Protein molecules and their interactions via protein-protein interactions (PPIs) are at the core of cellular functions. While such global PPI networks have been useful for analyzing gene function and effects of genetic variants, they do not resolve tissue and cell-typespecific interactions. Here we leverage recent advances in single-cell RNA sequencing (scRNA-seq) to reconstruct cell-type-specific PPI networks across different tissues to enable a context-sensitive analysis of immune cells’ gene-protein pathways. Targeting B cells, T cells, and macrophage cells as a proof-of-principle, we used scRNA-seq data across different tissues from the Tabula Muris mouse consortium. We mapped the protein-coding DEGs to a protein-protein interaction network database (STRING v.11). Topological and global similarity analysis of the networks revealed distinct properties between tissues highlighting tissue-specific behaviors for each cell type. For example, we found that degree and clustering coefficients distributions were tissue-specific. Different cell types and tissues displayed specific characteristics, and in particular, the splenic PPI networks were different compared to other analyzed tissues for all the immune cell types examined. For example, the pairwise comparison of the Jaccard index for node similarity and the mantel test correlation analysis showed that the spleen’ node and PPI networks are more different than any other tissues for each cell type examined. The physiological and anatomical properties that distinguish the spleen from other examined tissues might explain why the splenic PPI networks tend to be less similar compared to other tissues. The cell-type-specific network analyses using the different distance measures between the adjacency matrices on the hub nodes such as Euclidean, Manhattan, Jaccard, and Hamming distances showed a macrophage-specific behavior not observed in B cells and T cells, confirming their lineage differences. Finally, we explored the rewiring of selected hub nodes and transcription factors in the PPI networks along with their biological enrichments to validate our observations. The suggested biological validity of our results confirms the relevance of data-driven reconstruction of these context-sensitive networks using more advanced network inference algorithms. In conclusion, scRNA-seq enables the reconstruction of global unspecific PPI networks into cell and tissue-specific networks, thereby providing an increased resolution of the biological context.

DNA methylation patterns are sex and tissue specific in many species, yet many studies useblood samples, due to its accessibility, to establish links between the DNA methylation anddifferent phenotypes. This raises the question of whether DNA methylation in blood samplesreflect the DNA methylation pattern in other tissues that are more relevant to the phenotypebeing studied. In this research, samples were collected from the brain, blood, liver and gonadof 16 house sparrow (Passer domesticus), half of them were female, while the others weremale. Reduced representation bisulfite sequencing (RRBS) was performed to get themethylation profile in each sample. The result showed a tissue specific methylation profile inthe four investigated tissues, a strong and positive correlation between 0.74 – 0.85 was foundbetween tissues, in which a weaker correlation was found between blood and other tissue. Indifferential methylation analysis, most of the differently methylated sites between sexes werefound in gonads, while the fewest was found in blood, and Z chromosome wasoverrepresented place in all four tissues where the majority of the differently methylated sitesbetween sexes were found. Comparison with the house sparrow genome annotation foundabout half of the differentially methylated sites between sexes were within genes and about 20 % of them were in the exon or coding region of a gene. The result suggested that bloodcould be useful in reflecting the general DNA methylation level in other tissues, but it was nota reliable bioindicator for further detailed study in DNA methylation pattern or in geneontology enrichment pathway analysis.

