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Sample records for tca cycle function

  1. TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

    PubMed

    Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

    2016-01-21

    Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. PMID:26725009

  2. A Process-Based Model of TCA Cycle Functioning to Analyze Citrate Accumulation in Pre- and Post-Harvest Fruits.

    PubMed

    Etienne, Audrey; Génard, Michel; Bugaud, Christophe

    2015-01-01

    Citrate is one of the most important organic acids in many fruits and its concentration plays a critical role in organoleptic properties. The regulation of citrate accumulation throughout fruit development, and the origins of the phenotypic variability of the citrate concentration within fruit species remain to be clarified. In the present study, we developed a process-based model of citrate accumulation based on a simplified representation of the TCA cycle to predict citrate concentration in fruit pulp during the pre- and post-harvest stages. Banana fruit was taken as a reference because it has the particularity of having post-harvest ripening, during which citrate concentration undergoes substantial changes. The model was calibrated and validated on the two stages, using data sets from three contrasting cultivars in terms of citrate accumulation, and incorporated different fruit load, potassium supply, and harvest dates. The model predicted the pre and post-harvest dynamics of citrate concentration with fairly good accuracy for the three cultivars. The model suggested major differences in TCA cycle functioning among cultivars during post-harvest ripening of banana, and pointed to a potential role for NAD-malic enzyme and mitochondrial malate carriers in the genotypic variability of citrate concentration. The sensitivity of citrate accumulation to growth parameters and temperature differed among cultivars during post-harvest ripening. Finally, the model can be used as a conceptual basis to study citrate accumulation in fleshy fruits and may be a powerful tool to improve our understanding of fruit acidity. PMID:26042830

  3. A Process-Based Model of TCA Cycle Functioning to Analyze Citrate Accumulation in Pre- and Post-Harvest Fruits

    PubMed Central

    Etienne, Audrey; Génard, Michel; Bugaud, Christophe

    2015-01-01

    Citrate is one of the most important organic acids in many fruits and its concentration plays a critical role in organoleptic properties. The regulation of citrate accumulation throughout fruit development, and the origins of the phenotypic variability of the citrate concentration within fruit species remain to be clarified. In the present study, we developed a process-based model of citrate accumulation based on a simplified representation of the TCA cycle to predict citrate concentration in fruit pulp during the pre- and post-harvest stages. Banana fruit was taken as a reference because it has the particularity of having post-harvest ripening, during which citrate concentration undergoes substantial changes. The model was calibrated and validated on the two stages, using data sets from three contrasting cultivars in terms of citrate accumulation, and incorporated different fruit load, potassium supply, and harvest dates. The model predicted the pre and post-harvest dynamics of citrate concentration with fairly good accuracy for the three cultivars. The model suggested major differences in TCA cycle functioning among cultivars during post-harvest ripening of banana, and pointed to a potential role for NAD-malic enzyme and mitochondrial malate carriers in the genotypic variability of citrate concentration. The sensitivity of citrate accumulation to growth parameters and temperature differed among cultivars during post-harvest ripening. Finally, the model can be used as a conceptual basis to study citrate accumulation in fleshy fruits and may be a powerful tool to improve our understanding of fruit acidity. PMID:26042830

  4. Dysfunctional TCA-Cycle Metabolism in Glutamate Dehydrogenase Deficient Astrocytes.

    PubMed

    Nissen, Jakob D; Pajęcka, Kamilla; Stridh, Malin H; Skytt, Dorte M; Waagepetersen, Helle S

    2015-12-01

    Astrocytes take up glutamate in the synaptic area subsequent to glutamatergic transmission by the aid of high affinity glutamate transporters. Glutamate is converted to glutamine or metabolized to support intermediary metabolism and energy production. Glutamate dehydrogenase (GDH) and aspartate aminotransferase (AAT) catalyze the reversible reaction between glutamate and α-ketoglutarate, which is the initial step for glutamate to enter TCA cycle metabolism. In contrast to GDH, AAT requires a concomitant interconversion of oxaloacetate and aspartate. We have investigated the role of GDH in astrocyte glutamate and glucose metabolism employing siRNA mediated knock down (KD) of GDH in cultured astrocytes using stable and radioactive isotopes for metabolic mapping. An increased level of aspartate was observed upon exposure to [U-(13) C]glutamate in astrocytes exhibiting reduced GDH activity. (13) C Labeling of aspartate and TCA cycle intermediates confirmed that the increased amount of aspartate is associated with elevated TCA cycle flux from α-ketoglutarate to oxaloacetate, i.e. truncated TCA cycle. (13) C Glucose metabolism was elevated in GDH deficient astrocytes as observed by increased de novo synthesis of aspartate via pyruvate carboxylation. In the absence of glucose, lactate production from glutamate via malic enzyme was lower in GDH deficient astrocytes. In conclusions, our studies reveal that metabolism via GDH serves an important anaplerotic role by adding net carbon to the TCA cycle. A reduction in GDH activity seems to cause the astrocytes to up-regulate activity in pathways involved in maintaining the amount of TCA cycle intermediates such as pyruvate carboxylation as well as utilization of alternate substrates such as branched chain amino acids. PMID:26221781

  5. Metabolism: Part II. The Tricarboxylic Acid (TCA), Citric Acid, or Krebs Cycle.

    ERIC Educational Resources Information Center

    Bodner, George M.

    1986-01-01

    Differentiates the tricarboxylic acid (TCA) cycle (or Krebs cycle) from glycolysis, and describes the bridge between the two as being the conversion of pyruvate into acetyl coenzyme A. Discusses the eight steps in the TCA cycle, the results of isotopic labeling experiments, and the net effects of the TCA cycle. (TW)

  6. Mitochondrial engineering of the TCA cycle for fumarate production.

    PubMed

    Chen, Xiulai; Dong, Xiaoxiang; Wang, Yuancai; Zhao, Zihao; Liu, Liming

    2015-09-01

    Microbial fumarate production from renewable feedstock is a promising and sustainable alternative to petroleum-based chemical synthesis. Here, mitochondrial engineering was used to construct the oxidative pathway for fumarate production starting from the TCA cycle intermediate α-ketoglutarate in Candida glabrata. Accordingly, α-ketoglutarate dehydrogenase complex (KGD), succinyl-CoA synthetase (SUCLG), and succinate dehydrogenase (SDH) were selected to be manipulated for strengthening the oxidative pathway, and the engineered strain T.G-K-S-S exhibited increased fumarate biosynthesis (1.81 g L(-1)). To further improve fumarate production, the oxidative route was optimized. First, three fusion proteins KGD2-SUCLG2, SUCLG2-SDH1 and KGD2-SDH1 were constructed, and KGD2-SUCLG2 led to improved fumarate production (4.24 g L(-1)). In addition, various strengths of KGD2-SUCLG2 and SDH1 expression cassettes were designed by combinations of promoter strengths and copy numbers, resulting in a large increase in fumarate production (from 4.24 g L(-1) to 8.24 g L(-1)). Then, through determining intracellular amino acids and its related gene expression levels, argininosuccinate lyase in the urea cycle was identified as the key factor for restricting higher fumarate production. Correspondingly, after overexpression of it, the fumarate production was further increased to 9.96 g L(-1). Next, two dicarboxylic acids transporters facilitated an improvement of fumarate production, and, as a result, the final strain T.G-KS(H)-S(M)-A-2S reached fumarate titer of 15.76 g L(-1). This strategy described here paves the way to the development of an efficient pathway for microbial production of fumarate. PMID:25708514

  7. HSulf-1 deficiency dictates a metabolic reprograming of glycolysis and TCA cycle in ovarian cancer.

    PubMed

    Mondal, Susmita; Roy, Debarshi; Camacho-Pereira, Juliana; Khurana, Ashwani; Chini, Eduardo; Yang, Lifeng; Baddour, Joelle; Stilles, Katherine; Padmabandu, Seth; Leung, Sam; Kalloger, Steve; Gilks, Blake; Lowe, Val; Dierks, Thomas; Hammond, Edward; Dredge, Keith; Nagrath, Deepak; Shridhar, Viji

    2015-10-20

    Warburg effect has emerged as a potential hallmark of many cancers. However, the molecular mechanisms that led to this metabolic state of aerobic glycolysis, particularly in ovarian cancer (OVCA) have not been completely elucidated. HSulf-1 predominantly functions by limiting the bioavailability of heparan binding growth factors and hence their downstream signaling. Here we report that HSulf-1, a known putative tumor suppressor, is a negative regulator of glycolysis. Silencing of HSulf-1 expression in OV202 cell line increased glucose uptake and lactate production by upregulating glycolytic genes such as Glut1, HKII, LDHA, as well as metabolites. Conversely, HSulf-1 overexpression in TOV21G cells resulted in the down regulation of glycolytic enzymes and reduced glycolytic phenotype, supporting the role of HSulf-1 loss in enhanced aerobic glycolysis. HSulf-1 deficiency mediated glycolytic enhancement also resulted in increased inhibitory phosphorylation of pyruvate dehydrogenase (PDH) thus blocking the entry of glucose flux into TCA cycle. Consistent with this, metabolomic and isotope tracer analysis showed reduced glucose flux into TCA cycle. Moreover, HSulf-1 loss is associated with lower oxygen consumption rate (OCR) and impaired mitochondrial function. Mechanistically, lack of HSulf-1 promotes c-Myc induction through HB-EGF-mediated p-ERK activation. Pharmacological inhibition of c-Myc reduced HB-EGF induced glycolytic enzymes implicating a major role of c-Myc in loss of HSulf-1 mediated altered glycolytic pathway in OVCA. Similarly, PG545 treatment, an agent that binds to heparan binding growth factors and sequesters growth factors away from their ligand also blocked HB-EGF signaling and reduced glucose uptake in vivo in HSulf-1 deficient cells. PMID:26378042

  8. Prebiotic Metabolisms: Photo catalysis of the rTCA cycle by sphalerite colloids

    NASA Astrophysics Data System (ADS)

    Mangiante, D. M.; Bowen, B.; Northen, T.; Banfield, J. F.

    2010-12-01

    Explorations of mineral catalyzed reverse tricarboxylic acid (rTCA) cycle reactions provide a window into possible mechanisms for prebiotic metabolisms and the origins of life. The excitation of nano-scale semiconducting sphalerite minerals by ultra-violate light results in reducing electrons capable of catalyzing the reduction reactions present in the rTCA cycle. Current literature has utilized ion chromatography methods to characterize catalysis of two of the five redox active rTCA cycle compounds with high yield. This technique is unable to produce the untargeted analysis required to anticipate the myriad side reactions driven by excited photoelectrons and their ensuing radicals. By employing liquid chromatography coupled to mass spectrometry (LC-MS) we can examine the complete range of metabolites present across a reaction time series. The three dimensional LC-MS data set allows for the qualitative determination of individual metabolite features, while the comparison of intensities yields quantitative rates. These results allow us to describe the complete set of reactions resultant from a single rTCA cycle organic acid on a photo-activated sphalerite surface and provide a possible mechanism for how metabolic pathways could operate in enzyme free environments.

  9. Effects of intermediate metabolite carboxylic acids of TCA cycle on Microcystis with overproduction of phycocyanin.

    PubMed

    Bai, Shijie; Dai, Jingcheng; Xia, Ming; Ruan, Jing; Wei, Hehong; Yu, Dianzhen; Li, Ronghui; Jing, Hongmei; Tian, Chunyuan; Song, Lirong; Qiu, Dongru

    2015-04-01

    Toxic Microcystis species are the main bloom-forming cyanobacteria in freshwaters. It is imperative to develop efficient techniques to control these notorious harmful algal blooms (HABs). Here, we present a simple, efficient, and environmentally safe algicidal way to control Microcystis blooms, by using intermediate carboxylic acids from the tricarboxylic acid (TCA) cycle. The citric acid, alpha-ketoglutaric acid, succinic acid, fumaric acid, and malic acid all exhibited strong algicidal effects, and particularly succinic acid could cause the rapid lysis of Microcystis in a few hours. It is revealed that the Microcystis-lysing activity of succinic acid and other carboxylic acids was due to their strong acidic activity. Interestingly, the acid-lysed Microcystis cells released large amounts of phycocyanin, about 27-fold higher than those of the control. On the other hand, the transcription of mcyA and mcyD of the microcystin biosynthesis operon was not upregulated by addition of alpha-ketoglutaric acid and other carboxylic acids. Consider the environmental safety of intermediate carboxylic acids. We propose that administration of TCA cycle organic acids may not only provide an algicidal method with high efficiency and environmental safety but also serve as an applicable way to produce and extract phycocyanin from cyanobacterial biomass. PMID:25342454

  10. Glucose-independent glutamine metabolism via TCA cycling for proliferation and survival in B-cells

    PubMed Central

    Le, Anne; Lane, Andrew N.; Hamaker, Max; Bose, Sminu; Gouw, Arvin; Barbi, Joseph; Tsukamoto, Takashi; Rojas, Camilio J.; Slusher, Barbara S.; Zhang, Haixia; Zimmerman, Lisa J.; Liebler, Daniel C.; Slebos, Robbert J.C.; Lorkiewicz, Pawel K.; Higashi, Richard M.; Fan, Teresa W. M.; Dang, Chi V.

    2012-01-01

    Summary Because MYC plays a causal role in many human cancers, including those with hypoxic and nutrient-poor tumor microenvironments, we have determined the metabolic responses of a MYC-inducible human Burkitt lymphoma model P493 cell line to aerobic and hypoxic conditions, and to glucose deprivation, using Stable Isotope Resolved Metabolomics. Using [U-13C]-glucose as the tracer, both glucose consumption and lactate production were increased by MYC expression and hypoxia. Using [U-13C,15N]-glutamine as the tracer, glutamine import and metabolism through the TCA cycle persisted under hypoxia, and glutamine contributed significantly to citrate carbons. Under glucose deprivation, glutamine-derived fumarate, malate, and citrate were significantly increased. Their 13C labeling patterns demonstrate an alternative energy-generating glutaminolysis pathway involving a glucose-independent TCA cycle. The essential role of glutamine metabolism in cell survival and proliferation under hypoxia and glucose deficiency, makes them susceptible to the glutaminase inhibitor BPTES, and hence could be targeted for cancer therapy. PMID:22225880

  11. The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella

    PubMed Central

    Ricci, Vito; Loman, Nick; Pallen, Mark; Ivens, Alasdair; Fookes, Maria; Langridge, Gemma C.; Wain, John; Piddock, Laura J. V.

    2012-01-01

    Objectives The initial aim of this study was to use a systems biology approach to analyse a ciprofloxacin-selected multidrug-resistant (MDR) Salmonella enterica serotype Typhimurium, L664. Methods The whole genome sequence and transcriptome of L664 were analysed. Site-directed mutagenesis to recreate each mutation was carried out, followed by phenotypic characterization and mutation frequency analysis. As a mutation in the TCA cycle was detected we tested the controversial hypothesis regarding the bacterial response to bactericidal antibiotics, put forward by Kohanski et al. (Cell 2007; 130: 797–810 and Mol Cell 2010; 37: 311–20), that exposure of bacteria to agents such as ciprofloxacin produces reactive oxygen species (ROS), which transiently increase the mutation rate giving rise to MDR bacteria. Results L664 contained a mutation in ramR that conferred MDR. A mutation in tctA affected the TCA cycle and conferred the inability to grow on minimal agar. The virulence of L664 was not attenuated. Ciprofloxacin exposure produced ROS in L664 and SL1344 (tctA::aph), but it was reduced and occurred later. There were no significant differences in the rates of killing or mutations per generation to antibiotic resistance between the strains. Conclusions Whilst we confirm production of ROS in response to ciprofloxacin, we have no data to support the hypothesis that this leads to selection of MDR strains. Our results indicate that the mutations in tctA and glgA were random as they did not pre-exist in the parental strain, and that the mutation in tctA did not provide a survival advantage or disadvantage in the presence of antibiotic. PMID:22186876

  12. A Possibility for Piece-wise Ignitions of a TCA Cycle in a Prebiotic Hydrothermal Environment

    NASA Astrophysics Data System (ADS)

    Nemoto, A.; Ikeya, R.; Imai, E.; Hatori, K.; Honda, H.; Matsuno, K.

    We previously reported that formic and acetic acids were synthesized from the mixture of carbon dioxide and water in the presence of heated metal oxide serving as a catalyst (1). Fixation of carbon dioxide and monoxide could have been conceivable in the hydrothermal environment in the primitive ocean. We then considered a possibility of synthesizing major metabolites appearing in a TCA cycle in prebiotic conditions. Focused in this attempt was the vicinity of hydrothermal vents in the primitive ocean. We used a flow reactor to simulate hydrothermal circulation of seawater through hot vents (2). The experimental conditions we chose were that the hot chamber at 200 °C was connected to the cold chamber at 0 °C through a thin nozzle of its diameter 0.8 mm. The total volume of the reaction solution was 500 mL. The fluid was circulated through the flow reactor at the rate of 8 mL / min. As an initial attempt, we prepared the solution of acetic and formic acids. When iron chloride and copper sulfide were present in the solution, the products precipitated on the filter placed in the low-temperature chamber included di-carboxylic acids such as malic acid. We then proceeded to the reaction solution dissolving three different kinds of carboxylic acids, namely, succinate, fumarate, and oxoglutarate. We found that malic acid was in the solution after the operation of the flow-reactor. Formation and transformation of carboxylic acids were observed in our flow reactor. These observations, when combined together, may suggest a possibility of piece-wise ignitions of a TCA cycle even in the prebiotic ocean on the primitive earth. References (1) R. Terada, E. Imai, H. Honda, K. Hatori, and K. Matsuno.: Viva Origino 27, 197-208(1999). (2) E. Imai, H. Honda, K. Hatori, A. Brack, and K. Matsuno.: Science 283, 831-833(1999).

  13. Real Time Molecular Imaging of TCA Cycle Metabolism in vivo By Hyperpolarized 1-13C Diethyl Succinate

    PubMed Central

    Zacharias, Niki M.; Chan, Henry R.; Sailasuta, Napapon; Ross, Brian D.

    2011-01-01

    The Krebs tricarboxylic acid cycle (TCA) is central to metabolic energy production and is known to be altered in many disease states. Real time molecular imaging of TCA cycle in vivo will be important in understanding the metabolic basis of several diseases. Positron emission tomography (PET) using FDG-glucose (2-[18F]fluoro-2-deoxy-D-glucose) is already being used as a metabolic imaging agent in clinics. However, FDG-glucose does not reveal anything past glucose uptake and phosphorylation. We have developed a new metabolic imaging agent, hyperpolarized diethyl 1-13C 2,3-d2 succinate, that allows for real time in vivo imaging and spectroscopy of the TCA cycle. Diethyl succinate can be hyperpolarized using parahydrogen induced polarization (PHIP) in an aqueous solution with signal enhancement of 5000 compared to Boltzmann polarization. 13C magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) were achieved in vivo seconds after injection of 10 to 20 μmol of hyperpolarized diethyl succinate into normal mice. The downstream metabolites of hyperpolarized diethyl succinate were identified in vivo as malate, succinate, fumarate and aspartate. The metabolism of diethyl succinate was altered after exposing the animal to 3-nitropropionate, a known irreversible inhibitor of succinate dehydrogenase. Based on our results, hyperpolarized diethyl succinate allows for in real time in vivo MRI and MRS with a high signal to noise ratio and with visualization of multiple steps of the TCA cycle. Hyperpolarization of diethyl succinate and its in vivo applications may reveal an entirely new regime wherein the local status of TCA cycle metabolism is interrogated on the time scale of seconds to minutes with unprecedented chemical specificity and MR sensitivity. PMID:22146049

  14. Tracer-based assessments of hepatic anaplerotic and TCA cycle flux: practicality, stoichiometry, and hidden assumptions.

    PubMed

    Previs, Stephen F; Kelley, David E

    2015-10-15

    Two groups recently used different tracer methods to quantify liver-specific flux rates. The studies had a similar goal, i.e., to characterize mitochondrial oxidative function. These efforts could have a direct impact on our ability to understand metabolic abnormalities that affect the pathophysiology of fatty liver and allow us to examine mechanisms surrounding potential therapeutic interventions. Briefly, one method couples the continuous infusion of [(13)C]acetate with direct real-time measurements of [(13)C]glutamate labeling in liver; the other method administers [(13)C]propionate, in combination with other tracers, and subsequently measures the (13)C labeling of plasma glucose and/or acetaminophen-glucuronide. It appears that a controversy has arisen, since the respective methods yielded different estimates of the anaplerotic/TCA flux ratio (VANA:VTCA) in "control" subjects, i.e., the [(13)C]acetate- and [(13)C]propionate-derived VANA:VTCA flux ratios appear to be ∼1.4 and ∼5, respectively. While the deep expertise in the respective groups makes it somewhat trivial for each to perform the tracer studies, the data interpretation is inherently difficult. The current perspective was undertaken to examine potential factors that could account for or contribute to the apparent differences. Attention was directed toward 1) matters of practicality, 2) issues surrounding stoichiometry, and 3) hidden assumptions. We believe that the [(13)C]acetate method has certain weaknesses that limit its utility; in contrast, the [(13)C]propionate method likely yields a more correct answer. We hope our discussion will help clarify the differences in the recent reports. Presumably this will be of interest to investigators who are considering tracer-based studies of liver metabolism. PMID:26330343

  15. Application of citrate as a tricarboxylic acid (TCA) cycle intermediate, prevents diabetic-induced heart damages in mice

    PubMed Central

    Liang, Qianqian; Wang, Baoyu; Pang, Lingxia; Wang, Youpei; Zheng, Meiqin; Wang, Qing; Yan, Jingbin; Xu, Jinzhong

    2016-01-01

    Objective(s): Higher cellular reactive oxygen species (ROS) levels is important in reducing cellular energy charge (EC) by increasing the levels of key metabolic protein, and nitrosative modifications, and have been shown to damage the cardiac tissue of diabetic mice. However, the relation between energy production and heart function is unclear. Materials and Methods: Streptozotocin (STZ, 150 mg/kg body weight) was injected intraperitoneally once to mice that had been fasted overnight for induction of diabetes. After diabetic induction, mice received citrate (5 µg/kg) through intraperitoneal injection every other day for 5 weeks. The caspase-3, plasminogen activator inhibitor 1 (PAI1), protein kinase B (PKB), commonly known as AKT and phosphorylated-AKT (p-AKT) proteins were examined to elucidate inflammation and apoptosis in the heart. For histological analysis, heart samples were fixed with 10% formalin and stained with hematoxylin-eosin (HE) and Sirius red to assess pathological changes and fibrosis. The expression levels[AGA1] of marker proteins, tyrosine nitration, activity of ATP synthase and succinyl-CoA3-ketoacid coenzyme A transferase-1 (SCOT), and EC were measured. Results: Intraperitoneal injection of citrate significantly reduced caspase-3 and PAI-1 protein levels and increased p-AKT level on the 5th week; EC in the heart was found to be increased as well. Further, the expression level, activity, and tyrosine nitration of ATP synthase and SCOT were not affected after induction of diabetes. Conclusion: Results indicate that application of citrate, a tricarboxylic acid (TCA) cycle intermediate, might alleviate cardiac dysfunction by reducing cardiac inflammation, apoptosis, and increasing cardiac EC. PMID:27096063

  16. The Role of TCA Cycle Anaplerosis in Ketosis and Fatty Liver in Periparturient Dairy Cows.

    PubMed

    White, Heather M

    2015-01-01

    The transition to lactation period in dairy cattle is characterized by metabolic challenges, negative energy balance, and adipose tissue mobilization. Metabolism of mobilized adipose tissue is part of the adaptive response to negative energy balance in dairy cattle; however, the capacity of the liver to completely oxidize nonesterified fatty acids may be limited and is reflective of oxaloacetate pool, the carbon carrier of the tricarboxylic acid cycle. Alternative metabolic fates of acetyl-CoA from nonesterified fatty acids include esterification to triacylglycerides and ketogenesis, and when excessive, these pathways lead to fatty liver and ketosis. Examination of the anaplerotic and cataplerotic pull of oxaloacetate by the tricarboxylic acid cycle and gluconeogenesis may provide insight into the balance of oxidation and esterification of acetyl-CoA within the liver of periparturient dairy cows. PMID:26479386

  17. Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle.

    PubMed

    Alves, Tiago C; Pongratz, Rebecca L; Zhao, Xiaojian; Yarborough, Orlando; Sereda, Sam; Shirihai, Orian; Cline, Gary W; Mason, Graeme; Kibbey, Richard G

    2015-11-01

    Mass isotopomer multi-ordinate spectral analysis (MIMOSA) is a step-wise flux analysis platform to measure discrete glycolytic and mitochondrial metabolic rates. Importantly, direct citrate synthesis rates were obtained by deconvolving the mass spectra generated from [U-(13)C6]-D-glucose labeling for position-specific enrichments of mitochondrial acetyl-CoA, oxaloacetate, and citrate. Comprehensive steady-state and dynamic analyses of key metabolic rates (pyruvate dehydrogenase, β-oxidation, pyruvate carboxylase, isocitrate dehydrogenase, and PEP/pyruvate cycling) were calculated from the position-specific transfer of (13)C from sequential precursors to their products. Important limitations of previous techniques were identified. In INS-1 cells, citrate synthase rates correlated with both insulin secretion and oxygen consumption. Pyruvate carboxylase rates were substantially lower than previously reported but showed the highest fold change in response to glucose stimulation. In conclusion, MIMOSA measures key metabolic rates from the precursor/product position-specific transfer of (13)C-label between metabolites and has broad applicability to any glucose-oxidizing cell. PMID:26411341

  18. TCA cycle activity in Staphylococcus aureus is essential for iron-regulated synthesis of staphyloferrin A, but not staphyloferrin B: the benefit of a second citrate synthase.

    PubMed

    Sheldon, Jessica R; Marolda, Cristina L; Heinrichs, David E

    2014-05-01

    Staphylococcus aureus elaborates two citrate-containing siderophores, staphyloferrin A (SA) and staphyloferrin B (SB), that enhance growth under iron-restriction, yet, paradoxically, expression of the TCA cycle citrate synthase, CitZ, is downregulated during iron starvation. Iron starvation does, however, result in expression of SbnG, recently identified as a novel citrate synthase that is encoded from within the iron-regulated SB biosynthetic locus, suggesting an important role for SbnG in staphyloferrin production. We demonstrate that during growth of S. aureus in iron-restricted media containing glucose, SB is produced but, in contrast, SA production is severely repressed; accordingly, SB-deficient mutants grow poorly in these media. Hypothesizing that reduced TCA cycle activity hinders SA production, we show that a citZ mutant is capable of SB synthesis, but not SA synthesis, providing evidence that SbnG does not generate citrate for incorporation into SA. A citZ sbnG mutant synthesizes neither staphyloferrin, is severely compromised for growth in iron-restricted media, and is significantly more impaired for virulence than either of the single-deletion mutants. We propose that SB is the more important of the two siderophores for S. aureus insofar as it is synthesized, and supports iron-restricted growth, without need of TCA cycle activity. PMID:24666349

  19. The effect of Walterinnesia aegyptia venom proteins on TCA cycle activity and mitochondrial NAD(+)-redox state in cultured human fibroblasts.

    PubMed

    Ghneim, Hazem K; Al-Sheikh, Yazeed A; Aboul-Soud, Mourad A M

    2015-01-01

    Fibroblast cultures were used to study the effects of crude Walterinnesia aegyptia venom and its F1-F7 protein fractions on TCA cycle enzyme activities and mitochondrial NAD-redox state. Confluent cells were incubated with 10 μg of venom proteins for 4 hours at 37°C. The activities of all studied TCA enzymes and the non-TCA mitochondrial NADP(+)-dependent isocitrate dehydrogenase underwent significant reductions of similar magnitude (50-60% of control activity) upon incubation of cells with the crude venom and fractions F4, F5, and F7 and 60-70% for fractions F3 and F6. In addition, the crude and fractions F3-F7 venom proteins caused a drop in mitochondrial NAD(+) and NADP(+) levels equivalent to around 25% of control values. Whereas the crude and fractions F4, F5, and F7 venom proteins caused similar magnitude drops in NADH and NADPH (around 55% of control levels), fractions F3 and F6 caused a more drastic drop (60-70% of control levels) of both reduced coenzymes. Results indicate that the effects of venom proteins could be directed at the mitochondrial level and/or the rates of NAD(+) and NADP(+) biosynthesis. PMID:25705684

  20. The Effect of Walterinnesia aegyptia Venom Proteins on TCA Cycle Activity and Mitochondrial NAD+-Redox State in Cultured Human Fibroblasts

    PubMed Central

    Ghneim, Hazem K.; Al-Sheikh, Yazeed A.; Aboul-Soud, Mourad A. M.

    2015-01-01

    Fibroblast cultures were used to study the effects of crude Walterinnesia aegyptia venom and its F1–F7 protein fractions on TCA cycle enzyme activities and mitochondrial NAD-redox state. Confluent cells were incubated with 10 μg of venom proteins for 4 hours at 37°C. The activities of all studied TCA enzymes and the non-TCA mitochondrial NADP+-dependent isocitrate dehydrogenase underwent significant reductions of similar magnitude (50–60% of control activity) upon incubation of cells with the crude venom and fractions F4, F5, and F7 and 60–70% for fractions F3 and F6. In addition, the crude and fractions F3–F7 venom proteins caused a drop in mitochondrial NAD+ and NADP+ levels equivalent to around 25% of control values. Whereas the crude and fractions F4, F5, and F7 venom proteins caused similar magnitude drops in NADH and NADPH (around 55% of control levels), fractions F3 and F6 caused a more drastic drop (60–70% of control levels) of both reduced coenzymes. Results indicate that the effects of venom proteins could be directed at the mitochondrial level and/or the rates of NAD+ and NADP+ biosynthesis. PMID:25705684

  1. The Majority of Free-Living Autotrophic Bacteria use the Reductive TCA Cycle for Carbon Fixation at Deep-Sea Hydrothermal Vents

    NASA Astrophysics Data System (ADS)

    Campbell, B. J.; Cary, C.

    2003-12-01

    Deep-sea hydrothermal vents support large micro and macroscopic communities, without the input of photosynthesis. Autotrophic production at these vents is based on hydrothermal vent fluid chemistry. Primary production has been thought to occur mainly via hydrogen sulfide oxidation through the Calvin-Benson pathway, as measured by the presence of Rubisco in endosymbionts of several invertebrate hosts. Recently, we characterized two fosmids from a large insert library of the epsilon Proteobacterial episymbionts of Alvinella pompejana. Both contained sequences encoding ATP citrate lyase, a key enzyme in the reverse TCA cycle, an alternate carbon dioxide fixation pathway. Previous investigators have demonstrated the dominance of the epsilon subdivision in the free-living bacterial communities at hydrothermal vents. Based on these results, our working hypothesis is: The rTCA cycle is the dominant pathway for carbon fixation in the free-living bacterial communities at hydrothermal vents. A selection of free-living bacterial communities from various geographic locations (9N, East Pacific Rise and Guaymas Basin) were screened for the presence, diversity and expression (via RT-PCR) of Rubisco (forms I and II) and ATP citrate lyase. Our results indicate that the ATP citrate lyase gene is diverse and is consistently expressed in several types of vent communities. The two forms of Rubisco are not consistently present or expressed in the same environments. These results indicate that chemoautotrophic production in the free-living bacterial communities at deep-sea hydrothermal vents is dominated by bacteria that utilize the rTCA cycle, and parallels the phylogenetic dominance of members of the epsilon subdivision of Proteobacteria.

  2. Contribution of the tricarboxylic acid (TCA) cycle and the glyoxylate shunt in Saccharomyces cerevisiae to succinic acid production during dough fermentation.

    PubMed

    Rezaei, Mohammad N; Aslankoohi, Elham; Verstrepen, Kevin J; Courtin, Christophe M

    2015-07-01

    Succinic acid produced by yeast during bread dough fermentation can significantly affect the rheological properties of the dough. By introducing mutations in the model S288C yeast strain, we show that the oxidative pathway of the TCA cycle and the glyoxylate shunt contribute significantly to succinic acid production during dough fermentation. More specifically, deletion of ACO1 and double deletion of ACO1 and ICL1 resulted in a 36 and 77% decrease in succinic acid levels in fermented dough, respectively. Similarly, double deletion of IDH1 and IDP1 decreased succinic acid production by 85%, while also affecting the fermentation rate. By contrast, double deletion of SDH1 and SDH2 resulted in a two-fold higher succinic acid accumulation compared to the wild-type. Deletion of fumarate reductase activity (FRD1 and OSM1) in the reductive pathway of the TCA cycle did not affect the fermentation rate and succinic acid production. The changes in the levels of succinic acid produced by mutants Δidh1Δidp1 (low level) and Δsdh1Δsdh2 (high level) in fermented dough only resulted in small pH differences, reflecting the buffering capacity of dough at a pH of around 5.1. Moreover, Rheofermentometer analysis using these mutants revealed no difference in maximum dough height and gas retention capacity with the dough prepared with S288C. The impact of the changed succinic acid profile on the organoleptic or antimicrobial properties of bread remains to be demonstrated. PMID:25828707

  3. Increased anaplerosis, TCA cycling, and oxidative phosphorylation in the liver of dairy cows with intensive body fat mobilization during early lactation.

    PubMed

    Schäff, Christine; Börner, Sabina; Hacke, Sandra; Kautzsch, Ulrike; Albrecht, Dirk; Hammon, Harald M; Röntgen, Monika; Kuhla, Björn

    2012-11-01

    The onset of milk production lets mammals experience an enormous energy and nutrient demand. To meet these requirements, high-yielding dairy cows mobilize body fat resulting in an augmented hepatic oxidative metabolism, which has been suggested to signal for depressing hunger after calving. To examine how the extent of fat mobilization influences hepatic oxidative metabolism and thus potentially feed intake, blood and liver samples of 19 Holstein cows were taken throughout the periparturient period. Retrospectively grouped according to high (H) and low (L) liver fat content, H cows showed higher fatty acid but lower amino acid plasma concentrations and lower feed intake than L cows. The hepatic phospho-AMPK/total AMP ratio was not different between groups but decreased after parturition. A 2-DE coupled MALDI-TOF-TOF analysis and qRT-PCR studies revealed H cows having lower expressions of major enzymes involved in mitochondrial β-oxidation, urea cycling, and the pentose phosphate pathway but higher expressions of enzymes participating in peroxisomal and endoplasmic fatty acid degradation, pyruvate and TCA cycling, amino acid catabolism, oxidative phosphorylation, and oxidative stress defense. These data indicate that increasing lipolysis leads to augmenting nutrient catabolism for anaplerosis and mitochondrial respiration, providing a molecular link between hepatic oxidative processes and feed intake. PMID:23046364

  4. High night temperature strongly impacts TCA cycle, amino acid and polyamine biosynthetic pathways in rice in a sensitivity-dependent manner

    PubMed Central

    Glaubitz, Ulrike; Erban, Alexander; Kopka, Joachim; Hincha, Dirk K.; Zuther, Ellen

    2015-01-01

    Global climate change combined with asymmetric warming can have detrimental effects on the yield of crop plants such as rice (Oryza sativa L.). Little is known about metabolic responses of rice to high night temperature (HNT) conditions. Twelve cultivars with different HNT sensitivity were used to investigate metabolic changes in the vegetative stage under HNT compared to control conditions. Central metabolism, especially TCA cycle and amino acid biosynthesis, were strongly affected particularly in sensitive cultivars. Levels of several metabolites were correlated with HNT sensitivity. Furthermore, pool sizes of some metabolites negatively correlated with HNT sensitivity under control conditions, indicating metabolic pre-adaptation in tolerant cultivars. The polyamines putrescine, spermidine and spermine showed increased abundance in sensitive cultivars under HNT conditions. Correlations between the content of polyamines and 75 other metabolites indicated metabolic shifts from correlations with sugar-phosphates and 1-kestose under control to correlations with sugars and amino and organic acids under HNT conditions. Increased expression levels of ADC2 and ODC1, genes encoding enzymes catalysing the first committed steps of putrescine biosynthesis, were restricted to sensitive cultivars under HNT. Additionally, transcript levels of eight polyamine biosynthesis genes were correlated with HNT sensitivity. Responses to HNT in the vegetative stage result in distinct differences between differently responding cultivars with a dysregulation of central metabolism and an increase of polyamine biosynthesis restricted to sensitive cultivars under HNT conditions and a pre-adaptation of tolerant cultivars already under control conditions with higher levels of potentially protective compatible solutes. PMID:26208642

  5. Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast

    PubMed Central

    Lin, Kang-Wei; Yang, Chuan-Jun; Lian, Hui-Yong; Cai, Peng

    2016-01-01

    In this study, we investigated the transcriptional response to 50 Hz extremely low frequency electromagnetic field (ELF-EMF) and 2.0 GHz radio frequency electromagnetic field (RF-EMF) exposure by Illumina sequencing technology using budding yeast as the model organism. The transcription levels of 28 genes were upregulated and those of four genes were downregulated under ELF-EMF exposure, while the transcription levels of 29 genes were upregulated and those of 24 genes were downregulated under RF-EMF exposure. After validation by reverse transcription quantitative polymerase chain reaction (RT-qPCR), a concordant direction of change both in differential gene expression (DGE) and RT-qPCR was demonstrated for nine genes under ELF-EMF exposure and for 10 genes under RF-EMF exposure. The RT-qPCR results revealed that ELF-EMF and RF-EMF exposure can upregulate the expression of genes involved in glucose transportation and the tricarboxylic acid (TCA) cycle, but not the glycolysis pathway. Energy metabolism is closely related with the cell response to environmental stress including EMF exposure. Our findings may throw light on the mechanism underlying the biological effects of EMF.

  6. Combined effects of CO2 enrichment and elevated growth temperatures on metabolites in soybean leaflets: evidence for dynamic changes of TCA cycle intermediates.

    PubMed

    Sicher, Richard

    2013-08-01

    Soybean (Glycine max [Merr.] L.) was grown in indoor chambers with ambient (38 Pa) and elevated (70 Pa) CO2 and day/night temperature treatments of 28/20, 32/24 and 36/28 °C. We hypothesized that CO2 enrichment would mitigate the deleterious effects of elevated growth temperatures on metabolites in soybean leaflets. Net CO2 assimilation rates increased incrementally with growth temperature and were enhanced up to 24 % on average by CO2 enrichment. Stomatal conductance about doubled from the lowest to highest temperature but this was partially reversed by CO2 enrichment. Metabolites were measured thrice daily and 19 and 28 of 43 total leaf metabolites were altered by the 32/24 and 36/28 °C temperature treatments, respectively, in both CO2 treatments. Polyols, raffinose and GABA increased and 23 nonstructural carbohydrates, organic acids and amino acids decreased when the temperature was increased from 28 to 36 °C under ambient CO2. Citrate, aconitate and 2-oxoglutarate decreased over 90 % in the 36/28 °C compared to the 28/20 °C temperature treatment. Temperature-dependent changes of sugars, organic acids and all but three amino acids were almost completely eliminated by CO2 enrichment. The above findings suggested that specific TCA cycle intermediates were highly depleted by heat stress under ambient CO2. Mitigating effects of CO2 enrichment on soybean leaflet metabolites were attributed to altered rates of photosynthesis, photorespiration, dark respiration, the anaplerotic pathway and to possible changes of gene expression. PMID:23716183

  7. Tricarboxylic acid cycle intermediate pool size: functional importance for oxidative metabolism in exercising human skeletal muscle.

    PubMed

    Bowtell, Joanna L; Marwood, Simon; Bruce, Mark; Constantin-Teodosiu, Dumitru; Greenhaff, Paul L

    2007-01-01

    The tricarboxylic acid (TCA) cycle is the major final common pathway for oxidation of carbohydrates, lipids and some amino acids, which produces reducing equivalents in the form of nicotinamide adenine dinucleotide and flavin adenine dinucleotide that result in production of large amounts of adenosine triphosphate (ATP) via oxidative phosphorylation. Although regulated primarily by the products of ATP hydrolysis, in particular adenosine diphosphate, the rate of delivery of reducing equivalents to the electron transport chain is also a potential regulatory step of oxidative phosphorylation. The TCA cycle is responsible for the generation of approximately 67% of all reducing equivalents per molecule of glucose, hence factors that influence TCA cycle flux will be of critical importance for oxidative phosphorylation. TCA cycle flux is dependent upon the supply of acetyl units, activation of the three non-equilibrium reactions within the TCA cycle, and it has been suggested that an increase in the total concentration of the TCA cycle intermediates (TCAi) is also necessary to augment and maintain TCA cycle flux during exercise. This article reviews the evidence of the functional importance of the TCAi pool size for oxidative metabolism in exercising human skeletal muscle. In parallel with increased oxidative metabolism and TCA cycle flux during exercise, there is an exercise intensity-dependent 4- to 5-fold increase in the concentration of the TCAi. TCAi concentration reaches a peak after 10-15 minutes of exercise, and thereafter tends to decline. This seems to support the suggestion that the concentration of TCAi may be of functional importance for oxidative phosphorylation. However, researchers have been able to induce dissociations between TCAi pool size and oxidative energy provision using a variety of nutritional, pharmacological and exercise interventions. Brief periods of endurance training (5 days or 7 weeks) have been found to result in reduced TCAi pool

  8. Ames Optimized TCA Configuration

    NASA Technical Reports Server (NTRS)

    Cliff, Susan E.; Reuther, James J.; Hicks, Raymond M.

