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At least 163 records · Page 9

Transformative Impacts of Laser-Induced Breakdown Spectroscopy on Environmental and Biological Research at Oak Ridge National Laboratory

This manuscript will present an advancement of transformative research that has been conducted at Oak Ridge National Laboratory (ORNL) over a 25-year period (2000–2025) on a variety of environmental and biological matrices. These investigations derived a fundamental understanding of how elemental detection and analysis of these matrices led to the knowledge and discovery of natural processes in plants and the environment. Each project led to the initiation of a new research area which unearthed awesome and novel breakthroughs. Highlights are listed below: 1. The preliminary research at ORNL centered on the detection of aerosols utilizing Laser-induced Breakdown Spectroscopy (LIBS) technology. The Clean Air Act Amendment (CAAA) of 1990 highlighted the importance of identifying hazardous air pollutants (HAPs) due to their impact on environmental and human health, thereby underscoring the need to detect various toxic elements. Research in aerosol chemistry aimed to identify these harmful elements released by factories during periods of increased emissions in their manufacturing processes. LIBS emerged as the most effective method for real-time, in situ measurements of metal species in both gaseous and aerosol phases. 2. An understanding of the presence of total carbon in soils gives perspective on how to develop carbon sequestration strategies. The recognition that carbon sinks can evolve back to carbon sources to emit back to the atmosphere was an important consideration. Also, the concentration of carbon in soil indicates the health of land areas for growing crops successfully. 3. The direct detection of most of the elements in a wood sample in a single emission spectrum, without sample preparation, encouraged the research to use the LIBS technique for preservative treated wood coupled with use of multivariate statistical methodology. Additionally, it encouraged the researchers to try to differentiate natural woods from different parts of the country, and it was successfully demonstrated that LIBS coupled with MVA analysis could differentiate wood of different species from each other and of similar species grown in different environments based on their elemental spectra. This was a breakthrough since it revealed a systematic approach to connect elemental scarcity and abundance to either drought or typical rainfall conditions for the hardwood trees grown in specific areas. 4. Furthermore, the research progressed to reveal physiological and developmental processes contributing to biomass production such that the variation in leaf elemental composition increases our understanding of terrestrial nutrient cycles, as well as tracking the transfer of toxic elements from soils to living organisms. 5. Recently another breakthrough viz., ionomics initiated the correlation of elements to specific genes, uncovering the function that the element performed in the plant. More recently, this has been extended from plants to fungi as well as fungi growing in symbiotic relations with plants.

09 BIOMASS FUELS↗

Attaining the promise of plant gene editing at scale

Crop improvement relies heavily on genetic variation that arises spontaneously through mutation. Modern breeding methods are very adept at combining this genetic variation in ways that achieve remarkable improvements in plant performance. Novel traits have also been created through mutation breeding and transgenesis. The advent of gene editing, however, marks a turning point: With gene editing, synthetic variation will increasingly supplement and, in some cases, supplant the genetic variation that occurs naturally. We are still in the very early stages of realizing the opportunity provided by plant gene editing. At present, typically only one or a few genes are targeted for mutation at a time, and most mutations result in loss of gene function. New technological developments, however, promise to make it possible to perform gene editing at scale. RNA virus vectors, for example, can deliver gene-editing reagents to the germ line through infection and create hundreds to thousands of diverse mutations in the progeny of infected plants. With developmental regulators, edited somatic cells can be induced to form meristems that yield seed-producing shoots, thereby increasing throughput and shrinking timescales for creating edited plants. As these approaches are refined and others developed, they will allow for accelerated breeding, the domestication of orphan crops and the reengineering of metabolism in a more directed manner than has ever previously been possible.

