Michael L O'Leary

San Joaquin Valley Agricultural Sciences Center

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Lindsey P. Burbank

San Joaquin Valley Agricultural Sciences Center

Xigang Liu

Hebei Normal University

Xuemei Chen

Guangdong Medical College

Shengben Li

Nanjing Agricultural University

Thanh Theresa Dinh

Stanford University

Lei Gao

Shenzhen University

Pablo A. Manavella

Instituto de Agrobiotecnología del Litoral

Detlef Weigel

Max Planck Institute for Biology

Robert J. Schmitz

University of Georgia

R. L. Gilbertson

University of California, Davis

Cooperative Institutions

University of California, Riverside

Agricultural Research Service

Durham University

United States Department of Agriculture

Plant (United States)

Chinese Academy of Sciences

San Joaquin Valley Agricultural Sciences Center

University of California, Berkeley

Institute of Genetics and Developmental Biology

Consejo Superior de Investigaciones Científicas

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Comparative Genomics to Develop a Specific Multiplex PCR Assay for Detection of Clavibacter michiganensis

Phytopathology (2019)

Shree Prasad Thapa Michael L O'Leary Marie‐Agnès Jacques R. L. Gilbertson Gitta Coaker

Clavibacter michiganensis is a Gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial wilt and canker symptoms. Accurate detection is a crucial step in confirming outbreaks of bacterial canker and developing management strategies. A major problem with existing detection methods are false-positive and -negative results. Here, we report the use of comparative genomics of 37 diverse Clavibacter strains, including 21 strains sequenced in this study, to identify specific sequences that are C. michiganensis detection targets. Genome-wide phylogenic analyses revealed additional diversity within the genus Clavibacter. Pathogenic C. michiganensis strains varied in plasmid composition, highlighting the need for detection methods based on chromosomal targets. We utilized sequences of C. michiganensis-specific loci to develop a multiplex PCR-based diagnostic platform using two C. michiganensis chromosomal genes (rhuM and tomA) and an internal control amplifying both bacterial and plant DNA (16s ribosomal RNA). The multiplex PCR assay specifically detected C. michiganensis strains from a panel of 110 additional bacteria, including other Clavibacter spp. and bacterial pathogens of tomato. The assay was adapted to detect the presence of C. michiganensis in seed and tomato plant materials with high sensitivity and specificity. In conclusion, the described method represents a robust, specific tool for detection of C. michiganensis in tomato seed and infected plants.

Clavibacter michiganensis

Multiplex

Canker

10.1094/phyto-10-19-0405-r

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Invertibility

Michael L O'Leary

Since every linear transformation can be described by a matrix, the next goal should be to determine the standard matrix for the inverse of an invertible linear transformation. Since the inverse function is defined in terms of the given function, the sought-after standard matrix should also be found using the standard matrix of the given linear transformation. There is a close relationship between determinants and the inverses of square matrices. The goal of the definition of the determinant is to generalize the invertibility tests to arbitrary square matrices. The calculations of determinants are sometimes written using terminology that is intended to name the parts of the determinant equation. The determinant can be used to determine whether a square matrix is invertible. It can also be used to compute its inverse.

Matrix (chemical analysis)

Inverse function

Square (algebra)

Linear map

Involutory matrix

10.1002/9781119437437.ch4

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Isolation and characterization of behavioural mutants and genes of Agrobacterium tumefaciens

Journal of General Microbiology (1991)

C. H. Shaw Gary J. Loake Adrian P. Brown Christine Garrett William J. Deakin

Agrobacterium tumefaciens exhibits an unusual flagellation pattern in the electron microscope. The typical pattern is of two flagella in a polar or sub-polar tuft at one pole only, plus one or two lateral flagella on each side. Twenty independent behavioural mutants were isolated, after Tn5 mutagenesis, and divided into several classes. Fourteen non-motile mutants were differentiable into non-flagellate and flagellate subclasses, one non-chemotactic mutant appeared to have a defect in the intracellular signalling pathway, and one other mutant displayed an unusual pattern of polar cell pairing. Four mutants with impaired swarming ability were also isolated. Root colonization ability was impaired in the non-motile mutant for which this property was tested. From all but three of the mutants, the Tn5 insertion sites, including flanking sequences, have been cloned and used as probes to isolate a set of seven cosmids from a wild-type A. tumefaciens library. No hybridization to Escherichia coli or Pseudomonas DNA was detected for the A. tumefaciens mutant flanking sequences, but varying degrees of similarity to Rhizobium meliloti behavioural genes were detected. By complementation of A. tumefaciens behavioural mutants and hybridization of mutant flanking sequences, one cosmid insert was shown to contain at least nine behavioural loci, and another, linked to it on the chromosome, at least three. This suggests that, as in other organisms, behavioural genes are clustered in the A. tumefaciens genome.

Cosmid

10.1099/00221287-137-8-1939

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DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis

PLoS Genetics (2014)

Thanh Theresa Dinh Lei Gao Xigang Liu Dongming Li Shengben Li

RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology.