    1999-01-01

    Configuration design at Ames was carried out with the SYN87-SB (single block) Euler code using a 193 x 49 x 65 C-H grid. The Euler solver is coupled to the constrained (NPSOL) and the unconstrained (QNMDIF) optimization packages. Since the single block grid is able to model only wing-body configurations, the nacelle/diverter effects were included in the optimization process by SYN87's option to superimpose the nacelle/diverter interference pressures on the wing. These interference pressures were calculated using the AIRPLANE code. AIRPLANE is an Euler solver that uses a unstructured tetrahedral mesh and is capable of computations about arbitrary complete configurations. In addition, the buoyancy effects of the nacelle/diverters were also included in the design process by imposing the pressure field obtained during the design process onto the triangulated surfaces of the nacelle/diverter mesh generated by AIRPLANE. The interference pressures and nacelle buoyancy effects are added to the final forces after each flow field calculation. Full details of the (recently enhanced) ghost nacelle capability are given in a related talk. The pseudo nacelle corrections were greatly improved during this design cycle. During the Ref H and Cycle 1 design activities, the nacelles were only translated and pitched. In the cycle 2 design effort the nacelles can translate vertically, and pitch to accommodate the changes in the lower surface geometry. The diverter heights (between their leading and trailing edges) were modified during design as the shape of the lower wing changed, with the drag of the diverter changing accordingly. Both adjoint and finite difference gradients were used during optimization. The adjoint-based gradients were found to give good direction in the design space for configurations near the starting point, but as the design approached a minimum, the finite difference gradients were found to be more accurate. Use of finite difference gradients was limited by the

  9. Viscous Design of TCA Configuration

    NASA Technical Reports Server (NTRS)

    Krist, Steven E.; Bauer, Steven X. S.; Campbell, Richard L.

    1999-01-01

    The goal in this effort is to redesign the baseline TCA configuration for improved performance at both supersonic and transonic cruise. Viscous analyses are conducted with OVERFLOW, a Navier-Stokes code for overset grids, using PEGSUS to compute the interpolations between overset grids. Viscous designs are conducted with OVERDISC, a script which couples OVERFLOW with the Constrained Direct Iterative Surface Curvature (CDISC) inverse design method. The successful execution of any computational fluid dynamics (CFD) based aerodynamic design method for complex configurations requires an efficient method for regenerating the computational grids to account for modifications to the configuration shape. The first section of this presentation deals with the automated regridding procedure used to generate overset grids for the fuselage/wing/diverter/nacelle configurations analysed in this effort. The second section outlines the procedures utilized to conduct OVERDISC inverse designs. The third section briefly covers the work conducted by Dick Campbell, in which a dual-point design at Mach 2.4 and 0.9 was attempted using OVERDISC; the initial configuration from which this design effort was started is an early version of the optimized shape for the TCA configuration developed by the Boeing Commercial Airplane Group (BCAG), which eventually evolved into the NCV design. The final section presents results from application of the Natural Flow Wing design philosophy to the TCA configuration.

  10. Evolution and Functional Implications of the Tricarboxylic Acid Cycle as Revealed by Phylogenetic Analysis

    PubMed Central

    Cavalcanti, João Henrique Frota; Esteves-Ferreira, Alberto A.; Quinhones, Carla G.S.; Pereira-Lima, Italo A.; Nunes-Nesi, Adriano; Fernie, Alisdair R.; Araújo, Wagner L.

    2014-01-01

    The tricarboxylic acid (TCA) cycle, a crucial component of respiratory metabolism, is composed of a set of eight enzymes present in the mitochondrial matrix. However, most of the TCA cycle enzymes are encoded in the nucleus in higher eukaryotes. In addition, evidence has accumulated demonstrating that nuclear genes were acquired from the mitochondrial genome during the course of evolution. For this reason, we here analyzed the evolutionary history of all TCA cycle enzymes in attempt to better understand the origin of these nuclear-encoded proteins. Our results indicate that prior to endosymbiotic events the TCA cycle seemed to operate only as isolated steps in both the host (eubacterial cell) and mitochondria (alphaproteobacteria). The origin of isoforms present in different cell compartments might be associated either with gene-transfer events which did not result in proper targeting of the protein to mitochondrion or with duplication events. Further in silico analyses allow us to suggest new insights into the possible roles of TCA cycle enzymes in different tissues. Finally, we performed coexpression analysis using mitochondrial TCA cycle genes revealing close connections among these genes most likely related to the higher efficiency of oxidative phosphorylation in this specialized organelle. Moreover, these analyses allowed us to identify further candidate genes which might be used for metabolic engineering purposes given the importance of the TCA cycle during development and/or stress situations. PMID:25274566

  11. MicroTCA and AdvancedTCA equipment evaluation and customization for LHC experiments

    NASA Astrophysics Data System (ADS)

    Di Cosmo, M.; Bobillier, V.; Haas, S.; Joos, M.; Mico, S.; Vasey, F.

    2015-01-01

    The MicroTCA and AdvancedTCA industry standards are candidate modular electronics platforms for the upgrade of the current generation of high energy physics experiments at CERN. The PH-ESE group at CERN launched an xTCA evaluation project with the aim of performing technical evaluations and providing support for commercially available components. Over the past years, different equipment from different vendors has been acquired and evaluated. This paper summarizes our evaluation results of commercial MicroTCA and AdvancedTCA equipment. Special emphasis is put on the component requirements to be defined in view of future equipment procurement. Customized prototypes developed according to these generic specifications are presented for the first time.

  12. ATCA/muTCA for Physics

    SciTech Connect

    Jezynski, Tomasz; Larsen, Raymond; Le Du, Patrick; /Lyon, IPN

    2012-06-14

    ATCA/{mu}TCA platforms are attractive because of the modern serial link architecture, high availability features and many packaging options. Less-demanding availability applications can be met economically by scaling back speed and redundancy. The ATCA specification was originally targeted for the Telecom industry but has gained recently a much wider user audience. The purpose of this paper is to report on present hardware and software R and D efforts where ATCA and {mu}TCA are planned, already being used or in development using selected examples for accelerator and detectors in the Physics community. It will present also the status of a proposal for physics extensions to ATCA/{mu}TCA specifications to promote inter-operability of laboratory and industry designs for physics.

  13. Functional Family Therapy: A Life Cycle Perspective.

    ERIC Educational Resources Information Center

    Wetchler, Joseph L.

    1985-01-01

    Functional family therapy model assesses family behavior from perspectives of interactional process and functional payoffs for the individual family members. Illustrates that functional needs change as a result of development, and that by including a family life cycle perspective in the assessment process, clinicians will get a clearer picture of…

  14. MicroTCA and AdvancedTCA equipment evaluation and developments for LHC experiments

    NASA Astrophysics Data System (ADS)

    Bobillier, V.; Haas, S.; Joos, M.; Mendez, J.; Mico, S.; Vasey, F.

    2016-02-01

    The MicroTCA (MTCA) and AdvancedTCA (ATCA) industry standards have been selected as the platform for many of the current and planned upgrades of the off-detector electronic systems of two of the LHC experiments at CERN. We present a status update from an ongoing project to evaluate commercial MTCA and ATCA components with particular emphasis on infrastructure equipment such as shelves and power-supplies. Shelves customized for use in the existing LHC rack infrastructure have been tested, and electrical and cooling measurements and simulations were performed. In-house developments for hardware platform management will also be shown.

  15. SdhE-dependent formation of a functional Acetobacter pasteurianus succinate dehydrogenase in Gluconobacter oxydans--a first step toward a complete tricarboxylic acid cycle.

    PubMed

    Kiefler, Ines; Bringer, Stephanie; Bott, Michael

    2015-11-01

    The obligatory aerobic α-proteobacterium Gluconobacter oxydans 621H possesses an unusual metabolism in which the majority of the carbohydrate substrates are incompletely oxidized in the periplasm and only a small fraction is metabolized in the cytoplasm. The cytoplasmic oxidation capabilities are limited due to an incomplete tricarboxylic acid (TCA) cycle caused by the lack of succinate dehydrogenase (Sdh) and succinyl-CoA synthetase. As a first step to test the consequences of a functional TCA cycle for growth, metabolism, and bioenergetics of G. oxydans, we attempted to establish a heterologous Sdh in this species. Expression of Acetobacter pasteurianus sdhCDAB in G. oxydans did not yield an active succinate dehydrogenase. Co-expression of a putative sdhE gene from A. pasteurianus, which was assumed to encode an assembly factor for covalent attachment of flavin adenine dinucleotide (FAD) to SdhA, stimulated Sdh activity up to 400-fold to 4.0 ± 0.4 U (mg membrane protein)(‒1). The succinate/oxygen reductase activity of membranes was 0.68 ± 0.04 U (mg membrane protein)(‒1), indicating the formation of functional Sdh complex capable of transferring electrons from succinate to ubiquinone. A. pasteurianus SdhE could be functionally replaced by SdhE from the γ-proteobacterium Serratia sp. According to these results, the accessory protein SdhE was necessary and sufficient for heterologous synthesis of an active A. pasteurianus Sdh in G. oxydans. Studies with the Sdh-positive G. oxydans strain provided evidence for a limited functionality of the TCA cycle despite the absence of succinyl-CoA synthetase. PMID:26399411

  16. The TCA Pathway is an Important Player in the Regulatory Network Governing Vibrio alginolyticus Adhesion Under Adversity

    PubMed Central

    Huang, Lixing; Huang, Li; Yan, Qingpi; Qin, Yingxue; Ma, Ying; Lin, Mao; Xu, Xiaojin; Zheng, Jiang

    2016-01-01

    Adhesion is a critical step in the initial stage of Vibrio alginolyticus infection; therefore, it is important to understand the underlying mechanisms governing the adhesion of V. alginolyticus and determine if environmental factors have any effect. A greater understanding of this process may assist in developing preventive measures for reducing infection. In our previous research, we presented the first RNA-seq data from V. alginolyticus cultured under stress conditions that resulted in reduced adhesion. Based on the RNA-seq data, we found that the Tricarboxylic acid cycle (TCA pathway) might be closely related to adhesion. Environmental interactions with the TCA pathway might alter adhesion. To validate this, bioinformatics analysis, quantitative Real-Time PCR (qPCR), RNAi, and in vitro adhesion assays were performed, while V. alginolyticus was treated with various stresses including temperature, pH, salinity, and starvation. The expression of genes involved in the TCA pathway was confirmed by qPCR, which reinforced the reliability of the sequencing data. Silencing of these genes was capable of reducing the adhesion ability of V. alginolyticus. Adhesion of V. alginolyticus is influenced substantially by environmental factors and the TCA pathway is sensitive to some environmental stresses, especially changes in pH and starvation. Our results indicated that (1) the TCA pathway plays a key role in V. alginolyticus adhesion: (2) the TCA pathway is sensitive to environmental stresses. PMID:26870007

  17. Efficacy of Modified Jessner's Peel and 20% TCA Versus 20% TCA Peel Alone for the Treatment of Acne Scars

    PubMed Central

    Puri, Neerja

    2015-01-01

    Introduction: There is a paucity of studies on the use of chemical peels for acne scars among the Asian population. A trichloroacetic acid (TCA) and Jessner's combination chemical peel, originally described by Monheit, is said to be better than a TCA peel alone. Aims: The aim of the study was to compare the efficacy of 20% TCA and Jessner's solution versus 20% TCA alone for the treatment of acne scars. Materials and Methods : The patients were divided into two groups of 25 patients each. Chemical peeling was done in both the groups. In Group I, chemical peeling with Jessner's peel followed by 20% TCA was done and in Group II patients chemical peeling with 20% TCA peel alone was done. Results: In Group I (Jessner's peel and 20% TCA), mild improvement of acne scars was seen in 8% cases, moderate improvement in 32% cases and marked improvement of acne scars was seen in 60% patients. In Group II (20% TCA), mild improvement of acne scars was seen in 32% cases, moderate improvement in 40% cases and marked improvement of acne scars was seen in 28% patients. But, the difference in improvement of acne scars was not statistically significant in both the groups (P value > 0.05). PMID:25949022

  18. In folio respiratory fluxomics revealed by 13C isotopic labeling and H/D isotope effects highlight the noncyclic nature of the tricarboxylic acid "cycle" in illuminated leaves.

    PubMed

    Tcherkez, Guillaume; Mahé, Aline; Gauthier, Paul; Mauve, Caroline; Gout, Elizabeth; Bligny, Richard; Cornic, Gabriel; Hodges, Michael

    2009-10-01

    While the possible importance of the tricarboxylic acid (TCA) cycle reactions for leaf photosynthesis operation has been recognized, many uncertainties remain on whether TCA cycle biochemistry is similar in the light compared with the dark. It is widely accepted that leaf day respiration and the metabolic commitment to TCA decarboxylation are down-regulated in illuminated leaves. However, the metabolic basis (i.e. the limiting steps involved in such a down-regulation) is not well known. Here, we investigated the in vivo metabolic fluxes of individual reactions of the TCA cycle by developing two isotopic methods, (13)C tracing and fluxomics and the use of H/D isotope effects, with Xanthium strumarium leaves. We provide evidence that the TCA "cycle" does not work in the forward direction like a proper cycle but, rather, operates in both the reverse and forward directions to produce fumarate and glutamate, respectively. Such a functional division of the cycle plausibly reflects the compromise between two contrasted forces: (1) the feedback inhibition by NADH and ATP on TCA enzymes in the light, and (2) the need to provide pH-buffering organic acids and carbon skeletons for nitrate absorption and assimilation. PMID:19675152

  19. Coordination polymers of Fe(iii) and Al(iii) ions with TCA ligand: distinctive fluorescence, CO2 uptake, redox-activity and oxygen evolution reaction.

    PubMed

    Dhara, Barun; Sappati, Subrahmanyam; Singh, Santosh K; Kurungot, Sreekumar; Ghosh, Prasenjit; Ballav, Nirmalya

    2016-04-28

    Fe and Al belong to different groups in the periodic table, one from the p-block and the other from the d-block. In spite of their different groups, they have the similarity of exhibiting a stable 3+ oxidation state. Here we have prepared Fe(iii) and Al(iii) based coordination polymers in the form of metal-organic gels with the 4,4',4''-tricarboxyltriphenylamine (TCA) ligand, namely Fe-TCA and Al-TCA, and evaluated some important physicochemical properties. Specifically, the electrical conductivity, redox-activity, porosity, and electrocatalytic activity (oxygen evolution reaction) of the Fe-TCA system were noted to be remarkably higher than those of the Al-TCA system. As for the photophysical properties, almost complete quenching of the fluorescence originating from TCA was observed in case of the Fe-TCA system, whereas for the Al-TCA system a significant retention of fluorescence with red-shifted emission was observed. Quantum mechanical calculations based on density functional theory (DFT) were performed to unravel the origin of such discriminative behaviour of these coordination polymer systems. PMID:26961352

  20. Multi-layer canard cycles and translated power functions

    NASA Astrophysics Data System (ADS)

    Dumortier, Freddy; Roussarie, Robert

    The paper deals with two-dimensional slow-fast systems and more specifically with multi-layer canard cycles. These are canard cycles passing through n layers of fast orbits, with n⩾2. The canard cycles are subject to n generic breaking mechanisms and we study the limit cycles that can be perturbed from the generic canard cycles of codimension n. We prove that this study can be reduced to the investigation of the fixed points of iterated translated power functions.

  1. Functional interplay between the cell cycle and cell phenotypes.

    PubMed

    Chen, Wei-Chiang; Wu, Pei-Hsun; Phillip, Jude M; Khatau, Shyam B; Choi, Jae Min; Dallas, Matthew R; Konstantopoulos, Konstantinos; Sun, Sean X; Lee, Jerry S H; Hodzic, Didier; Wirtz, Denis

    2013-03-01

    Cell cycle distribution of adherent cells is typically assessed using flow cytometry, which precludes the measurements of many cell properties and their cycle phase in the same environment. Here we develop and validate a microscopy system to quantitatively analyze the cell-cycle phase of thousands of adherent cells and their associated cell properties simultaneously. This assay demonstrates that population-averaged cell phenotypes can be written as a linear combination of cell-cycle fractions and phase-dependent phenotypes. By perturbing the cell cycle through inhibition of cell-cycle regulators or changing nuclear morphology by depletion of structural proteins, our results reveal that cell cycle regulators and structural proteins can significantly interfere with each other's prima facie functions. This study introduces a high-throughput method to simultaneously measure the cell cycle and phenotypes at single-cell resolution, which reveals a complex functional interplay between the cell cycle and cell phenotypes. PMID:23319145

  2. Preliminary Evaluation of Nonlinear Effects on TCA Flutter

    NASA Technical Reports Server (NTRS)

    Arslan, Alan E.; Hartwich, Peter M.; Baker, Myles L.

    1998-01-01

    The objective of this study is to investigate the effect of nonlinear aerodynamics, especially at high angles-of-attack with leading-edge separation, on the TCA flutter properties at transonic speeds. In order to achieve that objective, flutter simulations with Navier-Stokes CFD must be performed. To this end, time-marching Navier-Stokes solutions are computed for the TCA wing/body configuration at high angles-of-attack in transonic flight regimes. The approach is to perform non-linear flutter calculations on the TCA at two angles-of-attack, the first one being a case with attached flow (a=2.8 degrees) and the second one being a high angle-of-attack case with a wing leading edge vortex (a=12.11 degrees). Comparisons of the resulting histories and frequency damping information for both angles-of-attack will evaluate the impact of high-alpha aerodynamics on flutter.

  3. TCA1, a single nuclear-encoded translational activator specific for petA mRNA in Chlamydomonas reinhardtii chloroplast.

    PubMed Central

    Wostrikoff, K; Choquet, Y; Wollman, F A; Girard-Bascou, J

    2001-01-01

    We isolated seven allelic nuclear mutants of Chlamydomonas reinhardtii specifically blocked in the translation of cytochrome f, a major chloroplast-encoded subunit of the photosynthetic electron transport chain encoded by the petA gene. We recovered one chloroplast suppressor in which the coding region of petA was now expressed under the control of a duplicated 5' untranslated region from another open reading frame of presently unknown function. Since we also recovered 14 nuclear intragenic suppressors, we ended up with 21 alleles of a single nuclear gene we called TCA1 for translation of cytochrome b(6)f complex petA mRNA. The high number of TCA1 alleles, together with the absence of genetic evidence for other nuclear loci controlling translation of the chloroplast petA gene, strongly suggests that TCA1 is the only trans-acting factor. We studied the assembly-dependent regulation of cytochrome f translation--known as the CES process--in TCA1-mutated contexts. In the presence of a leaky tca1 allele, we observed that the regulation of cytochrome f translation was now exerted within the limits of the restricted translational activation conferred by the altered version of TCA1 as predicted if TCA1 was the ternary effector involved in the CES process. PMID:11560891

  4. Description of sunspot cycles by orthogonal functions

    NASA Astrophysics Data System (ADS)

    Teuber, D. L.; Reichmann, E. J.; Wilson, R. M.

    1984-10-01

    Based on the principal component analysis technique and evidence for a 22-yr double-sunspot cycle periodicity. The time series of sunspot numbers is represented as a sum of mutually orthogonal eigenvectors in the time domain. It is shown that the first two eigenvectors account for about 90 percent of the cumulative 'signal power,' and that this is sufficient for reconstruction of the raw data curve. It is also noted that the second eigenvector behaves as the time derivative of the first, and that a phase-plane plot of these eigenvectors (i.e. a plot of a variable vs. its rate of change) suggests that the sun's sunspot cycle is driven by an oscillator; the implication is that, embedded within the sun, a chronometer is at work (e.g. Dicke, 1979).

  5. Description of sunspot cycles by orthogonal functions

    NASA Technical Reports Server (NTRS)

    Teuber, D. L.; Reichmann, E. J.; Wilson, R. M.

    1984-01-01

    Based on the principal component analysis technique and evidence for a 22-yr double-sunspot cycle periodicity. The time series of sunspot numbers is represented as a sum of mutually orthogonal eigenvectors in the time domain. It is shown that the first two eigenvectors account for about 90 percent of the cumulative 'signal power,' and that this is sufficient for reconstruction of the raw data curve. It is also noted that the second eigenvector behaves as the time derivative of the first, and that a phase-plane plot of these eigenvectors (i.e. a plot of a variable vs. its rate of change) suggests that the sun's sunspot cycle is driven by an oscillator; the implication is that, embedded within the sun, a chronometer is at work (e.g. Dicke, 1979).

  6. Identification of fuel cycle simulator functionalities for analysis of transition to a new fuel cycle

    DOE PAGESBeta

    Brown, Nicholas R.; Carlsen, Brett W.; Dixon, Brent W.; Feng, Bo; Greenberg, Harris R.; Hays, Ross D.; Passerini, Stefano; Todosow, Michael; Worrall, Andrew

    2016-06-09

    Dynamic fuel cycle simulation tools are intended to model holistic transient nuclear fuel cycle scenarios. As with all simulation tools, fuel cycle simulators require verification through unit tests, benchmark cases, and integral tests. Model validation is a vital aspect as well. Although compara-tive studies have been performed, there is no comprehensive unit test and benchmark library for fuel cycle simulator tools. The objective of this paper is to identify the must test functionalities of a fuel cycle simulator tool within the context of specific problems of interest to the Fuel Cycle Options Campaign within the U.S. Department of Energy smore » Office of Nuclear Energy. The approach in this paper identifies the features needed to cover the range of promising fuel cycle options identified in the DOE-NE Fuel Cycle Evaluation and Screening (E&S) and categorizes these features to facilitate prioritization. Features were categorized as essential functions, integrating features, and exemplary capabilities. One objective of this paper is to propose a library of unit tests applicable to each of the essential functions. Another underlying motivation for this paper is to encourage an international dialog on the functionalities and standard test methods for fuel cycle simulator tools.« less

  7. Analysis and Multipoint Design of the TCA Concept

    NASA Technical Reports Server (NTRS)

    Krist, Steven E.; Bauer, Steven X. S.; Buning, Pieter G.

    1999-01-01

    The goal in this effort is to analyze the baseline TCA concept at transonic and supersonic cruise, then apply the natural flow wing design concept to obtain multipoint performance improvements. Analyses are conducted with OVERFLOW, a Navier-Stokes code for overset grids, using PEGSUS to compute the interpolations between the overset grids.

  8. Glycation inhibits trichloroacetic acid (TCA)-induced whey protein precipitation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Four different WPI saccharide conjugates were successfully prepared to test whether glycation could inhibit WPI precipitation induced by trichloroacetic acid (TCA). Conjugates molecular weights after glycation were analyzed with SDS-PAGE. No significant secondary structure change due to glycation wa...

  9. Vesicular stomatitis virus P function depends on cellular growth cycle.

    PubMed

    Stanners, C P; Kennedy, S; Poliquin, L

    1987-09-01

    The P function of vesicular stomatitis virus (VSV) is defined as the viral function which results in a reduced rate of total protein synthesis (viral plus cellular) arising from a nonspecific reduction in the efficiency of the translational machinery in infected cells. The existence of P function has been challenged by Lodish and Porter who were unable to detect it in L-strain mouse cells infected with wild-type VSV (HR) or, as expected, with the P- mutant, T1026-R1. Although other groups have subsequently confirmed the existence of P function and the difference between HR and T1026-R1, we have sought an explanation for the difference between Lodish and Porter's results and those of other laboratories. We show that the VSV P function depends on the phase of the growth cycle of infected L-cell cultures. In very early exponential phase, as used by Lodish and Porter, HR has very little demonstrable P function; as the growth cycle proceeds toward stationary phase, P function becomes more and more manifest. Under the same conditions, T1026-R1 shows no P function throughout the growth cycle. Furthermore we show that the VSV M protein mutant tsG31 has a P++ phenotype reducing total protein synthesis below that seen with wild-type HR. P function can be observed in cells infected with tsG31, even early in the exponential phase of the cellular growth cycle. PMID:2820132

  10. Physical interactions between tricarboxylic acid cycle enzymes in Bacillus subtilis: evidence for a metabolon.

    PubMed

    Meyer, Frederik M; Gerwig, Jan; Hammer, Elke; Herzberg, Christina; Commichau, Fabian M; Völker, Uwe; Stülke, Jörg

    2011-01-01

    The majority of all proteins of a living cell is active in complexes rather than in an isolated way. These protein-protein interactions are of high relevance for many biological functions. In addition to many well established protein complexes an increasing number of protein-protein interactions, which form rather transient complexes has recently been discovered. The formation of such complexes seems to be a common feature especially for metabolic pathways. In the Gram-positive model organism Bacillus subtilis, we identified a protein complex of three citric acid cycle enzymes. This complex consists of the citrate synthase, the isocitrate dehydrogenase, and the malate dehydrogenase. Moreover, fumarase and aconitase interact with malate dehydrogenase and with each other. These five enzymes catalyze sequential reaction of the TCA cycle. Thus, this interaction might be important for a direct transfer of intermediates of the TCA cycle and thus for elevated metabolic fluxes via substrate channeling. In addition, we discovered a link between the TCA cycle and gluconeogenesis through a flexible interaction of two proteins: the association between the malate dehydrogenase and phosphoenolpyruvate carboxykinase is directly controlled by the metabolic flux. The phosphoenolpyruvate carboxykinase links the TCA cycle with gluconeogenesis and is essential for B. subtilis growing on gluconeogenic carbon sources. Only under gluconeogenic growth conditions an interaction of these two proteins is detectable and disappears under glycolytic growth conditions. PMID:20933603

  11. Nitrogen cycling in corals: the key to understanding holobiont functioning?

    PubMed

    Rädecker, Nils; Pogoreutz, Claudia; Voolstra, Christian R; Wiedenmann, Jörg; Wild, Christian

    2015-08-01

    Corals are animals that form close mutualistic associations with endosymbiotic photosynthetic algae of the genus Symbiodinium. Together they provide the calcium carbonate framework of coral reef ecosystems. The importance of the microbiome (i.e., bacteria, archaea, fungi, and viruses) to holobiont functioning has only recently been recognized. Given that growth and density of Symbiodinium within the coral host is highly dependent on nitrogen availability, nitrogen-cycling microbes may be of fundamental importance to the stability of the coral-algae symbiosis and holobiont functioning, in particular under nutrient-enriched and -depleted scenarios. We summarize what is known about nitrogen cycling in corals and conclude that disturbance of microbial nitrogen cycling may be tightly linked to coral bleaching and disease. PMID:25868684

  12. Intellectual Performance as a Function of Repression and Menstrual Cycle.

    ERIC Educational Resources Information Center

    Englander-Golden, Paula; And Others

    Performance on complex (Space Relations and Verbal Reasoning) and simple (Digit Symbol) tests was investigated as a function of Byrne's Repression-Sensitization (RS) dimension, phase of menstrual cycle and premenstrual-menstrual (PM) symptomatology in a group of females not taking oral contraceptives. Two control groups, consisting of males and…

  13. An ATP and oxalate generating variant tricarboxylic acid cycle counters aluminum toxicity in Pseudomonas fluorescens.

    PubMed

    Singh, Ranji; Lemire, Joseph; Mailloux, Ryan J; Chénier, Daniel; Hamel, Robert; Appanna, Vasu D

    2009-01-01

    Although the tricarboxylic acid (TCA) cycle is essential in almost all aerobic organisms, its precise modulation and integration in global cellular metabolism is not fully understood. Here, we report on an alternative TCA cycle uniquely aimed at generating ATP and oxalate, two metabolites critical for the survival of Pseudomonas fluorescens. The upregulation of isocitrate lyase (ICL) and acylating glyoxylate dehydrogenase (AGODH) led to the enhanced synthesis of oxalate, a dicarboxylic acid involved in the immobilization of aluminum (Al). The increased activity of succinyl-CoA synthetase (SCS) and oxalate CoA-transferase (OCT) in the Al-stressed cells afforded an effective route to ATP synthesis from oxalyl-CoA via substrate level phosphorylation. This modified TCA cycle with diminished efficacy in NADH production and decreased CO(2)-evolving capacity, orchestrates the synthesis of oxalate, NADPH, and ATP, ingredients pivotal to the survival of P. fluorescens in an Al environment. The channeling of succinyl-CoA towards ATP formation may be an important function of the TCA cycle during anaerobiosis, Fe starvation and O(2)-limited conditions. PMID:19809498

  14. Alternative reactions at the interface of glycolysis and citric acid cycle in Saccharomyces cerevisiae.

    PubMed

    van Rossum, Harmen M; Kozak, Barbara U; Niemeijer, Matthijs S; Duine, Hendrik J; Luttik, Marijke A H; Boer, Viktor M; Kötter, Peter; Daran, Jean-Marc G; van Maris, Antonius J A; Pronk, Jack T

    2016-05-01

    Pyruvate and acetyl-coenzyme A, located at the interface between glycolysis and TCA cycle, are important intermediates in yeast metabolism and key precursors for industrially relevant products. Rational engineering of their supply requires knowledge of compensatory reactions that replace predominant pathways when these are inactivated. This study investigates effects of individual and combined mutations that inactivate the mitochondrial pyruvate-dehydrogenase (PDH) complex, extramitochondrial citrate synthase (Cit2) and mitochondrial CoA-transferase (Ach1) in Saccharomyces cerevisiae. Additionally, strains with a constitutively expressed carnitine shuttle were constructed and analyzed. A predominant role of the PDH complex in linking glycolysis and TCA cycle in glucose-grown batch cultures could be functionally replaced by the combined activity of the cytosolic PDH bypass and Cit2. Strongly impaired growth and a high incidence of respiratory deficiency in pda1Δ ach1Δ strains showed that synthesis of intramitochondrial acetyl-CoA as a metabolic precursor requires activity of either the PDH complex or Ach1. Constitutive overexpression of AGP2, HNM1, YAT2, YAT1, CRC1 and CAT2 enabled the carnitine shuttle to efficiently link glycolysis and TCA cycle in l-carnitine-supplemented, glucose-grown batch cultures. Strains in which all known reactions at the glycolysis-TCA cycle interface were inactivated still grew slowly on glucose, indicating additional flexibility at this key metabolic junction. PMID:26895788

  15. Renal function and plasma volume following ultramarathon cycling.

    PubMed

    Neumayr, G; Pfister, R; Hoertnagl, H; Mitterbauer, G; Prokop, W; Joannidis, M

    2005-01-01

    In recreational cyclists marathon cycling influences renal function only on a minimal scale. Respective information on extreme ultramarathon cycling in better trained athletes is not available. The objective was to evaluate the renal and haematological effects of ultraendurance cycling in the world's best ultramarathon cyclists. Creatinine (CR), urea, haemoglobin (Hb), haematocrit (Hct) and plasma volume (PV) were investigated in 16 male ultramarathon cyclists during the 1st Race Across the Alps in 2001 (distance: 525 km; cumulative altitude difference: 12,600 m). All renal functional parameters were normal pre-exercise. During the race serum CR, urea and uric acid rose significantly by 33, 97 % and 18 % (p <0.001 respectively) and nearly normalised again on the following day. The decline in calculated CR clearance was 25 %. There was a negative correlation (r=- 0.575, p=0.02) between the rise in serum CR and the athlete's training kilometers. The serum urea/CR ratio rose above 40 in 12 athletes (75 %). Mean fractional sodium excretion and fractional uric acid excretion fell below 0.5 % (p <0.001) and 7 %, indicating reduced renal perfusion. The deflection of the renal functional parameters was temporary and nearly gone after 24 hours of recovery. Hct declined during the race from 0.44 to 0.42, and continued falling on the next day (0.42 --> 0.40; p <0.001). The corresponding rises in calculated PV were + 8 % and + 22 %. The study affirms that in world class cyclists the enormous strains of ultramarathon cycling influence renal function only on a minimal scale. The impact on the PV, however, is pronounced leading to marked haemodilution post-exercise. This very temporary "impairment of renal function" seems to be the physiological response to ultramarathon cycling and may be attenuated to some extent by preceding high-volume training. PMID:15643528

  16. Thioredoxin, a master regulator of the tricarboxylic acid cycle in plant mitochondria

    PubMed Central

    Daloso, Danilo M.; Müller, Karolin; Obata, Toshihiro; Florian, Alexandra; Tohge, Takayuki; Bottcher, Alexandra; Riondet, Christophe; Bariat, Laetitia; Carrari, Fernando; Nunes-Nesi, Adriano; Buchanan, Bob B.; Reichheld, Jean-Philippe; Araújo, Wagner L.; Fernie, Alisdair R.

    2015-01-01

    Plant mitochondria have a fully operational tricarboxylic acid (TCA) cycle that plays a central role in generating ATP and providing carbon skeletons for a range of biosynthetic processes in both heterotrophic and photosynthetic tissues. The cycle enzyme-encoding genes have been well characterized in terms of transcriptional and effector-mediated regulation and have also been subjected to reverse genetic analysis. However, despite this wealth of attention, a central question remains unanswered: “What regulates flux through this pathway in vivo?” Previous proteomic experiments with Arabidopsis discussed below have revealed that a number of mitochondrial enzymes, including members of the TCA cycle and affiliated pathways, harbor thioredoxin (TRX)-binding sites and are potentially redox-regulated. We have followed up on this possibility and found TRX to be a redox-sensitive mediator of TCA cycle flux. In this investigation, we first characterized, at the enzyme and metabolite levels, mutants of the mitochondrial TRX pathway in Arabidopsis: the NADP-TRX reductase a and b double mutant (ntra ntrb) and the mitochondrially located thioredoxin o1 (trxo1) mutant. These studies were followed by a comparative evaluation of the redistribution of isotopes when 13C-glucose, 13C-malate, or 13C-pyruvate was provided as a substrate to leaves of mutant or WT plants. In a complementary approach, we evaluated the in vitro activities of a range of TCA cycle and associated enzymes under varying redox states. The combined dataset suggests that TRX may deactivate both mitochondrial succinate dehydrogenase and fumarase and activate the cytosolic ATP-citrate lyase in vivo, acting as a direct regulator of carbon flow through the TCA cycle and providing a mechanism for the coordination of cellular function. PMID:25646482

  17. Novel functions of core cell cycle regulators in neuronal migration.

    PubMed

    Godin, Juliette D; Nguyen, Laurent

    2014-01-01

    The cerebral cortex is one of the most intricate regions of the brain, which required elaborated cell migration patterns for its development. Experimental observations show that projection neurons migrate radially within the cortical wall, whereas interneurons migrate along multiple tangential paths to reach the developing cortex. Tight regulation of the cell migration processes ensures proper positioning and functional integration of neurons to specific cerebral cortical circuits. Disruption of neuronal migration often lead to cortical dysfunction and/or malformation associated with neurological disorders. Unveiling the molecular control of neuronal migration is thus fundamental to understand the physiological or pathological development of the cerebral cortex. Generation of functional cortical neurons is a complex and stratified process that relies on decision of neural progenitors to leave the cell cycle and generate neurons that migrate and differentiate to reach their final position in the cortical wall. Although accumulating work shed some light on the molecular control of neuronal migration, we currently do not have a comprehensive understanding of how cell cycle exit and migration/differentiation are coordinated at the molecular level. The current chapter tends to lift the veil on this issue by discussing how core cell cycle regulators, and in particular p27(Kip1) acts as a multifunctional protein to control critical steps of neuronal migration through activities that go far beyond cell cycle regulation. PMID:24243100

  18. Functional Nanoscale Imaging of Synaptic Vesicle Cycling with Superfast Fixation.

    PubMed

    Schikorski, Thomas

    2016-01-01

    Functional imaging is the measurement of structural changes during an ongoing physiological process over time. In many cases, functional imaging has been implemented by tracking a fluorescent signal in live imaging sessions. Electron microscopy, however, excludes live imaging which has hampered functional imaging approaches on the ultrastructural level. This barrier was broken with the introduction of superfast fixation. Superfast fixation is capable of stopping and fixing membrane traffic at sufficient speed to capture a physiological process at a distinct functional state. Applying superfast fixation at sequential time points allows tracking of membrane traffic in a step-by-step fashion.This technique has been applied to track labeled endocytic vesicles at central synapses as they pass through the synaptic vesicle cycle. At synapses, neurotransmitter is released from synaptic vesicles (SVs) via fast activity-dependent exocytosis. Exocytosis is coupled to fast endocytosis that retrieves SVs components from the plasma membrane shortly after release. Fluorescent FM dyes that bind to the outer leaflet of the plasma membrane enter the endocytic vesicle during membrane retrieval and remain trapped in endocytic vesicles have been widely used to study SV exo-endocytic cycling in live imaging sessions. FM dyes can also be photoconverted into an electron-dense diaminobenzidine polymer which allows the investigation of SV cycling in the electron microscope. The combination of FM labeling with superfast fixation made it possible to track the fine structure of endocytic vesicles at 1 s intervals. Because this combination is not specialized to SV cycling, many other cellular processes can be studied. Furthermore, the technique is easy to set up and cost effective.This chapter describes activity-dependent FM dye labeling of SVs in cultured hippocampal neurons, superfast microwave-assisted fixation, photoconversion of the fluorescent endocytic vesicles, and the analysis of

  19. Reductive photo-dechlorination (RPD) technology for remediation of TCA

    SciTech Connect

    Lavid, M.; Gulati, S.K.; Teytelboym, M.

    1994-12-31

    The Reductive Photo-Dechlorination (RPD) technology uses ultraviolet light in a reducing atmosphere to remove chlorine atoms from organo-chlorine waste streams at low to moderate temperatures. Because chlorinated organics are destroyed in a reducing environment, process products include valuable hydrocarbons and hydrogen chloride with no toxic oxygenated chlorocarbon by-products. The RPD process is designed specifically to treat volatile chlorinated wastes in the liquid or gaseous phases. Field applications include organic wastes produced from soil venting operations and those adsorbed on activated carbon. The process can also be used to pretreat gas streams entering catalytic oxidation systems, reducing chlorine content and hereby protecting the catalyst against poisoning. This paper focuses on photo-thermal remediation of 1,1,1-trichloroethane (TCA). It describes bench-scale experimental results, kinetic modeling predictions, and selected design parameters for a pilot-scale demonstration.

  20. Cell Cycle Regulatory Functions of the KSHV Oncoprotein LANA

    PubMed Central

    Wei, Fang; Gan, Jin; Wang, Chong; Zhu, Caixia; Cai, Qiliang

    2016-01-01

    Manipulation of cell cycle is a commonly employed strategy of viruses for achieving a favorable cellular environment during infection. Kaposi’s sarcoma-associated herpesvirus (KSHV), the primary etiological agent of several human malignancies including Kaposi’s sarcoma, and primary effusion lymphoma, encodes several oncoproteins that deregulate normal physiology of cell cycle machinery to persist with endothelial cells and B cells and subsequently establish a latent infection. During latency, only a small subset of viral proteins is expressed. Latency-associated nuclear antigen (LANA) is one of the latent antigens shown to be essential for transformation of endothelial cells in vitro. It has been well demonstrated that LANA is critical for the maintenance of latency, episome DNA replication, segregation and gene transcription. In this review, we summarize recent studies and address how LANA functions as an oncoprotein to steer host cell cycle-related events including proliferation and apoptosis by interacting with various cellular and viral factors, and highlight the potential therapeutic strategy of disrupting LANA-dependent signaling as targets in KSHV-associated cancers. PMID:27065950

  1. Vx-770 potentiates CFTR function by promoting decoupling between the gating cycle and ATP hydrolysis cycle.

    PubMed

    Jih, Kang-Yang; Hwang, Tzyh-Chang

    2013-03-12

    Vx-770 (Ivacaftor), a Food and Drug Administration (FDA)-approved drug for clinical application to patients with cystic fibrosis (CF), shifts the paradigm from conventional symptomatic treatments to therapeutics directly tackling the root of the disease: functional defects of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel caused by pathogenic mutations. The underlying mechanism for the action of Vx-770 remains elusive partly because this compound not only increases the activity of wild-type (WT) channels whose gating is primarily controlled by ATP binding/hydrolysis, but also improves the function of G551D-CFTR, a disease-associated mutation that abolishes CFTR's responsiveness to ATP. Here we provide a unified theory to account for this dual effect of Vx-770. We found that Vx-770 enhances spontaneous, ATP-independent activity of WT-CFTR to a similar magnitude as its effects on G551D channels, a result essentially explaining Vx-770's effect on G551D-CFTR. Furthermore, Vx-770 increases the open time of WT-CFTR in an [ATP]-dependent manner. This distinct kinetic effect is accountable with a newly proposed CFTR gating model depicting an [ATP]-dependent "reentry" mechanism that allows CFTR shuffling among different open states by undergoing multiple rounds of ATP hydrolysis. We further examined the effect of Vx-770 on R352C-CFTR, a unique mutant that allows direct observation of hydrolysis-triggered gating events. Our data corroborate that Vx-770 increases the open time of WT-CFTR by stabilizing a posthydrolytic open state and thereby fosters decoupling between the gating cycle and ATP hydrolysis cycle. The current study also suggests that this unique mechanism of drug action can be further exploited to develop strategies that enhance the function of CFTR. PMID:23440202

  2. Vx-770 potentiates CFTR function by promoting decoupling between the gating cycle and ATP hydrolysis cycle

    PubMed Central

    Jih, Kang-Yang; Hwang, Tzyh-Chang

    2013-01-01

    Vx-770 (Ivacaftor), a Food and Drug Administration (FDA)-approved drug for clinical application to patients with cystic fibrosis (CF), shifts the paradigm from conventional symptomatic treatments to therapeutics directly tackling the root of the disease: functional defects of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel caused by pathogenic mutations. The underlying mechanism for the action of Vx-770 remains elusive partly because this compound not only increases the activity of wild-type (WT) channels whose gating is primarily controlled by ATP binding/hydrolysis, but also improves the function of G551D-CFTR, a disease-associated mutation that abolishes CFTR’s responsiveness to ATP. Here we provide a unified theory to account for this dual effect of Vx-770. We found that Vx-770 enhances spontaneous, ATP-independent activity of WT-CFTR to a similar magnitude as its effects on G551D channels, a result essentially explaining Vx-770’s effect on G551D-CFTR. Furthermore, Vx-770 increases the open time of WT-CFTR in an [ATP]-dependent manner. This distinct kinetic effect is accountable with a newly proposed CFTR gating model depicting an [ATP]-dependent “reentry” mechanism that allows CFTR shuffling among different open states by undergoing multiple rounds of ATP hydrolysis. We further examined the effect of Vx-770 on R352C-CFTR, a unique mutant that allows direct observation of hydrolysis-triggered gating events. Our data corroborate that Vx-770 increases the open time of WT-CFTR by stabilizing a posthydrolytic open state and thereby fosters decoupling between the gating cycle and ATP hydrolysis cycle. The current study also suggests that this unique mechanism of drug action can be further exploited to develop strategies that enhance the function of CFTR. PMID:23440202

  3. Evaluation results of xTCA equipment for HEP experiments at CERN

    NASA Astrophysics Data System (ADS)

    Di Cosmo, M.; Bobillier, V.; Haas, S.; Joos, M.; Mico, S.; Vasey, F.; Vichoudis, P.