Indiana University-Purdue University Indianapolis (IUPUI) / Imaging genetics is an emerging research field in neurodegenerative diseases. It studies the influence of genetic variants on brain structure and function. Genome-wide association studies (GWAS) of brain imaging has identified a few independent risk loci for individual imaging quantitative trait (iQT), which however display only modest effect size and explain limited heritability. This thesis focuses on mining high-level imaging genetic associations and their applications on neurodegenerative diseases. This thesis first presents a novel network-based GWAS framework for identifying functional modules, by employing a two-step strategy in a top-down manner. It first integrates tissue-specific network with GWAS of corresponding phenotype in regression models in addition to classification, to re-prioritize genome-wide associations. Then it detects densely connected and disease-relevant modules based on interactions among top reprioritizations. The discovered modules hold both phenotypical specificity and densely interaction. We applied it to an amygdala imaging genetics analysis in the study of Alzheimer's disease (AD). The proposed framework effectively detects densely interacted modules; and the reprioritizations achieve highest concordance with AD genes. We then present an extension of the above framework, named GWAS top-neighbor-based (tnGWAS); and compare it with previous approaches. This tnGWAS extracts densely connected modules from top GWAS findings, based on the hypothesis that relevant modules consist of top GWAS findings and their close neighbors. It is applied to a hippocampus imaging genetics analysis in AD research, and yields the densest interactions among top candidate genes. Experimental results demonstrate that precise context does help explore collective effects of genes with functional interactions specific to the studied phenotype. In the second part, a novel imaging genetic enrichment analysis (IGEA) paradigm is proposed for discovering complex associations among genetic modules and brain circuits. In addition to genetic modules, brain regions of interest also grouped to play role. We expand the scope of one-dimensional enrichment analysis into imaging genetics. This framework jointly considers meaningful gene sets (GS) and brain circuits (BC), and examines whether given GS-BC module is enriched in gene-iQT findings. We conduct the proof-of-concept study and demonstrate its performance by applying to a brain-wide imaging genetics study of AD.

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A doença Huanglongbing (HLB) associada a bactéria Candidatus Liberibacter spp., que coloniza os vasos do floema, é considerada uma das mais graves doenças de citros. Uma importante estratégia para o controle desta doença consiste na produção de plantas transgênicas, expressando genes que codificam peptídeos antibacterianos especificamente no local de colonização do patógeno. O objetivo deste trabalho foi obter plantas transgênicas de laranja doce, expressando o gene que codifica o peptídeo antibacteriano atacina A (attA) dirigido por promotores específicos para a expressão gênica no floema. O trabalho foi iniciado com a elaboração de construções gênicas contendo o gene attA (associado ou não ao peptídeo sinal), sob o controle dos promotores AtSuc2 (transportador de sacarose), AtPP2 (proteína de floema 2), clonados de Arabidopsis thaliana, ou CsPP2 (proteína de floema 2), clonado de Citrus sinensis. Os experimentos de transformação genética foram realizados com C. sinensis cv. \'Hamlin\', \'Valência\', \'Pêra\' e \'Natal\', via Agrobacterium tumefaciens, utilizando-se segmento de epicótilo como explante. A identificação de plantas transgênicas foi realizada por meio da análise de PCR. Plantas PCR+ foram aclimatizadas e transferidas para casa-de-vegetação específica para o cultivo de plantas transgênicas. Análises de Southern e Northern blot foram realizadas em plantas aclimatizadas, confirmando-se a integração e transcrição do gene attA, respectivamente. A expressão do gene attA também foi confirmada pela análise de RT-qPCR. Plantas de laranja \'Hamlin\' contendo o gene attA (associado ou não ao peptídeo sinal), sob o controle dos promotores AtSuc2 ou AtPP2 foram propagadas por enxertia, para futura avaliação da resistência a Candidatus Liberibacter asiaticus / Huanglongbing (HLB) associated to Candidatus Liberibacter spp., which colonizes the phloem, is considered one of the most serious diseases of citrus. One important strategy to control this disease consists of producing transgenic plants expressing, in the bacteria colonization tissue, genes encoding antibacterial peptides. The objective of this work was to produce transgenic sweet orange plants expressing genes encoding the antibacterial peptide attacin A (attA) driven by phoem-specific promoters. The work started with the development of the gene constructs, containing the attacin A gene (with or without signal peptide) controlled by either sucrose transporter gene (AtSuc2) or phloem protein 2 gene promoters (AtPP2) from Arabidopsis thaliana, or phloem protein 2 gene promotor (CsPP2) from Citrus sinensis. The genetic transformation of C. sinensis \'Hamlin\', \'Valencia\', \'Pera\' and \'Natal\' cultivars was done via Agrobacterium tumefaciens. Epicotyls segments collected from in vitro germinated seedlings were used as explants. Transgenic plants were identified by PCR analyses. PCR positive plants were acclimatized and transferred to specific greenhouse. Integration and transcription of the attA gene was confirmed in acclimatized transgenic plants by Southern and Northern blot analysis, respectively. The attA gene expression was validated by RT-qPCR analysis. \'Hamlin\' transgenic cultivars containing the AtSuc2 or AtPP2 promoters controlling the expression of attA (with or without signal peptide) were propagated by grafting, for future evaluation of Candidatus Liberibacter asiaticus resistance

In vivo, adipose tissue demonstrates only a limited capacity for self-repair, and the long-term treatment of subcutaneous defects remains an unresolved clinical problem. With the goal of regenerating healthy tissues, many tissue-engineering strategies have pointed to the potential of implementing three-dimensional (3-D), cell-seeded scaffolds for soft tissue augmentation and wound healing. In particular, microcarriers have shown promise as both cell expansion substrates and injectable cell-delivery vehicles for these applications. However, limited research has investigated the engineering of tissue-specific microcarriers, designed to closely mimic the native extracellular matrix (ECM) composition. In this work, methods were developed to fabricate microcarriers from decellularized adipose tissue (DAT) via non-cytotoxic protocols. Characterization by microscopy confirmed the efficacy of the fabrication protocols in producing stable beads, as well as the production of a microporous surface topography. The mean bead diameter was 934 ± 51 μm, while the porosity was measured to be 29 ± 4 % using liquid displacement. Stability and swelling behavior over 4 weeks indicated that the DAT-based microcarriers were effectively stabilized with the non-cytotoxic photochemical crosslinking agent rose bengal, with only low levels of protein release measured within a simulated physiological environment. In cell-based studies, the DAT-based microcarriers successfully supported the proliferation and adipogenic differentiation of human adipose-derived stem cells (hASCs) in a dynamic spinner flask system, with a more favorable response observed in terms of adhesion, proliferation, and adipogenesis on the DAT-based microcarriers relative to gelatin control beads. More specifically, dynamically-cultured hASCs on DAT-based microcarriers demonstrated greater lipid loading, as well as higher glycerol-3-phosphate dehydrogenase (GPDH) activity, a key enzyme involved in triacylglycerol biosynthesis, at 7 days and 14 days in culture in an inductive medium. Overall, the results indicated that the DAT-based microcarriers provided a uniquely supportive environment for adipogenesis. Established microcarrier sterility and injectability further support the broad potential of these tissue-specific microcarriers as a novel, adipogenic, clinically-translatable strategy for soft tissue engineering. / Thesis (Master, Chemical Engineering) -- Queen's University, 2010-12-01 14:28:14.628