59 BASIC BIOLOGICAL SCIENCES↗

Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP

Streptomyces are our principal source of antibiotics, which they generate concomitant with a complex developmental transition from vegetative hyphae to spores. c-di-GMP acts as a linchpin in this transition by binding and regulating the key developmental regulators, BldD and WhiG. Here we show that c-di-GMP also binds the glycogen-debranching-enzyme, GlgX, uncovering a direct link between c-di-GMP and glycogen metabolism in bacteria. Further, we show c-di-GMP binding is required for GlgX activity. We describe structures of apo and c-di-GMP-bound GlgX and, strikingly, their comparison shows c-di-GMP induces long-range conformational changes, reorganizing the catalytic pocket to an active state. Glycogen is an important glucose storage compound that enables animals to cope with starvation and stress. Our in vivo studies reveal the important biological role of GlgX in Streptomyces glucose availability control. Overall, we identify a function of c-di-GMP in controlling energy storage metabolism in bacteria, which is widespread in Actinobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Packaging “vegetable oils”: Insights into plant lipid droplet proteins

Abstract Plant neutral lipids, also known as “vegetable oils”, are synthesized within the endoplasmic reticulum (ER) membrane and packaged into subcellular compartments called lipid droplets (LDs) for stable storage in the cytoplasm. The biogenesis, modulation, and degradation of cytoplasmic LDs in plant cells are orchestrated by a variety of proteins localized to the ER, LDs, and peroxisomes. Recent studies of these LD-related proteins have greatly advanced our understanding of LDs not only as steady oil depots in seeds but also as dynamic cell organelles involved in numerous physiological processes in different tissues and developmental stages of plants. In the past 2 decades, technology advances in proteomics, transcriptomics, genome sequencing, cellular imaging and protein structural modeling have markedly expanded the inventory of LD-related proteins, provided unprecedented structural and functional insights into the protein machinery modulating LDs in plant cells, and shed new light on the functions of LDs in nonseed plant tissues as well as in unicellular algae. Here, we review critical advances in revealing new LD proteins in various plant tissues, point out structural and mechanistic insights into key proteins in LD biogenesis and dynamic modulation, and discuss future perspectives on bridging our knowledge gaps in plant LD biology.

Cai, Yingqi (ORCID:0000000203575809)↗

Foxtail mosaic virus-induced gene silencing (VIGS) in switchgrass (Panicum virgatum L.)

Abstract Background Although the genome for the allotetraploid bioenergy crop switchgrass ( Panicum virgatum ) has been established, limitations in mutant resources have hampered in planta gene function studies toward crop optimization. Virus-induced gene silencing (VIGS) is a versatile technique for transient genetic studies. Here we report the implementation of foxtail mosaic virus (FoMV)-mediated gene silencing in switchgrass in above- and below-ground tissues and at different developmental stages. Results The study demonstrated that leaf rub-inoculation is a suitable method for systemic gene silencing in switchgrass. For all three visual marker genes, Magnesium chelatase subunit D ( ChlD ) and I ( ChlI ) as well as phytoene desaturase ( PDS ), phenotypic changes were observed in leaves, albeit at different intensities. Gene silencing efficiency was verified by RT-PCR for all tested genes. Notably, systemic gene silencing was also observed in roots, although silencing efficiency was stronger in leaves (~ 63–94%) as compared to roots (~ 48–78%). Plants at a later developmental stage were moderately less amenable to VIGS than younger plants, but also less perturbed by the viral infection. Conclusions Using FoMV-mediated VIGS could be achieved in switchgrass leaves and roots, providing an alternative approach for studying gene functions and physiological traits in this important bioenergy crop.

59 BASIC BIOLOGICAL SCIENCES↗

Mycorrhiza‐induced mycocypins of Laccaria bicolor are potent protease inhibitors with nematotoxic and collembola antifeedant activity

Fungivory of mycorrhizal hyphae has a significant impact on fungal fitness and, by extension, on nutrient transfer between fungi and host plants in natural ecosystems. Mycorrhizal fungi have therefore evolved an arsenal of chemical compounds that are hypothesized to protect the hyphal tissues from being eaten, such as the protease inhibitors mycocypins. The genome of the ectomycorrhizal fungus Laccaria bicolor has an unusually high number of mycocypin-encoding genes. We have characterized the evolution of this class of proteins, identified those induced by symbiosis with a host plant and characterized the biochemical properties of two upregulated L. bicolor mycocypins. More than half of L. bicolor mycocypin-encoding genes are differentially expressed during symbiosis or fruiting body formation. We show that two L. bicolor mycocypins that are strongly induced during symbiosis are cysteine protease inhibitors and exhibit similar but distinct localization in fungal tissues at different developmental stages and during interaction with a host plant. Moreover, we show that these L. bicolor mycocypins have toxic and feeding deterrent effect on nematodes and collembolans, respectively. Therefore, L. bicolor mycocypins may be part of a mechanism by which this species deters grazing by different members of the soil food web.

