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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
15/12/2009 |
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Data da última atualização: |
13/10/2016 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
HERAI, R. H.; YAMAGISHI, M. E. B. |
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Afiliação: |
ROBERTO HIROCHI HERAI, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA. |
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Título: |
Detection of human interchromosomal trans-splicing in sequence databanks. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
Briefings in Bioinformatics, London, v. 2, n. 2, p. 198-209, 2010. |
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DOI: |
10.1093/bib/bbp041 |
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Idioma: |
Inglês |
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Conteúdo: |
Trans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, ?Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence??, we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent study has reported that trans-splicing may occur not only in malignant tissues, but in normal tissues as well. Our methodology can be applied to 5'-UTR, coding sequences and 3'-UTR in order to find new candidates for a posteriori experimental confirmation. MenosTrans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, ?Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence??, we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent stu... Mostrar Tudo |
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Palavras-Chave: |
Banco de dados; Bioinformática; Inter-chromosomal trans-splicing; Non-canonical splicing sites; TRNA-mediatedtrans-splicing. |
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Thesaurus Nal: |
Bioinformatics. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/148693/1/AP-Brief-Bioinform-2010-Herai-198-209.pdf
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Marc: |
LEADER 02445naa a2200217 a 4500
001 1577947
005 2016-10-13
008 2010 bl uuuu u00u1 u #d
024 7 $a10.1093/bib/bbp041$2DOI
100 1 $aHERAI, R. H.
245 $aDetection of human interchromosomal trans-splicing in sequence databanks.$h[electronic resource]
260 $c2010
520 $aTrans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, ?Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence??, we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent study has reported that trans-splicing may occur not only in malignant tissues, but in normal tissues as well. Our methodology can be applied to 5'-UTR, coding sequences and 3'-UTR in order to find new candidates for a posteriori experimental confirmation.
650 $aBioinformatics
653 $aBanco de dados
653 $aBioinformática
653 $aInter-chromosomal trans-splicing
653 $aNon-canonical splicing sites
653 $aTRNA-mediatedtrans-splicing
700 1 $aYAMAGISHI, M. E. B.
773 $tBriefings in Bioinformatics, London$gv. 2, n. 2, p. 198-209, 2010.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
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Biblioteca(s): |
Embrapa Solos. |
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Data corrente: |
16/09/2021 |
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Data da última atualização: |
16/09/2021 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
B - 5 |
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Autoria: |
BIGHI, K. N.; PAULA, R. R.; CALDEIRA, M. V. W.; BURAK, D. L.; MENDONÇA, E. de S.; SOUZA, P. H. de; DELARMELINA, W. M.; BALIEIRO, F. de C. |
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Afiliação: |
KELLY NERY BIGHI, UFES; RANIERI RIBEIRO PAULA, UFES; MARCOS VINÍCIUS WINCKLER CALDEIRA, UFES; DIEGO LANG BURAK, UFES; EDUARDO DE SÁ MENDONÇA, UFES; PAULO HENRIQUE DE SOUZA, IFMG; WILLIAM MACEDO DELARMELINA, IFES; FABIANO DE CARVALHO BALIEIRO, CNPS. |
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Título: |
Nitrogen pools in tropical plantations of N2-fixing and non-N2-fixing legume trees under different tree stand densities. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Nitrogen, v. 2, n. 1, p. 86-98, 2021. |
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DOI: |
https://doi.org/10.3390/nitrogen2010006 |
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Idioma: |
Inglês |
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Conteúdo: |
We investigated the nitrogen pools in monocultures of legume species widely used in reforestation in Brazil that have contrasting growth and nitrogen acquisition strategies. The plantations were established with the slow-growing and N2-fixing tree Anadenanthera peregrina var. peregrina, and the fast-growing and non-fixing tree Schizolobium parahyba var. amazonicum. The measurements of N pools in the tree biomass and the soil followed standard methods and were carried out on 54 experimental plots. The N2 fixation pools were evaluated by abundance natural of 15N and the N accretion methods. The soil N content was of similar magnitude between species and stand densities. The species showed similar amounts of N in the biomass, but divergent patterns of N accumulation, as well as the 15N signature on the leaves. S. parahyba accumulated most N in the stem, while A. peregrina accumulated N in the roots and leaves. However, the N accumulation in biomass of A. peregrina stand was less constrained by environment than in S. parahyba stands. The percentage of N derived from N2 fixation in A. peregrina stands decreased with the increase of stand density. The biological N2 fixation estimates depended on the method and the response of tree species to environment. |
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Palavras-Chave: |
15N natural abundance; Functional traits; N2 biological fixation. |
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Thesagro: |
Fixação de Nitrogênio; Floresta; Reflorestamento. |
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Thesaurus NAL: |
Forest plantations; Forest restoration; Nitrogen balance; Nitrogen fixation. |
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Categoria do assunto: |
P Recursos Naturais, Ciências Ambientais e da Terra |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/226110/1/Nitrogen-pools-in-tropical-plantations-2021.pdf
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Marc: |
LEADER 02309naa a2200337 a 4500
001 2134497
005 2021-09-16
008 2021 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.3390/nitrogen2010006$2DOI
100 1 $aBIGHI, K. N.
245 $aNitrogen pools in tropical plantations of N2-fixing and non-N2-fixing legume trees under different tree stand densities.$h[electronic resource]
260 $c2021
520 $aWe investigated the nitrogen pools in monocultures of legume species widely used in reforestation in Brazil that have contrasting growth and nitrogen acquisition strategies. The plantations were established with the slow-growing and N2-fixing tree Anadenanthera peregrina var. peregrina, and the fast-growing and non-fixing tree Schizolobium parahyba var. amazonicum. The measurements of N pools in the tree biomass and the soil followed standard methods and were carried out on 54 experimental plots. The N2 fixation pools were evaluated by abundance natural of 15N and the N accretion methods. The soil N content was of similar magnitude between species and stand densities. The species showed similar amounts of N in the biomass, but divergent patterns of N accumulation, as well as the 15N signature on the leaves. S. parahyba accumulated most N in the stem, while A. peregrina accumulated N in the roots and leaves. However, the N accumulation in biomass of A. peregrina stand was less constrained by environment than in S. parahyba stands. The percentage of N derived from N2 fixation in A. peregrina stands decreased with the increase of stand density. The biological N2 fixation estimates depended on the method and the response of tree species to environment.
650 $aForest plantations
650 $aForest restoration
650 $aNitrogen balance
650 $aNitrogen fixation
650 $aFixação de Nitrogênio
650 $aFloresta
650 $aReflorestamento
653 $a15N natural abundance
653 $aFunctional traits
653 $aN2 biological fixation
700 1 $aPAULA, R. R.
700 1 $aCALDEIRA, M. V. W.
700 1 $aBURAK, D. L.
700 1 $aMENDONÇA, E. de S.
700 1 $aSOUZA, P. H. de
700 1 $aDELARMELINA, W. M.
700 1 $aBALIEIRO, F. de C.
773 $tNitrogen$gv. 2, n. 1, p. 86-98, 2021.
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