Uric acid is a nitrogenous compound that is produced as an end product of the deamination of amino acids. Many insects and all reptiles and birds excrete the majority of excess nitrogen as solid uric acid granules that are suspended in the urine. However, the solid uric acid is not in crystalline form, but is packaged into small, spherical structures that are usually 3 - 15 μm in diameter. Further, the uric acid that is dissolved in the urine exceeds its aqueous solubility limit and the solubility limits of the potassium and sodium urate salts. Thus, a factor(s) in the urine is facilitating urate in exceeding its solubility limits and in causing urate to form spheres rather than crystals. I have reported that avian urine contains unusually high amounts of protein (1-3 mg/ml), and that the uric acid spheres also contain protein. Linear regression analysis shows that the amount of uric acid and protein in urine are positively correlated (r = 0.80, p<0.005), suggesting a functional relationship between the two. Equilibrium dialysis of urine before and after its treatment with protease shows the urinary protein capable of binding urate (and calcium). After isolating and purifying a sphere protein, I was able to generate sheep anti-sphere protein antibodies. By using these and commercially obtained anti-chicken serum albumin antibodies in a series of western blot analyses, I have identified serum albumin as the sphere protein and as a major urinary protein in birds. In summary, my data show serum albumin to playa significant role in the excretion of uric acid in birds. Because urine from all uricotelic species I have examined contains similar spheres, I am suggesting that all uricoteles may use like, or analogous, proteins to facilitate the excretion of urates.

The aim of this dissertation is to provide an analysis of central concepts in philosophy of science from the perspective of current molecular and developmental research. Each chapter explores the ways in which particular phenomena or discoveries in molecular biology influences our philosophical understanding of the nature of scientific knowledge. The introductory prologue draws some general connections between the various threads, which revolve around two central themes: causation and explanation. Chapter Two identifies a particular type of causal relation which is widespread across the sciences, but cannot be straightforwardly accommodated by extant accounts of causation and causal explanation. Chapter Three explores how the form of redundant causality identified in the previous chapter plays an important role in causal explanation, by making the effect stable and robust. Chapter Four offers a novel perspective on the debate over biological reductionism by distinguishing between different paradigms of molecular explanation. Chapter Five provides a philosophical analysis of the so-called "Developmental Synthesis" of evolutionary and developmental biology, and suggests a general account of scientific unification grounded in the notion of explanatory relevance. Chapter Six offers an account of dispositional properties inspired by mechanisms of gene regulation, according to which dispositions are not properties of entities, but properties that describe the behavior of abstract idealized models. Finally, Chapter Seven scrutinizes the concept of the molecular ecosystem, a metaphor frequently employed by biologists to describe cellular interactions, but seldom articulated in detail.

Hemorrhagic shock is a clinical syndrome involving widespread cellular dysfunction and resulting in injury to many organs. Resuscitation from hemorrhagic shock is similar to reperfusion after ischemia, but differs in that some blood flow persists during shock. Ischemia-reperfusion produces oxygen radicals in many organs, including the liver of the rat and the human. The hypothesis of this project was that oxygen radicals are produced and cause hepatic injury during resuscitation from hemorrhagic shock. The production of oxygen radicals within the liver should cause lipid peroxidation and tissue injury. Manipulation of defenses against oxygen radicals should decrease the hepatic injury caused by hemorrhagic shock and resuscitation. The blood pressure of Sprague-Dawley rats was reduced to 35-40 mm Hg by blood withdrawal for two hours, followed by reinfusion of withdrawn blood. Plasma alanine aminotransferase (ALT) levels rose and injury to hepatocytes and non-parenchymal cells was found on transmission electron microscopy. The presence of lipid peroxidation was determined by quantitation of ethane exhalation and hepatic content of thiobarbituric acid reactive substances (TBARS). Ethane exhalation was elevated during the hypotensive phase and after resuscitation. Hepatic TBARS levels were elevated after resuscitation only. The same hemorrhagic shock protocol was used to determine the effect of antioxidant manipulation on hepatic injury. The antioxidants superoxide dismutase, catalase, or deferoxamine produced no reduction in hepatic injury. The administration of phorone reduced hepatic non-protein sulfhydryl content and increased plasma ALT levels nine fold at 24 hours after resuscitation. The development of lipid peroxidation and the exacerbation of liver injury by the administration of phorone suggest that oxygen radicals are produced in the liver during hemorrhagic shock and resuscitation. However, the administration of antioxidants provided no protection. Therefore, it seems unlikely the oxygen radicals are involved in the pathogenesis of liver injury in this model. It is possible that the lipid peroxidation occurs after the cell is irreversible injured.

