Dave Schneider

• MS
• Professor at University of Saskatchewan

Background Canola (Brassica napus L.) has high phosphorus demand, but its seedlings are sensitive to seed-placed phosphorus fertilizers. Optimizing phosphorus fertilizer management for canola is critical and can benefit from insights into the root-associated microbiota, which enhances phosphorus availability through mineralization and solubilizatio...

Background Canola (Brassica napus L.) has high phosphorus demand, but its seedlings are sensitive to seed-placed phosphorus fertilizers. Optimizing phosphorus fertilizer managements (rates and placements) for canola is critical and can be aided by a better understanding of the root-associated microbiome, as it plays key roles in improving phosphoru...

Background Ribosomally-synthesized cyclic peptides are widely found in plants and exhibit useful bioactivities for humans. The identification of cyclic peptide sequences and their precursor proteins is facilitated by the growing number of sequenced genomes. While previous research largely focused on the chemical diversity of these peptides across v...

Background: Ribosomally-synthesized cyclic peptides are widely found in plants and show useful bioactivities for humans. The identification of cyclic peptide sequences and their precursor proteins is facilitated by the growing number of sequenced genomes. While previous research largely focused on the chemical diversity of these peptides across var...

Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (...

There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanis...

We introduce and study a variant of the Wasserstein distance on the space of probability measures, specially designed to deal with measures whose support has a dendritic, or treelike structure with a particular direction of orientation. Our motivation is the comparison of and interpolation between plants' root systems. We characterize barycenters w...

Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of poole...

Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myr-iad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pool...

Rationale The stable isotope ratios of water (δ²H and δ¹⁸O values) have been widely used to trace water in plants in a variety of physiological, ecohydrological, biogeochemical and hydrological studies. In such work, the analyte must first be extracted from samples, prior to isotopic analysis. While cryogenic vacuum distillation is currently the mo...

This work presents a new pipeline for digital optical phenotyping the root system architecture of agricultural crops. The pipeline begins with a 3D root-system imaging apparatus for hydroponically grown crop lines of interest. The apparatus acts as a self-containing dark room, which includes an imaging tank, motorized rotating bearing and digital c...

The bacterial plant pathogen Pseudomonas syringae adapts to changes in the environment by modifying its gene expression profile. In many cases, the response is mediated by the activation of extracytoplasmic function (ECF) sigma factors that direct RNA polymerase to transcribe specific sets of genes. In this study we focus on PSPTO_1043, one of ten...

The 137 regions of enrichment identified by CSDeconv in GFF format (https://www.sanger.ac.uk/resources/software/gff/spec.html). (GFF)

Orthologs of the PSPTO_1043 regulon in the sequenced Pseudomonadales. Reciprocal Best BLAST Hits (RBBH’s) were computed between DC3000 and 1028 genomes from the order Pseudomonadales and then used to identify orthologs of the genes in the PSPTO_1043 regulon. Once families of orthologous genes were identified, the regions upstream of each gene were...

A detailed discussion of the claim that the PSPTO_1043 binding sequence closely resembles the RpoERsp binding sequence identified in Rhodobacter and Caulobacter crescentus. (DOCX)

Assays to measure the effect of 1O2 and tBOOH on wildtype and ΔPSPTO_1043/1042 Pseudomonas syringae pv tomato DC3000. (DOCX)

The “naive” profile of the PSPTO_1043 ChIP-Seq reads that align to the DC3000 chromosome sequence. Naive profiles and file format is described in [17]. (ZIP)

Examples of ChIP-Seq peaks upstream of selected targets. (A) Peak upstream of the PSPTO_1043/1042 locus. (B) Peak upstream of phrB and other homologs of the RpoERsp-ChrR core regulon. The genomic profiles shown can be found in S2 Dataset. (TIFF)

Strains, plasmids, and primers used in this study. (DOCX)

Assays to measure growth of wildtype and ΔPSPTO_1043/1042 Pseudomonas syringae pv tomato DC3000 in Arabidopsis seedlings. (PDF)

The “sinister” profile of the PSPTO_1043 ChIP-Seq reads that align to the DC3000 chromosome sequence. Sinister profiles and file format is described in [17]. (ZIP)

A description of the method used to compute S2 Table. (DOCX)

The development of the Plant Root Imaging and Data Acquisition (PRIDA) hardware/software system enables researchers to collect digital images, along with all the relevant experimental details, of a range of hydroponically grown agricultural crop roots for 2D and 3D trait analysis. Previous efforts of image-based root phenotyping focused on young ce...

