Matching Items (64)
Description
The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of organic carbon into deep water, combined with the physical carbon pump, make the oceans the only long-term net sink for anthropogenic carbon dioxide. A full understanding of the workings of the biological carbon pump requires a knowledge of the role of different taxonomic groups of phytoplankton (protists and cyanobacteria) to organic carbon export. However, this has been difficult due to the degraded nature of particles sinking into particle traps, the main tools employed by oceanographers to collect sinking particulate matter in the ocean. In this study DNA-based molecular methods, including denaturing gradient gel electrophoresis, cloning and sequencing, and taxon-specific quantitative PCR, allowed for the first time for the identification of which protists and cyanobacteria contributed to the material collected by the traps in relation to their presence in the euphotic zone. I conducted this study at two time-series stations in the subtropical North Atlantic Ocean, one north of the Canary Islands, and one located south of Bermuda. The Bermuda study allowed me to investigate seasonal and interannual changes in the contribution of the plankton community to particle flux. I could also show that small unarmored taxa, including representatives of prasinophytes and cyanobacteria, constituted a significant fraction of sequences recovered from sediment trap material. Prasinophyte sequences alone could account for up to 13% of the clone library sequences of trap material during bloom periods. These observations contradict a long-standing paradigm in biological oceanography that only large taxa with mineral shells are capable of sinking while smaller, unarmored cells are recycled in the euphotic zone through the microbial loop. Climate change and a subsequent warming of the surface ocean may lead to a shift in the protist community toward smaller cell size in the future, but in light of these findings these changes may not necessarily lead to a reduction in the strength of the biological carbon pump.
ContributorsAmacher, Jessica (Author) / Neuer, Susanne (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Lomas, Michael (Committee member) / Wojciechowski, Martin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
The Cape Floral Region (CFR) in southwestern South Africa is one of the most diverse in the world, with >9,000 plant species, 70% of which are endemic, in an area of only ~90,000 km2. Many have suggested that the CFR's heterogeneous environment, with respect to landscape gradients, vegetation, rainfall, elevation, and soil fertility, is responsible for the origin and maintenance of this biodiversity. While studies have struggled to link species diversity with these features, no study has attempted to associate patterns of gene flow with environmental data to determine how CFR biodiversity evolves on different scales. Here, a molecular population genetic data is presented for a widespread CFR plant, Leucadendron salignum, across 51 locations with 5-kb of chloroplast (cpDNA) and 6-kb of unlinked nuclear (nuDNA) DNA sequences in a dataset of 305 individuals. In the cpDNA dataset, significant genetic structure was found to vary on temporal and spatial scales, separating Western and Eastern Capes - the latter of which appears to be recently derived from the former - with the highest diversity in the heart of the CFR in a central region. A second study applied a statistical model using vegetation and soil composition and found fine-scale genetic divergence is better explained by this landscape resistance model than a geographic distance model. Finally, a third analysis contrasted cpDNA and nuDNA datasets, and revealed very little geographic structure in the latter, suggesting that seed and pollen dispersal can have different evolutionary genetic histories of gene flow on even small CFR scales. These three studies together caution that different genomic markers need to be considered when modeling the geographic and temporal origin of CFR groups. From a greater perspective, the results here are consistent with the hypothesis that landscape heterogeneity is one driving influence in limiting gene flow across the CFR that can lead to species diversity on fine-scales. Nonetheless, while this pattern may be true of the widespread L. salignum, the extension of this approach is now warranted for other CFR species with varying ranges and dispersal mechanisms to determine how universal these patterns of landscape genetic diversity are.
ContributorsTassone, Erica (Author) / Verrelli, Brian C (Thesis advisor) / Dowling, Thomas (Committee member) / Cartwright, Reed (Committee member) / Rosenberg, Michael S. (Committee member) / Wojciechowski, Martin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Triops (Branchiopoda: Notostraca) and Streptocephalus (Branchiopoda: Anostraca) are two crustaceans which cohabitate in ephemeral freshwater pools. They both lay desiccation resistant eggs that disperse passively to new hydrologically isolated environments. The extent of genetic distance among regions and populations is of perennial interest in animals that live in such isolated habitats. Populations in six natural ephemeral pool habitats located in two different regions of the Sonoran Desert and a transition area between the Sonoran and Chihuahuan Deserts were sampled. Sequences from Genbank were used for reference points in the determination of species as well as to further identify regional genetic distance within species. This study estimated the amount of within and between genetic distance of individuals from each region and population through the use of a neutral marker, cytochrome oxidase I (COI). We concluded that, although the method of passive dispersal may differ between the two genera, the differences do not results in different patterns of genetic distances between regions and populations. Furthermore, we only found the putative species, Triops longicaudatus "short", with enough distinct speciation. Although Triops longicaudatus "long" and Triops newberryi may be in the early stages of speciation, this study does not find enough support to conclude that they have separated.
