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At least 145 records · Page 8

Stellar Rotation of T Tauri Stars in the Orion Star-forming Complex

We present a large-scale study of stellar rotation for T Tauri stars in the Orion star-forming complex. We use the projected rotational velocity ($v\sin (i)$) estimations reported by the APOGEE-2 collaboration as well as individual masses and ages derived from the position of the stars in the HR diagram, considering Gaia-EDR3 parallaxes and photometry plus diverse evolutionary models. We find an empirical trend for $v\sin (i)$ decreasing with age for low-mass stars (0.4M ⊙ < M $\star$ < 1.2M ⊙ ). Our results support the existence of a mechanism linking $v\sin (i)$ to the presence of accreting protoplanetary disks, responsible for regulating stellar rotation on timescales of about 6 Myr, which is the timescale in which most of the T Tauri stars lose their inner disk. Our results provide important constraints to models of rotation in the early phases of evolution of young stars and their disks.

79 ASTRONOMY AND ASTROPHYSICS↗

Distribution Grid Management in the Presence of Distributed Energy Resources

The global concerns over climate change, government policies, and incentives in support of distributed energy resources (DERs) are accelerating the growth of DERs in distribution networks. The growth in DER penetration levels can create various issues such as over/under voltages, reverse power flows, overloading, and protection miscoordination. State-of-the-art grid automation solutions such as advanced distribution management systems (ADMS) and distributed energy resource management systems (DERMS) can leverage the DERs to improve distribution grid operations. The ADMS offers advanced grid management functions such as Volt-VAR optimization (VVO), fault management, and outage management to the distribution operator to improve situational awareness and optimize network operations. The DERMS solutions aggregate the small-scale BTM DERs to provide grid services including demand response, voltage regulation, and situational awareness. In this presentation, distribution grid management approaches in the presence of DERs using ADMS and DERMS will be discussed.

ADMS↗

Nuclear Trade Atlas 2016-2020

Building on prior work developing a Strategic Trade Atlas promoting understanding of global trade flows of strategic goods, a Nuclear Trade Atlas was developed based on publicly available trade data. The Nuclear Trade Atlas examines trade patterns and trends for seventeen commodities based on a two-step assessment of the trade’s nuclear relevance: first estimating the probability that trade classified under a given Harmonized System (HS) code represents a specific commodity included in the export control lists of the Nuclear Suppliers Group, and second estimating the probability that the listed, often dual-use, commodity would be indicative of nuclear use. These estimates combine to provide a measure of the likelihood trade classified under a given HS code may be nuclear relevant. By exclusively focusing on the HS codes most highly ranked by this measure, the resulting data visualizations comprising the Nuclear Trade Atlas provide those responsible for regulating or monitoring nuclear trade greater understanding of relevant global trading patterns and trends. The Atlas includes both commodity- and country-based views of nuclear trade. It is published as a book and as an interactive tool. Besides trade data, the interactive Atlas also includes data about countries’ non-proliferation commitments, allowing users to take this information into consideration while analyzing specific trade flows.

strategic trade, world customs organization, trade↗

The starch-deficient plastidic PHOSPHOGLUCOMUTASE mutant of the constitutive crassulacean acid metabolism (CAM) species Kalanchoë fedtschenkoi impacts diel regulation and timing of stomatal CO2 responsiveness

Abstract Background and Aims Crassulacean acid metabolism (CAM) is a specialized type of photosynthesis characterized by a diel pattern of stomatal opening at night and closure during the day, which increases water-use efficiency. Starch degradation is a key regulator of CAM, providing phosphoenolpyruvate as a substrate in the mesophyll for nocturnal assimilation of CO2. Growing recognition of a key role for starch degradation in C3 photosynthesis guard cells for mediating daytime stomatal opening presents the possibility that starch degradation might also impact CAM by regulating the provision of energy and osmolytes to increase guard cell turgor and drive stomatal opening at night. In this study, we tested the hypothesis that the timing of diel starch turnover in CAM guard cells has been reprogrammed during evolution to enable nocturnal stomatal opening and daytime closure. Methods Biochemical and genetic characterization of wild-type and starch-deficient RNAi lines of Kalanchoë fedtschenkoi with reduced activity of plastidic phosphoglucomutase (PGM) constituted a preliminary approach for the understanding of starch metabolism and its implications for stomatal regulation in CAM plants. Key Results Starch deficiency reduced nocturnal net CO2 uptake but had negligible impact on nocturnal stomatal opening. In contrast, daytime stomatal closure was reduced in magnitude and duration in the starch-deficient rPGM RNAi lines, and their stomata were unable to remain closed in response to elevated concentrations of atmospheric CO2 administered during the day. Curtailed daytime stomatal closure was linked to higher soluble sugar contents in the epidermis and mesophyll. Conclusions Nocturnal stomatal opening is not reliant upon starch degradation, but starch biosynthesis is an important sink for carbohydrates, ensuring daytime stomatal closure in this CAM species.

59 BASIC BIOLOGICAL SCIENCES↗

De novo transcriptome sequencing of Capsicum frutescens . L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU ‐9

Abstract Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth–promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress‐treated plants grown in a microorganism‐controlled environment. Our previous reports have selected Bacillus atrophaeus WU‐9 as PGPR significantly alleviating pepper ( Capsicum frutescens . L) salt stress. In this work, the RNA‐seq analysis of salt stress‐treated and untreated plants, grown with and without WU‐9 in a microorganism‐controlled environment, was used to reveal the plant salt stress alleviating mechanisms of WU‐9. Twelve sequencing libraries, prepared by treating with WU‐9 and salt (150 mM NaCl for 36 h), were constructed by RNA‐Seq technique. Non‐inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene‐activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU‐9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress‐responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens . L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR.

Wang, Wenfei↗

A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and nonvascular plants

The phytohormone jasmonoyl-L-isoleucine (JA-Ile) regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein Coronatine Insensitive 1 (COI1) and a Jasmonate (JA) ZIM-domain (JAZ) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signaling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI–JAZ interaction and degradation of JAZ1 and JAZ9 in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation, and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana) COI1–JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1–JAZ also occurs in the liverwort Marchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signaling, J4 works as an antagonist of the closely related auxin signaling pathway, preventing Transport Inhibitor Response1/Aux–indole-3-acetic acid interaction and auxin responses in planta, including hormone-mediated degradation of an auxin repressor, gene expression, and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways. One-sentence summary: A chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and nonvascular plants.

59 BASIC BIOLOGICAL SCIENCES↗

Lawrence Livermore National Laboratory Annual Report for CY2024: Regulation for Reducing Greenhouse Gas Emissions from Gas-Insulated Equipment

This report is in response to the “Regulation for Reducing Greenhouse Gas Emissions from Gas Insulated Equipment (GIE),” Section 95355, Title 17, California Code of Regulations. This report includes GIE at Lawrence Livermore National Laboratory Site 200, located in Livermore, CA, and Site 300, located 10 miles west of the City of Tracy, in San Joaquin County.

42 ENGINEERING↗

Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light

As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.

59 BASIC BIOLOGICAL SCIENCES↗

An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp.

Abstract The transcription factor NODULE INCEPTION (NIN) has been studied extensively for its multiple roles in root nodule symbiosis within plants of the nitrogen-fixing clade (NFC) that associate with soil bacteria, such as rhizobia and Frankia. However, NIN homologs are present in plants outside the NFC, suggesting a role in other developmental processes. Here, we show that the biofuel crop Populus sp., which is not part of the NFC, contains eight copies of NIN with diversified protein sequence and expression patterns. Lipo-chitooligosaccharides (LCOs) are produced by rhizobia and a wide range of fungi, including mycorrhizal ones, and act as symbiotic signals that promote lateral root formation. RNAseq analysis of Populus sp. treated with purified LCO showed induction of the PtNIN2 subfamily. Moreover, the expression of PtNIN2b correlated with the formation of lateral roots and was suppressed by cytokinin treatment. Constitutive expression of PtNIN2b overcame the inhibition of lateral root development by cytokinin under high nitrate conditions. Lateral root induction in response to LCOs likely represents an ancestral function of NIN retained and repurposed in nodulating plants, as we demonstrate that the role of NIN in LCO-induced root branching is conserved in both Populus sp. and legumes. We further established a visual marker of LCO perception in Populus sp. roots, the putative sulfotransferase PtSS1 that can be used to study symbiotic interactions with the bacterial and fungal symbionts of Populus sp.

