Prickle1 is required for EMT and migration of zebrafish cranial neural crest

The neural crest—a key innovation of the vertebrates—gives rise to diverse cell types including melanocytes, neurons and glia of the peripheral nervous system, and chondrocytes of the jaw and skull. Proper development of the cephalic region is dependent on the tightly-regulated specification and migration of cranial neural crest cells (NCCs). The core PCP proteins Frizzled and Disheveled have previously been implicated in NCC migration. Here we investigate the functions of the core PCP proteins Prickle1a and Prickle1b in zebrafish cranial NCC development. Using analysis of pk1a and pk1b mutant embryos, we uncover similar roles for both genes in facilitating cranial NCC migration. Disruption of either gene causes pre-migratory NCCs to cluster together at the dorsal aspect of the neural tube, where they adopt aberrant polarity and movement. Critically, in investigating Pk1-deficient cells that fail to migrate ventrolaterally, we have also uncovered roles for pk1a and pk1b in the epithelial-to-mesenchymal transition (EMT) of pre-migratory NCCs that precedes their collective migration to the periphery. Normally, during EMT, pre-migratory NCCs transition from a neuroepithelial to a bleb-based and subsequently, mesenchymal morphology capable of directed migration. When either Pk1a or Pk1b is disrupted, NCCs continue to perform blebbing behaviors characteristic of pre-migratory cells over extended time periods, indicating a block in a key transition during EMT. Although some Pk1-deficient NCCs transition successfully to mesenchymal, migratory morphologies, they fail to separate from neighboring NCCs. Additionally, Pk1b-deficient NCCs show elevated levels of E-Cadherin and reduced levels of N-Cadherin, suggesting that Prickle1 molecules regulate Cadherin levels to ensure the completion of EMT and the commencement of cranial NCC migration. We conclude that Pk1 plays crucial roles in cranial NCCs both during EMT and migration. These roles are dependent on the regulation of E-Cad and N-Cad

Made-in-Canada system ecology: Explorations of the garment industry

The contemporary Made-In-Canada (MIC) local garment system is a vast departure from what Canada had in place 40 years ago. In the 1970’s, 70% of the Canadian consumer clothing demand was met with domestic production [Wyman, 2009]. At the time, both production capacity and labour skills existed inside of Canada, whereas in today’s market, these skills are significantly outsourced by Canadian businesses. This shift - driven in part by the capabilities available from globalization - has shrunk the domestic manufacturing sector in Canada, carrying with it many long-term economic, environmental and social implications. This paper examines the MIC system as it pertains to the garment industry; understanding how the current consumer market interest in fashion-forward timeliness and focus on price are impacting the garment system in Canada. This research also explores the dominant stakeholders influencing consumers’ ability to make informed choices about their garment purchases, particularly those which label themselves, Made-In-Canada. Three findings were revealed through the research process: a) Globalization is a critical driver in the system as deregulation made it difficult for local manufacturers to stay competitive; b) Consumer perceptions of value are driving demand for cheap prices as they are limited by what they see in the market; c) The MIC system in the garment industry is a ‘black box’ for consumers who are challenged to make an informed choice with a lack of access to information. As a result of this examination, the research identified emerging opportunities and interventions to assist consumers in making choices about their MIC garments in the future. Due to scope, the interventions identified in this paper initiate from the government, a key stakeholder, with a emphasis on possible policy interventions

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

BACKGROUND: Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. RESULTS: We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. CONCLUSIONS: The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0825-7) contains supplementary material, which is available to authorized users

Dynamics of nucleic acid mobility

Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species

Blockchain is not a silver bullet for agro-food supply chain sustainability: Insights from a coffee case study

Information sharing lies at the core of most governance interventions within agro-food commodity supply-chains, such as certification standards or direct trade relationships. However, actors have little information available to guide sustainable consumption decisions beyond simple labels. Blockchain technology can potentially alleviate the numerous sustainability problems related to agro-food commodity supply-chains by fostering traceability and transparency. Despite significant research on blockchain, there is limited understanding of the concrete barriers and benefits and potential applications of blockchain in real-world settings. Here, we present a case study of blockchain implementation in a coffee supply-chain. Our aim is to assess the potential of blockchain technology to promote sustainability in coffee supply chains through increased traceability and transparency and to identify barriers and opportunities for this. While our pilot implementation clearly illustrates certain benefits of blockchain, it also suggests that blockchain is no silver bullet for delivering agro-food supply chain sustainability. Knowledge on provenance and transparency of information on quality and sustainability can help trigger transformation of consumer behaviour, but the actual value lies in digitising the supply chain to increase efficiency and reduce costs, disputes, and fraud, while providing more insight end-to-end through product provenance and chain-of-custody information. We identify a need to understand and minimize supply chain barriers before we can reap the full benefits of digitalization and decentralization provided by blockchain technology

Modified Hawking temperatures of black holes in Lorentz violation theory

In this paper, the tunneling of scalar particles near the event horizons of Riemann space time, BTZ black hole and Schwarzschild-de Sitter black hole are investigated by applying Hamilton-Jacobi equation with Lorentz violation theory in curved space time. The modified Hamilton-Jacobi equation is derived from Klein-Gordon equation of scalar particles induced by Lorentz violation theory in curved space time. The Hawking temperatures of Riemann space time and the BTZ black hole are modified due to the effect of Lorentz violation theory. Moreover, the Bekenstein-Hawking entropy near the event horizon of Schwarzschild-de Sitter black hole is also modified due to Lorentz violation theory. It is observed that the modified values of Hawking temperatures and change in Bekenstein-Hawking entropy depend upon the ether-like vectors $u^\alpha$.Comment: Submitted in Int. J. Geom. Methods Mod. Phy

Biological relevance of CNV calling methods using familial relatedness including monozygotic twins

Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases and neurodevelopmental disorders. Common methods for CNV detection use SNP, CNV, or CGH arrays, where the signal intensities of consecutive probes are used to define the number of copies associated with a given genomic region. These practices pose a number of challenges that interfere with the ability of available methods to accurately call CNVs. It has, therefore, become necessary to develop experimental protocols to test the reliability of CNV calling methods from microarray data so that researchers can properly discriminate biologically relevant data from noise

Changes in DNA Sequence and Methylation Contribute to the Predisposition of Schizophrenia: Toward an Epigenetic Therapy

Schizophrenia has a heterogeneous and complex etiology that includes multiple candidate genes affected by a variety of mutational mechanisms including epigenetics, functional pathways, and environmental factors. This chapter mainly focuses on reviewing two sets of studies. The first one is whole‐genome next‐generation sequencing datasets involving monozygotic twins discordant for schizophrenia. The findings suggest that de novo sequence variations may underlie the discordance of monozygotic twins for schizophrenia. Second, whole‐genome DNA methylation study suggesting the role of DNA methylation in the mechanisms of actions of antipsychotic drugs in treating the disorder as well as the manifestation of side effects such as metabolic disorders. Furthermore, we are reporting original research results using next‐generation mitochondrial DNA sequence analysis of a pair of monozygotic twins discordant for schizophrenia as well as their mother. The chapter sheds light on the interplay between sequence variations and epigenetic signatures, including DNA methylation changes, in the etiology and pathophysiology of schizophrenia. Given the dynamic nature of methylation, it may be possible to develop a new treatment strategy for schizophrenia that is based on reversion of genomic methylation. This may involve environmental, dietary, and/or pharmaceutical approaches