Semigroup approach to the stability of a direct strain feedback control system of elastic vibration with structure damping

AbstractIn this paper, we relate a kind of second order hyperbolic system to an analytic semigroup, which is most often applied to the direct strain feedback (DSFB) control of flexible robot arms. The spectrum analysis is presented to confirm the positive function of DSFB

Mechanisms of Resistance to Aflatoxin Accumulation by Aspergillus Flavus in Maize Genotype GT-MAS:gk.

Maize genotype differences in aflatoxin production were observed when kernels of resistant GT-MAS:gk and thirteen susceptible commercial hybrids were inoculated with Aspergillus flavus using a laboratory kernel screening assay. GT-MAS:gk supported the lowest levels of aflatoxin in both intact and endosperm-wounded kernels. Treating intact kernels with KOH effected substantial increases in aflatoxin accumulation in GT-MAS:gk, but only marginal increases in Pioneer 3154. Removing wax from the surface of GT-MAS:gk kernels greatly increased aflatoxin accumulation. These results indicated that GT-MAS:gk resistance was associated with an intact pericarp (wax and cutin layers), acting as a physical barrier, along with internal biochemical factors. Kernels of GT-MAS:gk and Pioneer 3154 were tested for resistance to aflatoxin accumulation by A. flavus under different relative humidities (RH). Resistance in GT-MAS:gk was consistent across all RH levels. Preincubation at 100% RH for three days increased germination. In germinated kernels, aflatoxin levels decreased markedly in Pioneer 3154 but not GT-MAS:gk. When eight susceptible hybrids were evaluated under preincubation conditions, seven supported significantly lower aflatoxin levels than kernels not subjected to preincubation. Data suggested that an inhibitor of aflatoxin biosynthesis may be induced during kernel germination process. A. flavus can utilize cutin as sole carbon source, which suggests production of extracellular cutinase in vitro. This production was optimal at pH 8.0. Two esterases (cutinases) (36 kD and 22-23 kD) were isolated from A. flavus liquid cultures. Treatments with exogenous cutinase or DFP, an fungal cutinase inhibitor, markedly increased or decreased aflatoxin production, respectively. Results suggested that A. flavus produces cutinase and that this enzyme may play an important role in pathogenicity of A. flavus. Studies demonstrated that GT-MAS:gk kernels have more surface wax than do susceptible hybrids, and that this wax has antifungal activity against A. flavus. Wax from GT-MAS:gk kernels had a unique component, visualized using thin layer chromatography. This component was purified and examined using gas chromatography and mass spectrometry. A peak was identified that was absent in other genotypes. This compound may be a triterpenoid

Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection

<p>Abstract</p> <p>Background</p> <p>Peanut (<it>Arachis hypogaea </it>L.) is an important crop economically and nutritionally, and is one of the most susceptible host crops to colonization of <it>Aspergillus parasiticus </it>and subsequent aflatoxin contamination. Knowledge from molecular genetic studies could help to devise strategies in alleviating this problem; however, few peanut DNA sequences are available in the public database. In order to understand the molecular basis of host resistance to aflatoxin contamination, a large-scale project was conducted to generate expressed sequence tags (ESTs) from developing seeds to identify resistance-related genes involved in defense response against <it>Aspergillus </it>infection and subsequent aflatoxin contamination.</p> <p>Results</p> <p>We constructed six different cDNA libraries derived from developing peanut seeds at three reproduction stages (R5, R6 and R7) from a resistant and a susceptible cultivated peanut genotypes, 'Tifrunner' (susceptible to <it>Aspergillus </it>infection with higher aflatoxin contamination and resistant to TSWV) and 'GT-C20' (resistant to <it>Aspergillus </it>with reduced aflatoxin contamination and susceptible to TSWV). The developing peanut seed tissues were challenged by <it>A. parasiticus </it>and drought stress in the field. A total of 24,192 randomly selected cDNA clones from six libraries were sequenced. After removing vector sequences and quality trimming, 21,777 high-quality EST sequences were generated. Sequence clustering and assembling resulted in 8,689 unique EST sequences with 1,741 tentative consensus EST sequences (TCs) and 6,948 singleton ESTs. Functional classification was performed according to MIPS functional catalogue criteria. The unique EST sequences were divided into twenty-two categories. A similarity search against the non-redundant protein database available from NCBI indicated that 84.78% of total ESTs showed significant similarity to known proteins, of which 165 genes had been previously reported in peanuts. There were differences in overall expression patterns in different libraries and genotypes. A number of sequences were expressed throughout all of the libraries, representing constitutive expressed sequences. In order to identify resistance-related genes with significantly differential expression, a statistical analysis to estimate the relative abundance (<it>R</it>) was used to compare the relative abundance of each gene transcripts in each cDNA library. Thirty six and forty seven unique EST sequences with threshold of <it>R </it>> 4 from libraries of 'GT-C20' and 'Tifrunner', respectively, were selected for examination of temporal gene expression patterns according to EST frequencies. Nine and eight resistance-related genes with significant up-regulation were obtained in 'GT-C20' and 'Tifrunner' libraries, respectively. Among them, three genes were common in both genotypes. Furthermore, a comparison of our EST sequences with other plant sequences in the TIGR Gene Indices libraries showed that the percentage of peanut EST matched to <it>Arabidopsis thaliana</it>, maize (<it>Zea mays</it>), <it>Medicago truncatula</it>, rapeseed (<it>Brassica napus</it>), rice (<it>Oryza sativa</it>), soybean (<it>Glycine max</it>) and wheat (<it>Triticum aestivum</it>) ESTs ranged from 33.84% to 79.46% with the sequence identity ≥ 80%. These results revealed that peanut ESTs are more closely related to legume species than to cereal crops, and more homologous to dicot than to monocot plant species.</p> <p>Conclusion</p> <p>The developed ESTs can be used to discover novel sequences or genes, to identify resistance-related genes and to detect the differences among alleles or markers between these resistant and susceptible peanut genotypes. Additionally, this large collection of cultivated peanut EST sequences will make it possible to construct microarrays for gene expression studies and for further characterization of host resistance mechanisms. It will be a valuable genomic resource for the peanut community. The 21,777 ESTs have been deposited to the NCBI GenBank database with accession numbers <ext-link ext-link-type="gen" ext-link-id="ES702769">ES702769</ext-link> to <ext-link ext-link-type="gen" ext-link-id="ES724546">ES724546</ext-link>.</p