Irving, Thomas B. (ORCID:0000000330404543)↗

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗

ATM–dependent phosphorylation of CHD7 regulates morphogenesis-coupled DSB stress response in fetal radiation exposure

Following radiation exposure, unrepaired DNA double-strand breaks (DSBs) persist to some extent in a subset of cells as residual damage; they can exert adverse effects, including late-onset diseases. In search of the factor(s) that characterize(s) cells bearing such damage, we discovered ataxia-telangiectasia mutated (ATM)-dependent phosphorylation of the transcription factor chromodomain helicase DNA binding protein 7 (CHD7). CHD7 controls the morphogenesis of cell populations derived from neural crest cells during vertebrate early development. Indeed, malformations in various fetal bodies are attributable to CHD7 haploinsufficiency. Following radiation exposure, CHD7 becomes phosphorylated, ceases promoter/enhancer binding to target genes, and relocates to the DSB-repair protein complex, where it remains until the damage is repaired. Thus, ATM-dependent CHD7 phosphorylation appears to act as a functional switch. As such stress responses contribute to improved cell survival and canonical nonhomologous end joining, we conclude that CHD7 is involved in both morphogenetic and DSB-response functions. Thus, we propose that higher vertebrates have evolved intrinsic mechanisms underlying the morphogenesis-coupled DSB stress response. In fetal exposure, if the function of CHD7 becomes primarily shifted toward DNA repair, morphogenic activity is reduced, resulting in malformations.

59 BASIC BIOLOGICAL SCIENCES↗

Early growth response 2 (EGR2) is a novel regulator of the senescence programme

Abstract Senescence, a state of stable growth arrest, plays an important role in ageing and age‐related diseases in vivo. Although the INK4/ARF locus is known to be essential for senescence programmes, the key regulators driving p16 and ARF transcription remain largely underexplored. Using siRNA screening for modulators of the p16/pRB and ARF/p53/p21 pathways in deeply senescent human mammary epithelial cells (DS HMECs) and fibroblasts (DS HMFs), we identified EGR2 as a novel regulator of senescence. EGR2 expression is up‐regulated during senescence, and its ablation by siRNA in DS HMECs and HMFs transiently reverses the senescent phenotype. We demonstrate that EGR2 activates the ARF and p16 promoters and directly binds to both the ARF and p16 promoters. Loss of EGR2 down‐regulates p16 levels and increases the pool of p16− p21− ‘reversed’ cells in the population. Moreover, EGR2 overexpression is sufficient to induce senescence. Our data suggest that EGR2 is a direct transcriptional activator of the p16/pRB and ARF/p53/p21 pathways in senescence and a novel marker of senescence.

