Thesis (M.S.)--Middle East Technical University, 2004. / Keywords: Cytochrome P4501A1, EROD, PAH, PCB, dioxins, Izmir Bay, pollution, procarcinogen, ecotoxicology.

Thesis (M.S.) -- Middle East Technical University, 2005. / Keywords: Wheat immature inflorescence; Regeneration; Agrobacterium tumefaciens; GUS; Transient gene expression, Vernalization.

Predation pressure is a powerful agent of natural selection and is responsible for the evolution of various antipredator defence strategies in animals. Sensory thresholds for predator detection could play an important role in the evolution of defence strategies. I tested the hypothesis that the ability of animals to detect predators is correlated with defence strategy, with the prediction that animals with poor predator detection abilities rely more on preventative (primary) defence strategies than animals with low predator detection thresholds. Bats and their insect prey were used as a simple study system for these experiments due to the reliance on a single modality (hearing) for both predator and prey detection. Many insects have ears tuned to the ultrasonic echolocation calls of bats and can use this predator cue to initiate evasive action, but variation in auditory thresholds exists among species. In moths, a group in which the only known function of hearing is predator detection, a clear relationship was found between auditory thresholds for predatory ultrasound and a risky behaviour, nocturnal flight time. A more complicated situation exists when the sensory system serves more than one purpose, as with the ears of orthopteran insects used for both predator detection and mate localization. Some gleaning bats use calling song as a cue to locate these insects as prey, and both primary (reduced calling) and secondary (song cessation in response to ultrasound) defences have been identified in orthopterans. The auditory interneurons considered the “bat-detectors” in katydids and crickets most likely have context dependent functions in several groups, as a predator-detector in flight and mate-detector on the ground. The relationship between reliance on primary over secondary defence and auditory sensitivity in these insects appears to be influenced by the nature of the calling song of the species and their mating strategy.

<p> Land use change to meet economic and societal demands has negatively impacted the current state of our world's ecosystems and biodiversity. The alarming rate of landscape change and degradation has prompted ecologists to conserve intact areas and restore historical habitats in the hopes of mitigating the potential damage. As a result, restoration ecology was developed and has grown dramatically within the past couple decades. Historically, the Mississippi Alluvial Valley, provided services such as water enhancement and nutrient cycling, and the characteristic bottomland hardwood forests dominated the land cover and were suitable habitat for many organisms, especially neotropical migrants. As the Upper Mississippi Alluvial Valley was converted into agricultural fields and locks and dams were installed, many neotropical migrants had steady population declines. More recent surveys have noted that approximately two-thirds of the neotropical migrants have been declining for the past half-century. For the past two decades, the U.S. Army Corp of Engineers (USACE) has been responsible for the restoration of bottomland hardwood forests in the Upper Mississippi Valley. Using birds as model organisms, this project assessed the restoration success of this site by (1) comparing avian richness, diversity, and density among a chronosequence of forest restoration age classes to determine any significant differences in species assemblage in the chronosequence and (2) creating a predictive habitat model that assists in the formulation of appropriate recommendations for restoration planning and management in the future. I hypothesize that species richness and diversity is highest at intermediate sites since they will have habitat characteristics of both grasslands and forests and that my habitat models identifies structural variables, such vegetation height, and tree height and ground cover as significant determinants of avian presence. Our study included a chronosequence of nine restoration sites and two references in which bird surveys and vegetation surveys were completed. Avian surveys consisted of 25-m fixed radius point counts at five plots per site. Sites were visited three times for the spring and fall data collections. Spring data will continue May 2014 due to unusual flooding conditions. Within the 25-m radius, a 17.84-m radius vegetation plot was created. Tree species, tree health variables, diameter at breast height (DBH), and abundance were recorded, and the tree was tagged. Shrub stem count data was recorded in four belts within each vegetation plot, with the condition that a shrub is at least 1-m in height. The plot was divided into four belts, and five quadrats of 0.5 m2 were formed along each belt to record forb and grass cover and litter depth. Species richness, Antilog Shannon-Weiner's Diversity Index, and Simpson's Diversity Index was calculated, and the vegetation data was used in the predictive habitat modeling. I recorded 52 bird species during the spring and 79 bird species during that fall that were within the 25-m radius. Bird species richness and diversity differed among the sites, and richness and diversity generally increased as the age of the site increased. Grassland and shrubland birds did not have any significant trends for vegetation parameters. However, most open woodland birds had a significant association with DBH, and a majority of forest birds had significant associations with tree height and crown size. The observed richness and diversity values contradict several studies but may be attributed to the productivity rate of the sites chosen. Density estimates can also be enhanced through new surveying methods which would address detectability issues for naturally skittish birds. Future restoration efforts should include the planting of fast-growing trees and shrubs in order to increase structural diversity at faster rates. In addition, more sites should be acquired and restored in order to create close patches for neotropical migrants to facilitate travel. Continuing efforts in restoration and appropriate management should emphasize the causes of declines for land birds and identify them early enough to develop an appropriate management plan.</p>

