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Articles 1 - 8 of 8
Full-Text Articles in Genetics and Genomics
Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer
Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer
Dissertations, Theses, and Capstone Projects
The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …
Machine Learning Applications For Drug Repurposing, Hansaim Lim
Machine Learning Applications For Drug Repurposing, Hansaim Lim
Dissertations, Theses, and Capstone Projects
The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected …
Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang
Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang
Capstones
As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.
https://lucy-huang-9tge.squarespace.com/
Computational Investigation Of The Pore Formation Mechanism Of Beta-Hairpin Antimicrobial Peptides, Richard Lipkin
Computational Investigation Of The Pore Formation Mechanism Of Beta-Hairpin Antimicrobial Peptides, Richard Lipkin
Dissertations, Theses, and Capstone Projects
β-hairpin antimicrobial peptides (AMPs) are small, usually cationic peptides that provide innate biological defenses against multiple agents. They have been proposed as the basis for novel antibiotics, but their pore formation has not been directly observed on a molecular level. We review previous computational studies of peptide-induced membrane pore formation and report several new molecular dynamics simulations of β-hairpin AMPs to elucidate their pore formation mechanism. We simulated β-barrels of various AMPs in anionic implicit membranes, finding that most of the AMPs’ β-barrels were not as stable as those of protegrin. We also performed an optimization study of protegrin β-barrels …
Naturally-Derived Molecular Ensembles In Medicine, Materials Science And Evolutionary Biology: An Interdisciplinary Study, Silvio Panettieri
Naturally-Derived Molecular Ensembles In Medicine, Materials Science And Evolutionary Biology: An Interdisciplinary Study, Silvio Panettieri
Dissertations, Theses, and Capstone Projects
The first chapter will introduce the work carried out in collaboration with the Govind laboratory at CCNY. Our quest was set forth to investigate the intimate relationship lying between chronic inflammation and tumor development. For at least the last fifteen years much research has been conducted on this topic; yet, the level of complexity arising from exceedingly interwoven biochemical pathways in mammals has resulted in slow advancements in this field. This is why we resorted to a simple yet powerful immunogenetic model organism, the fruit fly Drosophila melanogaster, in combination with the administration of the most common anti-inflammatory drug, …
Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen
Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen
Dissertations, Theses, and Capstone Projects
Conservation biology is a scientific discipline that draws on methods from diverse fields to address specific conservation concerns and inform conservation actions. This field is overwhelmingly focused on charismatic animals and vascular plants, often ignoring other diverse and ecologically important groups. This trend is slowly changing in some ways; for example, increasing number of fungal species are being added to the IUCN Red-List. However, a strong taxonomic bias still exists. Here I contribute four research chapters to further the conservation of lichens, one group of frequently overlooked organisms. I address specific conservation concerns in eastern North America using modern methods. …
Metabolic Profiling And Polymer Formation Of Gene Silenced Potato Periderms, Qing Cai
Metabolic Profiling And Polymer Formation Of Gene Silenced Potato Periderms, Qing Cai
Dissertations, Theses, and Capstone Projects
Suberin is a biopolyester constituent of specialized plant periderm tissues formed within the phellem cell walls. Suberin and waxes of the periderm layer act to prevent water diffusion, mechanical breakdown and pathogenic invasion in plants. Ferulic esters, ω-hydroxyacids and α,ω-fatty diacids are considered to be the most important linkage between aliphatic and aromatic suberin domains and also linked with cell-wall polysaccharides. The potato gene FHT (fatty ω- hydroxyacid/fatty alcohol hydroxycinnamoyl transferase) esterifies ferulic acid to suberin. Diminished levels of feruloyl transferase activity have been associated with lowered amounts of feruloyl esters of fatty acids in both suberin-associated waxes and suberin …
Phylogeny And Population Genetics Of The Endangered Dwarf Bear-Poppy, Arctomecon Humilis Coville (Papaveraceae) Using Microsatellite Markers, Joshua Simpson
Phylogeny And Population Genetics Of The Endangered Dwarf Bear-Poppy, Arctomecon Humilis Coville (Papaveraceae) Using Microsatellite Markers, Joshua Simpson
Dissertations, Theses, and Capstone Projects
The genus Arctomecon (Papaveraceae) is comprised of three narrowly endemic rare species that are largely restricted to gypsum soils of the eastern Mojave Desert. The small, remaining populations of these species have become increasingly isolated by urban development and habitat fragmentation. Arctomecon humilis is federally listed as endangered due to its limited distribution within a ~15 km radius of an actively expanding city. Organizations involved with land management and conservation have called for greater insight into the genetic variation and population structure of the remaining subpopulations as they make important decisions regarding where to focus their efforts and resources.
The …