Plant form is a compromise between resource gathering, reproduction and
the tolerance to physical demands of the abiotic and biotic environment. In
an agricultural field in addition to the natural factors causing stress, humans
also introduce physical and mechanical stresses, and chemical pesticides
into the environment. Many of these factors...
A wealth of information on plant anatomy and morphology is available in the current and historical literature, and molecular biologists are producing massive amounts of transcriptome and genome data that can be used to gain better insights into the development, evolution, ecology, and physiological function of plant anatomical attributes. Integrating...
Premise of the study: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web....
The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Vertisols and other vertic-intergrade soils are found all over the globe, including many agricultural and urban areas. These soils are characterized by their cyclical shrinking and swelling behaviors, where bulk density and porosity distribution both vary as functions of time and/or soil moisture. In turn, alterations in physical soil parameters...
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
Full Text:
Kerhornou3, Brandon Walts3, Nuno
A. Fonseca3, Laura Huerta3, Maria Keays3, Y. Amy Tang3, Helen Parkinson3
Illegal fishing is a serious problem that threatens the sustainability of fisheries around the world. Historically, fisheries managers have attempted to increase the costs of illegal fishing through imposition of stricter sanctions and improvements to monitoring and enforcement programs. Non-monetary factors also influence illegal fishing behaviors, and failing to address...
There is an ever growing number of Latinas/os who reside and have settled permanently in rural America. Unbeknownst to most, rural Latinas/os face adversities unfamiliar to those living outside of this scope. As it stands, the barriers urban Latinas/os students face when transitioning to college has been well documented. However,...
The purpose of this study is to analyze women of colors's (WOC) experiences working within the United States Forest Service (USFS) accessing the challenges of recruitment, retention, and promotional efforts. Using testimonios and Anzaldúa's theory of mestiza consciousness, I found three themes that included white supremacist capitalist patriarchy, presumed incompetence,...
This M.S thesis presents an interactive software tool that I have developed in the course of the past two years. This interactive tool is called AISO. AISO is aimed at interactive image segmentation and annotation tool designed to allow users to segment an image – such as those produced with...
Concrete has been categorized as a key contributor of CO2 (carbon) emissions into the atmosphere. This is mostly associated with the production of ordinary portland cement (OPC). The concrete and cement industries are pursuing a path to reduce their carbon emissions generally in accordance with the climate change goals outlined...
Chilean society has been changing rapidly for the last few decades during a time of rapid economic growth. Some sociological and economical analyses state that when a nation grows, inequality between the rich and poor grows too, leaving the poor behind. The Chilean economy is the most rapidly growing in...
Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are valuable as pollinators. Thus, candidate pesticides in development pipelines must be assessed for toxicity to bees.
Leveraging a data set of 382 molecules with toxicity labels from honey bee exposure experiments, we...
In this article the authors examine the impact of recent
immigration on rates of serious property crime across communities in
Austin, Texas. The greater Austin foreign-born population has increased
by more than 580 percent since 1980, and Austin is considered a “pre-emerging” immigrant gateway city to the United States. The...
Quaking aspen, Populus tremuloides, has experienced severe declines in recent years in part due to the effects of changing climate and extreme drought. As the dominant deciduous tree in Western North American forests, aspen plays a critical role in forest biodiversity and ecosystem function. Therefore, the persistence of this species...
Environmental mycobacteria are important opportunistic pathogens for many hosts,
including humans, cattle, and fish. Two well-studied species are Mycobacterium
avium subsp. avium, a significant cause of disseminated bacterial disease in patients
with AIDS, and Mycobacterium avium subsp. paratuberculosis, the cause of Johne’s
disease in cattle. Many other species that are...
Over 76 cities throughout the United States have already adopted policies to limit the expansion of natural gas, mainly through updates to city codes that ban natural gas infrastructure in new construction. Rising concern over the environmental and public health impacts of methane - a greenhouse gas with a much...
In recent years, many studies have focused on the molecular and biochemical mechanisms regulating the development of wine grapes. The course of grape berry development is directed by genetic design and is mediated by phytohormones, which regulate grape berry growth and development by orchestrating a complex network of interacting genes,...
Mosses (Phylum Bryophyta) are widely considered to be among the most ancient groups of land plants (embryophytes) and they are the second most speciose embryophyte phylum with ~13,000 extant species. Despite their diversity and antiquity, mosses have a limited fossil record, which primarily consists of gametophytes entombed in Cenozoic amber....