    2013-12-01

    The MicroTCA and AdvancedTCA industry standards are candidate modular electronic platforms for the upgrade of the current generation of high energy physics experiments. The PH-ESE group at CERN launched in 2011 the xTCA evaluation project with the aim of performing technical evaluations and eventually providing support for commercially available components. Different devices from different vendors have been acquired, evaluated and interoperability tests have been performed. This paper presents the test procedures and facilities that have been developed and focuses on the evaluation results including electrical, thermal and interoperability aspects.

  4. Thermal-Cycle Memory Functions and Ising Dynamics

    NASA Astrophysics Data System (ADS)

    Johnson, Brad; Patrick, David

    2008-03-01

    The Ising model provides a rich system for the study of a variety of correlated systems. In this talk, we present the results of numerical studies of 2- and 3-dimensional Ising spin systems subjected to thermal cycling from an ordered state to states with a fixed order parameter (<1), but with differing overall morphologies, and back to a quenched state. We find that for systems with initial states generated by thermal disordering above Tc, the initial state of a given order parameter has larger `islands' of like-spin (than the case for random disorder with the same overall order parameter) and consequent quenches of the state to Tfunction we find is given by (B.Sinit), where Sinit is the order parameter of the initial state, is the average quenched order parameter, and B is a constant that depends upon the morphology of the initial state. The reason for the strong correlation stems from the energies associated with spins at the borders of large clusters. This `memory effect' does not occur in 3D (due to the larger number of near-neighbors). Finally, we discuss the `memory function' in the context of interfacial states of liquid crystals.

  5. ANALYSIS AND SIMULATION OF RECYCLE SO2-LIME SLURRY IN TCA (TURBULENT CONTACT ABSORBER) SCRUBBER SYSTEM

    EPA Science Inventory

    The report gives results of an analysis of flue gas desulfurization by a turbulent contact absorber (TCA) employing lime slurry, including the development of performance equations for the scrubber-hold tank recycle system. Performance characteristics investigated include pressure...

  6. Molecular evolution of SRP cycle components: functional implications.

    PubMed Central

    Althoff, S; Selinger, D; Wise, J A

    1994-01-01

    Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein that targets a subset of nascent presecretory proteins to the endoplasmic reticulum membrane. We have considered the SRP cycle from the perspective of molecular evolution, using recently determined sequences of genes or cDNAs encoding homologs of SRP (7SL) RNA, the Srp54 protein (Srp54p), and the alpha subunit of the SRP receptor (SR alpha) from a broad spectrum of organisms, together with the remaining five polypeptides of mammalian SRP. Our analysis provides insight into the significance of structural variation in SRP RNA and identifies novel conserved motifs in protein components of this pathway. The lack of congruence between an established phylogenetic tree and size variation in 7SL homologs implies the occurrence of several independent events that eliminated more than half the sequence content of this RNA during bacterial evolution. The apparently non-essential structures are domain I, a tRNA-like element that is constant in archaea, varies in size among eucaryotes, and is generally missing in bacteria, and domain III, a tightly base-paired hairpin that is present in all eucaryotic and archeal SRP RNAs but is invariably absent in bacteria. Based on both structural and functional considerations, we propose that the conserved core of SRP consists minimally of the 54 kDa signal sequence-binding protein complexed with the loosely base-paired domain IV helix of SRP RNA, and is also likely to contain a homolog of the Srp68 protein. Comparative sequence analysis of the methionine-rich M domains from a diverse array of Srp54p homologs reveals an extended region of amino acid identity that resembles a recently identified RNA recognition motif. Multiple sequence alignment of the G domains of Srp54p and SR alpha homologs indicates that these two polypeptides exhibit significant similarity even outside the four GTPase consensus motifs, including a block of nine contiguous amino acids in a location

  7. Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2

    PubMed Central

    Forbes, Elaine M; Nieduszynska, Siân R; Brunton, Fiona K; Gibson, Joanne; Glover, L Anne; Stansfield, Ian

    2007-01-01

    Background In the C. albicans retrotransposon Tca2, the gag and pol ORFs are separated by a UGA stop codon, 3' of which is a potential RNA pseudoknot. It is unclear how the Tca2 gag UGA codon is bypassed to allow pol expression. However, in other retroelements, translational readthrough of the gag stop codon can be directed by its flanking sequence, including a 3' pseudoknot. Results The hypothesis was tested that in Tca2, gag stop codon flanking sequences direct translational readthrough and synthesis of a gag-pol fusion protein. Sequence from the Tca2 gag-UGA-pol junction (300 nt) was inserted between fused lacZ and luciferase (luc) genes in a Saccharomyces cerevisiae dual reporter construct. Although downstream of UGA, luc was expressed, but its expression was unaffected by inserting additional stop codons at the 3' end of lacZ. Luc expression was instead being driven by a previously unknown minor promoter activity within the gag-pol junction region. Evidence together indicated that junction sequence alone cannot direct UGA readthrough. Using reporter genes in C. albicans, the activities of this gag-pol junction promoter and the Tca2 long terminal repeat (LTR) promoter were compared. Of the two promoters, only the LTR promoter was induced by heat-shock, which also triggers retrotransposition. Tca2 pol protein, epitope-tagged in C. albicans to allow detection, was also heat-shock induced, indicating that pol proteins were expressed from a gag-UGA-pol RNA. Conclusion This is the first demonstration that the LTR promoter directs Tca2 pol protein expression, and that pol proteins are translated from a gag-pol RNA, which thus requires a mechanism for stop codon bypass. However, in contrast to most other retroelement and viral readthrough signals, immediate gag UGA-flanking sequences were insufficient to direct stop readthrough in S. cerevisiae, indicating non-canonical mechanisms direct gag UGA bypass in Tca2. PMID:17961216

  8. Development of a cellular biosensor for the detection of 2,4,6-trichloroanisole (TCA).

    PubMed

    Varelas, Vassileios; Sanvicens, Nuria; M-Pilar-Marco; Kintzios, Spiridon

    2011-05-15

    2,4,6-trichloroanisole (TCA) is a microbial metabolite formed from chlorophenols through the activity of several natural fungal strains present on the cork oak bark. TCA is the primary compound responsible for the mousty/mould off-odour known as "cork taint" present in cork stoppers, wine, water and alcoholic beverages. Chromatographic and electrochemical methods are currently used for the determination of TCA, however its detection at low concentrations remains a technical challenge. The aim of this study was the development of a rapid novel biosensor system based on the Bioelectric Recognition Assay (BERA). The sensor measured the electric response of cultured membrane-engineered fibroblast cells suspended in an alginate gel matrix due to the change of their membrane potential in the presence of the analyte. Membrane-engineered cells were prepared by osmotic insertion of 0.5 μg/l of specific TCA antibodies into the membrane of the cells. The BERA-based sensor was able to detect TCA in a few minutes (3-5 min) at extremely low concentrations (10(-1)ppt), thus demonstrating higher sensitivity than the human sensory threshold. In addition, the assay was quite selective against other haloanisoles and halophenols structurally related to or co-occurring with TCA. Finally the sensor was tested against real white wine samples from cork soaks. At this real test, the BERA sensor was able to detect TCA from cork soaks rapidly (3-5 min) at very low concentrations (1.02-12 ng/l), covering the whole range for the detection threshold for wines (1.4-10 ng/l). Therefore, this novel biosensor offers new perspectives for ultra-rapid, ultra-sensitive and low-cost monitoring of TCA presence in cork and wine and possibly also other food commodities. PMID:21482306

  9. High-Level Functional and Operational Requirements for the Advanced Fuel Cycle Facilty

    SciTech Connect

    Charles Park

    2006-12-01

    High-Level Functional & Operational Requirements for the AFCF -This document describes the principal functional and operational requirements for the proposed Advanced Fuel Cycle Facility (AFCF). The AFCF is intended to be the world's foremost facility for nuclear fuel cycle research, technology development, and demonstration. The facility will also support the near-term mission to develop and demonstrate technology in support of fuel cycle needs identified by industry, and the long-term mission to retain and retain U.S. leadership in fuel cycle operations. The AFCF is essential to demonstrate a more proliferation-resistant fuel cycle and make long-term improvements in fuel cycle effectiveness, performance and economy.

  10. SWATCH: common control SW for the uTCA-based upgraded CMS L1 Trigger

    NASA Astrophysics Data System (ADS)

    Brooke, Jim; Bunkowski, Karol; Cali, Ivan; Ghabrous Larrea, Carlos; Lazaridis, Christos; Thea, Alessandro

    2015-12-01

    The CMS L1 Trigger electronics are composed of a large number of different cards based on the VMEBus standard. The majority of the system is being replaced to adapt the trigger to the higher collision rates the LHC will deliver after the LS1, the first phase on the CMS upgrade program. As a consequence, the software that controls, monitors and tests the hardware will need to be re-written. The upgraded trigger will consist of a set of general purpose boards of similar technology that follow the TCA specification, thus resulting in a more homogeneous system. A great effort has been made to identify the common firmware blocks and components shared across different cards, regardless of the role they play within the trigger data path. A similar line of work has been followed in order to identify all possible common functionalities in the control software, as well as in the database where the hardware initialisation and configuration data are stored. This will not only increase the homogeneity on the software and database sides, but it will also reduce the manpower needed to accommodate the online SW to the changes on hardware. Due to the fact that the upgrade will take place in different stages, it has been taken into consideration that these new components had to be integrated in the current SW framework. This paper presents the design of the control SW and configuration database for the upgraded L1 Trigger.

  11. Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum.

    PubMed

    Park, Yangshin; Cho, Yerim; Lee, Yong-Hwan; Lee, Yin-Won; Rhee, Sangkee

    2016-06-01

    The glyoxylate cycle bypasses a CO2-generating step in the tricarboxylic acid (TCA) cycle and efficiently assimilates C2 compounds into intermediates that can be used in later steps of the TCA cycle. It plays an essential role in pathogen survival during host infection such that the enzymes involved in this cycle have been suggested as potential drug targets against human pathogens. Isocitrate lyase (ICL) catalyzes the first-step reaction of the glyoxylate cycle, using isocitrate from the TCA cycle as the substrate to produce succinate and glyoxylate. In this study we report the crystal structure of Magnaporthe oryzae ICL in both the ligand-free form and as a complex with Mg(2+), glyoxylate, and glycerol, as well as the structure of the Fusarium graminearum ICL complexed with Mn(2+) and malonate. We also describe the ligand-induced conformational changes in the catalytic loop and C-terminal region, both of which are essential for catalysis. Using various mutant ICLs in an activity assay, we gained insight into the function of residues within the active site. These structural and functional analyses provide detailed information with regard to fungal ICLs. PMID:27016285

  12. Evaluation of a commercial AdvancedTCA board management controller solution (IPMC)

    NASA Astrophysics Data System (ADS)

    Mendez, J.; Bobillier, V.; Haas, S.; Joos, M.; Vasey, F.

    2016-02-01

    The MicroTCA (MTCA) and AdvancedTCA (ATCA) industry standards have been selected as the hardware platform for the upgrade of the electronic systems of some of the experiments at the Large Hadron Collider (LHC) . In this context, the electronics support group for experiments at CERN is running a project to perform technical evaluations of MTCA and ATCA equipment. As part of this activity, a commercial solution for an Intelligent Platform Management Controller (IPMC), an essential component of any ATCA blade design, is being evaluated. We validated the supported IPMC features, checked the interoperability and adapted the reference design for use on an existing ATCA carrier board.

  13. Metrological characterization of a cycle-ergometer to optimize the cycling induced by functional electrical stimulation on patients with stroke.

    PubMed

    Comolli, Lorenzo; Ferrante, Simona; Pedrocchi, Alessandra; Bocciolone, Marco; Ferrigno, Giancarlo; Molteni, Franco

    2010-05-01

    Functional electrical stimulation (FES) is a well established method in the rehabilitation of stroke patients. Indeed, a bilateral movement such as cycling induced by FES would be crucial for these patients who had an unilateral motor impairment and had to recover an equivalent use of limbs. The aim of this study was to develop a low-cost meteorologically qualified cycle-ergometer, optimized for patients with stroke. A commercial ergometer was instrumented with resistive strain gauges and was able to provide the torque produced at the right and left crank, independently. The developed system was integrated with a stimulator, obtaining a novel FES cycling device able to control in real-time the movement unbalance. A dynamic calibration of the sensors was performed and a total torque uncertainty was computed. The system was tested on a healthy subject and on a stroke patient. Results demonstrated that the proposed sensors could be successfully used during FES cycling sessions where the maximum torque produced is about 9Nm, an order of magnitude less than the torque produced during voluntary cycling. This FES cycling system will assist in future investigations on stroke rehabilitation by means of FES and in new exercise regimes designed specifically for patients with unilateral impairments. PMID:20171923

  14. IRIS Toxicological Review of Trichloroacetic Acid (TCA) (Interagency Science Discussion Draft)

    EPA Science Inventory

    EPA is releasing the draft report, Toxicological Review of Trichloroacetic Acid (TCA), that was distributed to Federal agencies and White House Offices for comment during the Science Discussion step of the IRIS Assessment Development ...

  15. IRIS Toxicological Review of Trichloroacetic Acid (TCA) (Interagency Science Consultation Draft)

    EPA Science Inventory

    On September 24, 2009, the Toxicological Review of Trichloroacetic Acid (TCA) and the charge to external peer reviewers were released for external peer review and public comment. The Toxicological Review and charge were reviewed internally by EPA and by other federal agencies an...

  16. PICMG xTCA Standards Extensions for Physics: New Developments & Future Plans

    SciTech Connect

    Larsen, R.S.; /SLAC

    2010-08-26

    After several years of planning and workshop meetings, a decision was reached in late 2008 to organize PICMG xTCA for Physics Technical Subcommittees to extend the ATCA and MTCA telecom standards for enhanced system performance, availability and interoperability for physics controls and applications hardware and software. Since formation in May-June 2009, the Hardware Technical Subcommittee has developed a number of ATCA, ARTM, AMC, MTCA and RTM extensions to be completed in mid-to-late 2010. The Software Technical Subcommittee is developing guidelines to promote interoperability of modules designed by industry and laboratories, in particular focusing on middleware and generic application interfaces such as Standard Process Model, Standard Device Model and Standard Hardware API. The paper describes the prototype design work completed by the lab-industry partners to date, the timeline for hardware releases to PICMG for approval, and the status of the software guidelines roadmap. The paper also briefly summarizes the program of the 4th xTCA for Physics Workshop immediately preceding the RT2010 Conference. he case for developing ATCA and MicroTCA (xTCA) specification extensions for physics has been covered in several previous papers. Briefly, ATCA and MicroTCA is the first all-serial communication platform available to the physics community to support both massively complex accelerator controls and massively large, high bandwidth and throughput experimental data acquisition systems. The major strength of xTCA is its multi-layer highly scalable managed platform architecture designed to achieve the highest possible system availability. Physics research imaging technologies have driven industrial applications in a wide range of medical scanners, for example, and in turn continue to evolve to exponentially higher speeds and resolution through new computer, communications industry and analog-to-digital conversion chip developments. The high availability managed platform is

  17. The functional cycle of visual arrestins in photoreceptor cells

    PubMed Central

    Gurevich, Vsevolod V.; Hanson, Susan M.; Song, Xiufeng; Vishnivetskiy, Sergey A.; Gurevich, Eugenia V.

    2011-01-01

    Visual arrestin-1 plays a key role in the rapid and reproducible shutoff of rhodopsin signaling. Its highly selective binding to light-activated phosphorylated rhodopsin is an integral part of the functional perfection of rod photoreceptors. Structure-function studies revealed key elements of the sophisticated molecular mechanism ensuring arrestin-1 selectivity and paved the way to the targeted manipulation of the arrestin-1 molecule to design mutants that can compensate for congenital defects in rhodopsin phosphorylation. Arrestin-1 self-association and light-dependent translocation in photoreceptor cells work together to keep a constant supply of active rhodopsin-binding arrestin-1 monomer in the outer segment. Recent discoveries of arrestin-1 interaction with other signaling proteins suggest that it is a much more versatile signaling regulator than previously thought, affecting the function of the synaptic terminals and rod survival. Elucidation of the fine molecular mechanisms of arrestin-1 interactions with rhodopsin and other binding partners is necessary for the comprehensive understanding of rod function and for devising novel molecular tools and therapeutic approaches to the treatment of visual disorders. PMID:21824527

  18. Impact of Polyphenol Antioxidants on Cycling Performance and Cardiovascular Function

    PubMed Central

    Trinity, Joel D.; Pahnke, Matthew D.; Trombold, Justin R.; Coyle, Edward F.

    2014-01-01

    This investigation sought to determine if supplementation with polyphenol antioxidant (PA) improves exercise performance in the heat (31.5 °C, 55% RH) by altering the cardiovascular and thermoregulatory responses to exercise. Twelve endurance trained athletes ingested PA or placebo (PLAC) for 7 days. Consecutive days of exercise testing were performed at the end of the supplementation periods. Cardiovascular and thermoregulatory measures were made during exercise. Performance, as measured by a 10 min time trial (TT) following 50 min of moderate intensity cycling, was not different between treatments (PLAC: 292 ± 33 W and PA: 279 ± 38 W, p = 0.12). Gross efficiency, blood lactate, maximal neuromuscular power, and ratings of perceived exertion were also not different between treatments. Similarly, performance on the second day of testing, as assessed by time to fatigue at maximal oxygen consumption, was not different between treatments (PLAC; 377 ± 117 s vs. PA; 364 ± 128 s, p = 0.61). Cardiovascular and thermoregulatory responses to exercise were not different between treatments on either day of exercise testing. Polyphenol antioxidant supplementation had no impact on exercise performance and did not alter the cardiovascular or thermoregulatory responses to exercise in the heat. PMID:24667134

  19. A phylogenetic approach to the early evolution of autotrophy: the case of the reverse TCA and the reductive acetyl-CoA pathways.

    PubMed

    Becerra, Arturo; Rivas, Mario; García-Ferris, Carlos; Lazcano, Antonio; Peretó, Juli

    2014-06-01

    In recent decades, a number of hypotheses on the autotrophic origin of life have been presented. These proposals invoke the emergence of reaction networks leading from CO or CO₂ to the organic molecules required for life. It has also been suggested that the last (universal) common ancestor (LCA or LUCA) of all extant cell lineages was a chemolitho-autotrophic thermophilic anaerobe. The antiquity of some carbon fixation pathways, the phylogenetic basal distribution of some autotrophic organisms, and the catalytic properties of iron-sulfur minerals have been advanced in support of these ideas. Here we critically examine the phylogenetic distribution and evolution of enzymes that are essential for two of the most ancient autotrophic means of metabolism: the reductive tricarboxylic acid (rTCA) cycle and the reductive acetyl-CoA pathway. Phylogenetic analysis of citryl-CoA synthetase and of citryl-CoA lyase, key enzymatic components of the rTCA cycle, and of CO dehydrogenase/acetyl-CoA synthase, a key enzyme in the reductive acetyl-CoA pathway, revealed that all three enzymes have undergone major lateral transfer events and therefore cannot be used as proof of the LCA's metabolic abilities nor as evidence of an autotrophic origin of life. PMID:26418853

  20. Treatment technologies and mechanisms for three odorants at trace level: IPMP, IBMP, and TCA.

    PubMed

    Li, Xin; Lin, Pengfei; Wang, Jun; Liu, Yuanyuan; Li, Yong; Zhang, Xiaojian; Chen, Chao

    2016-01-01

    Odour episodes caused by algal metabolites are gaining more and more attention in recent years. Besides geosmin and 2-methylisoborneol (MIB), 2-isopropyl-3-methoxypyrazine (IPMP), 2-isobutyl-3-methoxypyrazine (IBMP), and 2,4,6-trichloroanisole (TCA) have emerged to be important off-flavour sources. Their low odour threshold concentrations (several ng ·L(-1)), which are even lower than those of MIB and geosmin, pose challenges for treatment strategies. Hence, a practical and efficient mitigation technology is needed. The possible practical technologies, including powdered activated carbon (PAC) adsorption and oxidation by chlorine and potassium permanganate, were investigated. The results indicated that chlorine and potassium permanganate oxidation of the three odorants were unfeasible while PAC adsorption was effective. As for adsorption, TCA, followed by IBMP and IPMP, was most easily removed by PAC. The Freundlich model could well describe the adsorption isotherm data. The adsorption capacities for IPMP, IBMP, and TCA were described as follows: [Formula: see text], [Formula: see text], and [Formula: see text]. For five earthy/musty odorants including geosmin and MIB, octanol/water partition coefficient, molecular weight, and polarizability all promoted adsorption while aqueous solubility showed a negative influence. The hydrophobic interaction was believed to be the dominant force in the adsorption mechanism while the π-electron interaction enhanced adsorption when a benzene ring was present. This result could be used to predict the adsorption performance of emerging odorants. PMID:26150209

  1. Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle

    PubMed Central

    Zubarev, Dmitry Yu; Rappoport, Dmitrij; Aspuru-Guzik, Alán

    2015-01-01

    We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended. PMID:25620471

  2. Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle.

    PubMed

    Zubarev, Dmitry Yu; Rappoport, Dmitrij; Aspuru-Guzik, Alán

    2015-01-01

    We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended. PMID:25620471

  3. Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle

    NASA Astrophysics Data System (ADS)

    Zubarev, Dmitry Yu; Rappoport, Dmitrij; Aspuru-Guzik, Alán

    2015-01-01

    We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended.

  4. Menstrual Cycle-Related Changes of Functional Cerebral Asymmetries in Fine Motor Coordination

    ERIC Educational Resources Information Center

    Bayer, Ulrike; Hausmann, Markus

    2012-01-01

    Fluctuating sex hormone levels during the menstrual cycle have been shown to affect functional cerebral asymmetries in cognitive domains. These effects seem to result from the neuromodulatory properties of sex hormones and their metabolites on interhemispheric processing. The present study was carried out to investigate whether functional cerebral…

  5. Alternative functions of core cell cycle regulators in neuronal migration, neuronal maturation, and synaptic plasticity

    PubMed Central

    Frank, Christopher L.; Tsai, Li-Huei

    2009-01-01

    Recent studies have demonstrated that boundaries separating a cycling cell from a post-mitotic neuron are not as concrete as expected. Novel and unique physiological functions in neurons have been ascribed for proteins fundamentally required for cell cycle progression and control. These “core” cell cycle regulators serve diverse post-mitotic functions that span various developmental stages of a neuron, including neuronal migration, axonal elongation, axon pruning, dendrite morphogenesis, and synaptic maturation and plasticity. In this review, we detail the non-proliferative post-mitotic roles that these cell cycle proteins have recently been reported to play, the significance of their expression in neurons, mechanistic insight when available, and future prospects. PMID:19447088

  6. A Dysfunctional Tricarboxylic Acid Cycle Enhances Fitness of Staphylococcus epidermidis During β-Lactam Stress

    PubMed Central

    Chittezham Thomas, Vinai; Kinkead, Lauren C.; Janssen, Ashley; Schaeffer, Carolyn R.; Woods, Keith M.; Lindgren, Jill K.; Peaster, Jonathan M.; Chaudhari, Sujata S.; Sadykov, Marat; Jones, Joselyn; Mohamadi AbdelGhani, Sameh M.; Zimmerman, Matthew C.; Bayles, Kenneth W.; Somerville, Greg A.; Fey, Paul D.

    2013-01-01

    ABSTRACT A recent controversial hypothesis suggested that the bactericidal action of antibiotics is due to the generation of endogenous reactive oxygen species (ROS), a process requiring the citric acid cycle (tricarboxylic acid [TCA] cycle). To test this hypothesis, we assessed the ability of oxacillin to induce ROS production and cell death in Staphylococcus epidermidis strain 1457 and an isogenic citric acid cycle mutant. Our results confirm a contributory role for TCA-dependent ROS in enhancing susceptibility of S. epidermidis toward β-lactam antibiotics and also revealed a propensity for clinical isolates to accumulate TCA cycle dysfunctions presumably as a way to tolerate these antibiotics. The increased protection from β-lactam antibiotics could result from pleiotropic effects of a dysfunctional TCA cycle, including increased resistance to oxidative stress, reduced susceptibility to autolysis, and a more positively charged cell surface. PMID:23963176

  7. Dwell Time and Surface Parameter Effects on Removal of Silicone Oil From D6ac Steel Using TCA

    NASA Technical Reports Server (NTRS)

    Boothe, R. E.

    2003-01-01

    This study was conducted to evaluate the impact of dwell time, surface roughness, and the surface activation state on 1,1,1-trichloroethane's (TCA's) effectiveness for removing silicone oil from D6ac steel. Silicone-contaminated test articles were washed with TCA solvent, and then the surfaces were analyzed for residue, using Fourier transform infrared spectroscopy. The predominant factor affecting the ability to remove the silicone oil was surface roughness.

  8. Enhanced cycle performance of Li-S battery with a polypyrrole functional interlayer

    NASA Astrophysics Data System (ADS)

    Ma, Guoqiang; Wen, Zhaoyin; Jin, Jun; Wu, Meifen; Wu, Xiangwei; Zhang, Jingchao

    2014-12-01

    Polypyrrole functional interlayer is in-situ fabricated uniformly onto the surface of sulfur cathode to inhibit the dissolution of lithium polysulfides and protect sulfur cathode. Li-S battery with the functional inlayer shows an encouraging electrochemical performance. The initial discharge capacity is 719 mAh g-1 and the capacity retains at 846 mAh g-1 even after 200 cycles at 0.2C with an average coulombic efficiency of 94.2%. Moreover, the discharge capacities are 703 mAh g-1 and 533 mAh g-1 at 1C and 2C respectively even after 300 cycles.

  9. Animal Models for Studying the In Vivo Functions of Cell Cycle CDKs.

    PubMed

    Risal, Sanjiv; Adhikari, Deepak; Liu, Kui

    2016-01-01

    Multiple Cdks (Cdk4, Cdk6, and Cdk2) and a mitotic Cdk (Cdk1) are involved in cell cycle progression in mammals. Cyclins, Cdk inhibitors, and phosphorylations (both activating and inhibitory) at different cellular levels tightly modulate the activities of these kinases. Based on the results of biochemical studies, it was long believed that different Cdks functioned at specific stages during cell cycle progression. However, deletion of all three interphase Cdks in mice affected cell cycle entry and progression only in certain specialized cells such as hematopoietic cells, beta cells of the pancreas, pituitary lactotrophs, and cardiomyocytes. These genetic experiments challenged the prevailing biochemical model and established that Cdks function in a cell-specific, but not a stage-specific, manner during cell cycle entry and the progression of mitosis. Recent in vivo studies have further established that Cdk1 is the only Cdk that is both essential and sufficient for driving the resumption of meiosis during mouse oocyte maturation. These genetic studies suggest a minimal-essential cell cycle model in which Cdk1 is the central regulator of cell cycle progression. Cdk1 can compensate for the loss of the interphase Cdks by forming active complexes with A-, B-, E-, and D-type Cyclins in a stepwise manner. Thus, Cdk1 plays an essential role in both mitosis and meiosis in mammals, whereas interphase Cdks are dispensable. PMID:26231715

  10. Menstrual cycle-related changes of functional cerebral asymmetries in fine motor coordination.

    PubMed

    Bayer, Ulrike; Hausmann, Markus

    2012-06-01

    Fluctuating sex hormone levels during the menstrual cycle have been shown to affect functional cerebral asymmetries in cognitive domains. These effects seem to result from the neuromodulatory properties of sex hormones and their metabolites on interhemispheric processing. The present study was carried out to investigate whether functional cerebral asymmetries in fine motor coordination as reflected by manual asymmetries are also susceptible to natural sex hormonal variations during the menstrual cycle. Sixteen right-handed women with a regular menstrual cycle performed a finger tapping paradigm consisting of two conditions (simple, sequential) during the low hormone menstrual phase and the high estrogen and progesterone luteal phase. To validate the luteal phase, saliva levels of free progesterone (P) were analysed using chemiluminescence assays. As expected, normally cycling women showed a substantial decrease in manual asymmetries in a more demanding sequential tapping condition involving four fingers compared with simple (repetitive) finger tapping. This reduction in the degree of dominant (right) hand manual asymmetries was evident during the luteal phase. During the menstrual phase, however, manual asymmetries were even reversed in direction, indicating a slight advantage in favour of the non-dominant (left) hand. These findings suggest that functional cerebral asymmetries in fine motor coordination are affected by sex hormonal changes during the menstrual cycle, probably via hormonal modulations of interhemispheric interaction. PMID:22387299

  11. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect.

    PubMed

    Yergeau, Etienne; Kang, Sanghoon; He, Zhili; Zhou, Jizhong; Kowalchuk, George A

    2007-06-01

    Soil-borne microbial communities were examined via a functional gene microarray approach across a southern polar latitudinal gradient to gain insight into the environmental factors steering soil N- and C-cycling in terrestrial Antarctic ecosystems. The abundance and diversity of functional gene families were studied for soil-borne microbial communities inhabiting a range of environments from 51 degrees S (cool temperate-Falkland Islands) to 72 degrees S (cold rock desert-Coal Nunatak). The recently designed functional gene array used contains 24,243 oligonucleotide probes and covers >10,000 genes in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance and organic contaminant degradation (He et al. 2007). The detected N- and C-cycle genes were significantly different across different sampling locations and vegetation types. A number of significant trends were observed regarding the distribution of key gene families across the environments examined. For example, the relative detection of cellulose degradation genes was correlated with temperature, and microbial C-fixation genes were more present in plots principally lacking vegetation. With respect to the N-cycle, denitrification genes were linked to higher soil temperatures, and N2-fixation genes were linked to plots mainly vegetated by lichens. These microarray-based results were confirmed for a number of gene families using specific real-time PCR, enzymatic assays and process rate measurements. The results presented demonstrate the utility of an integrated functional gene microarray approach in detecting shifts in functional community properties in environmental samples and provide insight into the forces driving important processes of terrestrial Antarctic nutrient cycling. PMID:18043626

  12. Simultaneous determination of tricarboxylic acid cycle metabolites by high-performance liquid chromatography with ultraviolet detection.

    PubMed

    Shurubor, Yevgeniya I; Cooper, Arthur J L; Isakova, Elena P; Deryabina, Yulia I; Beal, M Flint; Krasnikov, Boris F

    2016-06-15

    Here we describe a simple high-performance liquid chromatography (HPLC) procedure for the simultaneous detection and quantitation in standard solutions of 13 important metabolites of cellular energy metabolism, including 9 tricarboxylic acid (TCA) cycle components and 4 additional metabolites. The metabolites are detected by their absorbance at 210 nm. The procedure does not require prior derivatization, and an analysis can be carried out at ambient temperature within 15 min. The significance of the current work is that the current HPLC procedure should motivate the development of simplified TCA cycle enzyme assays, isotopomer analysis, and determination of selected TCA metabolite levels in plasma/tissues. PMID:27001310

  13. Menstrual cycle influence on cognitive function and emotion processing—from a reproductive perspective

    PubMed Central

    Sundström Poromaa, Inger; Gingnell, Malin

    2014-01-01

    The menstrual cycle has attracted research interest ever since the 1930s. For many researchers the menstrual cycle is an excellent model of ovarian steroid influence on emotion, behavior, and cognition. Over the past years methodological improvements in menstrual cycle studies have been noted, and this review summarizes the findings of methodologically sound menstrual cycle studies in healthy women. Whereas the predominant hypotheses of the cognitive field state that sexually dimorphic cognitive skills that favor men are improved during menstrual cycle phases with low estrogen and that cognitive skills that favor women are improved during cycle phases with increased estrogen and/or progesterone, this review has not found sufficient evidence to support any of these hypotheses. Mental rotation has gained specific interest in this aspect, but a meta-analysis yielded a standardized mean difference in error rate of 1.61 (95% CI −0.35 to 3.57), suggesting, at present, no favor of an early follicular phase improvement in mental rotation performance. Besides the sexually dimorphic cognitive skills, studies exploring menstrual cycle effects on tasks that probe prefrontal cortex function, for instance verbal or spatial working memory, have also been reviewed. While studies thus far are few, results at hand suggest improved performance at times of high estradiol levels. Menstrual cycle studies on emotional processing, on the other hand, tap into the emotional disorders of the luteal phase, and may be of relevance for women with premenstrual disorders. Although evidence at present is limited, it is suggested that emotion recognition, consolidation of emotional memories, and fear extinction is modulated by the menstrual cycle in women. With the use of functional magnetic resonance imaging, several studies report changes in brain reactivity across the menstrual cycle, most notably increased amygdala reactivity in the luteal phase. Thus, to the extent that behavioral changes

  14. Precision control of soil N cycling via soil functional zone management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Managing the soil nitrogen (N) cycle is a major component of agricultural sustainability. Soil functional zone management (SFZM), a novel framework of agroecosystem management, may improve soil N management compared with conventional and no-tillage approaches by focusing on the timing and location (...

  15. CHLORINATION BY-PRODUCTS IN DRINKING WATER AND MENSTRUAL CYCLE FUNCTION

    EPA Science Inventory

    Chlorination by-Products in Drinking Water and Menstrual Cycle Function

    Gayle C. Windham1, Kirsten Waller2, Meredith Anderson2, Laura Fenster1, Pauline Mendola3, Shanna Swan4

    1California Department of Health Services, Division of Environmental and Occupational Disea...

  16. Functional cellular analyses reveal energy metabolism defect and mitochondrial DNA depletion in a case of mitochondrial aconitase deficiency.

    PubMed

    Sadat, Roa; Barca, Emanuele; Masand, Ruchi; Donti, Taraka R; Naini, Ali; De Vivo, Darryl C; DiMauro, Salvatore; Hanchard, Neil A; Graham, Brett H

    2016-05-01

    Defects in the tricarboxylic acid cycle (TCA) are associated with a spectrum of neurological phenotypes that are often difficult to diagnose and manage. Whole-exome sequencing (WES) led to a rapid expansion of diagnostic capabilities in such disorders and facilitated a better understanding of disease pathogenesis, although functional characterization remains a bottleneck to the interpretation of potential pathological variants. We report a 2-year-old boy of Afro-Caribbean ancestry, who presented with neuromuscular symptoms without significant abnormalities on routine diagnostic evaluation. WES revealed compound heterozygous missense variants of uncertain significance in mitochondrial aconitase (ACO2), which encodes the TCA enzyme ACO2. Pathogenic variants in ACO2 have been described in a handful of families as the cause of infantile cerebellar-retinal degeneration syndrome. Using biochemical and cellular assays in patient fibroblasts, we found that ACO2 expression was quantitatively normal, but ACO2 enzyme activity was <20% of that observed in control cells. We also observed a deficiency in cellular respiration and, for the first time, demonstrate evidence of mitochondrial DNA depletion and altered expression of some TCA components and electron transport chain subunits. The observed cellular defects were completely restored with ACO2 gene rescue. Our findings demonstrate the pathogenicity of two VUS in ACO2, provide novel mechanistic insights to TCA disturbances in ACO2 deficiency, and implicate mitochondrial DNA depletion in the pathogenesis of this recently described disorder. PMID:26992325

  17. The effect of physical activity across the menstrual cycle on reproductive function

    PubMed Central

    Ahrens, Katherine A.; Vladutiu, Catherine J.; Mumford, Sunni L.; Schliep, Karen C.; Perkins, Neil J.; Wactawski-Wende, Jean; Schisterman, Enrique F.

    2013-01-01

    Purpose To evaluate the association between physical activity (PA) across the menstrual cycle and reproductive function. Methods The BioCycle Study (2005–2007) followed 259, healthy premenopausal women not using hormonal contraceptives for up to two menstrual cycles (N=509 cycles). Serum leptin, estradiol, progesterone, luteinizing hormone, follicle-stimulating hormone, and testosterone were measured five to eight times per cycle. Linear mixed models were used to estimate the effect of past-week PA (measured four times during each cycle) on hormone levels. Past-week PA was categorized into tertiles based on metabolic equivalent [MET]-h/week (cut-points were 15.3 and 35.7). Risk ratios for sporadic anovulation were estimated using generalized linear models. Analyses adjusted for habitual PA (assessed at baseline), body mass index, race, age, and perceived stress. Linear mixed models used inverse probability weights to control for concurrent reproductive hormones and caloric intake. Results High past-week PA was inversely associated with leptin (−6.6%, 95% confidence interval [−10.6, −2.5]) and luteal phase progesterone (−22.1% [−36.2, −4.7]) as compared with low past-week PA. High past-week PA was not significantly associated with sporadic anovulation (adjusted risk ratio=1.5 [0.6, 3.4]). Conclusions High levels of PA were modestly associated with changes in select hormones, but not sporadic anovulation among moderate to highly active premenopausal women. PMID:24345590

  18. Effects of the Menstrual Cycle on Lung Function Variables in Women with Asthma

    PubMed Central

    Farha, Samar; Asosingh, Kewal; Laskowski, Daniel; Hammel, Jeffrey; Dweik, Raed A.; Wiedemann, Herbert P.; Erzurum, Serpil C.

    2009-01-01

    Rationale: Angiogenesis is a defining pathologic feature of airway remodeling and contributes to asthma severity. Women experience changes in asthma control over the menstrual cycle, a time when vessels routinely form and regress under the control of angiogenic factors. One vital function modulated over the menstrual cycle in healthy women is gas transfer, and this has been related to angiogenesis and cyclic expansion of the pulmonary vascular bed. Objectives: We hypothesized that changes in gas transfer and the pulmonary vascular bed occur in women with asthma over the menstrual cycle and are associated with worsening airflow obstruction. Methods: Twenty-three women, 13 with asthma and 10 healthy control subjects, were evaluated over the menstrual cycle with weekly measures of spirometry, gas transfer, nitric oxide, hemoglobin, factors affecting hemoglobin binding affinity, and proangiogenic factors. Measurements and Main Results: Airflow and lung diffusing capacity varied over the menstrual cycle with peak levels during menses that subsequently declined to nadir in early luteal phase. In contrast to healthy women, changes in lung diffusing capacity (DlCO) were associated with changes in membrane diffusing capacity and DlCO was not related to proangiogenic factors. DlCO did not differ between the two groups, although methemoglobin and carboxyhemoglobin were higher in women with asthma than in healthy women. Conclusions: Women with asthma experience cyclic changes in airflow as well as gas transfer and membrane diffusing capacity supportive of a hormonal effect on lung function. PMID:19520904

  19. Multiple functions of p21 in cell cycle, apoptosis and transcriptional regulation after DNA damage.

    PubMed

    Karimian, Ansar; Ahmadi, Yasin; Yousefi, Bahman

    2016-06-01

    An appropriate control over cell cycle progression depends on many factors. Cyclin-dependent kinase (CDK) inhibitor p21 (also known as p21(WAF1/Cip1)) is one of these factors that promote cell cycle arrest in response to a variety of stimuli. The inhibitory effect of P21 on cell cycle progression correlates with its nuclear localization. P21 can be induced by both p53-dependent and p53-independent mechanisms. Some other important functions attributed to p21 include transcriptional regulation, modulation or inhibition of apoptosis. These functions are largely dependent on direct p21/protein interactions and also on p21 subcellular localizations. In addition, p21 can play a role in DNA repair by interacting with proliferating cell nuclear antigen (PCNA). In this review, we will focus on the multiple functions of p21 in cell cycle regulation, apoptosis and gene transcription after DNA damage and briefly discuss the pathways and factors that have critical roles in p21 expression and activity. PMID:27156098

  20. Spur gears: Optimal geometry, methods for generation and Tooth Contact Analysis (TCA) program

    NASA Technical Reports Server (NTRS)

    Litvin, Faydor L.; Zhang, Jiao

    1988-01-01

    The contents of this report include the following: (1) development of optimal geometry for crowned spur gears; (2) methods for their generation; and (3) tooth contact analysis (TCA) computer programs for the analysis of meshing and bearing contact on the crowned spur gears. The method developed for synthesis is used for the determination of the optimal geometry for crowned pinion surface and is directed to reduce the sensitivity of the gears to misalignment, localize the bearing contact, and guarantee the favorable shape and low level of the transmission errors. A new method for the generation of the crowned pinion surface has been proposed. This method is based on application of the tool with a surface of revolution that slightly deviates from a regular cone surface. The tool can be used as a grinding wheel or as a shaver. The crowned pinion surface can also be generated by a generating plane whose motion is provided by an automatic grinding machine controlled by a computer. The TCA program simulates the meshing and bearing contact of the misaligned gears. The transmission errors are also determined.