A doença Huanglongbing (HLB) associada a bactéria Candidatus Liberibacter spp., que coloniza os vasos do floema, é considerada uma das mais graves doenças de citros. Uma importante estratégia para o controle desta doença consiste na produção de plantas transgênicas, expressando genes que codificam peptídeos antibacterianos especificamente no local de colonização do patógeno. O objetivo deste trabalho foi obter plantas transgênicas de laranja doce, expressando o gene que codifica o peptídeo antibacteriano atacina A (attA) dirigido por promotores específicos para a expressão gênica no floema. O trabalho foi iniciado com a elaboração de construções gênicas contendo o gene attA (associado ou não ao peptídeo sinal), sob o controle dos promotores AtSuc2 (transportador de sacarose), AtPP2 (proteína de floema 2), clonados de Arabidopsis thaliana, ou CsPP2 (proteína de floema 2), clonado de Citrus sinensis. Os experimentos de transformação genética foram realizados com C. sinensis cv. \'Hamlin\', \'Valência\', \'Pêra\' e \'Natal\', via Agrobacterium tumefaciens, utilizando-se segmento de epicótilo como explante. A identificação de plantas transgênicas foi realizada por meio da análise de PCR. Plantas PCR+ foram aclimatizadas e transferidas para casa-de-vegetação específica para o cultivo de plantas transgênicas. Análises de Southern e Northern blot foram realizadas em plantas aclimatizadas, confirmando-se a integração e transcrição do gene attA, respectivamente. A expressão do gene attA também foi confirmada pela análise de RT-qPCR. Plantas de laranja \'Hamlin\' contendo o gene attA (associado ou não ao peptídeo sinal), sob o controle dos promotores AtSuc2 ou AtPP2 foram propagadas por enxertia, para futura avaliação da resistência a Candidatus Liberibacter asiaticus / Huanglongbing (HLB) associated to Candidatus Liberibacter spp., which colonizes the phloem, is considered one of the most serious diseases of citrus. One important strategy to control this disease consists of producing transgenic plants expressing, in the bacteria colonization tissue, genes encoding antibacterial peptides. The objective of this work was to produce transgenic sweet orange plants expressing genes encoding the antibacterial peptide attacin A (attA) driven by phoem-specific promoters. The work started with the development of the gene constructs, containing the attacin A gene (with or without signal peptide) controlled by either sucrose transporter gene (AtSuc2) or phloem protein 2 gene promoters (AtPP2) from Arabidopsis thaliana, or phloem protein 2 gene promotor (CsPP2) from Citrus sinensis. The genetic transformation of C. sinensis \'Hamlin\', \'Valencia\', \'Pera\' and \'Natal\' cultivars was done via Agrobacterium tumefaciens. Epicotyls segments collected from in vitro germinated seedlings were used as explants. Transgenic plants were identified by PCR analyses. PCR positive plants were acclimatized and transferred to specific greenhouse. Integration and transcription of the attA gene was confirmed in acclimatized transgenic plants by Southern and Northern blot analysis, respectively. The attA gene expression was validated by RT-qPCR analysis. \'Hamlin\' transgenic cultivars containing the AtSuc2 or AtPP2 promoters controlling the expression of attA (with or without signal peptide) were propagated by grafting, for future evaluation of Candidatus Liberibacter asiaticus resistance

<p>  </p> <p>Zebrafish (<em>Danio rerio</em>) is a well-established model to study neutrophil biology. However, a lack of standard tissue-specific knockdown or knockout technique in the zebrafish field has limited the power of this model organism when studying developmental essential genes, such as those related to mitochondrial function. We have developed a robust and flexible neutrophil-restricted knockout in zebrafish based on CRISPR/Cas9 system, with which we gained insights into the role of Rac2 in regulating the actin cytoskeleton and the subcellular location of Rac activation in zebrafish neutrophils.</p> <p>Previous study in our lab using another neutrophil-specific knockout system addressed multiple mitochondrial proteins regulate neutrophil motility in zebrafish. Interestingly, we observed <em>Mfn2</em>-deficient neutrophils trapped in the vasculature in zebrafish embryos. Here we further characterized the function of MFN2 in regulating cell migration with neutrophil-like HL-60 cells and mice embryonic fibroblasts (MEFs). We found significant changes in actin organization in both <em>MFN2</em>-deficient neutrophil-like cells and MEFs and mechanistically, disrupted mitochondria-ER interaction, increased intracellular Ca2+ levels. We also investigated the cytoskeleton proteins and observed hyperactivation of RhoA and Myosin light chain kinase, along with accumulation of phosphorylated myosin light chain at the cell boundary in <em>MFN2</em>-deficient MEFs. These altered MFN2-Ca2+-RhoA/MLCK-myosin signaling finally affects the peripheral actin bundle architecture and forms the “Peripheral Actin Myosin Belt (PAMB)” structure. The formation of PAMB hampered cell adhesive migration in <em>Mfn2</em>-null MEFs. </p> <p>Altogether, our research gained new insights into the essential role of MFN2 in cytoskeleton regulation and the underlying molecular mechanisms, which may provide a new direction to understand the relevance of this gene in immune cell dysfunction and other MFN2-associated diseases.</p>

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