Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity

In light of rising energy costs, lignocellulosic ethanol has been identified as a renewable alternative to petroleum-based transportation fuels. In an attempt to reach government mandated ethanol production levels, potential plant biofeedstock candidates have been investigated, and cold-tolerant, perennial accessions within the C₄ grass genus Miscanthus have been identified as leading contenders in the Midwestern US. To facilitate the development of improved cultivars through marker-assisted breeding, a quantitative trait locus (QTL) study was conducted on a full-sib, F₁ mapping population segregating for flowering time, height, leaf width, and yield using a genetic map consisting of 846 segregating SNP and SSR markers. This was a 3 year study investigating the genetic architecture underlying traits important to biomass production in a population of 221 progeny from a cross between M. sinensis ‘Grosse Fountaine’ and M. sinensis ‘Undine’ established in the spring of 2010; 72 QTLs with LOD scores above the genome-wide, permuted threshold equivalent to a P-value of 0.05 were identified across 13 traits. Of the 36 QTLs identified in 2011, 22 were detected again the following year. Both the use of spring emergence and vigor rating as a covariate to account for variation related to differences in establishment increased the power to detect QTLs in the 2 year establishment period. Finally, a dry period in the middle of the 2012 growing season suggested that yield declines were due to a decrease in tiller diameter.     

Synthetic polyploid production of Miscanthus sacchariflorus,Miscanthus sinensis,and Miscanthus x giganteus

Plants from the genus Miscanthus are potential renewable sources of lignocellulosic biomass for energy production. A potential strategy for Miscanthus crop improvement involves interspecific manipulation of ploidy levels to generate superior germplasm and to circumvent reproductive barriers for the introduction of new genetic variation into core germplasm. Synthetic autotetraploid lines of Miscanthus sacchariflorus and Miscanthus sinensis, and autoallohexaploid Miscanthus x giganteus were produced in tissue culture from oryzalin treatments to seed‐ and immature inflorescence‐derived callus lines. This is the first report of the genome doubling of diploid M. sacchariflorus. Genome doubling of diploid M. sinensis, M. sacchariflorus, and triploid M. x giganteus to generate tetraploid and hexaploid lines was confirmed by stomata size, nuclear DNA content, and chromosome counts. A putative pentaploid line was also identified among the M. x giganteus synthetic polyploid lines by nuclear DNA content and chromosome counts. Comparisons of phenotypic performance of synthetic polyploid lines with their diploid and triploid progenitors in the greenhouse found species‐specific differences in plant tiller number, height, and flowering time among the doubled lines. Stem diameter tended to increase after polyploidization but there were no significant improvements in biomass traits. Under field conditions, M. x giganteus synthetic hexaploid lines showed greater phenotypic variation, in terms of plant height, stem diameter, and tiller number, than their progenitor lines. Production of synthetic autopolyploid lines displaying significant phenotypic variation suggests that ploidy manipulation can introduce useful genetic diversity in the limited Miscanthus germplasm currently available in the United States. The role of polyploidization in the evolution and breeding of the genus Miscanthus is discussed.     

Heterogeneity of ribosomal proteins among Streptomyces species and its application to identification

The ribosomal proteins from 11 Streptomyces strains representing various numerical taxonomic clusters were compared by two-dimensional PAGE. The protein patterns were specific for each species and were unaffected by acridine dye treatment, suggesting genetic stability of ribosomal proteins. An attempt was made to identify one strain of Streptomyces by both traditional taxonomic methods and analysis of the ribosomal protein patterns. Both methods identified the strain as Streptomyces lavendulae, and protein pattern analysis also showed that Streptomyces avidinii was closely related to this species. The practical application of ribosomal protein patterns in Streptomyces taxonomy was therefore demonstrated.     

Strategies for the enrichment and identification of basic proteins in proteome projects

Two-dimensional gel electrophoresis (2-DE) is currently the method of choice for separating complex mixtures of proteins for visual comparison in proteome analysis. This technology, however, is biased against certain classes of proteins including low abundance and hydrophobic proteins. Proteins with extremely alkaline isoelectric points (pI) are often very poorly represented using 2-DE technology, even when complex mixtures are separated using commercially available pH 6-11 or pH 7-10 immobilized pH gradients. The genome of the human gut pathogen, Helicobacter pylori, is dominated by genes encoding basic proteins, and is therefore a useful model for examining methodology suitable for separating such proteins. H. pylori proteins were separated on pH 6-11 and novel pH 9-12 immobilized pH gradients and 65 protein spots were subjected to matrix-assisted laser desorption/ionization-time of flight mass spectrometry, leading to the identification of 49 unique proteins. No proteins were characterized with a theoretical pI of greater than 10.23. A second approach to examine extremely alkaline proteins (pI > 9.0) utilized a prefractionation isoelectric focusing. Proteins were separated into two fractions using Gradiflow technology, and the extremely basic fraction subjected to both sodium dodecyl sulphate-polyacrylamide gel electrophoresis and liquid chromatography (LC) - tandem mass spectrometry post-tryptic digest, allowing the identification of 17 and 13 proteins, respectively. Gradiflow separations were highly specific for proteins with pI > 9.0, however, a single LC separation only allowed the identification of peptides from highly abundant proteins. These methods and those encompassing multiple LC 'dimensions' may be a useful complement to 2-DE for 'near-to-total' proteome coverage in the alkaline pH range.     

Study of the antioxidant capacity of Miscanthus sinensis lignins

The present work studied the antioxidant capacity of the lignin obtained from Miscanthus sinensis. As the lignin structure is very complex, extraction and separation processes highly influence obtained lignin structure and its properties, including the antioxidant activity. Lignin fractions were obtained from black liquor resulting from different fractionating and autohydrolysis processes of M. sinensis. Different lignin fractions with specific molecular weight were separated by ultrafiltration using different cut-off ceramic membranes (10 and 15 kDa). The physico-chemical properties, phenolic groups content and the antioxidant capacity of each lignin sample were studied. It was found that antiradical activity of the analyzed lignin samples was closely related with the used fractionating process (soda, organosolv and autohydrolysis treatments). The ultrafiltration process allows obtaining lignins with different antioxidant capacity, improving this property as the used cut-off was greater.     

Multidimensional protein profiling technology and its application to human plasma proteome

In clinical and diagnostic proteomics, it is essential to develop a comprehensive and robust system for proteome analysis. Although multidimensional liquid chromatography/tandem mass spectrometry (LC/MS/MS) systems have been recently developed as powerful tools especially for identification of protein complexes, these systems still some drawbacks in their application to clinical research that requires an analysis of a large number of human samples. Therefore, in this study, we have constructed a technically simple and high throughput protein profiling system comprising a two-dimensional (2D)-LC/MS/MS system which integrates both a strong cation exchange (SCX) chromatography and a microLC/MS/MS system with micro-flowing reversed-phase chromatography. Using the microLC/MS/MS system as the second dimensional chromatography, SCX separation has been optimized as an off-line first dimensional peptide fractionation. To evaluate the performance of the constructed 2D-LC/MS/MS system, the results of detection and identification of proteins were compared using digests mixtures of 6 authentic proteins with those obtained using one-dimensional microLC/MS/MS system. The number of peptide fragments detected and the coverage of protein sequence were found to be more than double through the use of our newly built 2D-LC/MS/MS system. Furthermore, this multidimensional protein profiling system has been applied to plasma proteome in order to examine its feasibility for clinical proteomics. The experimental results revealed the identification of 174 proteins from one serum sample depleted HSA and IgG which corresponds to only 1 microL of plasma, and the total analysis run time was less than half a day, indicating a fairly high possibility of practicing clinical proteomics in a high throughput manner.     

