Bioinformatics Applications in Neurodevelopmental Genetics and Genomics

Bioinformatics plays a crucial role in understanding neurodevelopmental genetics and genomics by integrating computational tools and large-scale datasets to analyze complex molecular interactions. This dissertation bridges experimental data and biological insights, uncovering genetic and epigenetic mechanisms underlying neurodevelopmental disorders.Chapter 2 introduces Rocketchip, a novel bioinformatics tool designed to automate and streamline data analysis for chromatin immunoprecipitation assays, including ChIP-seq, CUT&RUN, and CUT&Tag. It addresses challenges in genetics by enhancing analysis rigor and ensuring reproducibility while promoting the use of publicly available datasets to foster scientific collaboration.Chapter 3 applies Rocketchip to analyze newly generated ChIP-seq data targeting the transcription factor MeCP2, associated with Rett Syndrome, a neurodevelopmental disorder affecting approximately 1 in 10,000 females. This chapter investigates the DNA-binding activity of MeCP2 across various cell types and disease stages, highlighting genes and pathways contributing to Rett Syndrome progression.Chapter 4 evaluates the impact of excess folic acid on neurodevelopment using RNA-seq and whole genome bisulfite sequencing (WGBS) data from mice exposed to excess folic acid, identifying dysregulated or differentially methylated genes that affect neurodevelopment.Overall, these project chapters highlight the critical role of bioinformatics in advancing our understanding of neurodevelopmental genetics and genomics

The Spatial Ecology of Macroinvertebrates in Sierra Nevada Lakes and Ponds

Determining the factors that drive patterns of diversity across space and time is a major goal of ecology. Mountain lakes and ponds are uniquely suited for testing how environmental gradients shape the spatial and temporal patterns of population and community diversity. Additionally, mountains contain steep climate gradients and highly variable local contexts, both of which are likely to mediate how communities respond to climate warming. In this dissertation, I used a suite of theoretical and empirical frameworks to understand the factors shaping spatial patterns of population genetic diversity, patterns of community assembly among lakes and ponds, and community responses to a rapidly changing climate. For all chapters, the Sierra Nevada mountains of California served as the natural laboratory, while both historical and contemporary collections of littoral macroinvertebrates served as the subjects.In Chapter 1, I used a common lentic mayfly species (Callibaetis ferrugineus hageni) to explore how spatial patterns of genetic and genomic variation are influenced by the interaction of steep climate gradients, the landscape matrix, and local environmental quality. By using a combination of landscape genetic network models and genomic tools, I found that both at-site and among-site factors influence patterns of gene flow among lakes, while higher elevation populations showed enhanced signatures of local adaptation. Taken together, landscape-restricted gene flow likely allows for selection pressures to facilitate local adaptation in the mayfly populations of higher elevation lakes. In Chapter 2, I used a historical dataset of macroinvertebrates to understand how daily and seasonal temperature variation influence community assembly in lakes versus ponds. Relative to lakes, I found that ponds filter for taxa with wider thermal tolerance, which then constrains the diversity of functional traits in pond communities. My results also suggest that daily temperature variation may be a particularly important abiotic filter for pond communities, though future incorporation of in situ data will help confirm the relative roles of daily, seasonal, and interannual climate variation across categories of ecosystem size. In Chapter 3, I used both historical and contemporary datasets of lake macroinvertebrates to ask 1) if lake communities are responding to climate warming through colonizations by warm-adapted taxa, local extinctions of cold-adapted taxa, or both (i.e. thermophilization) and 2) if current responses to climate warming result in reduced beta diversity (i.e. homogenization). Over 20 years of declining winter snowpack and rising air temperatures, I found that colonizations by predators drove thermophilization in contemporary macroinvertebrate communities, but that thermophilization did not lead to significant homogenization in either taxonomic or functional measures.Collectively, my dissertation demonstrates the unique ways in which mountain environments shape freshwater populations and communities, while also mediating community responses to rapid climate warming