A plant's ability to maintain or improve its yield under limiting conditions, such as nutrient deficiency or drought, can be strongly influenced by root system architecture, the 3-dimensional distribution of the different root types in the soil. The ability to image, track and quantify these root system attributes in a dynamic fashion is a useful t...

Root system architecture is being studied more closely for improved nutrient acquisition, stress tolerance and carbon sequestration by relating the genetic material that corresponds to preferential physical features. This information can help direct plant breeders in addressing the growing concerns regarding the global demand on crops and fossil fu...

We consider a new reaction-transport framework, and apply it to the problem of advection-driven biotic transport. The are two compartments - the growth layer, coupled to a separate, advective layer. Density fronts propagate in both layers. Crucially, the downwind front speed goes to a finite value as the coupling goes to zero. We next include diffu...

We develop a new perturbation method for studying quasi-neutral competition in a broad class of stochastic competition models, and apply it to the analysis of fixation of competing strains in two epidemic models. The first model is a two-strain generalization of the stochastic Susceptible-Infected-Susceptible (SIS) model. Here we extend previous re...

Bacteria contain small non-coding RNAs (ncRNAs) that are typically responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they often regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae DC3000, spot 42 (now referred...

Branching processes have served as a model for chemical reactions, biological growth processes, and contagion (of disease, information, or fads). Through this connection, these seemingly different physical processes share some common universalities that can be elucidated by analyzing the underlying branching process. In this work we focus on couple...

Triticum aestivum aluminum-activated malate transporter (TaALMT1) is the founding member of a unique gene family of anion transporters (ALMTs) that mediate the efflux of organic acids. A small sub-group of root-localized ALMTs, including TaALMT1, is physiologically associated with in planta aluminum (Al) resistance. TaALMT1 exhibits significant enh...

Despite the enormous relevance of zoonotic infections to world- wide public health, and despite much effort in modeling individual zoonoses, a fundamental understanding of the disease dynamics and the nature of outbreaks arising in such systems is still lacking. We introduce a simple stochastic model of susceptible-infected- recovered dynamics in a...

Infection dynamics have been studied extensively on complex networks, yielding insight into the effects of heterogeneity in contact patterns on disease spread. Somewhat separately, metapopulations have provided a paradigm for modeling systems with spatially extended and "patchy" organization. In this paper we expand on the use of multitype networks...

Bacterial type III secretion systems (T3SSs) deliver proteins called effectors into eukaryotic cells. Although N-terminal amino acid sequences are required for translocation, the mechanism of substrate recognition by the T3SS is unknown. Almost all actively deployed T3SS substrates in the plant pathogen Pseudomonas syringae pathovar tomato strain D...

TEREE algorithm scores for annotated coding regions in P. s. phaseolicola 1448a. (XLSX)

TEREE algorithm scores for annotated coding regions in R. solanacearum GMI1000. (XLSX)

TEREE algorithm scores for annotated coding regions in P. s. tomato DC3000. (XLSX)

TEREE algorithm scores for proteins in T3SS substrate and negative training sets. (XLSX)

TEREE algorithm scores for annotated coding regions in S. e. Typhimurium LT2. (XLSX)

Fire blight is a devastating disease of rosaceous plants caused by the Gram-negative bacterium Erwinia amylovora. This pathogen delivers virulence proteins into host cells utilizing the type III secretion system (T3SS). Expression of the T3SS and of translocated and secreted substrates is activated by the alternative sigma factor HrpL, which recogn...

