of motion signals across space and time. A target moving on an extended trajectory amidst noise dots in Brownian motion is much more detectable than the sum of signals generated by independent motion energy units responding to the trajectory segments. This result suggests that facilitation occurs between motion units tuned to similar directions, lying along the trajectory path. We investigated whether the interaction between local motion units along the motion direction is mediated by contrast. One possibility is that contrast-driven signals from motion units early in the trajectory sequence are added to signals in subsequent units. If this were the case, then units later in the sequence would have a larger signal than those earlier in the sequence. To test this possibility, we compared contrast discrimination thresholds for the first and third patches of a triplet of sequentially presented Gabor patches, aligned along the motion direction. According to this simple additive model, contrast increment thresholds for the third patch should be higher than thresholds for the first patch.The lack of a measurable effect on contrast thresholds for these various manipulations suggests that the pooling of signals along a trajectory is not mediated by contrast-driven signals. Instead, these results are consistent with models that propose that the facilitation of trajectory signals is achieved by a second-level network that chooses the strongest local motion signals and combines them if they occur in a spatio-temporal sequence consistent with a trajectory. These results parallel the lack of increased apparent contrast along a static contour made up of similarly oriented elements.

Targeting MYCN-Driven Transcription By BET-Bromodomain Inhibition.

PubMed

Henssen, Anton; Althoff, Kristina; Odersky, Andrea; Beckers, Anneleen; Koche, Richard; Speleman, Frank; Schäfers, Simon; Bell, Emma; Nortmeyer, Maike; Westermann, Frank; De Preter, Katleen; Florin, Alexandra; Heukamp, Lukas; Spruessel, Annika; Astrahanseff, Kathy; Lindner, Sven; Sadowski, Natalie; Schramm, Alexander; Astorgues-Xerri, Lucile; Riveiro, Maria E; Eggert, Angelika; Cvitkovic, Esteban; Schulte, Johannes H

2016-05-15

Targeting BET proteins was previously shown to have specific antitumoral efficacy against MYCN-amplified neuroblastoma. We here assess the therapeutic efficacy of the BET inhibitor, OTX015, in preclinical neuroblastoma models and extend the knowledge on the role of BRD4 in MYCN-driven neuroblastoma. The efficacy of OTX015 was assessed in in vitro and in vivo models of human and murine MYCN-driven neuroblastoma. To study the effects of BET inhibition in the context of high MYCN levels, MYCN was ectopically expressed in human and murine cells. The effect of OTX015 on BRD4-regulated transcriptional pause release was analyzed using BRD4 and H3K27Ac chromatin immunoprecipitation coupled with DNA sequencing (ChIP-Seq) and gene expression analysis in neuroblastoma cells treated with OTX015 compared with vehicle control. OTX015 showed therapeutic efficacy against preclinical MYCN-driven neuroblastoma models. Similar to previously described BET inhibitors, concurrent MYCN repression was observed in OTX015-treated samples. Ectopic MYCN expression, however, did not abrogate effects of OTX015, indicating that MYCN repression is not the only target of BET proteins in neuroblastoma. When MYCN was ectopically expressed, BET inhibition still disrupted MYCN target gene transcription without affecting MYCN expression. We found that BRD4 binds to super-enhancers and MYCN target genes, and that OTX015 specifically disrupts BRD4 binding and transcription of these genes. We show that OTX015 is effective against mouse and human MYCN-driven tumor models and that BRD4 not only targets MYCN, but specifically occupies MYCN target gene enhancers as well as other genes associated with super-enhancers. Clin Cancer Res; 22(10); 2470-81. ©2015 AACR. ©2015 American Association for Cancer Research.

Transcriptome wide identification and characterization of starch branching enzyme in finger millet.

PubMed

Tyagi, Rajhans; Tiwari, Apoorv; Garg, Vijay Kumar; Gupta, Sanjay

2017-01-01

Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. In this study it was try to find out the gene sequence of starch branching enzyme and annotate the sequence and submit the sequence for further use. Rice SBE sequence was taken as reference and for characterization of the sequence different in silico tools were used. Four domains were found in the finger millet Starch branching enzyme like alpha amylase catalytic domain from 925 to2172 with E value 0, N-terminal Early set domain from 634 to 915 with E value 1.62 e-42, Alpha amylase, C-terminal all-beta domain from 2224 to 2511 with E value 5.80e-24 and 1,4-alpha-glucan-branching enzyme from 421 to 2517 with E value 0. Major binding interactions with the GLC (alpha-d-glucose), CA (calcium ion), GOL (glycerol), TRS (2-amino-2-hydroxymethylpropane- 1, 3-diol), MG (magnesium ion) and FLC (citrate anion) are fond with different residues. It was found in the phylogenetic study of the finger millet SBE with the 6 species of grass family that two clusters were form A and B. In cluster A, finger millet showed closeness with Oryzasativa and Setariaitalica, Sorghum bicolour and Zea mays while cluster B was formed with Triticumaestivum and Brachypodium distachyon. The nucleotide sequence of Finger millet SBE was submitted to NCBI with the accession no KY648913 and protein structure of SBE of finger millet was also submitted in PMDB with the PMDB id - PM0080938. This research presents a comparative overview of Finger millet SBE and includes their properties, structural and functional characteristics, and recent developments on their post-translational regulation.

Development of innovative technique that may be used as models for the increase of biomass production with grasses and other species

NASA Astrophysics Data System (ADS)

Burton, G. W.; Hanna, W. W.

1981-09-01

Techniques for biomass increase are discussed: irradiation breeding of sterile triploid turf bermuda grasses; irradiation breeding of sterile Coastcross-1, a forage grass hybrid to increase winter hardiness; heterosis resulting from crossing specific irradiation induced mutants with their normal inbred parent; use of mitomycin and streptomycin to create cytoplasmic male sterile mutants in pearl millet; biomass of napiergrass; evaluation of mutagen induced lignin mutants to maximize metabolizable energy in sorghum; interspecific crosses in Pennisetum; production of homozygous translocation tester stocks; use of radiation to induce and transfer reproductive behavior in plants; and genetics of radiation induced mutations.

Overview of the 2013 FireFlux II grass fire field experiment

Treesearch

C.B. Clements; B. Davis; D. Seto; J. Contezac; A. Kochanski; J.-B. Fillipi; N. Lareau; B. Barboni; B. Butler; S. Krueger; R. Ottmar; R. Vihnanek; W.E. Heilman; J. Flynn; M.A. Jenkins; J. Mandel; C. Teske; D. Jimenez; J. O' Brien; B. Lefer

2014-01-01

In order to better understand the dynamics of fire-atmosphere interactions and the role of micrometeorology on fire behaviour the FireFlux campaign was conducted in 2006 on a coastal tall-grass prairie in southeast Texas, USA. The FireFlux campaign dataset has become the international standard for evaluating coupled fire-atmosphere model systems. While FireFlux is one...

The neural dynamics of song syntax in songbirds

NASA Astrophysics Data System (ADS)

Jin, Dezhe

2010-03-01

Songbird is ``the hydrogen atom'' of the neuroscience of complex, learned vocalizations such as human speech. Songs of Bengalese finch consist of sequences of syllables. While syllables are temporally stereotypical, syllable sequences can vary and follow complex, probabilistic syntactic rules, which are rudimentarily similar to grammars in human language. Songbird brain is accessible to experimental probes, and is understood well enough to construct biologically constrained, predictive computational models. In this talk, I will discuss the structure and dynamics of neural networks underlying the stereotypy of the birdsong syllables and the flexibility of syllable sequences. Recent experiments and computational models suggest that a syllable is encoded in a chain network of projection neurons in premotor nucleus HVC (proper name). Precisely timed spikes propagate along the chain, driving vocalization of the syllable through downstream nuclei. Through a computational model, I show that that variable syllable sequences can be generated through spike propagations in a network in HVC in which the syllable-encoding chain networks are connected into a branching chain pattern. The neurons mutually inhibit each other through the inhibitory HVC interneurons, and are driven by external inputs from nuclei upstream of HVC. At a branching point that connects the final group of a chain to the first groups of several chains, the spike activity selects one branch to continue the propagation. The selection is probabilistic, and is due to the winner-take-all mechanism mediated by the inhibition and noise. The model predicts that the syllable sequences statistically follow partially observable Markov models. Experimental results supporting this and other predictions of the model will be presented. We suggest that the syntax of birdsong syllable sequences is embedded in the connection patterns of HVC projection neurons.

