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1.
BMC Genomics ; 14: 260, 2013 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-23594279

RESUMO

After publication of this article (Fernandez et al., BMC Genomics 2011, 12:604) it was brought to the Editors' attention that the data generated by the first author, Ariel Fernandez, seemed anomalous. One of the author's institutions found that the data were not reproducible from the described methods, but an investigation by the author's other institution did not find the data or their interpretation suspicious. Given the conflicting conclusions of these investigations, the Editors advise the readers to interpret the data with due caution. We apologize to all affected parties.

2.
BMC Evol Biol ; 11: 251, 2011 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-21917188

RESUMO

This Editorial highlights recent changes to the International Code of Botanical Nomenclature and the implications these changes have for electronic journals.


Assuntos
Botânica/normas , Plantas/classificação , Editoração , Terminologia como Assunto
3.
Nature ; 434(7032): 509-14, 2005 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-15791256

RESUMO

Vascular plants evolved in the Middle to Late Silurian period, about 420 million years ago. The fossil record indicates that these primitive plants had branched stems with sporangia but no leaves. Leaf-like lateral outgrowths subsequently evolved on at least two independent occasions. In extant plants, these events are represented by microphyllous leaves in lycophytes (clubmosses, spikemosses and quillworts) and megaphyllous leaves in euphyllophytes (ferns, gymnosperms and angiosperms). Our current understanding of how leaves develop is restricted to processes that operate during megaphyll formation. Because microphylls and megaphylls evolved independently, different mechanisms might be required for leaf formation. Here we show that this is not so. Gene expression data from a microphyllous lycophyte, phylogenetic analyses, and a cross-species complementation experiment all show that a common developmental mechanism can underpin both microphyll and megaphyll formation. We propose that this mechanism might have operated originally in the context of primitive plant apices to facilitate bifurcation. Recruitment of this pathway to form leaves occurred independently and in parallel in different plant lineages.


Assuntos
Evolução Biológica , Modelos Biológicos , Folhas de Planta/crescimento & desenvolvimento , Antirrhinum/genética , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Fósseis , Dosagem de Genes , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Teste de Complementação Genética , Meristema/crescimento & desenvolvimento , Dados de Sequência Molecular , Mutação/genética , Filogenia , Folhas de Planta/genética , Folhas de Planta/fisiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Ligação Proteica , RNA de Plantas/análise , RNA de Plantas/genética , Fatores de Transcrição/genética , Zea mays/genética
4.
Plant J ; 56(3): 432-44, 2008 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-18643989

RESUMO

In a number of land plants, Golden2-like (GLK) genes encode a pair of partially redundant nuclear transcription factors that are required for the expression of nuclear photosynthetic genes and for chloroplast development. As chloroplast biogenesis depends on close co-operation between the nuclear and plastid compartments, GLK gene function must be dependent on tight intracellular control. However, the extent to which GLK-mediated chloroplast development depends on intercellular communication is not known. Here we used sector analysis to show that GLK proteins operate cell-autonomously in leaf mesophyll cells. To establish whether GLK proteins are able to influence adjacent cell layers, we used tissue-specific promoters to restrict GLK gene expression to the epidermis and to the phloem. GLK genes driven by the Arabidopsis epidermal FIDDLEHEAD (FDH) and MERISTEM LAYER1 (AtML1) promoters failed to rescue the pale-green Atglk1 Atglk2 mutant phenotype, confirming the suggestion that GLK proteins can only influence chloroplast development intracellularly. An exception to this rule was seen in lines in which GLK genes were expressed in the phloem. However, we believe that the partial complementation of the mutant phenotype that was observed resulted from phloem unloading, as opposed to inherent properties of GLK proteins. We conclude that GLK proteins act in a cell-autonomous manner to coordinate and maintain the photosynthetic apparatus within individual cells. Significantly, this suggests that GLK proteins provide a means to fine-tune photosynthesis according to the differential requirements of cells within the leaf.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Cloroplastos/fisiologia , Regulação da Expressão Gênica de Plantas , Fatores de Transcrição/metabolismo , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/genética , Clorofila/metabolismo , Cloroplastos/genética , DNA de Plantas/genética , Regulação da Expressão Gênica no Desenvolvimento , Genes de Plantas , Microscopia Confocal , Microscopia Eletrônica de Transmissão , Mutação , Fenótipo , Floema/genética , Floema/metabolismo , Epiderme Vegetal/genética , Epiderme Vegetal/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Regiões Promotoras Genéticas , RNA de Plantas/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Transcrição/genética
5.
F1000Res ; 7: 969, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30135731

