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41.
Gautam?Aggarwal EA?Worthey Paul?D?McDonagh Peter?J?MylerEmail author 《BMC bioinformatics》2003,4(1):23
Background
Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces.Results
Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN) into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODON USAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence.Conclusion
An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.42.
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Serena Donadi Joëlle Westra Ellen J. Weerman Tjisse van der Heide Els M. van der Zee Johan van de Koppel Han Olff Theunis Piersma Henk W. van der Veer Britas Klemens Eriksson 《Ecosystems》2013,16(7):1325-1335
The importance of positive effects of ecosystem engineers on associated communities is predicted to increase with environmental stress. However, incorporating such non-trophic interactions into ecological theory is not trivial because facilitation of associated species is conditional on both the type of engineer and the type of abiotic stress. We tested the influence of two allogenic ecosystem engineers (lugworms, Arenicola marina L. and cockles, Cerastoderma edule L.) on the main primary producers (microphytobenthos) of the tidal flats, under different abiotic stresses controlled by reefs of blue mussels (Mytilus edulis L.). We added 25,000 cockles or 2,000 lugworms to 5 × 5 m plots, both in a muddy site with high sedimentation rates located coastward of a mussel bed, and in a sandy site without mussels and characterized by high hydrodynamic stress. After a year, cockles increased algal biomass in the sandy area, but not in the mussel bed site, where high values were measured in all plots. However, lugworms did not affect algal biomass in any of the sites. Field measurements suggest that cockles outweighed negative effects of water currents in the site without mussels by locally increasing sediment stability, whereas mussels overruled the effects of cockles in the wake of the reefs through hydrodynamic stress alleviation and/or biodeposition. Our results suggest that non-trophic interactions by ecosystem engineering bivalves control primary production of intertidal areas, and that the sediment-stabilizing effect of cockles plays a crucial role where the overruling effects of mussel beds are not present. 相似文献
44.
Kuzoff RK; Sweere JA; Soltis DE; Soltis PS; Zimmer EA 《Molecular biology and evolution》1998,15(3):251-263
18S ribosomal RNA genes are the most widely used nuclear sequences for
phylogeny reconstruction at higher taxonomic levels in plants. However, due
to a conservative rate of evolution, 18S rDNA alone sometimes provides too
few phylogenetically informative characters to resolve relationships
adequately. Previous studies using partial sequences have suggested the
potential of 26S or large-subunit (LSU) rDNA for phylogeny retrieval at
taxonomic levels comparable to those investigated with 18S rDNA. Here we
explore the patterns of molecular evolution of entire 26S rDNA sequences
and their impact on phylogeny retrieval. We present a protocol for PCR
amplification and sequencing of entire (approximately 3.4 kb) 26S rDNA
sequences as single amplicons, as well as primers that can be used for
amplification and sequencing. These primers proved useful in angiosperms
and Gnetales and likely have broader applicability. With these protocols
and primers, entire 26S rDNA sequences were generated for a diverse array
of 15 seed plants, including basal eudicots, monocots, and higher eudicots,
plus two representatives of Gnetales. Comparisons of sequence dissimilarity
indicate that expansion segments (or divergence domains) evolve 6.4 to 10.2
times as fast as conserved core regions of 26S rDNA sequences in plants.
Additional comparisons indicate that 26S rDNA evolves 1.6 to 2.2 times as
fast as and provides 3.3 times as many phylogenetically informative
characters as 18S rDNA; compared to the chloroplast gene rbcL, 26S rDNA
evolves at 0.44 to 1.0 times its rate and provides 2.0 times as many
phylogenetically informative characters. Expansion segment sequences
analyzed here evolve 1.2 to 3.0 times faster than rbcL, providing 1.5 times
the number of informative characters. Plant expansion segments have a
pattern of evolution distinct from that found in animals, exhibiting less
cryptic sequence simplicity, a lower frequency of insertion and deletion,
and greater phylogenetic potential.
相似文献
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46.