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites.

PubMed

Mikaelyan, Aram; Meuser, Katja; Brune, Andreas

2017-01-01

Symbiotic digestion of lignocellulose in higher termites (family Termitidae) is accomplished by an exclusively prokaryotic gut microbiota. By deep sequencing of amplified 16S rRNA genes, we had identified diet as the primary determinant of bacterial community structure in a broad selection of termites specialized on lignocellulose in different stages of humification. Here, we increased the resolution of our approach to account for the pronounced heterogeneity in microenvironmental conditions and microbial activities in the major hindgut compartments. The community structure of consecutive gut compartments in each species strongly differed, but that of homologous compartments clearly converged, even among unrelated termites. While the alkaline P1 compartments of all termites investigated contained specific lineages of Clostridiales, the posterior hindgut compartments (P3, P4) differed between feeding groups and were predominantly colonized by putatively fiber-associated lineages of Spirochaetes, Fibrobacteres and the TG3 phylum (wood and grass feeders) or diverse assemblages of Clostridiales and Bacteroidetes (humus and soil feeders). The results underscore that bacterial community structure in termite guts is driven by microenvironmental factors, such as pH, available substrates and gradients of O 2 and H 2 , and inspire investigations on the functional roles of specific bacterial taxa in lignocellulose and humus digestion. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

COMPUTATIONAL RESOURCES FOR BIOFUEL FEEDSTOCK SPECIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buell, Carol Robin; Childs, Kevin L

2013-05-07

While current production of ethanol as a biofuel relies on starch and sugar inputs, it is anticipated that sustainable production of ethanol for biofuel use will utilize lignocellulosic feedstocks. Candidate plant species to be used for lignocellulosic ethanol production include a large number of species within the Grass, Pine and Birch plant families. For these biofuel feedstock species, there are variable amounts of genome sequence resources available, ranging from complete genome sequences (e.g. sorghum, poplar) to transcriptome data sets (e.g. switchgrass, pine). These data sets are not only dispersed in location but also disparate in content. It will be essentialmore » to leverage and improve these genomic data sets for the improvement of biofuel feedstock production. The objectives of this project were to provide computational tools and resources for data-mining genome sequence/annotation and large-scale functional genomic datasets available for biofuel feedstock species. We have created a Bioenergy Feedstock Genomics Resource that provides a web-based portal or clearing house for genomic data for plant species relevant to biofuel feedstock production. Sequence data from a total of 54 plant species are included in the Bioenergy Feedstock Genomics Resource including model plant species that permit leveraging of knowledge across taxa to biofuel feedstock species.We have generated additional computational analyses of these data, including uniform annotation, to facilitate genomic approaches to improved biofuel feedstock production. These data have been centralized in the publicly available Bioenergy Feedstock Genomics Resource (http://bfgr.plantbiology.msu.edu/).« less

Using multi-approaches to investigate the effects of land cover on runoff and soil erosion in the Loess Plateau of China

NASA Astrophysics Data System (ADS)

Gao, G.; Fu, B.; Liu, Y.; Wang, Y.

2012-12-01

This study used the in-situ measurement, model simulation and radioisotope tracing methods to investigate the effects of land cover on runoff and soil erosion at plot and hillslope scales in the Loess Plateau of China. Three runoff plot groups covered by sparse young trees (Group 1), native shrubs (Group 2) and dense tussock (Group 3) with different revegetation time were established in the Yangjuangou catchment of Loess Plateau. Greater runoff was produced in plot groups (Group 2 and Group 3) with higher vegetation cover and longer restoration time as a result of soil compaction processes. Both of the runoff coefficient and soil loss rate decreased with increasing plot length in Group 2 and Group 3 plots. The runoff coefficient increased with plot length in Group 1 plots located at the early stage of revegetation, and the soil loss rates increased over an area threshold. Therefore, the effect of scale on runoff and soil erosion was dependent on restoration extent. The antecedent moisture condition (AMC) was explicitly incorporated in runoff production and initial abstraction of the SCS-CN model, and the direct effect of runoff on event soil loss was considered in the RUSLE model by adopting a rainfall-runoff erosivity factor. The modified SCS-CN and RUSLE models were coupled to link rainfall-runoff-erosion modeling. The modified SCS-CN model was accurate in predicting event runoff from the three plot groups with Nash-Sutcliffe model efficiency (EF) over 0.85, and the prediction accuracy of the modified RUSLE model was satisfactory with EF values being over 0.70. The 137Cs tracing technique was used to examine soil erosion under different land uses and land-use combinations. The results show that the order of erosion rate in different land uses increases sequentially from mature forest to grass to young forest to orchard to terrace crop. The land-use combinations of 'grass (6 years old) + mature forest (25 years old) + grass (25 years old)' and 'grass (6 years old) + young forest (6 years old) + mature forest (25 years old) + grass (25 years old)' are better for soil erosion control, lowering soil erosion amount by 42% compared with a mixtures of 'grass (6 years old) and shrub (6 years old)'. This study indicates that land cover type/pattern, vegetation cover, soil property, restoration time and scale effect as well as stand condition all contribute to the complex hydrological effects of restoring vegetation in the Loess Plateau. Each approach has its own advantages and limitations. Appropriate method should be chosen for specific purpose and study scale. It is better that the results from different approach can be checked with each other.

Detection of platinum species in plant material.

PubMed

Messerschmidt, J; Alt, F; Tölg, G

1995-05-01

Model experiments for the detection of platinum species in extracts from native and platinum-treated grass cultivations are described. The procedural steps are cultivation of the grass samples, extraction and concentration of the platinum species by ultrafiltration and freeze-drying, preparative separation of the species by gel chromatography followed by isotachophoresis, and sequential analytical detection of the separated platinum species by adsorptive voltammetry. After isotachophoresis, sharp peaks of platinum species could be detected. In the native grass extract only one platinum species (160-200 kDa) was found. In the platinum-treated grass extracts several platinum species were observed in the molecular mass range from 1 to > 1000 kDa. By an extremely sensitive platinum determination method (adsorptive voltammetry; detection limit, 2 pg Pt abs.) it was possible to detect platinum even in stained protein bands from horizontal gel electrophoresis of platinum containing fractions obtained after isotachophoresis.

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

PubMed Central

McKain, Michael R.; Tang, Haibao; McNeal, Joel R.; Ayyampalayam, Saravanaraj; Davis, Jerrold I.; dePamphilis, Claude W.; Givnish, Thomas J.; Pires, J. Chris; Stevenson, Dennis Wm.; Leebens-Mack, James H.

2016-01-01

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification. PMID:26988252

Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella.

PubMed

Noar, Jesse D; Buckley, Daniel H

2009-08-01

Strain 1a22T, a nitrogen-fixing bacterium, was isolated from soil associated with the rhizosphere of a perennial grass growing in a fallow agricultural field in Ithaca, New York, USA. Analysis of the 16S rRNA gene sequence placed the strain in the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch of the Betaproteobacteria and the closest characterized relative was the type strain of Ideonella dechloratans (97.7% 16S rRNA sequence similarity). Cells of strain 1a22T were Gram-negative, motile, straight rods, which formed polyhydroxybutyrate-like granules and were positive for oxidase and weakly positive for catalase. Cells were chemo-organotrophic, unable to grow by reduction of chlorate or nitrate and grew exclusively through aerobic respiration. Growth with mannitol on N-free solid media caused the strain to produce copious amounts of slime. The G+C content of the genomic DNA was 67.4 mol%. The major cellular fatty acids were C16:1 cis-9 and C16:0 and cells contained significant amounts of the hydroxy fatty acids C10:0 3-OH, C12:0 2-OH and C12:0 3-OH. Based on DNA-DNA hybridization studies, 16S rRNA gene sequence analysis, fatty acid analysis, and morphological and physiological characteristics, strain 1a22T represents a novel species in the genus Ideonella, for which the name Ideonella azotifigens sp. nov. is proposed. The type strain of Ideonella azotifigens is 1a22T (=JCM 15503T=DSM 21438T).

