The relationship between anthropogenic disturbance and the distribution of a nonindigenous species, Echinogammarus ischnus Stebbing, 1898 (Amphipoda: Gammaridae), at Great Lakes coastal margins

Invasive species are becoming increasingly common components of Great Lakes zoobenthic communities. Elton (1958) proposed that biotic resistance against exotic species establishment is greater in intact communities than in those disturbed by human activities. However, Baltz and Moyle (1993) suggested that if abiotic conditions are appropriate, invasion is likely, regardless of the biota already present. I tested these hypotheses by investigating the distribution of Echinogammarus ischnus Stebbing, 1898, an exotic amphipod, at U.S. Great Lakes coastal margin sites influenced by varying degrees of anthropogenic stress. Thirty-nine sites supporting Gammarus fasciatus Say, 1818, a common amphipod with habitat preferences similar to Echinogammarus ischnus, were evaluated (out of a total of 74 sites sampled across the entire U.S. Great Lakes coastline). A highly significant association was detected between Echinogammarus ischnus and Gammarus fasciatus (Yates corrected chi2 = 7.94, d.f. = 1, p \u3c 0.020, n = 74), consistent with the expectations of Baltz and Moyle\u27s hypothesis. (Abstract shortened by UMI.)Dept. of Biological Sciences. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2003 .K36. Source: Masters Abstracts International, Volume: 43-03, page: 0772. Adviser: Jan Ciborowski. Thesis (M.Sc.)--University of Windsor (Canada), 2003

HYDRAULIC PROPERTIES OF VARIABLY-SATURATED POROUS MEDIA DETERMINED USING QUANTITATIVE NEUTRON RADIOGRAPHY

The theoretical understanding of fluids in unsaturated porous media has improved substantially over the last several decades. Water retention curves remain a central pillar in the theoretical framework for modeling of water flow in unsaturated porous media. Use of the average water retention function in models to simulate water flow in porous media can result in inaccurate predictions due to the variations in water content and matric potential with elevation within the medium. As a result, point water retention curve data are needed for testing existing numerical and analytical models and for improving our ability to predict unsaturated water flow. Traditionally point water retention functions have been derived from average water retention curve data. The main objective of this research was to directly measure point water retention functions using neutron imaging. Neutron imaging provides a non-destructive tool for visualizing water flow in porous media due to its high sensitivity to hydrogen, and relative insensitivity to mineral solids. Using neutron imaging techniques we have explored the following research topics: (1) quantitative measurements of the equilibrium water content distribution in porous media, (2) measurement of average and point water retention functions using neutron radiography, (3) assessment of analytical models relating average and point water retention curves, and (4) investigation of the dynamics of unsaturated water flow. In the first two chapters of this dissertation we developed quantitative neutron imaging techniques to measure the 2-dimensional distribution of water in porous media and obtain the average water retention function for Flint sand by neutron radiography. In chapter III, point water retention functions were directly measured by neutron radiography and the resulting point functions were parameterized using the Brooks & Corey equation. The point water retention function constructed from the median values of the fitted Brooks and Corey parameters corresponded closely with the point curve for Flint sand obtained by inverse modeling of the average water retention curve data. In the final chapter of this dissertation we investigated capillary uptake of water in Berea Sandstone and estimated the sorptivity and unsaturated diffusivity function from analyses of the neutron radiographs

Patterns of biodiversity and co-occurrence of native and nonindigenous species at Great Lakes coastal margins

