Browsing by Author "Zhou, Peng"

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    Data for: Meta gene regulatory networks in maize highlight functionally relevant regulatory interactions
    (2020-03-12) Zhou, Peng; Springer, Nathan M.; zhoux379@umn.edu; Zhou, Peng; University of Minnesota Springer Lab
    Regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent a map of potential transcriptional regulation. A consistent analysis of a large number of public maize transcriptome datasets including >6000 RNA-Seq samples was used to generate 45 co- expression based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, tissue-and-genotype, etc). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes.
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    Defense-related gene families in the model legume, Medicago truncatula: computational analysis, pan-genome characterization, and structural variation
    (2015-06) Zhou, Peng
    Medicago truncatula is a model for investigating legume genetics and the evolution of legume-rhizobia symbiosis. Over the past two decades, two large gene families in M. truncatula, the nucleotide-binding site leucine-rich repeat (NBS-LRR) family and the nodule-specific, cysteine-rich (NCR) gene family, have received considerable attention due to their involvement in disease resistance and nodulation, large family size, and high nucleotide and copy number diversity. While NBS-LRRs have been found in all plant species and therefore relatively well characterized at the sequence level, members of the cysteine-rich protein (CRP) families, including NCRs, have generally been overlooked by popular similarity search tools and gene prediction techniques due to their (a) small size, (b) high sequence divergence among family members and (c) limited availability of expression evidence. In this thesis, I first developed a homology-based gene prediction program (Small Peptide Alignment Detection Algorithm, i.e., SPADA) to accurately predict small peptides including CRPs at the genome level. Given a high-quality profile alignment, SPADA identifies and annotates nearly all family members in tested genomes with better performance than all general-purpose gene prediction programs surveyed. Numerous mis-annotations in the current Arabidopsis and Medicago genome databases were found by SPADA, most supported by RNA-Seq data. As a homology-based gene prediction tool, SPADA works well on other classes of small secreted peptides in plants (e.g., self-incompatibility protein homologues) as well as non-secreted peptides outside the plant kingdom. I then comprehensively annotated the NBS-LRR and NCR gene families in the Medicago reference genome (version 4.0), and set out to characterize natural variation of these genes in diverse M. truncatula accessions. Previous studies using whole-genome sequence data to identify sequence polymorphisms (SNPs and short Insertion / Deletions) relied on mapping short reads to a single reference genome. However, limitations of read-mapping approaches have hindered variant detection, especially characterization of repeat-rich and highly divergent regions. As a result, studies of these large gene families are also hindered due to high sequence similarity among family members along with high divergence among accessions. In this work I constructed high-quality de novo assemblies for 15 M. truncatula accessions. This allowed me to detect novel genetic variation that would not have been found by mapping reads to a single reference. This analysis led to a within-species diversity estimate 70% higher than previous mapping-based resequencing efforts, even using a smaller sample size. These results clearly demonstrate that de novo assembly-based comparison is both more accurate and precise than mapping-based variant calling in exploring variation in repetitive and highly divergent regions. For the first time in plants, my results enable systematically identification and characterization of different types of structural variants (SVs) using a synteny-based approach. This analysis suggests that, depending on the divergence from the reference accession, 7% to 21% of the entire genome is involved in large structural changes, affecting 10% to 28% of all gene models. The results identify 64 Mbp of unique sequence segments absent in the reference, including 30 Mbp shared by at least 2 accessions and 34 Mbp of accessions-specific sequences, thus expanding the Medicago reference space (389-Mbp) by 16%. Evidence-based annotation of the 15 de novo assemblies revealed that more than half of reference gene models were structurally diverse (lower than 60% sequence similarity) in at least one other accession. Not surprisingly, the NBS-LRR gene family harbors by far the highest level of nucleotide diversity, large effect single nucleotide changes, mean pairwise protein distance and copy number variation (levels comparable with transposable elements), consistent with the rapidly-evolving dynamics of disease resistance phenotypes. Characterization of deletion and tandem duplication events in the NBS-LRR and NCR gene families suggests accession-specific subfamily expansion / contraction patterns. This work illustrates the value of multiple de novo assemblies and the strength of comparative genomics in exploring and characterizing novel genetic variation within a population, and provides insights in understanding the impact of SVs on genome architecture and large gene families underlying important traits.
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    Maize 509 line TE PAV calls
    (2020-10-28) Springer, Nathan M; Noshay, Jaclyn M; Hirsch, Candice N; Marand, Alexandre P; Anderson, Sarah N; Zhou, Peng; O'Connor, Christine; Crisp, Peter A; Schmitz, Robert J; Lu, Zefu; nosha003@umn.edu; Noshay, Jaclyn; University of Minnesota Springer Research Lab
    Transposable elements (TEs) have the potential to create regulatory variation both through disruption of existing DNA regulatory elements and through creation of novel DNA regulatory elements. In a species with a large genome, such as maize, the many TEs interspersed with genes creates opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22 or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes the TEs that carry ACRs exhibit an enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.