Lu, Yao. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

The effectiveness of estrogen replacement therapy in the prevention of postmenopausal osteoporosis has led to its current widespread use throughout the United States and much of Western Europe, and recently, clinical correlations between circulating androgen levels and structural bone integrity have been presented. Nevertheless, the biochemical mechanism through which estrogens and androgens act to protect and maintain bone has remained unclear. One possibility is that these hormones directly modulate the activity of cells responsible for bone formation. Therefore, studies were conducted to examine the effects of sex steroids on human osteoblast-like cells. In the first set of experiments, a finite human cell line was established from trabecular bone explants obtained from a 48 year-old woman. These cells, designated BG688, were characterized as osteoblast-like in phenotype using several independent criteria. In addition to classical osteoblast markers, BG688 cells also possess approximately 2400 high affinity (K(d) = 0.45nM) 17-β estradiol (E₂) binding sites per cell. The binding of E₂ to a subset of these sites was specific. BG688 cells were also shown to respond to a physiological concentration (10nM) of E₂, which elicits pleiotropic changes in several mRNA levels including a 2-fold increase in the steady state concentration of α₁(I)-procollagen mRNA. These results indicate that human osteoblast-like cells respond to E₂ via a receptor mediated mechanism, but that, unlike the reproductive tissues, osteoblasts are a less sensitive target. In the second series of experiments, the effects of androgenic hormones on the osteoblast-like, human osteosarcoma cell line, HOS TE85 were evaluated. Employing radiolabelled dihydrotestosterone (DHT), 2800 saturable, high-affinity (K(d) = 0.66nM) androgen binding sites were detected per HOS TE85 cell. Androgen binding was specific. The expression of androgen receptors in HOS TE85 cells was further substantiated by Northern analysis. Physiological concentrations of DHT and testosterone decreased HOS TE85 cell proliferation. This finding suggests that androgens may also play a role in osteoblast differentiation. In support of this hypothesis, treatment with testosterone enhanced the abundance of both α₁ (I)-procollagen mRNA and transforming growth factor- β mRNA. The non-aromatizable androgen DHT also elicited an increase in the steady state concentration of α₁(I)-procollagen mRNA. The findings presented herein are significant within the field of bone cell biology in that they demonstrate that osteoblasts are a target cell for the action of sex steroids, via their cognate, high-affinity receptors. These results also have important implications within the broader context of bone pathophysiology in that they suggest a direct modulation of bone forming and bone remodeling activity by sex steroids.

