Ethanolic fermentation: new functions for an old pathway

Ethanolic fermentation is an ancient metabolic pathway. In plants, it is a major route of {ATP} production under anaerobic conditions. In addition, recent developments suggest that the pathway has important functions in the presence of oxygen. Both of the enzymes required for the production of acetaldehyde and ethanol, pyruvate decarboxylase and alcohol dehydrogenase, are highly abundant in pollen, resulting in fermentation in fully oxygenated cells. Acetaldehyde toxicity is an inevitable side effect of aerobic fermentation. Could acetaldehyde be the elusive pollen factor that contributes to male sterility in cmsT maize? The versatility of this ancient pathway is also illustrated by the induction of aerobic fermentation by environmental stress and activation of a defense response by overexpression of pyruvate decarboxylase.

COMMUNITY-FOCUSED FUNCTIONS IN PUBLIC HEALTH NURSING: A COMPARISON OF PERCEPTIONS

This descriptive cross-sectional survey compared the perceptions of public health nursing practitioners, educators and administrators along two dimensions: the importance of community-focused functions in public health nursing and which occupational categories in public health are responsible for those functions. More than 50 percent of the mailed questionnaires that were sent to a systematic stratified nationwide sample of public health nurses were returned. In general, respondents: were female, were in their 40s, received their basic nursing education in baccalaureate programs, had either a baccalaureate or a master's degree, worked in official agencies or schools, and had approximately 14 years of experience in public health with six in their present position.^ Significant differences between practitioners, educators and administrators were found in their perceptions of both the importance of community-focused functions in public health nursing and in which occupational category they indicated as having the major responsibility to perform those functions. Educators and administrators perceived community-focused functions as more important than did practitioners. Overall the occupational category of administrator was indicated as having the major responsibility for performing community-focused functions.^

LOCALIZATION OF DNA REPAIR FUNCTIONS TO THE NUCLEAR MATRIX

The nucleus of a eukaryotic cell contains both structural and functional elements that contribute to the controlled operation of the cell. In this context, functional components refers to those nuclear constituents that perform metabolic activities such as DNA replication and RNA transcription. Structural nuclear components, designated nuclear matrix, organize the DNA into loops or domains and appear to provide a framework for nuclear DNA organization. However, the boundary between structural and functional components is not clear cut as evinced by reports of associations between metabolic functions and the nuclear matrix. The studies reported here attempt to determine the relationship of another nuclear function, DNA repair, to the nuclear matrix.^ One objective of these studies was to study the initiation of DNA repair by directly measuring the UV-incision activities in human cells and determine the influence of various extractable nuclear components on these activities. The assay for incision activities required the development of a nuclear isolation protocol that produced nuclei with intact DNA; the conformation of the nuclear DNA and its physical characteristics in response to denaturing conditions were determined.^ The nuclei produced with this protocol were then used as substrates for endogenous UV-specific nuclease activities. The isolated nuclei were shown to contain activities that cause breaks in nuclear DNA in response to UV-irradiation. These UV-responsive activities were tightly associated with nuclear components, being unextractable with salt concentration of up to 0.6 M.^ The tight association of the incision activities with salt-extracted nuclei suggested that other repair function might also be associated with salt-stable components of the nucleus. The site of unscheduled DNA synthesis (UDS) was determined in salt-extracted nuclei (nucleoids) using autoradiography and fluorescent microscopy. UDS was found to occur in association with the nuclear matrix following low-doses (2.55 J/M('2)) of ultraviolet light, but the association became looser after higher doses of ultraviolet light (10-30 J/m('2)). ^

Two prognostic factors in breast cancer: Novel functions of EGFR and beta-catenin

