Matching Items (2,057)
Filtering by
- Creators: School of Life Sciences
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
V(D)J recombination is responsible for generating an enormous repertoire of immunoglobulins and T cell receptors, therefore it is a centerpiece to the formation of the adaptive immune system. The V(D)J recombination process proceeds through two steps, site-specific cleavage at RSS (Recombination Signal Sequence) site mediated by the RAG recombinase (RAG1/2) and the subsequent imprecise resolution of the DNA ends, which is carried out by the ubiquitous non-homologous end joining pathway (NHEJ). The V(D)J recombination reaction is obliged to be tightly controlled under all circumstances, as it involves generations of DNA double strand breaks, which are considered the most dangerous lesion to a cell. Multifaceted regulatory mechanisms have been evolved to create great diversity of the antigen receptor repertoire while ensuring genome stability. The RAG-mediated cleavage reaction is stringently regulated at both the pre-cleavage stage and the post-cleavage stage. Specifically, RAG1/2 first forms a pre-cleavage complex assembled at the boarder of RSS and coding flank, which ensures the appropriate DNA targeting. Subsequently, this complex initiates site-specific cleavage, generating two types of double stranded DNA breaks, hairpin-ended coding ends (HP-CEs) and blunt signal ends (SEs). After the cleavage, RAG1/2 proteins bind and retain the recombination ends to form post-cleavage complexes (PCC), which collaborates with the NHEJ machinery for appropriate transfer of recombination ends to NHEJ for proper end resolution. However, little is known about the molecular basis of this collaboration, partly attributed to the lack of sensitive assays to reveal the interaction of PCC with HP-CEs. Here, for the first time, by using two complementary fluorescence-based techniques, fluorescence anisotropy and fluorescence resonance energy transfer (FRET), I managed to monitor the RAG1/2-catalyzed cleavage reaction in real time, from the pre-cleavage to the post-cleavage stages. By examining the dynamic fluorescence changes during the RAG-mediated cleavage reactions, and by manipulating the reaction conditions, I was able to characterize some fundamental properties of RAG-DNA interactions before and after cleavage. Firstly, Mg2+, known as a physiological cofactor at the excision step, also promotes the HP-CEs retention in the RAG complex after cleavage. Secondly, the structure of pre-cleavage complex may affect the subsequent collaborations with NHEJ for end resolution. Thirdly, the non-core region of RAG2 may have differential influences on the PCC retention of HP-CEs and SEs. Furthermore, I also provide the first evidence of RAG1-mediated regulation of RAG2. Our study provides important insights into the multilayered regulatory mechanisms, in modulating recombination events in developing lymphocytes and paves the way for possible development of detection and diagnotic markers for defective recombination events that are often associated immunodeficiency and/or lymphoid malignancy.
ContributorsWang, Guannan (Author) / Chang, Yung (Thesis advisor) / Levitus, Marcia (Committee member) / Misra, Rajeev (Committee member) / Anderson, Karen (Committee member) / Arizona State University (Publisher)
Created2012
Description
Teleosts have the most primitive adaptive immune system. However, in terms of functionality the teleost immune system is similar to birds and mammals. On the other hand, enteric bacterial pathogens of mammals and birds present conserved regulatory mechanisms that control virulence factors. In this context, deletion of conserved genes that control virulence factors have been successfully used as measure to construct live attenuated bacterial vaccines for mammals and birds. Here, I hypothesize that evolutionary conserved genes, which control virulence factors or are essential for bacterial physiology in Enterobacteriaceae, could be used as universal tools to design live attenuated recombinant bacterial vaccines from fish to mammals. The evolutionary conserved genes that control virulence factors, crp and fur, and the essential gene for the synthesis of the cell wall, asd, were studied in Edwardsiella ictaluri to develop a live recombinant vaccine for fish host. The genus Edwardsiella is one of the most ancient represent of the Enterobacteriaceae family. E. ictaluri, a host restricted pathogen of catfish (Ictalurus punctatus), is the causative agent of the enteric septicemia and one of the most important pathogens of this fish aquaculture. Although, crp and fur control different virulence factors in Edwardsiella, in comparison to other enterics, individual deletion of these genes triggered protective immune response at the systemic and mucosal level of the fish. Deletion of asdA gene allowed the creation of a balanced-lethal system to syntheses heterologous antigens. I concluded that crp, fur and asd could be universally used to develop live attenuate recombinant Enterobacteriaceae base vaccines for different hosts.