60 APPLIED LIFE SCIENCES↗

Onshore U.S. Carbon Pipeline Deployment: Siting, Safety, and Regulation

Carbon capture, utilization, and storage (CCUS) technology has significant potential to reduce greenhouse gas (GHG) emissions and mitigate the impact of climate change, particularly in hard to decarbonize industrial and commercial sectors. CCUS involves capturing carbon dioxide (CO 2 ) from industrial processes or power generation and utilizing it for other purposes, such as enhanced oil recovery (EOR), or storing the captured CO 2 underground. CCUS technology can reduce the environmental impact of continued fossil fuel use while smoothing the transition to a low-carbon economy. CCUS can create new economic opportunities, such as the development of new industries and job creation, and can enhance energy security by diversifying energy sources. For these reasons, enabling CCUS has become a key objective of the Biden-Harris administration’s clean energy policy and has received bipartisan support. Despite its environmental and economic potential, CCUS faces multiple barriers to widespread deployment. One of the main challenges is the high cost and technical difficulty of implementing and operating large-scale CCUS infrastructure. CCUS remains a relatively expensive way to reduce carbon emissions (e.g., compared to solar photovoltaic technology’s displacement of coal generation). Additionally, financial incentives and supportive policies like those enacted to support solar photovoltaic development, especially at the state level, are inconsistent or nonexistent, which can discourage investment in CCUS projects. There are also technical challenges associated with safe and secure underground CO 2 storage and the development of new carbon utilization technologies. Public opposition to various aspects of CCUS technologies, ranging from concerns that CCUS will extend reliance on fossil fuels to CCUS infrastructure being sited in disadvantaged communities, is a growing challenge. This paper focuses on another significant barrier to broad CCUS deployment: the need for considerable expansion of the dedicated land-based CO 2 pipeline network in the United States to meet CCUS goals and the unique regulatory challenges to its development. To reach carbon emissions targets in the United States by 2050, CCUS technology will need to be supported by tens of thousands of miles of CO 2 pipelines. Estimates range from a minimum of roughly 29,000 pipeline miles (according to a 2020 Great Plains Institute study) to 66,000 pipeline miles (as per a 2021 Princeton University–led study). As of October 2022, however, the U.S. Department of Transportation (U.S. DOT) reports fewer than 5,400 miles of U.S. pipelines carrying CO 2 . This deficit—and what it means for the prospect of moving substantially larger quantities of CO 2 from source to use or storage—threatens to stifle the development of CCUS projects and technologies identified as an important tool to meet emissions targets. The current regulatory landscape facing CO 2 pipeline development can best be described as uncertain. At the federal level, the U.S. DOT Pipeline and Hazardous Materials Safety Administration (PHMSA) oversees safety regulation of pipelines transporting hazardous materials, including CO 2 upon commencement of operation. However, PHMSA’s definition of CO 2 as “a fluid consisting of more than 90 percent CO 2 molecules compressed to a supercritical state” has not been updated since its 1991 addition to the Federal Register. Because CO 2 can be transported in a gaseous, liquid, or supercritical state (indeed, the physical state of CO 2 can fluctuate within a single pipeline due to environmental changes), doubts persist about the extent of PHMSA’s purview—and raise questions about what, if anything, states should do to address this apparent gap. PHMSA has begun a major revision of its existing rules, but the agency does not expect a first draft before 2024. Economic oversight of CO 2 pipelines is even less clear. The Federal Energy Regulatory Commission (FERC) and Surface Transportation Board (STB)—which regulate the rates of interstate oil/natural gas and non-energy pipelines, respectively—have both declined jurisdiction over interstate CO 2 pipelines. This presumably leaves economic regulation to state and/or local governments, but few if any states have the laws or resources in place to oversee just and reasonable rates. Further, the interstate nature of CO 2 pipeline development creates questions around how different states should align their rate-making decisions. Onshore U.S. Carbon Pipeline Deployment: Siting, Safety, and Regulation Currently, regulatory responsibilities regarding CO 2 pipeline siting and permitting fall to state and local governments. The variety of laws and regulations across the country, however, creates a maze of requirements for pipeline developers to navigate. To secure necessary permits, most states require pipeline companies to be “common carriers” that provide transport service to the public at uniform rates. However, the specific definition of that term varies. Some states require clear evidence that a pipeline services the public, while others automatically deem any pipeline company transporting energy products or hazardous materials to be a “common carrier”—with little consideration for accessibility to third parties. Other states have eschewed common-carrier terminology entirely, placing private and publicly accessible pipelines on equal footing. Much like the variation in common-carrier requirements, laws governing eminent domain authority to secure rights-of-way (ROW) to commence construction on a planned pipeline route differ by state. Several states have no laws or rules governing CO 2 pipelines. In addition to creating questions about whether long-standing rules for other pipelines (e.g., natural gas or petroleum products) apply to CO 2 , this policy vacuum leaves local governments as the sole authority over sections of pipe within their boundaries. With dozens of counties along a given route, the probability of inconsistent regulation of the same pipeline is significant. Even in states with CO 2 pipeline laws in place, local regulatory attempts to address rising concerns over pipeline routing and safety have triggered lawsuits by pipeline companies seeking to delimit areas of federal, state, and local government responsibility. Meanwhile, legislators across the country have introduced bills to restrict the application of eminent domain to CO 2 pipeline projects, which could threaten a key means of securing ROW that companies cannot secure through negotiation with landowners. Taken separately, any of these regulatory issues—the narrow federal definition of CO 2 , FERC’s and STB’s decisions that CO 2 pipelines are not within their jurisdiction, and the considerable variation in state and local governments’ laws regulating CO 2 pipeline technologies—are extremely difficult to resolve. Adding the required scale of CO 2 pipeline expansion and the currently identified narrow window of time in which to reach climate target goals, the task becomes even more difficult—and raises a host of urgent questions for regulators. How should CO 2 be defined in federal regulations to ensure consistent safety standards across the country? What is the potential impact radius of a CO 2 pipeline rupture, and how should that inform local emergency response? In the absence of centralized federal oversight, what should state legislatures do to increase alignment for interstate CO 2 pipeline projects? This paper intends to serve as a primer for regulators and stakeholders who seek to better understand the regulatory challenges and opportunities facing this critical infrastructure.

42 ENGINEERING↗

What are grana in chloroplasts of vascular plants good for?

