Phospho;#8208;dependent signaling during the general stress response by the atypical response regula
Explore the source record for details and available documents.
Schwartz, Jacob↗
SEARCH · Search NASA
Results for “REGULATIONS”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism
Abstract Circular RNAs (circRNAs) are closed‐loop RNAs forming a covalent bond between their 3′ and 5′ ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light‐grown and etiolated seedlings after 5 or 7 days post‐germination and identified a total of 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA, and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts.
Utley, Delecia [Department of Plant and Microbial ↗
Regulation of dhurrin pathway gene expression during Sorghum bicolor development
Plant defence models evaluate the costs and benefits of resource investments at different stages in the life cycle. Poor understanding of the molecular regulation of defence deployment and remobilization hampers accuracy of the predictions. Cyanogenic glucosides, such as dhurrin are phytoanticipins that release hydrogen cyanide upon bio-activation. In this study, RNA-seq was used to investigate the expression of genes involved in the biosynthesis, bio-activation and recycling of dhurrin in Sorghum bicolor . Genes involved in dhurrin biosynthesis were highly expressed in all young developing vegetative tissues (leaves, leaf sheath, roots, stems), tiller buds and imbibing seeds and showed gene specific peaks of expression in leaves during diel cycles. Genes involved in dhurrin bio-activation were expressed early in organ development with organ-specific expression patterns. Genes involved in recycling were expressed at similar levels in the different organ during development, although post-floral initiation when nutrients are remobilized for grain filling, expression of GSTL1 decreased > tenfold in leaves and NITB2 increased > tenfold in stems. Results are consistent with the establishment of a pre-emptive defence in young tissues and regulated recycling related to organ senescence and increased demand for nitrogen during grain filling. This detailed characterization of the transcriptional regulation of dhurrin biosynthesis, bioactivation and remobilization genes during organ and plant development will aid elucidation of gene regulatory networks and signalling pathways that modulate gene expression and dhurrin levels. In-depth knowledge of dhurrin metabolism could improve the yield, nitrogen use efficiency and stress resilience of Sorghum .
59 BASIC BIOLOGICAL SCIENCES↗
Ducted fuel injection with Low-Net-Carbon fuels as a solution for meeting future emissions regulations
Several studies have proven how ducted fuel injection (DFI) reduces soot emissions for compression-ignition engines. Nevertheless, no comprehensive study has investigated how DFI performs over a load range in combination with low-net-carbon fuels. In this study, optical-engine experiments were performed with four different fuels—conventional diesel and three low-net-carbon fuels—at low and moderate load, to measure emissions levels and performance. The 1.7-liter single-cylinder optical engine was equipped with a high-speed camera to capture natural luminosity images of the combustion event. Conventional diesel and DFI combustion were investigated at four different dilution levels (to simulate exhaust-gas recirculation effects), from 14 to 21 mol% oxygen in the intake. At a given dilution level, with commercial diesel fuel, DFI reduced soot by 82% at medium load, and 75% at low load without increasing NO x . The results further show how DFI with dilution reduces soot and NO x without compromising engine performance or other emission types, especially when combined with low-net-carbon fuels. DFI with the oxygenated low-net-carbon blend HEA67 simultaneously reduced soot and NO x by as much as 93 % and 82 %, respectively, relative to conventional diesel combustion with commercial diesel fuel. These soot and NO x reductions occurred while lifecycle CO 2 was reduced by at least 70 % when using low-net-carbon fuels instead of conventional diesel. All emissions changes were compared with future emissions regulations for different vehicle sectors to investigate how DFI can be used to facilitate achievement of the regulations. Finally, the results show how the DFI cases fall below several future emissions regulation levels, rendering less need for aftertreatment systems and giving a possible lower cost of ownership.
