Dissertation Defense Announcements

The invention of advanced Ni-containing concentrated solid solution alloys has significantly broadened the compositional space of alloy design. Unlike conventional alloys that typically consist of a principal solvent element with minor additions of various solute atoms, concentrated solid solution alloys involve multiple elements in equal or near-equal compositions. These concentrated solid solution alloys have exhibited remarkable properties such as exceptional toughness and superior radiation resistance. The exceptional performance of these concentrated solid solution alloys is generally attributed to specific intrinsic properties of concentrated solid solution alloys such as high entropy effect, severe lattice distortion and short ordering effect. However, being relatively new emerging materials, the theoretical understanding and experimental exploration of these alloys are still ongoing and not comprehensively understood.

This dissertation work will provide a systematic investigation on surface properties including mechanical properties and radiation damage of Ni-based concentrated solid solution alloys by using ex-situ and in-situ indentation techniques. The study explores the surface properties of a batch of Ni-containing concentrated solid solution alloys with addition of different 3d transition elements including binary NiCo, NiFe, Ni80Cr20, Ni80Mn20 and quaternary NiCoFeCr. First, initial investigations use ex-situ nanoindentation to obtain mechanical properties of five alloys including hardness, elastic modulus and strain rate sensitivity. A complete methodology is developed to acquire accurate property information directly from nanoindentation in a high throughput manner, which considers the indentation size effect and pile-up effect. Furthermore, the strengthening in Ni-concentrated solid solution alloys is attributed to being driven by solid solution strengthening induced by mismatch in atomic size. Notably, the intrinsic properties of alloying elements play a more critical role in strengthening than the number of alloying elements. Second, based on previous work, nanoindentation is further employed to evaluate the early-stage irradiation induced hardening in NiCo, NiFe and NiCoFeCr. It proposes using nanoindentation to detect early-stage irradiation-induced defects and hypothesizes that interactions between these defects and dislocations carried by deformation during indentation can quantify irradiation-induced defects. This approach successfully quantifies irradiation-induced hardening in NiCo, NiFe, and NiCoFeCr. Quantitative analysis reveals that irradiation-induced defects harden NiFe and NiCoFeCr, but no significant hardening is observed in NiCo. Additionally, irradiation-induced hardening is associated with the evolution of geometrically necessary dislocations and is interpreted by changes in the plastic zone during indentation. Finally, in-situ flat-punch indentation provides real-time observations of deformation behaviors, aiming to derive accurate stress-strain curves. A new protocol addresses thermal drift effects and contact issues, often neglected in measurements.

This comprehensive study on Ni-based concentrated solid solution alloys enhances understanding of their mechanical properties and irradiation resistance by using ex-situ and in-situ nano-mechanical techniques. Methodologies are developed for nanoindentations to acquire meaningful property information directly from surface in a high throughput manner. This systematic work offers valuable insights into the strengthening mechanisms and irradiation hardening mechanisms of Ni-based concentrated solid solution alloys. The robust experimental evidence supports that the exceptional properties of concentrated solid solution alloys are not solely determined by the number of elements but also determined by the intrinsic performance of alloying elements. These results provide new insights for alloying design strategy of concentrated solid solution alloys.

Recent advancements in single-cell RNA sequencing have revolutionized our understanding of gene expression regulation under various biological contexts, providing higher resolution and system-level insights compared to traditional bulk RNA sequencing methods. In this dissertation, we utilize single cell RNA-seq (scRNA-seq) along with various statistical tools to unveil the stress response and developmental transcriptomic landscape of four model organisms. First, we sequenced yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length single-cell RNA-Seq method. We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions as well as putative regulatory relationships between transcription factors and target genes.
Our results show that a full-length single-cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods. Second, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene, the diplotene, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the oocyte germline and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we attempt to delineate transcripts that may serve functions in the interaction between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon. Lastly, we profiled mature oocytes and 1-cell zygotes of mice and rats to uncover elusive transcriptomic dynamics in the maternal to zygote transition. We confirm the existence of early gene expression in the mouse zygotic while revealing a similar chain of events occurring in the rat zygote. We observe an increase in nascent transcription in both species. Moreover, we find subtle but pervasive signals of differential splicing of genes related to key early zygotic activities occurring in both species. Meanwhile, we find distinct profiles of alternative polyadenylation between zygotes and oocytes in both species, specifically in genes related to major processes within the zygote. Finally, although a more dynamic transcriptomic landscape exists in the mice zygote, the rat zygote also displays similar transcriptomic features, suggesting that minor zygotic activation in rat occurs earlier than originally thought.

Cis-regulatory modules (CRMs) can function as enhancers and/or silencers to promote and repress, respectively, the transcription of their target genes in a spatiotemporal manner, thereby playing critical roles in virtually all biological processes. However, despite recent progresses, the understanding of CRMs’ precise locations, landscape and architecture in terms of transcription factor (TF) binding sites (TFBSs) in the genomes as well as their functional types (enhancer or silencer), states (active or inactive) and target genes in various cell/tissue types of organisms is still limited.
We have recently predicted comprehensive maps of CRMs and constituent TFBSs in the human and mouse genomes, enabling us to investigate the organization and architecture of the CRMs in both genomes. We reveal common rules of the organization and architecture of CRMs in the genomes. We conclude that the rules governing the organization and architecture of CRMs in the human and mouse genomes are highly conserved.
Moreover, until recently research has long been focused on enhancers, and much less is known about silencers. To fill the gap, we develop two logistic regression models for predicting the functional states of our previously predicted 1.2M CRMs as enhancers and silencers in any cell/tissue types using five epigenetic marks data. Applying the models to 56 human cell/tissue types with the required data available, we predict that 793,140 of the 1.2M CRMs are active as enhancers or/and silencers in at least one of these cell/tissue types, of which 14.8% and 28.6% of them only function as enhancers (enhancer-predominant) and silencers (silencer-predominant), respectively, while 10.6% functioned both as enhancers and silencers (dual functional). Thus, both dual functional CRMs and silencers might be more prevalent than previously assumed. Most dual functional CRMs function either as enhancers or silencers in different cell/tissue types (Type I), while some have dual functions regulating different genes in the same cell/tissue types (Type II). Different types of CRMs display different lengths and TFBS densities, reflecting the complexity of their functions.
Furthermore, identifying their target genes of predicted or experimentally validated CRMs remains a challenge due to the low quality of the predicted CRMs and the fact that CRMs often do not regulate their closest genes. To fill this gap, we developed a method — correlation and physical proximity (CAPP) to not only predict the CRMs’ target genes but also their functional types using only chromatin accessibility (CA) and RNA-seq data in a panel of cell/tissue types plus Hi-C data in a few cell types. Applying CAPP to a panel of 107 human cell/tissue types with CA and RNA-seq data available, we predict target genes for 20% of the 1.2M CRMs, of which 4.5% are predicted as both enhancers and silencers (dual functional CRMs), 95.2% as exclusive enhancers and 0.3% as exclusive silencers. Different types of CRMs as well as their target genes and regulatory links exhibit distinct properties. CAPP predicts more enhancer-gene and silencer-gene links with higher accuracy than state-of-the-art methods.

Quality STEM education in secondary and post-secondary schools is vital to the advancement of knowledge and technology for the United States. Quality STEM education is found where evidence-based teaching practices are implemented in the classroom. This dissertation focuses on two programs and their impact on their participants with the goals of providing quality STEM education. The STEM Academy is a faculty learning community with goals to support faculty members in implementing new evidence-based teaching practices at UNC Charlotte. The second program is Summer Ventures in Science and Mathematics (SVSM) Nanoscale Science course for high school students in North Carolina. The data for investigating the experiences of the participants in the STEM Academy was collected through semi-structured individual interviews as well as focus groups. The transcripts of these were thematically coded to find consensus on the benefits of the STEM Academy and the barriers to implementing new evidence-based teaching practices. The data for investigating the impact of the SVSM Nanoscale Science course and its revisions was collected through the grading of student final papers using a rubric specific to the Big Ideas in Nanoscale Science (BINS) and the experimental design process. Also, students were given the Student Attitudes towards STEM (S-STEM) survey at the beginning and end of the course. The results of the STEM Academy interviews and focus groups yielded 11 themes; six describing benefits and five describing barriers identified by the participants. These results can help to reform and grow the STEM Academy for future participants to meet its goals of supporting faculty members in implementing evidence-based teaching practices in STEM classrooms at UNC Charlotte. The results of grading the student final papers from the SVSM Nanoscale Science course showed significant improvements to writing research questions, designing experiments, and writing conclusions about their findings for students in the second cohort compared to the first cohort. These findings indicate the revisions to the course had a positive impact on student outcomes. The S-STEM survey results show the students maintained or slightly improved their positive attitudes towards STEM after participating in the SVSM course.
Key words: Nanoscale Science, Evidence-Based Teaching Practices, Faculty Learning Community