Characterization of multiple nestin isoforms in the goldfish brain.

Nestin is an intermediate filament protein involved in neurogenesis in fish, mice, and humans. In this study we used rapid amplification of cDNA ends PCR to isolate goldfish nestin (nes). PCR analysis and sequencing revealed three different nes transcripts of 4003, 2446, and 2126 nucleotides, which are predicted to generate proteins of 860, 274, and 344 amino acids in length.

Diversity within the genus Elymus (Poaceae: Triticeae) II: analyses of variation within 5S nrDNA restrict membership in the genus to species with StH genomes.

The genus Elymus is a repository for a large number of species that have been difficult to classify by traditional techniques due to their remarkable levels of polymorphism. Following the genome analyses of Yen and Yang (Genus Elymus 5:58-362, 2013), we used sequences of the nr5SDNA to investigate diversity within those 24 species having St and H haplomes (Baum et al. Mol Genet Genomics 290:329-42, 2015) and for which the genome status was known.

Contrasting patterns of evolution of 45S and 5S rDNA families uncover new aspects in the genome constitution of the agronomically important grass Thinopyrum intermedium (Triticeae).

We employed sequencing of clones and in situ hybridization (genomic and fluorescent in situ hybridization [GISH and rDNA-FISH]) to characterize both the sequence variation and genomic organization of 45S (herein ITS1-5.8S-ITS2 region) and 5S (5S gene + nontranscribed spacer) ribosomal DNA (rDNA) families in the allohexaploid grass Thinopyrum intermedium. Both rDNA families are organized within several rDNA loci within all three subgenomes of the allohexaploid species.

A taxonomist's view on genomic authentication.

A brief history of taxonomy, for the most part plant oriented, is provided, which demonstrates the use of morphology early on, through the stages when different technologies became available at different times until the present use of genomic tools. Genomic authentication facilitates with greater precision than ever before the identification of an organism or part thereof. In this chapter I made an attempt to stress that, in general, but more so for genomic authentication, the use of the variation inherent in taxa down to the lowest level of the hierarchy of classification needs to be used to achieve a high degree of correct authentication.

The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae).

Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and these repeats often undergo rapid concerted evolution within and between arrays. Therefore, the rDNA ITS copies appear to be virtually identical and can sometimes be treated as a single gene. In this paper we examined ITS polymorphism within and among 13 diploid (A and C genomes), seven tetraploid (AB, AC and CC genomes) and four hexaploid (ACD genome) to infer the extent and direction of concerted evolution, and to reveal the phylogenetic and genome relationship among species of Avena.

Phylogenetic inferences in Avena based on analysis of FL intron2 sequences.

The development and application of molecular methods in oats has been relatively slow compared with other crops. Results from the previous analyses have left many questions concerning species evolutionary relationships unanswered, especially regarding the origins of the B and D genomes, which are only known to be present in polyploid oat species. To investigate the species and genome relationships in genus Avena, among 13 diploid (A and C genomes), we used the second intron of the nuclear gene FLORICAULA/LEAFY (FL int2) in seven tetraploid (AB and AC genomes), and five hexaploid (ACD genome) species.

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae).

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated.

Molecular confirmation of the genomic constitution of Douglasdeweya (Triticeae: Poaceae): demonstration of the utility of the 5S rDNA sequence as a tool for haplome identification.

A new genus Douglasdeweya containing the two species, Douglasdeweya deweyi and D. wangii was published in 2005 by Yen et al. based upon the results of cytogenetical and morphological findings.

Molecular evolution of dimeric alpha-amylase inhibitor genes in wild emmer wheat and its ecological association.

Background: alpha-Amylase inhibitors are attractive candidates for the control of seed weevils, as these insects are highly dependent on starch as an energy source. In this study, we aimed to reveal the structure and diversity of dimeric alpha-amylase inhibitor genes in wild emmer wheat from Israel and to elucidate the relationship between the emmer wheat genes and ecological factors using single nucleotide polymorphism (SNP) markers. Another objective of this study was to find out whether there were any correlations between SNPs in functional protein-coding genes and the environment.

Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae).

The molecular diversity of the rDNA sequences (5S rDNA units) in 71 accessions from 26 taxa of Avena was evaluated. The analyses, based on 553 sequenced clones, indicated that there were 6 unit classes, named according to the haplomes (genomes) they putatively represent, namely the long A1, long B1, long M1, short C1, short D1, and short M1 unit classes. The long and short M1 unit classes were found in the tetraploid A.

The 5S DNA sequences in Hordeum bogdanii and in the H. brevisubulatum complex, and the evolution and the geographic dispersal of the diploid Hordeum species (Triticeae: Poaceae).

The molecular diversity of 5S rDNA from the closely related Asiatic diploid species, Hordeum bogdanii and the H. brevisubulatum complex has been catalogued and analysed. As in previous studies in Hordeum, we found that the sequences are constrained in such an manner that unit classes can be defined.

Ancient differentiation of the H and I haplomes in diploid Hordeum species based on 5S rDNA.

5S rDNA clones from 12 South American diploid Hordeum species containing the HH genome and 3 Eurasian diploid Hordeum species containing the II genome, including the cultivated barley Hordeum vulgare, were sequenced and their sequence diversity was analyzed. The 374 sequenced clones were assigned to "unit classes", which were further assigned to haplomes. Each haplome contained 2 unit classes.

The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes - a test on cultivated wheat and wheat progenitors.

Data is presented on the evolutionary dynamics of non-transcribed spacers (NTSs) of 5S rRNA genes in some diploid and polyploid Triticum and Aegilops species. FISH experiments with probes representing different unit classes revealed presence and (or) absence of these sequences in genomes or separate chromosomes of the species. Among the three diploid species only Aegilops speltoides has all of the different unit classes in ribosomal clusters as detected by the probes.

Sequence assessment of comigrating AFLPTM bands in Echinacea -- implications for comparative biological studies.

The extent of sequence identity among clones derived from monomorphic and polymorphic AFLPTM polymorphism bands was quantified. A total of 79 fragments from a monomorphic band of 273 bp and 48 fragments from a polymorphic band of 159 bp, isolated from individuals belonging to different populations, varieties, and species of Echinacea, were cloned and sequenced. The monomorphic fragments exhibited above 90% sequence identity among clones within samples.

Phytochemistry of wild populations of Panax quinquefolius L. (North American ginseng).

A survey of the phytochemistry of Panax quinquefolius L. (North American ginseng) collected from wild populations in Ontario, Quebec, Maine, Vermont, and Wisconsin was undertaken. Reverse-phase HPLC was used to determine the natural variation of levels of ginsenosides Rg1, Re, Rf, Rb1, Rc, Rb2, and Rd and their total in leaf, stem, and root of authentic wild-grown material.

Phytochemical variation in echinacea from roots and flowerheads of wild and cultivated populations.

Quantitative phytochemical variation was determined from roots and inflorescences of native plant populations in the genus Echinacea. Specimens were collected in situ throughout the natural range of each putative taxon and transplanted to greenhouse cultivation. Ethanolic extracts from individual plants were separated by reversed-phase HPLC to quantify the alkamides, polyenes/ynes, and phenolics, and then grouped by age and taxonomically, according to a recent morphometric taxonomic revision of the genus.