David E. Matthews

Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat.

Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The publicly available collection of expressed sequence tags (ESTs) from several grass species can be used in the analysis of both structural and functional relationships in these genomes. We analyzed over 260 000 EST sequences from five different cereals for their potential use in developing simple sequence repeat (SSR) markers. The frequency of SSR-containing ESTs (SSR-ESTs) in this collection varied from 1.5% for maize to 4.7% for rice. In addition, we identified several ESTs that are related to the SSR-ESTs by BLAST analysis. The SSR-ESTs and the related sequences were clustered within each species in order to reduce the redundancy and to produce a longer consensus sequence. The consensus and singleton sequences from each species were pooled and clustered to identify cross-species matches. Overall a reduction in the redundancy by 85% was observed when the resulting consensus and singleton sequences (3569) were compared to the total number of SSR-EST and related sequences analyzed (24 606). This information can be useful for the development of SSR markers that can amplify across the grass genera for comparative mapping and genetics. Functional analysis may reveal their role in plant metabolism and gene evolution.

TREP: a database for Triticeae repetitive elements

wheat, barley and rye are large (5 × 109 to 17 × 109 bp) and contain 80% repetitive sequences. Although research on the molecular genetics of Triticeae concentrates on gene-rich regions, most genomic and some EST sequences isolated from these species are repetitive. Rapid identification of repetitive elements could significantly speed up the process of gene discovery and chromosome walking. Unfortunately, wading through the quagmire of repetitive sequences can be a difficult and uninspiring task. Classification and naming of such elements has been somewhat arbitrary and occasionally the same elements have even been classified and named differently by different researchers (e.g. ‘Sabrina’ [1] and ‘XA’ [2]). Often, repetitive elements are not present as complete copies but are fragmented by the insertion of other elements or by deletions, adding to the complexity of the analysis. In addition, frequently, only PCR fragments of conserved domains in repetitive elements (e.g. sequences encoding reverse transcriptase) are available.

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.

BackgroundA genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.ResultsNucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.ConclusionsIn a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

Identification and chromosomal locations of a family of cytochrome P-450 genes for pisatin detoxification in the fungus Nectria haematococca

SummaryThe ability to detoxify the phytoalexin, pisatin, an antimicrobial compound produced by pea (Pisum sativum L.), is one requirement for pathogenicity of the fungus Nectria haematococca on this plant. Detoxification is mediated by a cytochrome P-450, pisatin demethylase, encoded by any one of six Pda genes, which differ with respect to the inducibility and level of pisatin demethylase activity they confer, and which are associated with different levels of virulence on pea. A previously cloned Pda gene (PdaT9) was used in this study to characterize further the known genes and to identify additional members of the Pda family in this fungus by Southern analysis. DNA from all isolates which demethylate pisatin (Pda+ isolates) hybridized to PdaT9, while only one Pda− isolate possessed DNA homologous to the probe. Hybridization intensity and, in some cases, restriction fragment size, were correlated with enzyme inducibility. XhoI/BamHI restricted DNA from reference strains with a single active Pda allele had only one fragment with homology to PdaT9; no homology attributable to alleles associated with the Pda− phenotype was found. Homology to this probe was also limited to one or two restriction fragments in most of the 31 field isolates examined. Some unusual progeny from laboratory crosses that failed to inherit demethylase activity also lost the single restriction fragment homologous to PdaT9. At the chromosome level, N. haematococca is highly variable, each isolate having a unique electrophoretic karyotype. In most instances, PdaT9 hybridized to one or two chromosomes containing 1.6–2 million bases of DNA, while many Pda- isolates lacked chromosomes in this size class. The results from this study of the Pda family support the hypothesis that deletion of large amounts of genomic DNA is one mechanism that reduces the frequency of Pda genes in N. haematococca, while simultaneously increasing its karyotypic variation.

Safety and efficacy of office-based surgery with monitored anesthesia care/sedation in 4778 consecutive plastic surgery procedures.

&NA; Office‐based surgery has several potential benefits over hospital‐based surgery, including cost containment, ease of scheduling, and convenience to both patients and surgeons. Scrutiny of office‐based surgery by regulators and state‐licensing agencies has increased and must be addressed by improved documentation of safety and efficacy. To evaluate the safety and efficacy of the authors’ officebased plastic surgery, a review was undertaken of 3615 consecutive patients undergoing 4778 outpatient plastic surgery procedures under monitored anesthesia care/sedation in a single office. The charts of 3615 consecutive patients who had undergone office‐based surgery with monitored anesthesia care/sedation between May of 1995 and May of 2000 were reviewed. In all cases, the anesthesia protocol used included sedation with midazolam, propofol, and a narcotic administered by a board‐certified registered nurse anesthetist with local anesthesia provided by the surgeon. Charts were reviewed for patient profile, types of procedures, multiple procedures, duration of anesthesia, American Society of Anesthesiologists class, and complications related to anesthesia. Outcomes measured included death, airway compromise, dyspnea, hypotension, venous thrombosis, pulmonary emboli, protracted nausea and vomiting lasting more than 24 hours, and unplanned hospital admissions. Statistical analyses were performed using the Microsoft Excel program and the SAS package. Results were as follows: 92.3 percent of the patients were female and 7.7 percent were male, with a mean age of 42.7 years (range, 3 to 83 years). Patients underwent aesthetic (95.6 percent) and reconstructive (4.4 percent) plastic surgery procedures. Same‐session multiple procedures occurred in 24.8 percent of patients. The vast majority of patients were healthy: 84.3 percent of patients were American Society of Anesthesiologists class I, 15.6 percent were class II, and 0.1 percent were class III. The operations required a mean of 111 minutes. There were no deaths, ventilator requirements, deep venous thromboses, or pulmonary emboli. Complications were as follows: 0.05 percent (n = 2) of patients had dyspnea that resolved, 0.2 percent (n = 6) of patients had protracted nausea and vomiting, and 0.05 percent (n = 2) of patients had unplanned hospital admissions (<24 hours). One patient had an emergent intubation. No prolonged adverse effects were noted. There was a 30‐day follow‐up minimum. Outpatient surgery is an important aspect of plastic surgery. It was shown that office‐based surgery with intravenous sedation, performed by board‐certified plastic surgeons and nurse anesthetists, is safe. Appropriate accreditation, safe anesthesia protocols, and proper patient selection constitute the basis for safe and efficacious office‐based outpatient plastic surgery. (Plast. Reconstr. Surg. 111: 150, 2003.)

