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121.
Szklarczyk R Wanschers BF Cuypers TD Esseling JJ Riemersma M van den Brand MA Gloerich J Lasonder E van den Heuvel LP Nijtmans LG Huynen MA 《Genome biology》2012,13(2):R12-14
Background
Orthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs.Results
We have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase.Conclusions
Divergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs. 相似文献122.
Corn samples were collected in 1999 from three departments of Entre Réos province, Argentina, and were surveyed for mould
contamination and natural occurrence ofFusarium mycotoxins, ochratoxin A and aflatoxins.Fusarium verticillioides was the most prevalent fungal species recorded at all departments. Zearalenone, deoxynivalenol and ochratoxin A were not
found in any samples. Only one of the 52 corn samples analysed was contaminated with aflatoxin B1 (17 μg/kg). Fumonisin B1 was found in 58 % of samples (range of positive samples: 47– 3,347 μg/kg), fumonisin B2 in 33.0 % (range of positive samples: 23–537 μg/kg) and fumonisin B3 in 25.0 % (range of positive samples: 24–287 μg/kg) of them. This is the first report on the natural occurrence of mycotoxins
in corn from Entre Ríos province, Argentina. Levels of fumonisins were lower than detected in other Argentinian provinces. 相似文献
123.
A number of genera of soil fungi interact with plant roots to establish symbiotic associations whereby phosphate acquired by the fungus is exchanged for fixed carbon from the plant. Recent progress in investigating these associations, designated as mycorrhizae (sing., mycorrhiza), has led to the identification of specific steps in the establishment of the symbiosis in which the fungus and the plant interact in response to various molecular signals. Some of these signals are conserved with those of the Rhizobium-legume nitrogen-fixing symbiosis, suggesting that the two plant-microbe interactions share a common signal transduction pathway. Nevertheless, only legume hosts nodulate in response to Rhizobium, whereas the vast majority of flowering plants establish mycorrhizal associations. The key questions for the future are: what are the signal molecules produced by mycorrhizal fungi and how are they perceived by the plant? Copyright 1998 Academic Press. 相似文献
124.
Maria Benitez‐Guijarro Cesar Lopez‐Ruiz Žygimantė Tarnauskaitė Olga Murina Mahwish Mian Mohammad Thomas C Williams Adeline Fluteau Laura Sanchez Raquel Vilar‐Astasio Marta Garcia‐Canadas David Cano Marie‐Jeanne HC Kempen Antonio Sanchez‐Pozo Sara R Heras Andrew P Jackson Martin AM Reijns Jose L Garcia‐Perez 《The EMBO journal》2018,37(15)
125.
Gabriella Ujhelyi Jeroen P van Dijk Theo W Prins Marleen M Voorhuijzen AM Angeline Van Hoef Henriek G Beenen Dany Morisset Kristina Gruden Esther J Kok 《BMC biotechnology》2012,12(1):4
Background
With the increasing number of GMOs on the global market the maintenance of European GMO regulations is becoming more complex. For the analysis of a single food or feed sample it is necessary to assess the sample for the presence of many GMO-targets simultaneously at a sensitive level. Several methods have been published regarding DNA-based multidetection. Multiplex ligation detection methods have been described that use the same basic approach: i) hybridisation and ligation of specific probes, ii) amplification of the ligated probes and iii) detection and identification of the amplified products. Despite they all have this same basis, the published ligation methods differ radically. The present study investigated with real-time PCR whether these different ligation methods have any influence on the performance of the probes. Sensitivity and the specificity of the padlock probes (PLPs) with the ligation protocol with the best performance were also tested and the selected method was initially validated in a laboratory exchange study. 相似文献126.
AM. Bergman G. Cristalli S. Vittori J. Wang S. Eriksson Gj Peters 《Nucleosides, nucleotides & nucleic acids》2013,32(4-5):897-898
Abstract Several 1-deazapurine nucleosides were tested for their biological activity; anti-HIV-1, cytotoxicity and inhibition of adenosine deaminase (ADA). A2780 human ovarian cancer cells and the deoxycytidine kinase (dCK) deficient variant AG6000, used to determine whether dCK plays a role in their activation, showed a similar sensitivity to the analogs. This is in line with substrate specificity tests, which revealed a very low affinity of dCK. 相似文献
127.
Structural genes of the mouse major urinary protein are on chromosome 4 总被引:10,自引:0,他引:10
The major urinary proteins (MUPs) of mouse are a family of at least three major proteins which are synthesized in the liver of all strains of mice. The relative levels of synthesis of these proteins with respect to each other in the presence of testosterone is regulated by the Mup-a locus located on chromosome 4. In an effort to determine the mechanism of this regulation in molecular terms, a cDNA clone containing most of the coding region of a MUP protein has been isolated and identified by partial DNA sequence analysis. Using a combination of hybridization analysis and somatic cell genetics, the structural gene family has been unambiguously mapped to mouse chromosome 4. These data suggest that Mup-a regulation operates in a cis fashion and that models proposing trans regulation of MUP protein synthesis are unlikely. 相似文献
128.
Alpina Begossi Svetlana V Salivonchyk Luciana G Araujo Tainá B Andreoli Mariana Clauzet Claudia M Martinelli Allan GL Ferreira Luiz EC Oliveira Renato AM Silvano 《Journal of ethnobiology and ethnomedicine》2011,7(1):1-23
In this study, we sought to investigate the biology (diet and reproduction) and ethnobiology (fishers knowledge and fishing spots used to catch snappers) of five species of snappers (Lutjanidae), including Lutjanus analis, Lutjanus synagris, Lutjanus vivanus, Ocyurus chrysurus, and Romboplites saliens at five sites along the northeast (Riacho Doce, Maceió in Alagoas State, and Porto do Sauípe, Entre Rios at Bahia State) and the southeast (SE) Brazilian coast (Paraty and Rio de Janeiro cities at Rio de Janeiro State, and Bertioga, at São Paulo State.). We collected 288 snappers and interviewed 86 fishermen. The stomach contents of each fish were examined and macroscopic gonad analysis was performed. Snappers are very important for the fisheries of NE Brazil, and our results indicated that some populations, such as mutton snapper (L. analis) and lane snapper (L. synagris), are being caught when they are too young, at early juvenile stages. Local knowledge has been shown to be a powerful tool for determining appropriate policies regarding management of target species, and artisanal fishermen can be included in management processes. Other suggestions for managing the fisheries are discussed, including proposals that could provide motivation for artisanal fishermen to participate in programs to conserve resources, such as co-management approaches that utilize local knowledge, the establishment of fishing seasons, and compensation of fishermen, through 'payment for environmental services'. These suggestions may enhance the participation of local artisanal fishermen in moving to a more realistic and less top-down management approach of the fish population. 相似文献
129.
A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories,
New York, USA, November 2-5, 2011. 相似文献
130.