33 ADVANCED PROPULSION SYSTEMS↗
Improving the effectiveness and equity of fuel economy regulations with sales adjustment factors
Larger vehicles, such as sports utility vehicles, consume more energy than cars. Their increasing popularity runs contrary to the goal of fuel economy regulations to reduce fossil fuel consumption and greenhouse gas emissions and can be explained by consumer preference and lower regulation stringency, which is due to footprint, truck classification, and the omission of heterogenous lifetime vehicle distance traveled among vehicle classes. This study shows that, for both the US and China, large vehicles travel more, last longer, and are owned by higher income consumers. This means large vehicles and their high-income owners use more fuel and emit more pollutants than represented by current policy and thus raises both policy effectiveness and energy equity concerns. We propose and estimate Sales Adjustment Factors that weigh fuel economy standards based on vehicle lifetime usage and demonstrate the resultant significant improvements in the effectiveness and equity of fuel economy regulations.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Protein 4.1R negatively regulates P815 cells proliferation by inhibiting C-Kit-mediated signal transduction
The proliferation of mast cells (MCs) plays a crucial role in either physiological or pathological progression of human physical. C-Kit-mediated signaling pathway has been confirmed to play a key role in MCs proliferation, and the regulatory mechanisms of C-Kit-mediated MCs proliferation need to be further explored. Our previous study found that protein 4.1R could negatively regulate T cell receptor (TCR) mediated signal pathways in CD4{sup +} T cells. Little is known about the function of 4.1R in C-Kit-mediated proliferation of MCs. In this study, P815-4.1R{sup -/-} cells were constructed by using CRISPR/Cas9 technique. Lack of 4.1R significantly enhanced P815 cells proliferation by accelerating the progression of cell cycle. 4.1R could also significantly alleviate the clinical symptoms of systemic mastocytosis (SM) and improve the overall survival of SM mice. Further study showed that 4.1R could interact directly with C-Kit to inhibit the activation of C-Kit-mediated Ras-Raf-MAPKs and PI3K-AKT signal pathways. Taken together, our findings demonstrate that protein 4.1R, a novel negative regulator, negatively regulates MCs proliferation by inhibiting C-Kit-mediated signal transduction, which maybe provide a potential target to the prevention and treatment of abnormal MCs proliferation-related diseases.
60 APPLIED LIFE SCIENCES↗
AFF4 facilitates melanoma cell progression by regulating c-Jun activity
Melanoma is characterized by high mortality and poor prognosis due to metastasis. AFF4 (AF4/FMR2 family member 4), as a scaffold protein, is a component of the super elongation complex (SEC), and is involved in the progression of tumors, e.g., leukemia, head and neck squamous cell carcinoma (HNSCC). However, few studies on AFF4 have focused on melanoma. Here, AFF4 expression levels and clinicopathological features were evaluated in melanoma tissue samples. Then, we performed cell proliferation, migration and invasion assays in A375 and A2058 cells lines in vitro to evaluate the role of AFF4 in melanoma. The effects of AFF4 knockdown in vivo were characterized via a xenograft mouse model. Finally, the correlation between c-Jun and AFF4 protein levels in melanoma was analyzed by rescue assay and immunohistochemistry (IHC). We found that AFF4 expression was upregulated in melanoma tumor tissues and that AFF4 protein expression was also closely related to the prognosis of patients with cutaneous melanoma. Moreover, AFF4 could promote the invasion and migration of melanoma cells by mediating epithelial to mesenchymal transition (EMT). AFF4 might regulate c-Jun activity to promote the invasion and migration of melanoma cells. Importantly, c-Jun was regulated by the AFF4 promoted melanoma tumorigenesis in vivo. Taken together, AFF4 may be a novel oncogene that promotes melanoma progression through regulation of c-Jun activity.
60 APPLIED LIFE SCIENCES↗
Endothelial cells control vascular smooth muscle cell cholesterol levels by regulating 24-dehydrocholesterol reductase expression
Highlights: • Suspended endothelial and vascular smooth muscle cells organize to form spherical vascular organoids in hanging drops. • Vascular smooth muscle cells downregulate the expression of metabolism regulating genes in presence of endothelial cells. • Endothelial cells decrease the levels of 24-dehydrocholesterol reductase and cholesterol in vascular smooth muscle cells. • Diminished cholesterol biosynthesis inhibits vascular smooth muscle cell activity. Communication of vascular cells is essential for the control of organotypic functions of blood vessels. In this context, vascular endothelial cells (EC) act as potent regulators of vascular smooth muscle cell (VSMC) functions such as contraction and relaxation. However, the impact of ECs on the gene expression pattern of VSMCs is largely unknown. Here, we investigated changes of the VSMC transcriptome by utilizing 3D human vascular organoids organized as a core of VSMCs enclosed by a monolayer of ECs. Microarray-based analyses indicated that interaction with ECs for 48 h down-regulates expression of genes in VSMCs controlling rate-limiting steps of the cholesterol biosynthesis such as HMGCR, HMGCS1, DHCR24 and DHCR7. Protein analyses revealed a decrease in the abundance of DHCR24 (24-dehydrocholesterol reductase) and lower cholesterol levels in VSMCs co-cultured with ECs. On the functional level, the blockade of the DHCR24 activity impaired adhesion, migration and proliferation of VSMCs. Collectively, these findings indicate that ECs have the capacity to instruct VSMCs to shut down the expression of DHCR24 thereby limiting their cholesterol biosynthesis, which may support their functional steady state.
