Browsing by Author "Xu, Bin"

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    Biochemical Characterization of Thermocrispum agreste TheA: A Flavin-Dependent N-hydroxylating Enzyme
    Mena Aguilar, Didier Philippe (Virginia Tech, 2018-06-26)
    N-hydroxylating monooxygenases (NMOs) are Class B flavin-dependent monooxygenases found only in fungi and bacteria. These enzymes catalyze the hydroxylation of nucleophilic primary amines, such as those found in histamine, L-ornithine, L-lysine, and small aliphatic diamines. The hydroxamate moiety produced by this reaction is key for the production of siderophores, small chelating compounds that allow survival in iron limiting conditions. NMOs involved in siderophore biosynthesis have been shown to be essential for pathogenesis in organisms such as Aspergillus fumigatus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis. Therefore, NMOs are considered novel drug targets for the treatment associated with these diseases. Herein we present the characterization of TheA, an NMO from Thermocrispum agreste. The enzyme mechanism was studied using steady state kinetic measurements, thermostability, and stopped flow spectrophotometry assays. Using these techniques, the catalytic rates, substrate binding affinities, thermal stability, and coenzyme specificities were determined. Additionally, NADPH analogues were produced to use as tools to study FAD reduction in NMOs. An unspecific reduction reaction of NADP+ using NaB2H4 yielded [6-2H]-NADPH, [2-2H]-NADPH, and [4-2H]-NADPH. Compound identity was confirmed by mass spectrometry and unidimensional proton nuclear magnetic resonance (NMR). Results presented in this thesis lay the foundation for future studies of NMOs using NADPH analogues. In conjunction, these results will improve the general knowledge and understanding of flavoenzymes, ornithine monooxygenases, and their associated mechanisms.
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    Discovery and Mechanisms of Small Molecule Amyloid Formation Inhibitors
    Velander, Paul William (Virginia Tech, 2018-01-17)
    Current dogma suggests modulating or preventing amyloid assembly will prove critical to the armamentarium of therapeutic interventions that will likely be required to overcome the multifaceted pathology associated with amyloid diseases. The work described in this dissertation reveals substantial gains in understanding key aspects relating to the anti-amylin amyloid activities associated with both individual and broad groups of small molecule amyloid inhibitors. A main observation was the important role that the catechol functional group plays in modulating and preventing amyloid formation. In this context, each chapter provides unique yet complementary mechanistic insight that delineates a wide range of anti-amyloid activities associated with preventing amylin amyloid formation by mainly catechol-containing structural scaffolds. Structure activity studies show that the catechol moiety present within baicalein, oleuropein and rosmarinic acid are critical for their anti-amyloid functions, including exerting cell rescue effects against amylin induced cytotoxicity. We also demonstrate that in general, autoxidation enhances the anti-amyloid potency associated with many catechol containing amyloid inhibitors that may be mechanistically linked to a covalent mode of action. For example, we demonstrate that the O-quinone form of baicalein conjugates with amylin via a Schiff base mechanism. In contrast, we also show that catechol mediated formation of protein denaturant resistant aggregates, which requires autoxidation and that also stems from a predicted covalent mode of action, does not necessarily correlate with the enhanced anti-amyloid activities that occur upon catechol autoxidation. Regardless of the chemical mechanism(s) that drive catechol mediated anti-amyloid activity in vitro, the observed cell rescue effects exhibited by catechol containing molecules against amylin amyloid induced cytotoxicity is congruent with several recent in vivo studies that indicate polyphenols prevent toxic amyloid deposition as well as decades of population based studies that show regular consumption of diets rich in polyphenols are linked to a reduce incidence of age-related neurodegenerative amyloid disease. Indeed, advances in structure based drug discovery against amyloid formation may provide new avenues to optimize various catechol containing scaffolds that could be readily leveraged into improving diagnostic tools or perhaps accelerate the effort of discovering anti-amyloid therapeutics.
