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PART I The basic helix-loop-helix (bHLH) family of transcription factors are involved in a variety of developmental processes. MyoR is the mouse homologue of the human transcription factor ABF-1 . MyoR is classified as a class II basic-helix-loop-helix transcription factor. In order to better understand the relationship between MyoR and muscle cell differentiation, we analyzed the temporal expression at both the mRNA and protein level. Unlike previous studies, we have utilized reverse transcriptase quantitative PCR to analyze mRNA expression. This allows quantitative analysis of MyoR mRNA levels during muscle cell differentiation. We have also analyzed MyoR expression at the protein level. Our studies suggest that the temporal expression of MyoR at the mRNA level is similar to the expression profile seen at the protein level. To ascertain differences in the MyoR DNA-binding activity during myogenesis we performed EMSA. Results suggest that changes in MyoR expression fail to account for differences in the DNAbinding complexes to an E-box site. Part II Members of the basic helix-loop-helix (bHLH) family are required for a number of different developmental pathways, including lymphopoiesis, myogenesis, neurogenesis and sex determination. Screening a eDNA library prepared from silk-producing glands of the black widow spider, we have identified a new bHLH transcription factor named BW6. Within the bHLH region, BW6 shows considerable conservation with other HLH proteins, including Drosophila melanogaster achaete and scute, as well as three HLH proteins identified by gene prediction programs. The expression pattern of bw6 is restricted to a subset of silk producing glands, which includes the tubuliform and major ampullate glands. BW6 is capable of binding an E-box element as a heterodimer with E2A, but was unable to bind this motif as a homodimer. BW6 is also capable of inhibiting the transactivation of rE47 in mammalian cells. BW6 represents the first example of a silk-gland-restricted bHLH protein, and its expression pattern suggests that BW6 may play a role in regulating differentiation of cells in the spider that control silk gland formation or egg case silk gene expression.

The glenohumeral (GH) joint is the most mobile joint in the human body, but its mobility inherently increases the risk of instability. The humeral head sits in a shallow glenoid in the scapula like a golf ball sitting on a tee. The stability in this joint is provided by the rotator cuff muscles and tendons that actively pull the humerus back into the socket to prevent dislocation, especially during overhead motions. However, the rotator cuff is prone to tears, resulting in pain, loss of mobility, and recreational limitations. Surgical reattachment of the tendon to the bone is challenging due to the mechanical disparity between the two tissues, resulting in stress concentrations and a high risk of retear. Notably, the specialized tissue at the tendon-to-bone attachment, which facilitates stress transfer between tendon and bone in healthy joints, does not regenerate after surgical reattachment and healing, making tendon-to-bone repairs prone to re-tears. A comprehensive understanding of GH joint biomechanics is essential for developing early interventions to prevent rotator cuff injuries. Furthermore, improving tendon-to-bone fixation during rotator cuff repair is critical to improve post-surgery outcomes. In the last decade, bioinspired solutions have shown considerable promise for addressing several biomedical problems. This thesis draws bioinspiration from two animals that have evolved unique mechanical functions: (i) the bat shoulder joint, which facilitates repetitive overhead motions during flight and may offer insights into rotator cuff pathology and (ii) the curvature of python snake teeth, which enables secure grasping of prey without soft tissue tearing. In the first part of the thesis, the bat shoulder was studied for its unique characteristics relative to mice. Overhead motions in humans often lead to shoulder injuries, partly because the bony anatomy of the unstable GH joint places greater stress on the joint's surrounding soft tissues to stabilize these motions. Traditional animal models used to study shoulder pathology are quadrupeds, which lack the capacity for overhead motion. In contrast, bats consistently engage in overhead motion during flight, subjecting their shoulders to substantial loading throughout their relatively long lifespan. Remarkably, the biomechanical demands placed on a bat's shoulder are estimated to exceed those of a competitive swimmer’s by 45-fold, despite sharing similar coracoacromial arch anatomy with humans. We were inspired to study functional adaptations in the shoulders of bats that enable this overhead motion. We