RESUMO

Open peer review (OPR), as with other elements of open science and open research, is on the rise. It aims to bring greater transparency and participation to formal and informal peer review processes. But what is meant by `open peer review', and what advantages and disadvantages does it have over standard forms of review? How do authors or reviewers approach OPR? And what pitfalls and opportunities should you look out for? Here, we propose ten considerations for OPR, drawing on discussions with authors, reviewers, editors, publishers and librarians, and provide a pragmatic, hands-on introduction to these issues. We cover basic principles and summarise best practices, indicating how to use OPR to achieve best value and mutual benefits for all stakeholders and the wider research community.


Assuntos
Autoria , Políticas Editoriais , Revisão da Pesquisa por Pares , Humanos
6.
Res Integr Peer Rev ; 3: 3, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29556422

RESUMO

In May 2016, we launched Research Integrity and Peer Review, an international, open access journal with fully open peer review (reviewers are identified on their reports and named reports are published alongside the article) to provide a home for research on research and publication ethics, research reporting, and research on peer review. As the journal enters its third year, we reflect on recent events and highlights for the journal and explore how the journal is faring in terms of gender and diversity in peer review. We also share the particular interests of our Editors-in-Chief regarding models of peer review, reporting quality, common research integrity issues that arise during the publishing process, and how people interact with the published literature. We continue to encourage further research into peer review, research and publication ethics and research reporting, as we believe that all new initiatives should be evidence-based. We also remain open to constructive discussions of the developments in the field that offer new solutions.

7.
BMJ Open ; 6(11): e012047, 2016 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-27881524

RESUMO

OBJECTIVES: To assess why articles are retracted from BioMed Central journals, whether retraction notices adhered to the Committee on Publication Ethics (COPE) guidelines, and are becoming more frequent as a proportion of published articles. DESIGN/SETTING: Retrospective cross-sectional analysis of 134 retractions from January 2000 to December 2015. RESULTS: 134 retraction notices were published during this timeframe. Although they account for 0.07% of all articles published (190 514 excluding supplements, corrections, retractions and commissioned content), the rate of retraction is rising. COPE guidelines on retraction were adhered to in that an explicit reason for each retraction was given. However, some notices did not document who retracted the article (eight articles, 6%) and others were unclear whether the underlying cause was honest error or misconduct (15 articles, 11%). The largest proportion of notices was issued by the authors (47 articles, 35%). The majority of retractions were due to some form of misconduct (102 articles, 76%), that is, compromised peer review (44 articles, 33%), plagiarism (22 articles, 16%) and data falsification/fabrication (10 articles, 7%). Honest error accounted for 17 retractions (13%) of which 10 articles (7%) were published in error. The median number of days from publication to retraction was 337.5 days. CONCLUSIONS: The most common reason to retract was compromised peer review. However, the majority of these cases date to March 2015 and appear to be the result of a systematic attempt to manipulate peer review across several publishers. Retractions due to plagiarism account for the second largest category and may be reduced by screening manuscripts before publication although this is not guaranteed. Retractions due to problems with the data may be reduced by appropriate data sharing and deposition before publication. Adopting a checklist (linked to COPE guidelines) and templates for various classes of retraction notices would increase transparency of retraction notices in future.