Studies that assess the ecological processes that allow establishment by a nonindigenous species in the Laurentian Great Lakes can help elucidate general ecological processes. The Great Lakes has such varied habitats that observations of any general patterns in ecological processes, involving both native species and nonindigenous species, likely pertain elsewhere. Studies relating biotic interactions and interaction-neutral processes to invasibility are numerous, but they have been largely inconclusive. This thesis evaluates hypotheses linking biotic interaction (i.e., richness, evenness, and dominance) and neutral-interaction (i.e., dispersal/propagule pressure) processes of several taxonomic groups (birds, diatoms, fishes, macroinvertebrates, and wetland vegetation) to invasibility at various spatial scales and sample sizes. These hypotheses were assessed using synoptic sample collections from various locations throughout the US Laurentian Great Lakes coastal margins influenced by varying types and levels of anthropogenic disturbance. I tested hypotheses relating biotic resistance versus habitat suitability to invasion by a nonindigenous amphipod. Results supported the view that biotic facilitation by dreissenid mussels and distribution of suitable habitats better explain the distribution of the nonindigenous amphipod than anthropogenic disturbance and biotic resistance. I evaluated hypotheses relating richness, evenness, and relative species dominance to invasibility and the occurrence of native and nonindigenous species using data compiled for various taxonomic groups from several hundred locations along the US coastline of the Laurentian Great Lakes. Across taxonomic groups, trends of native and nonindigenous species distributions were inconsistent with regulation by biotic interaction related processes. Regulation by neutral processes, such as propagule pressure or habitat suitability may better explain patterns. Native species distributions were correlated with habitat suitability and habitat hydrogeomorphology, and ranges reflect biogeographic history. The factors that constrain nonindigenous species are arguably a variation of those that constrain native species distributions, thus indicating that similar factors constrain both native and nonindigenous species. The general accuracy of these synoptic findings was assessed by comparing biodiversity estimation performance of data resulting from intensive sampling protocols. A method proposed by Olszewski (2004), which is alternative to rarefaction and statistical estimators for species richness, was also tested. This method uses the evenness component of biodiversity and requires a limited number of samples for estimations. My findings indicated that true biodiversity measures cannot be attained efficiently from surveys. Since such measures are unattainable, interpretation of biodiversity studies would benefit from closer examination of detectable species (i.e., common species) that likely have a stronger impact on community processes, than rare and/or transient species. Nonindigenous species that become widespread and abundant are likely governed by the same factors that regulate common native species. Ecology would benefit from linking studies of the factors that regulate the distribution and abundances of common species, both native and nonindigenous, and the dynamics between biodiversity and ecosystem properties and processes

Quantification of soil organic carbon using mid- and near- DRIFT spectroscopy

New, rapid techniques to quantify the different pools of soil organic matter (SOM) are needed to improve our understanding of the dynamics and spatio-temporal variability of SOM in terrestrial ecosystems. In this study, total organic carbon (TOC) and oxidizable organic carbon (OCWB) fraction were calibrated and predicted by mid- and near-DRIFT spectroscopy in combination with partial least squares (PLS) regression method. PLS regression is a multivariate calibration method that can decompose spectral data (X) and soil property data (Y) into a new smaller set of latent variables and their scores that best describe all the variance in the data. Oxidizable organic carbon content was measured by a modified Walkley-Black method, and total organic carbon was measured by the carbon analyzer. The floodplain and Blackland Prairie soils in Texas were used for prediction of TOC and OCWB using mid- and near-DRIFT spectroscopy. Floodplain soil is mainly composed of quartz and kaolinite, whereas Blackland Prairie soils contain high concentrations of smectitic clays and low to high concentrations of carbonate minerals. The total organic carbon of 68 soil samples from two Texas sites varied between 0.19 and 4.36 wt.% C, and the oxidizable organic carbon of 26 samples from floodplain soils was in the range of 0.05 to 1.33 wt.% C. TOC and OCWB of soil were successfully calibrated and predicted by the PLS regression method using mid- and near-DRIFT spectroscopy. The correlation using mid-IR spectra for TOC (r = 0.96, RMSEV = 0.32 for calibration; r = 0.93, RMSEP = 0.44 for prediction) was about the same as the near-IR result (r = 0.95, RMSEV = 0.37; r = 0.93, RMSEP = 0.42). Therefore, we can also use mid-infrared region for quantification of total organic carbon in soils. The PLS1 regression model (r = 0.92) for prediction of OCWB using mid-IR spectra was more accurate than the PLS2 regression model (r = 0.90). PLS models showed better correlation with spectral data than the univariate least square regression method(r = 0.83) with TOC measured by the carbon analyzer. This study shows that the partial least squares (PLS1) method using mid-and near-IR spectra of neat soil samples can be used to predict both total organic carbon and oxidizable carbon fraction as a fast and routine quantitative method

Polymicrobial periodontal disease triggers a wide radius of effect and unique virome.

