human Mesenchymal Stem Cells Chronobiology: evaluating the crosstalk between the Embryonic and Circadian Clocks

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Mechanisms of vertebrate embryo segmentation: Common themes in trunk and limb development

Publication . Sheeba, C.J.; Andrade, Raquel P.; Palmeirim, Isabel

Various ultradian rhythms ensure proper temporal regulations during embryo development. The embryo molecular clock, which was first identified in the presomitic mesoderm (PSM) underlying periodic somite formation, is one among them. Somites are the earliest manifestation of the segmented vertebrate body and they are formed with strict temporal precision. The tetrapod limb is also a segmented structure and the formation of limb bone elements have also been associated with a molecular clock, operating in the distal limb mesenchyme. In both the PSM and the distal limb mesenchyme, the molecular clock (MC) is influenced by FGF, SHH and RA, which are also the key regulators of the development of these tissues. While somitogenesis has been continuously scrutinized to understand the mechanisms of the MC, the limb bud has served as an outstanding paradigm to study how a cohort of undifferentiated cells is organized into functional 3D structures. The fact that both the trunk and limb development are shaped by the MC and by common signaling molecules has prompted the exciting possibility of establishing parallelisms between somitogenesis and limb development. Systematically correlating various parameters during trunk and limb development will help us to appreciate the common principles underlying segmented structure formation and allow the rise of new questions in order to fill the gaps in our present understanding. In this review we have established the parallelisms between somitogenesis and limb development at the level of gene expression patterns and their regulation. Finally, we have also discussed the most evident new avenues this exercise could open to the scientific community. (C) 2016 Elsevier Ltd. All rights reserved.

2016-07Journal article

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rdml: A Mathematica package for parsing and importing Real-Time qPCR data

Publication . Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.; Palmeirim, Isabel

Objective The purpose and objective of the research presented is to provide a package for easy importing of Real-Time PCR data markup language (RDML) data to Mathematica. Results Real-Time qPCR is the most widely used experimental method for the accurate quantification of gene expression. To enable the straightforward archiving and sharing of qPCR data and its associated experimental information, an XML-based data standard was developed—the Real-Time PCR data markup language (RDML)—devised by the RDML consortium. Here, we present rdml, a package to parse and import RDML data into Mathematica, allowing the quick loading and extraction of relevant data, thus promoting the re-analysis, meta-analysis or experimental re-validation of gene expression data deposited in RDML format.

2017-06-12Journal article

Open Access

Getting a handle on embryo limb development: Molecular interactions driving limb outgrowth and patterning

Publication . Sheeba, C.J.; Andrade, Raquel P.; Palmeirim, Isabel

Development of the vertebrate embryo involves multiple segmentation processes to generate a functional, articulated organism. Cell proliferation, differentiation and patterning involve spatially and temporally regulated gene expression and signal transduction mechanisms. The developing vertebrate limb is an excellent model to study such fine-tuned regulations, whereby cells proliferate and are differentially sculptured along the proximal-distal, anterior-posterior and dorsal-ventral axes to form a functional limb. Complementary experimental approaches in different organisms have enhanced our knowledge on the molecular events underlying limb development. Herein, we summarize the current knowledge of the main signaling mechanisms governing vertebrate limb initiation, outgrowth, specification of limb segments and termination. (C) 2015 Elsevier Ltd. All rights reserved.

2016-07Journal article

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