Transcriptomic Analysis of the CAM Species Under Low- and High-Temperature Regimes.

Temperature stress is one of the major limiting environmental factors that negatively impact global crop yields. is an obligate crassulacean acid metabolism (CAM) plant species, exhibiting much higher water-use efficiency and tolerance to drought and heat stresses than C or C plant species. Previous studies on gene expression responses to low- or high-temperature stress have been focused on C and C plants.

Function and Evolution of the Plant MES Family of Methylesterases.

Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years.

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in leaves.

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ().

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization.

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance.

AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis.

In plants, pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance.

Diversification and conservation of DNA binding specificities of SPL family of transcription factors.

SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors in , providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins.

Biotechnology and Genomic Approaches to Mitigating Disease Impacts on Forest Health.

Outbreaks of insects and diseases are part of the natural disturbance regime of all forests. However, introduced pathogens have had outsized impacts on many dominant forest tree species over the past century. Mitigating these impacts and restoring these species are dilemmas of the modern era.

Aggregation-Induced Electrochemiluminescence of Ir(ppy)-Functionalized ZIF-8 for Microcystin-LR Detection via the -Cleavage Activity of CRISPR-Cas12a.

An efficient electrochemiluminescence (ECL) emitter, Ir(ppy)-based molecules has recently been reported to exhibit aggregation-induced electrochemiluminescence (AIECL) phenomenon. However, it remains a significant challenge to control the aggregation states of these molecules and achieve uniform aggregates with intense ECL emission. In this work, a biosensor was developed to detect microcystin-LR (MC-LR) based on Ir(ppy)-functionalized zeolitic imidazolate framework-8 (Ir-ZIF-8) as the ECL emitter and the -cleavage activity of CRISPR-Cas12a as the methodological strategy.

Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus.

Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study.

A novel split PEC sensor based on magneto-optic nanostructure and photocurrent polarity switching strategy.

Background: Photoelectrochemical (PEC) sensors have attracted much attention due to their low cost, simple instrumentation and high sensitivity. However, conventional PEC sensors require layer-by-layer modification of the photoelectrode surface, which has the disadvantages of being time-consuming and unstable. In addition, complex interfering substances in real samples may lead to false-positive or false-negative detection results.

Sulfur defect-engineered BiS/InS mediated signal enhancement of photoelectrochemical sensor for lead ions detection.

Lead ions (Pb) are heavy metal ions that are harmful to living organisms and ecosystems. It is important to realize sensitive detection of Pb in the environment. In this study, a signal enhancement photoelectrochemical (PEC) sensor with high sensitivity was constructed for the detection of Pb.

Oxygen vacancies-driven signal enhanced photoelectrochemical sensor for mercury ions detection.

Mercury ion (Hg) poses a serious threat to human health due to its high toxicity. In this study, a smartphone-based photoelectrochemical sensor based on oxygen vacancies (OVs) driven signal enhancement for mercury ion detection was designed. BiVO/BiS/AuNPs were combined with T-Hg-T recognition mode to construct a multi-sandwich photoelectrochemical sensor.

GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa.

Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants; however, the performance of these methods depends on the accuracy and scale of phenotyping.

Functional analysis of genes support roles for and as master regulators of sex determination.

The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate in tissue culture, previous studies investigating the mechanisms regulating sex in the genus have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow .

Photoelectrochemical Sensor with a Z-Scheme FeO/CdS Heterostructure for Sensitive Detection of Mercury Ions.

Mercury (Hg) is a highly toxic element and can seriously affect human health. This work proposed a photoelectrochemical (PEC) sensor with a Z-scheme FeO/CdS heterostructure and two thymine-rich DNA strands (DNA-1 and Au@DNA-2) for sensitive detection of Hg. The light excitation of the FeO/CdS composite accelerated the electron transfer among FeO, CdS, and the electrode to produce a stable photocurrent response.

Validation of a metabolite-GWAS network for family 1 UDP-glycosyltransferases.

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as , a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships.

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom.

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated.

Competitive photoelectrochemical aptamer sensor based on a Z-scheme FeO/g-CN heterojunction for sensitive detection of lead ions.

Lead ion (Pb) is one of the heavy metal contaminants within the environment, which can seriously affect biological health. Thus, it is very important to detect lead ions, especially exceeding the standard concentration (100 ng/mL). In this work, we have developed a photoelectrochemical (PEC) aptamer sensor with Z-scheme FeO/g-CN heterojunction as a substrate material for sensitive detection of Pb.

Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus.

Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans-eQTL were genes involved in plant hormone responses and root development.

Plant myo-inositol transport influences bacterial colonization phenotypes.

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites are consistently identified as important mediators of microbial interactions. We combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in seedlings of the model plant Arabidopsis thaliana to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions.

Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus.

Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy.