Evolution of C2H2-Zinc finger genes in mammalian genomes

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Catabolic flexibility of mammalian-associated lactobacilli

Metabolic flexibility may be generally defined as “the capacity for the organism to adapt fuel oxidation to fuel availability”. The metabolic diversification strategies used by individual bacteria vary greatly from the use of novel or acquired enzymes to the use of plasmid-localised genes and transporters. In this review, we describe the ability of lactobacilli to utilise a variety of carbon sources from their current or new environments in order to grow and survive. The genus Lactobacillus now includes more than 150 species, many with adaptive capabilities, broad metabolic capacity and species/strain variance. They are therefore, an informative example of a cell factory capable of adapting to new niches with differing nutritional landscapes. Indeed, lactobacilli naturally colonise and grow in a wide variety of environmental niches which include the roots and foliage of plants, silage, various fermented foods and beverages, the human vagina and the mammalian gastrointestinal tract (GIT; including the mouth, stomach, small intestine and large intestine). Here we primarily describe the metabolic flexibility of some lactobacilli isolated from the mammalian gastrointestinal tract, and we also describe some of the food-associated species with a proven ability to adapt to the GIT. As examples this review concentrates on the following species - Lb. plantarum, Lb. acidophilus, Lb. ruminis, Lb. salivarius, Lb. reuteri and Lb. sakei, to highlight the diversity and inter-relationships between the catabolic nature of species within the genus.

Evolution of C2H2-Zinc finger genes in mammalian genomes

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Effects of ocean acidification on embryo development: Does encapsulation matter?

As the concentration of CO2 in surface seawaters increases (ocean acidification, or OA) the saturation of calcium carbonate decreases, preventing marine organisms from creating shells and other calcified structures. These effects of elevated CO2 on calcification have been previously shown in free-spawning larvae, but are not as well-studied in larvae that spend their early life stages in encapsulation. The focus of our study was to determine what effects CO2 would have on a diversity of encapsulated embryos, and whether different types of encapsulating structures provided different levels of protection against OA. We found only a moderate larval response to low (600 ppm), medium (1050 ppm), and high (1500 ppm) CO2 concentrations across all species taken as a whole, but did observe that several species/ populations exhibited a decline in shell length with no corresponding decline in inorganic content. This suggests that while calcification was not significantly decreased by our OA conditions, perhaps the morphology of certain shells changed, becoming wider and shorter. Our hatch times, which increased with elevated CO2, confirmed that increased CO2 placed embryos under stress during development.

Factors influencing embryo morphology

info:eu-repo/semantics/published

Complementation of the embryo-lethal T-DNA insertion mutant of AUXIN-BINDING-PROTEIN 1 (ABP1) with abp1 point mutated versions reveals crosstalk of ABP1 and phytochromes

The function of the extracytoplasmic AUXIN-BINDING-PROTEIN1 (ABP1) is largely enigmatic. We complemented a homozygous T-DNA insertion null mutant of ABP1 in Arabidopsis thaliana Wassilewskia with three mutated and one wild-type (wt) ABP1 cDNA, all tagged C-terminally with a strepII-FLAG tag upstream the KDEL signal. Based on in silico modelling, the abp1 mutants were predicted to have altered geometries of the auxin binding pocket and calculated auxin binding energies lower than the wt. Phenotypes linked to auxin transport were compromised in these three complemented abp1 mutants. Red light effects, such as elongation of hypocotyls in constant red (R) and far-red (FR) light, in white light supplemented by FR light simulating shade, and inhibition of gravitropism by R or FR, were all compromised in the complemented lines. Using auxin-or light-induced expression of marker genes, we showed that auxininduced expression was delayed already after 10 min, and light-induced expression within 60 min, even though TIR1/AFB or phyB are thought to act as receptors relevant for gene expression regulation. The expression of marker genes in seedlings responding to both auxin and shade showed that for both stimuli regulation of marker gene expression was altered after 10-20 min in the wild type and phyB mutant. The rapidity of expression responses provides a framework for the mechanics of functional interaction of ABP1 and phyB to trigger interwoven signalling pathways.

Regulation of Glucose uptake in mammalian cells by phosphorylation networks

Objectives: Characterize the role of protein kinase WNK1 in the phosphorylation network regulating cellular glucose uptake

Fish nodavirus lytic cycle and semipermissive expression in mammalian and fish cell cultures

In this study, Dicentrarchus labrax encephalitis virus (DIEV), which causes sea bass encephalitis, was propagated in cell culture, thus allowing study of its lytic cycle, DIEV infection of mammalian and fish cells induced different patterns of expression of capsid proteins, which were assembled as virus-like particles, accumulating in the cytoplasm either as diffuse masses or in vesicles, as shown by electron microscopy, These particles correspond to virions, as shown by their ability to induce Secondary infection, Fish cells proved to be more permissive for DIEV than mammalian cells, although virus yield remained low, RNA analysis of infected sea bass cells revealed DIEV RNA3, in addition to genomic RNA1 and RNA2, and the presence of the RNA;! minus strand, thus demonstrating the replication of the DIEV genome, In addition, DIEV RNA-dependent RNA polymerase was associated with mature virions even after purification by a CsCl gradient, but it was dissociated when capsids were destabilized, In addition to providing more information about the relatedness of DIEV to the members of the family Nodaviridae, this study shows that fish nodaviruses may not be able to infect as wide a variety of cells as insect nodaviruses can.

Investigations of the Toxic Effect of Silver Nanoparticles on Mammalian Cell Lines

Silver nanoparticles are widely used for many applications. In this study silver nanoparticles have been tested for their toxic effect on fibroblasts (NIH-3T3), on a human lung adenocarcinoma epithelial cell line (A-549), on PC-12-cells, a rat adrenal pheochromocytoma cell line, and on HEP-G2-cells, a human hepatocellular carcinoma cell line. The viability of the cells cultivated with different concentrations of silver was determined by the MTT assay, a photometric method to determine cell metabolism. Dose-response curves were extrapolated and IC50, total lethal concentration (TLC), and no observable adverse effect concentration (NOAEC) values were calculated for each cell line. As another approach, ECIS (electric-cell-substrate-impedance-sensing) an automated method to monitor cellular behavior in real-time was applied to observe cells cultivated with silver nanoparticles. To identify the type of cell death the membrane integrity was analyzed by measurements of the lactate dehydrogenase releases and by determination of the caspase 3/7 activity. To ensure that the cytotoxic effect of silver nanoparticles is not traced back to the presence of Ag+ ions in the suspension, an Ag+ salt (AgNO3) has been examined at the same concentration of Ag+ present in the silver nanoparticle suspension that is assuming that the Ag particles are completely available as Ag+ ions.

Improving protein yield from mammalian cells by manipulation of stress response pathways

Monoclonal antibodies are a class of therapeutic that is an expanding area of the lucrative biopharmaceutical industry. These complex proteins are predominantly produced from large cultures of mammalian cells; the industry standard cell line being Chinese Hamster Ovary (CHO) cells. A number of optimisation strategies have led to antibody titres from CHO cells increasing by a hundred-fold, and it has been proposed that a further bottleneck in biosynthesis is in protein folding and assembly within the secretory pathway. To alleviate this bottleneck, a CHO-derived host cell line was generated by researchers at the pharmaceutical company UCB that stably overexpressed two critical genes: XBP1, a transcription factor capable of expanding the endoplasmic reticulum and upregulating protein chaperones; and Ero1α, an oxidase that replenishes the machinery of disulphide bond formation. This host cell line, named CHO-S XE, was confirmed to have a high yield of secreted antibody. The work presented in this thesis further characterises CHO-S XE, with the aim of using the information gained to lead the generation of novel host cell lines with more optimal characteristics than CHO-S XE. In addition to antibodies, it was found that CHO-S XE had improved production of two other secreted proteins: one with a simple tertiary structure and one complex multi-domain protein; and higher levels of a number of endogenous protein chaperones. As a more controlled system of gene expression to unravel the specific roles of XBP1 and Ero1α in the secretory properties of CHO-S XE, CHO cells with inducible overexpression of XBP1, Ero1α, or a third gene involved in the Unfolded Protein Response, GADD34, were generated. From these cell lines, it was shown that more antibody was secreted by cells with induced overexpression of XBP1; however, Ero1α and GADD34 overexpression did not improve antibody yield. Further investigation revealed that endogenous XBP1 splicing was downregulated in the presence of an abundance of the active form of XBP1. This result indicated a novel aspect of the regulation of the activity of IRE1, the stress-induced endoribonuclease responsible for XBP1 splicing. Overall, the work described in this thesis confirms that the overexpression of XBP1 has an enhancing effect on the secretory properties of CHO cells; information which could contribute to the development of host cells with a greater capacity for antibody production.

Insights into Neural Crest Evolution

Neural crest cells are unique to vertebrates and essential to the development and evolution of the craniofacial skeleton. Using a combination of DiI cell lineage tracing, transcriptomics, and analysis of key transcription factors of the Sox Family, I examined neural crest development in the sea lamprey, Petromyzon marinus, as the most basal extant vertebrate from which it is possible to get embryos. The results have uncovered distinct cranial and trunk neural crest subpopulations along the anterior-posterior axis of the lamprey embryo, with a clear separation between the two. However, no evidence of the presence of an intermediate vagal neural crest population was uncovered. Comparing cranial neural crest genes between lamprey and chick, either by examining individual candidate genes or whole genome transcriptome analysis, reveals significant changes in the cranial neural crest gene regulatory network of lamprey compared with chick. In particular, the lamprey cranial neural crest is "missing" several gnathostome cranial crest genes. We speculate that these may underlie the evolutionary divergence of craniofacial development between jawed and jawless vertebrates. Despite the absence of vagal neural crest, DiI-labeling shows that trunk neural crest-derived cells, likely homologous to mammalian Schwann cell precursors, contribute to the lamprey enteric nervous system, potentially representing the most primitive form of neural crest cells contribution to the ENS. Finally, I characterized key members of the Sox Family (Sox B-F) due to their importance in neural crest specification in other species. In comparative studies of the SoxC genes (Sox4, Sox11, and Sox12) in both lamprey and Xenopus, I found similar expression patterns and a novel key role in early neural crest specification, suggesting a conserved role of the SoxC genes amongst vertebrates. Taken together, this work represents important progress in characterizing the early evolution of the neural crest in vertebrates and its role in the transition from jawless to jawed vertebrates.

Studies to prevent degradation of recombinant fc-fusion protein expressed in mammalian cell line and protein characterization

Clipping of recombinant proteins is a major issue in animal cell cultures. A recombinant Fc-fusion protein, VEGFR1(D1-D3)-Fc expressed in CHOK1SV GS-KO cells was observed to be undergoing clippings in lab scale cultures. Partial cleaving of expressed protein initiated early on in cell culture and was observed to increase over time in culture and also on storage. In this study, a few parameters were explored in a bid to inhibit clipping in the fusion protein The effects of culture temperature, duration of culture, the addition of an anti-clumping agent, ferric citrate and use of protease inhibitor cocktail on inhibition of proteolysis of the Fc fusion were studied. Lowering of culture temperature from 37 to 30 °C alone appears to be the best solution for reducing protein degradation from the quality, cost and regulatory points of view. The obtained Fc protein was characterized and found to be in its stable folded state, exhibiting a high affinity for its ligand and also biological and functional activities.

Identification of differentially expressed genes in the heart precursor cells of the chick embryo

Genetic evidence has implicated several genes as being critical for heart development. However, the inducers of these genes as well as their targets and pathways they are involved with, remain largely unknown. Previous studies in the avian embryo showed that at HH4 Cerberus (cCer) transcripts are detected in the anterior endomesoderm including the heart precursor cells and later in the left lateral plate mesoderm. We have identified a promoter element of chick cCer able to drive EGFP expression in a population of cells that consistently exit from the anterior primitive streak region, from as early as stage HH3+, and that later will populate the heart. Using this promoter element as a tool allowed us to identify novel genes previously not known to potentially play a role in heart development. In order to identify and study genes expressed and involved in the correct development and differentiation of the vertebrate heart precursor cell (HPC) lineages, a differential screening using Affymetrix GeneChip system technologies was performed. Remarkably, this screening led to the identification of more than 700 transcripts differentially expressed in the heart forming regions (HFR). Bioinformatic tools allowed us to filter the large amount of data generated from this approach and to select a few transcripts for in vivo validation. Whole-mount in situ hybridization and sectioning of selected genes showed heart and vascular expression patterns for these transcripts during early chick development. We have developed an effective strategy to specifically identify genes that are differentially expressed in the HPC lineages. Within this set we have identified several genes that are expressed in the heart, blood and vascular lineages, which are likely to play a role in their development. These genes are potential candidates for future functional studies on early embryonic patterning.

Milk: milk of monotremes and marsupials

Lactation has evolved from an ancient reproductive strategy which appears to have been present long before the evolution of extantmammals. The ability to lactate is a feature only found among mammals and involves a facet of maternal care where mothers secretea nutrient-rich milk which is delivered to the young by the mammary gland. Evolutionary studies indicate that lactation was establishedprior to divergence of extant mammalian lineages. It also seems that lactation evolved long before gestation in utero. Secretionsof ancestral mammary glands may have had antimicrobial properties that protected either eggs or hatchlings and organiccomponents that supplemented offspring nutrition. Over the course of evolution, lactation became a highly efficient, effectiveand adaptable means of providing maternal care for neonates. The evolution of a placenta in eutherian mammals resulted inmore extensive intrauterine development of an embryo and the ability to lactate after birth became a critical part of the reproductivestrategy of mammalian species. Following development of highly nutritious milks, evolution produced diversity in milk compositionand function, quantity of milk output, length of lactation, length of intervals between nursing and contributions of lactation tooffspring nutrition.