In this study, we demonstrated the novel functions of two important prognostic markers in breast cancer, EGFR and b -catenin in proliferation and/or other transformation phenotype. ^ First we demonstrated that EGFR could be detected in the nucleus in highly proliferating tissues, including primary breast cancer samples and a breast cancer cell line. We found that EGFR contained a strong transactivation domain, complexed with an AT-rich consensus DNA sequence and activated promoters containing this sequence, including cyclin D1 promoter. Therefore, EGFR may function as a transcription factor to activate genes required for highly proliferating activity such as cyclin D1 in breast cancer. ^ In the second part of this study, we identified b -catenin as an important prognostic factor in breast cancer. We found that cyclin D1 was one of the genes regulated by b -catenin in breast cancer cells. The transactivation activity of b -catenin correlated significantly with cyclin D1 expression in both breast cancer cell lines and in breast cancer patient samples, in which high b -catenin activity correlated with poor prognosis of the patients. Moreover, blockage of b -catenin activity significantly inhibited transformation phenotypes in breast cancer cells. Therefore, our results indicate that b -catenin can be involved in breast cancer formation and/or progression and may serve as a target for breast cancer therapy. ^

A study in the molecular and cellular functions of GSK3beta in prostate adenocarcinoma

Kinases are part of a complex network of signaling pathways that enable a cell to respond to changes in environmental conditions in a regulated and coordinated way. For example, Glycogen Synthase Kinase 3 beta (GSK3β) modulates conformational changes, protein-protein interaction, protein degradation, and activation of unique domains in proteins that transduce signals from the extracellular milieu to the nucleus. ^ In this project, I investigated the expression and function that GSK3β exhibits in prostate cells. The capacity of GSK3β to regulate two transcription factors (JUN and CREB), which are known to be inversely utilized in prostate tumor cells, was measured. JUN/AP1 is constitutively activated in PC-3 cells; whereas, CREB/CRE activity is ∼20 fold less than the former. GSK3β overexpression obliterates JUN/AP1 activity. With respect to CREB GSK3β increases CREB/CRE activity. Cellular levels of active GSK3β can determine whether JUN or CREB is preferentially active in the PC-3s. Theoretically, in response to a particular cellular context or stimulus, a cell may coordinate JUN and CREB function by regulating GSK3β.^ A comparison of various prostate cell lines showed that active GSK3β is less expressed in normal prostate epithelial cells than in tumor cells. Differentially expressed active (GSK3β) may correlate with progression of prostate carcinoma. If a known marker associated with carcinoma of the prostate could be shown to be regulated by GSK3β then, further study of GSK3β may lead to a better understanding of both possible prevention of the disease and improved therapy for advanced stages. ^ The androgen receptor (AR) is an intriguing phosphoprotein whose regulation is potentially determined by a variety of kinases. One of these is (GSK3β) I found that (GSK3β) is a regulator of the androgen receptor in both the unliganded and liganded states. It can inhibit AR function as measured by reporter assays. Also, GSK3β associates with the AR at the DNA binding domain because deletion constructs expressing either the n-terminus or the c-terminus (both having the DBD in common) immunoprecipitated with GSK3β. Increased understanding of how GSK3β functions in prostate cancer would provide clues into how (1) certain signal pathways are coordinated and (2) the androgen receptor may be regulated. ^

The functions of pitx2 and Bmp signaling in craniofacial development

The formation of the vertebrate face is an extremely complex developmental process, which needs to coordinate the outgrowth of several facial primordia. Facial primordia are small buds made up of mesenchymal masses enclosed by an epithelial layer that surrounds the primitive mouth. The upper jaw is formed by the maxillary process, the lateral nasal process, and the frontonasal process while the mandibular process forms the lower jaw. Recent experiments using genetics in mice and bead implantation approaches have shown that the pitx2 homeobox gene and Bmp signaling play important roles in this complex developmental process. However, the molecular mechanisms underlying the function of pitx2 and Bmp in these events are still unclear. Here, we show that pitx2 is required for oral epithelium maintenance, and branchial arch signaling is pitx2 dosage sensitive by using pitx2 allelic combinations that encode varying levels of pitx2. Maintenance of fgf8 signaling requires only low pitx2 dosage while repression of Bmp signaling requires high pitx2 levels. Different incisor and molar phenotypes in low level pitx2 mutant embryos suggest a distinct requirement for pitx2 in tooth-type development. The results show that pitx2 is required for craniofacial muscle formation and expanded Bmp signaling results in excess bone formation in pitx2 mutant embryos. Fate-mapping studies show that ectopic bone results from excessive bone growth, instead of muscle transformation. Moreover, by using cre/loxp system we show that partial loss of Bmpr-IA in the facial primordia results in cleft lip/palate, abnormal teeth, ectopic teeth and tooth transformation. These phenotypes suggest that Bmp signaling has multiple functions during craniofacial development. The mutant palate shelves can fuse with each other when cultured in vitro, suggesting that cleft palate is secondary to the partial loss of Bmpr-IA. Furthermore, we prove that Bmp4, one of the ligands of Bmpr-IA, plays a role during lip fusion developmental process and partial loss of Bmp4 in the facial primordia results in the lip fusion delay. These results have provided insight to understand the complex signaling cascades that regulate craniofacial development. ^