ContributorsMurphy Jr., Patrick Joseph (Author) / Rutowski, Ronald (Thesis director) / Cartwright, Reed (Committee member) / Lessios, Nikos (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
There is a relative lack of basic information about early diverging species of the genus Medicago that, for the most part, were formerly considered to be in the genus Trigonella. Species boundaries are not always clear, for example, the most recent treatment of the genus Medicago submerged four previously recognized species into Medicago monantha, a widely distributed species in the Middle East. These species are recognized on the basis of morphological characters such as fruit number, shape, length and areole shape and size, but species identification is still challenging and further clarification of species boundaries is needed. There is also a lack of cytogenetic information. Some of the relatively few published chromosome numbers, e.g. 2n=28, and 44, differ from those of the rest of the genus, which are mostly 2n=16 or multiples thereof, although seven species are 2n=14. As part of a larger study of the genome and chromosome number evolution in the genus Medicago, we obtained genome size data using flow cytometry for 44 accessions of 14 currently recognized early diverging species, with a focus on Medicago monantha. Chromosome numbers were obtained using standard cytological methods. Our chromosome number data confirm a chromosome number of 2n=16 for M. brachycarpa (genome size of 1.33 pg), and M. monspeliaca (1.88 pg), and 2n=28 for M. polyceratia (2.77 pg) and give new numbers for some species; 2n=16 for M. biflora (2.7 pg), and a previously unknown chromosome number for these early diverging species of 2n=14 for Medicago fischeriana (~1.35 pg). Interestingly, our data support the hypothesis that there are at least two entities within M. monantha as currently recognized that differ in chromosome number and genome size; two accessions had chromosome numbers of 2n=26 and 30 with corresponding genome sizes of 2.68 and 2.85 pg and three other accessions had chromosome numbers 2n=36,44, and another 44 with genome sizes of 3.94, 3.89, and 4.04 pg. There are also some significant morphological differences between these two entities, such as fruit length and areole area. These data lead to both further clarification of the relationships of early diverging Medicago and help build a platform for more in-depth research concerning the evolution of chromosome number and genome size within Medicago.
ContributorsSteier, Julia Elizabeth (Author) / Steele, Kelly (Thesis director) / Wojciechowski, Martin (Committee member) / Fehlberg, Shannon (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Overexpression of AVP1 (Arabidopsis vacuolar pyrophosphatase), a type I H+ pyrophosphatase, results in greater biomass, possibly due to a function in sucrose transport within the phloem. Overexpression of the phloem lipid-associated family protein (PLAFP) was shown to increase the number of vascular bundles in Arabidopsis. Could these two phenotypes complement one another additively? In this work, double mutants overexpressing both AVP1 and PLAFP were characterized. These double mutants have enhanced biomass, greater leaf area, and a larger number of vascular bundles than the single mutant lines. Overexpression of PLAFP does not result in any increase in rhizosphere acidification capacity.
ContributorsWilson, Sean (Co-author) / Furstenau, Tara (Co-author) / Gaxiola, Roberto (Thesis director) / Mason, Hugh (Committee member) / Wojciechowski, Martin (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Type I H+-PPase encoding genes, such as AVP1 (Arabidopsis thaliana), TsVP (Thellungiella halophilla), TaVP,( Triticum aestivum), and OVP1 (Oryza sativa) are highly conserved and.traditionally known to operate as vacuolar proton translocating pyrophosphatases. It is worth mentioning that Rocha-Facanha and de Meis presented in vitro evidence with tonoplast fractions of maize coleoptiles and seeds consistent with the reverse function of the H+-PPase (1998). These authors suggested that given the appropriate thermodynamic conditions in vivo, the H+-PPase could operate as a system of energy conservation with a role in the maintenance of cytosolic PPi levels. Further evidence in support for a PPi-synthase activity of plant H+-PPases came from work done on tonoplasts from mature oranges where PPi synthesis was demonstrated when a ΔpH of 3 units was imposed (Marsh et al. 2000).
Futher research has shown that transgenics overexpressing type I H+-PPases develop more root and shoot biomass, and have enhanced rhizosphere acidification capacity than wild types. The increased root biomass suggests that previous reports describing the response of these plants to water scarcity as drought tolerance are incomplete. Larger root systems indicate that an important component of the response is drought resistance. The enhanced rhizosphere acidification capacity has also been associated with an increase in nutrient use efficiency, conferring a growth advantage under nitrogen and phosphorous deficient conditions.
While a vacuolar localized H+-PPase easily explains the salt tolerant phenotypes, it does little to provide a mechanism for an increase in root and shoot biomass and/or an augmented rhizosphere acidification capacity. Several groups have argued that higher levels and transport of the growth hormone auxin could be responsible for the above phenotypes. An alternative model focusing on the function of a plasma membrane bound H+-PPase in sieve elements and companion cells links these phenotypes with enhanced phloem sucrose loading and transport.