RNA-Directed DNA Methylation

10.1371/journal.pgen.1004446

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Inner Product Spaces

Michael L O'Leary

The dot product is used to find the angle between two nonzero vectors and to define what it means for vectors to be orthogonal. A vector space paired with an inner product is an inner product space. As computations of length, distance, and angle measure in ‚Ñùn can be made with the dot product, the inner product is used to compute these magnitudes in a general inner product space. This can be done because every inner product satisfies an important inequality. Although the inner product controls the geometry of the inner product space, the geometry is still Euclidean in that a key theorem proved by Euclid still holds. Every finite dimensional inner product space has an orthonormal basis.

Inner product space

Outer product

10.1002/9781119437437.ch6

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Abstract Vectors

Michael L O'Leary

This chapter discusses the concept of a vector abstract. Before delving deeper into the study of abstract vector spaces, it is useful to develop a small catalog of familiar, concrete systems which are vector spaces. It should be noted that every vector space is a subspace of itself. This subspace is called the improper subspace. This means that any property of a subspace is also a property of the vector space. Linear dependence and linear independence were determined by finding the solution set of a particular homogeneous system of linear equations. The sum of the rank of the linear transformation and its nullity equals the dimension of the domain of the transformation. This holds for all linear transformations. The linear transformation needs to be an isomorphism to preserve some of the stronger properties.

Linear map

Rank (graph theory)

Independence

Linear space

Isomorphism (crystallography)

10.1002/9781119437437.ch5

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Euclidean Space

Michael L O'Leary

Basic algebra is the study of ℝ with various operations, such as addition and multiplication. This is extended to ℝ × ℝ with equations for lines, distances between points, and angle measures. In calculus, eventually ℝ × ℝ × ℝ is studied. At this point, vectors are introduced, which are visualized as arrows either in a plane or in space. There are two standard operations on arrows. The first is arrow addition. The second operation is arrow scalar multiplication. The operations are read from left to right unless overridden by grouping symbols. The interpretations of vector as either a point or an arrow means that sets of vectors can be naturally viewed geometrically.

Scalar multiplication

10.1002/9781119437437.ch2

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Complete Genome Sequence Resource of a Strain of Curtobacterium flaccumfaciens pv. flaccumfaciens, the Causal Agent of Bacterial Wilt of Common Bean, from Turkey

Phytopathology (2020)

Michael L O'Leary R. L. Gilbertson

Curtobacterium flaccumfaciens pv. flaccumfaciens is the causal agent of bacterial wilt of common bean (Phaseolus vulgaris), a disease that can reduce yields of this economically important crop worldwide. Current genomics resources for this bacterial pathogen are limited. Therefore, long-read sequencing was used to determine the complete genome sequence of a pathogenic C. flaccumfaciens pv. flaccumfaciens strain isolated from common bean leaves showing irregular necrotic lesions with yellow borders collected in a commercial field in Turkey in 2015.

Bacterial wilt

Strain (injury)

10.1094/phyto-04-20-0131-a

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Complete Genome Resources for Xylella fastidiosa Strains AlmaEM3 and BB08-1 Reveal Prophage-Associated Structural Variation Among Blueberry-Infecting Strains

Phytopathology (2021)

Michael L O'Leary Luis F. Arias‐Giraldo Lindsey P. Burbank Leonardo De La Fuente Blanca B. Landa

Xylella fastidiosa is a gram-negative plant pathogenic bacterium with wide geographical distribution and host range. X. fastidiosa strains are separated into genetically distinct subspecies, and further categorized into sequence types (ST). Genetic characterization of X. fastidiosa strains infecting blueberry has revealed that strains of subspecies multiplex and fastidiosa are capable of causing bacterial leaf scorch disease of blueberry under field conditions. To better elucidate the relationships among blueberry-infecting X. fastidiosa subsp. multiplex strains, we completed the genomes of an ST 42 strain, AlmaEM3, and a ST 43 strain, BB08-1, using a hybrid assembly approach. Comparison of these assemblies reveals a large (0.95 Mb) chromosomal inversion in BB08-1 relative to AlmaEM3 and the reference strain M12, likely resulting from recombination between prophage regions.

Xylella fastidiosa

Prophage

Subspecies

Multiplex

Strain (injury)

10.1094/phyto-08-21-0317-a

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Logic and Set Theory

Michael L O'Leary

A sentence that is true or false but not both is called a statement. As the logical connectives enabled new statements to be written using given statements, the set operations allow new sets to be defined from given sets. A set is a collection of things called elements. Anything can be an element, but in linear algebra, elements are typically numbers, matrices, functions, or vectors. Functions are actually sets of ordered pairs. Because functions are sets, they are equal when they are subsets of each other. This implies that if the domains of two functions are not equal, the functions cannot be equal. The range and codomain of a function need not be equal, but there is a name for functions in which they are.

Statement (logic)

Set function

10.1002/9781119437437.ch1

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