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    Maize Mo17 SNPs
    (2018-07-11) Zhou, Peng; zhoux379@umn.edu; Zhou, Peng; University of Minnesota Springer Lab
    Genome resequencing of Mo17 was done as part of the bioMAP project (REF). 477 million 100bp paired-end reads were generated for Mo17 giving an average of 95x coverage. Reads were first trimmed by Trimmomatic (Bolger et al. 2014) and mapped to the maize B73 genome AGPv4 (Jiao et al. 2017) using BWA-MEM (Li and Durbin 2010). PCR duplicates were marked and removed using GATK (McKenna et al. 2010). Variants were called by GATK haplotypecaller and filtered using different filters for SNPs: (QD > 2, FS < 60, MQ > 40, MQRankSum > -12.5, ReadPosRankSum > -8, SOR < 4) and for InDels: (QD > 2, FS < 200, ReadPosRankSum > -20, SOR < 10). Moreover, variants located in regions with unusually high coverage (DP > Mean + 2*SD) and heterozygous calls (GT == '0/1') were also removed. The final variant file containing 8.04 million variants with 164 thousand CDS variants was deposited in DRUM.
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    MEMS-Based Purification and Sensing Technologies for Sustainable Water Management
    (2023-06) Zhou, Peng
    The management of water resources is a pressing global challenge. This research aims to address the issues of water pollution and scarcity by proposing micro-electromechanical systems (MEMS) based solutions for water purification and sensing. In particular, this research presents a new photoelectrocatalytic water purification system, an efficient valveless micropump, and a sensitive heavy metal ion sensor based on MEMS technologies, envisioning for a sensor-based closed-loop control water treatment platform.The photocatalytic degradation of organic matter by titanium dioxide was initially used to remove pollutants from water. A uniform and durable coating of titanium dioxide was successfully applied to various surfaces. These coated surfaces demonstrated high degradation efficiency and long-term stability in degrading organic matter in water. To further improve the photocatalytic degradation efficiency of titanium dioxide, graphene was introduced to form titanium dioxide/graphene nanocomposites. A new photoelectrocatalytic water purification system was developed by combining photocatalysis and electrochemistry. This scheme can be used to simultaneously remove both organic compounds and inorganic heavy metal ions from water. In this system, the working and counter electrodes are switched compared to traditional photoelectrocatalysis systems, with the metal or carbon electrode as the working electrode and the microchannels with photocatalyst serving as the counter electrode. A negative bias potential is applied to the working electrode to reduce the heavy metal ions, and the current flow through the circuit helps transfer the photo-excited electrons from the counter electrode (photocatalyst) to the working electrode. The inorganic heavy metal ions are thus reduced on the working electrodes while the photocatalytic degradation of organic pollutants on the counter electrode is enhanced. Next, a micropump suitable for the water treatment and detection platforms was researched and developed. Valveless fluidic diode micropumps without moving parts are considered suitable for water sensor systems due to their simple structure and rapid mixing. In the design, topology optimization is used to design two-dimensional, fixed-geometry, fluidic diodes of high diodicity, which is the ratio of pressure drops of forward to reverse flows. One of the fluidic diodes, of the Tesla type, shows a diodicity of over five. The numerical simulation was applied to simplify the structures, and the two-dimensional geometry was converted into three-dimensional model for micropumps. Three-dimensional and unsteady numerical analyses of micropump were conducted for pumps with the two diode designs. The experiments conducted with designed diodes showed reliable repeatability and precise control of flow, indicating positive prospects for potential applications. To achieve the envisioned closed-loop control water treatment platform, a highly sensitive low-cost sensor is essential. An electrochemical microfluidic sensor was developed for the high-sensitivity and low-cost detection of heavy metal ions in water. This sensor utilizes a glass carbon/graphene electrode synthesized through layer-by-layer self-assembly and subsequent pyrolysis. The electrode exhibited low overpotential, enabling detection of almost any heavy metal ions in aqueous solutions, and the incorporation of graphene resulted in a high sensitivity. To enhance mass transfer and sensitivity, a valveless micropump was integrated with the electrode, achieving two orders of higher sensitivity than those of measurements with a stationary solution and a detection limit as low as 20 ppt for lead and 100 ppt for cadmium. The developed sensor was employed to simultaneously detect lead and cadmium in water, investigating the mutual influence of heavy metal ions in electrochemistry. A neuron network model was adopted for data analysis. In summary, this study presents a comprehensive approach to addressing the worldwide challenge of sustainable water resource management through the removal of pollutants and the detection of water pollutants. The closed-looped control water treatment platform, based on high-performance sensors, micropumps, and advanced photoelectrocatalysis technologies, provides an efficient and cost-effective solution to water scarcity and pollution. This platform offers promising prospects for the development of effective water management systems, which can contribute to the improvement of global water resources management and enhance the quality of life for people around the world.