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    Early preclinical detection of prions in the skin of prion-infected animals
    Wang, Zerui; Manca, Matteo; Foutz, Aaron; Camacho, Manuel V.; Raymond, Gregory J.; Race, Brent; Orru, Christina D.; Yuan, Jue; Shen, Pingping; Li, Baiya; Lang, Yue; Dang, Johnny; Adornato, Alise; Williams, Katie; Maurer, Nicholas R.; Gambetti, Pierluigi; Xu, Bin; Surewicz, Witold; Petersen, Robert B.; Dong, Xiaoping; Appleby, Brian S.; Caughey, Byron; Cui, Li; Kong, Qingzhong; Zou, Wen-Quan (2019-01-16)
    A definitive pre-mortem diagnosis of prion disease depends on brain biopsy for prion detection currently and no validated alternative preclinical diagnostic tests have been reported to date. To determine the feasibility of using skin for preclinical diagnosis, here we report ultrasensitive serial protein misfolding cyclic amplification (sPMCA) and real-time quaking-induced conversion (RT-QuIC) assays of skin samples from hamsters and humanized transgenic mice (Tg40h) at different time points after intracerebral inoculation with 263K and sCJDMM1 prions, respectively. sPMCA detects skin PrPSc as early as 2 weeks post inoculation (wpi) in hamsters and 4 wpi in Tg40h mice; RT-QuIC assay reveals earliest skin prion-seeding activity at 3 wpi in hamsters and 20 wpi in Tg40h mice. Unlike 263K-inoculated animals, mock-inoculated animals show detectable skin/brain PrPSc only after long cohabitation periods with scrapie-infected animals. Our study provides the proof-of-concept evidence that skin prions could be a biomarker for preclinical diagnosis of prion disease.
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    An efficient protocol for perennial ryegrass mesophyll protoplast isolation and transformation, and its application on interaction study between LpNOL and LpNYC1
    Yu, Guohui; Cheng, Qiang; Xie, Zheni; Xu, Bin; Huang, Bingru; Zhao, Bingyu Y. (2017-06-05)
    Background Perennial ryegrass (Lolium perenne L.) is an important temperate grass used for turf and forage purposes. With the increasing accumulation of genomic and transcriptomic data of perennial ryegrass, an efficient protoplast and transient gene expression protocol is highly desirable for in vivo gene functional studies in its homologous system. Results In this report, a highly efficient protoplast isolation (5.6 × 107 protoplasts per gram of leaf material) and transient expression (plasmid transformation efficiency at 55.2%) was developed and the detailed protocol presented. Using this protocol, the subcellular locations of two ryegrass proteins were visualized in chloroplasts and nuclei, respectively, and protein–protein interaction between two chlorophyll catabolic enzymes (LpNOL and LpNYC1) was recorded in its homologous system for the first time. Conclusions This efficient protoplast isolation and transformation protocol is sufficient for studies on protein subcellular localization and protein–protein interaction, and shall be suitable for many other molecular biology applications where the mesophyll protoplast system is desirable in perennial ryegrass.
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    Fast Path Planning in Uncertain Environments: Theory and Experiments
    Xu, Bin (Virginia Tech, 2009-11-19)
    This dissertation addresses path planning for an autonomous vehicle navigating in a two dimensional environment for which an a priori map is inaccurate and for which the environment is sensed in real-time. For this class of application, planning decisions must be made in real-time. This work is motivated by the need for fast autonomous vehicles that require planning algorithms to operate as quickly as possible. In this dissertation, we first study the case in which there are only static obstacles in the environment. We propose a hybrid receding horizon control path planning algorithm that is based on level-set methods. The hybrid method uses global or local level sets in the formulation of the receding horizon control problem. The decision to select a new level set is made based on certain matching conditions that guarantee the optimality of the path. We rigorously prove sufficient conditions that guarantee that the vehicle will converge to the goal as long as a path to the goal exists. We then extend the proposed receding horizon formulation to the case when the environment possesses moving obstacles. Since all of the results in this dissertation are based on level-set methods, we rigorously investigate how level sets change in response to new information locally sensed by a vehicle. The result is a dynamic fast marching algorithm that usually requires significantly less computation that would otherwise be the case. We demonstrate the proposed dynamic fast marching method in a successful field trial for which an autonomous surface vehicle navigated four kilometers through a riverine environment.
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    Genetic Improvement of Switchgrass Cell Wall Content, Leaf Angle and Flowering Time
    Xu, Bin (Virginia Tech, 2011-06-10)
    Switchgrass (Panicum virgatum L.) is a candidate bioenergy crop. Somatic embryogenic (SE) calli are used for genetic transformation in switchgrass. A superior switchgrass line, HR8, was developed using recurrent tissue culture selection from cv. Alamo. HR8 SE calli were genetically transformable using Agrobacterium at an efficiency of ~12%. We used HR8 somatic embryogenic calli for genetic improvement of switchgrass. The lignin content of feedstock has been proposed as one key trait impacting biofuel production. 4-Coumarate: Coenzyme A ligase (4CL) is one of the key enzymes involved in the monolignol biosynthetic pathway. Two homologous 4CL genes, Pv4CL1 and Pv4CL2, were identified in switchgrass. Gene expression patterns and enzymatic activity assays suggested that Pv4CL1 is involved in monolignol biosynthesis. Stable transgenic plants were obtained with Pv4CL1 down-regulated. RNA interference of Pv4CL1 reduced extractable 4CL activity by 80%, leading to a reduction in lignin content with decreased guaiacyl unit composition. The transgenic plants had uncompromised biomass yield. After dilute acid pretreatment, the low lignin transgenic biomass had significantly increased cellulose hydrolysis (saccharification) efficiency for biofuel production. Erect leaf is a desirable trait to adjust the overall plant architecture to perceive more solar energy and thereby to increase the plant biomass production in a field population. We overexpressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Surprisingly, AtLOV1 induced smaller leaf angle by changing morphologies of epidermal cells in the leaf collar region, affecting lignin content and monolignol composition, and also causing delayed flowering time in switchgrass. Global gene-expression analysis of AtLOV1 transgenic plants demonstrated an array of genes has altered expressions. Potential downstream genes involved in the pleiotropic phenotypic traits of the transgenic plants are discussed.
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    GPR30 regulates diet-induced adiposity in female mice and adipogenesis in vitro
    Wang, Aihua; Luo, Jing; Moore, William; Alkhalidy, Hana; Wu, Ling; Zhang, Jinhua; Zhen, Wei; Wang, Yao; Clegg, Deborah J.; Xu, Bin; Cheng, Zhiyong; McMillan, Ryan P.; Hulver, Matthew W.; Liu, Dongmin (Nature Publishing Group, 2016-10-04)
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    Hexameric Aggregation Nucleation Core Sequences and Diversity of Pathogenic Tau Strains
    Wu, Ling; Madhavan, Sidharth S.; Tan, Christopher; Xu, Bin (MDPI, 2022-12-19)
    Tau aggregation associates with multiple neurodegenerative diseases including Alzheimer’s disease and rare tauopathies such as Pick’s disease, progressive supranuclear palsy, and corticobasal degeneration. The molecular and structural basis of tau aggregation and related diverse misfolded tau strains are not fully understood. To further understand tau-protein aggregation mechanisms, we performed systematic truncation mutagenesis and mapped key segments of tau proteins that contribute to tau aggregation, where it was determined that microtubule binding domains R2 and R3 play critical roles. We validated that R2- or R3-related hexameric PHF6 and PHF6* peptide sequences are necessary sequences that render tau amyloidogenicity. We also determined that the consensus VQI peptide sequence is not sufficient for amyloidogenicity. We further proposed single- and dual-nucleation core-based strain classifications based on recent cryo-EM structures. We analyzed the structural environment of the hexameric peptide sequences in diverse tau strains in tauopathies that, in part, explains why the VQI consensus core sequence is not sufficient to induce tau aggregation. Our experimental work and complementary structural analysis highlighted the indispensible roles of the hexameric core sequences, and shed light on how the interaction environment of these core sequences contributes to diverse pathogenic tau-strains formation in various tauopathy brains.
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    Hypothalamic Transcriptional Profiling and Quantitative Proteomics of Mice under 24-Hour Fasting
    Jiang, Hao (Virginia Tech, 2014-06-27)
    Energy balance includes energy intake and energy expenditure. Either excessive food intake or insufficient physical activity will increase the body mass and cause obesity, a worldwide health problem. In the US, more than two-thirds of people are obesity or overweight. Conversely, it is well accepted that reducing energy intake can increase the life span and the resistance to age-related diseases. MicroRNAs are highly conserved non-coding RNA molecules with a length of 21-23 nucleotides. Recent studies show that numerous microRNAs are associated with the regulation of oxidative stress, inflammation, insulin signaling, apoptosis, and angiogenesis that relate to obesity. However, the role of microRNAs in the regulation of energy balance in central nervous system remains unknown, especially within the hypothalamus, a primary site of energy balance control. In this project, microRNA, and mRNA were profiled using microarray technology. Furthermore, quantitative proteomics were used to identify differential protein levels during fasting, and in a genetically obese mouse model, Mice were given either a 24-hour fast, or ad libitum access to food. Hypothalamic RNA and microRNA samples were analyzed by microarray, using both the Affymetrix and Toray 3D mRNA and microRNA platforms. No microRNAs were found to be differentially expressed between two treatments, whereas numerous mRNAs were significantly regulated by fasting, including 7 cell cycle related genes. Hypothalamic protein samples from WT and N2KO mice treated either to ad lib feeding or 24-hour fasting were analyzed by MSE quantitative proteomics. Over 650 proteins were identified with some proteins showing significantly different abundances between or among the four groups. Between ad lib fed WT and N2KO mice, 53 proteins were differentially expressed, with some of these linked to neurodegeneration, NAD synthesis, and the citrate acid cycle (TCA). Overall, the results of this study suggest that while microRNA-mediated mechanisms are not significant modulators of hypothalamic gene expression upon a 24 hour fast, cell cycle gene expression changes represent a major contributor to the fasting response. Moreover, Nlhl2 might play an important role in the neurodegeneration and mitochondrial metabolism.
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    Identification of a Dual-Action Small Molecule with Potent Anti-diabetic and Anti-obesity Activity
    Wang, Yao (Virginia Tech, 2019-11-22)
    Type 2 diabetes (T2D) is one of the fasting growing chronic diseases, caused by insulin resistance and pancreatic β-cell dysfunction. While over thirty medications were approved to treat T2D in the United States, less than one in four patients treated with anti-diabetic drugs achieved the glycemic target. Thus, identifying more effective anti-diabetic drugs is still needed for improving glycemic control in T2D patients. Incretins are gut hormones that possess potent insulinotropic action, which have drawn considerable attention in research and developing treatment strategy for T2D. Specifically, glucagon like peptide 1 (GLP-1), the most important incretin that is secreted from enteroendocrine L-cells in response to food ingestion, plays a vital role in maintaining glycemic homeostasis via potentiating glucose stimulated insulin secretion (GSIS) and promoting pancreatic β-cell proliferation and survival. Therefore, targeting L-cells to induce GLP-1 secretion would be an alternative strategy for treating T2D. The goal of this research was to identify low-cost and safe naturally occurring agents as a primary or adjuvant treatment for T2D. Here, I found that a small molecule, elenolic acid (EA), which was generated in our lab but is also present in mature olive and extra virgin olive oil, dose-dependently stimulated GLP-1 secretion in mouse clonal L-cells and isolated mouse ileum crypts. EA induced a rapid increase in intracellular [Ca2+]i and the production of inositol trisphosphate in L-cells, indicating that EA activates phospholipase C (PLC)-mediated signaling. Consistently, inhibition of (PLC) ablated EA-stimulated increase of [Ca2+]i and GLP-1 secretion in L-cells. In addition, EA-triggered GLP-1 secretion from L-cells was blocked by YM-254890, a Gαq inhibitor. Consistent with our in vitro study, a single dose of EA acutely stimulated GLP-1 secretion in mice, accompanied with an improved oral glucose tolerance. Chronic administration of EA restored the impaired glucose and lipid homeostasis in DIO mice, which may be partially due to promoting GLP-1 secretion and reduced hepatic gluconeogenesis. In addition, EA suppressed appetite, reduced food intake and gastric emptying rate, as well as promoted weight loss in obese mice, demonstrating that it is also an anti-obesity agent. Further, EA treatment reduced lipid absorption, and promoted hepatic fatty acid oxidation, and reversed abnormal plasma lipid profiles in DIO mice. Consistently, EA exerted potent anti-diabetic action in db/db mice, and its blood glucose-lowering effect is comparable with that of liraglutide in blood glycemic control but is better than that of metformin in this overt diabetic model. Collectively, I have identified for the first time, as to the best of our knowledge, that EA could be a dual-action compound that exerts anti-diabetic effects via activation of the GLP-1 mediated metabolic pathway and suppression of hepatic gluconeogenesis, leading to effective control on food intake, body weight gain, and glycemia in T2D mice.