An integral projection model with YY-males and application to evaluating grass carp control

USGS Publications Warehouse

Erickson, Richard A.; Eager, Eric A.; Brey, Marybeth; Hansen, Michael J.; Kocovsky, Patrick

2017-01-01

Invasive fish species disrupt ecosystems and cause economic damage. Several methods have been discussed to control populations of invasive fish including the release of YY-males. YY-males are fish that have 2 male chromosomes compared to a XY-male. When YY-males mate, they only produce male (XY) offspring. This decreases the female proportion of the population and can, in theory, eradicate local populations by biasing the sex-ratio. YY-males have been used as a population control tool for brook trout in montane streams and lakes in Idaho, USA. The YY-male control method has been discussed for grass carp in Lake Erie, North America. We developed and presented an integral projection model for grass carp to model the use of YY-males as a control method for populations in this lake. Using only the YY-male control method, we found that high levels of YY-males would need to be release annually to control the species. Specifically, these levels were the same order of magnitude as the baseline adult population (e.g., 1000 YY-males needed to be released annual for 20 years to control a baseline adult population of 2500 grass carp). These levels may not be reasonable or obtainable for fisheries managers given the impacts of YY-males on aquatic vegetation and other constraints of natural resource management.

Genomic and metabolic characterisation of alkaloid biosynthesis by asexual Epichloë fungal endophytes of tall fescue pasture grasses.

PubMed

Ekanayake, Piyumi N; Kaur, Jatinder; Tian, Pei; Rochfort, Simone J; Guthridge, Kathryn M; Sawbridge, Timothy I; Spangenberg, German C; Forster, John W

2017-06-01

Symbiotic associations between tall fescue grasses and asexual Epichloë fungal endophytes exhibit biosynthesis of alkaloid compounds causing both beneficial and detrimental effects. Candidate novel endophytes with favourable chemotypic profiles have been identified in germplasm collections by screening for genetic diversity, followed by metabolite profile analysis in endogenous genetic backgrounds. A subset of candidates was subjected to genome survey sequencing to detect the presence or absence and structural status of known genes for biosynthesis of the major alkaloid classes. The capacity to produce specific metabolites was directly predictable from metabolic data. In addition, study of duplicated gene structure in heteroploid genomic constitutions provided further evidence for the origin of such endophytes. Selected strains were inoculated into meristem-derived callus cultures from specific tall fescue genotypes to perform isogenic comparisons of alkaloid profile in different host backgrounds, revealing evidence for host-specific quantitative control of metabolite production, consistent with previous studies. Certain strains were capable of both inoculation and formation of longer-term associations with a nonhost species, perennial ryegrass (Lolium perenne L.). Discovery and primary characterisation of novel endophytes by DNA analysis, followed by confirmatory metabolic studies, offers improvements of speed and efficiency and hence accelerated deployment in pasture grass improvement programs.

Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes.

PubMed

Srinivasachary; Dida, Mathews M; Gale, Mike D; Devos, Katrien M

2007-08-01

Finger millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the finger millet genome with that of rice. Six of the nine finger millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three finger millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the finger millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to finger millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and finger millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and finger millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of finger millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.

Lifelong learning of human actions with deep neural network self-organization.

PubMed

Parisi, German I; Tani, Jun; Weber, Cornelius; Wermter, Stefan

2017-12-01

Lifelong learning is fundamental in autonomous robotics for the acquisition and fine-tuning of knowledge through experience. However, conventional deep neural models for action recognition from videos do not account for lifelong learning but rather learn a batch of training data with a predefined number of action classes and samples. Thus, there is the need to develop learning systems with the ability to incrementally process available perceptual cues and to adapt their responses over time. We propose a self-organizing neural architecture for incrementally learning to classify human actions from video sequences. The architecture comprises growing self-organizing networks equipped with recurrent neurons for processing time-varying patterns. We use a set of hierarchically arranged recurrent networks for the unsupervised learning of action representations with increasingly large spatiotemporal receptive fields. Lifelong learning is achieved in terms of prediction-driven neural dynamics in which the growth and the adaptation of the recurrent networks are driven by their capability to reconstruct temporally ordered input sequences. Experimental results on a classification task using two action benchmark datasets show that our model is competitive with state-of-the-art methods for batch learning also when a significant number of sample labels are missing or corrupted during training sessions. Additional experiments show the ability of our model to adapt to non-stationary input avoiding catastrophic interference. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Sporophytic control of pollen tube growth and guidance in grasses.

