S-Adenosylmethionine Attenuates Oxidative Stress and Neuroinflammation Induced by Amyloid-β Through Modulation of Glutathione Metabolism.

PubMed

Li, Qian; Cui, Jing; Fang, Chen; Liu, Min; Min, Guowen; Li, Liang

2017-01-01

Oxidative stress and neuroinflammation are mainly involved in the pathogenic mechanisms of Alzheimer's disease (AD). Amyloid-β (Aβ), the main component of senile plaques, is a kind of strong inducer of oxidative stress. Glutathione is an endogenous antioxidant protecting cells from oxidative injury. S-adenosylmethionine (SAM) produced in the methionine cycle is the primary methyl donor and the precursor of glutathione. In this study, the Aβ intrahippocampal injection rat model and cultured SH-SY5Y cells were used to explore the neuroprotective effect of SAM. We found that SAM could protect cells against Aβ-induced cellular injury by inhibition of oxidative stress and neuroinflammation. SAM administration could increase the endogenous antioxidant glutathione and potentiate the antioxidant enzymes activities. SAM might act as an antioxidant and be a potential candidate therapy for AD patients.

Sensitivity of Antarctic sea ice to the Southern Annular Mode in coupled climate models

NASA Astrophysics Data System (ADS)

Holland, Marika M.; Landrum, Laura; Kostov, Yavor; Marshall, John

2017-09-01

We assess the sea ice response to Southern Annular Mode (SAM) anomalies for pre-industrial control simulations from the Coupled Model Intercomparison Project (CMIP5). Consistent with work by Ferreira et al. (J Clim 28:1206-1226, 2015. doi: 10.1175/JCLI-D-14-00313.1), the models generally simulate a two-timescale response to positive SAM anomalies, with an initial increase in ice followed by an eventual sea ice decline. However, the models differ in the cross-over time at which the change in ice response occurs, in the overall magnitude of the response, and in the spatial distribution of the response. Late twentieth century Antarctic sea ice trends in CMIP5 simulations are related in part to different modeled responses to SAM variability acting on different time-varying transient SAM conditions. This explains a significant fraction of the spread in simulated late twentieth century southern hemisphere sea ice extent trends across the model simulations. Applying the modeled sea ice response to SAM variability but driven by the observed record of SAM suggests that variations in the austral summer SAM, which has exhibited a significant positive trend, have driven a modest sea ice decrease. However, additional work is needed to narrow the considerable model uncertainty in the climate response to SAM variability and its implications for 20th-21st century trends.

Progress Report on SAM Reduced-Order Model Development for Thermal Stratification and Mixing during Reactor Transients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, R.

This report documents the initial progress on the reduced-order flow model developments in SAM for thermal stratification and mixing modeling. Two different modeling approaches are pursued. The first one is based on one-dimensional fluid equations with additional terms accounting for the thermal mixing from both flow circulations and turbulent mixing. The second approach is based on three-dimensional coarse-grid CFD approach, in which the full three-dimensional fluid conservation equations are modeled with closure models to account for the effects of turbulence.

SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches.

PubMed

Mirihana Arachchilage, Gayan; Sherlock, Madeline E; Weinberg, Zasha; Breaker, Ronald R

2018-03-04

Five distinct riboswitch classes that regulate gene expression in response to the cofactor S-adenosylmethionine (SAM) or its metabolic breakdown product S-adenosylhomocysteine (SAH) have been reported previously. Collectively, these SAM- or SAH-sensing RNAs constitute the most abundant collection of riboswitches, and are found in nearly every major bacterial lineage. Here, we report a potential sixth member of this pervasive riboswitch family, called SAM-VI, which is predominantly found in Bifidobacterium species. SAM-VI aptamers selectively bind the cofactor SAM and strongly discriminate against SAH. The consensus sequence and structural model for SAM-VI share some features with the consensus model for the SAM-III riboswitch class, whose members are mainly found in lactic acid bacteria. However, there are sufficient differences between the two classes such that current bioinformatics methods separately cluster representatives of the two motifs. These findings highlight the abundance of RNA structures that can form to selectively recognize SAM, and showcase the ability of RNA to utilize diverse strategies to perform similar biological functions.

Differences in reporting of perceived acute effects of alcohol use, marijuana use, and simultaneous alcohol and marijuana use.