Assuntos
Pesquisa Biomédica/normas , Editoração/normas , Retratação de Publicação como Assunto , Pesquisa Biomédica/ética , Estudos Transversais , Comissão de Ética , Guias como Assunto , Revisão por Pares , Editoração/tendências , Estudos Retrospectivos
8.
BMJ Open ; 5(9): e008707, 2015 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-26423855

RESUMO

OBJECTIVES: To assess whether reports from reviewers recommended by authors show a bias in quality and recommendation for editorial decision, compared with reviewers suggested by other parties, and whether reviewer reports for journals operating on open or single-blind peer review models differ with regard to report quality and reviewer recommendations. DESIGN: Retrospective analysis of the quality of reviewer reports using an established Review Quality Instrument, and analysis of reviewer recommendations and author satisfaction surveys. SETTING: BioMed Central biology and medical journals. BMC Infectious Diseases and BMC Microbiology are similar in size, rejection rates, impact factors and editorial processes, but the former uses open peer review while the latter uses single-blind peer review. The Journal of Inflammation has operated under both peer review models. SAMPLE: Two hundred reviewer reports submitted to BMC Infectious Diseases, 200 reviewer reports submitted to BMC Microbiology and 400 reviewer reports submitted to the Journal of Inflammation. RESULTS: For each journal, author-suggested reviewers provided reports of comparable quality to non-author-suggested reviewers, but were significantly more likely to recommend acceptance, irrespective of the peer review model (p<0.0001 for BMC Infectious Diseases, BMC Microbiology and the Journal of Inflammation). For BMC Infectious Diseases, the overall quality of reviewer reports measured by the Review Quality Instrument was 5% higher than for BMC Microbiology (p=0.042). For the Journal of Inflammation, the quality of reports was the same irrespective of the peer review model used. CONCLUSIONS: Reviewers suggested by authors provide reports of comparable quality to non-author-suggested reviewers, but are significantly more likely to recommend acceptance. Open peer review reports for BMC Infectious Diseases were of higher quality than single-blind reports for BMC Microbiology. There was no difference in quality of peer review in the Journal of Inflammation under open peer review compared with single blind.


Assuntos
Autoria , Biologia , Pesquisa Biomédica , Políticas Editoriais , Revisão por Pares/normas , Editoração , Relatório de Pesquisa/normas , Humanos , Julgamento , Revisão por Pares/métodos , Publicações Periódicas como Assunto , Satisfação Pessoal , Estudos Retrospectivos , Método Simples-Cego , Inquéritos e Questionários
10.
BMC Pharmacol Toxicol ; 15: 55, 2014 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-25266119

RESUMO

BMC Pharmacology and Toxicology was created from the merger of two journals within the BMC series published by BioMed Central: BMC Pharmacology and BMC Clinical Pharmacology. BMC Pharmacology operated anonymous peer review whereas BMC Clinical Pharmacology operated a fully open peer review policy where the identity of the reviewers was known to the editors, authors and readers. The merged journal also adopted a fully open peer review policy. Two years on we discuss the views and experiences of our Editorial Board Members towards open peer review on this biomedical journal.


Assuntos
Revisão da Pesquisa por Pares , Método Duplo-Cego , Método Simples-Cego
11.
BMC Sports Sci Med Rehabil ; 5: 1, 2013 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-23557003

RESUMO

This Editorial celebrates the launch of BMC Sports Science, Medicine and Rehabilitation within the BMC series of journals published by BioMed Central. BMC Sports Science, Medicine and Rehabilitation incorporates the recently closed Sports Medicine, Arthroscopy, Rehabilitation, Therapy & Technology (SMARTT) with an expanded scope and Editorial Board. BMC Sports Science, Medicine and Rehabilitation will fill its own niche in the BMC series alongside other companion journals including BMC Physiology, BMC Musculoskeletal Disorders and BMC Surgery.

