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Articles 1 - 10 of 10
Full-Text Articles in Life Sciences
Multi-Scale Simulations Of Dynamic Protein Structures And Interactions, Yumeng Zhang
Multi-Scale Simulations Of Dynamic Protein Structures And Interactions, Yumeng Zhang
Doctoral Dissertations
Intrinsically disordered proteins (IDPs) are functional proteins that lack stable tertiary structures in the unbound state. They frequently remain dynamic even within specific complexes and assemblies. IDPs are major components of cellular regulatory networks and have been associated with cancers, diabetes, neurodegenerative diseases, and other human diseases. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for mechanistic understanding of IDPs in biology, diseases, and therapeutics. However, accurate simulation of the heterogeneous ensembles and dynamic interactions of IDPs is extremely challenging because of both the prohibitive computational cost and demanding force field …
The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson
The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson
Doctoral Dissertations
This research focuses on a specific example of replicated evolution: the grass awn. Awns are typically extensions of the lemma, but may also appear on glumes or paleas. The lemma is a leaf-like organ on the exterior of the grass flower, the glumes are a pair of bracts subtending the basic unit of grass inflorescences, the spikelet, and the palea is the floral organ opposite the lemma. Awns are often described as "hair-" or "bristle-" like, but appear in many different shapes. Many awns are “twisted & geniculate", in which the awn has two sections, a lower twisted column, and …
Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro
Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro
Doctoral Dissertations
During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a …
Associations Between Early Childhood Sleep, Memory Function, And Brain Development Across The Nap Transition, Sanna Lokhandwala
Associations Between Early Childhood Sleep, Memory Function, And Brain Development Across The Nap Transition, Sanna Lokhandwala
Doctoral Dissertations
Preschool-age children often distribute their sleep across a midday nap and overnight sleep. Skipping the nap is suggested to increase the duration and depth of deep sleep (i.e., slow wave activity; SWA). Moreover, missing the midday nap has been shown to impair learning processes. This may be because children’s brains at this point in development are immature, necessitating the intervening nap period to strengthen memories before they are forgotten. Nonetheless, at some point during the preschool years, many children begin transitioning naturally out of napping. It is unclear whether the memory benefits of overnight SWA after a skipped nap depend …
Analysis Of Micro(Nano)Plastics In Food Using Raman Microscopy, Xin Guo
Analysis Of Micro(Nano)Plastics In Food Using Raman Microscopy, Xin Guo
Doctoral Dissertations
Microplastic pollution has emerged as a global concern in both aquatic and terrestrial environments. The presence of microplastics in the food chain poses a potential threat to human health. To accurately assess the risks associated with microplastics, it is crucial to have a reliable analytical technique capable of detecting, quantifying, and identifying microplastics of varying materials, sizes, and shapes in environmental, agricultural, and food samples. Spectroscopic techniques, specifically vibrational spectroscopy (Raman and Infrared), are extensively utilized in microplastic analysis. These techniques enable rapid and high-throughput identification, while also providing size and shape information. However, there are certain gaps in the …
High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre
High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre
Doctoral Dissertations
Polyoxometalates (POMs) are a class of inorganic molecule of increasing interest to the inorganic, bioinorganic and catalytic communities among many others. While their prevalence in research has increased, tools and methodologies for the analysis of their fundamental characteristics still need further development. Decavanadate (V10) specifically has been postulated to have several unique properties that have not been confirmed independently. Mass spectrometry (MS) and its ability to determine the composition of solution phase species by both mass and charge is uniquely well suited to the analysis of POMs. In this work we utilized high-resolution mass spectrometry to characterize V10 in aqueous …
A Ground-Based L-Band Radar System For Monitoring Forest Temporal Dynamics, Xingjian Chen
A Ground-Based L-Band Radar System For Monitoring Forest Temporal Dynamics, Xingjian Chen
Doctoral Dissertations
L-band FMCW radar is implemented for monitoring forest dynamics. It took short-term and long-term measurements with an internal calibration system that guarantees stability and precision. The radar data is compared to in-situ measurement, which infers causal relationships between radar backscatter signal and forest physiology index such as tree dielectric. This paper explains the relationship between radar signals and environmental components such as precipitation based on the measurement. The radar demonstrates some interesting observations, for example, trees' daily activity and freeze-thaw process.
The Impacts Of Environment And Host Evolutionary Relationships On Lemur Microbiota, Rachel B. Burten
The Impacts Of Environment And Host Evolutionary Relationships On Lemur Microbiota, Rachel B. Burten
Doctoral Dissertations
Recent studies have shown that the mammal microbiome is modified by environmental conditions, and that reduced microbiome functionality is associated with host health issues. Microbiome data in wild and captive primate populations can therefore be used to assess their health as they encounter a variety of environments. Comparative studies of the microbiome can also inform disease ecology, conservation, and captive management strategies tailored to different primate species. Therefore, this study examines how the hair, oral, and gut microbiota of nine wild and captive lemur species are determined by host phylogenetic relationships and host environment. I found that host species identity …
The Wild Tomato Clade Offers Insights Into Fleshy Fruit Trait Evolution At The Phenotypic And Molecular Levels, Jacob R. Barnett
The Wild Tomato Clade Offers Insights Into Fleshy Fruit Trait Evolution At The Phenotypic And Molecular Levels, Jacob R. Barnett
Doctoral Dissertations
Biologists have long been fascinated by the diversity of fleshy fruits, yet questions remain as to how this variety has evolved. According to the dispersal syndrome hypothesis, flowering plants improved their reproductive success by producing fleshy fruits with appealing combinations of traits that attract animal dispersers. However, animal preferences may not be the only selective pressure driving fruit trait diversity—conflicting forces include damage-inflicting seed predators and pathogens, abiotic habitat conditions, or constraints stemming from non-adaptive mechanical, developmental, or phylogenetic limitations. Few studies have examined the early stages of fleshy fruit evolution across an entire clade of recently diverged plant species. …
Development Of An Integrated Workflow For Nucleosome Modeling And Simulations, Ran Sun
Development Of An Integrated Workflow For Nucleosome Modeling And Simulations, Ran Sun
Doctoral Dissertations
Nucleosomes are the building blocks of eukaryotic genomes and thus fundamental to to all genetic processes. Any protein or drug that binds DNA must either cooperate or compete with nucleosomes. Given that a nucleosome contains 147 base pairs of DNA, there are approximately 4^147 or 10^88 possible sequences for a single nucleosome. Exhaustive studies are not possible. However, genome wide association studies can identify individual nucleosomes of interest to a specific mechanism, and today's supercomputers enable comparative simulation studies of 10s to 100s of nucleosomes. The goal of this thesis is to develop and present and end-to-end workflow that serves …