ContributorsSantander Morales, Javier Alonso (Author) / Curtiss, Roy Iii (Thesis advisor) / Chandler, Douglas (Committee member) / Chang, Yung (Committee member) / Shi, Yixin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Intrinsic antibiotic resistance is of growing concern in modern medical treatment. The primary action of multidrug resistant strains is through over-expression of active transporters which recognize a broad range of antibiotics. In Escherichia coli, the TolC-AcrAB complex has become a model system to understand antibiotic efflux. While the structures of these three proteins (and many of their homologs) are known, the exact mechanisms of interaction are still poorly understood. By mutational analysis of the TolC turn 1 residues, a drug hypersensitive mutant has been identified which is defective in functional interactions with AcrA and AcrB. Antibiotic resistant revertants carry alterations in both TolC and AcrA act by stabilizing functional complex assembly and opening of the TolC aperture, as monitored by stability of a labile TolC mutant and sensitivity to vancomycin, respectively. Alterations in the AcrB periplasmic hairpin loops lead to a similar antibiotic hypersensitivity phenotype and destabilized complex assembly. Likewise, alterations in TolC which constitutively open the aperture suppress this antibiotic sensitivity. Suppressor alterations in AcrA and AcrB partially restore antibiotic resistance by mediating stability of the complex. The AcrA suppressor alterations isolated in these studies map to the three crystallized domains and it is concluded they alter the AcrA conformation such that it is permanently fixed in an active state, which wild type only transiently goes through when activated by AcrB. Through this genetic evidence, a direct interaction between TolC and AcrB which is stabilized by AcrA has been proposed. In addition to stabilizing the interactions between TolC and AcrB, AcrA is also responsible for triggering opening of the TolC aperture by mediating energy flow from AcrB to TolC. By permanently altering the conformation of AcrA, suppressor mutants allow defective TolC or AcrB mutants to regain functional interactions lost by the initial mutations. The data provide the genetic proof for direct interaction between AcrB and that AcrA mediated opening of TolC requires AcrB as a scaffold.
ContributorsWeeks, Jon William (Author) / Misra, Rajeev (Thesis advisor) / Stout, Valerie (Committee member) / Shi, Yixin (Committee member) / Clark-Curtiss, Josephine (Committee member) / Arizona State University (Publisher)
Created2012
Description
The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the deposit are andesitic pyroclastic materials, which have been hydrothermally altered into argillic clay zones. High-sulfidation (acidic) alteration produced clay zones with elevated pyrite (18%), illite-smectite (I-S) (70% illite), elemental sulfur, kaolinite and carbonates. Low-sulfidation alteration at neutral pH generated clay zones with lower pyrite concentrations pyrite (4-6%), the mixed-layered I-S clay rectorite (R1, I-S) and quartz.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
ContributorsMorrison, Keith D (Author) / Williams, Lynda B (Thesis advisor) / Williams, Stanley N (Thesis advisor) / Misra, Rajeev (Committee member) / Shock, Everett (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2015
Description
The Multiple Antibiotic Resistance Regulator Family (MarR) are transcriptional regulators, many of which forms a dimer. Transcriptional regulation provides bacteria a stabilized responding system to ensure the bacteria is able to efficiently adapt to different environmental conditions. The main function of the MarR family is to create multiple antibiotic resistance from a mutated protein; this process occurs when the MarR regulates an operon. We hypothesized that different transcriptional regulator genes have interactions with each other. It is known that Salmonella pagC transcription is activated by three regulators, i.e., SlyA, MprA, and PhoP. Bacterial Adenylate Cyclase-based Two-Hybrid (BACTH) system was used to research the protein-protein interactions in SlyA, MprA, and PhoP as heterodimers and homodimers in vivo. Two fragments, T25 and T18, that lack endogenous adenylate cyclase activity, were used for construction of chimeric proteins and reconstruction of adenylate cyclase activity was tested. The significant adenylate cyclase activities has proved that SlyA is able to form homodimers. However, weak adenylate cyclase activities in this study has proved that MprA and PhoP are not likely to form homodimers, and no protein-protein interactions were detected in between SlyA, MprA and PhoP, which no heterodimers have formed in between three transcriptional regulators.
ContributorsTao, Zenan (Author) / Shi, Yixin (Thesis advisor) / Wang, Xuan (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2018
Description
Lignocellulosic biomass represents a renewable domestic feedstock that can support large-scale biochemical production processes for fuels and specialty chemicals. However, cost-effective conversion of lignocellulosic sugars into valuable chemicals by microorganisms still remains a challenge. Biomass recalcitrance to saccharification, microbial substrate utilization, bioproduct titer toxicity, and toxic chemicals associated with chemical pretreatments are at the center of the bottlenecks limiting further commercialization of lignocellulose conversion. Genetic and metabolic engineering has allowed researchers to manipulate microorganisms to overcome some of these challenges, but new innovative approaches are needed to make the process more commercially viable. Transport proteins represent an underexplored target in genetic engineering that can potentially help to control the input of lignocellulosic substrate and output of products/toxins in microbial biocatalysts. In this work, I characterize and explore the use of transport systems to increase substrate utilization, conserve energy, increase tolerance, and enhance biocatalyst performance.
