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WikiDust: a TinkerCell Plugin to Annotate and Share Network Models
(2011)
We present WikiDust, a software tool that (a) facilitates
searches for DNA components, and (b) produces annotated webready
images for improved sharing of designs. WikiDust is a plugin
for TinkerCell, a CAD design tool for genetic regulatory networks.
WikiDust leverages the SBOL standard to connect TinkerCell to the
Registry ...
Survey of Shell-boring Microorganisms Across a Depth Gradient at Point Caution, on San Juan Island, WA
(2011)
Although they are integral to many marine ecosystems, relatively little is known
about euendolithic (shell-boring) organisms outside the tropics. Here, I present a
short survey of euendoliths inhabiting a site on the Pacific coast of North
America. Shells were collected from sites in the intertidal and subtidal zone ...
Data set to support Ph.D Dissertation: Plant-Pollinator Interactions in an Ecological and Evolutionary Context: The Promising Role of 3D-Printing Technology and Mathematical Modeling
(2017-06-07)
table of the number of artificial flowers that were emptied (exploited) by a hawkmoth during each foraging trial.
original raw data files from the infrared sensors attached to each artificial flower
csv files of x,y coordinates from a custom automated moth flight-tracking program that I employed for my dissertation ...
Complex regulation and multiple developmental functions of misfire, the Drosophila melanogaster ferlin gene
(2007-03-26)
Background: Ferlins are membrane proteins with multiple C2 domains and proposed functions
in Ca2+ mediated membrane-membrane interactions in animals. Caenorhabditis elegans has two ferlin
genes, one of which is required for sperm function. Mammals have several ferlin genes and
mutations in the human dysferlin (DYSF) and ...
Evolution of Mutator Genes in Bacterial Populations: The Roles of Environmental Change and Timing
(Genetics Society of America, 2003-07)
Recent studies have found high frequencies of bacteria with increased genomic rates of mutation in both clinical and laboratory populations. These observations may seem surprising in light of earlier experimental and theoretical studies. Mutator genes (genes that elevate the genomic mutation rate) are likely to induce deleterious ...
Effect of human leukocyte antigen heterozygosity on infectious disease outcome: the need for allele-specific measures
(Biomed Central, 2003-01-24)
Background: Doherty and Zinkernagel, who discovered that antigen presentation is restricted by the major histocompatibility complex (MHC, called HLA in humans), hypothesized that individuals heterozygous at particular MHC loci might be more resistant to particular infectious diseases than the corresponding homozygotes because ...
Natural selection, infectious transfer, and the existence conditions for bacterial plasmids
(Genetics, 2000-08)
Despite the near-ubiquity of plasmids in bacterial populations and the profound contribution of plasmid-borne genes and infectious gene transfer to the adaptation and evolution of bacteria, the mechanisms responsible for the maintenance of plasmids in bacterial populations are poorly understood. In this report, we address the ...
Mathematical models of RNA silencing: Unidirectional amplification limits accidental self-directed reactions
(National Academy of Sciences USA, 2003-09-30)
RNA silencing, found broadly throughout the eukaryotes, post-transcriptionally suppresses the expression of aberrant genes including those of many viruses and transposons. Similar to the specific immune system of vertebrates, RNA silencing works by generating specific responses against foreign elements and rapidly amplifying ...
The role of evolution in the emergence of infectious diseases
(Nature, 2003)
It is unclear when, where and how novel pathogens such as human immunodeficiency virus (HIV), monkeypox and severe acute respiratory syndrome (SARS) will cross the barriers that separate their natural reservoirs from human populations and ignite an epidemic spread of novel infectious diseases. New pathogens are believed to ...
Models of CD8+ Responses: 1. What is the Antigen-independent Proliferation Program
(Elsevier Science, 2003)
Recent experimental results show that even brief stimulation with antigen can cause antigenspecic CD8 T-cells to undergo sustained proliferation followed by differentiation into memory cells. These results show that the dynamics of these immune responses are not governed by constant monitoring of antigen levels, but rather ...