Recent transcriptome data from yeast, worm, plants, and humans has shown that alternative polyadenylation (APA), a mechanism that enables expression of multiple 3′UTR isoforms for the same gene, is widespread in eukaryotic organisms. It is still poorly understood why metazoans require multiple 3′UTRs for the same gene, but accumulating evidence suggests that APA is largely regulated at a tissue-specific level. APA may direct combinatorial variation between cis-elements and microRNAs, perhaps to regulate gene expression in a tissue-specific manner. Apart from a few single gene anecdotes, this idea has not been systematically explored.
This dissertation research employs a systems biology approach to study the somatic tissue dynamics of APA and its impact on microRNA targeting networks in the small nematode C. elegans. In the first aim, tools were developed and applied to isolate and sequence mRNA from worm intestine and muscle tissues, which revealed pervasive tissue-specific APA correlated with microRNA regulation. The second aim provides genetic evidence that two worm genes use APA to escape repression by microRNAs in the body muscle. Finally, in aim three, mRNA from five additional somatic worm tissues was sequenced and their 3′ends mapped, allowing for an integrative study of APA and microRNA targeting dynamics in worms. Together, this work provides evidence that APA is a pervasive mechanism operating in somatic tissues of C. elegans with the potential to significantly rearrange their microRNA regulatory networks and precisely dose their gene expression.
materials for lithium-based batteries: silicon (Si) and metal lithium (Li). It will focus on
studying the mechanical behaviors of the two materials during charge and discharge and
understanding how these mechanical behaviors may affect their electrochemical
performance.
In the first part, amorphous Si anode will be studied. Despite many existing studies
on silicon (Si) anodes for lithium ion batteries (LIBs), many essential questions still exist
on compound formation, composition, and properties. Here it is shown that some
previously accepted findings do not truthfully reflect the actual lithiation mechanisms in
realistic battery configurations. Furthermore the correlation between structure and
mechanical properties in these materials has not been properly established. Here, a rigorous
and thorough study is performed to comprehensively understand the electrochemical
reaction mechanisms of amorphous-Si (a-Si) in a realistic LIB configuration. In-depth
microstructural characterization was performed and correlations were established between
Li-Si composition, volumetric expansion, and modulus/hardness. It is found that the
lithiation process of a-Si in a real battery setup is a single-phase reaction rather than the
accepted two-phase reaction obtained from in-situ TEM experiments. The findings in this
dissertation establish a reference to quantitatively explain many key metrics for lithiated a
Si as anodes in real LIBs, and can be used to rationally design a-Si based high-performance
LIBs guided by high-fidelity modeling and simulations.
In the second part, Li metal anode will be investigated. Problems related to dendrite
growth on lithium metal anodes such as capacity loss and short circuit present major
barriers to the next-generation high-energy-density batteries. The development of
successful mitigation strategies is impeded by the incomplete understanding of the Li
dendrite growth mechanisms. Here the enabling role of plating residual stress in dendrite
initiation through novel experiments of Li electrodeposition on soft substrates is confirmed,
and the observations is explained with a stress-driven dendrite growth model. Dendrite
growth is mitigated on such soft substrates through surface-wrinkling-induced stress
relaxation in deposited Li film. It is demonstrated that this new dendrite mitigation
mechanism can be utilized synergistically with other existing approaches in the form of
three-dimensional (3D) soft scaffolds for Li plating, which achieves superior coulombic
efficiency over conventional hard copper current collectors under large current density.
The pads were created using varying amounts of LM and matrix materials ranging from copper microspheres to diamond powder mixed into PDMS using a high-speed mixer. The material was then cast into molds and cured to create the pads. Once the pads were created, the difficulty came in quantifying their thermal properties. A stepped bar apparatus (SBA) following ASTM D5470 was created to measure the thermal resistance of the pads but it was determined that thermal conductivity was a more usable metric of the pads’ performance. This meant that the pad’s in-situ thickness was needed during testing, prompting the installation of a linear encoder to measure the thickness. The design and analysis of the necessary modification and proposed future design is further detailed in the following paper.
Strategies are needed to improve repopulation of decellularized lung scaffolds with stromal and functional epithelial cells. We demonstrate that decellularized mouse lungs recellularized in a dynamic low fluid shear suspension bioreactor, termed the rotating wall vessel (RWV), contained more cells with decreased apoptosis, increased proliferation and enhanced levels of total RNA compared to static recellularization conditions. These results were observed with two relevant mouse cell types: bone marrow-derived mesenchymal stromal (stem) cells (MSCs) and alveolar type II cells (C10). In addition, MSCs cultured in decellularized lungs under static but not bioreactor conditions formed multilayered aggregates. Gene expression and immunohistochemical analyses suggested differentiation of MSCs into collagen I-producing fibroblast-like cells in the bioreactor, indicating enhanced potential for remodeling of the decellularized scaffold matrix. In conclusion, dynamic suspension culture is promising for enhancing repopulation of decellularized lungs, and could contribute to remodeling the extracellular matrix of the scaffolds with subsequent effects on differentiation and functionality of inoculated cells.
Extra-intestinal pathogenic E. coli (ExPEC), including avian pathogenic E. coli (APEC), pose a considerable threat to both human and animal health, with illness causing substantial economic loss. APEC strain χ7122 (O78∶K80∶H9), containing three large plasmids [pChi7122-1 (IncFIB/FIIA-FIC), pChi7122-2 (IncFII), and pChi7122-3 (IncI2)]; and a small plasmid pChi7122-4 (ColE2-like), has been used for many years as a model strain to study the molecular mechanisms of ExPEC pathogenicity and zoonotic potential. We previously sequenced and characterized the plasmid pChi7122-1 and determined its importance in systemic APEC infection; however the roles of the other pChi7122 plasmids were still ambiguous. Herein we present the sequence of the remaining pChi7122 plasmids, confirming that pChi7122-2 and pChi7122-3 encode an ABC iron transport system (eitABCD) and a putative type IV fimbriae respectively, whereas pChi7122-4 is a cryptic plasmid. New features were also identified, including a gene cluster on pChi7122-2 that is not present in other E. coli strains but is found in Salmonella serovars and is predicted to encode the sugars catabolic pathways. In vitro evaluation of the APEC χ7122 derivative strains with the three large plasmids, either individually or in combinations, provided new insights into the role of plasmids in biofilm formation, bile and acid tolerance, and the interaction of E. coli strains with 3-D cultures of intestinal epithelial cells. In this study, we show that the nature and combinations of plasmids, as well as the background of the host strains, have an effect on these phenomena. Our data reveal new insights into the role of extra-chromosomal sequences in fitness and diversity of ExPEC in their phenotypes.