60 APPLIED LIFE SCIENCES↗
ANGPTL4 regulates CD163 expression and Kuppfer cell polarization induced cirrhosis via TLR4/NF-κB pathway
Angiopoietin like 4 (ANGPTL4) has been proved to play an important role in lipid and glucose metabolism disorders and related cardiovascular diseases, but its role in the formation of cirrhosis still needs to be further explored. Therefore, the aim of this study was to investigate the role of ANGPTL4 in the development of liver cirrhosis and its mechanism, as well as its effect on Kupffer cell polarization and hepatic stellate cell activation. The ELISA and RT-qPCR assay were used to detect the content of ANGPTL4 in serum and mRNA expression in cells and tissues respectively. The expression of ANGPTL4, Arg1 and Mrc2 in Kupffer cells was measured by Western blot. The percentage of CD163{sup +} and CD206{sup +} cells was measured by flow cytometry. Mice cirrhosis model was established, and the expression of ANGPTL4 was interfered by injecting sh-ANGPTL4 lentiviral vector into caudal vein. The results revealed that ANGPTL4 was significantly up-regulated in liver cirrhosis patients and HBV induced liver injury cell models. Further studies found that interference with ANGPTL4 regulated CD163 and inhibited the polarization and proinflammatory effects of KCsas well as inhibited the activation of hepatic stellate cells (HSCs) and fibrosis. More importantly, Interference with ANGPTL4 inhibits the progression of liver cirrhosis in mice. What's more, TLR4/NF-κB pathway was involved in the molecular mechanism of ANGPTL4 on Kupffer cells and hepatic stellate cells. It is suggested that the mechanism of sh-ANGPTL4 suppressing the polarization of KCs and the activation of hepatic stellate cells (HSCs) is to regulate the TLR4/NF-κB signaling pathways.
60 APPLIED LIFE SCIENCES↗
Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model
Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13 C-metabolic flux analysis ( 13 C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13 C labeling data were used with 13 C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.
59 BASIC BIOLOGICAL SCIENCES↗
Regulation of Iron Homeostasis through Parkin-Mediated Lactoferrin Ubiquitylation
Somatic mutations that perturb Parkin ubiquitin ligase activity and the misregulation of iron homeostasis have both been linked to Parkinson’s disease. Lactotransferrin (LTF) is a member of the family of transferrin iron binding proteins that regulate iron homeostasis, and increased levels of LTF and its receptor have been observed in neurodegenerative disorders like Parkinson’s disease. Here, we report that Parkin binds to LTF and ubiquitylates LTF to influence iron homeostasis. Parkin-dependent ubiquitylation of LTF occurred most often on lysines (K) 182 and 649. Substitution of K182 or K649 with alanine (K182A or K649A, respectively) led to a decrease in the level of LTF ubiquitylation, and substitution at both sites led to a major decrease in the level of LTF ubiquitylation. Importantly, Parkin-mediated ubiquitylation of LTF was critical for regulating intracellular iron levels as overexpression of LTF ubiquitylation site point mutants (K649A or K182A/K649A) led to an increase in intracellular iron levels measured by ICP-MS/MS. Consistently, RNAi-mediated depletion of Parkin led to an increase in intracellular iron levels in contrast to overexpression of Parkin that led to a decrease in intracellular iron levels. Together, these results indicate that Parkin binds to and ubiquitylates LTF to regulate intracellular iron levels. These results expand our understanding of the cellular processes that are perturbed when Parkin activity is disrupted and more broadly the mechanisms that contribute to Parkinson’s disease.