Rosângela V Andrade Hugo C Paes André M Nicola Maria José A de Carvalho Ana Lúcia Fachin Renato S Cardoso Simoneide S Silva Larissa Fernandes Silvana P Silva Eduardo A Donadi Elza T Sakamoto-Hojo Geraldo AS Passos Célia MA Soares Marcelo M Brígido Maria Sueli S Felipe 《BMC genomics》2006,7(1):1-13
Background
Bread wheat (Triticum aestivum) is an important staple food. However, wheat gluten proteins cause celiac disease (CD) in 0.5 to 1% of the general population. Among these proteins, the α-gliadins contain several peptides that are associated to the disease.Results
We obtained 230 distinct α-gliadin gene sequences from severaldiploid wheat species representing the ancestral A, B, and D genomes of the hexaploid bread wheat. The large majority of these sequences (87%) contained an internal stop codon. All α-gliadin sequences could be distinguished according to the genome of origin on the basis of sequence similarity, of the average length of the polyglutamine repeats, and of the differences in the presence of four peptides that have been identified as T cell stimulatory epitopes in CD patients through binding to HLA-DQ2/8. By sequence similarity, α-gliadins from the public database of hexaploid T. aestivum could be assigned directly to chromosome 6A, 6B, or 6D. T. monococcum (A genome) sequences, as well as those from chromosome 6A of bread wheat, almost invariably contained epitope glia-α9 and glia-α20, but never the intact epitopes glia-α and glia-α2. A number of sequences from T. speltoides, as well as a number of sequences fromchromosome 6B of bread wheat, did not contain any of the four T cell epitopes screened for. The sequences from T. tauschii (D genome), as well as those from chromosome 6D of bread wheat, were found to contain all of these T cell epitopes in variable combinations per gene. The differences in epitope composition resulted mainly from point mutations. These substitutions appeared to be genome specific.Conclusion
Our analysis shows that α-gliadin sequences from the three genomes of bread wheat form distinct groups. The four known T cell stimulatory epitopes are distributed non-randomly across the sequences, indicating that the three genomes contribute differently to epitope content. A systematic analysis of all known epitopes in gliadins and glutenins will lead to better understanding of the differences in toxiCity among wheat varieties. On the basis of such insight, breeding strategies can be designed to generate less toxic varieties of wheat which may be tolerated by at least part of the CD patient population. 相似文献47.
Soares CP Zuanon JA Teresa DB Fregonezi PA Neto CB Oliveira MR Donadi EA Martinelli-Kläy CP Soares EG 《Histology and histopathology》2006,21(7):721-728
The knowledge of cell-cycle control has shown that the capacity of malignant growth is acquired by the stepwise accumulation of defects in specific genes regulating cell growth. Histologic diagnosis might be improved by a quantitative evaluation of more specific diagnosis biomarkers, which could help to precisely identify pre-malignant and malignant oral lesions. The aim of the present study is to evaluate whether computer-based quantitative assessment of p53, PCNA and Ki-67 immunohistochemical expression, could be used clinically to foresee the risk of oral malignant transformation. This retrospective study was carried out in ninety-five oral biopsies, 27 were classified as fibrous inflammatory hyperplasia, 40 as leukoplakia and 28 as oral squamous cell carcinoma. Sixteen out of the 40 leukoplakia were diagnosed as non-dysplastic leukoplakia, the other 24 being dysplastic leukoplakia, of which 50.0% were classified as moderate to severe dysplasia. Comparison of the four groups of oral tissues showed significant rises in p53 and Ki-67 positivity index, which increased steadily in the order benign, pre-malignant, and malignant. In contrast, it was not possible to relate higher PCNA levels with pre-malignant and malignant oral lesions. We therefore conclude that PCNA immunohistochemistry expression is probably an inappropriate marker to identify oral carcinogenesis, whereas joint quantitative evaluation of p53 and Ki-67, appears to be useful as a tumor marker, providing a pre-diagnostic estimate of the potential for cell-cycle deregulation of the oral proliferate status. 相似文献
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Austin . N. Hansen J. P. Donadi S. Bergstrm U. Eriksson B. K. Sundblad G. Eklf J. S. 《Ecosystems》2021,24(7):1670-1686
Ecosystems - Ecosystem multifunctionality is an increasingly popular concept used to approximate multifaceted ecosystem functioning, which in turn may help advance ecosystem-based management.... 相似文献
50.
Biodiversity mediates top–down control in eelgrass ecosystems: a global comparative‐experimental approach 下载免费PDF全文
J. Emmett Duffy Pamela L. Reynolds Christoffer Boström James A. Coyer Mathieu Cusson Serena Donadi James G. Douglass Johan S. Eklöf Aschwin H. Engelen Britas Klemens Eriksson Stein Fredriksen Lars Gamfeldt Camilla Gustafsson Galice Hoarau Masakazu Hori Kevin Hovel Katrin Iken Jonathan S. Lefcheck Per‐Olav Moksnes Masahiro Nakaoka Mary I. O'Connor Jeanine L. Olsen J. Paul Richardson Jennifer L. Ruesink Erik E. Sotka Jonas Thormar Matthew A. Whalen John J. Stachowicz 《Ecology letters》2015,18(7):696-705
Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom–up and top–down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top–down and bottom–up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top–down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross‐site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large‐scale patterns corresponded strikingly with prior small‐scale experiments. Our results link global and local evidence that biodiversity and top–down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors. 相似文献