Physiological consequences of temperature stress on the marine snail, Lottia gigantea

<p> Early light induced proteins (ELIPs) are widely distributed in the plant kingdom. Members of the extended light harvesting complex (LHC) superfamily, <i> ELIP</i>s are expressed in the nucleus and the ELIP protein is transiently localized to the thylakoid membranes. Significant increase in expression of <i> ELIP</i>s has been reported in response to stresses such as high light, high and low temperature, exposure to UV and salinity. ELIP expression also increases at transitional stages of chloroplast development such as deetiolation, conversion to chromoplast, and senescence.</p><p> In search of <i>cis-</i>regulatory regions, the <i>A. thaliana ELIP1</i> gene promoter has been investigated in our lab. A double-SORLIP1 element was identified as a critical <i>cis-</i>regulatory region common in the promoters of <i>A. thaliana ELIP1</i> (At3g22840) and <i>ELIP2</i> (At4g14690). Point mutations in the double-SORLIP1 element led to significant decline in expression.</p><p> Due to the importance of the double-SORLIP1 element, a yeast-one-hybrid assay was set up to find the specific DNA-binding proteins that bind to this region. Light harvesting complex II (LHCA2) and the ortholog of sugar beet HS1 PRO-1 2, heat-shock-like protein 2 (HSPRO2), showed a high specificity in binding to the double-SORLIP1 element. Investigation of <i>lhca2</i> and <i>hspro2 Arabidopsis</i> mutants did not show any significant difference in high light induced expression of <i>ELIP1</i> or <i> ELIP2</i> as compared to wild type. However, the high frequency of LHCA2 clones selected by yeast-one-hybrid assay and the high specificity in binding to the double-SORLIP1 element cannot be ignored.</p><p> After reviewing the literature, I hypothesized that LHCA2 may be a new retrograde signal that regulates expression of <i>ELIP</i> genes. However, more experimental evidence is needed to support this proposed function. The potential regulatory role of HSPRO2 is also discussed.</p>

<p> The basal lamina of skeletal muscle is a specialized region of extracellular matrix (ECM) comprised primarily of type IV collagen. Remodeling of the basal lamina, through altered expression or degradation of type IV collagen, is an important component of muscle plasticity. Matrix metalloproteinase-9 (MMP-9) is an inducibly expressed enzyme that degrades type IV collagen, and thus its enzymatic activity may play a key role in maintenance and plasticity of muscle structure and function. The purpose of this dissertation was to investigate the role of MMP-9-induced remodeling during normal development, exercise-induced injury, post-injury repair and aging of skeletal muscle. </p><p> Inactivation of the MMP-9 gene by homologous recombination resulted in decreases in muscle cross sectional area and enrichment of fast-twitch fiber types in several adult hindlimb muscles. Despite these compositional changes force production in MMP-9 null muscle remained normal. </p><p> Using a downhill running model of injury, I found that plasma concentration of MMP-9 in WT mice increased immediately exercise, while inactivation of the MMP-9 gene resulted in a significant decrease in post-injury muscle sarcolemmal damage. The source of MMP-9 appeared to be white blood cells and not muscle tissue itself, indicating the enzyme's activity might be required for immune cell infiltration of damaged muscle. However, using a chemically induced model of muscle injury, I found that immune cell infiltration was not diminished in MMP-9 null mice. Similarly, MMP-9 inactivation did not impair muscle stem cell activity or muscle regeneration. Thus while MMP-9 is involved in the magnitude of the injury response it appears to be dispensable for critical aspects of the post-injury repair process. </p><p> Finally, hindlimb muscles of older WT mice had increased type IV collagen content compared to younger mice, despite the two age groups having similar levels of COL4a1 mRNA expression. Older mice also exhibited reduced MMP-2, but not MMP-9, expression in muscle, and MMP-9 inactivation did not alter collagen levels in older mice. Thus, while aging is accompanied by altered basal lamina composition MMP-9 does not appear to play a critical role in this phenomenon. </p><p> In summary, these findings demonstrate that MMP-9 is involved in most, but not all, of the remodeling events studied, with aging being the exception. </p>