performed comparative anatomy studies of the shoulders of bats and mice, similarly-sized quadrupeds. By quantifying the constraints imposed by the bony anatomy, we identified adaptations of the shoulder, including the rotator cuff tendons, that allow bats to sustain overhead motion in a high stress, repeated loading environment, without injury. In the second part of the thesis, python teeth were used as inspiration to develop a repair device optimized to grasp the rotator cuff without tearing. Rotator cuff repair surgeries fail frequently, with 20-94% of the 600,000 repairs performed annually in the United States resulting in retearing of the rotator cuff. The most common cause of failure is sutures tearing through tendons at grasping points. To address this issue, we examined the specialized teeth of snakes of the Pythonoidea superfamily, which effectively grasp soft tissues without tearing. To apply this non-damaging and effective gripping approach to the surgical repair of tendons, we developed and optimized a python-tooth inspired array as an adjunct to current rotator cuff suture repair, and found that it nearly doubled repair strength. Integrated simulations, 3D printing, and ex vivo experiments revealed a relationship between tooth shape and grasping mechanics, and enabled optimization of a tooth array device to enhance rotator cuff repair to distribute stresses and increase tendon-bone contact. The efficacy of the approach was demonstrated via human cadaver tests, suggesting an alternative to traditional suturing paradigms that may reduce tendon re-tearing. Collectively, these studies contribute to a better understanding of the biomechanics of the GH joint and offer novel, bioinspired approaches for rotator cuff repair. The functional adaptations of bats provide insight into developing new approaches to treat GH joint instability, and a clinically relevant python-tooth inspired device can ultimately reduce the high rates of re-rupture currently observed in rotator cuff repair.

This thesis documents three main projects performed during my PhD. Chapter 3 describes a published project in which detailed behavioral analysis based on machine learning approaches for pose-estimation were used to characterize a novel sensorimotor transformation in which mice use whisker information to rapidly modify their gait in order to rapidly avoid an obstacle in their path (Warren et al., 2021). I contributed to designing experiments, data collection and analysis related to this project spanning roughly from Aug. 2018 to Aug. 2019. Appendix 1 describes a follow-up study in which I performed multi-site silicon probe recordings and anatomical reconstruction of recording sites across the deep cerebellar nuclei in head-fixed mice performing the same obstacle avoidance behavior mentioned above. Data collection for this project spanned roughly from May 2019 to Jan. 2021. This data was initially analyzed in collaboration with Richard Warren and is currently being analyzed in collaboration with Ramin Kajeh in Dr. Larry Abbott’s group. Finally, Chapter 2 reports on the major independent work undertaken as part of my thesis, spanning from Sept. 2021 to present. As such, the Introduction relates solely to Chapter 2. The goal of this ongoing project is to extend the Sawtell laboratory studies of the mechanisms for sensory prediction and cancellation in the cerebellum-like circuitry of the electrosensory lobe (ELL) of electric fish to a cerebellum-like circuit in mammals, the dorsal cochlear nucleus (DCN) in the auditory brainstem. In particular, my work provides initial insights into the function of the cartwheel cell (CWC), a previously enigmatic cell type that occupies a similar place in the circuitry of the dorsal cochlear nucleus as the Purkinje cell of the cerebellum and the medium ganglion (MG) cell of the ELL. We have demonstrated that CWCs convey tonotopically-specific signals that are well-suited for canceling self-generated auditory responses in fusiform cells (FCs), the principal output cells in the DCN. Additionally, our findings reveal that the two characteristic types of spikes observed in CWCs—the axonal simple spikes (comparable to simple spikes in Purkinje cells and narrow spikes in MG cells) and dendritic complex spikes (similar to complex spikes in Purkinje cells and broad spikes in MG cells)—are distinctly modulated by both self-generated behavior and external acoustic stimuli, suggesting that these two types of spikes serve separate functional roles in the processing of the cancellation signal, as well as auditory information, within the DCN circuitry. This finding is consistent with the reported distinct functions of narrow and broad spikes in MG cells within the circuitry of the ELL, suggesting an evolutionarily conserved role of Purkinje-like cells in cerebellum-like circuits.

