Engineering topics

Liu, Lifeng

Publications and source records attributed to Liu, Lifeng.

8 records

DOE OSTI2024

Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression

Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.

Coomey, Joshua↗

DOE OSTI2023

The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum

Abstract Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

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

Abstract 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. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Exceptionally Fast Ion Diffusion in Block Copolymer-Based Porous Carbon Fibers

Confined ionic liquids in hydrophilic porous media have disrupted lattices and can be divided into two layers: An immobile ion layer adheres to the pore surfaces, and an inner layer exhibits faster mobility than the bulk. In this work, we report the first study of ionic liquids confined in block copolymer-based porous carbon fibers (PCFs) synthesized from polyacrylonitrile-block-polymethyl methacrylate (PAN-b-PMMA). The PCFs contain a network of unimodal mesopores of 13.6 nm in diameter and contain more hydrophilic surface functional groups than previously studied porous carbon. Elastic neutron scattering shows no freezing point for 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF 4 ) confined in PCFs down to 20 K. Quasi-elastic neutron scattering (QENS) is used to measure the diffusion of [BMIM]BF 4 confined in PCFs, which, surprisingly, is 7-fold faster than in the bulk. The unprecedentedly high ion diffusion remarks that PCFs hold exceptional potential for use in electrochemical catalysis, energy conversion, and storage.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Atomically Dispersed Pentacoordinated‐Zirconium Catalyst with Axial Oxygen Ligand for Oxygen Reduction Reaction

Single-atom catalysts (SACs), as promising alternatives to Pt-based catalysts, suffer from the limited choice of center metals and low single-atom loading. Here, we report a pentacoordinated Zr-based SAC with nontrivial axial O ligands (denoted O-Zr-N-C) for oxygen reduction reaction (ORR). The O ligand downshifts the d-band center of Zr and confers Zr sites with stable local structure and proper adsorption capability for intermediates. Consequently, the ORR performance of O-Zr-N-C prominently surpasses that of commercial Pt/C, achieving a half-wave potential of 0.91 V vs. reversible hydrogen electrode and outstanding durability (92% current retention after 130-hour operation). Moreover, the Zr site shows good resistance towards aggregation, enabling the synthesis of Zr-based SAC with high loading (9.1 wt%). With the high-loading catalyst, the zinc-air battery (ZAB) delivers a record-high power density of 324 mW cm -2 among those of SAC-based ZABs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance

Perennial grasses will account for approximately 16 billion gallons of renewable fuels by the year 2022, contributing significantly to carbon and nitrogen sequestration. However, perennial grasses productivity can be limited by severe freezing conditions in some geographical areas, although these risks could decrease with the advance of climate warming, the possibility of unpredictable early cold events cannot be discarded. We conducted a study on the model perennial grass Brachypodium sylvaticum to investigate the molecular mechanisms that contribute to cold and freezing adaption. The study was performed on two different B. sylvaticum accessions, Ain1 and Osl1, typical to warm and cold climates, respectively. Both accessions were grown under controlled conditions with subsequent cold acclimation followed by freezing stress. For each treatment a set of morphological parameters, transcription, metabolite, and lipid profiles were measured. State-of-the-art algorithms were employed to analyze cross-component relationships. Phenotypic analysis revealed higher adaption of Osl1 to freezing stress. Our analysis highlighted the differential regulation of the TCA cycle and the GABA shunt between Ain1 and Osl1. Osl1 adapted to freezing stress by repressing the GABA shunt activity, avoiding the detrimental reduction in fatty acid biosynthesis and the concomitant detrimental effects on membrane integrity.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Strategies for Semiconductor/Electrocatalyst Coupling toward Solar‐Driven Water Splitting

Abstract Hydrogen (H 2 ) has a significant potential to enable the global energy transition from the current fossil‐dominant system to a clean, sustainable, and low‐carbon energy system. While presently global H 2 production is predominated by fossil‐fuel feedstocks, for future widespread utilization it is of paramount importance to produce H 2 in a decarbonized manner. To this end, photoelectrochemical (PEC) water splitting has been proposed to be a highly desirable approach with minimal negative impact on the environment. Both semiconductor light‐absorbers and hydrogen/oxygen evolution reaction (HER/OER) catalysts are essential components of an efficient PEC cell. It is well documented that loading electrocatalysts on semiconductor photoelectrodes plays significant roles in accelerating the HER/OER kinetics, suppressing surface recombination, reducing overpotentials needed to accomplish HER/OER, and extending the operational lifetime of semiconductors. Herein, how electrocatalyst coupling influences the PEC performance of semiconductor photoelectrodes is outlined. The focus is then placed on the major strategies developed so far for semiconductor/electrocatalyst coupling, including a variety of dry processes and wet chemical approaches. This Review provides a comprehensive account of advanced methodologies adopted for semiconductor/electrocatalyst coupling and can serve as a guideline for the design of efficient and stable semiconductor photoelectrodes for use in water splitting.

Thalluri, Sitaramanjaneya Mouli↗