12.
BMC Pharmacol Toxicol ; 13: 1, 2012 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-22946996

RESUMO

This editorial celebrates the launch of BMC Pharmacology and Toxicology within the BMC series of journals published by BioMed Central. The scope of the journal is interdisciplinary encompassing toxicology, experimental and clinical pharmacology including clinical trials. In this editorial we discuss the origins of this new journal and the ethos and policies under which it will operate.


Assuntos
Publicações Periódicas como Assunto , Farmacologia , Comunicação Interdisciplinar
13.
BMC Biophys ; 4: 1, 2011 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-21595996

RESUMO

This editorial celebrates the re-launch of PMC Biophysics previously published by PhysMath Central, in its new format as BMC Biophysics published by BioMed Central with an expanded scope and Editorial Board. BMC Biophysics will fill its own niche in the BMC series alongside complementary companion journals including BMC Bioinformatics, BMC Medical Physics, BMC Structural Biology and BMC Systems Biology.

14.
Plant Cell ; 17(7): 1894-907, 2005 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-15923345

RESUMO

Land plant chloroplasts evolved from those found in the green algae. During land plant evolution, nuclear regulatory mechanisms have been modified to produce morphologically and functionally diverse chloroplasts in distinct developmental contexts. At least some of these mechanisms evolved independently in different plant lineages. In angiosperms, GOLDEN2-LIKE (GLK) transcription factors regulate the development of at least three chloroplast types. To determine whether GLK-mediated regulation of chloroplast development evolved within angiosperms or is a plesiomorphy within land plants, gene function was examined in the moss Physcomitrella patens. Gene expression patterns and loss-of-function mutant phenotypes suggested that GLK gene function is conserved between P. patens and Arabidopsis thaliana, species that diverged >400 million years ago. In support of this suggestion, moss genes partially complement Arabidopsis loss-of-function mutants. Therefore, GLK-mediated regulation of chloroplast development defines one of the most ancient conserved regulatory mechanisms identified in the plant kingdom.


Assuntos
Bryopsida/genética , Núcleo Celular/genética , Cloroplastos/genética , Sequência Conservada , Evolução Molecular , Fatores de Transcrição/genética , Arabidopsis/genética , Bryopsida/metabolismo , Diferenciação Celular/genética , Núcleo Celular/metabolismo , Cloroplastos/metabolismo , Cloroplastos/ultraestrutura , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta , Complexos de Proteínas Captadores de Luz/genética , Complexos de Proteínas Captadores de Luz/metabolismo , Magnoliopsida/genética , Dados de Sequência Molecular , Mutação/genética , Fenótipo , Fotossíntese/genética , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido Nucleico , Tilacoides/genética , Tilacoides/metabolismo , Tilacoides/ultraestrutura
15.
Am J Bot ; 91(5): 724-35, 2004 May.
Artigo em Inglês | MEDLINE | ID: mdl-21653427

RESUMO

Chloroplast trnL-F sequence data, nuclear ribosomal internal transcribed spacer (ITS) sequence data, and morphology were used to analyze phylogenetic relationships among members of the subtribe Strobilanthinae. Parsimony and maximum likelihood analyses of trnL-F indicate that the Strobilanthinae are a monophyletic group. While parsimony analysis of ITS recovers a nonmonophyletic subtribe, maximum likelihood analysis of ITS corroborates results from trnL-F and suggests that systematic error is impacting on ITS parsimony analysis. A combined ITS and trnL-F analysis strengthens the signal and also recovers a monophyletic subtribe. All analyses indicate that Hemigraphis, Sericocalyx, and Strobilanthes are nonmonophyletic. With one exception, all morphological characters included in a combined ITS and morphological analysis are homoplastic. The prospect for a new informative generic classification of the Strobilanthinae aiming to recognize and diagnose only monophyletic groups is considered. While some groups can be diagnosed, adequate diagnosis of the majority of groups remains problematic. Consequently, a single expanded genus Strobilanthes sensu lato is proposed at the level of the well-supported and monophyletic Strobilanthinae.

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