All plants and green algae contain stacked grana thylakoid membranes in their chloroplasts, underscoring an evolutionary pressure to maintain this unique structural feature. In addition, numerous studies have demonstrated that particular lateral and vertical dimensions of grana facilitate the function, regulation and repair of the photosynthetic machinery responsible for energy conversion. In this review, we present an updated overview of our understanding concerning the structure of grana thylakoids, the forces that contribute to their formation and their architectural dynamics. After establishing the structural foundation, we continue by reviewing the implications of grana formation on light harvesting, electron transport and protein maintenance in the thylakoid membranes of vascular plants. Regarding light harvesting, we discuss the implications of grana formation on energy spillover, macromolecular crowding, lateral versus vertical excitation energy transfer, and state transition. With respect to electron transport, we summarize recent findings regarding the functional connectivity of spatially separated photosystems facilitated by grana formation through small mobile electron carriers. We also explore how the dynamic responses of grana architecture regulate electron transport. Finally, we address how grana formation contributes to the organization of protein repair and biogenesis within thylakoid membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung

Interferon (IFN) cytokines induce an autonomous antiviral state in cells of the infected site to restrict virus spreading and critically regulate overall antiviral response. The antiviral state leads to host protection through expression of hundreds of IFN-stimulated genes that restrict viral infection through multiple mechanisms, for example, directly in viral genome degradation and indirectly through cellular metabolic inhibition. Young pigs were split into four treatment groups: control, porcine reproductive and respiratory syndrome virus (PRRSV, also known as porcine arterivirus) infected, influenza B virus (IBV) infected, and IBV/PRRSV coinfection. Lung tissue was collected at 3, 5, and 7 days post infection (dpi) for control, PRRSV and IBV/PRRSV coinfection, and at 3 and 5 dpi for IBV. Transcriptomic analysis, using usegalaxy.org tools, was performed against the S.scrofa 11.1 reference genome. Differentially expressed gene (DEG) analysis was carried out using DeSeq2 based on the model treatment + dpi + treatment:dpi + E. Downstream analysis examined the interaction of DEG at each dpi for over-enriched gene ontology (G.O.) terms and pathways. Comparisons of the infected groups vs. the controls yielded a total of (n = 1412) DEGs for the PRRSV group and (n = 1578) for the IBV/PRRSV group across all timepoints. The IBV group had (n = 64) total DEGs across 3 and 5 dpi. Expression data were considered statistically significant based on false discovery rate (FDR) ⫹ 0.1. Venn diagram comparisons of the DEGs across dpi showed that groups shared only 16 DEGs at 3 dpi, no DEGs were shared at 5 dpi, and for 7 dpi, only the PRRSV and IBV/PRRSV groups were compared and shared a total of 43 DEGs. Across the comparisons, differential expression was observed in antiviral genes such as IRF1, MX1, and OAS2. The IBV and IBV/PRRSV groups showed higher expression of antiviral genes at earlier dpi than the PRRSV group. Additionally, downregulated genes from the comparisons clustered around Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways effecting lung development and cellular integrity. Early expression of host IFN and antiviral genes may lead to viral RNA degradation, and assembly and transcription inhibition in the IBV infections. In comparison, expression of antiviral genes in the PRRSV group decreased across time. The decrease may explain why PRRSV infections persist, while IBV clears. Moreover, all infected groups showed prolonged upregulation in neutrophil degranulation pathway activity, possibly exacerbating symptomatic lung lesion pathology seen in these respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗

EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy

Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.

54 ENVIRONMENTAL SCIENCES↗

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated ß-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-?B signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

proteomics, PTM, automation, SP3, cysteine thiol o↗

Populus PtrbHLH011 Is a Transcriptional Co‐Regulator Involved in the Activation of Cell Wall Biosynthesis by Iron Deprivation

The lack of a mechanistic understanding of the environmental plasticity of secondary cell wall (SCW) biosynthesis restricts large-scale biomass and bioenergy production on marginal lands. Using Populus (poplar), a key bioenergy crop, we discovered that iron deprivation, a prevalent abiotic stress on marginal lands, stimulates SCW biosynthesis in stems. We identified the transcription factor PtrbHLH011 as a critical regulator underlying this response. Through integrated analyses involving phenotypic characterisation of PtrbHLH011 knockout and overexpression plants, functional genomics and molecular investigations, we established that PtrbHLH011 functions as a central regulator of SCW biosynthesis, iron homeostasis and flavonoid biosynthesis by directly repressing essential genes in these pathways. Iron deprivation downregulates PtrbHLH011 expression, subsequently activating these biosynthetic pathways. Notably, cytosine base editing-based knockout of PtrbHLH011 significantly enhanced plant growth, yielding up to a 110% increase in stem diameter and a 300% increase in leaf iron content. These findings present a novel regulatory mechanism linking environmental iron availability to SCW biosynthesis and illustrate a practical strategy to improve biomass yield on iron-deficient marginal lands. Furthermore, our mechanistic insights into PtrbHLH011 target recognition and regulation provide a valuable foundation for precise manipulation of gene regulatory networks, facilitating the development of high-performance bioenergy crops adapted to marginal environments.

59 BASIC BIOLOGICAL SCIENCES↗