The nuclear factor-kB (NF-kB) signaling cascade is comprised of two branches, the canonical and alternative NF-kB pathways. Signaling through the alternative NF-kB pathway culminates in the activation of the downstream transcription factor subunits, RELB and NF-kB2. The biological roles of RELB and NF-kB2 within the B cell lineage have been obscured in constitutional knockout mice by the diverse functions of these subunits in non-B cell types. To overcome these limitations, conditional alleles were generated to investigate the roles of RELB and NF-kB2 in B cell development. These alleles allowed the identification of complex functional requirements for RELB and/or NF-kB2 in naïve B cells, germinal center (GC) B cells and plasma cells (PCs). These functional requirements may have implications for B cell malignancies that display mutations that constitutively activate the alternative NF-kB pathway. A large body of work has demonstrated that B cell activating factor (BAFF) signaling is critical for the maintenance of mature B cells. However, the contribution of the alternative NF-kB subunits that are activated downstream of BAFF remained unclear, especially in regards to their specific target genes. We have identified critical, B cell-intrinsic roles for RELB and NF-kB2 in the maintenance of mature B cells. In response to BAFF, these subunits were found to control the expression of anti-apoptotic genes, genes that ensure correct positioning within the B cell niche, and genes involved in promoting B–T cell interactions that allow effective antigen-mediated activation. During the GC B cell reaction, light zone (LZ) B cells undergo affinity-based selection mediated by T follicular helper (Tfh) cells. A subset of LZ B cells show activation of the NF-kB signaling cascade, suggesting a critical role for NF-kB in the selection of high-affinity GC B cells. We here report that GC B cell development occurred normally in mice with conditional deletion of either relb (RELB) or nfkb2 (NF-kB2) in GC B cells. In contrast, the simultaneous ablation of both subunits caused rapid involution of established GCs, similar to what has been observed for ablation of the canonical NF-kB transcription factor subunit c-REL. Intriguingly, RNA-sequencing analysis of relb/nfkb2-deleted GC B cells revealed no overlap between the genes controlled by RELB/p52 and c-REL within GC B cells. This suggests that signaling through the separate NF-kB pathways in GC B cells results in the expression of different biological programs that are independently required for the maintenance of the GC reaction. In addition, we observed that human PCs and PC precursors within the LZ showed high protein levels of NF-kB2 compared to surrounding lymphocytes, suggesting a biological role for this subunit in PCs. Indeed, ablation of nfkb2 alone in GC B cells led to a dramatic decrease in antigen-specific serum IgG1 and antigen-specific IgG1-secreting cells. Interestingly however, the mice developed normal frequencies of PCs, suggesting a role for NF-kB2 in PC physiology rather than differentiation.

Finally, based on theoretical calculations and experiments, we present a development model (DDRA model) to describe the interaction between the protein and its solvent molecule. The parameters derived from this model provide good fits to the experimentally determined complex dielectric constant, making it of the model valuable benchmarks for other theoretical treatments of bio-molecular system. / Secondly, we focus our aims on investigating protein molecules due to the possibility of being able to explain the mechanism of molecular interactions more clearly. Two lands of labeled immunoglobulin G were investigated using a reflective THz-IDS system. The dielectric properties were sensitive to the conjugation of the antibody. Additionally, terahertz spectroscopy is able to evaluate the depth of the hydrogen shell and shows that the hydrogen-bonded networks of charged protein solutions play an important role in determining the dielectric. / The bio-molecular interaction has been one of the most challenging subjects to probe due to its complexity. In the thesis, we have been attempting to answer fundamental questions about bio-molecular interactions in the terahertz (THz) region from the macroscopic to microscopic level. Terahertz radiation (defined as 0.1--10 THz) can excite intermolecular interactions such as the librational and vibrational modes. These attributes make it feasible to probe the dynamic characteristics of the bio-molecular system. Furthermore, it is worth investigating whether terahertz technology could potentially be used as a novel tool in the biomedical diagnosis field in the near future. / Thirdly, using a transmission THz-TDS system we investigated a biomarker protein and observed distinct spectral differences at various temperatures. This work demonstrates that terahertz spectroscopy can be used to evaluate the anharmonicity of the vibrational potential. By comparing the absorption spectra of the THz-TDS and Synchrotron results it is possible to deduce the approximate localization of the vibrational modes within the molecular chain. / We develop a controlled study to investigate the effects of formalin fixing on the THz properties of two different tissue types. The optical properties are measured using THz reflection spectroscopy. The results present how the fixing process can affect image contrast in THz images of biological samples. / Sun, Yiwen. / Advisers: Emma MacPherson; Yuan-ting Zhang. / Source: Dissertation Abstracts International, Volume: 73-03, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 120-140). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