Detoxification of the phytoalexin pisatin by a fungal cytochrome P-450

The fungus Nectria haematococca, a pathogen of garden pea (Pisum sativum), can demethylate pisatin, an antimicrobial compound synthesized by infected pea tissue. The phenolic product is less toxic than pisatin to many microorganisms. Cell extracts catalyzing pisatin demethylation were obtained from N. haematococca, and the properties of the reaction were examined. The enzyme activity was greatest in the high-speed pellet fraction, in which rates up to 20 nmol/min/mg protein were observed. The Km for pisatin was relatively low, less than 5 microM. The reaction was dependent on NADPH, which could not be replaced by any other cofactor tested. However, in the presence of NADPH, NADH increased the rate of demethylation. Oxygen uptake by the enzyme was stimulated by addition of pisatin, the increment of oxygen utilization being approximately equimolar with pisatin added. Formaldehyde was a product of the reaction. The effects of various inhibitors were tested to determine whether this reaction is mediated by cytochrome P-450. The respiratory inhibitors KCN (1 mM) and antimycin A strongly inhibited the demethylation of pisatin by intact cells of the fungus, but not by the NADPH-supplemented enzyme. The cytochrome P-450 inhibitors SKF 525-A and 1-(2-isopropylphenyl)imidazole inhibited demethylation both in whole cells and in the enzyme preparation, though the latter compound was effective only at high concentrations. Most other cytochrome P-450 inhibitors tested had little effect. However the reaction was quite sensitive to CO, and this inhibition was readily reversed by light at wavelengths near 450 nm. It is concluded that pisatin demethylase is a cytochrome P-450 monooxygenase.

GrainGenes, the genome database for small-grain crops

GrainGenes, http://www.graingenes.org, is the international database for the wheat, barley, rye and oat genomes. For these species it is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with the help of many members of the research community, are integrated with sequence and bibliographic records selected from external databases and results of BLAST searches of the ESTs. Records are linked to corresponding records in other important databases, e.g. Gramenes EST homologies to rice BAC/PACs, TIGRs Gene Indices and GenBank. In addition to this information within the GrainGenes database itself, the GrainGenes homepage at http://wheat.pw.usda.gov provides many other community resources including publications (the annual newsletters for wheat, barley and oat, monographs and articles), individual datasets (mapping and QTL studies, polymorphism surveys, variety performance evaluations), specialized databases (Triticeae repeat sequences, EST unigene sets) and pages to facilitate coordination of cooperative research efforts in specific areas such as SNP development, EST-SSRs and taxonomy. The goal is to serve as a central point for obtaining and contributing information about the genetics and biology of these cereal crops.

GrainGenes 2.0. An Improved Resource for the Small-Grains Community

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.

Purification and characterization of cyanide hydratase from the phytopathogenic fungus Gloeocercospora sorghi

Previous studies have demonstrated that fungal pathogens of cyanogenic plants produce cyanide hydratase (CHT, EC 4.2.1.66), which converts HCN to formamide. Production of CHT in these fungi is thought to be a means of circumventing cyanide toxicity, and CHT is thus believed to be an important pathogenicity trait. In the present study, 13 species of fungi were assayed for CHT production, and all 7 species that were pathogens of sorghum, a cyanogenic plant, produced this enzyme. CHT was purified to apparent homogeneity from one of these sorghum pathogens, Gloeocercospora sorghi. The enzyme had a Km of 12 mM for KCN. Enzymatically functional CHT was obtained only as a large molecular entity of greater than 300 kDa. However, a polypeptide of approximately 45 kDa was identified as the only component of purified CHT detectable by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The 45-kDa polypeptide band could be resolved into three isozymes of pI 6.1, 6.3, and 6.5. Antibodies raised against the 45-kDa polypeptide inhibited the G. sorghi CHT activity and showed high specificity in Western blots to a polypeptide of approximately the same size. The evidence suggests that functional G. sorghi CHT is an aggregated protein that consists of 45-kDa polypeptides. A CHT with similar properties was also found in the fungus Colletotrichum graminicola, another pathogen of sorghum.

Differential toxicity of enantiomers of maackiain and pisatin to phytopathogenic fungi

Abstract Enantiomers of the isoflavonoid phytoalexins maackiain and pisatin were tested for toxicity to 36 fungal isolates representing 19 species. Nine of these species were pathogens of red clover, which synthesizes (−)maackiain; seven species were reported to be pathogenic on garden pea, which synthesizes predominantly (+)pisatin and minor amounts of (−)maackiain. In general, non-host phytoalexins were more inhibitory than host phytoalexins to growth of these pathogens. In addition, the opposite enantiomer of the host phytoalexin was often more inhibitory to a pathogenic fungus than the normally-occurring enantiomer. There was little correlation between the tolerance of fungi to (+) versus (−)pisatin and differential ability to metabolize the pisatin enantiomers. Nevertheless the data suggest that the production of non-host phytoalexins in transgenic plants might increase resistance of red clover and garden pea to some fungal pathogens.