59 BASIC BIOLOGICAL SCIENCES↗

β-Barrel proteins tether the outer membrane in many Gram-negative bacteria

Gram-negative bacteria have a cell envelope that comprises an outer membrane (OM), a peptidoglycan (PG) layer and an inner membrane (IM). The OM and PG are load-bearing, selectively permeable structures that are stabilized by cooperative interactions between IM and OM proteins. In Escherichia coli , Braun’s lipoprotein (Lpp) forms the only covalent tether between the OM and PG and is crucial for cell envelope stability; however, most other Gram-negative bacteria lack Lpp so it has been assumed that alternative mechanisms of OM stabilization are present. In this work we used a glycoproteomic analysis of PG to show that β-barrel OM proteins are covalently attached to PG in several Gram-negative species, including Coxiella burnetii, Agrobacterium tumefaciens and Legionella pneumophila . In C. burnetii , we found that four different types of covalent attachments occur between OM proteins and PG, with tethering of the β-barrel OM protein BbpA becoming most abundant in the stationary phase and tethering of the lipoprotein LimB similar throughout the cell cycle. Using a genetic approach, we demonstrate that the cell cycle-dependent tethering of BbpA is partly dependent on a developmentally regulated L,D-transpeptidase (Ldt). We use our findings to propose a model of Gram-negative cell envelope stabilization that includes cell cycle control and an expanded role for Ldts in covalently attaching surface proteins to PG.

59 BASIC BIOLOGICAL SCIENCES↗

Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize

Root anatomical phenotypes present a promising yet underexploited avenue to deliver major improvements in yield and climate resilience of crops by improving water and nutrient uptake. For instance, the formation of root cortical aerenchyma (RCA) significantly increases soil exploration and resource capture by reducing the metabolic costs of root tissue. A key bottleneck in studying such phenotypes has been the lack of robust high-throughput anatomical phenotyping platforms. We exploited a phenotyping approach based on laser ablation tomography, termed Anatomics , to quantify variation in RCA formation of 436 diverse maize lines in the field. Results revealed a significant and heritable variation for RCA formation. Genome-wide association studies identified a single-nucleotide polymorphism mapping to a root cortex-expressed gene-encoding transcription factor bHLH121. Functional studies identified that the bHLH121 Mu transposon mutant line and CRISPR/Cas9 loss-of-function mutant line showed reduced RCA formation, whereas an overexpression line exhibited significantly greater RCA formation when compared to the wild-type line. Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that bHLH121 is required for RCA formation developmentally as well as under studied abiotic stress. Overall functional validation of the bHLH121 gene’s importance in RCA formation provides a functional marker to select varieties with improved soil exploration and thus yield under suboptimal conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system

Understanding the regulatory mechanism by which cardiomyocyte proliferation transitions to endoreplication and cell cycle arrest during the neonatal period is crucial for identifying proproliferative factors and developing regenerative therapies. }We used a transgenic mouse model based on the fluorescent ubiquitination-based cell cycle indicator (FUCCI) system to isolate and characterize cycling cardiomyocytes at different cell cycle stages at a single-cell resolution. Single-cell transcriptome analysis of cycling and noncycling cardiomyocytes was performed at postnatal days 0 (P0) and 7 (P7). }The FUCCI system proved to be efficient for the identification of cycling cardiomyocytes with the highest mitotic activity at birth, followed by a gradual decline in the number of cycling and mitotic cardiomyocytes during the neonatal period. Cardiomyocytes showed premature cell cycle exit at G1/S shortly after birth and delayed G1/S progression during endoreplication at P7. Single-cell RNA-seq confirmed previously described signaling pathways involved in cardiomyocyte proliferation (Erbb2 and Hippo/YAP), and maturation-related transcriptional changes during postnatal development, including the metabolic switch from glycolysis to fatty acid oxidation in cardiomyocytes. Importantly, we generated transcriptional profiles specific to cell division and endoreplication in cardiomyocytes at different developmental stages that may facilitate the identification of genes important for adult cardiomyocyte proliferation and heart regeneration. }In conclusion, the FUCCI mouse provides a valuable system to study cardiomyocyte cell cycle activity at single cell resolution that can help to decipher the switch from cardiomyocyte proliferation to endoreplication, and to revert this process to facilitate endogenous repair.