ContributorsKurgan, Gavin (Author) / Wang, Xuan (Thesis advisor) / Nielsen, David (Committee member) / Misra, Rajeev (Committee member) / Nannenga, Brent (Committee member) / Arizona State University (Publisher)
Created2018
Description
This study investigates the relation between credit supply competition among banks and their clients’ conditional accounting conservatism (i.e., asymmetric timely loss recognition). The Interstate Banking and Branching Efficiency Act (IBBEA) of 1994 permits banks and bank holding companies to expand their business across state lines, introducing a positive shock to credit supply competition in the banking industry. The increase in credit supply competition weakens banks’ bargaining power in the negotiation process, which in turn may weaken their ability to demand conservative financial reporting from borrowers. Consistent with this prediction, results show that firms report less conservatively after the IBBEA is passed in their headquartered states. The effect of the IBBEA on conditional conservatism is particularly stronger for firms in states with a greater increase in competition among banks, firms whose operations are more concentrated in their headquarter states, firms with greater financial constraints, and firms subject to less external monitoring. Robustness tests confirm that the observed decline in conditional conservatism is causally related to the passage of IBBEA. Overall, this study highlights the impact of credit supply competition on financial reporting practices.
ContributorsHuang, Wei (Author) / Li, Yinghua (Thesis advisor) / Huang, Xiaochuan (Committee member) / Kaplan, Steve (Committee member) / Arizona State University (Publisher)
Created2018
Description摘要
在复杂多变的商业环境中，企业传统的人力资源管理已经难以应对日益频发的员工职业倦怠、人际间矛盾冲突、频繁跳槽等局面与问题。企业员工工作的价值与意义早已不再是传统的雇佣模式下，通过出卖劳动力或智力从而获得工资以实现“养家糊口”的目的那么单纯与简单，员工也希望通过辛勤的工作，以获得个体的幸福感、荣誉感与认同感等。对于现代企业的管理者而言，员工追求事业的提升、个人价值的实现，不仅体现在薪酬、福利待遇的提升，更重要的是员工个人的成长以及潜能和竞争力的提升。
随着组织行为学和心理学的不断发展与演变，与员工幸福感相关的研究备受关注。对现代企业而言，管理者借助制度设计对员工幸福积极管理，可以最大限度地发挥员工的积极性、主动性与创造性，实现员工与企业之间的利益相趋同，从而更为高效地实现组织的目标。基于此，本文以民营企业员工工作幸福感作为研究的切入点，借助理论分析、问卷调查和实证分析相结合的研究方法，系统深入地研究我国民营企业员工工作幸福感的构成、可控前因和绩效后果等问题。
本文研究发现：
第一，员工薪酬的提高有助于员工工作幸福感的提升，薪资对基层员工幸福感的影响显著高于其对高层员工幸福感的影响；
第二，完善的晋升机制对于中层员工而言更能提升其幸福感，完善的晋升机制更有利于中层员工；
第三，公平性的提高有助于提高员工工作幸福感，而且这种正效应更多体现在基层员工群体之中；
第四，高层员工更注重自我价值的实现，高层员工的工作挑战性越高，其自我实现需求获得的满足感则约高，但是对于基层员工和中层员工而言，其效果则恰恰相反，基础员工和高层员工更多地将工作挑战性和压力看作是一种负面的因素；