PubMed

Lausser, Andreas; Dresselhaus, Thomas

2010-04-01

Pollen tube growth and guidance in the female tissues of flowering plants is a long-studied and anatomically well-described process. A large number of gene products and chemical compounds involved have been identified in the last 20 years, and some underlying molecular mechanisms including self-incompatibility in the Brassicaceae, Solanaceae and Papaveraceae are now well understood. However, the largest part of the pollen tube pathway inside the transmitting tract towards the ovule harbouring the female gametophyte still requires intensive investigations. Especially in the economically most import plant family, the Poaceae or grasses, progamic pollen tube development is barely understood. Using maize as a model, we propose to divide pollen tube germination, growth and guidance towards the female gametophyte into five distinct phases. The model is adapted from Arabidopsis thaliana, taking anatomical differences and novel genetic and cellular studies into consideration. With the exception of Phase V, all phases seem to be under sporophytic control in grasses.

Leaf oxygen and Carbon Isotopic Signatures Reflect Drought Resistance and Water Use Efficiency in the C4 Grass, Setaria viridis

NASA Astrophysics Data System (ADS)

Ellsworth, P.; Cousins, A. B.

2014-12-01

Low water availability is a major constraint in crop production, especially as agriculture is pushed to marginal lands. Therefore, improving drought resistance such as increasing water use efficiency (WUE) through plant breeding is needed to expand the range of soil water availability adequate for food production. With the goal of finding the genomic basis for WUE in C4 grasses, Setaria viridis makes an ideal model species because of its small size, short lifespan, and sequenced genome. Also it is part of the panicoid grass clade, which is one of the most important clades for food and biofuel production. In plant breeding programs, large numbers of genotypes must be quickly screened for drought resistance traits, but there is no well-defined method of screening for WUE in C4 grasses. However, bulk leaf oxygen (Δ18OBL) and carbon (δ13C) isotopic signatures have shown potential as recorders of transpiration rate (E) and stomatal conductance (gs), and combined with biomass production potentially serve as a measure of WUE. Values of Δ18OBL record differences in transpiration rate because leaf water becomes more enriched as transpiration rate decreases, and leaf tissue records the isotopic composition of leaf water in which it is synthesized. Additionally, in C4 plants δ13C values decrease as gs decreases but the change in δ13C in response to gs may not be adequate to tease apart differences in WUE. In this study, we grew S. viridis plants under well-watered and water-limited conditions to determine if Δ18OBL and δ13C could be used as proxies for E and gs, and be used to screen S. viridis for differences in WUE in breeding programs. The Δ18OBL and δ13C were significantly different between well-watered and water-limited plants and correlated with each other and with E, gs, and instantaneous water use efficiency (Anet/gs). Therefore, Δ18OBL and δ13C can be useful proxies to screen genotypes for drought resistance by recording differences in E, gs, and WUE. Measuring Δ18OBL and δ13C are relatively simple and quick, requiring the collection of a single leaf sample from each genotype instead of making laborious gas exchange measurements of E and gs.

Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation1

PubMed Central

Draye, Xavier; Lin, Yann-Rong; Qian, Xiao-yin; Bowers, John E.; Burow, Gloria B.; Morrell, Peter L.; Peterson, Daniel G.; Presting, Gernot G.; Ren, Shu-xin; Wing, Rod A.; Paterson, Andrew H.