Behavioral resilience via dynamic circuit firing homeostasis

Homeostatic regulation ensures stable neural circuit output under changing conditions. We find that in Drosophila larvae, either presynaptic weakening due to perturbation of transmitter release or postsynaptic weakening due to perturbation of glutamate receptors at synapses between motor neuron (MN) and muscle has little impact on locomotion, suggesting a nonsynaptic compensatory mechanism. In vivo imaging shows that five different forms of synaptic weakening increase the duration of activity bouts in type I MNs. Strikingly, this compensation is input selective: occurring only in the tonic type Ib MN, not the phasic type Is MN that innervates the same muscle. Moreover, an inhibitory class of central pre-MNs that innervates the tonic-but not phasic-input decreases in activity. The adjustment in activity occurs remarkably quickly: within minutes of synapse perturbation. We propose that MN firing is dynamically regulated by two coordinated mechanisms: a cell-autonomous adjustment of MN excitability and a circuit adjustment of inhibitory central drive. The input selectivity of this process suggests homeostatic adjustment to maintain tonic drive but hold constant the phasic drive that organizes locomotory wave patterns

Exploring the genetic influences on equine analgesic efficacy through genome-wide association analysis of ranked pain responses

Multimodal analgesic administration is a promising strategy for mitigating side effects typically associated with analgesia; nevertheless, variation in analgesic effectiveness still poses a considerable safety concern for both horses and veterinarians. Pharmacogenomic studies have started delving into genetic influences on varying drug effectiveness and related side effects. However, current findings have narrow implications and are limited in their ability to individualize analgesic dosages in horses. Hydromorphone and detomidine were administered to a cohort of 48 horses at standardized time intervals, with dosage rates recorded. Analgesic effectiveness was scored (1-3) based on pain response to dura penetration during cerebrospinal fluid centesis. Genome-wide association (GWA) analyses identified two SNVs passing the nominal significance threshold (P < 1 ×10-5) in association with analgesic effectiveness. One SNV identified on chromosome 27 (rs1142378599) is contained within the LOC100630731 disintegrin and metalloproteinase domain-containing protein 5 gene. The second identified SNV is an intergenic variant located on chromosome 29 (rs3430772468) These SNVs accounted for 26.11 % and 31.72 % of explained variation in analgesic effectiveness respectively, with all eight of the horses with the lowest analgesic effectiveness expressing the A/C genotype at rs3430772468, with six of which also expressing the C/T genotype at rs1142872965. Whilst highlighting the multifactorial nature of analgesic efficacy, this study serves as an important step in the application of genome-wide approaches to better understand genetic factors underpinning commonly observed variation in analgesic effectiveness in horses, with the goal of tailoring analgesic dosage to minimize commonly observed side effects and improve the outcomes of equine pain management

Spatial transcriptomics defines the cell-specific RNA landscape of equine dorsal root ganglia.

Equine spinal neurodegenerative conditions are frequently encountered in sport and racing horses and may be career-ending diagnoses. To further define the spatial transcriptomic landscape of equine dorsal root ganglia (DRG) in healthy adult horses, we investigated gene expression differences in distinct DRG regions using the GeoMx Digital Spatial Profiling from NanoString. Four human cell markers demonstrated high fidelity for equine cells; microtubule-associated protein 2 (MAP2), myelin basic protein (MBP), allograft inflammatory 104 factor 1/ionized calcium-binding adaptor molecule 1 (IBA1/AIF1), and Syto83 nuclear marker. Geometric regions of interest were then selected as MBP-rich, IBA1-high, and IBA1-low, and gene expression was compared. Experimental validation was achieved, with genes involved in myelination enriched in MBP-rich regions, and the identification of glia-specific genes enriched in IBA1-high regions. Thus, spatial transcriptomics with human cell markers was successful in equine DRG and can now be applied to determine cell-specific transcriptional changes during disease states

A Description of Short-Stay Admissions from the Emergency Department among a Managed Care Population