PubMed

Lee, Christine M; Cadigan, Jennifer M; Patrick, Megan E

2017-11-01

Although there are serious negative harms associated with simultaneous alcohol and marijuana (SAM) use, little is known about the self-reported acute effects of SAM use and how they may be similar to or different than effects experienced when using alcohol or marijuana only. The current study examines the perceived acute effects of SAM use, compared to using alcohol or marijuana only, as well as demographic and substance use predictors of overall SAM effects. Participants were a community sample of young adults ages 18-23 participating in a longitudinal study on social role transitions and substance use during young adulthood. Young adults who reported SAM use at least once in their lifetime were selected for the present analyses (N=315; mean age=21.42; 58% female) and reported the effects they experienced from typical alcohol use, marijuana use, and SAM use. There were significant differences in the extent to which young adults perceived the effects depending on the substances used. Most effects (i.e., clumsy, confused, dizzy, difficulty concentrating) were rated strongest when engaging in SAM use, compared to typical alcohol or marijuana use alone. Feeling high and feeling marijuana effects were rated strongest when engaging in marijuana use alone compared to SAM use, but feeling drunk was greater during SAM use compared to alcohol use alone. Greater alcohol use and increased time spent high during typical SAM use were associated with greater overall SAM effects. When young adults engage in SAM use they report experiencing greater negative physiological and cognitive effects. Copyright © 2017 Elsevier B.V. All rights reserved.

Non-invasive vibrational SFG spectroscopy reveals that bacterial adhesion can alter the conformation of grafted "brush" chains on SAM.

PubMed

Bulard, Emilie; Guo, Ziang; Zheng, Wanquan; Dubost, Henri; Fontaine-Aupart, Marie-Pierre; Bellon-Fontaine, Marie-Noëlle; Herry, Jean-Marie; Briandet, Romain; Bourguignon, Bernard

2011-04-19

Understanding bacterial adhesion on a surface is a crucial step to design new materials with improved properties or to control biofilm formation and eradication. Sum Frequency Generation (SFG) vibrational spectroscopy has been employed to study in situ the conformational response of a self-assembled monolayer (SAM) of octadecanethiol (ODT) on a gold film to the adhesion of hydrophilic and hydrophobic ovococcoid model bacteria. The present work highlights vibrational SFG spectroscopy as a powerful and unique non-invasive biophysical technique to probe and control bacteria interaction with ordered surfaces. Indeed, the SFG vibrational spectral changes reveal different ODT SAM conformations in air and upon exposure to aqueous solution or bacterial adhesion. Furthermore, this effect depends on the bacterial cell surface properties. The SFG spectral modeling demonstrates that hydrophobic bacteria flatten the ODT SAM alkyl chain terminal part, whereas the hydrophilic ones raise this ODT SAM terminal part. Microorganism-induced alteration of grafted chains can thus affect the desired interfacial functionality, a result that should be considered for the design of new reactive materials. © 2011 American Chemical Society

Effect of functional end groups of silane self assembled monolayer surfaces on apatite formation, fibronectin adsorption and osteoblast cell function

PubMed Central

Toworfe, G.K.; Bhattacharyya, S.; Composto, R.J.; Adams, C.S.; Shapiro, I.M.; Ducheyne, P.

2008-01-01

Bioactive glass (BG) can directly bond to living bone without fibrous tissue encapsulation. Key mechanistic steps of BG’s activity are attributed to calcium phosphate formation, surface hydroxylation and fibronectin (FN) adsorption. In the present study, self-assembled monolayers (SAMs) of alkanesilanes with different surface chemistry (OH, NH2, and COOH) were used as a model system to mimic BG’s surface activity. Calcium phosphate (Ca-P) was formed on SAMs by immersion in a solution which simulates the electrolyte content of physiological fluids. FN adsorption kinetics and monolayer coverage was determined on SAMs with or without Ca-P coating. The surface roughness was also examined on these substrates before and after FN adsorption. The effects of FN-adsorbed, Ca-P coated SAMs on the function of MC3T3-E1 were evaluated by cell growth, expression of alkaline phosphatase activity, and actin cytoskeleton formation. We demonstrate that, although the FN monolayer coverage and the rms roughness are similar on −OH and −COOH terminated SAMs with or without Ca-P coating, higher levels of ALP activity, more actin cytoskeleton formation and more cell growth are obtained on −OH and −COOH terminated SAMs with Ca-P coating. In addition, although the FN monolayer coverage is higher on Ca-P coated −NH2 terminated SAMs and SiOx surfaces, higher levels of ALP activity and more cell growth are obtained on Ca-P coated −OH and −COOH terminated SAMs. Thus with same Ca-P coatings, different surface functional groups have different effects on the function of osteoblastic cells. These findings represent new insights into the mechanism of bioactivity of BG and, thereby, may lead to designing superior constructs for bone grafting. PMID:19012271

Reaction-diffusion pattern in shoot apical meristem of plants.

PubMed

Fujita, Hironori; Toyokura, Koichi; Okada, Kiyotaka; Kawaguchi, Masayoshi

2011-03-29

A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants.

Reaction-Diffusion Pattern in Shoot Apical Meristem of Plants

PubMed Central

Fujita, Hironori; Toyokura, Koichi; Okada, Kiyotaka; Kawaguchi, Masayoshi

2011-01-01

A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants. PMID:21479227

Recent Updates to the System Advisor Model (SAM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiOrio, Nicholas A

The System Advisor Model (SAM) is a mature suite of techno-economic models for many renewable energy technologies that can be downloaded for free as a desktop application or software development kit. SAM is used for system-level modeling, including generating performance pro the release of the code as an open source project on GitHub. Other additions that will be covered include the ability to download data directly into SAM from the National Solar Radiation Database (NSRDB) and up- dates to a user-interface macro that assists with PV system sizing. A brief update on SAM's battery model and its integration with themore » detailed photovoltaic model will also be discussed. Finally, an outline of planned work for the next year will be presented, including the addition of a bifacial model, support for multiple MPPT inputs for detailed inverter modeling, and the addition of a model for inverter thermal behavior.« less

Combining Fast-Walking Training and a Step Activity Monitoring Program to Improve Daily Walking Activity After Stroke: A Preliminary Study.

PubMed

Danks, Kelly A; Pohlig, Ryan; Reisman, Darcy S

2016-09-01

To determine preliminary efficacy and to identify baseline characteristics predicting who would benefit most from fast walking training plus a step activity monitoring program (FAST+SAM) compared with fast walking training (FAST) alone in persons with chronic stroke. Randomized controlled trial with blinded assessors. Outpatient clinical research laboratory. Individuals (N=37) >6 months poststroke. Subjects were assigned to either FAST, which was walking training at their fastest possible speed on the treadmill (30min) and overground 3 times per week for 12 weeks, or FAST+SAM. The step activity monitoring program consisted of daily step monitoring with an activity monitor, goal setting, and identification of barriers to activity and strategies to overcome barriers. Daily step activity metrics (steps/day [SPD], time walking per day), walking speed, and 6-minute walk test (6MWT) distance. There was a significant effect of time for both groups, with all outcomes improving from pre- to posttraining (all P values <.05). The FAST+SAM was superior to FAST for 6MWT (P=.018), with a larger increase in the FAST+SAM group. The interventions had differential effectiveness based on baseline step activity. Sequential moderated regression models demonstrated that for subjects with baseline levels of step activity and 6MWT distances that were below the mean, the FAST+SAM intervention was more effective than FAST (1715±1584 vs 254±933 SPD; P<.05 for overall model and ΔR(2) for SPD and 6MWT). The addition of a step activity monitoring program to a fast walking training intervention may be most effective in persons with chronic stroke who have initial low levels of walking endurance and activity. Regardless of baseline performance, the FAST+SAM intervention was more effective for improving walking endurance. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Combining fast walking training and a step activity monitoring program to improve daily walking activity after stroke: a preliminary study

PubMed Central

Danks, Kelly A.; Pohlig, Ryan; Reisman, Darcy S.

2016-01-01

Objective To determine preliminary efficacy and to identify baseline characteristics predicting who would benefit most from fast walking training plus a step activity monitoring program (FAST+SAM) compared to fast walking training alone (FAST) in persons with chronic stroke. Design Randomized controlled trial with blinded assessors Setting Outpatient clinical research laboratory Participants 37 individuals greater than 6 months post-stroke. Interventions Subjects were assigned to either FAST which was walking training at their fastest possible speed on the treadmill (30 minutes) and over ground 3 times/week for 12 weeks or FAST plus a step activity monitoring program (FAST+SAM). The step activity monitoring program consisted of daily step monitoring with a StepWatch Activity monitor, goal setting, and identification of barriers to activity and strategies to overcome barriers. Main Outcome Measures Daily step activity metrics (steps/day, time walking/day), walking speed and six minute walk test distance (6MWT). Results There was a significant effect of time for both groups with all outcomes improving from pre to post-training, (all p<0.05). The FAST+SAM was superior to FAST for 6MWT (p=0.018), with a larger increase in the FAST+SAM group. The interventions had differential effectiveness based on baseline step activity. Sequential moderated regression models demonstrated that for subjects with baseline levels of step activity and 6MWT distances that were below the mean, the FAST+SAM intervention was more effective than FAST (1715±1584 vs. 254±933 steps/day, respectively; p<0.05 for overall model and ΔR2 for steps/day and 6MWT). Conclusions The addition of a step activity monitoring program to a fast walking training intervention may be most effective in persons with chronic stroke that have initial low levels of walking endurance and activity. Regardless of baseline performance, the FAST + SAM intervention was more effective for improving walking endurance. PMID:27240430

Trapping effect of metal nanoparticle mono- and multilayer in the organic field-effect transistor

NASA Astrophysics Data System (ADS)

Lee, Keanchuan; Weis, Martin; Lin, Jack; Taguchi, Dai; Majková, Eva; Manaka, Takaaki; Iwamoto, Mitsumasa

2011-03-01

The effect of silver nanoparticles self-assembled monolayer (Ag NPs SAM) on charge transport in pentacene organic field-effect transistors (OFET) was investigated by both steady-state and transient-state methods, which are current-voltage measurements in steady-state and time-resolved microscopic (TRM) second harmonic generation (SHG) in transient-state, respectively. The analysis of electronic properties revealed that OFET with SAM exhibited significant charge trapping effect due to the space-charge field formed by immobile charges. Lower transient-state mobility was verified by the direct probing of carrier motion by TRM-SHG technique. It was shown that the trapping effect rises together with increase of SAM layers suggesting the presence of traps in the bulk of NP films. The model based on the electrostatic charge barrier is suggested to explain the phenomenon.

Methyl donor S-adenosylmethionine (SAM) supplementation attenuates breast cancer growth, invasion, and metastasis in vivo; therapeutic and chemopreventive applications

PubMed Central

Mahmood, Niaz; Cheishvili, David; Arakelian, Ani; Tanvir, Imrana; Khan, Haseeb Ahmed; Pépin, Anne-Sophie; Szyf, Moshe; Rabbani, Shafaat A.

2018-01-01

DNA hypomethylation coordinately targets various signaling pathways involved in tumor growth and metastasis. At present, there are no approved therapeutic modalities that target hypomethylation. In this regard, we examined the therapeutic plausibility of using universal methyl group donor S-adenosylmethionine (SAM) to block breast cancer development, growth, and metastasis through a series of studies in vitro using two different human breast cancer cell lines (MDA-MB-231 and Hs578T) and in vivo using an MDA-MB-231 xenograft model of breast cancer. We found that SAM treatment caused a significant dose-dependent decrease in cell proliferation, invasion, migration, anchorage-independent growth and increased apoptosis in vitro. These results were recapitulated in vivo where oral administration of SAM reduced tumor volume and metastasis in green fluorescent protein (GFP)-tagged MDA-MB-231 xenograft model. Gene expression analyses validated the ability of SAM to decrease the expression of several key genes implicated in cancer progression and metastasis in both cell lines and breast tumor xenografts. SAM was found to be bioavailable in the serum of experimental animals as determined by enzyme-linked immunosorbent assay and no notable adverse side effects were seen including any change in animal behavior. The results of this study provide compelling evidence to evaluate the therapeutic potential of methylating agents like SAM in patients with breast cancer to reduce cancer-associated morbidity and mortality. PMID:29435170

The SAM framework: modeling the effects of management factors on human behavior in risk analysis.

