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Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

The areas of reading comprehension theory that provide insights for writers are examined and the way in which a basic knowledge of reading theory provides a backdrop for explicating certain conventions and responding to certain problem area in student writing are explored. With the examples of successful classroom activities, it is shown how a teacher helps students become better writers by first helping them to understand the ways to construct meaning as readers.

Recombinant human manganese superoxide dismutase (MnSOD) were exposed to hydrogen peroxide, hypochlorous acid and tetranitromethane followed by exposure to several biochemical assays to determine the vulnerability of MnSOD to oxidative inactivation. The results suggested that the peroxynitrite-mediated inactivation of MnSOD involves nitration and oxidation of critical tyrosine residues. The results further revealed that hypochlorous acid can be a potent oxidant under certain conditions and hydrogen peroxide can oxidize methionine residues in proteins.

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Analysis of the effects of oxidants such as hypochlorite and peroxynitrite on yeast alcohol dehydrogenase suggests that the oxidants primarily target the zinc-thiolate moiety of the dehydrogenase. Enzyme inactivation by peroxynitrite or hypochlorite is associated with zinc release and thiol/thiolate oxidation. The zinc-thiolate moiety of dehydrogenase shows structural similarity with that in zinc finger proteins, confirming that oxidants target the zinc finger moiety for attack.

Western blot and polyacrylamide gel electrophoresis experiments to examine the effect of nitric oxide (.NO) on lung injuries reveal that simultaneous superoxide and .NO production by 3-morpholinosydnonimine (SIN-1) suppresses the function of surface protein A (SP-A). The suppression is dose-dependent, with the SP-A losing its lipid aggregation property. Urate, xanthine and xanthine oxidase block the inhibitory effect of SIN-1 on SP-A and the oxidation of dihydrorhodamine. Nitrotyrosine release by hydrogen peroxide and peroxynitrite also inhibits SP-A activity in the aggregating lipid.

Abstract Background Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP) markers for a complex polyploid species. Result The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2%) of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO) analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM) analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa) were clearly separated. Conclusion We used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System (http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications.

Abstract Background Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., Saccharomyces cerevisiae and Drosophila melanogaster), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes. Results A high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes. Conclusion These findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.

Abstract Background The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). Results We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. Conclusion This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.

Argues in favor of a specific component in technical writing courses devoted to the explanation, demonstration, and analysis of the reading comprehension process. Includes classroom activities for teaching this information, for working on writing problems relevant to ease of reading, and for analyzing writing problems in light of the reading process. (HTH)

Describes a study which compared a traditional approach to second language vocabulary instruction with the semantic field approach, which is based on the association between five related words and a key word that could be mentally substituted in context. Findings lend support to the use of the semantic field approach. (SED)

This article argues in favor of a receptive vocabulary component in foreign language courses through consideration of: productive vs. receptive vocabulary knowledge; misconceptions in receptive vocabulary instruction; and classroom-tested approaches and activities for receptive vocabulary development. (CB)

Carbon dioxide enhances nitration of surfactant protein A by activated alveolar macrophages. Am J Physiol Lung Cell Mol Physiol 278: L1025-L1031, 2000.--We assessed whether reactive oxygen-nitrogen intermediates generated by alveolar macrophages (AMs) oxidized and nitrated human surfactant protein (SP)A. SP-A was exposed to lipopolysaccharide (100 ng/ml)-activated AMs in 15 mM HEPES (pH 7.4) for 30 rain in the presence and absence of 1.2 mM [CO.sub.2]. In the presence of [CO.sub.2], lipopolysaccharide-stimulated AMs had significantly higher nitric oxide synthase (NOS) activity (as quantified by the conversion of L-[[U-.sup.14]C]arginine to L-[[U-.sup.14]C]citrulline) and secreted threefold higher levels of nitrate plus nitrite in the medium [28 [+ or -]_ 3 vs. 6 [+ or -] 1 (SE) nmol [multiplied by] 6.5 [h.sup.-1] [multiplied by] [10.sup.6] [AMs.sup.-1]. Western blotting studies of immunoprecipitated SP-A indicated that [CO.sub.2] enhanced SP-A nitration by AMs and decreased carbonyl formation. [CO.sub.2] (0-1.2 mM) also augmented peroxynitrite (0.5 mM)-induced SP-A nitration in a dose-dependent fashion. Peroxynitrite decreased the ability of SP-A to aggregate lipids, and this inhibition was augmented by 1.2 mM [CO.sub.2]. Mass spectrometry analysis of chymotryptic fragments of peroxynitrite-exposed SP-A showed nitration of two tyrosines ([Tyr.sup.164] and [Tyr.sup.166]) in the absence of [CO.sub.2] and three tyrosines ([Tyr.sup.164], [Tyr.sup.166], and [Tyr.sup.161]) in the presence of 1.2 mM [CO.sub.2]. These findings indicate that physiological levels of peroxynitrite, produced by activated AMs, nitrate SP-A and that [CO.sub.2] increased nitration, at least partially, by enhancing enzymatic nitric oxide production. nitric oxide; peroxynitrite; nitrotyrosine; protein oxidation; alveolar epithelium; acute respiratory distress syndrome; hypercapnia; mass spectrometry