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    Insights into Mechanisms of Amyloid Toxicity:  Molecular Dynamics Simulations of the Amyloid andbeta-peptide (Aandbeta) and Islet Amyloid Polypeptide (IAPP)
    Brown, Anne M. (Virginia Tech, 2016-04-07)
    Aggregation of proteins into amyloid deposits is a common feature among dozens of diseases. Two such diseases that feature amyloid deposits are Alzheimer's disease (AD) and type 2 diabetes (T2D). AD toxicity has been associated with the aggregation and accumulation of the amyloid β-peptide (Aβ); Aβ exerts its toxic effects through interactions with neuronal cell membranes. A characteristic feature of T2D is the deposition of the islet amyloid polypeptide (IAPP) in the pancreatic islets of Langerhans. It is currently unknown if IAPP aggregation is a cause or consequence of T2D, but it does lead to β-cell dysfunction and death, exacerbating the effects of diabetes. Characterizing the fundamental interactions between both Aβ and IAPP with lipid membranes and in solution will give greater insight into mechanisms of toxicity exhibited by amyloid proteins. In this work, molecular dynamics (MD) simulations were used to study the secondary, tertiary, and quatnary structure of Aβ and IAPP, in addition to peptide-membrane interactions and membrane perturbation as independently caused by both peptides. Studies were conducted to address the following questions: (1) what influence do solution conditions and oxidation state have on monomeric Aβ] (2) how and in what way does monomeric Aβ interact with model lipid membranes and what role does sequence play on these peptide-membrane interactions; (3) can MD simulations be utilized to understand Aβ tetramer formation, rearrangement, and tetramer-membrane interactions; (4) how does IAP interact with model membranes and how does that vary from non-toxic (rat) IAPP peptide-membrane interactions. These studies led to conclusions that showed variance in lipid affinity and degree of perturbation as based on peptide sequence, in addition to insight into the type of perturbation caused to membranes by these amyloid peptides. Understanding the differences in peptide-membrane interactions of amyloidogenic and non-amyloidogenic (rat) peptides gave insight into the overall mechanism of amyloidogenicity, leading to the detection of specific amino acids essential in peptide-membrane perturbation. These residues can then be targeted for novel therapeutic design to attenuate the perturbation and potential cell death as caused by these peptides.