Compact Singlet S Helium Wave functions(corrected)

This is a corrected version of the Phys. Rev. A 74,14501 (2006) article. The result is improved slightly from that in the original paper.

Advance P. Chem. Problems (I) Populations, Partition Functions, Particle in Box, Harmonic Oscillators, Angular Momentum and Rigid Rotor

This is a set of P. Chem. problems posed at slightly higher than the normal text book level, for students who are continuing in the study of this subject.

Legendre Polynomials, Dipole Moments, Generating Functions, etc..

A standard treatment of aspects of Legendre polynomials is treated here, including the dipole moment expansion, generating functions, etc..

The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation

A phosphorylation balance governed by Ipl1 Aurora kinase and the Glc7 phosphatase is essential for normal chromosome segregation in S. cerevisiae . Deletion of SET1, a histone K4 methyltransferase, suppresses the temperature sensitive phenotype of ipl1-2, and loss the catalytic activity of Set1 is important for this suppression. SET1 deletion also suppresses chromosome loss in ipl1-2 cells. Deletion of other Set1 complex components suppresses the temperature sensitivity of ipl1-2 as well. In contrast, SET1 deletion is synthetic lethal combined with glc7-127. Strikingly, these effects are independent of previously defined functions for Set1 in transcription initiation and histone H3 methylation. I find that Set1 methylates conserved lysines in a kinetochore protein, Dam1, a key mitotic substrate of Ipl1/Glc7. Biochemical and genetic experiments indicate that Dam1 methylation inhibits Ipl1-mediated phosphorylation of flanking serines. My studies demonstrate that Set1 has important, unexpected functions in mitosis through modulating the phosphorylation balance regulated by Ipl1/Glc7. Moreover, my findings suggest that antagonism between lysine methylation and serine phosphorylation is a fundamental mechanism for controlling protein function. ^

Nuclear functions of dynein light chain 1 in hormone action

It is widely accepted that the process of breast cancer tumorigenesis involves estrogen receptor-alpha (ER)-regulated stimulatory pathways, which feed into survival, cell cycle progression and proliferative response. Recent data from Kumar laboratory indicate that dynein light chain 1 (DLC1) plays a role in survival, motility and invasiveness, all of which are required for a successful tumorigenesis process. In the present research, we have discovered a mechanistic bidirectional regulatory link between the DLC1 and ER. We found that DLC1 facilitates ligand-induced ER transactivation involving the recruitment of the DLC1-ER complex to ER-target genes. To gain insights into the mechanism by which DLC1 regulates the ER pathway, we set out to identify novel DLC1-interacting proteins. Among other proteins, we identified KIBRA and Ciz1 as two novel DLC1-interacting proteins. We found that the KIBRA-DLC1 complex is recruited to ER-responsive promoters, and that KIBRA-DLC1 interaction is needed for the recruitment of ER to its targets as well as for ER's transactivation function. Finally, we found that KIBRA utilizes its histone H3interacting glutamic acid-rich region to regulate the transactivation activity of ER. During the course of this work, we also discovered that DLC1 interacts with Cdk2 and Ciz1, and such interactions play a direct accelerating role in the G1-S transition of breast cancer cells. While delineating the role of Ciz1 in hormone-responsive cancer cells, we found that Ciz1 is an estrogen-responsive gene, and acts as a co-regulator of ER. Accordingly, Ciz1 overexpression in breast cancer cells conferred estrogen hypersensitivity, promoted the growth-rate, anchorage-independency and tumorigenic properties. Collectively, findings made during the course of the present dissertation research introduced two new molecular players in the action of ER in breast cancer cells, with a particular focus on cell cycle progression and ER-chromatin target regulation. In addition, findings presented here provide novel mechanistic insight about the contribution of DLC1 and its interacting proteins in amplifying the hormone action and promoting the process of breast cancer tumorigenesis. ^