<p> mTOR (Mammalian Target ofRapamycin), PI3K (Phosphatidylinositol3-kinase) and MEK (Mitogen-activated protein kinase/ERK kinase) have been shown to be potent regulators ofS6Kl at G₁ phase of the cell cycle. Research has been concentrated at the Gt phase to elucidate mTOR's role in cell growth and proliferation. Limited information is available on the activity ofmTOR, PI3K and ERKl/2 in cell cycle phases other than G₁. Since we have observed that S6Kl is active in phases other than G₁ our goal was to ascertain ifmTOR, PI3K or ERKl/2 have a role in regulating S6Kl during these cell cycle phases. Using cell cycle analysis and immunoblot analysis we have determined here that mTORand PI3K could play a role in regulating S6Kl at the G₁/S transition iQ. the cell cycle but there is also indications that mTOR and PI3K are potentially involved in regulating S6Kl in the phases post-G₁/S of the cell cycle, indicating a complex interaction between the kinases used to regulate S6Kl during the cell cycle. ERKl/2 is demonstrated to have limited involvement in the regulation of S6Kl during the cell cycle.</p>

<p> I investigated the determinants of distributional patterns in the mussel <i> Mytilus californianus</i> in the Strait of Juan de Fuca in Washington State. A three pronged approach including evolutionary, geomorphological, and population ecology research methods elucidated processes determining the density and distribution of the species as well as forces impacting its future trajectory. Primary conclusions include: 1. Changes in aerial temperatures in Washington State in the near future are unlikely to dramatically influence the abundance and distribution of <i>Mytilus californianus.</i> 2. The interaction of sea level rise with the geomorphological features of rocky coasts has the potential to dramatically change the distribution and abundance of shallow water depth restricted species like <i>Mytilus californianus.</i> 3. Distributional patterns of <i> Mytilus californianus</i> occurring at multiple spatial scales are a result of the integration of population vital rates as determined by environmental gradients, and variation in vital rates are sometimes scale dependent (growth and recruitment rates) and sometimes not (survival rates). 4. Mussel populations were most sensitive to variation in growth rates, least sensitive to variation in recruitment rates, and intermediately sensitive to variation in survival. 5. <i>Mytilus californianus</i> density is unlikely to be primarily controlled by variation in growth rate or recruitment rate.</p>

Predation pressure is a powerful agent of natural selection and is responsible for the evolution of various antipredator defence strategies in animals. Sensory thresholds for predator detection could play an important role in the evolution of defence strategies. I tested the hypothesis that the ability of animals to detect predators is correlated with defence strategy, with the prediction that animals with poor predator detection abilities rely more on preventative (primary) defence strategies than animals with low predator detection thresholds. Bats and their insect prey were used as a simple study system for these experiments due to the reliance on a single modality (hearing) for both predator and prey detection. Many insects have ears tuned to the ultrasonic echolocation calls of bats and can use this predator cue to initiate evasive action, but variation in auditory thresholds exists among species. In moths, a group in which the only known function of hearing is predator detection, a clear relationship was found between auditory thresholds for predatory ultrasound and a risky behaviour, nocturnal flight time. A more complicated situation exists when the sensory system serves more than one purpose, as with the ears of orthopteran insects used for both predator detection and mate localization. Some gleaning bats use calling song as a cue to locate these insects as prey, and both primary (reduced calling) and secondary (song cessation in response to ultrasound) defences have been identified in orthopterans. The auditory interneurons considered the “bat-detectors” in katydids and crickets most likely have context dependent functions in several groups, as a predator-detector in flight and mate-detector on the ground. The relationship between reliance on primary over secondary defence and auditory sensitivity in these insects appears to be influenced by the nature of the calling song of the species and their mating strategy.