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    Modulation of Innate Immune Cell Signaling Pathways by Staphylococcus aureus and Omnigen-AF®
    Johnson, Anne Caitlin (Virginia Tech, 2013-11-08)
    Staphylococcus aureus causes chronic mastitis in bovines that is difficult to treat with current therapeutics. The goal of this research is to provide information about and improve innate immune responses to infection. Infection can result in host cell apoptosis or programmed cell death. Many pathogens can inhibit apoptosis; thereby acquiring a replicative niche, a reprieve from immune responses, and an escape from treatments. We hypothesize that S. aureus inhibits apoptosis in dendritic cells (DC). To investigate our hypothesis, DC were infected with live S. aureus (LSA), γ-irradiated S. aureus (ISA), or Streptococcus agalactiae (Strep ag.) for 2 hours. Stimulations of DC included ultraviolet light (UV) and lipoteichoic acid (LTA). Results indicate that γ-irradiated S. aureus can inhibit UV-induced apoptosis by upregulating LTA. This research provides information about S. aureus infections, but further research is needed to improve responses to this type of infection. One way to improve innate immune responses to infection is by supplementing bovines with OmniGen-AF®, a probiotic that restores neutrophil function during immunosuppression. To determine the mechanism by which OmniGen-AF® functions, wildtype, MyD88 KO, and TLR4 KO mice were fed either normal chow or supplemented with OmniGen-AF® for two weeks. Mice were immunosuppressed with dexamethasone and challenged with LTA. LTA overcame immunosuppression in a TLR4-depenent manner regardless of supplementation with OmniGen-AF®. Overall this research supplies knowledge about S. aureus inhibition of apoptosis in DC and S. aureus LTA activation of PMN regardless of immunosuppression or supplementation with OmniGen-AF®.
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    Modulation of Neutrophil Functions and Anti-Tumor Immune Responses by Innate Suppressors
    Lee, Christina K. (Virginia Tech, 2018-12-04)
    Neutrophils are known to be key innate defenders through performing vital and diverse functions such as degranulation, oxidative burst, and generation of extracellular trap (NET). Recent data suggest that neutrophils may also play key roles in modulating tissue inflammatory/immune environment by secreting soluble mediators as well as surface-attached co-activators. Furthermore, neutrophils may adopt distinct functional states either conducive or detrimental for tumor-growth through cellular contact with cancer cells and/or other immune cells such as T helper cells. However, molecular mechanisms that modulate functional adaptations of neutrophils are not well understood. The objective of my thesis is to identify the role of Tollip, a novel TLR signaling adaptor molecule, in modulating neutrophil functions by suppressing the inflammatory signaling pathway. Preliminary data from our lab suggest Tollip deficient neutrophils may be programed to exhibit enhanced anti-tumor activities. Based on these novel findings, I tested the hypothesis that neutrophils also have subsets with different functions similar to monocyte/macrophages, and Tollip deficient neutrophils may be programmed into an enhanced anti-tumor state through upregulating inflammatory signaling processes and mediators.
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    Non-resolving pro-inflammatory macrophage polarization by super-low doses of bacterial endotoxin
    Rahtes, Allison Anne (Virginia Tech, 2020-01-10)
    Subclinical endotoxemia (low levels of circulating bacterial endotoxin) has been observed in patients suffering from chronic inflammatory diseases such as atherosclerosis, diabetes, and obesity. However, the link between this condition and chronic inflammation is poorly understood. Previous work from our lab has shown that chronic exposure to super-low doses of bacterial endotoxin (LPS) aggravates atherosclerosis resulting in increased plaque size and instability in a macrophage-dependent manner in a mouse model of atherosclerosis. Further, we showed that super-low dose LPS (SLD-LPS) treatment was able to inhibit lysosomal fusion in immortalized macrophages. However, this was done under more acute treatment conditions. The aim of this project was to examine the molecular mechanisms by which chronic SLD-LPS may polarize macrophages to a non-resolving pro-inflammatory state consistent with chronic inflammation. This was carried out in two projects, the first a more broad phenotypic paper showing the disruption in homeostasis by chronic SLD-LPS in immortalized macrophages, while the second uses primary bone marrow-derived mouse macrophages to identify specific molecular signaling pathways used by chronic SLD-LPS. Here we show that chronic SLD-LPS led to the novel upregulation of pro-inflammatory mediators p62 and ccl2 with simultaneous downregulation of homeostatic mediators Nrf2 and slc40a1 in immortalized wild-type mouse macrophages. Further we showed this effect was reversed using the homeostatic restorative agent sodium phenylbutyrate (4-PBA), a newly reported activity for this reagent in mouse macrophages. This indicated that a disruption in homeostasis, possibly involving autophagy, may be responsible for the non-resolving pro-inflammatory polarization of macrophages. Therefore, in our second project, we further explored the effect of chronic SLD-LPS treatment on the homeostatic arm of the response by focusing on the Nrf2 inhibitor Keap1. Here we show that chronic SLD-LPS results in an accumulation of Keap1 in mouse bone marrow-derived macrophages, an effect specific to chronic SLD-LPS, as high doses of LPS failed to induce Keap1. We suggest that this effect may be related to a disruption in lysosomal fusion as evidenced by accumulation of autophagy flux markers MLKL and p62. Further, we show that these effects are dependent on the non-traditional TLR4 adaptor TRAM, suggesting an alternative dose-dependent signaling pathway for LPS. Together this work identifies novel signaling mechanisms involved in non-resolving pro-inflammatory polarization of murine macrophages, providing new insight behind how chronic super-low dose LPS exposure may lead to chronic inflammation.