Periodontal disease is a microbially-mediated inflammatory disease of tooth-supporting tissues that leads to bone and tissue loss around teeth. Although bacterially-mediated mechanisms of alveolar bone destruction have been widely studied, the effects of a polymicrobial infection on the periodontal ligament and microbiome/virome have not been well explored. Therefore, the current investigation introduced a new mouse model of periodontal disease to examine the effects of a polymicrobial infection on periodontal ligament (PDL) properties, changes in bone loss, the host immune response, and the microbiome/virome using shotgun sequencing. Periodontal pathogens, namely Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Fusobacterium nucleatum were used as the polymicrobial oral inoculum in BALB/cByJ mice. The polymicrobial infection triggered significant alveolar bone loss, a heightened antibody response, an elevated cytokine immune response, a significant shift in viral diversity and virome composition, and a widening of the PDL space; the latter two findings have not been previously reported in periodontal disease models. Changes in the PDL space were present at sites far away from the site of insult, indicating that the polymicrobial radius of effect extends beyond the bone loss areas and site of initial infection and wider than previously appreciated. Associations were found between bone loss, specific viral and bacterial species, immune genes, and PDL space changes. These findings may have significant implications for the pathogenesis of periodontal disease and biomechanical properties of the periodontium. This new polymicrobial mouse model of periodontal disease in a common mouse strain is useful for evaluating the features of periodontal disease

Doping Dependence of Spin-Lattice Coupling and Two-Dimensional Ordering in Multiferroic Hexagonal Y₁₋ₓLuₓMnO₃ (0 ≤ x ≤ 1)

We have examined a complete phase diagram of Y1-x Lu xMnO3 with 0≤x≤1 by using bulk measurements and neutron-diffraction studies. With increasing Lu concentration, Curie-Weiss temperature and Neel temperature are found to increase continuously while the two-dimensional nature of short-range magnetic correlation persists even in the paramagnetic phase throughout the entire doping range. At the same time, the lattice constants and the unit-cell volume get contracted with Lu doping, i.e., chemical pressure effect. This decrease in the lattice constants and the unit-cell volume then leads naturally to an increased magnetic exchange interaction as found in our local spin-density approximation band calculations. We also discover that there is strong correlation in the temperature dependence of a volume anomaly at TN and the magnetic moments

NFATc1 regulates the transcription of DNA damage-induced apoptosis suppressor

AbstractDNA damage induced apoptosis suppressor (DDIAS), or human Noxin (hNoxin), is strongly expressed in lung cancers. DDIAS knockdown induced apoptosis in non-small cell lung carcinoma A549 cells in response to DNA damage, indicating DDIAS as a potential therapeutic target in lung cancer. To understand the transcriptional regulation of DDIAS, we determined the transcription start site, promoter region, and transcription factor. We found that DDIAS transcription begins at nucleotide 212 upstream of the DDIAS translation start site. We cloned the DDIAS promoter region and identified NFAT2 as a major transcription factor (Im et al., 2016 [1]). We demonstrated that NFATc1 regulates DDIAS expression in both pancreatic cancer Panc-1 cells and lung cancer cells

Ring finger protein 126 (RNF126) suppresses ionizing radiation-induced p53-binding protein 1 (53BP1) focus formation