Unsaturated plots. (a). Unsaturated scatter plot of TAP-only treated biological replicate 1 (E1) compared to TAP-only treated biological replicated 2 (E2). (b) Unsaturated scatter plot of Exonuclease treated biological replicate 1 (E1+) compared to exonuclease treated biological replicate 2 (E2+). (c) Unsaturated scatter plot of Exonuclease treated...

A merged profile for the DC3000 chromosome that can be loaded into Artemis to visualize the sequencing results of biological replicates E1− and E2−. (RAR)

A merged profile for the DC3000 chromosome that can be loaded into Artemis to visualize the sequencing results of biological replicates E1+ and E2+. (RAR)

A profile for the DC3000 chromosome containing the classification of each genomic location. (RAR)

gff file of E12+Top peaks. (RAR)

A histogram of the ratios of RNA-Seq read counts downstream and upstream of TSS's. These ratios were computed by first counting the number of reads in the RNA-Seq sinister profile, 10 bp upstream and 10 bp downstream of the 5′-end of all 1827merged E12+Top peaks. Then, for each peak, we compute the ratio: log10(1+downstream_count) log10(1+upstream_...

A histogram of the log_10 of the distances from TSS's to start codons. To compute these distances, we first selected the set of E12+Top peaks that fell within 1000 bps upstream of annotated CDSs. This set included 1552 of the 2510 TSSs. The mean length of these 5′UTR regions was 77.8 bps. (TIF)

Summary of 5′-end RNA-Seq data for P. syringae DC3000. (XLSX)

Distribution of unique positions. (XLS)

gff file containing the resulting ranges for 40 bps upstream of E12+Top peaks. (RAR)

MEME results. (RAR)

Transcriptional start sites confirmed by 5′RACE. (XLS)

Transcriptional start sites for putative RpoF regulated genes. (XLSX)

A profile for the DC3000 chromosome that can be loaded into Artemis to visualize the sequencing results of the Tap only treated sample E1−. (RAR)

A profile for the DC3000 chromosome that can be loaded into Artemis to visualize the sequencing results of the Tap only treated sample E2−. (RAR)

A profile for the DC3000 chromosome that can be loaded into Artemis to visualize the sequencing results of the exonuclease and Tap treated sample E1+. (RAR)

A profile for the DC3000 chromosome that can be loaded into Artemis to visualize the sequencing results of the exonuclease and Tap treated sample E2+. (RAR)

Python script, make-class-scatter.py, for the three-way classification of 5′-ends. (RAR)

Data file containing the FASTA file of 40 bps upstream of E12+Top peaks. (RAR)

RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina's high-throughput sequencing technology, we globally identified 5'-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 5'-ends obtained by thi...

Estimation of times in years since most recent common ancestor of T1-like strains with Bayesian 95% Highest Posterior Density intervals assuming a yearly mutation rate per bp of 5×10–6. (XLS)

SNPs identified between Max4, LNPV 17.41, T1, K40, and NCPPB1108 by aligning Illumina reads against the genome of Pto strain DC3000. (XLS)

Predicted type III effector repertoires of T1-like strains (positions refer to whole genome shotgun sequences deposited at NCBI, besides Max4. which was not deposited). (XLS)

List of strains with continent and year of isolation, MLST genotype, SNP genotype, and results for several virulence factors based on PCR (and sequencing of PCR products for hopM1). (XLS)

Core genome SNPs identified between Pto strains T1, Max4, NCPPB1108, K40, and LNPV17.41 by aligning Illumina reads against the T1 draft genome and only considering those SNPs located within core genome genes. (XLS)

DNA sequences corresponding to the MLST and SNP genotypes listed in Table 1 (only nucleotides corresponding to SNPs are shown and were used for molecular evolutionary analyses, i.e. nucleotides identical in all analyzed strains were ignored. (XLS)

Primers. (XLS)

The plant pathogen Pseudomonas syringae pv. tomato DC3000 (DC3000) is found in a wide variety of environments and must monitor and respond to various environmental signals such as the availability of iron, an essential element for bacterial growth. An important regulator of iron homeostasis is Fur (ferric uptake regulator), and here we present the...

Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography. Here, we report a genome-based micro-evolutionary study of a bacterial plant pathogen, Pseudomonas syringae pv. tomato. Only 267 mutations were identified between five sequenced is...

In this work, we explore the connections between parameter fitting and statistical thermodynamics using the maxent principle of Jaynes as a starting point. In particular, we show how signal averaging may be described by a suitable one particle partition function, modified for the case of a variable number of particles. These modifications lead to a...

When E. O. Wilson proclaimed that insects are the “little creatures who run the world” ([ 1 ][1]), he was simply reaffirming the long-recognized dominance of the largest class of animals on our planet. Insects constitute approximately 53% of all living species, with one group alone (the ants),

Burkholderia cenocepacia is an opportunistic pathogen of humans that encodes two genes that resemble the acylhomoserine lactone synthase gene luxI of Vibrio fischeri and three genes that resemble the acylhomoserine lactone receptor gene luxR. Of these, CepI synthesizes octanoylhomoserine lactone (OHL), while CepR is an OHL-dependent transcription f...

The three-dimensional Poisson's equation is solved by iterative methods and the resulting electric field is used in Newton's equation to simulate electron transfer in a charge-coupled device (CCD). The time dependence of charge transfer is studied through a random walk simulation of Newton's equation. Potential obstacles of the order of 0.03 V are...

We have simulated the dynamical failure of three-dimensional notched solids under tension using molecular dynamics and up to 100 million atoms. We discovered a dynamical brittle-to-ductile transition in the rapid cleavage of rare-gas solids when the crack velocity approaches one-third of the Rayleigh sound speed. At this transition, the crack tip h...

Methods of statistical geometry are introduced which allow one to estimate, on the basis of computable criteria, the conditions under which maximally informative data may be collected. We note the important role of constraints which introduce curvature into parameter space and discuss the appropriate mathematical tools for treating curvature effect...

Non-coding RNAs (ncRNAs) are important components of many regulatory pathways and have key roles in regulating diverse functions. In the Pseudomonads, the two-component system, GacA/S, directly regulates at least two well-characterized ncRNAs, RsmZ and RsmY, which act by sequestration of translation repressor proteins to control expression of vario...

Molecular factors enabling microbial pathogens to cause plant diseases have been sought with increasing efficacy over three research eras that successively introduced the tools of disease physiology, single-gene molecular genetics, and genomics. From this work emerged a unified model of the interactions of biotrophic and hemibiotrophic pathogens, w...

The growth of a model plant pathogen, Pseudomonas syringae pv. tomato DC3000, was investigated using a chemostat culture system to examine environmentally regulated responses. Using minimal medium with iron as the limiting nutrient, four different types of responses were obtained in a customized continuous culture system: (1) stable steady state, (...

Erwinia amylovora causes the economically important disease fire blight that affects rosaceous plants, especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation...

To fully understand how bacteria respond to their environment, it is essential to assess genome-wide transcriptional activity. New high-throughput sequencing technologies make it possible to query the transcriptome of an organism in an efficient unbiased manner. We applied a strand-specific method to sequence bacterial transcripts using Illumina's...

Virtually all crop plants are attacked by pathogenic microbes, including bacteria, fungi, oomycetes, and nematodes. In many cases, bacterial diseases are still poorly controlled with century-old agents like copper, and cause serious losses, as seen with the recent citrus canker outbreak in Florida (Schubert et al., 2001). Pathogenicity has evolved...

In this paper, we describe the context sensitivity problem encountered in partitioning a heterogeneous biological sequence into statistically homogeneous segments. After showing signatures of the problem in the bacterial genomes of Escherichia coli K-12 MG1655 and Pseudomonas syringae DC3000, when these are segmented using two entropic segmentation...