60 APPLIED LIFE SCIENCES↗

Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics

In plants, as in other species, genotypic variation in combination with environmental variation leads to differences in the biochemical makeup of cells, measurable as molecular phenotypes. These in turn influence physiological and developmental traits such as organ formation and plant growth, and eventually traits relevant in agriculture, such as yield and stress tolerance. Thus, relating genotypes to phenotypes yields fundamental insights into the regulation of important processes in plant development and physiology, but also provides the ability to predict yield and quality traits in specific environments, which is essential in basic plant science and molecular breeding of resilient plants in changing environments.

59 BASIC BIOLOGICAL SCIENCES↗

Reactivation of a developmentally silenced embryonic globin gene

The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) of open, acetylated chromatin and interacts with the α-globin super-enhancer. By contrast, in adult erythroid cells, the ζ-gene is packaged within a small (~10 kb) sub-domain of hypoacetylated, facultative heterochromatin within the acetylated sub-TAD and that it no longer interacts with its enhancers. The ζ-gene can be partially re-activated by acetylation and inhibition of histone de-acetylases. In addition to suggesting therapies for severe α-thalassemia, these findings illustrate the general principles by which reactivation of developmental genes may rescue abnormalities arising from mutations in their adult paralogues.

59 BASIC BIOLOGICAL SCIENCES↗

Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation

Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin ‘egg-box’ structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. Here, these changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

36 MATERIALS SCIENCE↗

RNAi-Mediated Manipulation of Cuticle Coloration Genes in Lygus hesperus Knight (Hemiptera: Miridae)

Cuticle coloration in insects is a consequence of the accumulation of pigments in a species-specific pattern. Numerous genes are involved in regulating the underlying processes of melanization and sclerotization, and their manipulation can be used to create externally visible markers of successful gene editing. To clarify the roles for many of these genes and examine their suitability as phenotypic markers in Lygus hesperus Knight (western tarnished plant bug), transcriptomic data were screened for sequences exhibiting homology with the Drosophila melanogaster proteins. Complete open reading frames encoding putative homologs for six genes (aaNAT, black, ebony, pale, tan, and yellow) were identified, with two variants for black. Sequence and phylogenetic analyses supported preliminary annotations as cuticle pigmentation genes. In accord with observable difference in color patterning, expression varied for each gene by developmental stage, adult age, body part, and sex. Knockdown by injection of dsRNA for each gene produced varied effects in adults, ranging from the non-detectable (black 1, yellow), to moderate decreases (pale, tan) and increases (black 2, ebony) in darkness, to extreme melanization (aaNAT). Based solely on its expression profile and highly visible phenotype, aaNAT appears to be the best marker for tracking transgenic L. hesperus.

59 BASIC BIOLOGICAL SCIENCES↗

Phenylpropanoid Biosynthesis Gene Expression Precedes Lignin Accumulation During Shoot Development in Lowland and Upland Switchgrass Genotypes

Efficient conversion of lignocellulosic biomass into biofuels is influenced by biomass composition and structure. Lignin and other cell wall phenylpropanoids, such as para -coumaric acid ( p CA) and ferulic acid (FA), reduce cell wall sugar accessibility and hamper biochemical fuel production. Toward identifying the timing and key parameters of cell wall recalcitrance across different switchgrass genotypes, this study measured cell wall composition and lignin biosynthesis gene expression in three switchgrass genotypes, A4 and AP13, representing the lowland ecotype, and VS16, representing the upland ecotype, at three developmental stages [Vegetative 3 (V3), Elongation 4 (E4), and Reproductive 3 (R3)] and three segments (S1–S3) of the E4 stage under greenhouse conditions. A decrease in cell wall digestibility and an increase in phenylpropanoids occur across development. Compared with AP13 and A4, VS16 has significantly less lignin and greater cell wall digestibility at the V3 and E4 stages; however, differences among genotypes diminish by the R3 stage. Gini correlation analysis across all genotypes revealed that lignin and p CA, but also pectin monosaccharide components, show the greatest negative correlations with digestibility. Lignin and p CA accumulation is delayed compared with expression of phenylpropanoid biosynthesis genes, while FA accumulation coincides with expression of these genes. The different cell wall component accumulation profiles and gene expression correlations may have implications for system biology approaches to identify additional gene products with cell wall component synthesis and regulation functions.