Differentially expressed genes in Populus simonii×Populus nigra in response to NaCl stress using cDNA-AFLP

Salinity is an important environmental factor limiting growth and productivity of plants, and affects almost every aspect of the plant physiology and biochemistry. The objective of this study was to apply cDNA-AFLP and to identify differentially expressed genes in response to NaCl stress vs. no-stress in Populus simonii × Populus nigra in order to develop genetic resources for genetic improvement. Selective amplification with 64 primer combinations allowed the visualization of 4407 transcript-derived fragments (TDFs), and 2027 were differentially expressed. Overall, 107 TDFs were re-sequenced successfully, and 86 unique sequences were identified in 10 functional categories based on their putative functions. A subset of these genes was selected for real-time PCR validation, which confirmed the differential expression patterns in the leaf tissues under NaCl stress vs. no stress. Differential expressed genes will be studied further for association with salt or drought-tolerance in P. simonii×P. nigra. This study suggests that cDNA-AFLP is a useful tool to serve as an initial step for characterizing transcriptional changes induced by NaCl salinity stress in P. simonii×P. nigra and provides resources for further study and application in genetic improvement and breeding. All unique sequences have been deposited in the Genbank as accession numbers GW672587–GW672672 for public use

Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

<p>Abstract</p> <p>Background</p> <p>Lack of sufficient molecular markers hinders current genetic research in peanuts (<it>Arachis hypogaea </it>L.). It is necessary to develop more molecular markers for potential use in peanut genetic research. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining.</p> <p>Results</p> <p>In this study, we investigated 24,238 ESTs for the identification and development of SSR markers. In total, 881 SSRs were identified from 780 SSR-containing unique ESTs. On an average, one SSR was found per 7.3 kb of EST sequence with tri-nucleotide motifs (63.9%) being the most abundant followed by di- (32.7%), tetra- (1.7%), hexa- (1.0%) and penta-nucleotide (0.7%) repeat types. The top six motifs included AG/TC (27.7%), AAG/TTC (17.4%), AAT/TTA (11.9%), ACC/TGG (7.72%), ACT/TGA (7.26%) and AT/TA (6.3%). Based on the 780 SSR-containing ESTs, a total of 290 primer pairs were successfully designed and used for validation of the amplification and assessment of the polymorphism among 22 genotypes of cultivated peanuts and 16 accessions of wild species. The results showed that 251 primer pairs yielded amplification products, of which 26 and 221 primer pairs exhibited polymorphism among the cultivated and wild species examined, respectively. Two to four alleles were found in cultivated peanuts, while 3–8 alleles presented in wild species. The apparent broad polymorphism was further confirmed by cloning and sequencing of amplified alleles. Sequence analysis of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the microsatellite regions. In addition, a few single base mutations were observed in the microsatellite flanking regions.</p> <p>Conclusion</p> <p>This study gives an insight into the frequency, type and distribution of peanut EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated peanut. These EST-SSR markers could enrich the current resource of molecular markers for the peanut community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, and genetic diversity studies in cultivated peanut as well as related <it>Arachis </it>species. All of the 251 working primer pairs with names, motifs, repeat types, primer sequences, and alleles tested in cultivated and wild species are listed in Additional File <supplr sid="S1">1</supplr>.</p> <suppl id="S1"> <title> <p>Additional File 1</p> </title> <text> <p><b>List of EST-SSR primers developed from cultivated peanut ESTs</b>. The file contains a table that lists primer names, repeat motifs, primer sequences, allele number and product length for the newly developed EST-SSR markers.</p> </text> <file name="1471-2229-9-35-S1.xls"> <p>Click here for file</p> </file> </suppl

