Dave Schneider

Dave Schneider
University of Saskatchewan | U of S · School of Environment and Sustainability

MS

About

140
Publications
18,670
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7,416
Citations
Citations since 2016
24 Research Items
2039 Citations
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300
2016201720182019202020212022050100150200250300

Publications

Publications (140)
Article
Full-text available
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...
Article
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 (...
Article
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...
Article
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Presentation
Full-text available
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...
Article
Full-text available
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...
Data
The 137 regions of enrichment identified by CSDeconv in GFF format (https://www.sanger.ac.uk/resources/software/gff/spec.html). (GFF)
Data
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...
Data
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)
Data
Assays to measure the effect of 1O2 and tBOOH on wildtype and ΔPSPTO_1043/1042 Pseudomonas syringae pv tomato DC3000. (DOCX)
Data
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)
Data
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)
Data
Strains, plasmids, and primers used in this study. (DOCX)
Data
Assays to measure growth of wildtype and ΔPSPTO_1043/1042 Pseudomonas syringae pv tomato DC3000 in Arabidopsis seedlings. (PDF)
Data
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)
Data
A description of the method used to compute S2 Table. (DOCX)
Presentation
Full-text available
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...
Article
Full-text available
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...
Poster
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Data
TEREE algorithm scores for annotated coding regions in P. s. phaseolicola 1448a. (XLSX)
Data
TEREE algorithm scores for annotated coding regions in R. solanacearum GMI1000. (XLSX)
Data
TEREE algorithm scores for annotated coding regions in P. s. tomato DC3000. (XLSX)
Data
TEREE algorithm scores for proteins in T3SS substrate and negative training sets. (XLSX)
Data
TEREE algorithm scores for annotated coding regions in S. e. Typhimurium LT2. (XLSX)
Data
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...
Data
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)
Data
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)
Data
A profile for the DC3000 chromosome containing the classification of each genomic location. (RAR)
Data
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_...
Data
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)
Data
Summary of 5′-end RNA-Seq data for P. syringae DC3000. (XLSX)
Data
gff file containing the resulting ranges for 40 bps upstream of E12+Top peaks. (RAR)
Data
Transcriptional start sites confirmed by 5′RACE. (XLS)
Data
Transcriptional start sites for putative RpoF regulated genes. (XLSX)
Data
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)
Data
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)
Data
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)
Data
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)
Data
Python script, make-class-scatter.py, for the three-way classification of 5′-ends. (RAR)
Data
Data file containing the FASTA file of 40 bps upstream of E12+Top peaks. (RAR)
Article
Full-text available
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...
Article
Full-text available
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...
Data
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)
Data
SNPs identified between Max4, LNPV 17.41, T1, K40, and NCPPB1108 by aligning Illumina reads against the genome of Pto strain DC3000. (XLS)
Data
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)
Data
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)
Data
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)
Data
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)
Article
Full-text available
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...
Article
Full-text available
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...