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    O-GlcNAcylation of SIRT1 Protects against Cold Stress-Induced Skeletal Muscle Damage via Amelioration of Mitochondrial Homeostasis
    Cao, Yu; Zhang, Meng; Li, Ye; Lu, Jingjing; Zhou, Wanhui; Li, Xiaoshuang; Shi, Hao; Xu, Bin; Li, Shize (MDPI, 2022-11-22)
    Cold stress disturbs cellular metabolic and energy homeostasis, which is one of the causes of stress-induced illnesses. O-GlcNAcylation is a nutrient-sensing pathway involved in a myriad of cellular processes. It plays a key role in metabolic homeostasis. Nevertheless, a specific sensing mechanism linking skeletal muscle to O-GlcNAcylation in cold stress is unknown. In this study, O-GlcNAcylation of SIRT1 was targeted to explore the mechanism of skeletal muscle adaptation to cold stress. Ogt mKO aggravated skeletal muscle fibrosis induced by cold stress. At the same time, Ogt gene deletion accelerated the homeostasis imbalance and oxidative stress of skeletal muscle mitochondria induced by cold stress. In vitro results showed that inhibition of SIRT1’s O-GlcNAcylation accelerated mild hypothermia induced mitochondrial homeostasis in mouse myogenic cells (C2C12 cells). However, overexpression of SIRT1’s O-GlcNAcylation improved the above phenomena. Thus, these results reveal a protective role of OGT-SIRT1 in skeletal muscle’s adaptation to cold stress, and our findings will provide new avenues to combat stress-induced diseases.
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    An olive-derived elenolic acid stimulates hormone release from L-cells and exerts potent beneficial metabolic effects in obese diabetic mice
    Wang, Yao; Wu, Yajun; Wang, Aiping; Wang, Aihua; Alkhalidy, Hana; Helm, Richard; Zhang, Shijun; Ma, Hongguang; Zhang, Yan; Gilbert, Elizabeth R.; Xu, Bin; Liu, Dongmin (Frontiers, 2022-11-01)
    Insulin resistance and progressive decline in functional β-cell mass are two key factors for developing type 2 diabetes (T2D), which is largely driven by overweight and obesity, a significant obstacle for effective metabolic control in many patients with T2D. Thus, agents that simultaneously ameliorate obesity and act on multiple pathophysiological components could be more effective for treating T2D. Here, we report that elenolic acid (EA), a phytochemical, is such a dual-action agent. we show that EA dose-dependently stimulates GLP-1 secretion in mouse clonal L-cells and isolated mouse ileum crypts. In addition, EA induces L-cells to secrete peptide YY (PYY). EA induces a rapid increase in intracellular [Ca2+]i and the production of inositol trisphosphate in L-cells, indicating that EA activates phospholipase C (PLC)-mediated signaling. Consistently, inhibition of (PLC) or Gαq ablates EA-stimulated increase of [Ca2+]i and GLP-1 secretion. In vivo, a single dose of EA acutely stimulates GLP-1 and PYY secretion in mice, accompanied with an improved glucose tolerance and insulin levels. Oral administration of EA at a dose of 50 mg/kg/day for 2 weeks normalized the fasting blood glucose and restored glucose tolerance in high-fat diet-induced obese (DIO) mice to levels that were comparable to chow-fed mice. In addition, EA suppresses appetite, reduces food intake, promotes weight loss, and reverses perturbated metabolic variables in obese mice. These results suggest that EA could be a dual-action agent as an alternative or adjuvant treatment for both T2D and obesity.