The ability of a genetically-engineered <i>Erwirzia carotovora</i> subsp. <i>carotovora</I> (Ecc) strain to transfer recombinant chromosomal DNA or plasmids to wildtype Ecc or <i>Pseudomonas fluorescens</i> was tested on filters, within soil microcosms, and <i>in planta</i>. Ecc was engineered by chromosomal insertion of a disarmed <i>endo</i>-pectate lyase gene marked with a 1.4kb DNA fragment conferring kanamycin resistance. Plasmids RPI and pBR322 were introduced separately into engineered Ecc clones. These strains served as donors in genetic transfer experiments. No transfer of the inserted kan marker or of pBR322 was observed under any experimental condition. In filter matings, RPI was transferred to wildtype Ecc at a frequency of 3.6 X 10⁻² transconjugants per donor (TPD) and to P. <i>fluorescens</i> at a frequency of 2.4 X 10⁻⁵ TPD. In matings conducted in potato tubers inoculated using sewing needles, the respective frequencies were 4.0 X 10⁻³ and 2.0 X 10⁻³, while matings on potato slices yielded frequencies of 4.7 X 10⁻² and 2.3 X 10⁻². In soil microcosms, the maximum transfer frequencies observed were 2.3 X 10³ and 8.4 X 10⁻⁵ TPD. / Master of Science

Isogenic clonal fish lines are a powerful resource for aquaculture-related research. Fully inbred individuals, clone founders, can be produced either through mitotic gynogenesis or androgenesis and a further generation from those propagates fully inbred clonal lines. Despite rapid generation, as opposed to successive generation of sibling mating as in mice, the production of such lines may be hampered due to (i) potential residual contribution from irradiated gametes associated with poorly optimised protocols, (ii) reduced survival of clone founders and (iii) spontaneous arisal of meiotic gynogenetics with varying degree of heterozygosity, contaminating fully homozygous progenies. This research set out to address challenges and gain insights into isogenic clonal fish lines development by using double-digest RADseq (ddRADseq) to generate large numbers of genetic markers covering the genome of interest. Analysis of potential contribution from irradiated sperm indicated successful uniparental inheritance in meiotic and mitotic gynogenetics European seabass. Exclusive transmission of maternal alleles was detected in G1 progeny of Atlantic salmon (with a duplicated genome), while G2 progenies presented varying levels of sire contribution suggesting sub-optimal UV irradiation which was undetected previously with 27 microsatellite markers. Identification of telomeric markers in European seabass, with higher recombination frequencies for efficient differentiation of meiotic and mitotic gynogenetics was successful, and a genetic linkage map was generated from this data. One clear case of a spontaneous meiotic gynogenetic fish was detected among 18 putative DH fish in European seabass, despite earlier screening for isogenicity using 11 microsatellite markers. An unidentified larval DNA restriction digestion inhibition mechanism observed in Nile tilapia prevented the construction of SNP-based genetic linkage map. In summary, this study provides strong evidence on efficacy of NGS technologies for the development and verification of isogenic clonal fish lines. Reliable establishment of isogenic clonal fish lines is critical for their utility as a research tool.

Indiana University-Purdue University Indianapolis (IUPUI) / Polyacetylenic natural products, compounds containing multiple carbon-carbon triple bonds, have been found in a large collection of organisms. Radiochemical tracer studies have indicated that these bioactive metabolites are synthesized from fatty acid precursors through a series of uncharacterized desaturation and acetylenation steps. To date, there are three main pathways believed to be involved in acetylenic natural product biosynthesis. However, it is apparent that the crepenynic acid pathway is the origin of a vast majority of the known plant and fungal acetylenic products. This investigation provides concrete evidence that the polyacetylenic natural products found in the fungus Fistulina hepatica and the medicinal plant species Echinacea purpurea are biosynthesized from crepenynic acid. Through heterologous expression in Yarrowia lipolytica, two acetylenases capable of producing crepenynic acid were identified from E. purpurea. Furthermore, heterologous expression of two diverged desaturases isolated from F. hepatica, uncovered a ∆12-acetylenase and the first multifunctional enzyme capable of ∆14-/∆16- desaturation and ∆14-acetylenation.