SurR is a master regulator of the primary electron flow pathways in the order Thermococcales: SurR controls electron flow pathways in thermococcales
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Biochemistry & Molecular Biology↗
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Results for “REGULATION”
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Anaerobic benzene oxidation in Geotalea daltonii involves activation by methylation and is regulated by the transition state regulator AbrB
ABSTRACT Benzene is a widespread groundwater contaminant that persists under anoxic conditions. The aim of this study was to more accurately investigate anaerobic microbial degradation pathways to predict benzene fate and transport. Preliminary genomic analysis of Geotalea daltonii strain FRC-32, isolated from contaminated groundwater, revealed the presence of putative aromatic-degrading genes. G. daltonii was subsequently shown to conserve energy for growth on benzene as the sole electron donor and fumarate or nitrate as the electron acceptor. The hbs gene, encoding for 3-hydroxybenzylsuccinate synthase (Hbs), a homolog of the radical-forming, toluene-activating benzylsuccinate synthase (Bss), was upregulated during benzene oxidation in G. daltonii , while the bss gene was upregulated during toluene oxidation. Addition of benzene to the G. daltonii whole-cell lysate resulted in toluene formation, indicating that methylation of benzene was occurring. Complementation of σ 54 - (deficient) E. coli transformed with the bss operon restored its ability to grow in the presence of toluene, revealing bss to be regulated by σ 54 . Binding sites for σ 70 and the transition state regulator AbrB were identified in the promoter region of the σ 54 -encoding gene rpoN, and binding was confirmed. Induced expression of abrB during benzene and toluene degradation caused G. daltonii cultures to transition to the death phase. Our results suggested that G. daltonii can anaerobically oxidize benzene by methylation, which is regulated by σ 54 and AbrB. Our findings further indicated that the benzene, toluene, and benzoate degradation pathways converge into a single metabolic pathway, representing a uniquely efficient approach to anaerobic aromatic degradation in G. daltonii . IMPORTANCE The contamination of anaerobic subsurface environments including groundwater with toxic aromatic hydrocarbons, specifically benzene, toluene, ethylbenzene, and xylene, has become a global issue. Subsurface groundwater is largely anoxic, and further study is needed to understand the natural attenuation of these compounds. This study elucidated a metabolic pathway utilized by the bacterium Geotalea daltonii capable of anaerobically degrading the recalcitrant molecule benzene using a unique activation mechanism involving methylation. The identification of aromatic-degrading genes and AbrB as a regulator of the anaerobic benzene and toluene degradation pathways provides insights into the mechanisms employed by G. daltonii to modulate metabolic pathways as necessary to thrive in anoxic contaminated groundwater. Our findings contribute to the understanding of novel anaerobic benzene degradation pathways that could potentially be harnessed to develop improved strategies for bioremediation of groundwater contaminants.
Bullows, James E.↗
Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica
Many yeasts undergo a morphological transition from yeast-to-hyphal growth in response to environmental conditions. We used forward and reverse genetic techniques to identify genes regulating this transition in Yarrowia lipolytica . We confirmed that the transcription factor Yl msn2 is required for the transition to hyphal growth and found that signaling by the histidine kinases Yl chk1 and Yl nik1 as well as the MAP kinases of the HOG pathway (Yl ssk2 , Yl pbs2 , and Yl hog1 ) regulates the transition to hyphal growth. These results suggest that Y. lipolytica transitions to hyphal growth in response to stress through multiple kinase pathways. Intriguingly, we found that a repetitive portion of the genome containing telomere-like and rDNA repeats may be involved in the transition to hyphal growth, suggesting a link between this region and the general stress response.
59 BASIC BIOLOGICAL SCIENCES↗
A distal 594 bp ECR specifies Hmx1 expression in pinna and lateral facial morphogenesis and is regulated by the Hox-Pbx-Meis complex
Hmx1 encodes a homeodomain transcription factor expressed in the developing lateral craniofacial mesenchyme, retina and sensory ganglia. Mutation or mis-regulation of Hmx1 underlies malformations of the eye and external ear in multiple species. Deletion or insertional duplication of an evolutionarily conserved region (ECR) downstream of Hmx1 has recently been described in rat and cow, respectively. Here, we demonstrate that the impact of Hmx1 loss is greater than previously appreciated, with a variety of lateral cranioskeletal defects, auriculofacial nerve deficits, and duplication of the caudal region of the external ear. Using a transgenic approach, we demonstrate that a 594 bp sequence encompassing the ECR recapitulates specific aspects of the endogenous Hmx1 lateral facial expression pattern. Moreover, we show that Hoxa2, Meis and Pbx proteins act cooperatively on the ECR, via a core 32 bp sequence, to regulate Hmx1 expression. In conclusion, these studies highlight the conserved role for Hmx1 in BA2-derived tissues and provide an entry point for improved understanding of the causes of the frequent lateral facial birth defects in humans.
59 BASIC BIOLOGICAL SCIENCES↗
Data for The Stem Cell-Type Transcriptome of Bioenergy Sorghum Reveals the Spatial Regulation of Secondary Cell Wall Networks
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.
Software↗
A Real-Time Greedy-Index Dispatching Policy for using PEVs to Provide Frequency Regulation Service
This article presents a real-time greedy-index dispatching policy (GIDP) for using plug-in electric vehicles (PEVs) to provide frequency regulation services. A new service cost allocation mechanism is proposed to award PEVs based on the amount of service they provided, while considering compensations for delayed-charging and reduction of battery lifetime due to participation of the service. The GIDP transforms the optimal dispatch problem from a high-dimensional space into a one-dimensional space while preserving the solution optimality. When solving the transformed problem in real-time, the global optimality of the GIDP solution can be guaranteed by mathematically proved “indexability”. Because the GIDP index can be calculated upon the PEV’s arrival and used for the entire decision making process till its departure, the computational burden is minimized and the complexity of the aggregator dispatch process is significantly reduced. Finally, simulation results are used to evaluate the proposed GIDP, and to demonstrate the potential profitability from providing frequency regulation service by using PEVs.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Valve Regulated Lead Acid Battery Evaluation under Peak Shaving and Frequency Regulation Duty Cycles
This work highlights the performance metrics and the fundamental degradation mechanisms of lead-acid battery technology and maps these mechanisms to generic duty cycles for peak shaving and frequency regulation grid services. Four valve regulated lead acid batteries have been tested for two peak shaving cycles at different discharge rates and two frequency regulation duty cycles at different SOC ranges. Reference performance and pulse resistance tests are done periodically to evaluate battery degradation over the time. The results of the studies are expected to provide a valuable understanding of lead acid battery technology suitability for grid energy-storage applications.
25 ENERGY STORAGE↗
Status of French regulation regulations concerning nuclear criticality safety - 14585
Hitherto, in France, licensees used to demonstrate compliance with Fundamental Safety Rule I.3.c. This Rule sets out the principles for demonstrating Nuclear Criticality Safety in all nuclear facilities (excluding reactors). Although there is a good level of consensus between the licensees and the Regulator, this Rule is now somewhat dated (it came into force in 1984) and does not cover all aspects. The French Nuclear Safety Authority (ASN) used the 2006 Law on Transparency and Nuclear Safety as the catalyst for a thorough revision and updating of its regulatory documentation. Thus, in 2010, ASN decided to set up a 'criticality working group' involving ASN, the licensees (AREVA, CEA, EDF...) and the Technical Safety Organization (IRSN). This group was tasked with drafting a regulatory text (a 'resolution') and a criticality guide. The objectives were to update Rule I.3.c, clearly defining the scope for reactors and transport packages of fissile material, to further develop areas not covered in the existing rule and to take account of the feedback and lessons learned from past events. Thus, this paper presents the status of French regulations concerning Nuclear Criticality Safety (NCS). Firstly, it focuses on the existing Rule I.3.c and then explains how this will be modified by the forthcoming improvements to the resolution and the criticality guide. It in particular addresses the scope of the new regulations (concerning reactors and the transport of fissile material), how the principle of defence in depth is to be applied to criticality safety, the double contingency principle, control modes, the reference fissile medium, the organization, the role of the Criticality Engineer, admissibility criteria, validation, etc. (authors)
42 ENGINEERING↗
Lactoferrin inhibits dexamethasone-induced chondrocyte impairment from osteoarthritic cartilage through up-regulation of extracellular signal-regulated kinase 1/2 and suppression of FASL, FAS, and Caspase 3
Highlights: •Dex exerts dose-dependant inhibition of HACs viability and induction of apoptosis. •Dex-induced impairment of chondrocytes was attenuated by rhLF. •ERK and FASL/FAS signaling are involved in the effects of rhLF. •OA patients with glucocorticoid-induced cartilage damage may benefit from treatment with rhLF. -- Abstract: Dexamethasone (Dex) is commonly used for osteoarthritis (OA) with excellent anti-inflammatory and analgesic effect. However, Dex also has many side effects following repeated use over prolonged periods mainly through increasing apoptosis and inhibiting proliferation. Lactoferrin (LF) exerts significantly anabolic effect on many cells and little is known about its effect on OA chondrocytes. Therefore, the aim of this study is to investigate whether LF can inhibit Dex-induced OA chondrocytes apoptosis and explore its possible molecular mechanism involved in. MTT assay was used to determine the optimal concentration of Dex and recombinant human LF (rhLF) on chondrocytes at different time and dose points. Chondrocytes were then stimulated with Dex in the absence or presence of optimal concentration of rhLF. Cell proliferation and viability were evaluated using MTT and LIVE/DEAD assay, respectively. Cell apoptosis was evaluated by multi-parameter apoptosis assay kit using both confocal microscopy and flow cytometry, respectively. The expression of extracellular signal-regulated kinase (ERK), FAS, FASL, and Caspase-3 (CASP3) at the mRNA and protein levels were examined by real-time polymerase chain reaction (PCR) and immunocytochemistry, respectively. The optimal concentration of Dex (25 μg/ml) and rhLF (200 μg/ml) were chosen for the following experiments. rhLF significantly reversed the detrimental effect of Dex on chondrocytes proliferation, viability, and apoptosis. In addition, rhLF significantly prevented Dex-induced down-regulation of ERK and up-regulation of FAS, FASL, and CASP3. These findings demonstrated that rhLF acts as an anabolic effect on chondrocytes through significantly reversing Dex-induced chondrocytes apoptosis. This study may contribute to further investigating the clinical application of LF on OA.
60 APPLIED LIFE SCIENCES↗
Numb positively regulates autophagic flux via regulating lysosomal function
Autophagy is a lysosome-dependent catabolic process involving in the degradation and recycling of unnecessary or damaged proteins and organelles. Emerging evidence indicates that autophagy dysfunction is closely related to various human diseases including cancer, aging, myopathies and neurodegenerative disorders. Here, using genetic knockdown, we uncover the role of Numb, an endocytic adaptor protein, in regulating the late steps of autophagy. We found that Numb depletion led to the accumulation of autophagic vacuole, as verified by RFP-LC3 staining combined with transmission electron microscopy. Further investigation indicated that Numb depletion impaired autophagic degradation through inhibiting the activities of lysosomal enzymes (Cathepsin D, β-glucuronidase and β-glucosidase). Moreover, Numb depletion induced elevation of lysosomal pH values and decrease of glycosylated lysosome-associated membrane proteins. We further observed that Rab7 activity was inhibited in Numb-depleted cells. Together, our findings revealed a novel function of Numb and its likely mechanism in regulation of autophagy events. - Highlights: • Numb depletion induces the accumulation of autophagic vacuole in MCF-7 cells. • Numb depletion impairs autophagic degradation and lysosomal enzymes activities. • Numb depletion elevates lysosomal pH but decreases glycosylated LAMPs. • Numb may regulate lysosome maturation by facilitating Rab7 activation.
60 APPLIED LIFE SCIENCES↗
Down-regulated lncRNA MEG3 promotes osteogenic differentiation of human dental follicle stem cells by epigenetically regulating Wnt pathway
Our previous long noncoding RNA (lncRNA) microarray results showed that lncRNA MEG3 (maternally expressed 3) was significantly downregulated in human dental follicle cells than human periodontal ligament cells. Latest studies show that MEG3 contributes to polycomb repressive complex 2 (PRC2) recruitment to silence gene expression. The enhancer of zeste homolog 2 (EZH2), a crucial catalytic subunit of PRC2, mediates gene silencing and participates in cell lineage determination via methyltransferase activity. In this study, we found that the expression of EZH2 and H3K27me3 (trimethylation on lysine 27 in histone H3) decreased during osteogenesis of human dental follicle stem cells (hDFSCs). Knockdown studies of MEG3 and EZH2 by siRNA showed that MEG3/EZH2 negatively regulated osteogenesis of hDFSCs. We investigated the role of Wnt signaling pathway during the osteogenesis of hDFSCs and its relationship with EZH2. Besides, we studied the key genes of the canonical/noncanonical Wnt signaling pathway which might be related to EZH2. ChIP (chromatin immunoprecipitation) analysis showed that these effects were due to the EZH2 regulation of H3K27me3 level on the Wnt genes promotors. We first demonstrated that the decrease of MEG3 or EZH2 activated the Wnt/β-catenin signaling pathway via epigenetically regulating the H3K27me3 level on the Wnt genes promotors. Our research offers a new target for periodontal tissue engineering and osteogenic tissue regeneration.
60 APPLIED LIFE SCIENCES↗
Mitotic regulators and the SHP2-MAPK pathway promote IR endocytosis and feedback regulation of insulin signaling
Insulin controls glucose homeostasis and cell growth through bifurcated signaling pathways. Dysregulation of insulin signaling is linked to diabetes and cancer. The spindle checkpoint controls the fidelity of chromosome segregation during mitosis. Here, we show that insulin receptor substrate 1 and 2 (IRS1/2) cooperate with spindle checkpoint proteins to promote insulin receptor (IR) endocytosis through recruiting the clathrin adaptor complex AP2 to IR. A phosphorylation switch of IRS1/2 orchestrated by extracellular signal-regulated kinase 1 and 2 (ERK1/2) and Src homology phosphatase 2 (SHP2) ensures selective internalization of activated IR. SHP2 inhibition blocks this feedback regulation and growth-promoting IR signaling, prolongs insulin action on metabolism, and improves insulin sensitivity in mice. We propose that mitotic regulators and SHP2 promote feedback inhibition of IR, thereby limiting the duration of insulin signaling. Targeting this feedback inhibition can improve insulin sensitivity.
59 BASIC BIOLOGICAL SCIENCES↗
Cardiac myosin filaments are directly regulated by calcium
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Ma, Weikang↗
The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii
The accumulation of carbon storage compounds by many unicellular algae after nutrient deprivation occurs despite declines in their photosynthetic apparatus. To understand the regulation and roles of photosynthesis during this potentially bioenergetically valuable process, we analyzed photosynthetic structure and function after nitrogen deprivation in the model alga Chlamydomonas reinhardtii. Transcriptomic, proteomic, metabolite, and lipid profiling and microscopic time course data were combined with multiple measures of photosynthetic function. Levels of transcripts and proteins of photosystems I and II and most antenna genes fell with differing trajectories; thylakoid membrane lipid levels decreased, while their proportions remained similar and thylakoid membrane organization appeared to be preserved. Cellular chlorophyll (Chl) content decreased more than 2-fold within 24 h, and we conclude from transcript protein and 13 C labeling rates that Chl synthesis was down-regulated both pre- and posttranslationally and that Chl levels fell because of a rapid cessation in synthesis and dilution by cellular growth rather than because of degradation. Photosynthetically driven oxygen production and the efficiency of photosystem II as well as P700 + reduction and electrochromic shift kinetics all decreased over the time course, without evidence of substantial energy overflow. The results also indicate that linear electron flow fell approximately 15% more than cyclic flow over the first 24 h. Comparing Calvin-Benson cycle transcript and enzyme levels with changes in photosynthetic 13 CO 2 incorporation rates also pointed to a coordinated multilevel down-regulation of photosynthetic fluxes during starch synthesis before the induction of high triacylglycerol accumulation rates.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of the Francisella response regulator QseB receiver domain, and characterization of QseB inhibition by antibiofilm 2-aminoimidazole-based compounds: Inhibition of response regulator QseB by antibiofilm compounds
With antibiotic resistance increasing at alarming rates, targets for new antimicrobial therapies must be identified. A particularly promising target is the bacterial two-component system. Two-component systems allow bacteria to detect, evaluate and protect themselves against changes in the environment, such as exposure to antibiotics and also to trigger production of virulence factors. Drugs that target the response regulator portion of two-component systems represent a potent new approach so far unexploited. Here, we focus efforts on the highly virulent bacterium Francisella tularensis tularensis. Francisella contains only three response regulators, making it an ideal system to study. In this study, we initially present the structure of the N-terminal domain of QseB, the response regulator responsible for biofilm formation. Subsequently, using binding assays, computational docking and cellular studies, we show that QseB interacts with2-aminoimidazole based compounds that impede its function. This information will assist in tailoring compounds to act as adjuvants that will enhance the effect of antibiotics.
60 APPLIED LIFE SCIENCES↗
Network-based approaches for understanding gene regulation and function in plants
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Plant Sciences↗
Sostdc1 Regulates NK Cell Maturation and Cytotoxicity [Sostdc1 regulates natural killer cell maturation and cytotoxicity]
NK cells are innate-like lymphocytes that eliminate virally infected and cancerous cells, but the mechanisms that control NK cell development and cytotoxicity are incompletely understood. We identified roles for sclerostin domain–containing-1 ( Sostdc1 ) in NK cell development and function. Sostdc1 -knockout ( Sostdc1 –/– ) mice display a progressive accumulation of transitional NK cells (tNKs) (CD27 + CD11b + ) with age, indicating a partial developmental block. The NK cell Ly49 repertoire in Sostdc1 –/– mice is also changed. Lower frequencies of Sostdc1 –/– splenic tNKs express inhibitory Ly49G2 receptors, but higher frequencies express activating Ly49H and Ly49D receptors. Yet, the frequencies of Ly49I + , G2 + , H + , and D + populations were universally decreased at the most mature (CD27 – CD11b + ) stage. We theorized that the Ly49 repertoire in Sostdc1 –/– mice would correlate with NK killing ability and observed that Sostdc1 –/– NK cells are hyporesponsive against MHC class I–deficient cell targets in vitro and in vivo, despite higher CD107a surface levels and similar IFN-γ expression to controls. Consistent with Sostdc1’s known role in Wnt signaling regulation, Tcf7 and Lef1 levels were higher in Sostdc1 –/– NK cells. Expression of the NK development gene Id2 was decreased in Sostdc1 –/– immature NK and tNK cells, but Eomes and Tbx21 expression was unaffected. Reciprocal bone marrow transplant experiments showed that Sostdc1 regulates NK cell maturation and expression of Ly49 receptors in a cell-extrinsic fashion from both nonhematopoietic and hematopoietic sources. Taken together, these data support a role for Sostdc1 in the regulation of NK cell maturation and cytotoxicity, and identify potential NK cell niches.
59 BASIC BIOLOGICAL SCIENCES↗