Organization and function of the phage Lambda chromosome

The process of prophage integration by phage λ and the function and structure of the chromosomal elements required for λ integration have been studied with the use of λ deletion mutants. Since att^φ, the substrate of the integration enzymes, is not essential for λ growth, and since att^φ resides in a portion of the λ chromosome which is not necessary for vegetative growth, viable λ deletion mutants were isolated and examined to dissect the structure of att^φ.

Deletion mutants were selected from wild type populations by treating the phage under conditions where phage are inactivated at a rate dependent on the DNA content of the particles. A number of deletion mutants were obtained in this way, and many of these mutants proved to have defects in integration. These defects were defined by analyzing the properties of Int-promoted recombination in these att mutants.

The types of mutants found and their properties indicated that att^φ has three components: a cross-over point which is bordered on either side by recognition elements whose sequence is specifically required for normal integration. The interactions of the recognition elements in Int-promoted recombination between att mutants was examined and proved to be quite complex. In general, however, it appears that the λ integration system can function with a diverse array of mutant att sites.

The structure of att^φ was examined by comparing the genetic properties of various att mutants with their location in the λ chromosome. To map these mutants, the techniques of heteroduplex DNA formation and electron microscopy were employed. It was found that integration cross-overs occur at only one point in att^φ and that the recognition sequences that direct the integration enzymes to their site of action are quite small, less than 2000 nucleotides each. Furthermore, no base pair homology was detected between att^φ and its bacterial analog, att^B. This result clearly demonstrates that λ integration can occur between chromosomes which have little, if any, homology. In this respect, λ integration is unique as a system of recombination since most forms of generalized recombination require extensive base pair homology.

An additional study on the genetic and physical distances in the left arm of the λ genome was described. Here, a large number of conditional lethal nonsense mutants were isolated and mapped, and a genetic map of the entire left arm, comprising a total of 18 genes, was constructed. Four of these genes were discovered in this study. A series of λdg transducing phages was mapped by heteroduplex electron microscopy and the relationship between physical and genetic distances in the left arm was determined. The results indicate that recombination frequency in the left arm is an accurate reflection of physical distances, and moreover, there do not appear to be any undiscovered genes in this segment of the genome.

Symmetric representation of an integral domain over a subdomain

Let F(θ) be a separable extension of degree n of a field F. Let Δ and D be integral domains with quotient fields F(θ) and F respectively. Assume that Δ ᴝ D. A mapping φ of Δ into the n x n D matrices is called a Δ/D rep if (i) it is a ring isomorphism and (ii) it maps d onto dI_n whenever d ϵ D. If the matrices are also symmetric, φ is a Δ/D symrep.

Every Δ/D rep can be extended uniquely to an F(θ)/F rep. This extension is completely determined by the image of θ. Two Δ/D reps are called equivalent if the images of θ differ by a D unimodular similarity. There is a one-to-one correspondence between classes of Δ/D reps and classes of Δ ideals having an n element basis over D.

The condition that a given Δ/D rep class contain a Δ/D symrep can be phrased in various ways. Using these formulations it is possible to (i) bound the number of symreps in a given class, (ii) count the number of symreps if F is finite, (iii) establish the existence of an F(θ)/F symrep when n is odd, F is an algebraic number field, and F(θ) is totally real if F is formally real (for n = 3 see Sapiro, “Characteristic polynomials of symmetric matrices” Sibirsk. Mat. Ž. 3 (1962) pp. 280-291), and (iv) study the case D = Z, the integers (see Taussky, “On matrix classes corresponding to an ideal and its inverse” Illinois J. Math. 1 (1957) pp. 108-113 and Faddeev, “On the characteristic equations of rational symmetric matrices” Dokl. Akad. Nauk SSSR 58 (1947) pp. 753-754).

The case D = Z and n = 2 is studied in detail. Let Δ’ be an integral domain also having quotient field F(θ) and such that Δ’ ᴝ Δ. Let φ be a Δ/Z symrep. A method is given for finding a Δ’/Z symrep ʘ such that the Δ’ ideal class corresponding to the class of ʘ is an extension to Δ’ of the Δ ideal class corresponding to the class of φ. The problem of finding all Δ/Z symreps equivalent to a given one is studied.

Some generalizations of commutativity for linear transformations on a finite dimensional vector space

Let L be the algebra of all linear transformations on an n-dimensional vector space V over a field F and let A, B, ƐL. Let A_i+1 = A_iB - BA_i, i = 0, 1, 2,…, with A = A_o. Let f_k (A, B; σ) = A_2K+1 - ^σ1^A2K-1 ^{+ σ}2^A2K-3 -… +(-1)^Kσ_KA₁ where σ = (σ₁, σ₂,…, σ_K), σ_i belong to F and K = k(k-1)/2. Taussky and Wielandt [Proc. Amer. Math. Soc., 13(1962), 732-735] showed that f_n(A, B; σ) = 0 if σ_i is the i^th elementary symmetric function of (β₄- β_s)², 1 ≤ r ˂ s ≤ n, i = 1, 2, …, N, with N = n(n-1)/2, where β₄ are the characteristic roots of B. In this thesis we discuss relations involving f_k(X, Y; σ) where X, Y Ɛ L and 1 ≤ k ˂ n. We show: 1. If F is infinite and if for each X Ɛ L there exists σ so that f_k(A, X; σ) = 0 where 1 ≤ k ˂ n, then A is a scalar transformation. 2. If F is algebraically closed, a necessary and sufficient condition that there exists a basis of V with respect to which the matrices of A and B are both in block upper triangular form, where the blocks on the diagonals are either one- or two-dimensional, is that certain products X₁, X₂…X_r belong to the radical of the algebra generated by A and B over F, where X_i has the form f₂(A, P(A,B); σ), for all polynomials P(x, y). We partially generalize this to the case where the blocks have dimensions ≤ k. 3. If A and B generate L, if the characteristic of F does not divide n and if there exists σ so that f_k(A, B; σ) = 0, for some k with 1 ≤ k ˂ n, then the characteristic roots of B belong to the splitting field of g_k(w; σ) = w^2K+1 - σ₁w^2K-1 + σ₂w^2K-3 - …. +(-1)^K σ_Kw over F. We use this result to prove a theorem involving a generalized form of property L [cf. Motzkin and Taussky, Trans. Amer. Math. Soc., 73(1952), 108-114]. 4. Also we give mild generalizations of results of McCoy [Amer. Math. Soc. Bull., 42(1936), 592-600] and Drazin [Proc. London Math. Soc., 1(1951), 222-231].