2001-01-01

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a “grass genome model.” Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. “Diversity maps,” which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA—progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis. PMID:11244113

Structural Redesigning Arabidopsis Lignins into Alkali-Soluble Lignins through the Expression of p-Coumaroyl-CoA:Monolignol Transferase PMT1

PubMed Central

Sibout, Richard; Le Bris, Philippe; Cézard, Laurent

2016-01-01

Grass lignins can contain up to 10% to 15% by weight of p-coumaric esters. This acylation is performed on monolignols under the catalysis of p-coumaroyl-coenzyme A monolignol transferase (PMT). To study the impact of p-coumaroylation on lignification, we first introduced the Brachypodium distachyon Bradi2g36910 (BdPMT1) gene into Arabidopsis (Arabidopsis thaliana) under the control of the constitutive maize (Zea mays) ubiquitin promoter. The resulting p-coumaroylation was far lower than that of lignins from mature grass stems and had no impact on stem lignin content. By contrast, introducing either the BdPMT1 or the Bradi1g36980 (BdPMT2) gene into Arabidopsis under the control of the Arabidopsis cinnamate-4-hydroxylase promoter boosted the p-coumaroylation of mature stems up to the grass lignin level (8% to 9% by weight), without any impact on plant development. The analysis of purified lignin fractions and the identification of diagnostic products confirmed that p-coumaric acid was associated with lignins. BdPMT1-driven p-coumaroylation was also obtained in the fah1 (deficient for ferulate 5-hydroxylase) and ccr1g (deficient for cinnamoyl-coenzyme A reductase) lines, albeit to a lower extent. Lignins from BdPMT1-expressing ccr1g lines were also found to be feruloylated. In Arabidopsis mature stems, substantial p-coumaroylation of lignins was achieved at the expense of lignin content and induced lignin structural alterations, with an unexpected increase of lignin units with free phenolic groups. This higher frequency of free phenolic groups in Arabidopsis lignins doubled their solubility in alkali at room temperature. These findings suggest that the formation of alkali-leachable lignin domains rich in free phenolic groups is favored when p-coumaroylated monolignols participate in lignification in a grass in a similar manner. PMID:26826222

Invasion of the Brazilian campo rupestre by the exotic grass Melinis minutiflora is driven by the high soil N availability and changes in the N cycle.

PubMed

Ribeiro, Pâmella C D; Menendez, Esther; da Silva, Danielle L; Bonieck, Douglas; Ramírez-Bahena, Martha Helena; Resende-Stoianoff, Maria Aparecida; Peix, Alvaro; Velázquez, Encarna; Mateos, Pedro F; Scotti, Maria Rita

2017-01-15

The Serra do Rola Moça State Park (PESRM) in Minas Gerais State, Brazil is a preserved site representative of the campo rupestre biome over an ironstone outcrop that has a high level of plant diversity. Almost 60% of this grassy field has been invaded by the exotic molasses grass (Melinis minutiflora), which constitutes a severe threat to the biodiversity and survival of this biome, particularly due to the impacts of annual fires and inappropriate restoration interventions. Many invasive species exhibit a high demand for nitrogen (N). Hence, this work aimed to study the N cycle alterations promoted by M. minutiflora in a site of the campo rupestre, where the leguminous species Mimosa pogocephala was prevalent. The biome's soils exhibited a high natural N fertility and low C:N ratio. The main N source in this biome resulted from the biological N fixation performed by M. pogocephala associated with Burkholderia nodosa, as evidenced by the total leaf N content, leaf δ 15 N signature, nodule occupation and bacterial molecular identification analyses. The displacement of native species by molasses grass was associated with changes in the soil N forms, namely the nitrate increased as the ammonium decreased. The latter was the dominant N form in the native species plots, as observed in the soil analysis of total N, ammonium and nitrate contents. The dominant ammonium form was changed to the nitric form by the stimulation of ammonia-oxidising bacteria populations due to the invasive species. Therefore, the key mechanism behind the invasiveness of the exotic grass and the concomitant displacement of the native species may be associated with changes in the soil N chemical species. Based on this finding and on the high N-based soil fertility found in the campo rupestre N fertilisation procedures for restoration of invaded areas should be strictly avoided in this biome. Copyright © 2016 Elsevier B.V. All rights reserved.