60 APPLIED LIFE SCIENCES↗
Function, Structure, and Regulation of Nitrogen Fixation-like Metalloproteins for Nitrogen, Energy, Carbon, and Sulfur Metabolism
Nitrogenases (N 2 ases) and nitrogen fixation-like (NFL) systems play distinct roles in nitrogen, carbon, sulfur, and energy metabolism based on their fundamental differences in structure and metallocofactor identity. As new NFL systems have recently been identified and characterized, striking parallels and differences compared to N 2 ase structure, catalysis, and regulation have emerged. NFL systems use metallocofactors that span from simple [4Fe-4S] clusters to complex clusters akin to FeMo-co, previously only thought to occur in N 2 ase. This review describes the present state of knowledge on the function, structure, catalytic mechanisms, and regulation of NFL systems that perform distinct biological roles across all three domains of life. Recent advancements in N 2 ase spectroscopic techniques for probing metallocofactor structure and electronic states guide current and future work on how each NFL system catalyzes its specific biological reaction(s). Key knowledge gaps and needed areas of research for uncovering the specific metallocofactors and structural motifs that are at the heart of NFL system reaction specificity, along with how these systems are regulated, are discussed.
Bacteria↗
Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators
Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.
Cell signaling↗
River Regulation Alleviates the Impacts of Climate Change on US Thermoelectricity Production
Climate change and anthropogenic activities can both influence stream temperature, which is a critical indicator of thermoelectric power generation potential. Previous studies emphasized the vulnerability of power-generation systems to climate warming (ref 1, 2). Despite the fact that two-thirds of the global rivers are regulated by dams (ref 3), the relative impacts of water management and climate change on stream temperature and thermoelectric production have not yet been evaluated. Using an integrated modeling system applied to the conterminous United States, simulations confirm the dominant role of climate change in shaping the future trends of stream temperature. However, water management, reservoir regulation in particular, can mitigate the stream temperature warming and reduce the frequency and magnitude of extreme high stream temperatures through redistribution of the seasonal streamflow. Moreover, water management can alleviate the loss of power plant usable capacity from climate change to the level of reduced warming from emission mitigation. By regulating the flow and temperature regimes, water management is a promising adaptation measure to alleviate climate change induced effects in the water-energy nexus.
Zhang, Xiao↗
Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel
Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
59 BASIC BIOLOGICAL SCIENCES↗
Light-independent regulation of algal photoprotection by CO 2 availability
Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO 2 conditions. When light energy exceeds CO 2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO 2 Concentrating Mechanism (CCM). How light and CO 2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO 2 concentrations and that depletion of CO 2 drives these responses, even in total darkness. High CO 2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO 2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO 2 levels.
59 BASIC BIOLOGICAL SCIENCES↗
Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding
The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we describe DarR-c-di-AMP and DarR-DNA structures and complementary biochemical assays. The DarR-c-di-AMP structure reveals a unique effector binding site for a TFR, located between DarR dimer subunits. Strikingly, we show this motif also binds cAMP. The location of the adenine nucleotide binding site between subunits suggests this interaction may facilitate dimerization and hence DNA binding. Indeed, biochemical assays show cAMP enhances DarR DNA binding. Finally, DarR-DNA structures reveal a distinct TFR DNA-binding mechanism involving two interacting dimers on the DNA. Thus, the combined data unveil a newly described second messenger binding motif and DNA binding mode for this important family of regulators.
59 BASIC BIOLOGICAL SCIENCES↗
M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation
Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection of the archaeal Methanosarcina mazei ( Mm ) GS and its regulation. We show that Mm GS forms unstable dodecamers. Strikingly, we show this Mm GS oligomerization property is leveraged for a unique mode of regulation whereby labile Mm GS hexamers are stabilized by binding the nitrogen regulatory protein, GlnK1. Our GS-GlnK1 structure shows that GlnK1 functions as molecular glue to affix GS hexamers together, stabilizing formation of GS active-sites. These data, therefore, reveal the structural basis for a unique form of enzyme regulation by oligomer modulation.
59 BASIC BIOLOGICAL SCIENCES↗