  1. Topology of modified helical gears and Tooth Contact Analysis (TCA) program

    NASA Technical Reports Server (NTRS)

    Litvin, Faydor L.; Zhang, Jiao

    1989-01-01

    The contents of this report covers: (1) development of optimal geometries for crowned helical gears; (2) a method for their generation; (3) tooth contact analysis (TCA) computer programs for the analysis of meshing and bearing contact of the crowned helical gears; and (4) modelling and simulation of gear shaft deflection. The developed method for synthesis was used to determine the optimal geometry for a crowned helical pinion surface and was directed to localize the bearing contact and guarantee favorable shape and a low level of transmission errors. Two new methods for generation of the crowned helical pinion surface are proposed. One is based on the application of a tool with a surface of revolution that slightly deviates from a regular cone surface. The tool can be used as a grinding wheel or as a shaver. The other is based on a crowning pinion tooth surface with predesigned transmission errors. The pinion tooth surface can be generated by a computer-controlled automatic grinding machine. The TCA program simulates the meshing and bearing contact of the misaligned gears. The transmission errors are also determined. The gear shaft deformation was modelled and investigated. It was found that the deflection of gear shafts has the same effect as gear misalignment.

  2. Structural and functional insights into enzymes of the vitamin K cycle.

    PubMed

    Tie, J-K; Stafford, D W

    2016-02-01

    Vitamin K-dependent proteins require carboxylation of certain glutamates for their biological functions. The enzymes involved in the vitamin K-dependent carboxylation include: gamma-glutamyl carboxylase (GGCX), vitamin K epoxide reductase (VKOR) and an as-yet-unidentified vitamin K reductase (VKR). Due to the hydrophobicity of vitamin K, these enzymes are likely to be integral membrane proteins that reside in the endoplasmic reticulum. Therefore, structure-function studies on these enzymes have been challenging, and some of the results are notably controversial. Patients with naturally occurring mutations in these enzymes, who mainly exhibit bleeding disorders or are resistant to oral anticoagulant treatment, provide valuable information for the functional study of the vitamin K cycle enzymes. In this review, we discuss: (i) the discovery of the enzymatic activities and gene identifications of the vitamin K cycle enzymes; (ii) the identification of their functionally important regions and their active site residues; (iii) the membrane topology studies of GGCX and VKOR; and (iv) the controversial issues regarding the structure and function studies of these enzymes, particularly, the membrane topology, the role of the conserved cysteines and the mechanism of active site regeneration of VKOR. We also discuss the possibility that a paralogous protein of VKOR, VKOR-like 1 (VKORL1), is involved in the vitamin K cycle, and the importance of and possible approaches for identifying the unknown VKR. Overall, we describe the accomplishments and the remaining questions in regard to the structure and function studies of the enzymes in the vitamin K cycle. PMID:26663892

  3. Levels of Ycg1 Limit Condensin Function during the Cell Cycle

    PubMed Central

    Arsenault, Heather E.; Benanti, Jennifer A.

    2016-01-01

    During mitosis chromosomes are condensed to facilitate their segregation, through a process mediated by the condensin complex. Although several factors that promote maximal condensin activity during mitosis have been identified, the mechanisms that downregulate condensin activity during interphase are largely unknown. Here, we demonstrate that Ycg1, the Cap-G subunit of budding yeast condensin, is cell cycle-regulated with levels peaking in mitosis and decreasing as cells enter G1 phase. This cyclical expression pattern is established by a combination of cell cycle-regulated transcription and constitutive degradation. Interestingly, overexpression of YCG1 and mutations that stabilize Ycg1 each result in delayed cell-cycle entry and an overall proliferation defect. Overexpression of no other condensin subunit impacts the cell cycle, suggesting that Ycg1 is limiting for condensin complex formation. Consistent with this possibility, we find that levels of intact condensin complex are reduced in G1 phase compared to mitosis, and that increased Ycg1 expression leads to increases in both levels of condensin complex and binding to chromatin in G1. Together, these results demonstrate that Ycg1 levels limit condensin function in interphase cells, and suggest that the association of condensin with chromosomes must be reduced following mitosis to enable efficient progression through the cell cycle. PMID:27463097

  4. Canard cycles for predator-prey systems with Holling types of functional response

    NASA Astrophysics Data System (ADS)

    Li, Chengzhi; Zhu, Huaiping

    By using the singular perturbation theory developed by Dumortier and Roussarie and recent work of De Maesschalck and Dumortier, we study the canard phenomenon for predator-prey systems with response functions of Holling types. We first develop a formula for computing the slow divergence integrals. By using the formula we prove that for the systems with the response function of Holling types III and IV the cyclicity of any limit periodic set is at most two, that is at most two families of hyperbolic limit cycles or at most one family of limit cycles with multiplicity two can bifurcate from the limit periodic set by small perturbations. We also indicate the regions in parameter space where the corresponding limit periodic set has cyclicity at most one or at most two.

  5. Functional profiles of orphan membrane transporters in the life cycle of the malaria parasite.

    PubMed

    Kenthirapalan, Sanketha; Waters, Andrew P; Matuschewski, Kai; Kooij, Taco W A

    2016-01-01

    Assigning function to orphan membrane transport proteins and prioritizing candidates for detailed biochemical characterization remain fundamental challenges and are particularly important for medically relevant pathogens, such as malaria parasites. Here we present a comprehensive genetic analysis of 35 orphan transport proteins of Plasmodium berghei during its life cycle in mice and Anopheles mosquitoes. Six genes, including four candidate aminophospholipid transporters, are refractory to gene deletion, indicative of essential functions. We generate and phenotypically characterize 29 mutant strains with deletions of individual transporter genes. Whereas seven genes appear to be dispensable under the experimental conditions tested, deletion of any of the 22 other genes leads to specific defects in life cycle progression in vivo and/or host transition. Our study provides growing support for a potential link between heavy metal homeostasis and host switching and reveals potential targets for rational design of new intervention strategies against malaria. PMID:26796412

  6. Functional profiles of orphan membrane transporters in the life cycle of the malaria parasite

    PubMed Central

    Kenthirapalan, Sanketha; Waters, Andrew P.; Matuschewski, Kai; Kooij, Taco W. A.

    2016-01-01

    Assigning function to orphan membrane transport proteins and prioritizing candidates for detailed biochemical characterization remain fundamental challenges and are particularly important for medically relevant pathogens, such as malaria parasites. Here we present a comprehensive genetic analysis of 35 orphan transport proteins of Plasmodium berghei during its life cycle in mice and Anopheles mosquitoes. Six genes, including four candidate aminophospholipid transporters, are refractory to gene deletion, indicative of essential functions. We generate and phenotypically characterize 29 mutant strains with deletions of individual transporter genes. Whereas seven genes appear to be dispensable under the experimental conditions tested, deletion of any of the 22 other genes leads to specific defects in life cycle progression in vivo and/or host transition. Our study provides growing support for a potential link between heavy metal homeostasis and host switching and reveals potential targets for rational design of new intervention strategies against malaria. PMID:26796412

  7. Fresh insight to functioning of selected enzymes of the nitrogen cycle.

    PubMed

    Eady, Robert R; Antonyuk, Svetlana V; Hasnain, S Samar

    2016-04-01

    The global nitrogen cycle is the process in which different forms of environmental N are interconverted by microorganisms either for assimilation into biomass or in respiratory energy-generating pathways. This short review highlights developments over the last 5 years in our understanding of functionality of nitrogenase, Cu-nitrite reductase, NO reductase and N2O reductase, complex metalloenzymes that catalyze electron/proton-coupled substrate reduction reactions. PMID:26963700

  8. Integrative Functional Genomics of Hepatitis C Virus Infection Identifies Host Dependencies in Complete Viral Replication Cycle

    PubMed Central

    Li, Qisheng; Zhang, Yong-Yuan; Chiu, Stephan; Hu, Zongyi; Lan, Keng-Hsin; Cha, Helen; Sodroski, Catherine; Zhang, Fang; Hsu, Ching-Sheng; Thomas, Emmanuel; Liang, T. Jake

    2014-01-01

    Recent functional genomics studies including genome-wide small interfering RNA (siRNA) screens demonstrated that hepatitis C virus (HCV) exploits an extensive network of host factors for productive infection and propagation. How these co-opted host functions interact with various steps of HCV replication cycle and exert pro- or antiviral effects on HCV infection remains largely undefined. Here we present an unbiased and systematic strategy to functionally interrogate HCV host dependencies uncovered from our previous infectious HCV (HCVcc) siRNA screen. Applying functional genomics approaches and various in vitro HCV model systems, including HCV pseudoparticles (HCVpp), single-cycle infectious particles (HCVsc), subgenomic replicons, and HCV cell culture systems (HCVcc), we identified and characterized novel host factors or pathways required for each individual step of the HCV replication cycle. Particularly, we uncovered multiple HCV entry factors, including E-cadherin, choline kinase α, NADPH oxidase CYBA, Rho GTPase RAC1 and SMAD family member 6. We also demonstrated that guanine nucleotide binding protein GNB2L1, E2 ubiquitin-conjugating enzyme UBE2J1, and 39 other host factors are required for HCV RNA replication, while the deubiquitinating enzyme USP11 and multiple other cellular genes are specifically involved in HCV IRES-mediated translation. Families of antiviral factors that target HCV replication or translation were also identified. In addition, various virologic assays validated that 66 host factors are involved in HCV assembly or secretion. These genes included insulin-degrading enzyme (IDE), a proviral factor, and N-Myc down regulated Gene 1 (NDRG1), an antiviral factor. Bioinformatics meta-analyses of our results integrated with literature mining of previously published HCV host factors allows the construction of an extensive roadmap of cellular networks and pathways involved in the complete HCV replication cycle. This comprehensive study of HCV host

  9. Solar Magnetic Flux as a Function of Disk Position over the Solar Cycle

    NASA Astrophysics Data System (ADS)

    Berger, T.

    2005-05-01

    A novel analysis of a SOHO/MDI full-disk magnetogram time series from March 1996 to November 2004 is presented. Each of the 26,052 magnetograms in the series are segmented into sectors of constant μ = cos θ, each sector having a width of Δμ = 0.05. Within each sector, a histogram of signed magnetic flux density, corrected for the line-of-sight angle θ, is compiled. For each magnetogram we thus obtain a distribution of signed magnetic flux density as a function of μ. Summing the signed flux in each μ bin gives the total signed flux as a function of μ. Plotting these totals for each μ-sector as a function of time over the course of Solar Cycle 22 reveals that cycle minimum and maximum are differentiated only by the magnitude of the flux distributions. In other words, in contrast to analogous plots of flux versus heliocentric latitude, there is no discernible pattern, or "Butterfly Diagram", of flux seen on the solar disk from Earth. The finding is relevant to investigations of total solar irradiance (TSI) since it is known that the primary cause of the ~ 0.1% TSI variation over the solar cycle is the distribution of non-sunspot magnetic flux at smaller μ-values (so-called "faculae").

  10. Trichloroacetic acid (TCA) and trifluoroacetic acid (TFA) mixture toxicity to the macrophytes Myriophyllum spicatum and Myriophyllum sibiricum in aquatic microcosms.

    PubMed

    Hanson, Mark L; Sibley, Paul K; Mabury, Scott A; Solomon, Keith R; Muir, Derek C G

    2002-02-21

    Trichloroacetic acid (TCA) and trifluoroacetic acid (TFA) have been detected together in environmental water samples throughout the world. TCA may enter into aquatic systems via rainout as the degradation product of chlorinated solvents, herbicide use, as a by-product of water disinfection and from emissions of spent bleach liquor of kraft pulp mills. Sources of TFA include degradation of hydrofluorocarbons (HFCs) refrigerants and pesticides. These substances are phytotoxic and widely distributed in aquatic environments. A study to assess the risk of a binary mixture of TCA and TFA to macrophytes in aquatic microcosms was conducted as part of a larger study on haloacetic acids. M. spicatum and M. sibiricum were exposed to 0.1, 1, 3 and 10 mg/l of both TCA and TFA (neutralized with sodium hydroxide) in replicate (n = 3) 12000 l aquatic microcosms for 49 days in an one-way analysis of variance design. Each microcosm was stocked with 14 individual apical shoots per species. The plants were sampled at regular intervals and assessed for the somatic endpoints of plant length, root growth, number of nodes and wet and dry mass and the biochemical endpoints of chlorophyll-a, chlorophyll-b, carotenoid content and citric acid levels. Results indicate that there were statistically significant effects of the TCA/TFA mixture on certain pigment concentrations immediately after the start of exposure (2-7 days), but the plants showed no signs of stress thereafter. These data suggest that TCA/TFA mixtures at environmentally relevant concentrations do not pose a significant risk to these aquatic macrophytes. PMID:11878273

  11. Abrupt shifts in ecosystem function and intensification of global biogeochemical cycle driven by hydroclimatic extremes

    NASA Astrophysics Data System (ADS)

    Ma, Xuanlong; Huete, Alfredo; Ponce-Campos, Guillermo; Zhang, Yongguang; Xie, Zunyi; Giovannini, Leandro; Cleverly, James; Eamus, Derek

    2016-04-01

    Amplification of the hydrologic cycle as a consequence of global warming is increasing the frequency, intensity, and spatial extent of extreme climate events globally. The potential influences resulting from amplification of the hydro-climatic cycle, coupled with an accelerating warming trend, pose great concerns on the sustainability of terrestrial ecosystems to sequester carbon, maintain biodiversity, provide ecosystem services, food security, and support human livelihood. Despite the great implications, the magnitude, direction, and carry-over effect of these extreme climate events on ecosystem function, remain largely uncertain. To address these pressing issues, we conducted an observational, interdisciplinary study using satellite retrievals of atmospheric CO2 and photosynthesis (chlorophyll fluorescence), and in-situ flux tower measures of ecosystem-atmosphere carbon exchange, to reveal the shifts in ecosystem function across extreme drought and wet periods. We further determine the factors that govern ecosystem sensitivity to hydroclimatic extremes. We focus on Australia but extended our analyses to other global dryland regions due to their significant role in global biogeochemical cycles. Our results revealed dramatic impacts of drought and wet hydroclimatic extremes on ecosystem function, with abrupt changes in vegetation productivity, carbon uptake, and water-use-efficiency between years. Drought resulted in widespread reductions or collapse in the normal patterns of vegetation growth seasonality such that in many cases there was no detectable phenological cycle during extreme drought years. We further identified a significant increasing trend (p < 0.001) in extreme wet year precipitation amounts over Australia and many other global regions, resulting in an increasing trend in magnitude of the episodic carbon sink pulses coupled to each La Niña-induced wet years. This finding is of global biogeochemical significance, with the consequence of amplifying

  12. Seat Pressure Changes after Eight Weeks of Functional Electrical Stimulation Cycling: A Pilot Study

    PubMed Central

    2013-01-01

    Background: Pressure ulcers (PUs) are a common secondary condition associated with spinal cord injury (SCI). PUs can potentially interfere with activities of daily living, occupational duties, and rehabilitation programs, and in severe cases they may threaten life. Functional electrical stimulation (FES) cycling has been proposed as an activity that may decrease the risk of PUs through the promotion of increased blood flow and thickening of the gluteus maximus. The purpose of this pilot study was to measure the effects of home-based FES cycling on the average and maximal seat pressure of wheelchair-reliant individuals with SCI. Method: Eight male veterans with C5-T6 SCI participated in FES cycling 3 times per week. Cycling parameters were individualized depending on the comfort of the participants and the amount of current needed to perform the cycling activity. Pressure mapping was completed immediately before and after the 8 weeks of FES cycling with the measurement performed by a force sensitive application (FSA) 4 pressure mapping system. Results: The mean average seat pressure decreased by 3.69 ± 4.46 mm Hg (35.57 ± 11.99 to 31.88 ± 13.02), while the mean maximum seat pressure decreased by 14.56 ±18.45 mm Hg (112 ± 34.73 to 98.36 ± 25.89). Although neither measurement was statistically significant, there was a strong trend toward a reduction in average and maximal seat pressure (P = .052 and P = .061, respectively). Conclusion: The positive trend of decreased seat pressure in our study creates incentive for further investigation of the effects of electrical stimulation activities on seat pressure and the prevention of PUs. PMID:23960706

  13. Sexual dimorphism in immune function changes during the annual cycle in house sparrows

    NASA Astrophysics Data System (ADS)

    Pap, Péter László; Czirják, Gábor Árpád; Vágási, Csongor István; Barta, Zoltán; Hasselquist, Dennis

    2010-10-01

    Difference between sexes in parasitism is a common phenomenon among birds, which may be related to differences between males and females in their investment into immune functions or as a consequence of differential exposure to parasites. Because life-history strategies change sex specifically during the annual cycle, immunological responses of the host aiming to reduce the impact of parasites may be sexually dimorphic. Despite the great complexity of the immune system, studies on immunoecology generally characterise the immune status through a few variables, often overlooking potentially important seasonal and gender effects. However, because of the differences in physiological and defence mechanisms among different arms of the immune system, we expect divergent responses of immune components to environmental seasonality. In male and female house sparrows ( Passer domesticus), we measured the major components of the immune system (innate, acquired, cellular and humoral) during four important life-history stages across the year: (1) mating, (2) breeding, (3) moulting and (4) during the winter capture and also following introduction to captivity in aviary. Different individuals were sampled from the same population during the four life cycle stages. We found that three out of eight immune variables showed a significant life cycle stage × sex interaction. The difference in immune response between the sexes was significant in five immune variables during the mating stage, when females had consistently stronger immune function than males, while variables varied generally non-significantly with sex during the remaining three life cycle stages. Our results show that the immune system is highly variable between life cycle stages and sexes, highlighting the potential fine tuning of the immune system to specific physiological states and environmental conditions.

  14. Sexual dimorphism in immune function changes during the annual cycle in house sparrows.

    PubMed

    Pap, Péter László; Czirják, Gábor Arpád; Vágási, Csongor István; Barta, Zoltán; Hasselquist, Dennis

    2010-10-01

    Difference between sexes in parasitism is a common phenomenon among birds, which may be related to differences between males and females in their investment into immune functions or as a consequence of differential exposure to parasites. Because life-history strategies change sex specifically during the annual cycle, immunological responses of the host aiming to reduce the impact of parasites may be sexually dimorphic. Despite the great complexity of the immune system, studies on immunoecology generally characterise the immune status through a few variables, often overlooking potentially important seasonal and gender effects. However, because of the differences in physiological and defence mechanisms among different arms of the immune system, we expect divergent responses of immune components to environmental seasonality. In male and female house sparrows (Passer domesticus), we measured the major components of the immune system (innate, acquired, cellular and humoral) during four important life-history stages across the year: (1) mating, (2) breeding, (3) moulting and (4) during the winter capture and also following introduction to captivity in aviary. Different individuals were sampled from the same population during the four life cycle stages. We found that three out of eight immune variables showed a significant life cycle stage × sex interaction. The difference in immune response between the sexes was significant in five immune variables during the mating stage, when females had consistently stronger immune function than males, while variables varied generally non-significantly with sex during the remaining three life cycle stages. Our results show that the immune system is highly variable between life cycle stages and sexes, highlighting the potential fine tuning of the immune system to specific physiological states and environmental conditions. PMID:20706704

  15. Four weeks of functional electrical stimulated cycling after spinal cord injury: a clinical cohort study.

    PubMed

    Kuhn, Daniel; Leichtfried, Veronika; Schobersberger, Wolfgang

    2014-09-01

    The aim of this study was to determine the efficacy and the effects of functional electrical stimulated cycling (FES cycling) in patients with spinal cord injury during their rehabilitation in a special acute care unit. Thirty patients [10 with American Spinal Injury Association Impairment Scale (AIS) grade A, three with AIS grade B, 15 with AIS grade C, two with AIS grade D] aged 44±15.5 years and 2 (median) (interquartile range, 1.0-4.25) months after spinal cord injury were included in the study. The patients participated in a 20-min FES-cycling program 2 days per week for 4 weeks during their acute inpatient rehabilitation. The influence on muscle cross-section, muscle and leg circumference, spasticity, and the walking ability parameter (distance, time, aids) was measured. Muscle stimulation intensity and output parameters (pedalling time and distance) were also recorded. Spasticity decreased during hip abduction and adduction (70 and 98.1%, respectively). Spasticity during knee flexion and knee extension decreased by 66.8 and 76.6%, and a decrease was found during dorsal foot extension (67.8%; for all, P<0.05). Presession-postsession comparisons showed that after 4 weeks of FES cycling, an increase in the circumference of the cross-sectional area of 15.3% on the left and of 17% on the right m. rectus femoris could be observed in group AIS A+B. In the AIS C+D group, the circumference of the left m. rectus femoris increased by 25% and that of the right m. rectus femoris by 21% (for all, P<0.05). The results of the study show that FES cycling in combination with function-oriented physiotherapy and occupational therapy can have a positive influence on spasticity, walking ability, and muscular reactivation. It seems to support circulatory processes within the rehabilitation of paraplegics already after a 4-week intervention. PMID:24802976

  16. A cell cycle-dependent co-repressor mediates photoreceptor cell-specific nuclear receptor function

    PubMed Central

    Takezawa, Shinichiro; Yokoyama, Atsushi; Okada, Maiko; Fujiki, Ryoji; Iriyama, Aya; Yanagi, Yasuo; Ito, Hiroaki; Takada, Ichiro; Kishimoto, Masahiko; Miyajima, Atsushi; Takeyama, Ken-ichi; Umesono, Kazuhiko; Kitagawa, Hirochika; Kato, Shigeaki

    2007-01-01

    Photoreceptor cell-specific nuclear receptor (PNR) (NR2E3) acts as a sequence-specific repressor that controls neuronal differentiation in the developing retina. We identified a novel PNR co-repressor, Ret-CoR, that is expressed in the developing retina and brain. Biochemical purification of Ret-CoR identified a multiprotein complex that included E2F/Myb-associated proteins, histone deacetylases (HDACs) and NCoR/HDAC complex-related components. Ret-CoR appeared to function as a platform protein for the complex, and interacted with PNR via two CoRNR motifs. Purified Ret-CoR complex exhibited HDAC activity, co-repressed PNR transrepression function in vitro, and co-repressed PNR function in PNR target gene promoters, presumably in the retinal progenitor cells. Notably, the appearance of Ret-CoR protein was cell-cycle-stage-dependent (from G1 to S). Therefore, Ret-CoR appears to act as a component of an HDAC co-repressor complex that supports PNR repression function in the developing retina, and may represent a co-regulator class that supports transcriptional regulator function via cell-cycle-dependent expression. PMID:17255935

  17. Design and evaluation of a downconverter based on MicroTCA.4

    NASA Astrophysics Data System (ADS)

    Gan, Nan; Liu, Rong; Ma, Xin-Peng; Chi, Yun-Long

    2016-07-01

    Modern low-level RF (LLRF) control systems of particle accelerators are designed to achieve extremely precise field amplitude and phase regulation inside the accelerating cavities. The RF field signal is usually converted to an intermediate frequency (IF) before being sampled by ADC. As the down-conversion is an important procedure of digital signal processing in LLRF system, designing a high performance and broad band downconverter compatible with various accelerators is important. In this paper, the design of a downconverter based on MicroTCA and its performance evaluation on different frequency points are presented. The major design objective of this module is a wider operating frequency range and more flexibility in application.

  18. Fabrication of functionally gradient nanocomposite coatings by plasma electrolytic oxidation based on variable duty cycle

    NASA Astrophysics Data System (ADS)

    Aliofkhazraei, M.; Rouhaghdam, A. Sabour

    2012-01-01

    Plasma electrolytic oxidation (PEO) was applied on the surface of commercially pure titanium substrates in a mixed aluminate-phosphate electrolyte in the presence of silicon nitride nanoparticles as suspension in the electrolyte in order to fabricate nanocomposite coatings. Pulsed current was applied based on variable duty cycle in order to synthesize functionally gradient coatings (FGC). Different rates of variable duty cycle (3, 1.5 and 1%/min), applied current densities (0.06-0.14 A/cm2) and concentrations of nanoparticles in the electrolyte (2, 4, 6, 8 and 10 g l-1) were investigated. The nanopowder and coated samples were analyzed by atomic force microscope, scanning electron microscope and transmission electron microscope. The influence of different rates of variable duty cycle (or treatment times) on the growth rate of nanocomposite coatings and their microhardness values was investigated. The experimental results revealed that the content of Si3N4 nanoparticulates in the layer increases with the increase of its concentration in the plasma electrolysis bath. Nanocomposite coatings fabricated with lower rate of variable duty cycle have higher microhardness with smoother microhardness profile.

  19. Modeling the High Speed Research Cycle 2B Longitudinal Aerodynamic Database Using Multivariate Orthogonal Functions

    NASA Technical Reports Server (NTRS)

    Morelli, E. A.; Proffitt, M. S.

    1999-01-01

    The data for longitudinal non-dimensional, aerodynamic coefficients in the High Speed Research Cycle 2B aerodynamic database were modeled using polynomial expressions identified with an orthogonal function modeling technique. The discrepancy between the tabular aerodynamic data and the polynomial models was tested and shown to be less than 15 percent for drag, lift, and pitching moment coefficients over the entire flight envelope. Most of this discrepancy was traced to smoothing local measurement noise and to the omission of mass case 5 data in the modeling process. A simulation check case showed that the polynomial models provided a compact and accurate representation of the nonlinear aerodynamic dependencies contained in the HSR Cycle 2B tabular aerodynamic database.

  20. Energy-containing beverages: reproductive hormones and ovarian function in the BioCycle Study123

    PubMed Central

    Schliep, Karen C; Mumford, Sunni L; Pollack, Anna Z; Perkins, Neil J; Ye, Aijun; Zhang, Cuilin J; Stanford, Joseph B; Porucznik, Christina A; Hammoud, Ahmad O; Wactawski-Wende, Jean

    2013-01-01

    Background: Energy-containing beverages are widely consumed among premenopausal women, but their association with reproductive hormones is not well understood. Objective: The objective was to assess the association of energy-containing beverages, added sugars, and total fructose intake with reproductive hormones among ovulatory cycles and sporadic anovulation in healthy premenopausal women. Design: Women (n = 259) in the BioCycle Study were followed for up to 2 menstrual cycles; they provided fasting blood specimens during up to 8 visits/cycle and four 24-h dietary recalls/cycle. Results: Women who consumed ≥1 cup (1 cup = 237 mL) sweetened soda/d had 16.3% higher estradiol concentrations compared with women who consumed less sweetened soda (86.5 pg/mL compared with 74.4 pg/mL, P = 0.01) after adjustment for age, BMI, race, dietary factors, and physical activity. Similarly elevated estradiol concentrations were found for ≥1 cup cola/d and noncola soda intake. Neither artificially sweetened soda nor fruit juice intake ≥1 cup/d was significantly associated with reproductive hormones. Added sugar above the average US woman's intake (≥73.2 g/d) or above the 66th percentile in total fructose intake (≥41.5 g/d) was associated with significantly elevated estradiol but not consistently across all models. No associations were found between beverages, added sugars, or total fructose intake and anovulation after multivariate adjustment. Conclusions: Even at moderate consumption amounts, sweetened soda is associated with elevated follicular estradiol concentrations among premenopausal women but does not appear to affect ovulatory function. Further research into the mechanism driving the association between energy-containing beverages and reproductive hormones, and its potential implications for women's health, is warranted. PMID:23364018

  1. Comparison of ultracentrifugation and density gradient separation methods for isolating Tca8113 human tongue cancer cell line-derived exosomes

    PubMed Central

    ZHANG, ZHUOYUAN; WANG, CHENXING; LI, TANG; LIU, ZHE; LI, LONGJIANG

    2014-01-01

    The aim of the present study was to compare the method of ultracentrifugation and density gradient separation for isolating Tca8113 human tongue squamous cell carcinoma cell line-derived exosomes. The exosomes were obtained from the culture supernatant of cultured Tca8113 cells, respectively, followed by identification with transmission electron microscopy observation and western blot analysis. The two different methods were then compared by the morphology, the distribution range of the particle size and the concentration of proteins of the extracted exosomes. In vitro, Tca8113 cells can secrete a large amount of vesicle-like structures, which are identified as exosomes by the presence of the surface markers, Hsp-70 and Alix. The protein profile of the two products are almost the same, however the particle size distribution of the exosomes extracted with density gradient centrifugation are more limited, between 40–120 nm, and these have a higher protein concentration. The results indicate that Tca8113 cells can secrete exosomes in vitro, and the density gradient separation methods for purifying exosomes is improved, which is helpful for future research and application of exosomes. PMID:25202395

  2. 1H nuclear magnetic resonance-based extracellular metabolomic analysis of multidrug resistant Tca8113 oral squamous carcinoma cells

    PubMed Central

    WANG, HUI; CHEN, JIAO; FENG, YUN; ZHOU, WENJIE; ZHANG, JIHUA; YU, YU; WANG, XIAOQIAN; ZHANG, PING

    2015-01-01

    A major obstacle of successful chemotherapy is the development of multidrug resistance (MDR) in the cancer cells, which is difficult to reverse. Metabolomic analysis, an emerging approach that has been increasingly applied in various fields, is able to reflect the unique chemical fingerprints of specific cellular processes in an organism. The assessment of such metabolite changes can be used to identify novel therapeutic biomarkers. In the present study, 1H nuclear magnetic resonance (NMR) spectroscopy was used to analyze the extracellular metabolomic spectrum of the Tca8113 oral squamous carcinoma cell line, in which MDR was induced using the carboplatin (CBP) and pingyangmycin (PYM) chemotherapy drugs in vitro. The data were analyzed using the principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) methods. The results demonstrated that the extracellular metabolomic spectrum of metabolites such as glutamate, glycerophosphoethanol amine, α-Glucose and β-Glucose for the drug-induced Tca8113 cells was significantly different from the parental Tca8113 cell line. A number of biochemicals were also significantly different between the groups based on their NMR spectra, with drug-resistant cells presenting relatively higher levels of acetate and lower levels of lactate. In addition, a significantly higher peak was observed at δ 3.35 ppm in the spectrum of the PYM-induced Tca8113 cells. Therefore, 1H NMR-based metabolomic analysis has a high potential for monitoring the formation of MDR during clinical tumor chemotherapy in the future. PMID:26137105

  3. Extraction-less, rapid assay for the direct detection of 2,4,6-trichloroanisole (TCA) in cork samples.

    PubMed

    Apostolou, Theofylaktos; Pascual, Nuria; Marco, M-Pilar; Moschos, Anastassios; Petropoulos, Anastassios; Kaltsas, Grigoris; Kintzios, Spyridon

    2014-07-01

    2,4,6-trichloroanisole (TCA), the cork taint molecule, has been the target of several analytical approaches over the few past years. In spite of the development of highly efficient and sensitive tools for its detection, ranging from advanced chromatography to biosensor-based techniques, a practical breakthrough for routine cork screening purposes has not yet been realized, in part due to the requirement of a lengthy extraction of TCA in organic solvents, mostly 12% ethanol and the high detectability required. In the present report, we present a modification of a previously reported biosensor system based on the measurement of the electric response of cultured fibroblast cells membrane-engineered with the pAb78 TCA-specific antibody. Samples were prepared by macerating cork tissue and mixing it directly with the cellular biorecognition elements, without any intervening extraction process. By using this novel approach, we were able to detect TCA in just five minutes at extremely low concentrations (down to 0.2 ppt). The novel biosensor offers a number of practical benefits, including a very considerable reduction in the total assay time by one day, and a full portability, enabling its direct employment for on-site, high throughput screening of cork in the field and production facilities, without requiring any type of supporting infrastructure. PMID:24840453

  4. Lipotoxicity in steatohepatitis occurs despite an increase in tricarboxylic acid cycle activity.

    PubMed

    Patterson, Rainey E; Kalavalapalli, Srilaxmi; Williams, Caroline M; Nautiyal, Manisha; Mathew, Justin T; Martinez, Janie; Reinhard, Mary K; McDougall, Danielle J; Rocca, James R; Yost, Richard A; Cusi, Kenneth; Garrett, Timothy J; Sunny, Nishanth E

    2016-04-01

    The hepatic tricarboxylic acid (TCA) cycle is central to integrating macronutrient metabolism and is closely coupled to cellular respiration, free radical generation, and inflammation. Oxidative flux through the TCA cycle is induced during hepatic insulin resistance, in mice and humans with simple steatosis, reflecting early compensatory remodeling of mitochondrial energetics. We hypothesized that progressive severity of hepatic insulin resistance and the onset of nonalcoholic steatohepatitis (NASH) would impair oxidative flux through the hepatic TCA cycle. Mice (C57/BL6) were fed a high-trans-fat high-fructose diet (TFD) for 8 wk to induce simple steatosis and NASH by 24 wk. In vivo fasting hepatic mitochondrial fluxes were determined by(13)C-nuclear magnetic resonance (NMR)-based isotopomer analysis. Hepatic metabolic intermediates were quantified using mass spectrometry-based targeted metabolomics. Hepatic triglyceride accumulation and insulin resistance preceded alterations in mitochondrial metabolism, since TCA cycle fluxes remained normal during simple steatosis. However, mice with NASH had a twofold induction (P< 0.05) of mitochondrial fluxes (μmol/min) through the TCA cycle (2.6 ± 0.5 vs. 5.4 ± 0.6), anaplerosis (9.1 ± 1.2 vs. 16.9 ± 2.2), and pyruvate cycling (4.9 ± 1.0 vs. 11.1 ± 1.9) compared with their age-matched controls. Induction of the TCA cycle activity during NASH was concurrent with blunted ketogenesis and accumulation of hepatic diacylglycerols (DAGs), ceramides (Cer), and long-chain acylcarnitines, suggesting inefficient oxidation and disposal of excess free fatty acids (FFA). Sustained induction of mitochondrial TCA cycle failed to prevent accretion of "lipotoxic" metabolites in the liver and could hasten inflammation and the metabolic transition to NASH. PMID:26814015

  5. Oral contraceptive pill use and menstrual cycle phase are associated with altered resting state functional connectivity.

    PubMed

    Petersen, Nicole; Kilpatrick, Lisa A; Goharzad, Azaadeh; Cahill, Larry

    2014-04-15

    At rest, brain activity can be characterized not by an absence of organized activity but instead by spatially and temporally correlated patterns of activity. In this experiment, we investigated whether and to what extent resting state functional connectivity is modulated by sex hormones in women, both across the menstrual cycle and when altered by oral contraceptive pills. Sex hormones have been shown to have important effects on task-related activity, but few studies have investigated the extent to which they can influence the behavior of functional networks at rest. These hormones are dramatically altered by the use of hormonal contraception, which is used by approximately 100 million women worldwide. However, potential cognitive side effects of hormonal contraception have been given little attention. Here, we collected resting state data for naturally-cycling women (n=45) and women using combined oral contraceptive pills (n=46) and evaluated the differences in resting state activity between these two groups using independent component analysis. We found that in the default mode network and in a network associated with executive control, resting state dynamics were altered both by the menstrual cycle and by oral contraceptive use. Specifically, the connectivity of the left angular gyrus, the left middle frontal gyrus, and the anterior cingulate cortex were different between groups. Because the anterior cingulate cortex and left middle frontal gyrus are important for higher-order cognitive and emotional processing, including conflict monitoring, changes in the relationship of these structures to the functional networks with which they interact may have important consequences for attention, affect, and/or emotion regulation. PMID:24365676

  6. Adenosine Kinase Deficiency Disrupts the Methionine Cycle and Causes Hypermethioninemia, Encephalopathy, and Abnormal Liver Function

    PubMed Central

    Bjursell, Magnus K.; Blom, Henk J.; Cayuela, Jordi Asin; Engvall, Martin L.; Lesko, Nicole; Balasubramaniam, Shanti; Brandberg, Göran; Halldin, Maria; Falkenberg, Maria; Jakobs, Cornelis; Smith, Desiree; Struys, Eduard; von Döbeln, Ulrika; Gustafsson, Claes M.; Lundeberg, Joakim; Wedell, Anna

    2011-01-01

    Four inborn errors of metabolism (IEMs) are known to cause hypermethioninemia by directly interfering with the methionine cycle. Hypermethioninemia is occasionally discovered incidentally, but it is often disregarded as an unspecific finding, particularly if liver disease is involved. In many individuals the hypermethioninemia resolves without further deterioration, but it can also represent an early sign of a severe, progressive neurodevelopmental disorder. Further investigation of unclear hypermethioninemia is therefore important. We studied two siblings affected by severe developmental delay and liver dysfunction. Biochemical analysis revealed increased plasma levels of methionine, S-adenosylmethionine (AdoMet), and S-adenosylhomocysteine (AdoHcy) but normal or mildly elevated homocysteine (Hcy) levels, indicating a block in the methionine cycle. We excluded S-adenosylhomocysteine hydrolase (SAHH) deficiency, which causes a similar biochemical phenotype, by using genetic and biochemical techniques and hypothesized that there was a functional block in the SAHH enzyme as a result of a recessive mutation in a different gene. Using exome sequencing, we identified a homozygous c.902C>A (p.Ala301Glu) missense mutation in the adenosine kinase gene (ADK), the function of which fits perfectly with this hypothesis. Increased urinary adenosine excretion confirmed ADK deficiency in the siblings. Four additional individuals from two unrelated families with a similar presentation were identified and shown to have a homozygous c.653A>C (p.Asp218Ala) and c.38G>A (p.Gly13Glu) mutation, respectively, in the same gene. All three missense mutations were deleterious, as shown by activity measurements on recombinant enzymes. ADK deficiency is a previously undescribed, severe IEM shedding light on a functional link between the methionine cycle and adenosine metabolism. PMID:21963049

  7. Nitrogen cycling in Yellowstone National Park thermal features: using gene expression to reveal ecological function

    NASA Astrophysics Data System (ADS)

    Lafree, S. T.; Burton, M. S.; Meyer-Dombard, D. R.

    2010-12-01

    Studies of biodiversity, metabolic strategies, and functional ecology in modern hydrothermal systems have the potential to provide insight into the metabolism and evolution of life. The geochemical and microbial diversity present at Yellowstone National Park (YNP), Wyoming, USA, makes it an ideal place for studying the functional ecology and metabolic processes of prokaryotic organisms. While much work in terrestrial hydrothermal features is focused on phylogenetic and geochemical analyses, a few recent investigations in YNP and other hydrothermal areas have focused on “gene hunting”: screening thermal sediment and biofilm samples for the presence of genes utilized in specific metabolic processes [2, 3, 6, 7, 8]. Although research has evaluated and confirmed the presence of many of these genes in various thermophilic microbial communities, the existence of a gene in the DNA of an organism does not verify its use, and few researchers have done work to confirm the utilization (expression) of the genes discovered in thermal samples [1, 6, 7, 8]. Disequilibrium between reduced hydrothermal fluid of YNP thermal features and the atmosphere provides a copious source of potential energy to be harnessed through microbial metabolic processes, with NO3- and NO2- serving as the preferred electron acceptors and top energy sources after O2 [4, 5]. Consequentially, nitrogen cycling likely plays a vital role in microbial metabolic processes, as well as nutrient availability. This study explores the presence and utilization of functional genes that are key in steps of the nitrogen cycle, such as nitrogen fixation (NifH), denitrification (nirKS), and ammonia oxidation (amoA). Both DNA and RNA were extracted from thermal sediment and streamer biofilm communities collected in the chemosynthetic zone of various thermal features of the Sentinel Meadows Group in Lower Geyser Basin, YNP. Extracted DNA and reverse transcribed RNA (cDNA) were amplified using the polymerase chain

  8. Functional near infrared spectroscopy study of age-related difference in cortical activation patterns during cycling with speed feedback.

    PubMed

    Lin, Pei-Yi; Lin, Sang-I; Chen, Jia-Jin J

    2012-01-01

    Functional decline of lower-limb affects the ability of locomotion and the age-related brain differences have been elucidated among the elderly. Cycling exercise is a common training program for restoring motor function in the deconditioned elderly or stroke patients. The provision of speed feedback has been commonly suggested to clinical therapists for facilitating learning of controlled cycling performance and maintaining motivation in training programs with elderly participants. However, the cortical control of pedaling movements and the effect of external feedback remain poorly understanding. This study investigated the regional cortical activities detected by functional near infrared spectroscopy (fNIRS) in 12 healthy young and 13 healthy elderly subjects under conditions of cycling without-(free cycling) and with feedback (target cycling). The elderly exhibited predominant activation of the sensorimotor cortex during free cycling similar to young subjects but with poorer cycling performance. The cycling performance improved in both groups, and the elderly showed increased brain activities of the supplementary motor area and premotor cortex under target cycling condition. These findings demonstrated age-related changes in the cortical control in processing external feedback and pedaling movements. Use of fNIRS to evaluate brain activation patterns after training may facilitate brain-based design of tailored therapeutic rehabilitation strategies. PMID:21984524

  9. Acute Bouts of Assisted Cycling Improves Cognitive and Upper Extremity Movement Functions in Adolescents with Down Syndrome

    ERIC Educational Resources Information Center

    Ringenbach, Shannon D. R; Albert, Andrew R.; Chen, Chih-Chia; Alberts, Jay L.

    2014-01-01

    The aim of this study was to examine the effectiveness of 2 modes of exercise on cognitive and upper extremity movement functioning in adolescents with Down syndrome (DS). Nine participants randomly completed 3 interventions over 3 consecutive weeks. The interventions were: (a) voluntary cycling (VC), in which participants cycled at their…

  10. Sparstolonin B Inhibits Pro-Angiogenic Functions and Blocks Cell Cycle Progression in Endothelial Cells

    PubMed Central

    Bateman, Henry R.; Liang, Qiaoli; Fan, Daping; Rodriguez, Vanessa; Lessner, Susan M.

    2013-01-01

    Sparstolonin B (SsnB) is a novel bioactive compound isolated from Sparganium stoloniferum, an herb historically used in Traditional Chinese Medicine as an anti-tumor agent. Angiogenesis, the process of new capillary formation from existing blood vessels, is dysregulated in many pathological disorders, including diabetic retinopathy, tumor growth, and atherosclerosis. In functional assays, SsnB inhibited endothelial cell tube formation (Matrigel method) and cell migration (Transwell method) in a dose-dependent manner. Microarray experiments with human umbilical vein endothelial cells (HUVECs) and human coronary artery endothelial cells (HCAECs) demonstrated differential expression of several hundred genes in response to SsnB exposure (916 and 356 genes, respectively, with fold change ≥2, p<0.05, unpaired t-test). Microarray data from both cell types showed significant overlap, including genes associated with cell proliferation and cell cycle. Flow cytometric cell cycle analysis of HUVECs treated with SsnB showed an increase of cells in the G1 phase and a decrease of cells in the S phase. Cyclin E2 (CCNE2) and Cell division cycle 6 (CDC6) are regulatory proteins that control cell cycle progression through the G1/S checkpoint. Both CCNE2 and CDC6 were downregulated in the microarray data. Real Time quantitative PCR confirmed that gene expression of CCNE2 and CDC6 in HUVECs was downregulated after SsnB exposure, to 64% and 35% of controls, respectively. The data suggest that SsnB may exert its anti-angiogenic properties in part by downregulating CCNE2 and CDC6, halting progression through the G1/S checkpoint. In the chick chorioallantoic membrane (CAM) assay, SsnB caused significant reduction in capillary length and branching number relative to the vehicle control group. Overall, SsnB caused a significant reduction in angiogenesis (ANOVA, p<0.05), demonstrating its ex vivo efficacy. PMID:23940584

  11. Sparstolonin B inhibits pro-angiogenic functions and blocks cell cycle progression in endothelial cells.

    PubMed

    Bateman, Henry R; Liang, Qiaoli; Fan, Daping; Rodriguez, Vanessa; Lessner, Susan M

    2013-01-01

    Sparstolonin B (SsnB) is a novel bioactive compound isolated from Sparganium stoloniferum, an herb historically used in Traditional Chinese Medicine as an anti-tumor agent. Angiogenesis, the process of new capillary formation from existing blood vessels, is dysregulated in many pathological disorders, including diabetic retinopathy, tumor growth, and atherosclerosis. In functional assays, SsnB inhibited endothelial cell tube formation (Matrigel method) and cell migration (Transwell method) in a dose-dependent manner. Microarray experiments with human umbilical vein endothelial cells (HUVECs) and human coronary artery endothelial cells (HCAECs) demonstrated differential expression of several hundred genes in response to SsnB exposure (916 and 356 genes, respectively, with fold change ≥2, p<0.05, unpaired t-test). Microarray data from both cell types showed significant overlap, including genes associated with cell proliferation and cell cycle. Flow cytometric cell cycle analysis of HUVECs treated with SsnB showed an increase of cells in the G1 phase and a decrease of cells in the S phase. Cyclin E2 (CCNE2) and Cell division cycle 6 (CDC6) are regulatory proteins that control cell cycle progression through the G1/S checkpoint. Both CCNE2 and CDC6 were downregulated in the microarray data. Real Time quantitative PCR confirmed that gene expression of CCNE2 and CDC6 in HUVECs was downregulated after SsnB exposure, to 64% and 35% of controls, respectively. The data suggest that SsnB may exert its anti-angiogenic properties in part by downregulating CCNE2 and CDC6, halting progression through the G1/S checkpoint. In the chick chorioallantoic membrane (CAM) assay, SsnB caused significant reduction in capillary length and branching number relative to the vehicle control group. Overall, SsnB caused a significant reduction in angiogenesis (ANOVA, p<0.05), demonstrating its ex vivo efficacy. PMID:23940584

  12. The Functional Breakdown Structure (FBS) and Its Relationship to Life Cycle Cost

    NASA Technical Reports Server (NTRS)

    DeHoff, Bryan; Levack, Danie J. H.; Rhodes, Russell E.

    2009-01-01

    The Functional Breakdown Structure (FBS) is a structured, modular breakdown of every function that must be addressed to perform a generic mission. It is also usable for any subset of the mission. Unlike a Work Breakdown Structure (WBS), the FBS is a function-oriented tree, not a product-oriented tree. The FBS details not products, but operations or activities that should be performed. The FBS is not tied to any particular architectural implementation because it is a listing of the needed functions, not the elements, of the architecture. The FBS for Space Transportation Systems provides a universal hierarchy of required functions, which include ground and space operations as well as infrastructure - it provides total visibility of the entire mission. By approaching the systems engineering problem from the functional view, instead of the element or hardware view, the SPST has created an exhaustive list of potential requirements which the architecture designers can use to evaluate the completeness of their designs. This is a new approach that will provide full accountability of all functions required to perform the planned mission. It serves as a giant check list to be sure that no functions are omitted, especially in the early architectural design phase. A significant characteristic of a FBS is that if architecture options are compared using this approach, then any missing or redundant elements of each option will be ' identified. Consequently, valid Life Cycle Costs (LCC) comparisons can be made. For example, one architecture option might not need a particular function while another option does. One option may have individual elements to perform each of three functions while another option needs only one element to perform the three functions. Once an architecture has been selected, the FBS will serve as a guide in development of the work breakdown structure, provide visibility of those technologies that need to be further developed to perform required functions

  13. Neuromuscular function and fatigue resistance of the plantar flexors following short-term cycling endurance training

    PubMed Central

    Behrens, Martin; Weippert, Matthias; Wassermann, Franziska; Bader, Rainer; Bruhn, Sven; Mau-Moeller, Anett

    2015-01-01

    Previously published studies on the effect of short-term endurance training on neuromuscular function of the plantar flexors have shown that the H-reflex elicited at rest and during weak voluntary contractions was increased following the training regime. However, these studies did not test H-reflex modulation during isometric maximum voluntary contraction (iMVC) and did not incorporate a control group in their study design to compare the results of the endurance training group to individuals without the endurance training stimulus. Therefore, this randomized controlled study was directed to investigate the neuromuscular function of the plantar flexors at rest and during iMVC before and after 8 weeks of cycling endurance training. Twenty-two young adults were randomly assigned to an intervention group and a control group. During neuromuscular testing, rate of torque development, isometric maximum voluntary torque and muscle activation were measured. Triceps surae muscle activation and tibialis anterior muscle co-activation were assessed by normalized root mean square of the EMG signal during the initial phase of contraction (0–100, 100–200 ms) and iMVC of the plantar flexors. Furthermore, evoked spinal reflex responses of the soleus muscle (H-reflex evoked at rest and during iMVC, V-wave), peak twitch torques induced by electrical stimulation of the posterior tibial nerve at rest and fatigue resistance were evaluated. The results indicate that cycling endurance training did not lead to a significant change in any variable of interest. Data of the present study conflict with the outcome of previously published studies that have found an increase in H-reflex excitability after endurance training. However, these studies had not included a control group in their study design as was the case here. It is concluded that short-term cycling endurance training does not necessarily enhance H-reflex responses and fatigue resistance. PMID:26029114

  14. An Estimate of the Size and Shape of Sunspot Cycle 24 Based on its Early Cycle Behavior using the Hathaway-Wilson-Reichmann Shape-Fitting Function

    NASA Technical Reports Server (NTRS)

    Wilson, Robert M.

    2011-01-01

    On the basis of 12-month moving averages (12-mma) of monthly mean sunspot number (R), sunspot cycle 24 had its minimum amplitude (Rm = 1.7) in December 2008. At 12 mo past minimum, R measured 8.3, and at 18 mo past minimum, it measured 16.4. Thus far, the maximum month-to-month rate of rise in 12-mma values of monthly mean sunspot number (AR(t) max) has been 1.7, having occurred at elapsed times past minimum amplitude (t) of 14 and 15 mo. Compared to other sunspot cycles of the modern era, cycle 24?s Rm and AR(t) max (as observed so far) are the smallest on record, suggesting that it likely will be a slow-rising, long-period sunspot cycle of below average maximum amplitude (RM). Supporting this view is the now observed relative strength of cycle 24?s geomagnetic minimum amplitude as measured using the 12-mma value of the aa-geomagnetic index (aam = 8.4), which also is the smallest on record, having occurred at t equals 8 and 9 mo. From the method of Ohl (the inferred preferential association between RM and aam), one predicts RM = 55 +/- 17 (the ?1 se prediction interval) for cycle 24. Furthermore, from the Waldmeier effect (the inferred preferential association between the ascent duration (ASC) and RM) one predicts an ASC longer than 48 mo for cycle 24; hence, maximum amplitude occurrence should be after December 2012. Application of the Hathaway-Wilson-Reichmann shape-fitting function, using an RM = 70 and ASC = 56 mo, is found to adequately fit the early sunspot number growth of cycle 24.

  15. Acute bouts of assisted cycling improves cognitive and upper extremity movement functions in adolescents with Down syndrome.

    PubMed

    Ringenbach, Shannon D R; Albert, Andrew R; Chen, Chih-Chia J J; Alberts, Jay L

    2014-04-01

    The aim of this study was to examine the effectiveness of 2 modes of exercise on cognitive and upper extremity movement functioning in adolescents with Down syndrome (DS). Nine participants randomly completed 3 interventions over 3 consecutive weeks. The interventions were: (a) voluntary cycling (VC), in which participants cycled at their self-selected pedaling rate; (b) assisted cycling (AC), in which the participants' voluntary pedaling rates were augmented with a motor to ensure the maintenance of 80 rpm; and (c) no cycling (NC), in which the participants sat and listened to music. Manual dexterity improved after AC, but not after VC or NC. Measures of cognitive function, including reaction time and cognitive planning, also improved after AC, but not after the other interventions. Future research will try to uncover the mechanisms involved in the behavioral improvements found after an acute bout of assisted cycling in adolescents with DS. PMID:24725111

  16. A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

    PubMed

    Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

    2015-01-01

    Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution. PMID:26263551

  17. Assessment of LV systolic function in atrial fibrillation using an index of preceding cardiac cycles.

    PubMed

    Tabata, T; Grimm, R A; Greenberg, N L; Agler, D A; Mowrey, K A; Wallick, D W; Zhang, Y; Zhuang, S; Mazgalev, T N; Thomas, J D

    2001-08-01

    The clinical assessment of left ventricular (LV) systolic function during atrial fibrillation (AF) is unreliable and difficult because of beat-to-beat variability. We evaluated an index for the estimation of LV systolic function in AF that is based on the relationship between the preceding (R-R1) and prepreceding (R-R2) R-R intervals. LV Doppler stroke volume (SV), ejection fraction (EF), peak aortic flow rate (AoF) and the maximum value of the first derivative of the LV pressure curve (dP/dt(max)) were evaluated in 13 healthy open-chest dogs during triggered AF. All parameters showed a significantly strong positive linear relationship with the ratio of R-R1/R-R2 (r = 0.65, 0.74, 0.75, and 0.70 for SV, EF, AoF, and dP/dt(max), respectively). The calculated value of LV systolic parameters at R-R1/R-R2 = 1 in the linear regression line showed a good relationship and an agreement with the measured average value of the parameter over all cardiac cycles (SV, 12.1 vs. 12.8 ml; EF, 49.6 vs. 51.2%; AoF, 1.37 vs. 1.48 l/min; and dP/dt(max), 2,323 vs. 2,454 mmHg/s). Using the LV systolic parameters estimated at R-R1/R-R2 = 1 in the linear regression line allows the LV contractile function to be accurately and reproducibly evaluated during AF and obviates the less-reliable process of averaging multiple cardiac cycles. PMID:11454559

  18. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

    PubMed Central

    Handley, Kim M; VerBerkmoes, Nathan C; Steefel, Carl I; Williams, Kenneth H; Sharon, Itai; Miller, Christopher S; Frischkorn, Kyle R; Chourey, Karuna; Thomas, Brian C; Shah, Manesh B; Long, Philip E; Hettich, Robert L; Banfield, Jillian F

    2013-01-01

    Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used proteogenomics to test the hypothesis that excess input of acetate activates complex community functioning and syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer and recovered during microbial sulfate reduction. De novo reconstruction of community sequences yielded near-complete genomes of Desulfobacter (Deltaproteobacteria), Sulfurovum- and Sulfurimonas-like Epsilonproteobacteria and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen fixation and acetate oxidation to CO2 during amendment. Results indicate less abundant Desulfuromonadales, and possibly Bacteroidetes, also actively contributed to CO2 production via the tricarboxylic acid (TCA) cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. We infer that high acetate concentrations, aimed at stimulating anaerobic heterotrophy, led to the co-enrichment of, and carbon fixation in Epsilonproteobacteria. Results give an insight into ecosystem behavior following addition of simple organic carbon to the subsurface, and demonstrate a range of biological processes and community interactions were stimulated. PMID:23190730

  19. Power Effects on High Lift, Stability and Control Characteristics of the TCA Model Tested in the LaRC 14 x 22 Ft Wind Tunnel

    NASA Technical Reports Server (NTRS)

    Glessner, Paul T.

    1999-01-01

    The TCA-2 wind-tunnel test was the second in a series of planned tests utilizing the 5% Technology Concept Airplane (TCA) model. Each of the tests was planned to utilize the unique capabilities of the NASA Langley 14'x22' and the NASA Ames 12' test facilities, in order to assess specific aspects of the high lift and stability and control characteristics of the TCA configuration. However, shortly after the completion of the TCA-1 test, an early projection of the Technology Configuration (TC) identified the need for several significant changes to the baseline TCA configuration. These changes were necessary in order to meet more stringent noise certification levels, as well as, to provide a means to control dynamic structural modes. The projected changes included a change to the outboard wing (increased aspect ratio and lower sweep) and a reconfiguration of the longitudinal control surfaces to include a medium size canard and a reduced horizontal tail. The impact of these proposed changes did not affect the TCA-2 test, because it was specifically planned to address power effects on the empennage and a smaller horizontal tail was in the plan to be tested. However, the focus of future tests was reevaluated and the emphasis was shifted away from assessment of TCA specific configurations to a more general assessment of configurations that encompass the projected design space for the TC.

  20. Plasmodial HSP70s are functionally adapted to the malaria parasite life cycle

    PubMed Central

    Przyborski, Jude M.; Diehl, Mathias; Blatch, Gregory L.

    2015-01-01

    The human malaria parasite, Plasmodium falciparum, encodes a minimal complement of six heat shock protein 70s (PfHSP70s), some of which are highly expressed and are thought to play an important role in the survival and pathology of the parasite. In addition to canonical features of molecular chaperones, these HSP70s possess properties that reflect functional adaptation to a parasitic life style, including resistance to thermal insult during fever periods and host–parasite interactions. The parasite even exports an HSP70 to the host cell where it is likely to be involved in host cell modification. This review focuses on the features of the PfHSP70s, particularly with respect to their adaptation to the malaria parasite life cycle. PMID:26167469

  1. Plasmodial HSP70s are functionally adapted to the malaria parasite life cycle.

    PubMed

    Przyborski, Jude M; Diehl, Mathias; Blatch, Gregory L

    2015-01-01

    The human malaria parasite, Plasmodium falciparum, encodes a minimal complement of six heat shock protein 70s (PfHSP70s), some of which are highly expressed and are thought to play an important role in the survival and pathology of the parasite. In addition to canonical features of molecular chaperones, these HSP70s possess properties that reflect functional adaptation to a parasitic life style, including resistance to thermal insult during fever periods and host-parasite interactions. The parasite even exports an HSP70 to the host cell where it is likely to be involved in host cell modification. This review focuses on the features of the PfHSP70s, particularly with respect to their adaptation to the malaria parasite life cycle. PMID:26167469

  2. Viral Membrane Channels: Role and Function in the Virus Life Cycle

    PubMed Central

    Sze, Ching Wooen; Tan, Yee-Joo

    2015-01-01

    Viroporins are small, hydrophobic trans-membrane viral proteins that oligomerize to form hydrophilic pores in the host cell membranes. These proteins are crucial for the pathogenicity and replication of viruses as they aid in various stages of the viral life cycle, from genome uncoating to viral release. In addition, the ion channel activity of viroporin causes disruption in the cellular ion homeostasis, in particular the calcium ion. Fluctuation in the calcium level triggers the activation of the host defensive programmed cell death pathways as well as the inflammasome, which in turn are being subverted for the viruses’ replication benefits. This review article summarizes recent developments in the functional investigation of viroporins from various viruses and their contributions to viral replication and virulence. PMID:26110585

  3. Defective Cell Cycle Checkpoint Functions in Melanoma Are Associated with Altered Patterns of Gene Expression

    PubMed Central

    Kaufmann, William K.; Nevis, Kathleen R.; Qu, Pingping; Ibrahim, Joseph G.; Zhou, Tong; Zhou, Yingchun; Simpson, Dennis A.; Helms-Deaton, Jennifer; Cordeiro-Stone, Marila; Moore, Dominic T.; Thomas, Nancy E.; Hao, Honglin; Liu, Zhi; Shields, Janiel M.; Scott, Glynis A.; Sharpless, Norman E.

    2009-01-01

    Defects in DNA damage responses may underlie genetic instability and malignant progression in melanoma. Cultures of normal human melanocytes (NHMs) and melanoma lines were analyzed to determine whether global patterns of gene expression could predict the efficacy of DNA damage cell cycle checkpoints that arrest growth and suppress genetic instability. NHMs displayed effective G1 and G2 checkpoint responses to ionizing radiation-induced DNA damage. A majority of melanoma cell lines (11/16) displayed significant quantitative defects in one or both checkpoints. Melanomas with B-RAF mutations as a class displayed a significant defect in DNA damage G2 checkpoint function. In contrast the epithelial-like subtype of melanomas with wild-type N-RAS and B-RAF alleles displayed an effective G2 checkpoint but a significant defect in G1 checkpoint function. RNA expression profiling revealed that melanoma lines with defects in the DNA damage G1 checkpoint displayed reduced expression of p53 transcriptional targets, such as CDKN1A and DDB2, and enhanced expression of proliferation-associated genes, such as CDC7 and GEMININ. A Bayesian analysis tool was more accurate than significance analysis of microarrays for predicting checkpoint function using a leave-one-out method. The results suggest that defects in DNA damage checkpoints may be recognized in melanomas through analysis of gene expression. PMID:17597816

  4. Differences in plantarflexor function during a stretch-shortening cycle task due to limb preference.

    PubMed

    Furlong, Laura-Anne M; Harrison, Andrew J

    2015-01-01

    Most healthy humans move symmetrically at gross limb level but large kinetic and kinematic asymmetries have been observed at joint level during locomotion. The aim of this study was to assess muscle function asymmetries in healthy, active adults using an adapted force sledge apparatus which isolates the plantarflexors during a stretch-shortening cycle (SSC) task. Peak force, rate of force development and SSC function of preferred and non-preferred limbs were assessed in 21 healthy, active individuals using the adapted sledge and three-dimensional motion analysis. Between-limb differences and relationships were determined using paired t-tests/Wilcoxon Signed-rank test, Cohen's dz, absolute symmetry index and Pearson's r/Spearman's rho. Significant differences with moderate effect size (ES) were observed in peak force (ES: 0.66), rate of peak force development (ES: 0.78), rate of force development in the first 50 ms (ES: 0.76), flight time (ES: 0.64) and SSC function (0.68), with no difference in contact time or duration of eccentric loading. A small ES (0.56) was observed in rate of force development in the first 30 ms. The upper range of asymmetry observed (up to 44.6%) was larger than previously reported for healthy individuals, indicating compensations occur at proximal joints during locomotion to ensure symmetrical movement. PMID:24877621

  5. Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities

    PubMed Central

    Ramírez, Santiago R; Hernández, Carlos; Link, Andres; López-Uribe, Margarita M

    2015-01-01

    Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of declining bee populations. Male euglossine bees collect, store, and accumulate odoriferous compounds (perfumes) to subsequently use during courtship display. Thus, synthetic chemical baits can be used to attract and monitor euglossine bee populations. We conducted monthly censuses of orchid bees in three sites in the Magdalena valley of Colombia – a region where Central and South American biotas converge – to investigate the structure, diversity, and assembly of euglossine bee communities through time in relation to seasonal climatic cycles. In particular, we tested the hypothesis that phylogenetic community structure and functional trait diversity changed in response to seasonal rainfall fluctuations. All communities exhibited strong to moderate phylogenetic clustering throughout the year, with few pronounced bursts of phylogenetic overdispersion that coincided with the transition from wet-to-dry seasons. Despite the heterogeneous distribution of functional traits (e.g., body size, body mass, and proboscis length) and the observed seasonal fluctuations in phylogenetic diversity, we found that functional trait diversity, evenness, and divergence remained constant during all seasons in all communities. However, similar to the pattern observed with phylogenetic diversity, functional trait richness fluctuated markedly with rainfall in all sites. These results emphasize the importance of considering seasonal fluctuations in community assembly

  6. Form and function of the corpus luteum during the human menstrual cycle

    PubMed Central

    BAERWALD, A. R.; ADAMS, G. P.; PIERSON, R. A.

    2010-01-01

    Objective To characterize the growth and regression of the corpus luteum (CL) during an interovulatory interval (IOI) using serial transvaginal ultrasonography. Methods Fifty healthy women of reproductive age with a history of regular menstrual cycles underwent daily transvaginal ultrasonography for one IOI. Measurements of luteal area and luteal numerical pixel value (NPV) were recorded each day after ovulation until the CL could no longer be detected. Blood was drawn every third day during the IOI to measure serum concentrations of progesterone and estradiol-17β. Results Corpora lutea were of two morphological types: those with a central fluid-filled cavity (CFFC) (78%) and those without (22%). Eighty-eight percent of women exhibited a CL containing a CFFC 2 days after ovulation, followed by 34% 13 days after ovulation and 2% 27 days after ovulation. Luteal area, progesterone concentration and estradiol concentration increased for approximately the first 6 days following ovulation followed by a subsequent decline. Luteal NPV decreased from days 1 to 11 and increased during days 11–16. Changes in luteal area, NPV, progesterone and estradiol concentrations did not differ in women with two versus three waves of follicular development. Conclusions Peak luteal function, as determined by maximum luteal area, progesterone concentration and estradiol concentration, is observed 6 days following ovulation. Luteal NPV is reflective of morphological and endocrinological changes in the CL. The development of a CFFC during luteinization is a normal physiological phenomenon. The CL can be detected, but is not functional, during the follicular phase of the menstrual cycle. PMID:15846762

  7. DNA Damage Response and Spindle Assembly Checkpoint Function throughout the Cell Cycle to Ensure Genomic Integrity

    PubMed Central

    Lawrence, Katherine S.; Chau, Thinh; Engebrecht, JoAnne

    2015-01-01

    Errors in replication or segregation lead to DNA damage, mutations, and aneuploidies. Consequently, cells monitor these events and delay progression through the cell cycle so repair precedes division. The DNA damage response (DDR), which monitors DNA integrity, and the spindle assembly checkpoint (SAC), which responds to defects in spindle attachment/tension during metaphase of mitosis and meiosis, are critical for preventing genome instability. Here we show that the DDR and SAC function together throughout the cell cycle to ensure genome integrity in C. elegans germ cells. Metaphase defects result in enrichment of SAC and DDR components to chromatin, and both SAC and DDR are required for metaphase delays. During persistent metaphase arrest following establishment of bi-oriented chromosomes, stability of the metaphase plate is compromised in the absence of DDR kinases ATR or CHK1 or SAC components, MAD1/MAD2, suggesting SAC functions in metaphase beyond its interactions with APC activator CDC20. In response to DNA damage, MAD2 and the histone variant CENPA become enriched at the nuclear periphery in a DDR-dependent manner. Further, depletion of either MAD1 or CENPA results in loss of peripherally associated damaged DNA. In contrast to a SAC-insensitive CDC20 mutant, germ cells deficient for SAC or CENPA cannot efficiently repair DNA damage, suggesting that SAC mediates DNA repair through CENPA interactions with the nuclear periphery. We also show that replication perturbations result in relocalization of MAD1/MAD2 in human cells, suggesting that the role of SAC in DNA repair is conserved. PMID:25898113

  8. The N cycle in Earth subsurface. Reactivity of functional genes to anthropogenic CO2 injections.

    NASA Astrophysics Data System (ADS)

    Trias, Rosalia; Gérard, Emmanuelle; Le Campion, Paul; Gíslason, Sigurður R.; Aradóttir, Edda S.; Alfreðsson, Helgui A.; Mesfin, Kiflom G.; Snæbjörnsdóttir, Sandra Ó.; Ménez, Bénédicte

    2014-05-01

    The Nitrogen cycle has been widely studied in surface ecosystems, due to the importance of this nutrient for the organisms' development, and to the impact in the environment of most of the N forms, many of them being considered pollutants. However, little is known about the importance of the N-related metabolisms in subsurface systems now recognized to host diverse and active microbial life. In this study, we have periodically sampled the subsurface aquifers of the Icelandic pilot site for CO2 storage associated with the geothermal plant of Hellisheidi (operated by Reykjavik Energy; http://www.or.is/en/projects/carbfix). With the aim of understanding the dynamics of N-cycle in the subsurface, and its reactivity to CO2 injections, we quantified through qPCR the functional genes amoA (archaea), amoA (bacteria), nirK, nirS, nosZ, nifH, and the 16SrRNA genes of the anammox, total archaea and total bacteria. The 16SrRNA gene quantification provided values of around 107 gene copies/l at non injection periods. CO2 injection caused first a slight decrease probably due to pH decrease or toxicity by oxygen contamination during the injections. Two months after injection, the copy numbers increased up to 109 gene copies/l, and slowly returned to pre-injection values. The archaeal 16S rDNA copy numbers showed a similar reaction, with higher toxicity effects, and a lower increase afterwards. Due to the high reactivity of the microbial populations to CO2 injections, all the N cycle quantifications were related to the total 16S rDNA copies for normalization. Nitrifying genes (amoA) were mainly represented by the ammonia oxidizing archaea, and were apparently not affected by CO2 injections. Anammox bacteria were present in a very low percentage, and the obtained copy numbers tended to decrease after the injection. These results were surprising due to the autotrophic character of ammonia oxidizers, but could be explained by a competitive exclusion. On the contrary, N-fixation (nif

  9. Renal Function in Kidney and Liver Transplant Recipients After A 130-km Road Cycling Race

    PubMed Central

    Mosconi, Giovanni; Roi, Giulio Sergio; Totti, Valentina; Zancanaro, Marco; Tacconi, Alessandra; Todeschini, Paola; Ramazzotti, Eric; Di Michele, Rocco; Trerotola, Manuela; Donati, Carlo; Nanni Costa, Alessandro

    2015-01-01

    Abstract Background A few patients, after receiving solid organ transplantation, return to performing various sports and competitions; however, at present, data no study had evaluated the effects of endurance cycling races on their renal function. Methods Race times and short form (36) health survey questionnaires of 10 kidney transplant recipients (KTR) and 8 liver transplant recipients (LTR) transplanted recipients involved in a road cycling race (130 km) were compared with 35 healthy control subjects (HCS), also taking laboratory blood and urine tests the day before the race, at the end of the race, and 18 to 24 hours after competing. Results The 3 groups showed similar race times (KTR, 5 hours 59 minutes ± 0 hours 39 minutes; LTR, 6 hours 20 minutes ± 1 hour 11 minutes; HCS, 5 hours 40 minutes ± 1 hour 28 minutes), similar short form (36) health survey scores, and similar trend of laboratory parameters which returned to baseline after 18 to 24 hours. After the race, there was an increase in creatinine (0.24 mg/dL; effect size [ES] = 0.78; P < 0.001), urea (22 mg/dL; ES = 1.42; P < 0.001), and a decrease of estimated glomerular filtration rate (−17 mL/min; ES = 0.85; P < 0.001). The increase of blood uric acid was more remarkable in HCS and KTR (2.3 mg/dL; ES = 1.39; P < 0.001). The KTR showed an increase of microalbuminuria (167.4 mg/L; ES = 1.20; P < 0.001) and proteinuria (175 mg/mL; ES = 0.97; P < 0.001) similar to LTR (microalbuminuria: 176.0 mg/L; ES = 1.26; P < 0.001; proteinuria: 213 mg/mL; ES = 1.18; P < 0.001), with high individual variability. The HCS had a nonsignificant increase of microalbuminuria (4.4 mg/L; ES = 0.03; P = 0.338) and proteinuria (59 mg/mL; ES = 0.33; P = 0.084). Conclusions Selected and well-trained KTR and LTR patients can participate to an endurance cycling race showing final race times and temporary modifications of kidney function similar to those of HCS group, despite some differences related to baseline clinical

  10. Tumor cycling hypoxia induces chemoresistance in glioblastoma multiforme by upregulating the expression and function of ABCB1

    PubMed Central

    Chou, Chii-Wen; Wang, Chi-Chung; Wu, Chung-Pu; Lin, Yu-Jung; Lee, Yu-Chun; Cheng, Ya-Wen; Hsieh, Chia-Hung

    2012-01-01

    Tumor cycling hypoxia is now a well-recognized phenomenon in animal and human solid tumors. However, how tumor cycling hypoxia impacts chemotherapy is unclear. In the present study, we explored the impact and the mechanism of cycling hypoxia on tumor microenvironment-mediated chemoresistance. Hoechst 33342 staining and hypoxia-inducible factor–1 (HIF-1) activation labeling together with immunofluorescence imaging and fluorescence-activated cell sorting were used to isolate hypoxic tumor subpopulations from human glioblastoma xenografts. ABCB1 expression, P-glycoprotein function, and chemosensitivity in tumor cells derived from human glioblastoma xenografts or in vitro cycling hypoxic stress-treated glioblastoma cells were determined using Western blot analysis, drug accumulation and efflux assays, and MTT assay, respectively. ABCB1 expression and P-glycoprotein function were upregulated under cycling hypoxia in glioblastoma cells concomitant with decreased responses to doxorubicin and BCNU. However, ABCB1 knockdown inhibited these effects. Moreover, immunofluorescence imaging and flow cytometric analysis for ABCB1, HIF-1 activation, and Hoechst 3342 in glioblastoma revealed highly localized ABCB1 expression predominantly in potentially cycling hypoxic areas with HIF-1 activation and blood perfusion in the solid tumor microenvironment. The cycling hypoxic tumor cells derived from glioblastoma xenografts exhibited higher ABCB1 expression, P-glycoprotein function, and chemoresistance, compared with chronic hypoxic and normoxic cells. Tumor-bearing mice that received YC-1, an HIF-1α inhibitor, exhibited suppressed tumor microenvironment-induced ABCB1 induction and enhanced survival rate in BCNU chemotherapy. Cycling hypoxia plays a vital role in tumor microenvironment-mediated chemoresistance through the HIF-1–dependent induction of ABCB1. HIF-1 blockade before and concurrent with chemotherapy could suppress cycling hypoxia-induced chemoresistance. PMID:22946104

  11. Cycling with Functional Electrical Stimulation Before and After a Distal Femur Fracture in a Man with Paraplegia

    PubMed Central

    Marino, Ralph J.; Oleson, Christina V.; Schmidt-Read, Mary; Modlesky, Christopher M.

    2015-01-01

    Case Presentation: A man with chronic paraplegia sustained a distal femur fracture following an unrelated fall while enrolled in a study examining musculoskeletal changes after 6 months of cycling with functional electrical stimulation (FES). After healing, he restarted and completed the study. Management and Outcome: Study measures included areal bone mineral density, trabecular bone microarchitecture, cortical bone macroarchitecture, serum bone formation/resorption markers, and muscle volume. The patient made small gains in bone- and muscle-related measures. Bone markers had not returned to baseline prior to restarting cycling, which may have impacted results. Discussion: This case shows that cycling with FES may be safely resumed after distal femur fracture. PMID:26689692

  12. Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae.

    PubMed

    Gibson, Daniel G; Bell, Stephen P; Aparicio, Oscar M

    2006-06-01

    Chromosomal replication initiates through the assembly of a prereplicative complex (pre-RC) at individual replication origins in the G1-phase, followed by activation of these complexes in the S-phase. In Saccharomyces cerevisiae, the origin recognition complex (ORC) binds replication origins throughout the cell cycle and participates in pre-RC assembly. Whether the ORC plays an additional role subsequent to pre-RC assembly in replication initiation or any other essential cell cycle process is not clear. To study the function of the ORC during defined cell cycle periods, we performed cell cycle execution point analyses with strains containing a conditional mutation in the ORC1, ORC2 or ORC5 subunit of ORC. We found that the ORC is essential for replication initiation, but is dispensable for replication elongation or later cell cycle events. Defective initiation in ORC mutant cells results in incomplete replication and mitotic arrest enforced by the DNA damage and spindle assembly checkpoint pathways. The involvement of the spindle assembly checkpoint implies a defect in kinetochore-spindle attachment or sister chromatid cohesion due to incomplete replication and/or DNA damage. Remarkably, under semipermissive conditions for ORC1 function, the spindle checkpoint alone suffices to block proliferation, suggesting this checkpoint is highly sensitive to replication initiation defects. We discuss the potential significance of these overlapping checkpoints and the impact of our findings on previously postulated role(s) of ORCs in other cell cycle functions. PMID:16716188

  13. A systematic analysis of TCA Escherichia coli mutants reveals suitable genetic backgrounds for enhanced hydrogen and ethanol production using glycerol as main carbon source.

    PubMed

    Valle, Antonio; Cabrera, Gema; Muhamadali, Howbeer; Trivedi, Drupad K; Ratray, Nicholas J W; Goodacre, Royston; Cantero, Domingo; Bolivar, Jorge

    2015-09-01

    Biodiesel has emerged as an environmentally friendly alternative to fossil fuels; however, the low price of glycerol feed-stocks generated from the biodiesel industry has become a burden to this industry. A feasible alternative is the microbial biotransformation of waste glycerol to hydrogen and ethanol. Escherichia coli, a microorganism commonly used for metabolic engineering, is able to biotransform glycerol into these products. Nevertheless, the wild type strain yields can be improved by rewiring the carbon flux to the desired products by genetic engineering. Due to the importance of the central carbon metabolism in hydrogen and ethanol synthesis, E. coli single null mutant strains for enzymes of the TCA cycle and other related reactions were studied in this work. These strains were grown anaerobically in a glycerol-based medium and the concentrations of ethanol, glycerol, succinate and hydrogen were analysed by HPLC and GC. It was found that the reductive branch is the more relevant pathway for the aim of this work, with malate playing a central role. It was also found that the putative C4-transporter dcuD mutant improved the target product yields. These results will contribute to reveal novel metabolic engineering strategies for improving hydrogen and ethanol production by E. coli. PMID:26058953

  14. Changes in vascular plant functional types drive carbon cycling in peatlands

    NASA Astrophysics Data System (ADS)

    Zeh, Lilli; Bragazza, Luca; Erhagen, Björn; Limpens, Juul; Kalbitz, Karsten

    2016-04-01

    Northern peatlands store a large organic carbon (C) pool that is highly exposed to future environmental changes with consequent risk of releasing enormous amounts of C. Biotic changes in plant community structure and species abundance might have an even stronger impact on soil organic C dynamics in peatlands than the direct effects of abiotic changes. Therefore, a sound understanding of the impact of vegetation dynamics on C cycling will help to better predict the response of peatlands to environmental changes. Here, we aimed to assess the role of plant functional types (PFTs) in affecting peat decomposition in relation to climate warming. To this aim, we selected two peatlands at different altitude (i.e. 1300 and 1700 m asl) on the south-eastern Alps of Italy. The two sites represent a contrast in temperature, overall vascular plant biomass and relative ericoids abundance, with the highest biomass and ericoids occurrence at the low latitude. Within the sites we selected 20 plots of similar microtopographical position and general vegetation type (hummocks). All plots contained both graminoids and ericoids and had a 100% cover of Sphagnum mosses. The plots were subjected to four treatments (control, and three clipping treatments) in which we selectively removed aboveground biomass of ericoids, graminoids or both to explore the contribution of the different PFTs for soil respiration (n=5) and peat chemistry. Peat chemical composition was determined by the analysis of C and N and their stable isotopes in association with pyrolysis GC/MS. Soil respiration was measured after clipping with a Licor system. Preliminary findings suggest that peat decomposition pathway and rate depend on plant species composition and particularly on differences in root activity between PFTs. Finally, this study underlines the importance of biotic drivers to predict the effects of future environmental changes on peatland C cycling.

  15. Ingestion of sodium plus water improves cardiovascular function and performance during dehydrating cycling in the heat.

    PubMed

    Hamouti, N; Fernández-Elías, V E; Ortega, J F; Mora-Rodriguez, R

    2014-06-01

    We studied if salt and water ingestion alleviates the physiological strain caused by dehydrating exercise in the heat. Ten trained male cyclists (VO2max : 60 ± 7 mL/kg/min) completed three randomized trials in a hot-dry environment (33 °C, 30% rh, 2.5 m/s airflow). Ninety minutes before the exercise, participants ingested 10 mL of water/kg body mass either alone (CON trial) or with salt to result in concentrations of 82 or 164 mM Na(+) (ModNa(+) or HighNa(+) trial, respectively). Then, participants cycled at 63% of VO2 m ⁢ a x for 120 min immediately followed by a time-trial. After 120 min of exercise, the reduction in plasma volume was lessened with ModNa(+) and HighNa(+) trials (-11.9 ± 2.1 and -9.8 ± 4.2%) in comparison with CON (-16.4 ± 3.2%; P < 0.05). However, heat accumulation or dissipation (forearm skin blood flow and sweat rate) were not improved by salt ingestion. In contrast, both salt trials maintained cardiac output (∼ 1.3 ± 1.4 L/min; P < 0.05) and stroke volume (∼ 10 ± 11 mL/beat; P < 0.05) above CON after 120 min of exercise. Furthermore, the salt trials equally improved time-trial performance by 7.4% above CON (∼ 289 ± 42 vs 269 ± 50 W, respectively; P < 0.05). Our data suggest that pre-exercise ingestion of salt plus water maintains higher plasma volume during dehydrating exercise in the heat without thermoregulatory effects. However, it maintains cardiovascular function and improves cycling performance. PMID:23253191

  16. Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle

    NASA Astrophysics Data System (ADS)

    Zubarev, Dmitry; Rappoport, Dmitrij; Aspuru-Guzik, Alan

    2015-03-01

    We consider the much discussed hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach that quantifies the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for the investigations of the origin of the common metabolic core should be significantly extended. This work was supported by a grant from the Simons Foundation (SCOL 291937, Dmitry Zubarev).

  17. Insulin signalling and glucose transport in the ovary and ovarian function during the ovarian cycle.

    PubMed

    Dupont, Joëlle; Scaramuzzi, Rex J

    2016-06-01

    Data derived principally from peripheral tissues (fat, muscle and liver) show that insulin signals via diverse interconnecting intracellular pathways and that some of the major intersecting points (known as critical nodes) are the IRSs (insulin receptor substrates), PI3K (phosphoinositide kinase)/Akt and MAPK (mitogen-activated protein kinase). Most of these insulin pathways are probably also active in the ovary and their ability to interact with each other and also with follicle-stimulating hormone (FSH) and luteinizing hormone (LH) signalling pathways enables insulin to exert direct modulating influences on ovarian function. The present paper reviews the intracellular actions of insulin and the uptake of glucose by ovarian tissues (granulosa, theca and oocyte) during the oestrous/menstrual cycle of some rodent, primate and ruminant species. Insulin signals through diverse pathways and these are discussed with specific reference to follicular cell types (granulosa, theca and oocyte). The signalling pathways for FSH in granulosa cells and LH in granulosa and theca cells are summarized. The roles of glucose and of insulin-mediated uptake of glucose in folliculogenesis are discussed. It is suggested that glucose in addition to its well-established role of providing energy for cellular function may also have insulin-mediated signalling functions in ovarian cells, involving AMPK (AMP-dependent protein kinase) and/or hexosamine. Potential interactions of insulin signalling with FSH or LH signalling at critical nodes are identified and the available evidence for such interactions in ovarian cells is discussed. Finally the action of the insulin-sensitizing drugs metformin and the thiazolidinedione rosiglitazone on follicular cells is reviewed. PMID:27234585

  18. Insulin signalling and glucose transport in the ovary and ovarian function during the ovarian cycle

    PubMed Central

    Dupont, Joëlle; Scaramuzzi, Rex J.