Gene regulation is a complex mechanism that controls the spatial and temporal expression of genes in a living cell. My dissertation studies focus on two problems. First, tissue-specific gene expression prediction from DNA sequence and chromatin state, and second, the accurate discovery of small over-represented regulatory circuits in gene regulatory...
Chemistry of preparing dense film from solution deposition is explored with several cases in this thesis. Surface dense structure, conversion at melting point, and ion exchange in aqueous solution are the main topics covered here for the thin films of aluminum oxide phosphate and tin dioxide. Thin film density, optical...
Research relying on remotely sensed data on land use and deforestation has exploded in recent years. While satellite-based measures have clear advantages in terms of coverage, the presence of measurement error within these products is often overlooked. Here, we detail the econometric implications of these errors when analyzing the determinants...
How do fishing guides of the Cascade and Coast Range rivers negotiate the conflicting tensions between their client’s desire to experience the wild and the extractive nature based tourism of their role as fishing guides? How do they position their services relative to the environment and an imagined landscape that...
Few remote health monitoring (RHM) studies have included Mexican-origin Latinos, and even fewer have explored RHM acceptance and utility, reasons for RHM uptake success or failure, or how cultural values influence RHM use among this population. The primary purpose of this study was to determine the remote health monitoring (RHM)...
Wine is particularly vulnerable to infection by Brettanomyces bruxellensis during or shortly after malolactic fermentation (MLF). While different methods and techniques enable winemakers to prevent wine spoilage due to this organism, no single intervention is universally sufficient. Moreover application of sulfur dioxide, the most commonly used of these methods, is...
Characterization of the determinants of economically important phenotypes
showing complex inheritance should lead to more effective use of genetic
resources. This study was conducted to determine the number, genome location and
effects of QTLs determining malting quality and agronomic traits in the two North
American barley quality standards. Using a...
Woody biomass transportation costs and market values/costs are strongly correlated with the woody biomass moisture content. Properly managing moisture content can potentially lead to economic and environmental advantages in biomass energy markets. Good management requires accurate moisture content measurements. Therefore, availability of accurate, precise, reliable, and efficient tools to assess...
For the last 30 years, the population of Mexico has grappled with overweight, obesity, and associated chronic diseases, such as type-2 diabetes and hypertension. To standardize care among healthcare providers and dietitians, an official nutritional guideline was published in the early 2000s, which included a non-modifiable food-based dietary guideline in...
This thesis is an offering, request, testimonio, refusal, and compliance to the discipline of anthropology and higher education. In this thesis, I engage with different forms of storytelling to highlight the relationships of mixed-status families in the United States. To accomplish this, I draw on the experiences of my mother...
During the Last Glacial Maximum (LGM, ∼ 21 ky before present) the atmospheric CO2 concentration was about 100 ppm lower than its pre-industrial (PI)value. The missing carbon from the atmosphere must have been stored in thedeep ocean during this period, but the mechanisms driving such re-distribution ofthe carbon cycle are...
Biological di-nitrogen (N₂) fixation is a key process in open-ocean ecosystems, where the new nitrogen (N) provided by marine diazotrophs can support a large fraction of primary productivity and carbon (C) drawdown. Recent laboratory studies have shown that elevated pCO₂ enhances the rate of N₂ fixation by select laboratory isolates...
Both conflicts and new identities result when indigenous' traditional values of landscape and resource management are superimposed with federal governments' management of archaeological and forest resources in federally designated protected areas. This thesis examines the relationship and discourse between two Cuicatec towns in Oaxaca, Mexico and three Mexican government agencies...
Although dam construction has been an integral tool in development initiatives for nearly a century, dams can have significant negative impacts on local residents, particularly those who are permanently displaced from their homes and must be resettled elsewhere. Dams have unique impacts on indigenous peoples. As a result, many dam...
The search for the stand density that optimizes growth and hence generates the maximum amount of wood is one of the philosopher’s stone in modern forestry. Since scientific methods were applied to forestry, numerous generations of foresters have studied the relations between stocking density and growth, obtaining diverse results and...
Archaeological excavations of the Cooper's Ferry site in the Lower Salmon River Canyon, Idaho, have revealed a stratified record of cultural occupation, spanning the late Pleistocene and early Holocene periods. The purpose of this study was to contribute to the understanding of cultural adaptive strategies represented in the archaeological record...