The evolution and regulation of DNA-binding by the nickel-dependent transcription factor NikR

Transition metal homeostasis is critical for all cells to balance cellular metal requirements with metal availability. One common homeostatic mechanism in bacteria is metal-dependent transcriptional regulation. The Ni2+-dependent transcription factor NikR is a member of the ribbon-helix-helix: RHH) family of DNA-binding proteins and is widespread among bacteria and archea with vastly different nickel physiologies. The goal of this thesis was to better understand basic aspects of cellular transition metal homeostasis by examining the activity and regulatory properties of NikR family members from different bacterial species. One organism that exhibits a prominent and well-defined nickel physiology is Helicobacter pylori, making it an ideal system with which to examine various aspects of metal homeostasis. Genetic studies demonstrated that NikR activation is controlled by a hierarchy of nickel-trafficking in H. pylori, where nickel is preferentially trafficked to the urease assembly pathway. NikR differentially regulates multiple nickel-related genes in response to distinct extracellular nickel concentrations, functioning to coordinate multiple activities important for metal homeostasis. Differential gene regulation resulted from NikR binding to promoters from different genes with a range of affinities and in distinct conformations, due to a flexible N-terminal arm that makes different DNA contacts at two promoters. In addition, the arm expands the specific DNA interactions by NikR as compared to previously characterized RHH transcription factors. Examination of additional previously uncharacterized NikR family members revealed that the N-terminal arm has been adapted differently in some cases but is also critical for DNA-binding affinity and specificity. This structural feature provides a molecular basis for tuning NikR activity to the physiology of the cell. These studies provide insight into how multiple metal-dependent activities in cells are coordinated and controlled in response to fluctuations in environmental metal. Further, they establish a robust experimental system with which to further investigate the molecular details of the evolution of transcriptional regulation, an integral component of metal homeostasis

Asymptotics for Graded Capelli Polynomials

The finite dimensional simple superalgebras play an important role in the theory of PI-algebras in characteristic zero. The main goal of this paper is to characterize the T 2-ideal of graded identities of any such algebra by considering the growth of the corresponding supervariety. We consider the T 2-ideal Γ M+1,L+1 generated by the graded Capelli polynomials C a p M+1[Y,X] and C a p L+1[Z,X] alternanting on M+1 even variables and L+1 odd variables, respectively. We prove that the graded codimensions of a simple finite dimensional superalgebra are asymptotically equal to the graded codimensions of the T 2-ideal Γ M+1,L+1, for some fixed natural numbers M and L. In particular csupn(Γk2+l2+1,2kl+1)≃csupn(Mk,l(F)) and csupn(Γs2+1,s2+1)≃csupn(Ms(F⊕tF)). These results extend to finite dimensional superalgebras a theorem of Giambruno and Zaicev [6] giving in the ordinary case the asymptotic equality csupn(Γk2+1,1)≃csupn(Mk(F)) between the codimensions of the Capelli polynomials and the codimensions of the matrix algebra M k (F)

Computing with rational symmetric functions and applications to invariant theory and PI-algebras

Let the formal power series f in d variables with coefficients in an arbitrary field be a symmetric function decomposed as a series of Schur functions, and let f be a rational function whose denominator is a product of binomials of the form (1 - monomial). We use a classical combinatorial method of Elliott of 1903 further developed in the Partition Analysis of MacMahon in 1916 to compute the generating function of the multiplicities (i.e., the coefficients) of the Schur functions in the expression of f. It is a rational function with denominator of a similar form as f. We apply the method to several problems on symmetric algebras, as well as problems in classical invariant theory, algebras with polynomial identities, and noncommutative invariant theory.Comment: 37 page

Defining Relations of Minimal Degree of the Trace Algebra of 3×33 \times 3 Matrices

The trace algebra C(n,d) over a field of characteristic 0 is generated by all traces of products of d generic nxn matrices, n,d>1. Minimal sets of generators of C(n,d) are known for n=2 and n=3 for any d as well as for n=4 and n=5 and d=2. The defining relations between the generators are found for n=2 and any d and for n=3, d=2 only. Starting with the generating set of C(3,d) given by Abeasis and Pittaluga in 1989, we have shown that the minimal degree of the set of defining relations of C(3,d) is equal to 7 for any d>2. We have determined all relations of minimal degree. For d=3 we have also found the defining relations of degree 8. The proofs are based on methods of representation theory of the general linear group and easy computer calculations with standard functions of Maple

Polynomial identities on superalgebras and exponential growth

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Lubricants Optimized for use with R-32 and Related Low GWP Refrigerant Blends

Lubricants are important components of almost all air conditioning and refrigeration systems. Their primary function is to lubricate the compressor, provide sealing of clearances between low and high pressure sides of the compressor and remove frictional heat. But the lubricant is in contact with refrigerant at all times and plays a thermo-fluidic role in the air conditioning system that can impact both system capacity and coefficient of performance (COP). Lubricants can influence capacity by altering the refrigerant-side heat transfer coefficients, and increasing pressure drop required to maintain set point temperatures. Lubricants can also affect the isentropic efficiency of the compressor. The transition to lower global warming potential (GWP) alternative refrigerants is critical to the realization of environmentally sustainable and more energy efficient refrigeration technologies. Leading candidates to replace R-22 and R-410A in air conditioning and heat pump applications include R-32 (difluoromethane) and a plethora of HFC/hydrofluoro-olefin blends with GWPs in the range of 400-650. Considerable data has been generated comparing R-410A with various low GWP alternative refrigerants in full system tests. Most notable is the work sponsored by AHRI under the Alternative Refrigerant Evaluation Program (AREP). But these studies have either been refrigerant “drop in” tests to commercial R-410A systems or “soft optimized” tests, where minor component modifications were made to better adapt a system to the properties of the new refrigerants. In all cases, the lubricants used for these studies were the commercial polyol ester (POE) lubricants used with R-410A. But commercial POE lubricants used today are much less compatible with R-32 and HFC/HFO blends. There is concern that issues may arise with long term reliability of compressors due to inadequate lubrication, poor oil return to the compressor and undesirable lubricant hold up in the system; problems that would not be observed in the short term capacity and energy efficiency tests. But regardless, there is also interest in understanding if properly optimized lubricants can improve the overall performance of low GWP-based systems. This paper presents the results of a study of the solution phase behavior and lubricating performance of several commercial and new developmental POE lubricants with low GWP R-410A replacement refrigerants. The results suggest that POE lubricants used today with R-410A may not be acceptable for use with R-32 or related HFC/HFO blends. An undesirable miscibility gap is observed in mixtures of traditional POEs with R-32 in the concentration range of 10-40 wt% lubricant in refrigerant. In addition, the viscosity dilution of refrigerant/lubricant mixtures at high lubricant concentrations (typical of those observed in the compressor sump) is as much as 50% more pronounced with R-32 than R-410A. Studies conducted with a new class of advanced polyol esters show that it is possible to design synthetic lubricants optimized for R-32, combining good refrigerant miscibility with limited viscosity dilution