第五，员工幸福感的确会给企业带来正向的绩效。
本文的研究框架和实证结论不仅可以丰富学术界有关员工工作幸福感的研究，而且为企业管理者进行绩效管理以及员工工作质量的提升提供理论和实证借鉴。
在复杂多变的商业环境中，企业传统的人力资源管理已经难以应对日益频发的员工职业倦怠、人际间矛盾冲突、频繁跳槽等局面与问题。企业员工工作的价值与意义早已不再是传统的雇佣模式下，通过出卖劳动力或智力从而获得工资以实现“养家糊口”的目的那么单纯与简单，员工也希望通过辛勤的工作，以获得个体的幸福感、荣誉感与认同感等。对于现代企业的管理者而言，员工追求事业的提升、个人价值的实现，不仅体现在薪酬、福利待遇的提升，更重要的是员工个人的成长以及潜能和竞争力的提升。
随着组织行为学和心理学的不断发展与演变，与员工幸福感相关的研究备受关注。对现代企业而言，管理者借助制度设计对员工幸福积极管理，可以最大限度地发挥员工的积极性、主动性与创造性，实现员工与企业之间的利益相趋同，从而更为高效地实现组织的目标。基于此，本文以民营企业员工工作幸福感作为研究的切入点，借助理论分析、问卷调查和实证分析相结合的研究方法，系统深入地研究我国民营企业员工工作幸福感的构成、可控前因和绩效后果等问题。
本文研究发现：
第一，员工薪酬的提高有助于员工工作幸福感的提升，薪资对基层员工幸福感的影响显著高于其对高层员工幸福感的影响；
第二，完善的晋升机制对于中层员工而言更能提升其幸福感，完善的晋升机制更有利于中层员工；
第三，公平性的提高有助于提高员工工作幸福感，而且这种正效应更多体现在基层员工群体之中；
第四，高层员工更注重自我价值的实现，高层员工的工作挑战性越高，其自我实现需求获得的满足感则约高，但是对于基层员工和中层员工而言，其效果则恰恰相反，基础员工和高层员工更多地将工作挑战性和压力看作是一种负面的因素；
第五，员工幸福感的确会给企业带来正向的绩效。
本文的研究框架和实证结论不仅可以丰富学术界有关员工工作幸福感的研究，而且为企业管理者进行绩效管理以及员工工作质量的提升提供理论和实证借鉴。
ContributorsShu, Man (Author) / Shen, Wei (Thesis advisor) / Wu, Fei (Thesis advisor) / Chen, Xin (Committee member) / Arizona State University (Publisher)
Created2019
Description当前，上市公司的盈余管理问题已是我国资本市场中普遍存在的突出问题。一般来说，一些企业为了满足资本市场对于上市、增发等条件的要求,以及为有效推动企业的并购、重组等行为的顺利实现,甚至为了谋求公司管理层的个别利益,往往运用盈余管理等举措实施公司财报及关键指标的粉饰修正，让不知情的股民蒙受一定的损失。普遍分析显示，我国股市中民营企业比其他企业遭遇的问题和压力更多、更大、更突出,因此民营企业从客观上来说拥有更强的盈余管理动机。而从当前我国资本市场的实际情况来看，我国相关专家学者对盈余管理的系统性深入研究，一般都瞄准了上市企业群体或持续亏损企业，对盈余管理的研究不系统、不全面、不深入，这将对我国进一步提升盈余管理监管水平构成一定不利影响。当前，由于我国民企在自身管理及发展动力方面的特殊性,我国民企的管理、盈余管理特点和国外上市公司还存在着很大的不同,进一步深入研究我国民企上市公司自身管理方面的突出特点，以及其对企业盈余管理等方面的深层次影响,有助于监管层对症下药，更有针对性地研究出台全新的监管措施,进一步提升管理水平。这还可以为公司发展的决策层及相关会计信息使用人员提供一定的决策参考, 因此其拥有十分重要的意义。
本文首先认真总结分析了有关上市企业治理结构和盈余管理等方面的历史文献资料，依托当前资本市场上普遍运用的委托代理、内部人控制和契约等理论，系统研究了我国民企上市公司在自身治理结构方面的突出特征以及其对盈余管理方面所构成影响的深层次原理。在此基础上，本文通过2015-2017年我国上市企业数据，基于截面Jones模型对民营企业和非民营企业盈余管理程度进行测算和比较分析，发现民营企业盈余管理程度更高；从四个层面系统研究民企公司自身的治理结构突出特点,设立回归模型论证了民营企业独特的公司治理结构特征对盈余管理程度确实会产生影响；最后,本文进一步利用修正的费尔萨姆一奥尔森估价模型对民营上市公司盈余管理有公司价值的关系进行了验证，发现两者具有显著相关性。
本文首先认真总结分析了有关上市企业治理结构和盈余管理等方面的历史文献资料，依托当前资本市场上普遍运用的委托代理、内部人控制和契约等理论，系统研究了我国民企上市公司在自身治理结构方面的突出特征以及其对盈余管理方面所构成影响的深层次原理。在此基础上，本文通过2015-2017年我国上市企业数据，基于截面Jones模型对民营企业和非民营企业盈余管理程度进行测算和比较分析，发现民营企业盈余管理程度更高；从四个层面系统研究民企公司自身的治理结构突出特点,设立回归模型论证了民营企业独特的公司治理结构特征对盈余管理程度确实会产生影响；最后,本文进一步利用修正的费尔萨姆一奥尔森估价模型对民营上市公司盈余管理有公司价值的关系进行了验证，发现两者具有显著相关性。
ContributorsChen, Hui (Author) / Shen, Wei (Thesis advisor) / Chang, Chun (Thesis advisor) / Huang, Xiaochuan (Committee member) / Arizona State University (Publisher)
Created2019