CARD9 functions as a key regulator in monocyte homeostasis and pathogen clearance

Mononuclear phagocytes are designed to neutralize systemic bacterial and fungal infections. However, the exact regulation of these functions are largely unknown. CARD9 was first identified as an immune-specific adaptor protein of unclear function. Here, we have found that Card9 is specifically expressed in monocyte-origin cell populations. To better understand the biological function of Card9, we have generated Card9-deficient (Card9-/-) mice. Hematologic profiling and histological analysis of Card9-/- mice revealed a decreased leukocyte/myeloid cell count, delayed monocyte maturation in bone marrow as well as monocyte counts in the peripheral blood. Upon M-CSF stimulation, Card9-/- macrophages further exhibit a partial loss in IKK phosphorylation. As a consequence, in vivo challenge with Listeria monocytogenes in Card9-/- mice results in a higher susceptibility to infection-associated inflammation and fatality. Collectively, these data suggest that CARD9 is required for monocyte development and function. ^ At the cellular level, Card9-/- macrophages are defective in killing Listeria and the production of pro-inflammatory cytokines. Molecular characterizations have further demonstrated that CARD9 inducibly interacts with NOD2, controls p38 MAPK activation, and regulates ROS production during Listeria infections. Cytotrap screening showed that CARD9 could physically associate with various g&barbelow;uanine e&barbelow;xchange f&barbelow;actor (GEF) proteins that are essential for regulating ROS production. In summary, we have first identified and provided genetic evidence that CARD9 functions as a novel regulator during monocyte development and serves as an essential protein adaptor for p38 MAPK activation during bacterial clearance processes in macrophages. ^

Assessing time-by-covariate interactions in Cox proportional hazards regression models using cubic spline functions

This dissertation develops and explores the methodology for the use of cubic spline functions in assessing time-by-covariate interactions in Cox proportional hazards regression models. These interactions indicate violations of the proportional hazards assumption of the Cox model. Use of cubic spline functions allows for the investigation of the shape of a possible covariate time-dependence without having to specify a particular functional form. Cubic spline functions yield both a graphical method and a formal test for the proportional hazards assumption as well as a test of the nonlinearity of the time-by-covariate interaction. Five existing methods for assessing violations of the proportional hazards assumption are reviewed and applied along with cubic splines to three well known two-sample datasets. An additional dataset with three covariates is used to explore the use of cubic spline functions in a more general setting. ^

DISTRIBUTION FUNCTIONS, MEAN SQUARED ERRORS, AND CONFIDENCE LIMITS FOR RIDGE REGRESSION ESTIMATORS

A large number of ridge regression estimators have been proposed and used with little knowledge of their true distributions. Because of this lack of knowledge, these estimators cannot be used to test hypotheses or to form confidence intervals.^ This paper presents a basic technique for deriving the exact distribution functions for a class of generalized ridge estimators. The technique is applied to five prominent generalized ridge estimators. Graphs of the resulting distribution functions are presented. The actual behavior of these estimators is found to be considerably different than the behavior which is generally assumed for ridge estimators.^ This paper also uses the derived distributions to examine the mean squared error properties of the estimators. A technique for developing confidence intervals based on the generalized ridge estimators is also presented. ^