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    Overcoming Biomass Recalcitrance by Combining Genetically Modified Switchgrass and Cellulose Solvent-Based Lignocellulose Pretreatment
    Sathitsuksanoh, Noppadon; Xu, Bin; Zhao, Bingyu Y.; Zhang, Y. H. Percival (2013-09-27)
    Decreasing lignin content of plant biomass by genetic engineering is believed to mitigate biomass recalcitrance and improve saccharification efficiency of plant biomass. In this study, we compared two different pretreatment methods (i.e., dilute acid and cellulose solvent) on transgenic plant biomass samples having different lignin contents and investigated biomass saccharification efficiency. Without pretreatment, no correlation was observed between lignin contents of plant biomass and saccharification efficiency. After dilute acid pretreatment, a strong negative correlation between lignin content of plant samples and overall glucose release was observed, wherein the highest overall enzymatic glucan digestibility was 70% for the low-lignin sample. After cellulose solvent- and organic solvent-based lignocellulose fractionation pretreatment, there was no strong correlation between lignin contents and high saccharification efficiencies obtained (i.e., 80-90%). These results suggest that the importance of decreasing lignin content in plant biomass to saccharification was largely dependent on pretreatment choice and conditions.
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    Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering Time
    Xu, Bin; Sathitsuksanoh, Noppadon; Tang, Yuhong; Udvardi, Michael K.; Zhang, Ji-Yi; Shen, Zhengxing; Balota, Maria; Harich, Kim; Zhang, Y. H. Percival; Zhao, Bingyu Y. (2012-12-26)
    Background: Switchgrass (Panicum virgatum L.) is a prime candidate crop for biofuel feedstock production in the United States. As it is a self-incompatible polyploid perennial species, breeding elite and stable switchgrass cultivars with traditional breeding methods is very challenging. Translational genomics may contribute significantly to the genetic improvement of switchgrass, especially for the incorporation of elite traits that are absent in natural switchgrass populations. Methodology/Principal Findings: In this study, we constitutively expressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Overexpression of AtLOV1 in switchgrass caused the plants to have a smaller leaf angle by changing the morphology and organization of epidermal cells in the leaf collar region. Also, overexpression of AtLOV1 altered the lignin content and the monolignol composition of cell walls, and caused delayed flowering time. Global gene-expression analysis of the transgenic plants revealed an array of responding genes with predicted functions in plant development, cell wall biosynthesis, and flowering. Conclusions/Significance: To our knowledge, this is the first report of a single ectopically expressed transcription factor altering the leaf angle, cell wall composition, and flowering time of switchgrass, therefore demonstrating the potential advantage of translational genomics for the genetic improvement of this crop.
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    Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
    Yan, Haidong; Sun, Min; Zhang, Zhongren; Jin, Yarong; Zhang, Ailing; Lin, Chuang; Wu, Bingchao; He, Min; Xu, Bin; Wang, Jing; Qin, Peng; Mendieta, John Pablo; Nie, Gang; Wang, Jianping; Jones, Chris S. S.; Feng, Guangyan; Srivastava, Rakesh K. K.; Zhang, Xinquan; Bombarely, Aureliano; Luo, Dan; Jin, Long; Peng, Yuanying; Wang, Xiaoshan; Ji, Yang; Tian, Shilin; Huang, Linkai (Nature Portfolio, 2023-03)
    Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate. A graph-based pan-genome constructed using de novo genome assemblies of ten pearl millet accessions adapted to different climates worldwide identifies structural variations and their contribution to heat tolerance in pearl millet.
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    siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass
    Yan, Haidong; Bombarely, Aureliano; Xu, Bin; Frazier, Taylor P.; Wang, Chengran; Chen, Peilin; Chen, Jing; Hasing, Tomas; Cui, Chenming; Zhang, Xinquan; Zhao, Bingyu Y.; Huang, Linkai (2018-07-24)
    Background Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. Results We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar ‘Alamo’ using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. Conclusions This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.