In this paper, we extend a previously developed recursive entropic segmentation scheme for applications to biological sequences. Instead of Bernoulli chains, we model the statistically stationary segments in a biological sequence as Markov chains, and define a generalized Jensen-Shannon divergence for distinguishing between two Markov chains. We th...

The gamma-proteobacterial plant pathogen Pseudomonas syringae pv. tomato DC3000 uses the type III secretion system to inject ca. 28 Avr/Hop effector proteins into plants, which enables the bacterium to grow from low inoculum levels to produce bacterial speck symptoms in tomato, Arabidopsis thaliana, and (when lacking hopQ1-1) Nicotiana benthamiana....

Growth of the ΔhopQ1-1ΔavrPtoΔavrPtoB mutant in N. benthamiana leaves is partially restored by complementation with avrPtoB. N. benthamiana leaves were infiltrated with the indicated strains at 3×104 CFU/ml (2.5 log CFU/cm2 leaf tissue) with a blunt syringe. The avrPtoB gene was expressed from PavrPto in pBBR derivative pCPP5372. Bacterial populati...

A CUCPB5500 derivative grows on minimal media and translocates AvrPto-Cya as well as wild type DC3000. (A) DC3000 and CUCPB5506 (a CUCPB5500 derivative with the phytotoxin coronatine biosynthesis cfa cluster deleted) were simultaneously streaked on mannitol glutamate (MG) and Hrp minimal medium (HMM) and then photographed 4 days later to reveal any...

Structural alignment of selected HopR1 homologs. The alignment was generated using the MUSCLE algorithm and is displayed in strict CLUSTAL W format. (0.06 MB TXT)

In this paper, the multiclass supervised training problem is considered when a discrete set of classes is assumed. Upon generating affine models for finite data sets, we have observed the invariance of certain measures of performance after a trained classifier has been presented with test data of unknown classification. Specifically, after construc...

Pseudomonas syringae pv tomato DC3000 (DC3000) is a Gram-negative model plant pathogen that is found in a wide variety of environments. To survive in these diverse conditions it must sense and respond to various environmental cues. One micronutrient required for most forms of life is iron. Bioavailable iron has been shown to be an important global...

Although chemically defined media have been developed and widely used to study the expression of virulence factors in the model plant pathogen Pseudomonas syringae, it has been difficult to link specific medium components to the induction response. Using a chemostat system, we found that iron is the limiting nutrient for growth in the standard hrp-...

Diverse gene products including phytotoxins, pathogen-associated molecular patterns, and type III secreted effectors influence interactions between Pseudomonas syringae strains and plants, with additional yet uncharacterized factors likely contributing as well. Of particular interest are those interactions governing pathogen-host specificity. Compa...

p-0.01_average_uncentered_clustering.cdt. This CDT file can be used also with the accompanying GTR file to display the gene clustering of differentially regulated genes at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.

Logos of RpoD and Fur motifs. This png file contains the sequence logos used to scan the DC3000 genome for putative gene targets of these regulators.

Tables of differentially regulated genes. This Excel file contains tables of all differentially regulated genes identified with different p value cut-offs. Excel table of genes in the correct order from the pair-wise average linkage with un-centered correlation distance (Figure 5A) and the pair-wise average linkage with absolute un-centered correla...

p-0.01_average_absolute_uncentered_clustering.cdt. This CDT file can be used also with the accompanying GTR file to display the gene clustering of differentially regulated genes (without considering the direction of change) at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.

p-0.01_average_uncentered_clustering.gtr. This GTR file can be used also with the accompanying CDT file to display the gene clustering of differentially regulated genes at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.

p-0.01_average_absolute_uncentered_clustering.gtr. This GTR file can be used also with the accompanying CDT file to display the gene clustering of differentially regulated genes (without considering the direction of change) at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.

Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3,000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacter...