Joshua S Yuan

Texas A&M University, College Station, Texas, United States

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Publications (43)203.2 Total impact

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    ABSTRACT: Lignin utilization during biomass conversion has been a major challenge for lignocellulosic biofuel. In particular, the conversion of lignin along with carbohydrate for fungible fuels and chemicals will both improve the overall carbon efficiency and reduce the need for chemical pretreatments. However, few biomass-converting microorganisms have the capacity to degrade all cell wall components including lignin, cellulose, and hemicellulose. We hereby evaluated a unique oleaginous fungus strain Cunninghamella echinulata FR3 for its capacity to degrade lignin during biomass conversion to lipid, and the potential to carry out consolidated fermentation without chemical pretreatment, especially when combined with sorghum (Sorghum bicolor) bmr mutants with reduced lignin content. The study clearly showed that lignin was consumed together with carbohydrate during biomass conversion for all sorghum samples, which indicates this organism has the potential for biomass conversion without chemical pretreatment. Even though dilute acid pretreatment of biomass resulted in more weight loss during fungal fermentation than untreated biomass, the lipid yields were comparable for untreated bmr6/bmr12 double mutant and dilute acid-pretreated wild-type biomass samples. The mechanisms for lignin degradation in oleaginous fungi were further elucidated through transcriptomics and chemical analysis. The studies showed that in C. echinulata FR3, Fenton Reaction may play an important role in lignin degradation. This discovery is among the first to show that a mechanism for lignin degradation similar to ones found in white and brown rot basidiomycetous fungi exists in an oleaginous fungus. This study suggests that oleaginous fungus such as C. echinulata FR3 can be employed for complete biomass utilization in a consolidated platform without chemical pretreatment, or can be used to convert lignin waste into lipids.
    Green Chemistry 12/2014; · 6.83 Impact Factor
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    Shangxian Xie, Ryan Syrenne, Su Sun, Joshua S Yuan
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    ABSTRACT: Efficient degradation and utilization of lignocellulosic biomass remains a challenge for sustainable and affordable biofuels. Various natural biomass utilization systems (NBUS) evolved the capacity to combat the recalcitrance of plant cell walls. The study of these NBUS could enable the development of efficient and cost-effective biocatalysts, microorganisms, and bioprocesses for biofuels and bioproducts. Here, we reviewed the recent research progresses for several NBUS, ranging from single cell microorganisms to consortiums such as cattle rumen and insect guts. These studies aided the discovery of biomass-degrading enzymes and the elucidation of the evolutionary and functional relevance in these systems. In particular, advances in the next generation 'omics' technologies offered new opportunities to explore NBUS in a high-throughput manner. Systems biology helped to facilitate the rapid biocatalyst discovery and detailed mechanism analysis, which could in turn guide the reverse design of engineered microorganisms and bioprocesses for cost-effective and efficient biomass conversion.
    Current Opinion in Biotechnology 03/2014; 27C:195-203. · 8.04 Impact Factor
  • Wusheng Liu, Joshua S Yuan, C Neal Stewart Jr
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    ABSTRACT: Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.
    Nature Reviews Genetics 10/2013; · 41.06 Impact Factor
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    ABSTRACT: Genetically engineered (GE) ringspot virus-resistant papayas cultivars 'Rainbow' and 'SunUp' have been grown in Hawai'i for over 10 years. In Hawai'i, the introduction of GE papayas into regions where non-GE cultivars are grown and where feral non-GE papayas exist have been accompanied with concerns associated with transgene flow. Of particular concern is the possibility of transgenic seeds being found in non-GE papaya fruits via cross-pollination. Development of high-throughput methods to reliably detect the adventitious presence of such transgenic material would benefit both the scientific and regulatory communities. We assessed the accuracy of using conventional qualitative polymerase chain reaction (PCR) as well as real-time PCR-based assays to quantify the presence of transgenic DNA from bulk samples of non-GE papaya seeds. In this study, an optimized method of extracting high quality DNA from dry seeds of papaya was standardized. A reliable, sensitive real-time PCR method for detecting and quantifying viral coat protein (cp) transgenes in bulk seed samples utilizing the endogenous papain gene is presented. Quantification range was from 0.01 to 100 ng/mul of GE-papaya DNA template with a detection limit as low as 0.01% (10 pg). To test this system, we simulated transgene flow using known quantities of GE and non-GE DNA and determined that 0.038% (38 pg) GE papaya DNA could be detected using real-time PCR. We also validated this system by extracting DNA from known ratios of GE seeds to non-GE seeds of papaya followed by real-time PCR detection and observed a reliable detection limit of 0.4%. This method for the quick and sensitive detection of transgenes in bulked papaya seed lots using conventional as well as real-time PCR-based methods will benefit numerous stakeholders. In particular, this method could be utilized to screen selected fruits from maternal non-GE papaya trees in Hawai'i for the presence of transgenic seed at typical regulatory threshold levels. Incorporation of subtle differences in primers and probes for variations in cp worldwide should allow this method to be utilized elsewhere when and if deregulation of transgenic papaya occurs.
    BMC Biotechnology 09/2013; 13(1):69. · 2.17 Impact Factor
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    ABSTRACT: High abundance proteins like Ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. In order to address this challenge, we developed and evaluated Polyethyleneimine (PEI) Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery.
    Molecular &amp Cellular Proteomics 08/2013; · 7.25 Impact Factor
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    Yixiang Zhang, Peng Gao, Joshua S Yuan
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    ABSTRACT: Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications.
    PLoS Genetics 02/2013; 9(1):e1003131. · 8.52 Impact Factor
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    Shangxian Xie, Su Sun, Susie Y. Dai, Joshua S.Yuan
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    ABSTRACT: To overcome the daunting technical barriers of algae biofuels and photosynthetic biorefineries, a novel cultivation technology has been developed to concentrate, harvest, and enhance microalgae-based biofuels and bioproducts through pelletization. The technology involves the co-cultivation of microalgae with fungi to achieve optimized pelletization with a 2-to-10-mm diameter. This pelletization enables the complete removal of single algal cells from the liquid medium to allow their extraction and harvest by simple filtration. In addition, the pelletization process results in significantly increased biomass, lipid, and bioproduct yields. If successfully scaled up, this technology has the potential to improve the sustainability and economic viability of the production of algal biofuels.
    Algal Research. 01/2013; 2(1):28–33.
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    ABSTRACT: Multidimensional protein identification technology (MudPIT)-based shot-gun proteomics has been proven to be an effective platform for functional proteomics. In particular, the various sample preparation methods and bioinformatics tools can be integrated to improve the proteomics platform for applications like target organelle proteomics. We have recently integrated a rapid sample preparation method and bioinformatics classification system for comparative analysis of plant responses to two plant hormones, zeatin and brassinosteroid (BR). These hormones belong to two distinct classes of plant growth regulators, yet both can promote cell elongation and growth. An understanding of the differences and the cross-talk between the two types of hormone responses will allow us to better understand the molecular mechanisms and to identify new candidate genes for plant engineering. As compared to traditional organelle proteomics, the organelle-enrichment method both simplifies the sample preparation and increases the number of proteins identified in the targeted organelle as well as the entire sample. Both zeatin and BR induce dramatic changes in signaling and metabolism. Their shared-regulated protein components indicate that both hormones may down-regulate some key components in auxin responses. However, they have shown distinct induction and suppression of metabolic pathways in mitochondria and chloroplast. For zeatin, the metabolic pathways in sucrose and starch biosynthesis and utilization were significantly changed, yet the lipid biosynthesis remained unchanged. For BR, lipid biosynthesis and β-oxidation were both down-regulated, yet the changes in sucrose and starch metabolism were minor. We present a rapid sample preparation method and bioinformatics classification for effective proteomics analysis of plant hormone responses. The study highlighted the largely differing response to zeatin and brassinosteroid by the metabolic pathways in chloroplast and mitochondria.
    BMC Bioinformatics 09/2012; 13 Suppl 15:S8. · 3.02 Impact Factor
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    ABSTRACT: NAC domain transcription factors are important transcriptional regulators involved in plant growth, development and stress responses. Recent studies have revealed several classes of NAC transcriptional factors crucial for controlling secondary cell wall biosynthesis. These transcriptional factors mainly include three classes, SND, NST and VND. Despite progress, most current analysis is carried out in the model plant Arabidopsis. Moreover, many downstream genes regulated by these transcriptional factors are still not clear. In order to identify the key homologue genes across species and discover the network controlling cell wall biosynthesis, we carried out comparative genome analysis of NST, VND and SND genes across 19 higher plant species along with computational modelling of genes regulated or co-regulated with these transcriptional factors. The comparative genome analysis revealed that evolutionarily the secondary-wall-associated NAC domain transcription factors first appeared in Selaginella moellendorffii. In fact, among the three groups, only VND genes appeared in S. moellendorffii, which is evolutionarily earlier than the other two groups. The Arabidopsis and rice gene expression analysis showed specific patterns of the secondary cell wall-associated NAC genes (SND, NST and VND). Most of them were preferentially expressed in the stem, especially the second internodes. Furthermore, comprehensive co-regulatory network analysis revealed that the SND and MYB genes were co-regulated, which indicated the coordinative function of these transcriptional factors in modulating cell wall biosynthesis. In addition, the co-regulatory network analysis revealed many novel genes and pathways that could be involved in cell wall biosynthesis and its regulation. The gene ontology analysis also indicated that processes like carbohydrate synthesis, transport and stress response, are coordinately regulated toward cell wall biosynthesis. Overall, we provided a new insight into the evolution and the gene regulatory network of a subgroup of the NAC gene family controlling cell wall composition through bioinformatics data mining and bench validation. Our work might benefit to elucidate the possible molecular mechanism underlying the regulation network of secondary cell wall biosynthesis.
    BMC Bioinformatics 09/2012; 13 Suppl 15:S10. · 3.02 Impact Factor
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    ABSTRACT: Background: Insect gut symbionts are essential for biomass degradation, nutrient synthesis and toxin detoxification. We carried out comparative analysis of gut symbionts from four insect species to investigate the adaptation to different food types and to evaluate the potential for biofuel applications. Results: The study revealed significant variation of insect gut symbiont composition as a function to adapt to different food types. The composition–function relationship has been discussed from different perspectives, including biomass utilization and nutrient biosynthesis. The existence of species such as Klebsiella oxytoca and the capacity for these species to produce unique biomass degradation enzymes indicated that grasshopper and woodborer gut systems may be enriched resources for biofuel applications. For functional verification and concept validation, we have cloned and characterized a β-glucosidase from K. oxytoca in the grasshopper gut system. Conclusion: The research suggested that different insect gut systems can be good resources for biocatalyst and microbial strain discovery for bioenergy applications.
    Biofuels. 09/2011; 2(5):529-544.
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    ABSTRACT: After herbivore damage, many plants increase their emission of volatile compounds, with terpenes usually comprising the major group of induced volatiles. Populus trichocarpa is the first woody species with a fully sequenced genome, enabling rapid molecular approaches towards characterization of volatile terpene biosynthesis in this and other poplar species. We identified and characterized four terpene synthases (PtTPS1-4) from P. trichocarpa which form major terpene compounds of the volatile blend induced by gypsy moth (Lymantria dispar) feeding. The enzymes were heterologously expressed and assayed with potential prenyl diphosphate substrates. PtTPS1 and PtTPS2 accepted only farnesyl diphosphate and produced (-)-germacrene D and (E,E)-α-farnesene as their major products, respectively. In contrast, PtTPS3 and PtTPS4 showed both mono- and sesquiterpene synthase activity. They produce the acyclic terpene alcohols linalool and nerolidol but exhibited opposite stereospecificity. qRT-PCR analysis revealed that the expression of the respective terpene synthase genes was induced after feeding of gypsy moth caterpillars. The TPS enzyme products may play important roles in indirect defense of poplar to herbivores and in mediating intra- and inter-plant signaling.
    Phytochemistry 04/2011; · 3.35 Impact Factor
  • Weibing Shi, Shi-You Ding, Joshua S. Yuan
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    ABSTRACT: Insect guts represent unique natural biocatalyst systems for biocatalyst discovery and biomass deconstruction mechanism studies. In order to guide the further research for enzyme discovery and biodiversity analysis, we carried out comprehensive xylanase and cellulase activity assays for the gut contents of three insect species representing different orders and food sources. The three insect species are grasshopper (Acrididae sp.), woodborer (Cerambycidae spp.), and silkworm (Bombyx mori) to represent the wood-consuming, grass-consuming, and leaf-consuming insects from Orthoptera, Coleoptera, and Lepidoptera orders, respectively. Generally speaking, the enzyme activity assays have shown that the cellulase and xylanase activities for grasshopper and woodborer guts are significantly higher than those of silkworm under various conditions. In addition, both pH and temperature have a significant impact on the enzyme activities in the gut contents. For the grasshopper gut, the means of xylanase and cellulase activities at pH7 were 3,397 and 404μM mg−1 min−1, which are significantly higher than the activities at pH4 and 10 (P < 0.05). However, woodborer guts have shown the highest cellulase activity at pH10. The results suggested that systems similar to woodborer guts could be good resources for discovering alkaline-tolerant enzymes. Moreover, the enzyme activities in response to different substrate concentrations were also analyzed, which indicated that grasshopper gut had particularly high cellulase activity. The enzyme activities in response to the reaction time were also examined, and we found that the enzyme activities (micromolar per milligram per minute) of different insect gut juices in response to the increase of incubation time fit well to the power function equation (E c = K ⋅ t b ) with high coefficients (r 2 > 0.99). The newly developed model serves well to compare the characteristics of the enzyme mixtures among different insect species, which can be applied to other studies of natural biocatalyst systems for the future. Overall, the data indicated that grasshopper and woodborer guts are valuable resources for discovering the novel biocatalysts for various biorefinery applications. KeywordsInsect gut-Cellulase-Xylanase-Natural biocatalyst system
    BioEnergy Research 01/2011; 4(1):1-10. · 4.25 Impact Factor
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    ABSTRACT: BACKGROUND: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2. IMPLEMENTATION AND RESULTS: HDXanalyzer package contains three major modules, the data processing module, the statistical analysis module, and the user interface. RPY2 is employed to enable the connection of these three components, where the data processing module is implemented using Python and the statistical analysis module is implemented with R. RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing. The data processing module generates the centroid for the peptides in form of m/z value, and the differences of centroids between the peptides derived from apo and ligand-bound protein allow us to evaluate whether the regions have significant changes in structure dynamics or not. Another option of the software is to calculate the deuterium incorporation rate for the comparison. The two types of statistical analyses are Paired Student's t-test and the linear combination of the intercept for multiple regression and ANCOVA model. The user interface is implemented with wxpython to facilitate the data visualization in graphs and the statistical analysis output presentation. In order to evaluate the software, a previously published xylanase HDX mass spectrometry analysis dataset is processed and presented. The results from the different statistical analysis methods are compared and shown to be similar. The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme. CONCLUSION: Statistical analysis provides crucial evaluation of whether a protein region is significantly protected or unprotected during the HDX mass spectrometry studies. Although there are several other available software programs to process HDX experimental data, HDXanalyzer is the first software program to offer multiple statistical methods to evaluate the changes in protein structure dynamics based on HDX mass spectrometry analysis. Moreover, the statistical analysis can be carried out for both m/z value and deuterium incorporation rate. In addition, the software package can be used for the data generated from a wide range of mass spectrometry instruments.
    BMC Bioinformatics 01/2011; 12 Suppl 1:S43. · 3.02 Impact Factor
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    ABSTRACT: The de novo transcriptome sequencing of a weedy plant using GS-FLX 454 technologies is reported. Horseweed (Conyza canadensis L.) was the first broadleaf weed to evolve glyphosate resistance in agriculture, and also is the most widely distributed glyphosate-resistant weed in the United States and the world. However, available sequence data for this species are scant. The transcriptomic sequence should be useful for gene discovery, and to help elucidate the non-target-based glyphosate resistance mechanism and the genomic basis of weediness. Sequencing experiments yielded 411 962 raw reads, an average read length of 233 bp and a total dataset of 95.8 Mb (NCBI accession number SRA010952). After trimming and quality control, 379 152 high-quality sequences were retained and assembled into contigs. The assembly resulted in 31 783 unique transcripts, including 16 102 contigs and 15 681 singletons. The average coverage depth for each contig and each nucleotide position was 22-fold and 12-fold respectively. A total of 16 306 unique sequences were annotated by searching a custom plant protein database. The utility of the transcriptome data was demonstrated by further exploration of ABC transporters, which were previously hypothesized to play a role in non-target glyphosate resistance. Real-time RT-PCR primers were designed from the transcriptome data, which made it possible to assess expression patterns of 17 ABC transporters from resistant and susceptible horseweed accessions from Tennessee, with and without glyphosate treatment. These results show that GS-FLX 454 sequencing is a powerful and cost-effective platform for the development of functional genomic tools for a weed species.
    Pest Management Science 10/2010; 66(10):1053-62. · 2.74 Impact Factor
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    ABSTRACT: Abstract Insect gut symbiotic microbiota play essential roles in the growth, development, pathogenesis and environmental adaptation of host insects. The molecular and systems level analysis of insect gut symbiotic microbial community will allow us to discover novel biocatalysts for biomass deconstruction and to develop innovative strategies for pest management. We hereby review the various molecular biology techniques as applied to insect gut symbiont analysis. This review aims to serve as an informative resource for experimental design and research strategy development in the field. We first discuss various strategies for sample preparation and their pros and cons. The traditional molecular techniques like DGGE, RFLP and FISH are covered with respect to how they are applied to study the composition, diversity and dynamics of insect gut symbiotic microbiota. We then focus on the various ‘omics’ techniques. The metagenome analysis together with the recent advancements in next-generation sequencing will provide enormous sequencing information, allowing in-depth microbial diversity analysis and modeling of pathways for biological processes such as biomass degradation. The metagenome sequencing will also enable the study of system dynamics and gene expression with metatranscriptome and metaproteome methods. The integration of different ‘omics’ level data will allow us to understand how insect gut works as a system to carry out its functions. The molecular and systems-level understanding will also guide the reverse design of next-generation biorefinery.
    Insect Science 06/2010; 17(3):199 - 219. · 1.79 Impact Factor
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    ABSTRACT: The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis. Nomenclature: Glyphosate, horseweed, Conyza canadensis (L.) Cronq. ERICA
    Weed Science 04/2010; · 1.76 Impact Factor
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    Yixiang Zhang, Peng Gao, Joshua S Yuan
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    ABSTRACT: Protein-protein interaction network represents an important aspect of systems biology. The understanding of the plant protein-protein interaction network and interactome will provide crucial insights into the regulation of plant developmental, physiological, and pathological processes. In this review, we will first define the concept of plant interactome and the protein-protein interaction network. The significance of the plant interactome study will be discussed. We will then compare the pros and cons for different strategies for interactome mapping including yeast two-hybrid system (Y2H), affinity purification mass spectrometry (AP-MS), bimolecular fluorescence complementation (BiFC), and in silico prediction. The application of these platforms on specific plant biology questions will be further discussed. The recent advancements revealed the great potential for plant protein-protein interaction network and interactome to elucidate molecular mechanisms for signal transduction, stress responses, cell cycle control, pattern formation, and others. Mapping the plant interactome in model species will provide important guideline for the future study of plant biology.
    Current Genomics 03/2010; 11(1):40-6. · 2.48 Impact Factor
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    ABSTRACT: Enzyme dynamics has recently been shown to be crucial for structure-function relationship. Among various structure dynamics analysis platforms, HDX (hydrogen deuterium exchange) mass spectrometry stands out as an efficient and high-throughput way to analyze protein dynamics upon ligand binding. Despite the potential, limited research has employed the HDX mass spec platform to probe regional structure dynamics of enzymes. In particular, the technique has never been used for analyzing cell wall degrading enzymes. We hereby used xylanase as a model to explore the potential of HDX mass spectrometry for studying cell wall degrading enzymes. HDX mass spectrometry revealed significant intrinsic dynamics for the xylanase enzyme. Different regions of the enzymes are differentially stabilized in the apo enzyme. The comparison of substrate-binding enzymes revealed that xylohexaose can significantly stabilize the enzyme. Several regions including those near the reaction centres were significantly stabilized during the xylohexaose binding. As compared to xylohexaose, xylan induced relatively less protection in the enzyme, which may be due to the insolubility of the substrate. The structure relevance of the enzyme dynamics was discussed with reference to the three dimensional structure of the enzyme. HDX mass spectrometry revealed strong dynamics-function relevance and such relevance can be explored for the future enzyme improvement. Ligand-binding can lead to the significant stabilization at both regional and global level for enzymes like xylanase. HDX mass spectrometry is a powerful high-throughput platform to identify the key regions protected during the ligand binding and to explore the molecular mechanisms of the enzyme function. The HDX mass spectrometry analysis of cell wall degrading enzymes has provided a novel platform to guide the rational design of enzymes.
    BMC Bioinformatics 01/2010; 11 Suppl 6:S12. · 3.02 Impact Factor
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    Chao Di, Wenying Xu, Zhen Su, Joshua S Yuan
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    ABSTRACT: PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.
    BMC Bioinformatics 01/2010; 11 Suppl 6:S22. · 3.02 Impact Factor

Publication Stats

1k Citations
203.20 Total Impact Points

Institutions

  • 2008–2014
    • Texas A&M University
      • • Department of Plant Pathology and Microbiology
      • • Institute for Plant Genomics and Biotechnology
      College Station, Texas, United States
  • 2006–2013
    • The University of Tennessee Medical Center at Knoxville
      Knoxville, Tennessee, United States
    • University of Michigan
      • Department of Molecular, Cellular and Developmental Biology
      Ann Arbor, MI, United States
  • 2010
    • China Agricultural University
      • China State Key Laboratory of Plant Physiology and Biochemistry
      Beijing, Beijing Shi, China
  • 2006–2010
    • University of Tennessee
      • Department of Plant Sciences
      Knoxville, TN, United States