Mapping of the Physcomitrella patens proteome

The moss Physcomitrella patens is unique among land plants due to the high rate of homologous recombination in its nuclear DNA. The feasibility of gene targeting makes Physcomitrella an unrivalled model organism in the field of plant functional genomics. To further extend the potentialities of this seed-less plant we aimed at exploring the P. patens proteome. Experimental conditions had to be adopted to meet the special requirements connected to the investigations of this moss. Here we describe the identification of 306 proteins from the protonema of Physcomitrella. Proteins were separated by two dimensional electrophoresis, excised form the gel and analysed by means of mass spectrometry. This reference map will lay the basis for further profound studies in the field of Physcomitrella proteomics.     

Predominant identification of RNA-binding proteins in Fas-induced apoptosis by proteome analysis

Proteome analysis of Jurkat T cells was performed in order to identify proteins that are modified during apoptosis. Subtractive analysis of two-dimensional gel patterns of apoptotic and nonapoptotic cells revealed differences in 45 protein spots. 37 protein spots of 21 different proteins were identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization mass spectrometry. The hnRNPs A0, A2/B1, A3, K, and R; the splicing factors p54(nrb), SRp30c, ASF-2, and KH-type splicing regulatory protein (FUSE-binding protein 2); and alpha NAC, NS1-associated protein 1, and poly(A)-binding protein 4 were hitherto unknown to be involved in apoptosis. The putative cleavage sites of the majority of the proteins could be calculated by the molecular masses and isoelectric points in the two-dimensional electrophoresis gel, the peptide mass fingerprints, and after translation by treatment with recombinant caspase-3. Remarkably, 15 of the 21 identified proteins contained the RNP or KH motif, the best characterized RNA-binding motifs.     

金属矿区芒草种群对重金属的积累及其与土壤特性的关系

通过分析大型综合金属矿区中经历不同污染强度与污染时间胁迫的芒草（Miscanthus sinensis）种群对4种主要重金属的积累状况,初步揭示芒草对这些重金属的积累特性与土壤重金属含量的关系。结果表明,1芒草根茎叶对4种重金属的的积累顺序为：根〉叶〉茎;2芒草对Cd、Pb的积累量与土壤中这两种重金属含量之间存在显著（P〈0．05）正相关关系;对Cu、Zn的积累量与土壤含量之间无显著相关,主要是因为土壤最高Cu与Zn含量已超过芒草对这两种元素积累所需的最大量,成为对芒草构成胁迫的主要因子。在该矿区的酸性条件下,芒草对Pb、Zn、Cu3种重金属的吸收率随pH值升高而升高,pH接近的样地,芒草的吸收率主要受土壤重金属含量的影响。结合各种群对四种重金属的积累状况判断,强度胁迫下的种群可能已发生耐性分化,从而产生较其它种群更强的耐重金属特性。总体上芒草是一种多重金属耐性植物,对这四种重金属的耐性顺序是：Cd〈Cu〈Zn-Pb。     

New insights into the rat spermatogonial proteome: identification of 156 additional proteins

Despite the essential role played by spermatogonia in testicular function, little is known about these cells. To improve our understanding of their biology, our group recently identified a set of 53 spermatogonial proteins using two-dimensional (2-D) gel electrophoresis and mass spectrometry. To continue this work, we investigated a subset of the spermatogonial proteome using narrow range immobilized pH gradients to favor the detection of less abundant proteins. A 2-D reference map of spermatogonia in the pH range 4-9 was created, and protein entities fractionated in a pH 5-6 2-D gel were further processed for protein identification. A new set of 156 polypeptides was identified by peptide mass fingerprinting and tandem mass spectrometry. These polypeptides corresponded to 102 different proteins, which reflect the complexity of post-translational modifications. Seventy-nine of these proteins were identified for the first time in spermatogonia. All identified proteins were classified into functional groups. This work represents a first step toward the establishment of a systematic spermatogonia protein database.     

