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1.
PLoS One ; 14(6): e0217195, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31185025

RESUMO

[This corrects the article DOI: 10.1371/journal.pone.0208078.].

2.
PLoS One ; 14(1): e0208078, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30682020

RESUMO

This paper provides a statistical methodology for quantifying causality in complex dynamical systems, based on analysis of multidimensional time series data of the state variables. The methodology integrates Granger's causality analysis based on the log-likelihood function expansion (Partial pair-wise causality), and Akaike's power contribution approach over the whole frequency domain (Total causality). The proposed methodology addresses a major drawback of existing methodologies namely, their inability to use time series observation of state variables to quantify causality in complex systems. We first perform a simulation study to verify the efficacy of the methodology using data generated by several multivariate autoregressive processes, and its sensitivity to data sample size. We demonstrate application of the methodology to real data by deriving inter-species relationships that define key food web drivers of the Barents Sea ecosystem. Our results show that the proposed methodology is a useful tool in early stage causality analysis of complex feedback systems.


Assuntos
Simulação por Computador , Ecossistema , Algoritmos , Animais , Cadeia Alimentar , Modelos Teóricos , Dinâmica Populacional , Temperatura
3.
Am J Bot ; 105(9): 1453-1468, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30179250

RESUMO

PREMISE OF THE STUDY: The apical meristem generates indeterminate apical growth of the stem and root of vascular plants. Our previous examination showed that shoot apical meristems (SAMs) can be classified into two types based on plasmodesmatal networks (PNs), which are important elements in symplasmic signaling pathways within the apical meristem. Here, we examined the PNs of root apical meristems (RAMs) in comparison with those of SAMs. METHODS: Root apical meristems of 18 families and 22 species of lycophytes and euphyllophytes were analyzed. Plasmodesmata (PD) in cell walls in median longitudinal sections of RAMs were enumerated using transmission electron micrographs, and the PD density per 1 µm2 of each cell wall was calculated. KEY RESULTS: Root apical meristems with prominent apical cells of monilophytes (euphyllophytes) and Selaginellaceae (lycophytes) had high PD densities, while RAMs with plural initial cells of gymnosperms and angiosperms (euphyllophytes), and of Lycopodiaceae and Isoetaceae (lycophytes) had low PD densities. This correlation between structures of apical meristems and PD densities is identical to that in SAMs already described. CONCLUSIONS: Irrespective of their diversified structures, the RAMs of vascular plants can be classified into two types with respect to PNs: the fern (monilophyte) type, which has a lineage-specific PN with only primary PD, and the seed-plant type, which has an interspecific PN with secondary PD in addition to primary PD. PNs may have played a key role in the evolution of apical meristems in vascular plants.


Assuntos
Meristema/anatomia & histologia , Plantas/anatomia & histologia , Plasmodesmos/ultraestrutura , Evolução Biológica , Cycadopsida/anatomia & histologia , Cycadopsida/citologia , Cycadopsida/ultraestrutura , Magnoliopsida/anatomia & histologia , Magnoliopsida/citologia , Magnoliopsida/ultraestrutura , Meristema/citologia , Meristema/ultraestrutura , Raízes de Plantas , Plantas/ultraestrutura
4.
Mol Oncol ; 5(1): 61-76, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21212030

RESUMO

Breast cancer is a heterogeneous disease that can be divided in subtypes based on histology, gene expression profiles as well as differences in genomic aberrations. Distinct global DNA methylation profiles have been reported in normal breast epithelial cells as well as in breast tumors. However, the influence of the tumor methylome on the previously described subgroups of breast cancer is not fully understood. Here we report the DNA methylation profiles of 80 breast tumors using a panel of 807 cancer related genes interrogating 1505 CpG sites. We identified three major clusters based on the methylation profiles; one consisting of mainly tumors of myoepithelial origin and two other clusters with tumors of predominantly luminal epithelial origin. The clusters were different with respect to estrogen receptor status, TP53 status, ErbB2 status and grade. The most significantly differentially methylated genes including HDAC1, TFF1, OGG1, BMP3, FZD9 and HOXA11 were confirmed by pyrosequencing. Gene Ontology analysis revealed enrichment for genes involved in developmental processes including homeobox domain genes (HOXA9, HOXA11, PAX6, MYBL2, ISL1 and IPF1) and (ETS1, HDAC1, CREBBP, GAS7, SPI1 and TBX1). Extensive correlation to mRNA expression was observed. Pathway analyses identified a significant association with canonical (curated) pathways such as hepatic fibrosis including genes like EGF, NGFR and TNF, dendritic cell maturation and the NF-κB signaling pathway. Our results show that breast tumor expression subtypes harbor major epigenetic differences and tumors with similar gene expression profiles might belong to epigenetically different subtypes. Some of the transcription factors identified, with key roles in differentiation and development might play a role in inducing and maintaining the different phenotypes.


Assuntos
Neoplasias da Mama/genética , Metilação de DNA , Mutação , Receptores de Estrogênio/metabolismo , Proteína Supressora de Tumor p53/metabolismo , Neoplasias da Mama/metabolismo , Feminino , Humanos , RNA Mensageiro/genética , Receptores de Estrogênio/genética , Proteína Supressora de Tumor p53/genética
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