PubMed

Murphy, D M; Paté-Cornell, M E

1996-08-01

Complex engineered systems, such as nuclear reactors and chemical plants, have the potential for catastrophic failure with disastrous consequences. In recent years, human and management factors have been recognized as frequent root causes of major failures in such systems. However, classical probabilistic risk analysis (PRA) techniques do not account for the underlying causes of these errors because they focus on the physical system and do not explicitly address the link between components' performance and organizational factors. This paper describes a general approach for addressing the human and management causes of system failure, called the SAM (System-Action-Management) framework. Beginning with a quantitative risk model of the physical system, SAM expands the scope of analysis to incorporate first the decisions and actions of individuals that affect the physical system. SAM then links management factors (incentives, training, policies and procedures, selection criteria, etc.) to those decisions and actions. The focus of this paper is on four quantitative models of action that describe this last relationship. These models address the formation of intentions for action and their execution as a function of the organizational environment. Intention formation is described by three alternative models: a rational model, a bounded rationality model, and a rule-based model. The execution of intentions is then modeled separately. These four models are designed to assess the probabilities of individual actions from the perspective of management, thus reflecting the uncertainties inherent to human behavior. The SAM framework is illustrated for a hypothetical case of hazardous materials transportation. This framework can be used as a tool to increase the safety and reliability of complex technical systems by modifying the organization, rather than, or in addition to, re-designing the physical system.

Carbon tax effects on the poor: a SAM-based approach

NASA Astrophysics Data System (ADS)

Chapa, Joana; Ortega, Araceli

2017-09-01

A SAM-based price model for Mexico is developed in order to assess the effects of the carbon tax, which was part of the fiscal reform approved in 2014. The model is formulated based on a social accounting matrix (SAM) that distinguishes households by the official poverty condition and geographical area. The main results are that the sector that includes coke, refined petroleum and nuclear fuel shows the highest price increase due to the direct impact of the carbon tax; in addition, air transport and inland transport are the most affected sectors, in an indirect manner, because both employ inputs from the former sector. Also, it is found that welfare diminishes more in the rural strata than in the urban one. In the urban area, the carbon tax is regressive: the negative impact of carbon tax on family welfare is greater on the poorest families.

Analytical techniques for retrieval of atmospheric composition with the quadrupole mass spectrometer of the Sample Analysis at Mars instrument suite on Mars Science Laboratory

NASA Astrophysics Data System (ADS)

B. Franz, Heather; G. Trainer, Melissa; H. Wong, Michael; L. K. Manning, Heidi; C. Stern, Jennifer; R. Mahaffy, Paul; K. Atreya, Sushil; Benna, Mehdi; G. Conrad, Pamela; N. Harpold, Dan; A. Leshin, Laurie; A. Malespin, Charles; P. McKay, Christopher; Thomas Nolan, J.; Raaen, Eric

2014-06-01

The Sample Analysis at Mars (SAM) instrument suite is the largest scientific payload on the Mars Science Laboratory (MSL) Curiosity rover, which landed in Mars' Gale Crater in August 2012. As a miniature geochemical laboratory, SAM is well-equipped to address multiple aspects of MSL's primary science goal, characterizing the potential past or present habitability of Gale Crater. Atmospheric measurements support this goal through compositional investigations relevant to martian climate evolution. SAM instruments include a quadrupole mass spectrometer, a tunable laser spectrometer, and a gas chromatograph that are used to analyze martian atmospheric gases as well as volatiles released by pyrolysis of solid surface materials (Mahaffy et al., 2012). This report presents analytical methods for retrieving the chemical and isotopic composition of Mars' atmosphere from measurements obtained with SAM's quadrupole mass spectrometer. It provides empirical calibration constants for computing volume mixing ratios of the most abundant atmospheric species and analytical functions to correct for instrument artifacts and to characterize measurement uncertainties. Finally, we discuss differences in volume mixing ratios of the martian atmosphere as determined by SAM (Mahaffy et al., 2013) and Viking (Owen et al., 1977; Oyama and Berdahl, 1977) from an analytical perspective. Although the focus of this paper is atmospheric observations, much of the material concerning corrections for instrumental effects also applies to reduction of data acquired with SAM from analysis of solid samples. The Sample Analysis at Mars (SAM) instrument measures the composition of the martian atmosphere. Rigorous calibration of SAM's mass spectrometer was performed with relevant gas mixtures. Calibration included derivation of a new model to correct for electron multiplier effects. Volume mixing ratios for Ar and N2 obtained with SAM differ from those obtained with Viking. Differences between SAM and Viking volume mixing ratios are under investigation.

SAM Works! A Systems Approach Model for Adult Education Programming.