Wheat leaf proteome analysis using sequence data of proteins separated by two-dimensional electrophoresis

Identifying wheat leaf protein expression is a major challenge of functional genomics. Using two-dimensional gel electrophoresis 541 wheat leaf proteins were separated and 55 of them were sequenced by nano liquid chromatography-tandem mass spectrometry. Peptide sequence data were screened against protein banks and expressed sequence tag public banks. Among these 55 spots, 20 proteins were found in wheat and 21 in other grass families (http://www.ncbi.nlm.nih.gov/). Twelve proteins showed similarities with other eukaryotic plant species. One protein showed homology to a bacterial sequence and another protein remained unknown. In 18 cases a significant score was found for the wheat TUC (Tentative Unique Contigs) of the PlantGDB (http://www.plantgdb.org/) data. In several cases, different spots were identified as corresponding to the same protein that can probably be attributed to the hexaploid structure of wheat. The identified proteins were classified in six groups and their role is discussed. Most of them (31/55) are involved in carbohydrate metabolism.     

Micropropagation and plant regeneration from embryogenic callus of Miscanthus sinensis

Miscanthus sinensis (Poaceae) is a typical perennial giant grass of East Asia. Due to its high photosynthetic efficiency, low input requirements, and high biomass production, M. sinensis shows outstanding potential as a biofuel feedstock. However, the lack of an efficient tissue culture system may limit its utilization potential. Different explants of M. sinensis were evaluated to develop an efficient tissue culture system. Shoot apices from in vitro-germinated seedling explants were tested for adventitious bud proliferation. The highest level of proliferation (multiplication coefficient 6.69) was obtained when shoot apices were cultured on Murashige and Skoog (MS) medium supplemented with 1.0 mg L⁻¹ 6-benzyladenine (BA), 2.0 mg L⁻¹ kinetin, 0.05 mg L⁻¹ α-naphthalene acetic acid (NAA), 3% sucrose, and 0.8% agar. The highest rooting percentage (95.4%) was obtained when adventitious buds were cultured on half-strength MS medium supplemented with 0.2 mg L⁻¹ NAA, 3% sucrose, and 0.8% agar. Significant differences were found in the formation of embryogenic callus among different explant types. The embryogenic callus derived from epicotyls had the highest regeneration capacity when cultured on a medium supplemented with 2.0 mg L⁻¹ 2,4-dichlorophenoxyacetic acid, 0.5 mg L⁻¹ BA, and 0.1 mg L⁻¹ thiamine. Under these conditions, the callus induction percentage was 82%.     

Environmental Tolerances of Miscanthus sinensis in Invasive and Native Populations

Miscanthus sinensis is a moderately invasive ornamental grass species being considered as a bioenergy species in the USA and elsewhere. In this study, we show the range of environmental conditions tolerated by this species in wild populations in the USA and in Japan. Six naturalized populations in the USA and five native populations in Japan were sampled in summer 2009. In each population, environmental factors (canopy cover and soil fertility) were measured, along with measurements of size and morphology for 30 plants. Relationships between M. sinensis size and environmental variables in the two countries were determined using linear mixed effects models. Results indicated that M. sinensis can tolerate extremely wide variation in soil and climate conditions in the populations we sampled across both ranges, suggesting that it could be successfully grown across a wide distribution in the USA, both intentionally as a bioenergy crop and unintentionally as an escaped invader. Plant size generally responded to different environmental conditions in both ranges, with USA plants being negatively influenced by canopy cover and Japanese plants being positively influenced by soil fertility measures. We recommend caution in growing M. sinensis for bioenergy or ornamental purposes to minimize escape outside of its native range.     