Gene expression profiling in peanut using high density oligonucleotide microarrays

<p>Abstract</p> <p>Background</p> <p>Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology.</p> <p>Results</p> <p>We have developed a high-density oligonucleotide microarray for peanut using 49,205 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues. Results from this experiment showed 108 putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to peg, leaf, stem, or root. The transcripts significantly over-represented in pod include genes responsible for seed storage proteins and desiccation (e.g., late-embryogenesis abundant proteins, aquaporins, legumin B), oil production, and cellular defense. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes.</p> <p>Conclusion</p> <p>The peanut oligonucleotide array represents the majority of publicly available peanut ESTs and can be used as a tool for expression profiling studies in diverse tissues.</p

Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application

Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function

Gene Expression Profiling and Identification of Resistance Genes to Aspergillus flavus Infection in Peanut through EST and Microarray Strategies

Aspergillus flavus and A. parasiticus infect peanut seeds and produce aflatoxins, which are associated with various diseases in domestic animals and humans throughout the world. The most cost-effective strategy to minimize aflatoxin contamination involves the development of peanut cultivars that are resistant to fungal infection and/or aflatoxin production. To identify peanut Aspergillus-interactive and peanut Aspergillus-resistance genes, we carried out a large scale peanut Expressed Sequence Tag (EST) project which we used to construct a peanut glass slide oligonucleotide microarray. The fabricated microarray represents over 40% of the protein coding genes in the peanut genome. For expression profiling, resistant and susceptible peanut cultivars were infected with a mixture of Aspergillus flavus and parasiticus spores. The subsequent microarray analysis identified 62 genes in resistant cultivars that were up-expressed in response to Aspergillus infection. In addition, we identified 22 putative Aspergillus-resistance genes that were constitutively up-expressed in the resistant cultivar in comparison to the susceptible cultivar. Some of these genes were homologous to peanut, corn, and soybean genes that were previously shown to confer resistance to fungal infection. This study is a first step towards a comprehensive genome-scale platform for developing Aspergillus-resistant peanut cultivars through targeted marker-assisted breeding and genetic engineering

Development of trinucleotide (GGC)n SSR markers in peanut ( Arachis hypogaea L.)

Cultivated peanut ( Arachis hypogaea L.) is an oilseed crop of economic importance. It is native to South America, and it is grown extensively in the semi-arid tropics of Asia, Africa, and Latin America. Given an extremely narrow genetic base, efforts are being made to develop simple sequence repeat (SSR) markers to provide useful genetic and genomic tools for the peanut research community. A SSR-enriched library to isolate trinucleotide (GGC)n SSRs in peanut was constructed. A total of 143 unique sequences containing (GGC)n repeats were identified. One hundred thirty eight primer pairs were successfully designed at the flanking regions of SSRs. A suitable polymerase was chosen to amplify these GC-rich sequences. Although a low level of polymorphism was observed in cultivated peanut by these new developed SSRs, a high level of transferability to wild species would be beneficial to increasing the number of SSRs in wild species

Expression Analysis of Stress-Related Genes in Kernels of Different Maize (Zea mays L.) Inbred Lines with Different Resistance to Aflatoxin Contamination

This research examined the expression patterns of 94 stress-related genes in seven maize inbred lines with differential expressions of resistance to aflatoxin contamination. The objective was to develop a set of genes/probes associated with resistance to A. flavus and/or aflatoxin contamination. Ninety four genes were selected from previous gene expression studies with abiotic stress to test the differential expression in maize lines, A638, B73, Lo964, Lo1016, Mo17, Mp313E, and Tex6, using real-time RT-PCR. Based on the relative-expression levels, the seven maize inbred lines clustered into two different groups. One group included B73, Lo1016 and Mo17, which had higher levels of aflatoxin contamination and lower levels of overall gene expression. The second group which included Tex6, Mp313E, Lo964 and A638 had lower levels of aflatoxin contamination and higher overall levels of gene expressions. A total of six “cross-talking” genes were identified between the two groups, which are highly expressed in the resistant Group 2 but down-regulated in susceptible Group 1. When further subjected to drought stress, Tex6 expressed more genes up-regulated and B73 has fewer genes up-regulated. The transcript patterns and interactions measured in these experiments indicate that the resistant mechanism is an interconnected process involving many gene products and transcriptional regulators, as well as various host interactions with environmental factors, particularly, drought and high temperature