    2016-01-01

    Data derived principally from peripheral tissues (fat, muscle and liver) show that insulin signals via diverse interconnecting intracellular pathways and that some of the major intersecting points (known as critical nodes) are the IRSs (insulin receptor substrates), PI3K (phosphoinositide kinase)/Akt and MAPK (mitogen-activated protein kinase). Most of these insulin pathways are probably also active in the ovary and their ability to interact with each other and also with follicle-stimulating hormone (FSH) and luteinizing hormone (LH) signalling pathways enables insulin to exert direct modulating influences on ovarian function. The present paper reviews the intracellular actions of insulin and the uptake of glucose by ovarian tissues (granulosa, theca and oocyte) during the oestrous/menstrual cycle of some rodent, primate and ruminant species. Insulin signals through diverse pathways and these are discussed with specific reference to follicular cell types (granulosa, theca and oocyte). The signalling pathways for FSH in granulosa cells and LH in granulosa and theca cells are summarized. The roles of glucose and of insulin-mediated uptake of glucose in folliculogenesis are discussed. It is suggested that glucose in addition to its well-established role of providing energy for cellular function may also have insulin-mediated signalling functions in ovarian cells, involving AMPK (AMP-dependent protein kinase) and/or hexosamine. Potential interactions of insulin signalling with FSH or LH signalling at critical nodes are identified and the available evidence for such interactions in ovarian cells is discussed. Finally the action of the insulin-sensitizing drugs metformin and the thiazolidinedione rosiglitazone on follicular cells is reviewed. PMID:27234585

  19. Parametric Flutter Analysis of the TCA Configuration and Recommendation for FFM Design and Scaling

    NASA Technical Reports Server (NTRS)

    Baker, Myles; Lenkey, Peter

    1997-01-01

    The current HSR Aeroelasticity plan to design, build, and test a full span, free flying transonic flutter model in the TDT has many technical obstacles that must be overcome for a successful program. One technical obstacle is the determination of a suitable configuration and point in the sky to use in setting the scaling point for the ASE models program. Determining this configuration and point in the sky requires balancing several conflicting requirements, including model buildability, tunnel test safety, and the ability of the model to represent the flutter mechanisms of interest. As will be discussed in detail in subsequent sections, the current TCA design exhibits several flutter mechanisms of interest. It has been decided that the ASE models program will focus on the low frequency symmetric flutter mechanism, and will make no attempt to investigate high frequency flutter mechanisms. There are several reasons for this choice. First, it is believed that the high frequency flutter mechanisms are similar in nature to classical wing bending/torsion flutter, and therefore there is more confidence that this mechanism can be predicted using current techniques. The low frequency mode, on the other hand, is a highly coupled mechanism involving wing, body, tail, and engine motion which may be very difficult to predict. Second, the high frequency flutter modes result in very small weight penalties (several hundred pounds), while suppression of the low frequency mechanism inside the flight envelope causes thousands of pounds to be added to the structure. In order to successfully test the low frequency flutter mode of interest, a suitable starting configuration and point in the sky must be identified. The configuration and point in the sky must result in a wind tunnel model that (1) represents the low-frequency wing/body/engine/empennage flutter mechanisms that are unique to HSCT configurations, (2) flutters at an acceptably low frequency in the tunnel, (3) flutters at an

  20. Estrogenic effects of Pueraria mirifica on the menstrual cycle and hormone-related ovarian functions in cyclic female cynomolgus monkeys.

    PubMed

    Trisomboon, Hataitip; Malaivijitnond, Suchinda; Watanabe, Gen; Taya, Kazuyoshi

    2004-01-01

    This study investigated the estrogenic effect of Pueraria mirifica (P. mirifica) on menstrual cycle length and hormone-related ovarian function. Nine normal cyclic monkeys (Macaca fascicularis) were separated into 3 groups; each group was force fed with a single dose of 10, 100, and 1,000 mg of P. mirifica. The experimental schedule was separated into the pre-treatment and post-treatment periods. Blood samples were collected on days 3, 9 - 14, 19, 24, 29, and every 10 days until the next menstruation for one and two menstrual cycles during two consecutive periods and assayed for serum levels of gonadotropins and ovarian hormones. The result showed a significant increase in lengths of the follicular phase and total menstrual cycle in monkeys treated with 1,000 mg of P. mirifica, but no change in menstrual cycle length in monkeys treated with 10 and 100 mg of P. mirifica. Serum levels of follicle stimulating hormone, luteinizing hormone, estradiol, progesterone, or immunoreactive-inhibin did not change during the first and second menstrual cycles of the post-treatment period for all monkey groups. Our findings demonstrate that although changes in hormonal levels could not be observed in this study, a single dose of 1,000 mg of P. mirifica can disturb ovarian function and menstrual cycle in monkeys. PMID:14745118

  1. Intravenous administration of Honokiol provides neuroprotection and improves functional recovery after traumatic brain injury through cell cycle inhibition.

    PubMed

    Wang, Haiquan; Liao, Zhengbu; Sun, Xiaochuan; Shi, Quanhong; Huo, Gang; Xie, Yanfeng; Tang, Xiaolan; Zhi, Xinggang; Tang, Zhaohua

    2014-11-01

    Recently, increasing evidence has shown that cell cycle activation is a key factor of neuronal death and neurological dysfunction after traumatic brain injury (TBI). This study aims to investigate the effects of Honokiol, a cell cycle inhibitor, on attenuating the neuronal damage and facilitating functional recovery after TBI in rats, in an attempt to unveil its underlying molecular mechanisms in TBI. This study suggested that delayed intravenous administration of Honokiol could effectively ameliorate TBI-induced sensorimotor and cognitive dysfunctions. Meanwhile, Honokiol treatment could also reduce the lesion volume and increase the neuronal survival in the cortex and hippocampus. The neuronal degeneration and apoptosis in the cortex and hippocampus were further significantly attenuated by Honokiol treatment. In addition, the expression of cell cycle-related proteins, including cyclin D1, CDK4, pRb and E2F1, was significantly increased and endogenous cell cycle inhibitor p27 was markedly decreased at different time points after TBI. And these changes were significantly reversed by post-injury Honokiol treatment. Furthermore, the expression of some of the key cell cycle proteins such as cyclin D1 and E2F1 and the associated apoptosis in neurons were both remarkably attenuated by Honokiol treatment. These results show that delayed intravenous administration of Honokiol could effectively improve the functional recovery and attenuate the neuronal cell death, which is probably, at least in part, attributed to its role as a cell cycle inhibitior. This might give clues to developing attractive therapies for future clinical trials. PMID:24973706

  2. Effect of adjusting pulse durations of functional electrical stimulation cycling on energy expenditure and fatigue after spinal cord injury.

    PubMed

    Gorgey, Ashraf S; Poarch, Hunter J; Dolbow, David D; Castillo, Teodoro; Gater, David R

    2014-01-01

    The purpose of the current study was to determine the effects of three different pulse durations (200, 350, and 500 microseconds [P200, P350, and P500, respectively]) on oxygen uptake (VO2), cycling performance, and energy expenditure (EE) percentage of fatigue of the knee extensor muscle group immediately and 48 to 72 h after cycling in persons with spinal cord injury (SCI). A convenience sample of 10 individuals with motor complete SCI participated in a repeated-measures design using a functional electrical stimulation (FES) cycle ergometer over a 3 wk period. There was no difference among the three FES protocols on relative VO2 or cycling EE. Delta EE between exercise and rest was 42% greater in both P500 and P350 compared with P200 (p = 0.07), whereas recovery VO2 was 23% greater in P350 compared with P200 (p = 0.03). There was no difference in the outcomes of the three pulse durations on muscle fatigue. Knee extensor torque significantly decreased immediately after (p < 0.001) and 48 to 72 h after (p < 0.001) FES leg cycling. Lengthening pulse duration did not affect submaximal or relative VO2 or EE, total EE, and time to fatigue. Greater recovery VO2 and delta EE were noted in P350 and P500 compared with P200. An acute bout of FES leg cycling resulted in torque reduction that did not fully recover 48 to 72 h after cycling. PMID:25803753

  3. Clusterin and DNA repair: a new function in cancer for a key player in apoptosis and cell cycle control.

    PubMed

    Shannan, B; Seifert, M; Boothman, D A; Tilgen, W; Reichrath, J

    2006-09-01

    The glycoprotein clusterin (CLU), has two known isoforms generated in human cells. A nuclear form of CLU protein (nCLU) is pro-apoptotic, while a secretory form (sCLU) is pro-survival. Both forms are implicated in various cell functions, including DNA repair, cell cycle regulation, and apoptotic cell death. CLU expression has been associated with tumorigenesis and the progression of various malignancies. In response to DNA damage, cell survival can be enhanced by activation of DNA repair mechanisms, while simultaneously stimulating energy-expensive cell cycle checkpoints that delay the cell cycle progression to allow more time for DNA repair. This review summarizes our current understanding of the role of clusterin in DNA repair, apoptosis, and cell cycle control and the relevance. PMID:17048076

  4. Existence of limit cycles and homoclinic bifurcation in a plant-herbivore model with toxin-determined functional response

    NASA Astrophysics Data System (ADS)

    Zhao, Yulin; Feng, Zhilan; Zheng, Yiqiang; Cen, Xiuli

    2015-04-01

    In this paper we study a two-dimensional toxin-determined functional response model (TDFRM). The toxin-determined functional response explicitly takes into consideration the reduction in the consumption of plants by herbivore due to chemical defense, which generates more complex dynamics of the plant-herbivore interactions. The purpose of the present paper is to analyze the existence of limit cycles and bifurcations of the model. By applying the theories of rotated vector fields and the extended planar termination principle, we establish the conditions for the existence of limit cycles and homoclinic loop. It is shown that a limit cycle is generated in a supercritical Hopf bifurcation and terminated in a homoclinic bifurcation, as the parameters vary. Analytic proofs are provided for all results, which generalize the results presented in [11].

  5. BB0323 function is essential for Borrelia burgdorferi virulence and persistence through tick-rodent transmission cycle

    PubMed Central

    Zhang, Xinyue; Yang, Xiuli; Kumar, Manish; Pal, Utpal

    2010-01-01

    Borrelia burgdorferi bb0323 encodes an immunogenic protein in mammalian hosts including humans. An analysis of bb0323 expression in vivo showed variable transcription throughout the spirochete infection cycle, with elevated expression during tick-mouse transmission. Deletion of bb0323 in infectious B. burgdorferi did not affect microbial survival in vitro, despite significant alterations in growth kinetics and cell morphology. bb0323 mutants were unable to infect either mice or ticks, and were quickly eliminated from immunocompetent and immunodeficient hosts and the vector, within the first few days of inoculation. Chromosomal complementation of the mutant with native bb0323 and phenotypic analysis in vivo indicated the significant restoration of spirochete virulence and persistence throughout the mouse-tick infection cycle. BB0323 may serve an indispensable physiological function that is more pronounced during microbial persistence and transitions between the host and the vector in vivo. Strategies to interfere with BB0323 function may interrupt the infectious cycle of spirochetes. PMID:19754308

  6. Advanced oxidation degradation kinetics as a function of ultraviolet LED duty cycle.

    PubMed

    Duckworth, Kelsey; Spencer, Michael; Bates, Christopher; Miller, Michael E; Almquist, Catherine; Grimaila, Michael; Magnuson, Matthew; Willison, Stuart; Phillips, Rebecca; Racz, LeeAnn

    2015-01-01

    Ultraviolet (UV) light emitting diodes (LEDs) may be a viable option as a UV light source for advanced oxidation processes (AOPs) utilizing photocatalysts or oxidizing agents such as hydrogen peroxide. The effect of UV-LED duty cycle, expressed as the percentage of time the LED is powered, was investigated in an AOP with hydrogen peroxide, using methylene blue (MB) to assess contaminant degradation. The UV-LED AOP degraded the MB at all duty cycles. However, adsorption of MB onto the LED emitting surface caused a linear decline in reactor performance over time. With regard to the effect of duty cycle, the observed rate constant of MB degradation, after being adjusted to account for the duty cycle, was greater for 5 and 10% duty cycles than higher duty cycles, providing a value approximately 160% higher at 5% duty cycle than continuous operation. This increase in adjusted rate constant at low duty cycles, as well as contaminant fouling of the LED surface, may impact design and operational considerations for pulsed UV-LED AOP systems. PMID:25945855

  7. Unique requirement for Rb/E2F3 in neuronal migration: evidence for cell cycle-independent functions.

    PubMed

    McClellan, Kelly A; Ruzhynsky, Vladimir A; Douda, David N; Vanderluit, Jacqueline L; Ferguson, Kerry L; Chen, Danian; Bremner, Rod; Park, David S; Leone, Gustavo; Slack, Ruth S

    2007-07-01

    The cell cycle regulatory retinoblastoma (Rb) protein is a key regulator of neural precursor proliferation; however, its role has been expanded to include a novel cell-autonomous role in mediating neuronal migration. We sought to determine the Rb-interacting factors that mediate both the cell cycle and migration defects. E2F1 and E2F3 are likely Rb-interacting candidates that we have shown to be deregulated in the absence of Rb. Using mice with compound null mutations of Rb and E2F1 or E2F3, we asked to what extent either E2F1 or E2F3 interacts with Rb in neurogenesis. Here, we report that E2F1 and E2F3 are both functionally relevant targets in neural precursor proliferation, cell cycle exit, and laminar patterning. Each also partially mediates the Rb requirement for neuronal survival. Neuronal migration, however, is specifically mediated through E2F3, beyond its role in cell cycle regulation. This study not only outlines overlapping and distinct functions for E2Fs in neurogenesis but also is the first to establish a physiologically relevant role for the Rb/E2F pathway beyond cell cycle regulation in vivo. PMID:17452454

  8. Effects of Functional Electric Stimulation Cycle Ergometry Training on Lower Limb Musculature in Acute Sci Individuals

    PubMed Central

    Demchak, Timothy J.; Linderman, Jon K.; Mysiw, W. Jerry; Jackson, Rebecca; Suun, Jihong; Devor, Steven T.

    2005-01-01

    The purpose of this study was to compare three different intervals for a between sets rest period during a common isokinetic knee extension strength-testing protocol of twenty older Brazilian men (66.30 ± 3.92 yrs). The volunteers underwent unilateral knee extension (Biodex System 3) testing to determine their individual isokinetic peak torque at 60, 90, and 120° ·s-1. The contraction speeds and the rest periods between sets (30, 60 and 90 s) were randomly performed in three different days with a minimum rest period of 48 hours. Significant differences between and within sets were analyzed using a One Way Analysis of Variance (ANOVA) with repeated measures. Although, at angular velocity of 60°·s-1 produced a higher peak torque, there were no significant differences in peak torque among any of the rest periods. Likewise, there were no significant differences between mean peak torque among all resting periods (30, 60 and 90s) at angular velocities of 90 and 120°·s-1. The results showed that during a common isokinetic strength testing protocol a between set rest period of at least 30 s is sufficient for recovery before the next test set in older men. Key Points Muscle fiber cross sectional area (CSAf ) decreased 38% following spinal cord injury (SCI). Early intervention with functional electric stimulation cycle ergometry (FES-CE) prevented further loss of CSAf in SCI patients and increased power output. Muscle myosin heavy chain (MHC) and myonuclear density were unaffected by SCI or FES-CE PMID:24453530

  9. Effects of functional electric stimulation cycle ergometry training on lower limb musculature in acute sci individuals.

    PubMed

    Demchak, Timothy J; Linderman, Jon K; Mysiw, W Jerry; Jackson, Rebecca; Suun, Jihong; Devor, Steven T

    2005-09-01

    The purpose of this study was to compare three different intervals for a between sets rest period during a common isokinetic knee extension strength-testing protocol of twenty older Brazilian men (66.30 ± 3.92 yrs). The volunteers underwent unilateral knee extension (Biodex System 3) testing to determine their individual isokinetic peak torque at 60, 90, and 120° ·s-1. The contraction speeds and the rest periods between sets (30, 60 and 90 s) were randomly performed in three different days with a minimum rest period of 48 hours. Significant differences between and within sets were analyzed using a One Way Analysis of Variance (ANOVA) with repeated measures. Although, at angular velocity of 60°·s-1 produced a higher peak torque, there were no significant differences in peak torque among any of the rest periods. Likewise, there were no significant differences between mean peak torque among all resting periods (30, 60 and 90s) at angular velocities of 90 and 120°·s-1. The results showed that during a common isokinetic strength testing protocol a between set rest period of at least 30 s is sufficient for recovery before the next test set in older men. Key PointsMuscle fiber cross sectional area (CSAf ) decreased 38% following spinal cord injury (SCI).Early intervention with functional electric stimulation cycle ergometry (FES-CE) prevented further loss of CSAf in SCI patients and increased power output.Muscle myosin heavy chain (MHC) and myonuclear density were unaffected by SCI or FES-CE. PMID:24453530

  10. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

    PubMed Central

    Penton, C. Ryan; Johnson, Timothy A.; Quensen, John F.; Iwai, Shoko; Cole, James R.; Tiedje, James M.

    2013-01-01

    Targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, dbfA1, and carAa. The majority of obtained environmental sequences were classified into novel sequence clusters, illustrating the discovery value of the approach. For the nitrite reductase step in denitrification, the well-known nirK primers exhibited deficiencies in reference database coverage, illustrating the need to refine primer-binding sites and/or to design multiple primers, while nirS primers exhibited bias against five phyla. Amino acid-based OTU clustering of these two N-cycle genes from soil samples yielded only 114 unique nirK and 45 unique nirS genus-level groupings, likely a reflection of constricted primer coverage. Finally, supervised and non-supervised OTU analysis methods were compared using the nifH gene of nitrogen fixation, with generally similar outcomes, but the clustering (non-supervised) method yielded higher diversity estimates and stronger site-based differences. High throughput amplicon sequencing can provide inexpensive and rapid access to nature's related sequences by circumventing the culturing barrier, but each unique gene requires individual considerations in terms of primer design and sequence processing and classification. PMID:24062736

  11. Stable isotope approaches for tracking C cycling and function in microbial communities

    NASA Astrophysics Data System (ADS)

    Pett-Ridge, J.

    2008-12-01

    Identifying the microorganisms responsible for specific processes in C cycling remains a major challenge in environmental microbiology, one that requires integration of multiple techniques. Stable isotope probing, or SIP, has come to represent a variety of powerful approaches that allow simultaneous identification of identity and function in microbial communities. Bulk methods such as DNA/RNA-SIP and PLFA-SIP are well developed and allow tracking of a multitude of C substrates (acetate, cellulose, CH4, CO2, and plant litter) into specific microbial consumers. However, to understand the spatio-temporal context of may key C transformations and microbial interactions, new imaging technologies are needed to analyze processes and properties of macromolecule complexes, microbes, plant root cells, soil (micro)aggregates, phytoplankton and marine snow as they undergoes formation and decomposition. New and sensitive in situ approaches include NanoSIMS single cell analysis, isotope arrays, and combinations of immuno- or FISH labeling with high resolution isotope imaging. Recent work illustrates how these powerful new techniques use targeted stable isotope probing to measure biological, physical and chemical processes and can be used in soil systems to study microbial mats or rhizosphere interactions. In both terrestrial and aquatic systems, they allow us to directly link C and other nutrient metabolism at the organismal level. Lastly, these new aproaches may be of great use in the study of trophic cascades and metabolic networks. While cross-feeding is often thought of as a confounding effect in SIP-type studies, with fine scale temporal sampling and FISH-SIMS analysis, we have the opportunity trace C flows through microbial foodwebs and to their eventual fate in stabilized organic-mineral complexes.

  12. Influence of exercise duration and hydration status on cognitive function during prolonged cycling exercise.

    PubMed

    Grego, F; Vallier, J-M; Collardeau, M; Rousseu, C; Cremieux, J; Brisswalter, J

    2005-01-01

    The purpose of the present study was to examine the influence of submaximal aerobic exercise duration on simple and complex cognitive performance. Eight well-trained male subjects agreed to participate in this study (trial group). A control group of eight regularly trained male subjects was included for comparative purposes. For the trial group, the experiment involved a critical flicker fusion test (CFF) and a map recognition task performed before, every 20 min during, and immediately after, a 3-h cycling task at an intensity corresponding to approximately 60 % of VO2max. Data were obtained over two experimental sessions with fluid ingestion (F) or no fluid (NF) ingestion. For the control group the experiment was the same but without exercise and fluid ingestion. In the trial group, a significant effect of hydration status was observed on physiological parameters (p <0.05). No effect was found on cognitive performance. A significant decrease in CFF performance was observed after 120 min of exercise when compared with the first 20 min (respectively for CFFmdi: 2.6 vs. 3.8 Hz), irrespective of experimental condition. A significant improvement in speed of response (respectively: 3291 vs. 3062 msec for 20 and 120 min, respectively) and a decrease in error number (21.5 % vs. 6.0 % for 20 and 120 min, respectively) during the map recognition task were recorded between 80 min and 120 min when compared with the first 20 min of exercise. After 120 min the number of recorded errors was significantly greater indicating a shift in the accuracy-speed trade-off (6.0 % vs. 14.1 % for 120 and 180 min, respectively). These results provide some evidence for exercise-induced facilitation of cognitive function. However this positive effect disappears during prolonged exercise--as evidenced within our study by an increase in errors during the complex task and an alteration in perceptual response (i.e. the appearance of symptoms of central fatigue). PMID:15643531

  13. Sexual functioning and commitment to their current relationship among breastfeeding and regularly cycling women in Manila, Philippines.

    PubMed

    Escasa-Dorne, Michelle J

    2015-03-01

    This project investigates the relationship between lactation and female sexual functioning and relationship commitment among partnered women in urban Manila. Previous literature suggests that the time after giving birth is often rife with lower sexual functioning and relationship dissatisfaction. Given the important role of caregiving by multiple individuals in humans, the current cross-sectional study suggests that female sexuality may decline immediately after giving birth but then may increase afterwards. Non-cycling, breastfeeding (n = 86); cycling, breastfeeding (n = 48); and nulliparous, regularly cycling (n = 105) women were recruited from neighborhood health centers in Manila to complete questionnaires that assessed sexual functioning and relationship satisfaction, along with demographic variables. Cycling, breastfeeding women report the highest sexual functioning scores and commitment scores. Females undergoing life history trade-offs between mating effort and parenting effort during the postpartum phase may employ a strategy in which they continue investment both in their offspring and in a romantic relationship. Variations in self-reported sexual functioning, level of commitment in a relationship, and love toward her current partner may indicate that breastfeeding women engage in sexual activities as part of a relationship maintenance strategy. Cultural and life history factors will serve as a framework for the findings. The current findings suggest women in Manila may experience a post-birth increase in sexual functioning that may be higher than pre-pregnancy levels. Future studies should incorporate a longitudinal component or a memory recall on pre-pregnancy and post-birth sexual functioning levels. PMID:25847056

  14. Subcellular location and photodynamic therapeutic effect of chlorin e6 in the human tongue squamous cell cancer Tca8113 cell line

    PubMed Central

    LUO, WEI; LIU, RONG-SEN; ZHU, JIAN-GUO; LI, YING-CHAO; LIU, HONG-CHEN

    2015-01-01

    The present study aimed to investigate the distribution and photodynamic therapeutic effect of chlorin e6 (Ce6) in the human tongue squamous cell carcinoma Tca8113 cell line in vitro. The distribution of Ce6 in the Tca8113 cells was observed in situ combined with mitochondrial and lysosomal fluorescent probes. Next, 630-nm semiconductor laser irradiation was performed. The MTS colorimetric method was used to determine cell survival. Annexin V fluorescein isothiocyanate/propidium iodide (PI) double staining was used to detect early apoptosis following photodynamic therapy (PDT). The flow cytometer was used to analyze the DNA content subsequent to PI-staining. It was observed that Ce6 could combine with the cellular membrane following 30 min of incubation with the Tca8113 cells. As the length of incubation increased, Ce6 gradually entered the cells in a particular distribution and reached saturation by 3 h. Co-localization analysis demonstrated that Ce6 was more likely to be present in the mitochondria than in the lysosomes. The cells incubated with 5 μg/ml Ce6 for 24 h exhibited a low toxicity of 5%, however, following light irradiation, Ce6-PDT was able to kill the Tca8113 cells in vitro. The cell toxicity was positively correlated with Ce6 concentration and light dose, therefore, the effect of Ce6 was concentration/dose-dependent (P<0.01). The lower Ce6 concentrations and light doses could significantly induce apoptosis in the Tca8113 cells, while higher doses increased necrosis/percentage of dead cells. In summary, Ce6 saturated the Tca8113 cells following 3 h of incubation. Furthermore, Ce6-PDT effectively killed the cultured Tca8113 cells in vitro at a safe concentration. At a low concentration and light dose, Ce6 is more likely to induce cell apoptosis via the mitochondria than the lysosomes. PMID:25621023

  15. The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control

    SciTech Connect

    Yang, Yunfeng; McCue, Lee Ann; Parsons, Andrea; Feng, Sheng; Zhou, Jizhong

    2010-01-01

    Background: It is well established in E. coli and Vibrio cholerae that strains harboring mutations in the ferric uptake regulator gene (fur) are unable to utilize tricarboxylic acid (TCA) compounds, due to the down-regulation of key TCA cycle enzymes, such as AcnA and SdhABCD. This down-regulation is mediated by a Fur-regulated small regulatory RNA named RyhB. It is unclear in the g-proteobacterium S. oneidensis whether TCA is also regulated by Fur and RyhB. Results: In the present study, we showed that a fur deletion mutant of S. oneidensis could utilize TCA compounds. Consistently, expression of the TCA cycle genes acnA and sdhA was not down-regulated in the mutant. To explore this observation further, we identified a ryhB gene in Shewanella species and experimentally demonstrated the gene expression. Further experiments suggested that RyhB was up-regulated in fur mutant, but that AcnA and SdhA were not controlled by RyhB. Conclusions: These cumulative results delineate an important difference of the Fur-RyhB regulatory cycle between S. oneidensis and other g-proteobacteria. This work represents a step forward for understanding the unique regulation in S. oneidensis.

  16. ENVIRONMENTAL AUDITING: The Functional Unit in the Life Cycle Inventory Analysis of Degreasing Processes in the Metal-Processing Industry

    PubMed

    Finkbeiner; Hoffmann; Kreisel

    1997-07-01

    / In 1986 degreasing processes in the German metal-processing industry contributed about 70,000 t to the emission of chlorinated C1 and C2 hydrocarbons (trichloroethane, trichloroethene, tetrachloroethene, dichloromethane). Measures aiming at the reduction of toxic emissions and ozone depletion potential (ODP) may possibly lead to a shift of environmental impacts towards higher energy consumption, emission of waste water, and volatile organic compounds (VOC) with photochemical oxidant creation potential (POCP). The present article concerns itself with a life cycle assessment of the three main degreasing processes in order to compare their integral environmental impacts with one another. This is supplemented by presenting the methodology of the life cycle inventory life cycle inventory analysis (LCI). Generally, the applicability of the established LCI method can be shown quite clearly. However, some difficulties arise, especially at the stage of the goal definition, as the use of the process and the functional unit cannot be pinned down as easily and neatly as for most other products. The definition of the use of the process and the functional unit is not as straightforward as for most products. Among the potential functional units identified are the mass of removed impurities, cleaning time, cleaning work, percentage of purity, throughput of parts, loads, mass or surface and virtual coefficients. The mass of removed impurities turned out to be the most suitable parameter for measuring the technical performance of degreasing processes. The article discusses background, purpose, scope, system boundaries, target group, process tree and representativeness of the present study.KEY WORDS: Functional unit; Life cycle assessment; Life cycle inventory analysis; Degreasing processes; Metal processing PMID:9175550

  17. Non-target effects of repeated chlorothalonil application on soil nitrogen cycling: The key functional gene study.

    PubMed

    Zhang, Manyun; Xu, Zhihong; Teng, Ying; Christie, Peter; Wang, Jun; Ren, Wenjie; Luo, Yongming; Li, Zhengao

    2016-02-01

    The widespread and increasing application of chlorothalonil (CTN) raises concerns about its non-target impacts, but little information is available on the effect of CTN on the key functional genes related to soil nitrogen (N) cycling, especially in the case of repeated applications. In the present study, a microcosm incubation was conducted to determine CTN residues and the impacts on the abundances of key functional genes related to N cycling after repeated CTN applications. The results demonstrated that repeated CTN applications at the recommended application rate and five times the recommended rate led to the accumulation of CTN residue in soil at concentrations of 5.59 and 78.79 mg kg(-1), respectively, by the end of incubation. Real time PCR (RT-PCR) revealed that repeated CTN applications had negative effects on the chiA and aprA gene abundances. There were significantly negative correlations between CTN residues and abundances of AOA and AOB genes. In addition, the abundances of key functional genes involved in soil denitrification were declined by repeated CTN applications with the sole exception of the nosZ gene. This study suggests that repeated CTN applications could lead to the accumulation of CTN residue and generate somewhat inconsistent and erratic effects on the abundances of key functional genes related to soil N cycling. PMID:26613517

  18. Li-Ion polymer cells thermal property changes as a function of cycle-life

    SciTech Connect

    Maleki, Hossein; Wang, Hsin; Porter, Wallace D; Hallmark, Jerry

    2014-01-01

    The impact of elevated temperature chargeedischarge cycling on thermal conductivity (K-value) of Lithium Ion Polymer (LIP) cells of various chemistries from three different manufacturers was investigated. These included high voltage (Graphite/LiCoO2:3.0e4.35 V), wide voltage (Si:C/LiCoO2:2.7e4.35 V) and conventional (Graphite/LiCoO2:3.0e4.2 V) chemistries. Investigation results show limited variability within the in-plane and through-plane K-values for the fresh cells with graphite-based anodes from all three suppliers. After 500 cycles at 45 C, in-plane and through-plane K-values of the high voltage cells reduced less vs. those for the wide voltage cells. Such results suggest that high temperature cycling could have a greater impact on thermal properties of Si:C cells than on the LIP cells with graphite (Gr) anode cells we tested. This difference is due to the excess swelling of Si:C-anode based cells vs. Gr-anode cells during cycling, especially at elevated temperatures. Thermal modeling is used to evaluate the impact of K-value changes, due to cycles at 45 C, on the cells internal heat propagation under internal short circuit condition that leads to localized meltdown of the separator.

  19. Diosmin pretreatment improves cardiac function and suppresses oxidative stress in rat heart after ischemia/reperfusion.

    PubMed

    Senthamizhselvan, Oomaidurai; Manivannan, Jeganathan; Silambarasan, Thangarasu; Raja, Boobalan

    2014-08-01

    Reperfusion of ischemic tissue leads to the generation of oxygen derived free radicals which plays an important role in cellular damage. Objective of the current study is to evaluate the cardio-protective and antioxidant effect of diosmin on ischemia-reperfusion related cardiac dysfunction, oxidative stress and apoptosis. Diosmin (50 and 100 mg/kg body weight (bw)) was given every day to the rats orally throughout the experimental period. Ischemia/reperfusion protocol was carried out ex vivo using langendorff perfusion method and the cardiac functional recovery was assessed in terms of percentage rate pressure product. Coronary effluents of LDH and CK-MB activities, antioxidant enzyme activities, lipid peroxidation products, activity of TCA cycle enzymes were evaluated. Moreover, in vitro superoxide anion and hydroxyl radical scavenging potential of diosmin was also quantified. Finally, quantitative real-time PCR was used for assessing Bcl-2 mRNA expression in heart. Cardiac functional recovery was impaired after reperfusion compared with continuously perfused heart. It was significantly prevented by diosmin treatment. Impaired antioxidant enzyme activities and elevated lipid peroxidation products level were also significantly suppressed. The activity of TCA cycle enzymes was protected against reperfusion stress. Down regulated Bcl-2 was also significantly increased. This study concluded that diosmin pretreatment prevents all the impaired patterns including cardiac function, oxidative stress and apoptosis associated with reperfusion in control heart by its antioxidant role. PMID:24769512

  20. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    PubMed

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. PMID:26974565

  1. Functional Dissection of Caenorhabditis elegans CLK-2/TEL2 Cell Cycle Defects during Embryogenesis and Germline Development

    PubMed Central

    Moser, Sandra C.; von Elsner, Sophie; Büssing, Ingo; Alpi, Arno; Schnabel, Ralf; Gartner, Anton

    2009-01-01

    CLK-2/TEL2 is essential for viability from yeasts to vertebrates, but its essential functions remain ill defined. CLK-2/TEL2 was initially implicated in telomere length regulation in budding yeast, but work in Caenorhabditis elegans has uncovered a function in DNA damage response signalling. Subsequently, DNA damage signalling defects associated with CLK-2/TEL2 have been confirmed in yeast and human cells. The CLK-2/TEL2 interaction with the ATM and ATR DNA damage sensor kinases and its requirement for their stability led to the proposal that CLK-2/TEL2 mutants might phenocopy ATM and/or ATR depletion. We use C. elegans to dissect developmental and cell cycle related roles of CLK-2. Temperature sensitive (ts) clk-2 mutants accumulate genomic instability and show a delay of embryonic cell cycle timing. This delay partially depends on the worm p53 homolog CEP-1 and is rescued by co-depletion of the DNA replication checkpoint proteins ATL-1 (C. elegans ATR) and CHK-1. In addition, clk-2 ts mutants show a spindle orientation defect in the eight cell stages that lead to major cell fate transitions. clk-2 deletion worms progress through embryogenesis and larval development by maternal rescue but become sterile and halt germ cell cycle progression. Unlike ATL-1 depleted germ cells, clk-2–null germ cells do not accumulate DNA double-strand breaks. Rather, clk-2 mutant germ cells arrest with duplicated centrosomes but without mitotic spindles in an early prophase like stage. This germ cell cycle arrest does not depend on cep-1, the DNA replication, or the spindle checkpoint. Our analysis shows that CLK-2 depletion does not phenocopy PIKK kinase depletion. Rather, we implicate CLK-2 in multiple developmental and cell cycle related processes and show that CLK-2 and ATR have antagonising functions during early C. elegans embryonic development. PMID:19360121

  2. Cuckoo Search Algorithm Based on Repeat-Cycle Asymptotic Self-Learning and Self-Evolving Disturbance for Function Optimization.

    PubMed

    Wang, Jie-sheng; Li, Shu-xia; Song, Jiang-di

    2015-01-01

    In order to improve convergence velocity and optimization accuracy of the cuckoo search (CS) algorithm for solving the function optimization problems, a new improved cuckoo search algorithm based on the repeat-cycle asymptotic self-learning and self-evolving disturbance (RC-SSCS) is proposed. A disturbance operation is added into the algorithm by constructing a disturbance factor to make a more careful and thorough search near the bird's nests location. In order to select a reasonable repeat-cycled disturbance number, a further study on the choice of disturbance times is made. Finally, six typical test functions are adopted to carry out simulation experiments, meanwhile, compare algorithms of this paper with two typical swarm intelligence algorithms particle swarm optimization (PSO) algorithm and artificial bee colony (ABC) algorithm. The results show that the improved cuckoo search algorithm has better convergence velocity and optimization accuracy. PMID:26366164

  3. Cuckoo Search Algorithm Based on Repeat-Cycle Asymptotic Self-Learning and Self-Evolving Disturbance for Function Optimization

    PubMed Central

    Wang, Jie-sheng; Li, Shu-xia; Song, Jiang-di

    2015-01-01

    In order to improve convergence velocity and optimization accuracy of the cuckoo search (CS) algorithm for solving the function optimization problems, a new improved cuckoo search algorithm based on the repeat-cycle asymptotic self-learning and self-evolving disturbance (RC-SSCS) is proposed. A disturbance operation is added into the algorithm by constructing a disturbance factor to make a more careful and thorough search near the bird's nests location. In order to select a reasonable repeat-cycled disturbance number, a further study on the choice of disturbance times is made. Finally, six typical test functions are adopted to carry out simulation experiments, meanwhile, compare algorithms of this paper with two typical swarm intelligence algorithms particle swarm optimization (PSO) algorithm and artificial bee colony (ABC) algorithm. The results show that the improved cuckoo search algorithm has better convergence velocity and optimization accuracy. PMID:26366164

  4. Functional activity of sphingomyelin cycle in rat liver in chronic toxic hepatitis.

    PubMed

    Serebrov, V Yu; Kuzmenko, D I; Burov, P G; Novitsky, S V

    2008-12-01

    Activities of sphingomyelinase and ceramidase decreased in the liver in chronic toxic hepatitis and the balance between the levels of proapoptotic ceramide and antiapoptotic sphyngosine-1-phosphate shifts towards the latter substance. Pronounced changes in the qualitative and quantitative composition of fatty acids in the sphingomyelin cycle effector molecules were revealed. PMID:19513367

  5. Patterns of matrix metalloproteinase expression in cycling endometrium imply differential functions and regulation by steroid hormones.

    PubMed Central

    Rodgers, W H; Matrisian, L M; Giudice, L C; Dsupin, B; Cannon, P; Svitek, C; Gorstein, F; Osteen, K G

    1994-01-01

    Matrix metalloproteinases are a highly regulated family of enzymes, that together can degrade most components of the extracellular matrix. These proteins are active in normal and pathological processes involving tissue remodeling; however, their sites of synthesis and specific roles are poorly understood. Using in situ hybridization, we determined cellular distributions of matrix metalloproteinases and tissue inhibitor of metalloproteinase-1, an inhibitor of matrix metalloproteinases, in endometrium during the reproductive cycle. The mRNAs for all the metalloproteinases were detected in menstrual endometrium, but with different tissue distributions. The mRNA for matrilysin was localized to epithelium, while the others were detected in stromal cells. Only the transcripts for the 72-kD gelatinase and tissue inhibitor of metalloproteinases-1 were detected throughout the cycle. Transcripts for stromelysin-2 and the 92-kD gelatinase were only detected in late secretory and menstrual endometrium, while those for matrilysin, the 72-kD gelatinase, and stromelysin-3 were also consistently detected in proliferative endometrium. These data indicate that matrix metalloproteinases are expressed in cell-type, tissue, and reproductive cycle-specific patterns, consistent with regulation by steroid hormones, and with specific roles in the complex tissue growth and remodeling processes occurring in the endometrium during the reproductive cycle. Images PMID:8083380

  6. Spatial Distribution of Cellular Function: The Partitioning of Proteins between Mitochondria and the Nucleus in MCF7 Breast Cancer Cells

    PubMed Central

    Qattan, Amal T.; Radulovic, Marko; Crawford, Mark; Godovac-Zimmermann, Jasminka

    2014-01-01

    Concurrent proteomics analysis of the nuclei and mitochondria of MCF7 breast cancer cells identified 985 proteins (40% of all detected proteins) present in both organelles. Numerous proteins from all five complexes involved in oxidative phosphorylation (e.g., NDUFA5, NDUFB10, NDUFS1, NDUF2, SDHA, UQRB, UQRC2, UQCRH, COX5A, COX5B, MT-CO2, ATP5A1, ATP5B, ATP5H, etc.), from the TCA-cycle (DLST, IDH2, IDH3A, OGDH, SUCLAG2, etc.), and from glycolysis (ALDOA, ENO1, FBP1, GPI, PGK1, TALDO1, etc.) were distributed to both the nucleus and mitochondria. In contrast, proteins involved in nuclear/mitochondrial RNA processing/translation and Ras/Rab signaling showed different partitioning patterns. The identity of the OxPhos, TCA-cycle, and glycolysis proteins distributed to both the nucleus and mitochondria provides evidence for spatio-functional integration of these processes over the two different subcellular organelles. We suggest that there are unrecognized aspects of functional coordination between the nucleus and mitochondria, that integration of core functional processes via wide subcellular distribution of constituent proteins is a common characteristic of cells, and that subcellular spatial integration of function may be a vital aspect of cancer. PMID:23051583

  7. ROCK inhibitor Y-27632 inhibits the growth, migration, and invasion of Tca8113 and CAL-27 cells in tongue squamous cell carcinoma.

    PubMed

    Wang, Zhi-Ming; Yang, Dong-Sheng; Liu, Jie; Liu, Hong-Bo; Ye, Ming; Zhang, Yu-Fei

    2016-03-01

    The objective of this study is to determine the effects of Rho-associated coiled-coil containing protein kinase (ROCK) inhibitor Y-27632 on the growth, invasion, and migration of Tca8113 and CAL-27 cells in tongue squamous cell carcinoma (TSCC). The methods of the study are as follows: After being routinely cultured for 24 h, Tca8113 and CAL-27 cells were treated with Y-27632 solution. The morphological change of Y-27632-treated cells was observed under an optical microscope and an inverted microscope; MTT assay was performed to measure the optical density (OD) of cells and calculate cell growth inhibition rate; the change of apoptosis was detected by AnnexinV-FITC/PI assay; cell invasion and migration were measured by Transwell assay. The results were as follows: (1) With increasing concentration of Y-27632, cell morphology changed and cell apoptosis appeared; (2) MTT assay showed that inhibition effect of Y-27632 on Tca8113 and CAL-27 cells was enhanced with increasing concentrations and time (all P < 0.01); (3) Apoptosis showed that, compared with controls, the number of apoptosis cells in experimental groups was significantly increased (all P < 0.01). Apoptosis rate was elevated with increasing concentrations of Y-27632; (4) Transwell assay showed, after a treatment with Y-27632, the number of migrated and invaded Tca8113 and CAL-27 cells in each group was statistically different (all P < 0.01); compared with controls, the number of migrated cell in groups treated with Y-27632 was decreased and less Tca8113 and CAL-27 cells in experimental groups passed through polycarbonate membrane (all P < 0.05). The study concludes that Y-27632 can inhibit the growth, invasion, and migration of Tca8113 and CAL-27 cells, suggesting that Y-27632 may be therapeutically useful in TSCC. PMID:26468018

  8. Test bed with force-measuring crank for static and dynamic investigations on cycling by means of functional electrical stimulation.

    PubMed

    Gföhler, M; Angeli, T; Eberharter, T; Lugner, P; Mayr, W; Hofer, C

    2001-06-01

    Cycling by means of functional electrical stimulation (FES) is an attractive training method for individuals with paraplegia. The physiological benefits of FES are combined with the psychological incentive of independent locomotion. In addition, cycling has the advantage in that the generated muscle forces are converted into drive power with relatively high efficiency compared to other means of locomotion, e.g., walking. For the design of an appropriate cycling device and the development of optimal stimulation patterns, it has to be investigated how the geometry for FES cycling, influenced by individual parameters of the FES-generated drive torques and the magnitude of variations among subjects with paraplegia, can be optimized. This study shows the design of a freely adjustable test bed with additional motor drive which allows static and dynamic measurements of force components and drive torque at the crank. Furthermore, the influence of geometry and various individual parameters on FES pedaling can be tested for each subject individually. A pedal path realized by a three-bar linkage that was optimized according to preliminary simulations further increases leg cycling efficiency. Safety precautions avoid injuries in case of excessive forces, e.g., spasms. Test results illustrate the application of the test bed and measurement routines. A test series with four paraplegic test persons showed that the presented static and dynamic measurement routines allow to provide optimal stimulation patterns for individual paraplegic subjects. While pedaling with these optimal stimulation patterns only negligible negative active drive torques, due to active muscle forces, were applied to the crank and sufficient drive power was generated to power a cycle independently. PMID:11474970

  9. Computational functions in biochemical reaction networks.

    PubMed Central

    Arkin, A; Ross, J

    1994-01-01

    In prior work we demonstrated the implementation of logic gates, sequential computers (universal Turing machines), and parallel computers by means of the kinetics of chemical reaction mechanisms. In the present article we develop this subject further by first investigating the computational properties of several enzymatic (single and multiple) reaction mechanisms: we show their steady states are analogous to either Boolean or fuzzy logic gates. Nearly perfect digital function is obtained only in the regime in which the enzymes are saturated with their substrates. With these enzymatic gates, we construct combinational chemical networks that execute a given truth-table. The dynamic range of a network's output is strongly affected by "input/output matching" conditions among the internal gate elements. We find a simple mechanism, similar to the interconversion of fructose-6-phosphate between its two bisphosphate forms (fructose-1,6-bisphosphate and fructose-2,6-bisphosphate), that functions analogously to an AND gate. When the simple model is supplanted with one in which the enzyme rate laws are derived from experimental data, the steady state of the mechanism functions as an asymmetric fuzzy aggregation operator with properties akin to a fuzzy AND gate. The qualitative behavior of the mechanism does not change when situated within a large model of glycolysis/gluconeogenesis and the TCA cycle. The mechanism, in this case, switches the pathway's mode from glycolysis to gluconeogenesis in response to chemical signals of low blood glucose (cAMP) and abundant fuel for the TCA cycle (acetyl coenzyme A). Images FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 7 FIGURE 10 FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 PMID:7948674

  10. Muscle Synergies in Cycling after Incomplete Spinal Cord Injury: Correlation with Clinical Measures of Motor Function and Spasticity

    PubMed Central

    Barroso, Filipe O.; Torricelli, Diego; Bravo-Esteban, Elisabeth; Taylor, Julian; Gómez-Soriano, Julio; Santos, Cristina; Moreno, Juan C.; Pons, José L.

    2016-01-01

    Background: After incomplete spinal cord injury (iSCI), patients suffer important sensorimotor impairments, such as abnormal locomotion patterns and spasticity. Complementary to current clinical diagnostic procedures, the analysis of muscle synergies has emerged as a promising tool to study muscle coordination, which plays a major role in the control of multi-limb functional movements. Objective: Based on recent findings suggesting that walking and cycling share similar synergistic control, the analysis of muscle synergies during cycling might be explored as an early descriptor of gait-related impaired control. This idea was split into the following two hypotheses: (a) iSCI patients present a synergistic control of muscles during cycling; (b) muscle synergies outcomes extracted during cycling correlate with clinical measurements of gait performance and/or spasticity. Methods: Electromyographic (EMG) activity of 13 unilateral lower limb muscles was recorded in a group of 10 healthy individuals and 10 iSCI subjects during cycling at four different cadences. A non-negative matrix factorization (NNMF) algorithm was applied to identify synergistic components (i.e., activation coefficients and muscle synergy vectors). Reconstruction goodness scores (VAF and r2) were used to evaluate the ability of a given number of synergies to reconstruct the EMG signals. A set of metrics based on the similarity between pathologic and healthy synergies were correlated with clinical scales of gait performance and spasticity. Results: iSCI patients preserved a synergistic control of muscles during cycling. The similarity with the healthy reference was consistent with the degree of the impairment, i.e., less impaired patients showed higher similarities with the healthy reference. There was a strong correlation between reconstruction goodness scores at 42 rpm and motor performance scales (TUG, 10-m test and WISCI II). On the other hand, the similarity between the healthy and affected

  11. Aircraft Emission Scenarios Projected in Year 2015 for the NASA Technology Concept Aircraft (TCA) High Speed Civil Transport

    NASA Technical Reports Server (NTRS)

    Baughcum, Steven L.; Henderson, Stephen C.

    1998-01-01

    This report describes the development of a three-dimensional database of aircraft fuel burn and emissions (fuel burned, NOx, CO, and hydrocarbons) from projected fleets of high speed civil transports (HSCTs) on a universal airline network. Inventories for 500 and 1000 HSCT fleets, as well as the concurrent subsonic fleets, were calculated. The HSCT scenarios are calculated using the NASA technology concept airplane (TCA) and update an earlier report. These emissions inventories are available for use by atmospheric scientists conducting the Atmospheric Effects of Stratospheric Aircraft (AESA) modeling studies. Fuel burned and emissions of nitrogen oxides (NOx as NO2), carbon monoxide, and hydrocarbons have been calculated on a 1 degree latitude x 1 degree longitude x 1 kilometer pressure altitude grid and delivered to NASA as electronic files.

  12. Converting chemical energy into electricity through a functionally cooperating device with diving-surfacing cycles.

    PubMed

    Song, Mengmeng; Cheng, Mengjiao; Ju, Guannan; Zhang, Yajun; Shi, Feng

    2014-11-01

    A smart device that can dive or surface in aqueous medium has been developed by combining a pH-responsive surface with acid-responsive magnesium. The diving-surfacing cycles can be used to convert chemical energy into electricity. During the diving-surfacing motion, the smart device cuts magnetic flux lines and produces a current, demonstrating that motional energy can be realized by consuming chemical energy of magnesium, thus producing electricity. PMID:25146589

  13. Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis

    PubMed Central

    Kümper, Sandra; Mardakheh, Faraz K; McCarthy, Afshan; Yeo, Maggie; Stamp, Gordon W; Paul, Angela; Worboys, Jonathan; Sadok, Amine; Jørgensen, Claus; Guichard, Sabrina

    2016-01-01

    Rho-associated kinases 1 and 2 (ROCK1/2) are Rho-GTPase effectors that control key aspects of the actin cytoskeleton, but their role in proliferation and cancer initiation or progression is not known. Here, we provide evidence that ROCK1 and ROCK2 act redundantly to maintain actomyosin contractility and cell proliferation and that their loss leads to cell-cycle arrest and cellular senescence. This phenotype arises from down-regulation of the essential cell-cycle proteins CyclinA, CKS1 and CDK1. Accordingly, while the loss of either Rock1 or Rock2 had no negative impact on tumorigenesis in mouse models of non-small cell lung cancer and melanoma, loss of both blocked tumor formation, as no tumors arise in which both Rock1 and Rock2 have been genetically deleted. Our results reveal an indispensable role for ROCK, yet redundant role for isoforms 1 and 2, in cell cycle progression and tumorigenesis, possibly through the maintenance of cellular contractility. DOI: http://dx.doi.org/10.7554/eLife.12203.001 PMID:26765561

  14. Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis.

    PubMed

    Kümper, Sandra; Mardakheh, Faraz K; McCarthy, Afshan; Yeo, Maggie; Stamp, Gordon W; Paul, Angela; Worboys, Jonathan; Sadok, Amine; Jørgensen, Claus; Guichard, Sabrina; Marshall, Christopher J

    2016-01-01

    Rho-associated kinases 1 and 2 (ROCK1/2) are Rho-GTPase effectors that control key aspects of the actin cytoskeleton, but their role in proliferation and cancer initiation or progression is not known. Here, we provide evidence that ROCK1 and ROCK2 act redundantly to maintain actomyosin contractility and cell proliferation and that their loss leads to cell-cycle arrest and cellular senescence. This phenotype arises from down-regulation of the essential cell-cycle proteins CyclinA, CKS1 and CDK1. Accordingly, while the loss of either Rock1 or Rock2 had no negative impact on tumorigenesis in mouse models of non-small cell lung cancer and melanoma, loss of both blocked tumor formation, as no tumors arise in which both Rock1 and Rock2 have been genetically deleted. Our results reveal an indispensable role for ROCK, yet redundant role for isoforms 1 and 2, in cell cycle progression and tumorigenesis, possibly through the maintenance of cellular contractility. PMID:26765561

  15. Gluconeogenesis is associated with high rates of tricarboxylic acid and pyruvate cycling in fasting northern elephant seals.

    PubMed

    Champagne, Cory D; Houser, Dorian S; Fowler, Melinda A; Costa, Daniel P; Crocker, Daniel E

    2012-08-01

    Animals that endure prolonged periods of food deprivation preserve vital organ function by sparing protein from catabolism. Much of this protein sparing is achieved by reducing metabolic rate and suppressing gluconeogenesis while fasting. Northern elephant seals (Mirounga angustirostris) endure prolonged fasts of up to 3 mo at multiple life stages. During these fasts, elephant seals maintain high levels of activity and energy expenditure associated with breeding, reproduction, lactation, and development while maintaining rates of glucose production typical of a postabsorptive mammal. Therefore, we investigated how fasting elephant seals meet the requirements of glucose-dependent tissues while suppressing protein catabolism by measuring the contribution of glycogenolysis, glycerol, and phosphoenolpyruvate (PEP) to endogenous glucose production (EGP) during their natural 2-mo postweaning fast. Additionally, pathway flux rates associated with the tricarboxylic acid (TCA) cycle were measured specifically, flux through phosphoenolpyruvate carboxykinase (PEPCK) and pyruvate cycling. The rate of glucose production decreased during the fast (F(1,13) = 5.7, P = 0.04) but remained similar to that of postabsorptive mammals. The fractional contributions of glycogen, glycerol, and PEP did not change with fasting; PEP was the primary gluconeogenic precursor and accounted for ∼95% of EGP. This large contribution of PEP to glucose production occurred without substantial protein loss. Fluxes through the TCA cycle, PEPCK, and pyruvate cycling were higher than reported in other species and were the most energetically costly component of hepatic carbohydrate metabolism. The active pyruvate recycling fluxes detected in elephant seals may serve to rectify gluconeogeneic PEP production during restricted anaplerotic inflow in these fasting-adapted animals. PMID:22673783

  16. Regulation of leukocyte tricarboxylic acid cycle in drug-naïve Bipolar Disorder.

    PubMed

    de Sousa, Rafael T; Streck, Emilio L; Forlenza, Orestes V; Brunoni, Andre R; Zanetti, Marcus V; Ferreira, Gabriela K; Diniz, Breno S; Portela, Luis V; Carvalho, André F; Zarate, Carlos A; Gattaz, Wagner F; Machado-Vieira, Rodrigo

    2015-09-25

    Several lines of evidence suggest a role for mitochondrial dysfunction in the pathophysiology of bipolar disorder (BD). The tricarboxylic acid cycle (TCA cycle) is fundamental for mitochondrial energy production and produces substrates used in oxidative phosphorylation by the mitochondrial electron transport chain. The activity of the key TCA cycle enzymes citrate synthase, malate dehydrogenase, and succinate dehydrogenase has never been evaluated in BD. In the present study, these enzymes were assayed from leukocytes of drug-naïve BD patients in a major depressive episode (n=18) and compared to 24 age-matched healthy controls. Drug-naïve BD patients did not show differences in activities of citrate synthase (p=0.79), malate dehydrogenase (p=0.17), and succinate dehydrogenase (p=0.35) compared with healthy controls. No correlation between any TCA cycle enzyme activity and severity of depressive symptoms was observed. Overall, these data suggest that the activities of the TCA cycle enzymes are not altered in major depressive episodes of recent-onset BD, which may support the concept of illness staging and neuroprogression in BD. PMID:26297865

  17. A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei

    PubMed Central

    Chikne, Vaibhav; Doniger, Tirza; Rajan, K. Shanmugha; Bartok, Osnat; Eliaz, Dror; Cohen-Chalamish, Smadar; Tschudi, Christian; Unger, Ron; Hashem, Yaser; Kadener, Sebastian; Michaeli, Shulamit

    2016-01-01

    The protozoan parasite Trypanosoma brucei, which causes devastating diseases in humans and animals in sub-Saharan Africa, undergoes a complex life cycle between the mammalian host and the blood-feeding tsetse fly vector. However, little is known about how the parasite performs most molecular functions in such different environments. Here, we provide evidence for the intriguing possibility that pseudouridylation of rRNA plays an important role in the capacity of the parasite to transit between the insect midgut and the mammalian bloodstream. Briefly, we mapped pseudouridines (Ψ) on rRNA by Ψ-seq in procyclic form (PCF) and bloodstream form (BSF) trypanosomes. We detected 68 Ψs on rRNA, which are guided by H/ACA small nucleolar RNAs (snoRNA). The small RNome of both life cycle stages was determined by HiSeq and 83 H/ACAs were identified. We observed an elevation of 21 Ψs modifications in BSF as a result of increased levels of the guiding snoRNAs. Overexpression of snoRNAs guiding modification on H69 provided a slight growth advantage to PCF parasites at 30 °C. Interestingly, these modifications are predicted to significantly alter the secondary structure of the large subunit (LSU) rRNA suggesting that hypermodified positions may contribute to the adaption of ribosome function during cycling between the two hosts. PMID:27142987

  18. A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei.

    PubMed

    Chikne, Vaibhav; Doniger, Tirza; Rajan, K Shanmugha; Bartok, Osnat; Eliaz, Dror; Cohen-Chalamish, Smadar; Tschudi, Christian; Unger, Ron; Hashem, Yaser; Kadener, Sebastian; Michaeli, Shulamit

    2016-01-01

    The protozoan parasite Trypanosoma brucei, which causes devastating diseases in humans and animals in sub-Saharan Africa, undergoes a complex life cycle between the mammalian host and the blood-feeding tsetse fly vector. However, little is known about how the parasite performs most molecular functions in such different environments. Here, we provide evidence for the intriguing possibility that pseudouridylation of rRNA plays an important role in the capacity of the parasite to transit between the insect midgut and the mammalian bloodstream. Briefly, we mapped pseudouridines (Ψ) on rRNA by Ψ-seq in procyclic form (PCF) and bloodstream form (BSF) trypanosomes. We detected 68 Ψs on rRNA, which are guided by H/ACA small nucleolar RNAs (snoRNA). The small RNome of both life cycle stages was determined by HiSeq and 83 H/ACAs were identified. We observed an elevation of 21 Ψs modifications in BSF as a result of increased levels of the guiding snoRNAs. Overexpression of snoRNAs guiding modification on H69 provided a slight growth advantage to PCF parasites at 30 °C. Interestingly, these modifications are predicted to significantly alter the secondary structure of the large subunit (LSU) rRNA suggesting that hypermodified positions may contribute to the adaption of ribosome function during cycling between the two hosts. PMID:27142987

  19. Replication of a unit-copy plasmid F in the bacterial cell cycle: a replication rate function analysis.

    PubMed

    Morrison, Paul F; Chattoraj, Dhruba K

    2004-07-01

    For stability, the replication of unit-copy plasmids ought to occur by a highly controlled process. We have characterized the replication dynamics of a unit-copy plasmid F by a replication rate function defined as the probability per unit age interval of the cell cycle that a plasmid will initiate replication. Analysis of baby-machine data [J. Bacteriol. 170 (1988) 1380; J. Bacteriol. 179 (1997) 1393] by stochastics that make no detailed reference to underlying mechanism revealed that this rate function increased monotonically over the cell cycle with rapid increase near cell division. This feature is highly suggestive of a replication control mechanism that is designed to force most plasmids to replicate before cells undergo division. The replication rate function is developed anew from a mechanistic model incorporating the hypotheses that initiators are limiting and that steric hindrance of origins by handcuffing control initiation of replication. The model is based on correctly folded initiator protein monomers arising from an inactive dimer pool via chaperones in limiting amounts, their random distribution to high affinity sites (iterons) at the origin (ori) and an outside locus (incC), the statistical mechanics of bound monomer participation in pairing the two loci (cis-handcuffing), and initiation probability as proportional to the number of non-handcuffed ori-saturated plasmids. Provided cis-handcuffing is present, this model closely accounts for the shape of the replication rate function derived from experiment, and reproduces the observation that replication occurs throughout the cell cycle. Present concepts of iteron-based molecular mechanisms thus appear capable of yielding a quantitative description of unit-copy-number plasmid replication dynamics. PMID:15212889

  20. Immune function in a free-living bird varies over the annual cycle, but seasonal patterns differ between years.

    PubMed

    Hegemann, Arne; Matson, Kevin D; Both, Christiaan; Tieleman, B Irene

    2012-11-01

    A central hypothesis of eco-immunology proposes trade-offs between immune defences and competing physiological and behavioural processes, leading to immunological variation within and among annual-cycle stages, as has been revealed for some species. However, few studies have simultaneously investigated patterns of multiple immune indices over the entire annual cycle in free-living birds, and none has investigated the consistency of seasonal patterns across multiple years. We quantified lysis, agglutination, haptoglobin, leukocyte profiles, and body mass in free-living skylarks (Alauda arvensis) through two complete annual cycles and within and between four breeding seasons. The skylarks' annual cycle is characterised by annually repeated changes in energy and time budgets, social structure and diet. If trade-offs relating to these cyclic changes shape evolution, predictable intra-annual immune patterns may result. Alternatively, intra-annual immune patterns may vary among years if fluctuating environmental changes affect the cost-benefit balances of immune function. We found significant variation in immune indices and body mass across the annual cycle, and these patterns differed between years. Immune parameters differed between four breeding seasons, and in all years, lysis and agglutination increased as the season progressed independent of average levels. Population-level patterns (intra-annual, inter-annual, within breeding season) were consistent with within-individual patterns based on repeated measurements. We found little evidence for sex differences, and only haptoglobin was correlated (negatively) with body mass. We conclude that immune modulation is not simply a pre-programmed phenomenon that reflects predictable ecological changes. Instead, fluctuating environmental conditions that vary among years likely contribute to the immunological variation that we observed. PMID:22562421

  1. Microprocessor-controlled phase analysis for a 2-mm microwave interferometer on the TCA tokamak

    SciTech Connect

    Lister, J.B.; Means, R.W.; Oberson, P.

    1982-05-01

    The method of phase analysis is presented for a 2-mm microwave interferometer built to measure the plasma density in a tokamak. Use is made of a fast phase shifter (FPS) constructed from a switchable four-port circulator to resolve the phase ambiguity inherent in a simple interferometer. The phase between 0--2..pi.. is calculated by a microprocessor accessing a look-up table and the total phase is calculated by taking the 0 to 2..pi.. crossings into consideration. It is software controlled and the complete sampling and analysis cycle takes 24 ..mu..s which is sufficiently rapid for the application considered. The phase information is available in analog and digital form.

  2. Microprocessor-controlled phase analysis for a 2-mm microwave interferometer on the TCA tokamak

    NASA Astrophysics Data System (ADS)

    Lister, J. B.; Means, R. W.; Oberson, P.

    1982-05-01

    The method of phase analysis is presented for a 2-mm microwave interferometer built to measure the plasma density in a tokamak. Use is made of a fast phase shifter (FPS) constructed from a switchable four-port circulator to resolve the phase ambiguity inherent in a simple interferometer. The phase between 0-2π is calculated by a microprocessor accessing a look-up table and the total phase is calculated by taking the 0 to 2π crossings into consideration. It is software controlled and the complete sampling and analysis cycle takes 24 μs which is sufficiently rapid for the application considered. The phase information is available in analog and digital form.

  3. Multi-function ring magnet power supply for rapid-cycling synchrotrons

    SciTech Connect

    Praeg, W.F.

    1985-01-01

    Ring magnet power supply (RMPS) circuits that produce a wide range of magnet current waveshapes for rapid-cycling synchrotrons (RCS) are described. The shapes range from long flat-tops separated by a biased dual frequency cosine wave to those having a flat-bottom (injection), followed by a lower frequency cosine half wave (acceleration), a flat-top (extraction), and a higher frequency cosine half wave (magnet reset). Applications of these circuits for proposed synchrotrons are outlined. Solid-state switching circuits and the results of proof-of-concept tests are shown. 8 refs., 12 figs.

  4. Dynamics and function of the tear film in relation to the blink cycle

    PubMed Central

    Braun, R.J.; King-Smith, P.E.; Begley, C.G.; Li, Longfei; Gewecke, N.R.

    2014-01-01

    Great strides have recently been made in quantitative measurements of tear film thickness and thinning, mathematical modeling thereof and linking these to sensory perception. This paper summarizes recent progress in these areas and reports on new results. The complete blink cycle is used as a framework that attempts to unify the results that are currently available. Understanding of tear film dynamics is aided by combining information from different imaging methods, including fluorescence, retroillumination and a new high-speed stroboscopic imaging system developed for studying the tear film during the blink cycle. During the downstroke of the blink, lipid is compressed as a thick layer just under the upper lid which is often released as a narrow thick band of lipid at the beginning of the upstroke. “Rippling” of the tear film/air interface due to motion of the tear film over the corneal surface, somewhat like the flow of water in a shallow stream over a rocky streambed, was observed during lid motion and treated theoretically here. New mathematical predictions of tear film osmolarity over the exposed ocular surface and in tear breakup are presented; the latter is closely linked to new in vivo observations. Models include the effects of evaporation, osmotic flow through the cornea and conjunctiva, quenching of fluorescence, tangential flow of aqueous tears and diffusion of tear solutes and fluorescein. These and other combinations of experiment and theory increase our understanding of the fluid dynamics of the tear film and its potential impact on the ocular surface. PMID:25479602

  5. Environmental impacts on the diversity of methane-cycling microbes and their resultant function

    PubMed Central

    Aronson, Emma L.; Allison, Steven D.; Helliker, Brent R.

    2013-01-01

    Methane is an important anthropogenic greenhouse gas that is produced and consumed in soils by microorganisms responding to micro-environmental conditions. Current estimates show that soil consumption accounts for 5–15% of methane removed from the atmosphere on an annual basis. Recent variability in atmospheric methane concentrations has called into question the reliability of estimates of methane consumption and calls for novel approaches in order to predict future atmospheric methane trends. This review synthesizes the environmental and climatic factors influencing the consumption of methane from the atmosphere by non-wetland, terrestrial soil microorganisms. In particular, we focus on published efforts to connect community composition and diversity of methane-cycling microbial communities to observed rates of methane flux. We find abundant evidence for direct connections between shifts in the methane-cycling microbial community, due to climate and environmental changes, and observed methane flux levels. These responses vary by ecosystem and associated vegetation type. This information will be useful in process-based models of ecosystem methane flux responses to shifts in environmental and climatic parameters. PMID:23966984

  6. Dynamics and function of the tear film in relation to the blink cycle.

    PubMed

    Braun, R J; King-Smith, P E; Begley, C G; Li, Longfei; Gewecke, N R

    2015-03-01

    Great strides have recently been made in quantitative measurements of tear film thickness and thinning, mathematical modeling thereof and linking these to sensory perception. This paper summarizes recent progress in these areas and reports on new results. The complete blink cycle is used as a framework that attempts to unify the results that are currently available. Understanding of tear film dynamics is aided by combining information from different imaging methods, including fluorescence, retroillumination and a new high-speed stroboscopic imaging system developed for studying the tear film during the blink cycle. During the downstroke of the blink, lipid is compressed as a thick layer just under the upper lid which is often released as a narrow thick band of lipid at the beginning of the upstroke. "Rippling" of the tear film/air interface due to motion of the tear film over the corneal surface, somewhat like the flow of water in a shallow stream over a rocky streambed, was observed during lid motion and treated theoretically here. New mathematical predictions of tear film osmolarity over the exposed ocular surface and in tear breakup are presented; the latter is closely linked to new in vivo observations. Models include the effects of evaporation, osmotic flow through the cornea and conjunctiva, quenching of fluorescence, tangential flow of aqueous tears and diffusion of tear solutes and fluorescein. These and other combinations of experiment and theory increase our understanding of the fluid dynamics of the tear film and its potential impact on the ocular surface. PMID:25479602

  7. Beyond Vmax and Km: How details of enzyme function influence geochemical cycles

    NASA Astrophysics Data System (ADS)

    Steen, A. D.

    2015-12-01

    Enzymes catalyze the vast majority of chemical reactions relevant to geomicrobiology. Studies of the activities of enzymes in environmental systems often report Vmax (the maximum possible rate of reaction; often proportional to the concentration of enzymes in the system) and sometimes Km (a measure of the affinity between enzymes and their substrates). However, enzyme studies - particularly those related to enzymes involved in organic carbon oxidation - are often limited to only those parameters, and a relatively limited and mixed set of enzymes. Here I will discuss some novel methods to assay and characterize the specific sets of enzymes that may be important to the carbon cycle in aquatic environments. First, kinetic experiments revealed the collective properties of the complex mixtures of extracellular peptidases that occur where microbial communities are diverse. Crystal structures combined with biochemical characterization of specific enzymes can yield more detailed information about key steps in organic carbon transformations. These new techniques have the potential to provide mechanistic grounding to geomicrobiological models.

  8. Modeling forest carbon cycle response to tree mortality: Effects of plant functional type and disturbance intensity

    NASA Astrophysics Data System (ADS)

    Frasson, Renato Prata de Moraes; Bohrer, Gil; Medvigy, David; Matheny, Ashley M.; Morin, Timothy H.; Vogel, Christoph S.; Gough, Christopher M.; Maurer, Kyle D.; Curtis, Peter S.

    2015-11-01

    Natural and anthropogenic disturbances influence ecological succession and impact the carbon cycle. Understanding disturbance effects and ecosystem recovery is essential to carbon modeling. We hypothesized that (1) species-specific disturbances impact the carbon cycle differently from nonspecific disturbances. In particular, disturbances that target early-successional species will lead to higher carbon uptake by the postrecovery, middle- and late-successional community and (2) disturbances that affect the midsuccessional deciduous species have more intense and long-lasting impacts on carbon uptake than disturbances of similar intensity that only affect the early-successional species. To test these hypotheses, we employed a series of simulations conducted with the Ecosystem Demography model version 2 to evaluate the sensitivity of a temperate mixed-deciduous forest to disturbance intensity and type. Our simulation scenarios included a control (undisturbed) case, a uniform disturbance case where we removed 30% of all trees regardless of their successional status, five cases where only early-successional deciduous trees were removed with increasing disturbance intensity (30%, 70%, 85%, and 100%), and four cases of midsuccessional disturbances with increasing intensity (70%, 85%, and 100%). Our results indicate that disturbances affecting the midsuccessional deciduous trees led to larger decreases in carbon uptake as well as longer recovery times when compared to disturbances that exclusively targeted the early-successional deciduous trees at comparable intensities. Moreover, disturbances affecting 30% to 100% of early-successional deciduous trees resulted in an increased carbon uptake, beginning 6 years after the disturbance and sustained through the end of the 100 year simulation.

  9. Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships.

    PubMed

    Lau, Maggie C Y; Cameron, Connor; Magnabosco, Cara; Brown, C Titus; Schilkey, Faye; Grim, Sharon; Hendrickson, Sarah; Pullin, Michael; Sherwood Lollar, Barbara; van Heerden, Esta; Kieft, Thomas L; Onstott, Tullis C

    2014-01-01

    Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes. PMID:25400621

  10. Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

    PubMed Central

    Lau, Maggie C. Y.; Cameron, Connor; Magnabosco, Cara; Brown, C. Titus; Schilkey, Faye; Grim, Sharon; Hendrickson, Sarah; Pullin, Michael; Sherwood Lollar, Barbara; van Heerden, Esta; Kieft, Thomas L.; Onstott, Tullis C.

    2014-01-01

    Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes. PMID:25400621

  11. C2 from Beet curly top virus meddles with the cell cycle: a novel function for an old pathogenicity factor.

    PubMed

    Lozano-Duran, Rosa; Caracuel, Zaira; Bejarano, Eduardo R

    2012-12-01

    Geminiviruses are ssDNA plant viruses that infect a wide range of crops. Since geminiviruses often infect terminally differentiated cells, they must induce cell cycle re-entry in order to replicate; until recently, only two viral proteins, the replication-associated protein Rep and the curtoviral pathogenicity factor C4, had been assigned a role in the restoration of cell competency. In a recent work, we demonstrated that C2 from Beet curly top virus activates the expression of host genes involved in DNA replication and/or control of the G2/M transition in a manner consistent with cell cycle re-entry. As expected, expression of BCTV C2 results in enhanced replication of DNA viruses. We conclude that BCTV C2 acts as a re-activator of the cell cycle in infected cells, enhancing the DNA replication competency and providing a cell environment favorable for replication of geminiviruses. Potential mechanisms for this novel function are discussed in light of our findings. PMID:23073019

  12. Ovarian function of the Algerian wild Libyan jird, Meriones libycus during seasonal reproductive cycle: histological and immunohistochemical expression.

    PubMed

    Smaï-Hamdidouche, S; Gernigon-Spychalowicz, T; Khammar, F; Exbrayat, J M

    2013-01-01

    Meriones libycus (Libyan jird), a nocturnal Saharan rodent, is characterized by a seasonal reproductive cycle with a short active phase (spring and early summer) and a long resting period (late summer, autumn, winter). Histological and immunohistochemical techniques were performed in order to study the seasonal variations in mature ovaries. During the breeding season, the ovary showed a continuous cyclical activity, the various stages of folliculogenesis from primordial to preovulatory follicles were observed; broken follicles and corpora lutea were also observed. During sexual quiescence, the ovarian cycle was interrupted; anovulation was observed without any corpus luteum. Non mature antral follicles entered the atretic process. Steroid and steroidogenic enzyme activities were studied using indirect immunohistochemistry. 17β-estradiol, progesterone, testosterone hormones and P450 aromatase (P450 arom) were detected in the different components of the ovary and in various stages of healthy and atretic follicles during the seasonal reproductive cycle. Our results indicate that during ovarian folliculogenesis in breeding season steroids hormone and P450 arom present important activities. In comparison with the resting period, steroidogenesis and steroidogenic enzyme activity became less pronounced in the healthy preantral follicle; it seemed that steroid biosynthesis was reduced and could be involved in the stimulation and maintenance of the ovarian structural integrity in early follicle development. In conclusion, the histological and immunohistochemical seasonal variations of ovaries in Meriones libycus support the hypothesis that seasonal fluctuations are indirectly involved in regulating reproduction, inducing significant changes in both ovarian morphology and its hormonal function. PMID:23233063

  13. Reproductive functional anatomy and oestrous cycle pattern of the female brush-tailed porcupine (Atherurus africanus, Gray 1842) from Gabon.

    PubMed

    Mayor, P; López-Béjar, M; Jori, F; Fenech, M; López-Gatius, F

    2003-07-15

    In the present study, we examined certain features of the functional anatomy of the female genital tract of the wild brush-tailed porcupine (Atherurus africanus) to obtain data on the reproductive biology of this African forest rodent. Two consecutive experiments were performed. The aim of the first was to establish macroscopic and microscopic features of the genital organs, and to explore correlations between predominant ovarian structures and vaginal contents in 20 wild, mature females. In the second experiment, we inspected the external genitalia and vaginal smears of a further 10 females in captivity on a daily basis for 90 days. The uterus of the brush-tailed porcupine is bicornuate and composed of two separated uterine horns, a uterine body and cervix. The genital tract does not present a vaginal vestibule. Thus, there is no portion common to genital and urinary tracts. Females in the follicular phase of the oestrous cycle showed increased cornification of the vaginal epithelium and a high density of eosinophilic cells in vaginal smears. The vulva and vaginal opening were open, reddish and tumefacted. In luteal phase or in pregnancy, epithelial cornification and eosinophilic features were notably reduced and the vagina presented a pale, non-tumefacted vulva and a vaginal closure membrane. Females in captivity showed spontaneous cycles, a polyoestrous reproduction pattern and, based on features of the external genitalia and vaginal smears, their oestrous cycle length was 27.1+/-6.4 days (n=12). PMID:12695058

  14. c-Myb Regulates Cell Cycle-Dependent Expression of Erbin: An Implication for a Novel Function of Erbin

    PubMed Central

    Zhang, Hao; Qian, Lu; Yu, Ming; Hu, Meiru; Zhang, Ruihong; Wang, Tianyou; Han, Caili; Duan, Huijun; Guo, Ning

    2012-01-01

    In the present study, we demonstrated the cell cycle periodicity of Erbin expression with the maximal expression of Erbin in G2/M phase. A significant increase in Erbin promoter activity was observed in G2/M phase-synchronized cells. Sequence analysis revealed a c-Myb site in the core promoter region of Erbin. Mutagenesis of c-Myb consensus sequences abrogated the increased Erbin promoter activity in G2/M phase. ChIP and oligonucleotide pull-down assays validated that the recruitment of c-Myb to the consensus sequences was specific. The interaction of c-Myb with c-Myb site in the Erbin promoter was significantly enhanced in G2/M phase. Ectopic overexpression of c-Myb led to the up-regulation of Erbin promoter activity and c-Myb silencing by small interfering RNA significantly decreased Erbin protein level. Transfection of c-Myb rescued Erbin expression that was impaired by c-Myb knockdown. It proves that c-Myb and the c-Myb response element mediate the cell cycle-dependent expression of Erbin. Inactivation of Erbin causes an acceleration of the G1/S transition, the formation of multipolar spindles and abnormal chromosome congression. These results unravel a critical role of c-Myb in promoting Erbin transcription in G2/M phase and also predict an unappreciated function of Erbin in cell cycle progression. PMID:22880131

  15. EFFECTS OF LAND USE CHANGES ON THE FUNCTIONING OF SOILS AND WATERSHEDS OF CENTRAL BRAZIL SAVANNAS: PHASE 2, IMPACTS ON NUTRIENT AND CARBON CYCLES AND TRACE GAS EXCHANGE

    EPA Science Inventory

    This research is funded through an interagency agreement with NASA. The research in this project is contributing to assessments of the effects of land use in central Brazil on: 1) the stocks and cycling rates of carbon and nutrient cycling; 2) the function and structure of soil ...

  16. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

    SciTech Connect

    Handley, KM; Verberkmoes, Nathan C; Steefel, Carl I; Sharon, I; Williams, Ken; Miller, CS; Frischkorn, Kyle C; Chourey, Karuna; Thomas, Brian; Shah, Manesh B; Long, Phil; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2013-01-01

    Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used community proteogenomics to test the hypothesis that excess input of acetate activates syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer. Genomic sequences from the community recovered during microbial sulfate reduction were used to econstruct, de novo, near-complete genomes for Desulfobacter (Deltaproteobacteria) and relatives of Sulfurovum and Sulfurimonas (Epsilonproteobacteria), and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2 during amendment. Results suggest less abundant Desulfuromonadales and Bacteroidetes also actively contributed to CO2 production via the TCA cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. Modeling shows that this reaction was thermodynamically possible, and kinetically favorable relative to acetate-dependent denitrification. We conclude that high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.

  17. Delineating potential epileptogenic areas utilizing resting functional magnetic resonance imaging (fMRI) in epilepsy patients.

    PubMed

    Pizarro, Ricardo; Nair, Veena; Meier, Timothy; Holdsworth, Ryan; Tunnell, Evelyn; Rutecki, Paul; Sillay, Karl; Meyerand, Mary E; Prabhakaran, Vivek

    2016-08-01

    Seizure localization includes neuroimaging like electroencephalogram, and magnetic resonance imaging (MRI) with limited ability to characterize the epileptogenic network. Temporal clustering analysis (TCA) characterizes epileptogenic network congruent with interictal epileptiform discharges by clustering together voxels with transient signals. We generated epileptogenic areas for 12 of 13 epilepsy patients with TCA, congruent with different areas of seizure onset. Resting functional MRI (fMRI) scans are noninvasive, and can be acquired quickly, in patients with different levels of severity and function. Analyzing resting fMRI data using TCA is quick and can complement clinical methods to characterize the epileptogenic network. PMID:27362339

  18. Carnitine palmitoyltransferase 1A functions to repress FoxO transcription factors to allow cell cycle progression in ovarian cancer.

    PubMed

    Shao, Huanjie; Mohamed, Esraa M; Xu, Guoyan G; Waters, Michael; Jing, Kai; Ma, Yibao; Zhang, Yan; Spiegel, Sarah; Idowu, Michael O; Fang, Xianjun

    2016-01-26

    Cancer cells rely on hyperactive de novo lipid synthesis for maintaining malignancy. Recent studies suggest involvement in cancer of fatty acid oxidation, a process functionally opposite to lipogenesis. A mechanistic link from lipid catabolism to oncogenic processes is yet to be established. Carnitine palmitoyltransferase 1 (CPT1) is a rate-limiting enzyme of fatty acid β-oxidation (FAO) that catalyzes the transfer of long-chain acyl group of the acyl-CoA ester to carnitine, thereby shuttling fatty acids into the mitochondrial matrix for β-oxidation. In the present study, we demonstrated that CPT1A was highly expressed in most ovarian cancer cell lines and primary ovarian serous carcinomas. Overexpression of CPT1A correlated with a poor overall survival of ovarian cancer patients. Inactivation of CPT1A decreased cellular ATP levels and induced cell cycle arrest at G0/G1, suggesting that ovarian cancer cells depend on or are addicted to CPT1A-mediated FAO for cell cycle progression. CPT1A deficiency also suppressed anchorage-independent growth and formation of xenografts from ovarian cancer cell lines. The cyclin-dependent kinase inhibitor p21WAF1 (p21) was identified as most consistently and robustly induced cell cycle regulator upon inactivation of CPT1A. Furthermore, p21 was transcriptionally upregulated by the FoxO transcription factors, which were in turn phosphorylated and activated by AMP-activated protein kinase and the mitogen-activated protein kinases JNK and p38. Our results established the oncogenic relevance of CPT1A and a mechanistic link from lipid catabolism to cell cycle regulation, suggesting that CPT1A could be a prognostic biomarker and rational target for therapeutic intervention of cancer. PMID:26716645

  19. Carnitine palmitoyltransferase 1A functions to repress FoxO transcription factors to allow cell cycle progression in ovarian cancer

    PubMed Central

    Shao, Huanjie; Mohamed, Esraa M.; Xu, Guoyan G.; Waters, Michael; Jing, Kai; Ma, Yibao; Zhang, Yan; Spiegel, Sarah; Idowu, Michael O.; Fang, Xianjun

    2016-01-01

    Cancer cells rely on hyperactive de novo lipid synthesis for maintaining malignancy. Recent studies suggest involvement in cancer of fatty acid oxidation, a process functionally opposite to lipogenesis. A mechanistic link from lipid catabolism to oncogenic processes is yet to be established. Carnitine palmitoyltransferase 1 (CPT1) is a rate-limiting enzyme of fatty acid β-oxidation (FAO) that catalyzes the transfer of long-chain acyl group of the acyl-CoA ester to carnitine, thereby shuttling fatty acids into the mitochondrial matrix for β-oxidation. In the present study, we demonstrated that CPT1A was highly expressed in most ovarian cancer cell lines and primary ovarian serous carcinomas. Overexpression of CPT1A correlated with a poor overall survival of ovarian cancer patients. Inactivation of CPT1A decreased cellular ATP levels and induced cell cycle arrest at G0/G1, suggesting that ovarian cancer cells depend on or are addicted to CPT1A-mediated FAO for cell cycle progression. CPT1A deficiency also suppressed anchorage-independent growth and formation of xenografts from ovarian cancer cell lines. The cyclin-dependent kinase inhibitor p21WAF1 (p21) was identified as most consistently and robustly induced cell cycle regulator upon inactivation of CPT1A. Furthermore, p21 was transcriptionally upregulated by the FoxO transcription factors, which were in turn phosphorylated and activated by AMP-activated protein kinase and the mitogen-activated protein kinases JNK and p38. Our results established the oncogenic relevance of CPT1A and a mechanistic link from lipid catabolism to cell cycle regulation, suggesting that CPT1A could be a prognostic biomarker and rational target for therapeutic intervention of cancer. PMID:26716645

  20. Anaplerotic Triheptanoin Diet Enhances Mitochondrial Substrate Use to Remodel the Metabolome and Improve Lifespan, Motor Function, and Sociability in MeCP2-Null Mice

    PubMed Central

    Li, Qun; Degano, Alicia L.; Penati, Judith; Zhuo, Justin; Roe, Charles R.; Ronnett, Gabriele V.

    2014-01-01

    Rett syndrome (RTT) is an autism spectrum disorder (ASD) caused by mutations in the X-linked MECP2 gene that encodes methyl-CpG binding protein 2 (MeCP2). Symptoms range in severity and include psychomotor disabilities, seizures, ataxia, and intellectual disability. Symptom onset is between 6-18 months of age, a critical period of brain development that is highly energy-dependent. Notably, patients with RTT have evidence of mitochondrial dysfunction, as well as abnormal levels of the adipokines leptin and adiponectin, suggesting overall metabolic imbalance. We hypothesized that one contributor to RTT symptoms is energy deficiency due to defective nutrient substrate utilization by the TCA cycle. This energy deficit would lead to a metabolic imbalance, but would be treatable by providing anaplerotic substrates to the TCA cycle to enhance energy production. We show that dietary therapy with triheptanoin significantly increased longevity and improved motor function and social interaction in male mice hemizygous for Mecp2 knockout. Anaplerotic therapy in Mecp2 knockout mice also improved indicators of impaired substrate utilization, decreased adiposity, increased glucose tolerance and insulin sensitivity, decreased serum leptin and insulin, and improved mitochondrial morphology in skeletal muscle. Untargeted metabolomics of liver and skeletal muscle revealed increases in levels of TCA cycle intermediates with triheptanoin diet, as well as normalizations of glucose and fatty acid biochemical pathways consistent with the improved metabolic phenotype in Mecp2 knockout mice on triheptanoin. These results suggest that an approach using dietary supplementation with anaplerotic substrate is effective in improving symptoms and metabolic health in RTT. PMID:25299635

  1. Anaplerotic triheptanoin diet enhances mitochondrial substrate use to remodel the metabolome and improve lifespan, motor function, and sociability in MeCP2-null mice.

    PubMed

    Park, Min Jung; Aja, Susan; Li, Qun; Degano, Alicia L; Penati, Judith; Zhuo, Justin; Roe, Charles R; Ronnett, Gabriele V

    2014-01-01

    Rett syndrome (RTT) is an autism spectrum disorder (ASD) caused by mutations in the X-linked MECP2 gene that encodes methyl-CpG binding protein 2 (MeCP2). Symptoms range in severity and include psychomotor disabilities, seizures, ataxia, and intellectual disability. Symptom onset is between 6-18 months of age, a critical period of brain development that is highly energy-dependent. Notably, patients with RTT have evidence of mitochondrial dysfunction, as well as abnormal levels of the adipokines leptin and adiponectin, suggesting overall metabolic imbalance. We hypothesized that one contributor to RTT symptoms is energy deficiency due to defective nutrient substrate utilization by the TCA cycle. This energy deficit would lead to a metabolic imbalance, but would be treatable by providing anaplerotic substrates to the TCA cycle to enhance energy production. We show that dietary therapy with triheptanoin significantly increased longevity and improved motor function and social interaction in male mice hemizygous for Mecp2 knockout. Anaplerotic therapy in Mecp2 knockout mice also improved indicators of impaired substrate utilization, decreased adiposity, increased glucose tolerance and insulin sensitivity, decreased serum leptin and insulin, and improved mitochondrial morphology in skeletal muscle. Untargeted metabolomics of liver and skeletal muscle revealed increases in levels of TCA cycle intermediates with triheptanoin diet, as well as normalizations of glucose and fatty acid biochemical pathways consistent with the improved metabolic phenotype in Mecp2 knockout mice on triheptanoin. These results suggest that an approach using dietary supplementation with anaplerotic substrate is effective in improving symptoms and metabolic health in RTT. PMID:25299635

  2. A Functional Tricarboxylic Acid Cycle Operates during Growth of Bordetella pertussis on Amino Acid Mixtures as Sole Carbon Substrates

    PubMed Central

    Garnier, Dominique; Speck, Denis

    2015-01-01

    It has been claimed that citrate synthase, aconitase and isocitrate dehydrogenase activities are non-functional in Bordetella pertussis and that this might explain why this bacterium’s growth is sometimes associated with accumulation of polyhydroxybutyrate (PHB) and/or free fatty acids. However, the sequenced genome includes the entire citric acid pathway genes. Furthermore, these genes were expressed and the corresponding enzyme activities detected at high levels for the pathway when grown on a defined medium imitating the amino acid content of complex media often used for growth of this pathogenic microorganism. In addition, no significant PHB or fatty acids could be detected. Analysis of the carbon balance and stoichiometric flux analysis based on specific rates of amino acid consumption, and estimated biomass requirements coherent with the observed growth rate, clearly indicate that a fully functional tricarboxylic acid cycle operates in contrast to previous reports. PMID:26684737

  3. Targeting and functional mechanisms of the cytokinesis-related F-BAR protein Hof1 during the cell cycle.

    PubMed

    Oh, Younghoon; Schreiter, Jennifer; Nishihama, Ryuichi; Wloka, Carsten; Bi, Erfei

    2013-05-01

    F-BAR proteins are membrane-associated proteins believed to link the plasma membrane to the actin cytoskeleton in cellular processes such as cytokinesis and endocytosis. In the budding yeast Saccharomyces cerevisiae, the F-BAR protein Hof1 localizes to the division site in a complex pattern during the cell cycle and plays an important role in cytokinesis. However, the mechanisms underlying its localization and function are poorly understood. Here we show that Hof1 contains three distinct targeting domains that contribute to cytokinesis differentially. The N-terminal half of Hof1 localizes to the bud neck and the sites of polarized growth during the cell cycle. The neck localization is mediated mainly by an interaction between the second coiled-coil region in the N-terminus and the septin Cdc10, whereas the localization to the sites of polarized growth is mediated entirely by the F-BAR domain. In contrast, the C-terminal half of Hof1 interacts with Myo1, the sole myosin-II heavy chain in budding yeast, and localizes to the bud neck in a Myo1-dependent manner from the onset to the completion of cytokinesis. We also show that the SH3 domain in the C-terminus plays an important role in maintaining the symmetry of Myo1 ring constriction during cytokinesis and that Hof1 interacts with Chs2, a chitin synthase that is required for primary septum formation. Together these data define a mechanism that accounts for the localization of Hof1 during the cell cycle and suggest that Hof1 may function in cytokinesis by coupling actomyosin ring constriction to primary septum formation through interactions with Myo1 and Chs2. PMID:23468521

  4. Raf-1 Physically Interacts with Rb and Regulates Its Function: a Link between Mitogenic Signaling and Cell Cycle Regulation

    PubMed Central

    Wang, Sheng; Ghosh, Richik N.; Chellappan, Srikumar P.

    1998-01-01

    Cells initiate proliferation in response to growth factor stimulation, but the biochemical mechanisms linking signals received at the cell surface receptors to the cell cycle regulatory molecules are not yet clear. In this study, we show that the signaling molecule Raf-1 can physically interact with Rb and p130 proteins in vitro and in vivo and that this interaction can be detected in mammalian cells without overexpressing any component. The binding of Raf-1 to Rb occurs subsequent to mitogen stimulation, and this interaction can be detected only in proliferating cells. Raf-1 can inactivate Rb function and can reverse Rb-mediated repression of E2F1 transcription and cell proliferation efficiently. The region of Raf-1 involved in Rb binding spanned residues 1 to 28 at the N terminus, and functional inactivation of Rb required a direct interaction. Serum stimulation of quiescent human fibroblast HSF8 cells led to a partial translocation of Raf-1 into the nucleus, where it colocalized with Rb. Further, Raf-1 was able to phosphorylate Rb in vitro quite efficiently. We believe that the physical interaction of Raf-1 with Rb is a vital step in the growth factor-mediated induction of cell proliferation and that Raf-1 acts as a direct link between cell surface signaling cascades and the cell cycle machinery. PMID:9819434

  5. The Arabidopsis CDC25 induces a short cell length when overexpressed in fission yeast: evidence for cell cycle function.

    PubMed

    Sorrell, D A; Chrimes, D; Dickinson, J R; Rogers, H J; Francis, D

    2005-02-01

    The putative mitotic inducer gene, Arath;CDC25 cloned in Arabidopsis thaliana, was screened for cell cycle function by overexpressing it in Schizosaccharomyces pombe (fission yeast). The expression pattern of Arath;CDC25 was also examined in different tissues of A. thaliana. Fission yeast was transformed with plasmids pREP1 and pREP81 with the Arath;CDC25 gene under the control of the thiamine-repressible nmt promoter. Using reverse transcription-polymerase chain reaction (RT-PCR), the expression of Arath;CDC25 was examined in seedlings, flower buds, mature leaves and stems of A. thaliana; actin (ACT2) was used as a control. In three independent transformants of fission yeast, cultured in the absence of thiamine (T), pREP1::Arath;CDC25 induced a highly significant reduction in mitotic cell length compared with wild type, pREP::Arath;CDC25 +T, and empty vector (pREP1 +/- T). The extent of cell shortening was greater using the stronger pREP1 compared with the weaker pREP81. However, Arath;CDC25 was expressed at low levels in all tissues examined. The data indicate that Arath;CDC25 can function as a mitotic accelerator in fission yeast. However, unlike other plant cell cycle genes, expression of Arath;CDC25 was not enhanced in rapidly dividing compared with non-proliferative Arabidopsis tissues. PMID:15720653

  6. Study of nickel electrode oxidation as a function of 80% depth of discharge cycling

    SciTech Connect

    Pickett, D.F. Jr.; Scoles, D.L.; Johnson, Z.W.; Hayden, J.W.; Pennington, R.D.

    1997-12-31

    Oxidation of nickel sinter used in nickel oxide electrodes in aerospace nickel cadmium cells leads to hydrogen gassing and the potential for cell rupture. The oxidation is directly related to loss of overcharge protection built into the cell during manufacturing. In nickel hydrogen cells, excessive oxidation of the nickel sinter can eventually lead to a burst before leak situation and is a potential source of failure. It is well known that nickel cadmium cells having nylon separators contribute to loss of overcharge via a hydrolysis reaction of the nylon in the potassium hydroxide electrolyte environment in the cell. The hydrolysis reaction produces lower chain organics which are oxidized by the positive electrode and oxygen. Oxidation of the organics diminishes the overcharge protection. With introduction of the Super NiCd{trademark} and the Magnum{trademark} nickel cadmium cells the nylon hydrolysis reaction is eliminated, but any reducing agent in the cell such as nickel or an organic additive can contribute to loss of overcharge protection. The present effort describes chemical analyses made to evaluate the extent of overcharge protection loss in nickel cadmium cells which do not have nylon hydrolysis, and quantifies the amount of hydrogen buildup in nickel hydrogen cells which are subjected to 80% depth of discharge cycling with and without the presence of cadmium in the positive electrode.

  7. From low- to high-potential bioenergetic chains: Thermodynamic constraints of Q-cycle function.

    PubMed

    Bergdoll, Lucie; Ten Brink, Felix; Nitschke, Wolfgang; Picot, Daniel; Baymann, Frauke

    2016-09-01

    The electrochemical parameters of all cofactors in the supercomplex formed by the Rieske/cytb complex and the SoxM/A-type O2-reductase from the menaquinone-containing Firmicute Geobacillus stearothermophilus were determined by spectroelectrochemistry and EPR redox titrations. All redox midpoint potentials (Em) were found to be lower than those of ubi- or plastoquinone-containing systems by a value comparable to the redox potential difference between the respective quinones. In particular, Em values of +200mV, -360mV, -220mV and -50mV (at pH7) were obtained for the Rieske cluster, heme bL, heme bH and heme ci, respectively. Comparable values of -330mV, -200mV and +120mV for hemes bL, bH and the Rieske cluster were determined for an anaerobic Firmicute, Heliobacterium modesticaldum. Thermodynamic constraints, optimization of proton motive force build-up and the necessity of ROS-avoidance imposed by the rise in atmospheric O2 2.5billionyears ago are discussed as putative evolutionary driving forces resulting in the observed redox upshift. The close conservation of the entire redox landscape between low and high potential systems suggests that operation of the Q-cycle requires the precise electrochemical tuning of enzyme cofactors to the quinone substrate as stipulated in P. Mitchell's hypothesis. PMID:27328272

  8. Arabidopsis CSLD5 Functions in Cell Plate Formation in a Cell Cycle-Dependent Manner.

    PubMed

    Gu, Fangwei; Bringmann, Martin; Combs, Jonathon R; Yang, Jiyuan; Bergmann, Dominique C; Nielsen, Erik

    2016-07-01

    In plants, the presence of a load-bearing cell wall presents unique challenges during cell division. Unlike other eukaryotes, which undergo contractile cytokinesis upon completion of mitosis, plants instead synthesize and assemble a new dividing cell wall to separate newly formed daughter cells. Here, we mine transcriptome data from individual cell types in the Arabidopsis thaliana stomatal lineage and identify CSLD5, a member of the Cellulose Synthase Like-D family, as a cell wall biosynthesis enzyme uniquely enriched in rapidly dividing cell populations. We further show that CSLD5 is a direct target of SPEECHLESS, the master transcriptional regulator of these divisions during stomatal development. Using a combination of genetic analysis and in vivo localization of fluorescently tagged fusion proteins, we show that CSLD5 preferentially accumulates in dividing plant cells where it participates in the construction of newly forming cell plates. We show that CSLD5 is an unstable protein that is rapidly degraded upon completion of cell division and that the protein turnover characteristics of CSLD5 are altered in ccs52a2 mutants, indicating that CSLD5 turnover may be regulated by a cell cycle-associated E3-ubiquitin ligase, the anaphase-promoting complex. PMID:27354558

  9. Characterization of MAT gene functions in the life cycle of Sclerotinia sclerotiorum reveals a lineage-specific MAT gene functioning in apothecium morphogenesis.

    PubMed

    Doughan, Benjamin; Rollins, Jeffrey A

    2016-09-01

    Sclerotinia sclerotiorum (Lib.) de Bary is a phytopathogenic fungus that relies on the completion of the sexual cycle to initiate aerial infections. The sexual cycle produces apothecia required for inoculum dispersal. In this study, insight into the regulation of apothecial multicellular development was pursued through functional characterization of mating-type genes. These genes are hypothesized to encode master regulatory proteins required for aspects of sexual development ranging from fertilization through fertile fruiting body development. Experimentally, loss-of-function mutants were created for the conserved core mating-type genes (MAT1-1-1, and MAT1-2-1), and the lineage-specific genes found only in S. sclerotiorum and closely related fungi (MAT1-1-5, and MAT1-2-4). The MAT1-1-1, MAT1-1-5, and MAT1-2-1 mutants are able to form ascogonia but are blocked in all aspects of apothecium development. These mutants also exhibit defects in secondary sexual characters including lower numbers of spermatia. The MAT1-2-4 mutants are delayed in carpogenic germination accompanied with altered disc morphogenesis and ascospore production. They too produce lower numbers of spermatia. All four MAT gene mutants showed alterations in the expression of putative pheromone precursor (Ppg-1) and pheromone receptor (PreA, PreB) genes. Our findings support the involvement of MAT genes in sexual fertility, gene regulation, meiosis, and morphogenesis in S. sclerotiorum. PMID:27567717

  10. The Closure of the Cycle: Enzymatic Synthesis and Functionalization of Bio-Based Polyesters.

    PubMed

    Pellis, Alessandro; Herrero Acero, Enrique; Ferrario, Valerio; Ribitsch, Doris; Guebitz, Georg M; Gardossi, Lucia

    2016-04-01

    The polymer industry is under pressure to mitigate the environmental cost of petrol-based plastics. Biotechnologies contribute to the gradual replacement of petrol-based chemistry and the development of new renewable products, leading to the closure of carbon circle. An array of bio-based building blocks is already available on an industrial scale and is boosting the development of new generations of sustainable and functionally competitive polymers, such as polylactic acid (PLA). Biocatalysts add higher value to bio-based polymers by catalyzing not only their selective modification, but also their synthesis under mild and controlled conditions. The ultimate aim is the introduction of chemical functionalities on the surface of the polymer while retaining its bulk properties, thus enlarging the spectrum of advanced applications. PMID:26806112

  11. Soil warming alters nitrogen cycling in a New England forest: implications for ecosystem function and structure.

    PubMed

    Butler, S M; Melillo, J M; Johnson, J E; Mohan, J; Steudler, P A; Lux, H; Burrows, E; Smith, R M; Vario, C L; Scott, L; Hill, T D; Aponte, N; Bowles, F

    2012-03-01

    Global climate change is expected to affect terrestrial ecosystems in a variety of ways. Some of the more well-studied effects include the biogeochemical feedbacks to the climate system that can either increase or decrease the atmospheric load of greenhouse gases such as carbon dioxide and nitrous oxide. Less well-studied are the effects of climate change on the linkages between soil and plant processes. Here, we report the effects of soil warming on these linkages observed in a large field manipulation of a deciduous forest in southern New England, USA, where soil was continuously warmed 5°C above ambient for 7 years. Over this period, we have observed significant changes to the nitrogen cycle that have the potential to affect tree species composition in the long term. Since the start of the experiment, we have documented a 45% average annual increase in net nitrogen mineralization and a three-fold increase in nitrification such that in years 5 through 7, 25% of the nitrogen mineralized is then nitrified. The warming-induced increase of available nitrogen resulted in increases in the foliar nitrogen content and the relative growth rate of trees in the warmed area. Acer rubrum (red maple) trees have responded the most after 7 years of warming, with the greatest increases in both foliar nitrogen content and relative growth rates. Our study suggests that considering species-specific responses to increases in nitrogen availability and changes in nitrogen form is important in predicting future forest composition and feedbacks to the climate system. PMID:21983640

  12. The CMS fast beams condition monitor back-end electronics based on MicroTCA technology: status and development

    NASA Astrophysics Data System (ADS)

    Zagozdzinska, Agnieszka A.; Dabrowski, Anne E.; Pozniak, Krzysztof T.

    2015-09-01

    The Fast Beams Condition Monitor (BCM1F), upgraded for LHC Run II, is used to measure the online luminosity and machine induced background for the CMS experiment. The detector consists of 24 single-crystal CVD diamond sensors that are read out with a custom fast front-end chip fabricated in 130 nm CMOS technology. Since the signals from the sensors are used for real time monitoring of the LHC conditions they are processed by dedicated back-end electronics to measure separately rates corresponding to LHC collision products, machine induced background and residual activation exploiting different arrival times. The system is built in MicroTCA technology and uses high speed analog-to-digital converters. In operational modes of high rates, consecutive events, spaced in time by less than 12.5 ns, may cause partially overlapping events. Hence, novel signal processing techniques are deployed to resolve overlapping peaks. The high accuracy qualification of the signals is crucial to determine the luminosity and the machine induced background rates for the CMS experiment and the LHC.

  13. The role of surface chemical analysis in a study to select replacement processes for TCA vapor degreasing

    NASA Technical Reports Server (NTRS)

    Lesley, Michael W.; Davis, Lawrence E.; Moulder, John F.; Carlson, Brad A.

    1995-01-01

    The role of surface-sensitive chemical analysis (ESCA, AES, and SIMS) in a study to select a process to replace 1, 1, 1-trichloroethane (TCA) vapor degreasing as a steel and aluminum bonding surface preparation method is described. The effort was primarily concerned with spray-in-air cleaning processes involving aqueous alkaline and semi-aqueous cleaners and a contamination sensitive epoxy-to-metal bondline. While all five cleaners tested produced bonding strength results equal to or better than those produced by vapor degreasing, the aqueous alkaline cleaners yielded results which were superior to those produced by the semi-aqueous cleaners. The main reason for the enhanced performance appears to be a silicate layer left behind by the aqueous alkaline cleaners. The silicate layer increases the polarity of the surface and enhances epoxy-to-metal bonding. On the other hand, one of the semi-aqueous cleaners left a nonpolar carbonaceous residue which appeared to have a negative effect on epoxy-to-metal bonding. Differences in cleaning efficiency between cleaners/processes were also identified. These differences in surface chemistry, which were sufficient to affect bonding, were not detected by conventional chemical analysis techniques.

  14. xCT expression modulates cisplatin resistance in Tca8113 tongue carcinoma cells

    PubMed Central

    ZHANG, PENG; WANG, WEI; WEI, ZHENHUI; XU, LI; YANG, XUANNING; DU, YUANHONG

    2016-01-01

    Tongue squamous cell carcinoma (TSCC), which is a subtype of head and neck cancer, is the most common type of oral cancer. Due to its high recurrence rate and chemoresistance, the average survival rate for patients with TSCC remains unsatisfactory. At present, cisplatin (CDDP) is utilized as the first-line treatment for numerous solid neoplasms, including TSCC. CDDP resistance develops in the majority of patients; however, the mechanism of such resistance remains unknown. Therefore, the present study aimed to clarify the mechanism of CDDP resistance and attempted to reduce chemoresistance. The results indicated that CDDP significantly increased expression of xCT, which is the light chain and functional subunit of the glutamate/cysteine transporter system xc−, and a subsequent increase in glutathione (GSH) levels was observed. The present study demonstrated that the upregulation of xCT expression and intercellular GSH levels contributed to CDDP resistance in TSCC cells. Furthermore, xCT suppression, induced by small interfering RNA or pharmacological inhibitors, sensitized TSCC cells to CDDP treatment. In conclusion, the present study revealed that CDDP-induced xCT expression promotes CDDP chemoresistance, and xCT inhibition sensitizes TSCC cells to CDDP treatment. These results provide a novel insight into the molecular mechanisms involved in TSCC cell chemoresistance. PMID:27347143

  15. A “footprint” of plant carbon fixation cycle functions during the development of a heterotrophic fungus

    PubMed Central

    Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

    2015-01-01

    Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution. PMID:26263551

  16. An N-Myristoylated Globin with a Redox-Sensing Function That Regulates the Defecation Cycle in Caenorhabditis elegans

    PubMed Central

    Tilleman, Lesley; De Henau, Sasha; Pauwels, Martje; Nagy, Nora; Pintelon, Isabel; Braeckman, Bart P.; De Wael, Karolien; Van Doorslaer, Sabine; Adriaensen, Dirk; Timmermans, Jean-Pierre; Moens, Luc; Dewilde, Sylvia

    2012-01-01

    Globins occur in all kingdoms of life where they fulfill a wide variety of functions. In the past they used to be primarily characterized as oxygen transport/storage proteins, but since the discovery of new members of the globin family like neuroglobin and cytoglobin, more diverse and complex functions have been assigned to this heterogeneous family. Here we propose a function for a membrane-bound globin of C. elegans, GLB-26. This globin was predicted to be myristoylated at its N-terminus, a post-translational modification only recently described in the globin family. In vivo, this globin is found in the membrane of the head mesodermal cell and in the tail stomato-intestinal and anal depressor muscle cells. Since GLB-26 is almost directly oxidized when exposed to oxygen, we postulate a possible function as electron transfer protein. Phenotypical studies show that GLB-26 takes part in regulating the length of the defecation cycle in C. elegans under oxidative stress conditions. PMID:23251335

  17. Sociological functionalism, exchange theory and life-cycle analysis: a call for more explicit theoretical bridges.

    PubMed

    Bengtson, V L; Dowd, J J

    There has been a notable lack of articulation between mainstream sociological theory and the work of social gerontologists. This paper suggests four reasons for this, and reviews the basic assumptions and applications to gerontology of two well-established frameworks in sociological theory: structural-functionalism and exchange. With more rigorous and systematic integration of gerontological data with social and social psychological theory, more comprehensive explanations of life course phenomena would result. Moreover, the age variable would be considerably by other sociologists as less of a control and more of a relevant variable in its own right. PMID:7203672

  18. Variations in structure and function during the life cycle of malarial parasites*

    PubMed Central

    Aikawa, M.

    1977-01-01

    The fine structure of malarial parasites is reviewed and the function of the intracellular organelles is discussed. When the erythrocytic, exoerythrocytic, and mosquito stages of plasmodia are compared, substantial differences are seen. The major differences involve the amount of surface coat of the motile forms, the structure and function of the mitochondria, and the ingestion and digestion of nutrients. Significant structural differences are also observed between comparable stages of mammalian and avian parasites. These differences indicate that malarial parasites adapt themselves to the different environments in which the parasite resides. When host cell changes induced by malarial parasite infection are reviewed, alterations characteristic of the infecting plasmodia are observed in erythrocytes. Erythrocyte changes include caveola—vesicle complexes, excrescences, and clefts. The caveola—vesicle complexes possess malarial antigens and exhibit pinocytotic activities. The excrescences form focal junctions with adjacent cells and may be responsible for infected erythrocyte sequestration in organs. The significance of these host cell changes specific to certain species of malarial parasite is still unknown. ImagesFig. 9Fig. 8Fig. 2Fig. 6Fig. 3Fig. 1Fig. 7Fig. 4Fig. 10Fig. 5 PMID:338177

  19. The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control

    SciTech Connect

    Yang, Yunfeng; McCue, Lee Ann; Parsons, Andrea B.; Feng, Sheng; Zhou, Jizhong

    2010-10-26

    It is well established in E. coli and Vibrio cholerae that strains harboring mutations in the ferric uptake regulator gene (fur) are unable to utilize tricarboxylic acid (TCA) compounds, due to the down-regulation of key TCA cycle enzymes, such as AcnA and SdhABCD. This down-regulation is mediated by a Fur-regulated small regulatory RNA named RyhB. In this study, we showed that a fur deletion mutant of the γ-proteobacterium S. oneidensis could utilize TCA compounds. In addition, expression of the TCA cycle genes acnA and sdhA was not down-regulated in the mutant. To explore this observation further, we identified a ryhB gene in Shewanella species and demonstrated its expression experimentally. Further experiments suggested that RyhB was up-regulated in fur mutant, but that AcnA and SdhA were not controlled by RyhB. This work delineates an important difference of the Fur-RyhB regulatory cycle between S. oneidensis and other γ-proteobacteria.

  20. The role of biodiversity for the carbon cycle: Implementation of functional diversity in a dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Sakschewski, Boris; Boit, Alice; von Bloh, Werner; Rammig, Anja; Thonicke, Kirsten

    2013-04-01

    Most dynamic global vegetation models (DGVMs) condense natural plant diversity to plant functional types (PFTs). A single PFT usually represents a whole biome, e.g. the PFT "tropical broadleaved evergreen tree" and its constant set of functional trait parameters covers entire regions in the model. This approach minimizes functional diversity and neglects the effects of functional diversity on the modeled vegetation and carbon dynamics. Our work aims to overcome this limitation and extend functional diversity in the vegetation model LPJmL to explore the role of biodiversity in climate change mitigation. Our approach improves the representation of biodiversity in the model by incorporating the natural ranges and eco-physiological interrelations of relevant plant traits. Empirical data on plant traits is provided by the TRY data base (www.try-db.org) and the ROBIN project (www.robinproject.info). A first sensitivity analysis revealed that simulated carbon stocks are very stable under a large range of trait combinations. However, several model output variables appeared highly sensitive to small changes of plant trait parameters and thus the introduction of trait ranges requires several improvements of the PFT concept of LPJmL. One possible way of improvement is to implement missing plant-trait tradeoffs, which will be used to simulate the growth of individual plants with flexible parameter combinations at the landscape scale. Our improved model will enable for the simulation of local competition and complementarity of individual plants which, according to their trait values and ranges, can then be categorized into a much broader variety of PFTs. This modeling approach will allow for investigating the role of bio- and functional diversity in the global carbon cycle as well as in regional vegetation dynamics.

  1. Passive hind-limb cycling improves cardiac function and reduces cardiovascular disease risk in experimental spinal cord injury

    PubMed Central

    West, Christopher R; Crawford, Mark A; Poormasjedi-Meibod, Malihe-Sadat; Currie, Katharine D; Fallavollita, Andre; Yuen, Violet; McNeill, John H; Krassioukov, Andrei V

    2014-01-01

    Spinal cord injury (SCI) causes altered autonomic control and severe physical deconditioning that converge to drive maladaptive cardiac remodelling. We used a clinically relevant experimental model to investigate the cardio-metabolic responses to SCI and to establish whether passive hind-limb cycling elicits a cardio-protective effect. Initially, 21 male Wistar rats were evenly assigned to three groups: uninjured control (CON), T3 complete SCI (SCI) or T3 complete SCI plus passive hind-limb cycling (SCI-EX; 2 × 30 min day−1, 5 days week−1 for 4 weeks beginning 6 days post-SCI). On day 32, cardio-metabolic function was assessed using in vivo echocardiography, ex vivo working heart assessments, cardiac histology/molecular biology and blood lipid profiles. Twelve additional rats (n = 6 SCI and n = 6 SCI-EX) underwent in vivo echocardiography and basal haemodynamic assessments pre-SCI and at days 7, 14 and 32 post-SCI to track temporal cardiovascular changes. Compared with CON, SCI exhibited a rapid and sustained reduction in left ventricular dimensions and function that ultimately manifested as reduced contractility, increased myocardial collagen deposition and an up-regulation of transforming growth factor beta-1 (TGFβ1) and mothers against decapentaplegic homolog 3 (Smad3) mRNA. For SCI-EX, the initial reduction in left ventricular dimensions and function at day 7 post-SCI was completely reversed by day 32 post-SCI, and there were no differences in myocardial contractility between SCI-EX and CON. Collagen deposition was similar between SCI-EX and CON. TGFβ1 and Smad3 were down-regulated in SCI-EX. Blood lipid profiles were improved in SCI-EX versus SCI. We provide compelling novel evidence that passive hind-limb cycling prevents cardiac dysfunction and reduces cardiovascular disease risk in experimental SCI. PMID:24535438

  2. The evolutionary armistice: attachment bonds moderate the function of ovulatory cycle adaptations.

    PubMed

    Eastwick, Paul W; Finkel, Eli J

    2012-02-01

    Natural selection modified the attachment-behavioral system to bond adult mating partners in early members of the genus Homo, thus facilitating increased investment, especially paternal investment, in offspring. Previously existing adaptations that fostered intersexual conflict (e.g., ovulatory adaptations) could have threatened attachment bonds; therefore, the attachment-behavioral system might have evolved the ability to mute or refocus such adaptations for the purpose of strengthening the bond. Two studies offer support for this prediction. Women who were strongly attached to their romantic partner revealed positive associations of fertility with reports of romantic physical intimacy, but these associations were negative among unbonded women. This moderational effect of attachment bond strength was robust beyond dispositional attachment anxiety and avoidance, relationship satisfaction, relationship commitment, and partner physical attractiveness, none of which revealed robust moderational effects. Findings highlight how researchers can use the timeline of hominid evolution (i.e., phylogeny) as a tool to complement functional, adaptationist hypotheses. PMID:21933989

  3. The Relationship between Sleep-Wake Cycle and Cognitive Functioning in Young People with Affective Disorders

    PubMed Central

    Carpenter, Joanne S.; Robillard, Rébecca; Lee, Rico S. C.; Hermens, Daniel F.; Naismith, Sharon L.; White, Django; Whitwell, Bradley; Scott, Elizabeth M.; Hickie, Ian B.

    2015-01-01

    Although early-stage affective disorders are associated with both cognitive dysfunction and sleep-wake disruptions, relationships between these factors have not been specifically examined in young adults. Sleep and circadian rhythm disturbances in those with affective disorders are considerably heterogeneous, and may not relate to cognitive dysfunction in a simple linear fashion. This study aimed to characterise profiles of sleep and circadian disturbance in young people with affective disorders and examine associations between these profiles and cognitive performance. Actigraphy monitoring was completed in 152 young people (16–30 years; 66% female) with primary diagnoses of affective disorders, and 69 healthy controls (18–30 years; 57% female). Patients also underwent detailed neuropsychological assessment. Actigraphy data were processed to estimate both sleep and circadian parameters. Overall neuropsychological performance in patients was poor on tasks relating to mental flexibility and visual memory. Two hierarchical cluster analyses identified three distinct patient groups based on sleep variables and three based on circadian variables. Sleep clusters included a ‘long sleep’ cluster, a ‘disrupted sleep’ cluster, and a ‘delayed and disrupted sleep’ cluster. Circadian clusters included a ‘strong circadian’ cluster, a ‘weak circadian’ cluster, and a ‘delayed circadian’ cluster. Medication use differed between clusters. The ‘long sleep’ cluster displayed significantly worse visual memory performance compared to the ‘disrupted sleep’ cluster. No other cognitive functions differed between clusters. These results highlight the heterogeneity of sleep and circadian profiles in young people with affective disorders, and provide preliminary evidence in support of a relationship between sleep and visual memory, which may be mediated by use of antipsychotic medication. These findings have implications for the personalisation of treatments

  4. The relationship between sleep-wake cycle and cognitive functioning in young people with affective disorders.

    PubMed

    Carpenter, Joanne S; Robillard, Rébecca; Lee, Rico S C; Hermens, Daniel F; Naismith, Sharon L; White, Django; Whitwell, Bradley; Scott, Elizabeth M; Hickie, Ian B

    2015-01-01

    Although early-stage affective disorders are associated with both cognitive dysfunction and sleep-wake disruptions, relationships between these factors have not been specifically examined in young adults. Sleep and circadian rhythm disturbances in those with affective disorders are considerably heterogeneous, and may not relate to cognitive dysfunction in a simple linear fashion. This study aimed to characterise profiles of sleep and circadian disturbance in young people with affective disorders and examine associations between these profiles and cognitive performance. Actigraphy monitoring was completed in 152 young people (16-30 years; 66% female) with primary diagnoses of affective disorders, and 69 healthy controls (18-30 years; 57% female). Patients also underwent detailed neuropsychological assessment. Actigraphy data were processed to estimate both sleep and circadian parameters. Overall neuropsychological performance in patients was poor on tasks relating to mental flexibility and visual memory. Two hierarchical cluster analyses identified three distinct patient groups based on sleep variables and three based on circadian variables. Sleep clusters included a 'long sleep' cluster, a 'disrupted sleep' cluster, and a 'delayed and disrupted sleep' cluster. Circadian clusters included a 'strong circadian' cluster, a 'weak circadian' cluster, and a 'delayed circadian' cluster. Medication use differed between clusters. The 'long sleep' cluster displayed significantly worse visual memory performance compared to the 'disrupted sleep' cluster. No other cognitive functions differed between clusters. These results highlight the heterogeneity of sleep and circadian profiles in young people with affective disorders, and provide preliminary evidence in support of a relationship between sleep and visual memory, which may be mediated by use of antipsychotic medication. These findings have implications for the personalisation of treatments and improvement of functioning in

  5. In situ Expression of Functional Genes Reveals Nitrogen Cycling at High Temperatures in Terrestrial Hydrothermal Systems

    NASA Astrophysics Data System (ADS)

    Loiacono, S. T.; Meyer-Dombard, D. R.

    2011-12-01

    An essential element for life, nitrogen occurs in all living organisms and is critical for the synthesis of amino acids, proteins, nucleic acids, and other forms of biomass. Thus, nitrogen cycling likely plays a vital role in microbial metabolic processes as well as nutrient availability. For microorganisms in "extreme" environments, this means developing adaptations that allow them to survive in harsh conditions and still perform the metabolisms essential to sustain life. Recent studies have screened biofilms and thermal sediments of Yellowstone National Park (YNP) thermal features for the presence of nifH genes, which code for a key enzyme in the nitrogen fixation process [1-4]. Furthermore, analysis of nitrogen isotopes in biofilms across a temperature and chemical gradient revealed that nitrogen fixation likely varies across the chemosynthetic/photosynthetic ecotone [5]. Although research has evaluated and confirmed the presence of nifH genes in various thermophilic microbial communities, the existence of a gene in the DNA of an organism does not verify its use. Instead, other methods, such as culturing, isotope tracer assays, and gene expression studies are required to provide direct evidence of biological nitrogen fixation. Culturing and isotope tracer approaches have successfully revealed high-temperature biological nitrogen fixation in both marine hydrothermal vent microbial communities [6] and in acidic, terrestrial hydrothermal sediment [3]. Transcriptomics-based techniques (using mRNA extracted from samples to confirm in situ expression of targeted genes) have been much more limited in number, and only a few studies have, to date, investigated in situ expression of the nifH gene in thermophilic microbial communities [2, 7]. This study explores the presence and expression of nifH genes in several features of the Lower Geyser Basin (LGB) of YNP. Nucleic acids from chemosynthetic and photosynthetic microbial communities were extracted and then amplified

  6. Chloroplastic thioredoxin m functions as a major regulator of Calvin cycle enzymes during photosynthesis in vivo.

    PubMed

    Okegawa, Yuki; Motohashi, Ken

    2015-12-01

    Thioredoxins (Trxs) regulate the activity of various chloroplastic proteins in a light-dependent manner. Five types of Trxs function in different physiological processes in the chloroplast of Arabidopsis thaliana. Previous in vitro experiments have suggested that the f-type Trx (Trx f) is the main redox regulator of chloroplast enzymes, including Calvin cycle enzymes. To investigate the in vivo contribution of each Trx isoform to the redox regulatory system, we first quantified the protein concentration of each Trx isoform in the chloroplast stroma. The m-type Trx (Trx m), which consists of four isoforms, was the most abundant type. Next, we analyzed several Arabidopsis Trx-m-deficient mutants to elucidate the physiological role of Trx m in vivo. Deficiency of Trx m impaired plant growth and decreased the CO2 assimilation rate. We also determined the redox state of Trx target enzymes to examine their photo-reduction, which is essential for enzyme activation. In the Trx-m-deficient mutants, the reduction level of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase was lower than that in the wild type. Inconsistently with the historical view, our in vivo study suggested that Trx m plays a more important role than Trx f in the activation of Calvin cycle enzymes. PMID:26468055

  7. How useful are plant functional types in global simulations of the carbon, water, and energy cycles?

    NASA Astrophysics Data System (ADS)

    Alton, Paul B.

    2011-03-01

    Land-surface and vegetation models divide the globe into discrete vegetation classes or plant functional types (PFTs). The current study quantifies some of the limitations of this simplification on global predictions of carbon, water, and energy fluxes. First, a state-of-the-art land-surface model, JULES-SF, is optimized against a diversity of calibration data sets (eddy covariance fluxes, field measurements of net primary production (NPP), and remotely sensed surface albedo) in order to retrieve a range of values for four key plant parameters within each PFT. This is done for 112 sites and 1200 1° land points. Second, global simulations are compared in which the parameter values per PFT are either fixed (standard method) or vary according to either the retrieved parameter range or the satellite-observed range (new methods). Retrieved key plant parameters exhibit a broad range, and the range overlap between PFTs is significant. The impact on the global simulation depends on the surface flux/state in question. Thus, the difference between the new and old method is small for albedo, net shortwave radiation, and continental runoff (0.005, 0.7%, and 2%, respectively) compared to current model-observation differences (0.05, 7%, and 20%, respectively). In contrast, carbon fluxes are more sensitive to the categorization of plant properties, with predicted global NPP varying by ≤15% (6.2 Gt yr-1) according to whether the standard or one of the new methods is implemented.

  8. Mapping the conformation of a client protein through the Hsp70 functional cycle.

    PubMed

    Sekhar, Ashok; Rosenzweig, Rina; Bouvignies, Guillaume; Kay, Lewis E

    2015-08-18

    The 70 kDa heat shock protein (Hsp70) chaperone system is ubiquitous, highly conserved, and involved in a myriad of diverse cellular processes. Its function relies on nucleotide-dependent interactions with client proteins, yet the structural features of folding-competent substrates in their Hsp70-bound state remain poorly understood. Here we use NMR spectroscopy to study the human telomere repeat binding factor 1 (hTRF1) in complex with Escherichia coli Hsp70 (DnaK). In the complex, hTRF1 is globally unfolded with up to 40% helical secondary structure in regions distal to the binding site. Very similar conformational ensembles are observed for hTRF1 bound to ATP-, ADP- and nucleotide-free DnaK. The patterns in substrate helicity mirror those found in the unfolded state in the absence of denaturants except near the site of chaperone binding, demonstrating that DnaK-bound hTRF1 retains its intrinsic structural preferences. To our knowledge, our study presents the first atomic resolution structural characterization of a client protein bound to each of the three nucleotide states of DnaK and establishes that the large structural changes in DnaK and the associated energy that accompanies ATP binding and hydrolysis do not affect the overall conformation of the bound substrate protein. PMID:26240333

  9. Structure and diversity of functional guilds in the microbial nitrogen cycle of estuarine sediments

    NASA Astrophysics Data System (ADS)

    Ward, B. B.; Francis, C. A.; Taroncher-Oldenburg, G.; Cornwell, J.

    2002-12-01

    Denitrification is a major flux of nitrogen in Chesapeake Bay, an estuary with a long residence time and high organic and inorganic nutrient inputs from the large surrounding watershed. The estuarine system spans a complex gradient of salinity and many correlated chemical constituents, from its upper bay and river freshwater end members to its nearly full strength seawater lower Bay. Denitrification rates in sediments, computed from net nitrogen fluxes in simulated in situ core incubations, show distinct reproducible patterns along the Bay. Highest rates are observed in sediments from the low salinity, high nitrate upper stations in the Bay and Choptank River. Lower rates occur in the low nitrate, oxygen depleted mid bay sediments and in the metabolically less active south Bay sediments. Gene sequences for nitrite reductase, the key enzyme in denitrification, show very high diversity in Bay and River sediments. On the basis of clone library sequences alone, however, there are distinct clades and patterns indicating highest diversity in the upper Bay and River sediments and lower diversity in the lower Bay sediments. Using a DNA microarray containing many individual nitrite reductase sequences, we investigated the population structure of denitrification genes along the estuarine gradient. Evaluation of gene expression patterns, in addition to presence/absence or abundance of individual genes, will allow a direct assessment of the links between diversity and biogeochemical transformation rates for particular functional guilds. The rate of denitrification and its regulation by environmental variables may be reflected in patterns of guild composition and activity.

  10. Establishment and consolidation of the sleep-wake cycle as a function of attachment pattern.

    PubMed

    Pennestri, Marie-Hélène; Moss, Ellen; O'Donnell, Katherine; Lecompte, Vanessa; Bouvette-Turcot, Andrée-Anne; Atkinson, Leslie; Minde, Klaus; Gruber, Reut; Fleming, Alison S; Meaney, Michael J; Gaudreau, Hélène

    2015-01-01

    The development of sleep-wake regulation in infants depends upon brain maturation as well as various environmental factors. The aim of the present study was to evaluate sleep duration and quality as a function of child attachment to the mother. One hundred and thirty-four mother-child dyads enrolled in the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) project were included in this study. Attachment was assessed with the Strange Situation procedure at 36 months and maternal sleep reports were collected at 6, 12, 24 and 36 months. Differences in sleep characteristics were assessed with mixed models with one factor (attachment group) and one repeated measure (age). Children classified as disorganized had a significantly lower duration of nocturnal sleep, went to bed later, signaled more awakenings, had shorter periods of uninterrupted sleep (only at 12 months) and had shorter periods of time in bed (only at 6 months) than children classified as secure and/or ambivalent (p < 0.05). This is the first study to show that children with insecure disorganized attachment present a distinct sleep pattern in comparison with those with secure or ambivalent attachment between 6 and 36 months of age. Sleep disturbances could exacerbate difficulties in these families that are already considered vulnerable. PMID:25231054