09 BIOMASS FUELS↗

An extensible vector toolkit and parts library for advanced engineering of plant genomes

Abstract Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T‐DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site‐specific recombinases. Finally, we use a series of dual‐luciferase assays to measure contributions to expression from promoters, terminators, and from cross‐cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.

42 ENGINEERING↗

Transcription Factors Controlling the Rhizobium–Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment

Abstract Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium–legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium–legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium–legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium–legume symbiosis.

Cell Biology↗

40th Eastern Regional Photosynthesis Conference

Photosynthesis has shaped global biochemistry and geochemistry in its production of almost all atmospheric oxygen, and almost every electron that supports the processes of life on Earth was extracted from water by the light-dependent reactions, many of which were then used to fix carbon in the dark reactions. To humans, that fixed carbon is the originator of all fossil fuels and a critical step in conversion of solar photons to human-usable energy. The Eastern Regional Photosynthesis Conference (ERPC) serves as a forum for advancement of science in this field. As a regional-level conference, it specializes in providing developmental opportunities for early-career researchers from undergraduates to pre-tenure professors, as well as broadening the field in terms of participating scholars and research approaches to produce new interdisciplinary collaborations. Funding from the Department of Energy is used to mitigate registration and attendance costs for junior (non-PI) researchers. The ERPC is one of the three regional conferences in the field of photosynthesis research in the United States, alongside the Western Photosynthesis Conference (currently in California) and the Midwestern Photosynthesis Conference (Turkey Run, Indiana). A longstanding incubator for scientific discourse, discovery, and collaborations, this conference has spawned many collaborations which led to Department of Energy-funded projects and brought two full generations of scientists into the field. In 2023 the landmark 40th such conference was held at the Woods Hole Marine Biological Laboratory in Massachusetts. The conference was held April 14th-16th, 2023. The majority of the total attendees are traditionally undergraduates, graduate students, and postdoctoral researchers, whose scientific development greatly benefits from conferences like these. Almost all talks besides the ones given by invited speakers were given by young scientists who benefited from this award. Many posters presented at this conference were also the work of junior scientists. This conference is many young scientists' first exposure to the photosynthesis research community and its primary goal is to provide a positive atmosphere for those attendees, as exemplified by the three poster sessions and dedicated interactions between senior and junior scientists. Additionally, this was the first year of a successful equitable outreach and speaker recruitment plan to provide fair representation at the conference in line with Department of Energy policies and mission. The central focus of the ERPC is the understanding of energy flow from photons to usable chemical products in both natural and artificial photosynthesis. We support the DOE-BES aim of understanding of the biochemical/biophysical processes of photosynthesis to inform new technology development and field applications. This year’s theme, “Photosynthesis Across Scales,” reflected the scope of work being done from the individual exciton to the crop scale. This research encompasses applied biology, chemistry, physics, and materials engineering. The aim of this conference is to present new discoveries, techniques, and questions which can be sourced from any of these disciplines and provide an audience which is broadly qualified to use or respond to these developments.

08 HYDROGEN↗

Extending juvenility in grasses

The present invention relates to compositions and methods for modulating the juvenile to adult developmental growth transition in plants, such as grasses (e.g. maize). In particular, the invention provides methods for enhancing agronomic properties in plants by modulating expression of GRMZM2G362718, GRMZM2G096016, or homologs thereof. Modulation of expression of one or more additional genes which affect juvenile to adult developmental growth transition such as Glossy15 or Cg1, in conjunction with such modulation of expression is also contemplated. Nucleic acid constructs for down-regulation of GRMZM2G362718 and/or GRMZM2G096016 are also contemplated, as are transgenic plants and products produced there from, that demonstrate altered, such as extended juvenile growth, and display associated phenotypes such as enhanced yield, improved digestibility, and increased disease resistance. Plants described herein may be used, for example, as improved forage or feed crops or in biofuel production.

59 BASIC BIOLOGICAL SCIENCES↗