Browsing Genetics by Title
Now showing items 62-81 of 146
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Identification and characterization of genes that modify tubulogenesis defects caused by over-expression of Imaginal Disc Growth Factor-3 using the Drosophila dorsal appendage model, a partial genomic expedition
Biological tube formation underlies organ development, and when disrupted, can cause severe birth defects. To investigate the genetic basis of tubulogenesis, I study the formation of Drosophila melanogaster eggshell ... -
Identification of candidate substrates of the leucine rich repeat kinase 2 by mass spectrometry-based phosphoproteomics
Mutations in the kinase domain of the leucine rich repeat kinase (LRRK2) have been implicated in heritable forms of Parkinson’s disease (PD). Specifically, a glycine to serine mutation (G2019S) has demonstrated hyperactive ... -
Identifying Neural Pathways of Stress and Fear with Retrograde Viral Tracing and Single Cell RNA Sequencing
The brain is made up of millions of neurons, often making thousands of connections each. Interrogating individual neurons activated by stressors is the equivalent of finding a needle in a haystack. Here we describe ... -
Identifying New Genes for Inherited Breast Cancer by Exome Sequencing
(2014-02-24)Breast cancer is the most common cancer among American women and family history is an important risk factor for its occurrence. More than 20 genes have been identified with inherited mutations that lead to significantly ... -
Immune consequences and therapeutic targeting of disrupted RNA splicing in cancer
Immunotherapies, such as checkpoint blockade, CAR-T cells, and vaccines, have proven to be a valuable tool to treat various types of cancer. This class of therapy capitalizes on the immune system’s natural ability to ... -
Improving peptide detection in mass spectrometry-based proteomics
Over the last 30 years, the field of computational mass spectrometry-based proteomics has made great strides. Specifically, the development of database search engines has allowed for the automatic annotation of observed ... -
Inferring whole-genome 3D chromatin structures from diploid Hi-C data
The three-dimensional organization of the genome plays an important part in regulating numerous basic cellular functions, including gene regulation, differentiation, the cell cycle, DNA replication, and DNA repair. Assays ... -
Insights into mechanisms of Pseudomonas aeruginosa virulence: cyanide as a weapon and the complexity of its regulation
(2001)This dissertation presents investigations into virulence mechanisms and virulence-gene regulatory circuitry in the bacterium Pseudomonas aeruginosa . P. aeruginosa is a medically important human pathogen that causes serious ... -
Interpreting variation in pharmacogenes using multiplex assays
With the advent of genome sequencing technologies, our ability to read DNA sequences is unprecedented. However, understanding how the variation we encounter impacts humans is a formidable challenge. Technologies like ... -
Investigating the duplication and evolution of essential fertilization proteins
Duplication processes such as whole gene duplication and tandem domain expansion are important for the evolution and functional diversification of essential protein families. While whole gene duplications are well established ... -
Learning from Large-scale Mutagenesis Data
Mutations can have profound effects on protein function. For example, mutations can increase or decrease enzymatic activity, influence aggregation propensity, or lead to novel protein functions. Mastery of the rules governing ... -
Learning from the past: Searching for novel TRIM, CypA, and TRIMCyp antiviral factors in primates
(2013-07-23)The evolutionary history and genetic composition of mammals has been strongly influenced by viruses. This is reflected by evolved mechanisms of host defense mediated by restriction factors that are in an arms race to win ... -
Leveraging natural isolates and experimental evolution to characterize biofilm-related phenotypes in Saccharomyces cerevisiae
Biofilm formation is a protective community building behavior in which microbes participate to respond to external stress or colonize new ecological niches. It is a primary mechanism used by pathogenic yeast to persist on ... -
Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. One way in which cis-regulatory elements can be delineated is by their characteristic ... -
Maps and mechanisms of three-dimensional genome organization
The three-dimensional organization of the genome inside the nucleus both impacts and is influenced by its functions, including transcription and DNA replication. Recent technological advances, particularly the high-throughput ... -
Massively parallel analysis of nucleic acid strucure
A goal amongst modern biologists is to “compute” cellular and organismal function. This “computation” necessitates a holistic understanding of the biochemical mechanisms underlying different cellular states. Methods that ... -
Massively parallel analysis of the functional effects of mutations
Massively parallel assays can dramatically advance our understanding of biological processes. Coupling them with modern mutagenesis techniques allows for fine mapping of the link between genotype and phenotype. In this ... -
Massively parallel characterization of enhancers in evolution and disease
On average, protein-coding sequence is over 99.9% identical between humans, yet some individuals develop disease while others do not. Similarly, protein-coding sequences are over 99% identical between human and chimpanzees ... -
Massively parallel functional dissection of regulatory elements
(2013-02-25)Massively parallel sequencing has accelerated the cataloging of cis-regulatory elements in mammalian genomes. However, it remains challenging to estimate the functional effects of variation in cis-regulatory elements. The ... -
Mechanisms of buffering of phenotypic variation in A. thaliana: Features of HSP90 and characterization of AGO1 as a new regulator of robustness
Biological systems have molecular mechanisms that allow them to maintain a constant phenotype despite environmental and genetic perturbations. These mechanisms can take the form of master regulator of robustness, gene ...