Chiu, Wang Kei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 95-110). / Abstracts in English and Chinese. / Abstract --- p.i / 摘要 --- p.iii / Contents --- p.v / Acknowledgements --- p.viii / Abbreviations --- p.ix / List of tables --- p.xii / List of figures --- p.xii / Chapter 1. --- Literature Review --- p.1 / Chapter 1.1 --- Cell cycle and chromosome replication --- p.1 / Chapter 1.2 --- Telomere-associated proteins --- p.4 / Chapter 1.3 --- Telomere repair protein --- p.6 / Chapter 1.4 --- Function of telomere --- p.9 / Chapter 1.5 --- Telomerase --- p.10 / Chapter 1.6 --- Factors affecting telomere length --- p.14 / Chapter 1.7 --- Stress and telomere length --- p.14 / Chapter 1.8 --- Definition of Stress --- p.16 / Chapter 1.9 --- Central nervous system components involved in stress response --- p.17 / Chapter 1.10 --- Glucocorticoid --- p.17 / Chapter 1.11 --- Physiological effects under the activation of stress system --- p.19 / Chapter 1.12 --- Effects of chronic hyperactivation of the stress system --- p.20 / Chapter 1.13 --- Hypothesis --- p.23 / Chapter 2. --- Materials and Methods --- p.24 / Chapter 2.1 --- Materials --- p.24 / Chapter 2.2 --- Experiment animals --- p.25 / Chapter 2.3 --- Methods --- p.26 / Chapter 2.3.1 --- Treatment schedule --- p.26 / Chapter 2.3.2 --- Organ extraction and serum preparation --- p.27 / Chapter 2.4 --- Serum corticosteroid assay --- p.27 / Chapter 2.5 --- Telomere length assay --- p.30 / Chapter 2.5.1 --- Genomic DNA extraction --- p.30 / Chapter 2.5.2 --- Genomic DNA digestion --- p.31 / Chapter 2.5.3 --- Southern blotting procedure --- p.32 / Chapter 2.6 --- Telomeric Repeat Amplification Protocol (TRAP) assay --- p.37 / Chapter 2.6.1 --- Extract preparation and protein concentration quanititation --- p.38 / Chapter 2.6.2 --- Real-time PCR reaction --- p.39 / Chapter 2.6.3 --- Melt Curve --- p.41 / Chapter 2.7 --- Detection of mouse telomerase reverse transcriptase component (mTERT) mRNA expression by reverse transcriptase- polymerase chain reaction (RT-PCR) --- p.42 / Chapter 2.7.1 --- Total RNA extraction --- p.42 / Chapter 2.7.2 --- RT-PCR --- p.44 / Chapter 2.7.3 --- Agarose gel electrophoresis of RT-PCR products --- p.45 / Chapter 2.8 --- Detection of mouse TERT (mTERT) by Western blotting --- p.46 / Chapter 2.8.1 --- Nuclear protein extraction --- p.46 / Chapter 2.8.2 --- Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) --- p.47 / Chapter 2.9 --- Statistics --- p.49 / Chapter 3. --- Results --- p.51 / Chapter 3.1 --- Body and spleen weights of study animals --- p.51 / Chapter 3.2 --- Serum corticosterone level --- p.54 / Chapter 3.3 --- Telomere lengths of spleen --- p.54 / Chapter 3.4 --- Telomerase activity of spleen tissue --- p.58 / Chapter 3.5 --- Correlation between serum corticosterone level and telomere length --- p.65 / Chapter 3.6 --- Correlation between serum corticosterone level and telomerase activity --- p.66 / Chapter 3.7 --- Correlation between telomere length and telomerase activity --- p.67 / Chapter 3.8 --- Detection of telomerase reverse transcriptase component (mTERT) mRNA expression by RT-PCR --- p.69 / Chapter 3.9 --- Detection of mTERT by Western blotting --- p.72 / Chapter 3.10 --- Correlation between serum corticosterone level and mTERT mRNA /protein expression --- p.75 / Chapter 4. --- Discussion --- p.77 / Chapter 4.1 --- Serum corticosterone level in mice --- p.78 / Chapter 4.2 --- Mice body weight and spleen weight --- p.80 / Chapter 4.3 --- Telomere lengths in the spleen tissue --- p.83 / Chapter 4.4 --- Telomerase activity in spleens --- p.84 / Chapter 4.5 --- Correlation between serum corticosterone level and telomere length --- p.87 / Chapter 4.6 --- Correlation between serum corticosterone level and telomerase activity --- p.89 / Chapter 4.7 --- Mouse telomerase reverse transcriptase component (mTERT) mRNA expression --- p.89 / Chapter 4.8 --- Expression of mTERT protein --- p.90 / Chapter 4.9 --- Conclusion --- p.92 / Chapter 5. --- References --- p.95 / Chapter 6. --- Appendix --- p.111

Indiana University-Purdue University Indianapolis (IUPUI) / Sensitization to the locomotor stimulant effects of alcohol (ethanol) is thought to be a heritable risk factor for the development of alcoholism that reflects progressive increases in the positive motivational effects of this substance. However, very little is known about the genetic influences involved in this phenomenon or the extent to which ethanol’s positive motivational effects are altered in parallel to its development. The first goal of this work was to determine the heritability of ethanol-induced locomotor sensitization in mice using short-term behavioral selection. Genetically heterogeneous C57BL/6J (B6) x DBA/2J (D2) F2 mice were generated from B6D2F1 progenitors, phenotyped for the expression of locomotor sensitization, and bred for high (HLS) and low (LLS) expression of this behavior. A secondary goal was to characterize possible line differences in ethanol’s positive motivational effects using a conditioned place preference assay. There were large and significant differences in locomotor sensitization between HLS and LLS lines by the fourth generation. Twenty-two percent of the observed line difference(s) were attributable to genes (h2=.22). However, there were no significant differences in conditioned place preference between lines despite significant line differences in ethanol-stimulated locomotion following repeated exposures. The results of this work have several implications. First, that changes in ethanol sensitivity following repeated exposures are in part genetically regulated highlights the relevance of studies aimed at determining how genes regulate susceptibility to ethanol-induced behavioral and neural adaptations. Additionally, the lack of line differences in ethanol-induced CPP, and the observation that CPP and ethanol sensitization are dissociable, suggests that 1) different genes regulate these two behaviors and 2) the utility of locomotor sensitization as a model of alterations in ethanol’s positive motivational effects is, at best, still unclear. Together these studies provide evidence that genes are capable of regulating alterations in ethanol-induced locomotor behavior but provide little support for ethanol-induced locomotor sensitization as a model for increases in ethanol’s positive subjective effects in mice.

The combinatorial code of cPcdh isoforms creates a diversified cell-surface molecular signature for cell-cell recognition in neural networks. This genetic architecture, combined with a regulated expression pattern and trans-homophilic binding properties, provides insights into cell specialization and signaling. Anomalies in cPcdhs, which include genetic mutations, epigenetic modifications, structural variations, and altered gene expression profiles, are associated with several neurological, neuropsychiatric, and systemic conditions, highlighting the importance of cPcdh investigations. This study focuses on the transcriptional regulation of the Pcdhα gene cluster. Each neuron displays a specific Pcdhα alternate exon repertoire, necessitating an understanding of the transcriptional dynamics. Using the SK-N-SH human neuroblastoma cell line and methodologies such as cRNA-seq and Start-Seq, these dynamics are examined. The application of CRISPR-Cas9 gene editing and a dCas9-VPR gain-of-function assay in the HEK293T cell line reveals the role of as-lncRNA and its interaction with DNA methylation within the Pcdhα gene cluster. This study identifies the role of noncoding as-lncRNA in RNA transcription and provides information on CTCF binding and Pcdhα promoter activation. The research also examines the gastrointestinal domain, as cPcdhs are linked to various diseases. Shifting focus from the canonical realm of the CNS, the research embarks on a preliminary yet pivotal exploration of the gastrointestinal domain. As cPcdhs intersect with a plethora of diseases, an incisive understanding of their expression could yield revelations into tissue susceptibilities with potential disease ramifications. Employing a novel single-domain antibody technique coupled with immunohistochemistry, the endeavor casts a precise lens into the gastrointestinal expression dynamics of Pcdhα and Pcdhγ. These insights not only fortify the understanding of cPcdh within neural structures but also beckon a deeper inquiry into their multifaceted biological roles.

Indiana University-Purdue University Indianapolis (IUPUI) / Extrasynaptic GABAA receptors, often identified as those containing both α4 and δ subunits, appear to be a target for the actions of alcohol (ethanol) at relatively low concentrations, perhaps suppressing the activity of GABAergic interneurons which regulate activity in the mesolimbocortical circuit. Pharmacological studies in rodents using the δ-subunit selective agonist Gaboxadol (THIP) have found both promotional and inhibitory effects on alcohol consumption. The goal of this project was to determine the role of extrasynaptic GABAA receptors located in the infralimbic cortex (ILC) in the binge-like alcohol intake of male C57BL/6J (B6) mice. The ILC is of interest due to its demonstrated involvement in stress reactivity and alcohol exposure has been shown to interfere with extinction learning; impairments of which may be related to inflexible behavior (i.e. problematic alcohol consumption). Adult male B6 mice were bilaterally implanted with stainless steel guide cannulae aimed at the ILC and were offered limited access to 20% ethanol or 5% sucrose for 6 days. On day 7, mice were bilaterally injected with 50 or 100 ng THIP (25 or 50 ng per side respectively) or saline vehicle into the ILC. It was found that the highest dose of THIP (100 ng/mouse) increased alcohol intake relative to vehicle controls, although control animals consumed relatively little ethanol following infusion. Furthermore, THIP had no effect on sucrose consumption (p > 0.05), suggesting that the effect of THIP was selective for ethanol consumption. Together, these findings suggest that the mice that consumed ethanol may have been particularly reactive to the microinfusion process relative to animals that consumed sucrose, perhaps because ethanol consumption was not as reinforcing as sucrose consumption. In addition, the observation that THIP effectively prevented the decrease in ethanol intake on day 7 induced by the microinjection process may be related to a role for the ILC in adaptive learning processes, which in turn, promote behavioral flexibility.

Indiana University-Purdue University Indianapolis (IUPUI) / It has traditionally been posited that women show a "telescoped" development of alcohol use disorders (Kuhn, 2011). In particular, a number of clinical studies support striking sex differences in the progression from initial use of alcohol to dependence on the compound; with women showing a faster progression through landmark events associated with the development of alcohol addiction (Randall et al., 1999). However, recent studies have challenged this tenet (Keyes et al., 2010). The work presented herein was designed to determine whether females are indeed more vulnerable to the development of behavioral maladaptations following binge drinking and whether sex differences in GABA(A) receptor regulation might underlie this vulnerability. Using a mouse model of binge drinking this dissertation established that, compared to males, females escalate their binge drinking at a faster rate and maintain altered responsivity to the locomotor effects of alcohol after extended abstinence from binge drinking. Female mice also displayed significant increases in ethanol preference and intake in a continuous, two-bottle choice protocol following a shorter history of binge drinking than males. The final goal was to determine if binge drinking results in unique patterns of anxiety- or depressive-like symptoms in males and females and whether these behaviors would be associated with the dimorphic regulation of GABAA receptor subunits across the prefrontal cortex and hippocampus. Male binge drinkers displayed anxiety-like behavior during early withdrawal that dissipated after 2 weeks of abstinence. There were no significant changes in the expression of delta or gamma2 GABAA receptor subunit mRNA at this time point in the regions analyzed. Females also showed temporary anxiety-like behavior during early withdrawal from binge drinking. Additionally, females displayed significant depressive-like behavior after 2 weeks of abstinence from binge drinking. In particular, diestrus-phase females displayed significantly greater immobility in the forced-swim test after ethanol exposure and no longer maintained the reduced swim-time behavior associated with this phase of the cycle at baseline (when compared to the estrus-phase). qPCR analysis of hippocampal tissues from diestrus females supported a significant reduction in expression of gamma2 GABA(A) subunit mRNA after binge drinking. This effect was not noted for RNA isolated from hippocampal tissues taken during the estrus phase of bingers. These final data suggest possible interaction of estrous-cycle and binge drinking history that may result in the unique expression of deficits following binge drinking for females. Taken together, this work supports sex and estrous dependent effects of binge drinking on behavior and gene regulation.