Cells have evolved sophisticated mechanisms to maintain genomic integrity in response to DNA damage. Ionizing radiation (IR)-induced DNA damage results in the formation of IR-induced foci (iRIF) in the nucleus. The iRIF formation is part of the DNA damage response (DDR), which is an essential signaling cascade that must be strictly regulated because either the loss of or an augmented DDR leads to loss of genome integrity. Accordingly, negative regulation of the DDR is as critical as its activation. In this study, we have identified ring finger protein 126 (RNF126) as a negative regulator of the DDR from a screen of iRIF containing 53BP1. RNF126 overexpression abolishes not only the formation of 53BP1 iRIF but also of RNF168, FK2, RAP80, and BRCA1. However, the iRIF formation of H2AX, MDC1, and RNF8 is maintained, indicating that RNF126 acts between RNF8 and RNF168 during the DDR. In addition, RNF126 overexpression consistently results in the loss of RNF168-mediated H2A monoubiquitination at lysine 13/15 and inhibition of the non-homologous end joining capability. Taken together, our findings reveal that RNF126 is a novel factor involved in the negative regulation of DDR, which is important for sustaining genomic integrity

Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome.

An unbalanced microbial ecosystem on the human skin is closely related to skin diseases and has been associated with inflammation and immune responses. However, little is known about the role of the skin microbiome on skin aging. Here, we report that the Streptococcus species improved the skin structure and barrier function, thereby contributing to anti-aging. Metagenomic analyses showed the abundance of Streptococcus in younger individuals or those having more elastic skin. Particularly, we isolated Streptococcus pneumoniae, Streptococcus infantis, and Streptococcus thermophilus from face of young individuals. Treatment with secretions of S. pneumoniae and S. infantis induced the expression of genes associated with the formation of skin structure and the skin barrier function in human skin cells. The application of culture supernatant including Streptococcal secretions on human skin showed marked improvements on skin phenotypes such as elasticity, hydration, and desquamation. Gene Ontology analysis revealed overlaps in spermidine biosynthetic and glycogen biosynthetic processes. Streptococcus-secreted spermidine contributed to the recovery of skin structure and barrier function through the upregulation of collagen and lipid synthesis in aged cells. Overall, our data suggest the role of skin microbiome into anti-aging and clinical applications

Biobanking for glomerular diseases: a study design and protocol for KOrea Renal biobank NEtwoRk System TOward NExt-generation analysis (KORNERSTONE)

Abstract Backgrounds Glomerular diseases, a set of debilitating and complex disease entities, are related to mortality and morbidity. To gain insight into pathophysiology and novel treatment targets of glomerular disease, various types of biospecimens linked to deep clinical phenotyping including clinical information, digital pathology, and well-defined outcomes are required. We provide the rationale and design of the KOrea Renal biobank NEtwoRk System TOward Next-generation analysis (KORNERSTONE). Methods The KORNERSTONE, which has been initiated by Korea Centres for Disease Control and Prevention, is designed as a multi-centre, prospective cohort study and biobank for glomerular diseases. Clinical data, questionnaires will be collected at the time of kidney biopsy and subsequently every 1 year after kidney biopsy. All of the clinical data will be extracted from the electrical health record and automatically uploaded to the web-based database. High-quality digital pathologies are obtained and connected in the database. Various types of biospecimens are collected at baseline and during follow-up: serum, urine, buffy coat, stool, glomerular complementary DNA (cDNA), tubulointerstitial cDNA. All data and biospecimens are processed and stored in a standardised manner. The primary outcomes are mortality and end-stage renal disease. The secondary outcomes will be deterioration renal function, remission of proteinuria, cardiovascular events and quality of life. Discussion Ethical approval has been obtained from the institutional review board of each participating centre and ethics oversight committee. The KORNERSTONE is designed to deliver pioneer insights into glomerular diseases. The study design allows comprehensive, integrated and high-quality data collection on baseline laboratory findings, clinical outcomes including administrative data and digital pathologic images. This may provide various biospecimens and information to many researchers, establish the rationale for future more individualised treatment strategies for glomerular diseases. Trial registration NCT03929887