The following paper reviews publications in which the H+-PPase overexpression technology has been used since 2006 in an attempt to identify cues that could help us test the compatibility of the the proposed models with the actual data.
Futher research has shown that transgenics overexpressing type I H+-PPases develop more root and shoot biomass, and have enhanced rhizosphere acidification capacity than wild types. The increased root biomass suggests that previous reports describing the response of these plants to water scarcity as drought tolerance are incomplete. Larger root systems indicate that an important component of the response is drought resistance. The enhanced rhizosphere acidification capacity has also been associated with an increase in nutrient use efficiency, conferring a growth advantage under nitrogen and phosphorous deficient conditions.
While a vacuolar localized H+-PPase easily explains the salt tolerant phenotypes, it does little to provide a mechanism for an increase in root and shoot biomass and/or an augmented rhizosphere acidification capacity. Several groups have argued that higher levels and transport of the growth hormone auxin could be responsible for the above phenotypes. An alternative model focusing on the function of a plasma membrane bound H+-PPase in sieve elements and companion cells links these phenotypes with enhanced phloem sucrose loading and transport.
The following paper reviews publications in which the H+-PPase overexpression technology has been used since 2006 in an attempt to identify cues that could help us test the compatibility of the the proposed models with the actual data.
ContributorsCoulter, Joshua (Author) / Gaxiola, Roberto (Thesis director) / Wojciechowski, Martin (Committee member) / Pizzio, Gaston (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
The evolution of blindness in cave animals has been heavily studied; however, little research has been done on the interaction of migration and drift on the development of blindness in these populations. In this study, a model is used to compare the effect that genetic drift has on the fixation of a blindness allele for varying amounts of migration and selection. For populations where the initial frequency is quite low, genetic drift plays a much larger role in the fixation of blindness than populations where the initial frequency is high. In populations where the initial frequency is high, genetic drift plays almost no role in fixation. Our results suggest that migration plays a greater role in the fate of the blindness allele than selection.
ContributorsMerry, Alexandra Leigh (Author) / Cartwright, Reed (Thesis director) / Rosenberg, Michael (Committee member) / Schwartz, Rachel (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
It is important to consider factors that contribute to successful fertilization and the development of viable offspring. Better understanding the factors that contribute to infertility can be used to assist in the development of viable offspring, especially for human beings looking to successfully reproduce. Identifying paternal effect genes, genes that come from the father, introduces more targets that can be manipulated to produce specific reproductive effects. Use of Drosophila melanogaster as a model to study reproduction has increased, in part, due to the use of the GAL4 system. In this system, the GAL4 gene encodes an 881 amino acid protein that binds to the 4-site Upstream Activating Sequence (UAS) to induce transcription of the gene of interest. These sequences constitute the two components of the system: the driver (GAL4) and the responder (gene of interest) \u2014 each of which is maintained as a separate parental line. Effects of the GAL4 driver line "driving" transcription of the responder can be assessed by examining the offspring. One of the more common uses of the GAL4 system involves analyzing phenotypic effects of reducing or eliminating expression of a target gene through the induction of RNAi transcription, which often results in toxicity, lethality, or reduced viability. Utilizing these principles, we strove to demonstrate the effect of knocking down the expression of testis-specific sperm-leucyl-aminopeptidases gene CG13340 on progeny by inducing expression of RNAi with two distinct GAL4 driver lines - one with a nonspecific actin-binding activation sequence and the other with a testis-specific activation sequence. Comparison of both GAL4 driver lines to crosses using N01 wild type ("wt") flies verify that inducing RNAi transcription using the GAL4 system results in reduction of proper offspring development. Further studies using D. melanogaster and the GAL4 system can improve knowledge of factors contributing to male fertility and also be applied to better understand mammalian, specifically human, fertility.
ContributorsEvans, Donna Marie (Author) / Karr, Timothy L. (Thesis director) / Roland, Kenneth (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of English (Contributor)
Created2014-05
Description
The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern web development technologies, Genie was developed as a simulator to help educators in biology, genetics, and evolution classrooms teach their students about population genetics. Because Genie was designed for the modern web, it is highly accessible to both educators and students, who can access the web application using any modern web browser on virtually any device. Genie demonstrates the efficacy of web devel- opment technologies for demonstrating and simulating complex processes, and it will be a unique educational tool for educators who teach population genetics.
ContributorsRoos, Benjamin Hirsch (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Mayron, Liam (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
Description
Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
ContributorsSchwartz, Rachel (Author) / Harkins, Kelly (Author) / Stone, Anne (Author) / Cartwright, Reed (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-06-11