Objectives: Emergency Department (ED) boarding of admitted patients is associated with worsened patient outcomes, delays in medical care, increased ED crowding and reduced patient satisfaction.  Utilization of alternatives to hospital admission such as ED observation, hospital at home/home health and the Medicare Skilled Nursing Facility 3-day waiver program, which are all value-based care programs, can help alleviate ED boarding.  Identifying details associated with short-stay admissions (those in which patients are discharged within 24 hours of admission) may help optimize use of these alternatives to hospital admission.  At our health system, we have a large managed care population for which these value-based initiatives are fundamental to cost-effective care.  This study aimed to identify and characterize short stay admissions from the ED among managed care patients with the larger, long-term goal of optimizing ED dispositions and utilization of alternatives to admissions.    Methods: This retrospective, observational descriptive cohort study was conducted at an academic health system’s two EDs over 12 months.  Included were managed care commercial and Medicare patients attributed to our health system who had an ED visit that resulted in an inpatient or observation admission lasting  Results/Findings: Over the study time period, 198 managed care patients with short-stay admissions were identified.  71.2% (n= 141) of the patients were >/= 65 years.  The average LACE+ score was 64 with a median of 68.  91 patients (46%) were admitted to a Medicine service.  107 patients (54%) were admitted to a Specialty Service.  The most frequent diagnoses among the Medicine admission cohort were those disease conditions or symptoms relating to infection (n=13 or 6.6%), pulmonary (n=7 or 3.5%) and gastroenterology (n=7 or 3.5%%) and among the Specialty Service admission cohort were those disease conditions or symptoms relating to cardiology (n=29 or 14.7%), neurology (n=15 or 7.6%), gynecology (n=5 or 2.5%), and Urology (n=6, 3%).  The remaining admissions among both cohorts involved varied disease conditions or symptoms (n=116 , 58.6%).  The majority of patients (n= 167 or 84.3%) were discharged home, 19 patients (9.6%) were discharged to a SNF, rehab facility or transferred to another hospital.  12 patients (6.1%) left Against Medical Advice.      Conclusion: In this population of managed care, short-stay admission patients with a medium to high risk of readmission based on LACE+ score, approximately half the patients were admitted to a Medicine service with the most frequent admitting diagnoses related to infection.  Among the patients admitted to a Specialty Service, the most frequent admitting diagnosis or symptoms related to a cardiac condition.  The majority of patients were discharged to home.  Understanding this population may help to focus opportunities in which alternatives to admission may be leveraged, when appropriate. &nbsp

Spatially explicit terrestrial carbon densities for calibrating the carbon cycle in human-Earth system Models

Soil and vegetation carbon stocks play a critical role in human-Earth system models. These stocks (denominated as densities in MgC/ha) affect variables such as land use change emissions and also influence land use change pathways under climate forcing scenarios where terrestrial carbon is assigned a carbon price. Here we present reharmonized soil and vegetation carbon densities both at the 5-arcmin resolution grid cell level and also aggregated to 235 water sheds for 4 land use types (Cropland, Grazed land, Urban land and unmanaged vegetation) and 15 unmanaged land cover types. Moreover, we use the distribution of carbon within and across pixels to define statistical “states” of carbon, once again differentiated by land type. These statistical states are used to define a range of possible carbon values that can be used for defining initial conditions of soil and vegetation carbon in human-Earth system models. We implement these data in a state-of-the-art multi sector dynamics model, namely the Global Change Analysis Model (GCAM), and show that these new data improve several land use responses, especially when terrestrial carbon is assigned a carbon price

“Paid to a Forged Order”: Counterfeit Continental Pay Orders and Their Impact on Veterans in Early Republic Massachusetts

Between 1783 and 1800, dozens of Continental Army veterans approached the Massachusetts House of Representatives to petition for their wages, which had been paid out to criminals in possession of forged pay orders. The legislature responded to these requests with direct, individual action, as well as with legislation punishing the forgery of payment certificates. These forgeries are situated within the broader context of an epidemic of counterfeiting in the Early Republic and the intricacies of Continental Army payment. However, due to their overlap in both of these fields, forged orders themselves have not been studied. What has also been overlooked is the impact of counterfeiting on its victims, which has largely been ignored in favor of research into the forgers and falsified documents themselves. Examination of the many petitions which were filed by veterans who fell victim to forged orders, as well as the resolutions that the Massachusetts House of Representatives passed on the matter, reveal the massive scale of counterfeited pay certificates in this period, as well as the devastating impact that such forgeries had on the veterans who lost their wages to forgeries. This article demonstrates the consequences of this pervasive counterfeiting on ordinary Americans whose struggle, despite their service to their new-found nation, has been largely ignored in history

Appalachia As Ghost

A poem in the "Verse in Place" section of Parks Stewardship Forum