Analysis of lignocelluloses and lignins from Arundo donax L. and Miscanthus sinensis Anderss., and hydroliquefaction of Miscanthus

In a comparative investigation of the chemical composition of Arundo donax L. and Miscanthus sinensis Anderss. the following experiments were performed: ash determination and ash characterization by energy dispersive X-ray analysis; determination of solubility in cyclohexane/ ethanol, hot water, 1% hydrochloric acid and sodium hydroxide; C, H and N determination; determination of Klason lignin and acid soluble lignin content; sulfuric acid hydrolysis followed by borate complex ion exchange chromatography of the monomeric sugars; isolation of milled wood lignins (MWL) and dioxane lignins (DIL) and their analysis by C, H, and OMe determination; quantitative FTIR spectroscopy of MWL; recording the molecular weight distribution curves using high performance size exclusion chromatography (HPSEC); calculation of average molecular weights, such as M_w and M_n; calculation of the heating values of the lignocellulosics and their components. The quantitative composition of the lignin from the three basic phenylpropane units is presented.M. sinensis was submitted to hydroliquefaction. The conversion process yielded 35% of a net product oil (NPO) with low oxygen content (11%), low viscosity (10⁻² NS m⁻²), low asphaltene content (3·5%) low molecular weight (M_w 200) and with a specific gravity of c. 0·93 g cm⁻³. The NPO has a heating value of 39·4 MJ kg⁻¹ and contains 55% of the carbon of the starting material and 59% of the combined heating value from the biomass and the hydrogen used for hydroliquefaction. The process yields 28% water which contains 58% of the original oxygen of the biomass. The process gives rise to 9 g solids and 32–35 g gases, whose energy content can easily be recovered.     

Development of SCAR marker for simultaneous identification of Miscanthus sacchariflorus, M. sinensis and M. x giganteus

The sequence-characterized amplified region (SCAR) marker for simultaneous identification of Miscanthus sacchariflorus, Miscanthus sinensis, and Miscanthus x giganteus was developed. In this study, it was attempted for the first time to develop the SCAR marker for detecting the molecular phenotypes among Miscanthus species. Randomly amplified polymorphic DNA technique was applied for this study and one fragment which is unique to M. sacchariflorus was identified and then sequenced. Based on the specific fragment, one SCAR primer pair designated as MS62-5F and MS62-5R was designed to amplify an approximately 1,000 bp DNA fragment within the sequenced region. Diagnostic PCR was performed using the primer pair. Using this SCAR marker, approximately 1,000 bp and 1,200 bp DNA fragments were obtained in M. sacchariflorus and M. sinensis, respectively. Moreover, M. x giganteus was obtained both bands at the same time. The result showed that this SCAR marker can clearly distinguish the M. sacchariflorus, M. sinensis, and M. x giganteus, respectively.     

Mapping the membrane proteome of Corynebacterium glutamicum

In order to avoid the specific problems with intrinsic membrane proteins in proteome analysis, a new procedure was developed which is superior to the classical two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) method in terms of intrinsic membrane proteins. For analysis of the membrane proteome from Corynebacterium glutamicum, we replaced the first separation dimension, i.e., the isoelectric focusing step, by anion-exchange chromatography, followed by sodium dodecyl sulfate (SDS)-PAGE in the second separation dimension. Enrichment of the membrane intrinsic subproteome was achieved by washing with 2.5 M NaBr which removed more than 35% of the membrane-associated soluble proteins. For the extraction and solubilization of membrane proteins, the detergent amidosulfobetaine 14 (ASB-14) was most efficient in a detailed screening procedure and proved also suitable for chromatography. 356 gel bands were spotted, and out of 170 different identified proteins, 50 were membrane-integral. Membrane proteins with one up to 13 transmembrane helices were found. Careful analysis revealed that this new procedure covers proteins from a wide pI range (3.7-10.6) and a wide mass range of 10-120 kDa. About 50% of the identified membrane proteins belong to various functional categories like energy metabolism, transport, signal transduction, protein translocation, and proteolysis while for the others a function is not yet known, indicating the potential of the developed method for elucidation of membrane proteomes in general.