Lq estimates for rearrangements of Fourier series

This work is concerned with estimating the upper envelopes S* of the absolute values of the partial sums of rearranged trigonometric sums. A.M. Garsia [Annals of Math. 79 (1964), 634-9] gave an estimate for the L₂ norms of the S*, averaged over all rearrangements of the original (finite) sum. This estimate enabled him to prove that the Fourier series of any function in L₂ can be rearranged so that it converges a.e. The main result of this thesis is a similar estimate of the L_q norms of the S*, for all even integers q. This holds for finite linear combinations of functions which satisfy a condition which is a generalization of orthonormality in the L₂ case. This estimate for finite sums is extended to Fourier series of L_q functions; it is shown that there are functions to which the Men’shov-Paley Theorem does not apply, but whose Fourier series can nevertheless be rearranged so that the S* of the rearranged series is in L_q.

Spectral density of first order Piecewise linear systems excited by white noise

The Fokker-Planck (FP) equation is used to develop a general method for finding the spectral density for a class of randomly excited first order systems. This class consists of systems satisfying stochastic differential equations of form ẋ + f(x) = m/Ʃ/j = 1 h_j(x)n_j(t) where f and the h_j are piecewise linear functions (not necessarily continuous), and the n_j are stationary Gaussian white noise. For such systems, it is shown how the Laplace-transformed FP equation can be solved for the transformed transition probability density. By manipulation of the FP equation and its adjoint, a formula is derived for the transformed autocorrelation function in terms of the transformed transition density. From this, the spectral density is readily obtained. The method generalizes that of Caughey and Dienes, J. Appl. Phys., 32.11.

This method is applied to 4 subclasses: (1) m = 1, h₁ = const. (forcing function excitation); (2) m = 1, h₁ = f (parametric excitation); (3) m = 2, h₁ = const., h₂ = f, n₁ and n₂ correlated; (4) the same, uncorrelated. Many special cases, especially in subclass (1), are worked through to obtain explicit formulas for the spectral density, most of which have not been obtained before. Some results are graphed.

Dealing with parametrically excited first order systems leads to two complications. There is some controversy concerning the form of the FP equation involved (see Gray and Caughey, J. Math. Phys., 44.3); and the conditions which apply at irregular points, where the second order coefficient of the FP equation vanishes, are not obvious but require use of the mathematical theory of diffusion processes developed by Feller and others. These points are discussed in the first chapter, relevant results from various sources being summarized and applied. Also discussed is the steady-state density (the limit of the transition density as t → ∞).

Stationary absolute distributions for chains of infinite order

Let {Ƶ_n}^∞_{n = -∞} be a stochastic process with state space S₁ = {0, 1, …, D – 1}. Such a process is called a chain of infinite order. The transitions of the chain are described by the functions

Q_i(i⁽⁰⁾) = Ƥ(Ƶ_n = i | Ƶ_{n - 1} = i ⁽⁰⁾₁, Ƶ_{n - 2} = i ⁽⁰⁾₂, …) (i ɛ S₁), where i⁽⁰⁾ = (i⁽⁰⁾₁, i⁽⁰⁾₂, …) ranges over infinite sequences from S₁. If i⁽ⁿ⁾ = (i⁽ⁿ⁾₁, i⁽ⁿ⁾₂, …) for n = 1, 2,…, then i⁽ⁿ⁾ → i⁽⁰⁾ means that for each k, i⁽ⁿ⁾_k = i⁽⁰⁾_k for all n sufficiently large.

Given functions Q_i(i⁽⁰⁾) such that

(i) 0 ≤ Q_i(i⁽⁰) ≤ ξ ˂ 1

(ii)D – 1/Ʃ/i = 0 Q_i(i⁽⁰⁾) Ξ 1

(iii) Q_i(i⁽ⁿ⁾) → Q_i(i⁽⁰⁾) whenever i⁽ⁿ⁾ → i⁽⁰⁾,

we prove the existence of a stationary chain of infinite order {Ƶ_n} whose transitions are given by

Ƥ (Ƶ_n = i | Ƶ_{n - 1}, Ƶ_{n - 2}, …) = Q_i(Ƶ_{n - 1}, Ƶ_{n - 2}, …)

With probability 1. The method also yields stationary chains {Ƶ_n} for which (iii) does not hold but whose transition probabilities are, in a sense, “locally Markovian.” These and similar results extend a paper by T.E. Harris [Pac. J. Math., 5 (1955), 707-724].

Included is a new proof of the existence and uniqueness of a stationary absolute distribution for an Nth order Markov chain in which all transitions are possible. This proof allows us to achieve our main results without the use of limit theorem techniques.