ERIC Educational Resources Information Center

Murk, Peter J.; Wells, John H.

The Systems Approach Model (SAM) is a dynamic approach to planning adult and continuing education that is intended to provide the flexibility, creativity, and meaningfulness necessary to meet the needs and interests of an ever-expanding and ever-aging student population. The SAM model consists of the following dynamically interrelated and…

Integration, Validation, and Application of a PV Snow Coverage Model in SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, Janine M.; Ryberg, David Severin

2017-08-01

Due to the increasing deployment of PV systems in snowy climates, there is significant interest in a method capable of estimating PV losses resulting from snow coverage that has been verified for a variety of system designs and locations. Many independent snow coverage models have been developed over the last 15 years; however, there has been very little effort verifying these models beyond the system designs and locations on which they were based. Moreover, major PV modeling software products have not yet incorporated any of these models into their workflows. In response to this deficiency, we have integrated the methodologymore » of the snow model developed in the paper by Marion et al. (2013) into the National Renewable Energy Laboratory's (NREL) System Advisor Model (SAM). In this work, we describe how the snow model is implemented in SAM and we discuss our demonstration of the model's effectiveness at reducing error in annual estimations for three PV arrays. Next, we use this new functionality in conjunction with a long term historical data set to estimate average snow losses across the United States for two typical PV system designs. The open availability of the snow loss estimation capability in SAM to the PV modeling community, coupled with our results of the nationwide study, will better equip the industry to accurately estimate PV energy production in areas affected by snowfall.« less

High performance computation of landscape genomic models including local indicators of spatial association.

PubMed

Stucki, S; Orozco-terWengel, P; Forester, B R; Duruz, S; Colli, L; Masembe, C; Negrini, R; Landguth, E; Jones, M R; Bruford, M W; Taberlet, P; Joost, S

2017-09-01

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an F ST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Teleconnection stationarity, variability and trends of the Southern Annular Mode (SAM) during the last millennium

NASA Astrophysics Data System (ADS)

Dätwyler, Christoph; Neukom, Raphael; Abram, Nerilie J.; Gallant, Ailie J. E.; Grosjean, Martin; Jacques-Coper, Martín; Karoly, David J.; Villalba, Ricardo

2017-11-01

The Southern Annular Mode (SAM) is the leading mode of atmospheric interannual variability in the Southern Hemisphere (SH) extra-tropics. Here, we assess the stationarity of SAM spatial correlations with instrumental and paleoclimate proxy data for the past millennium. The instrumental period shows that temporal non-stationarities in SAM teleconnections are not consistent across the SH land areas. This suggests that the influence of the SAM index is modulated by regional effects. However, within key-regions with good proxy data coverage (South America, Tasmania, New Zealand), teleconnections are mostly stationary over the instrumental period. Using different stationarity criteria for proxy record selection, we provide new austral summer and annual mean SAM index reconstructions over the last millennium. Our summer SAM reconstructions are very robust to changes in proxy record selection and the selection of the calibration period, particularly on the multi-decadal timescale. In contrast, the weaker performance and lower agreement in the annual mean SAM reconstructions point towards changing teleconnection patterns that may be particularly important outside the summer months. Our results clearly portend that the temporal stationarity of the proxy-climate relationships should be taken into account in the design of comprehensive regional and hemispherical climate reconstructions. The summer SAM reconstructions show no significant relationship to solar, greenhouse gas and volcanic forcing, with the exception of an extremely strong negative anomaly following the AD 1257 Samalas eruption. Furthermore, reconstructed pre-industrial summer SAM trends are very similar to trends obtained by model control simulations. We find that recent trends in the summer SAM lie outside the 5-95% range of pre-industrial natural variability.

Defects in subventricular zone pigmented epithelium-derived factor niche signaling in the senescence-accelerated mouse prone-8.

PubMed

Castro-Garcia, Paola; Díaz-Moreno, María; Gil-Gas, Carmen; Fernández-Gómez, Francisco J; Honrubia-Gómez, Paloma; Álvarez-Simón, Carmen Belén; Sánchez-Sánchez, Francisco; Cano, Juan Carlos Castillo; Almeida, Francisco; Blanco, Vicente; Jordán, Joaquín; Mira, Helena; Ramírez-Castillejo, Carmen

2015-04-01

We studied potential changes in the subventricular zone (SVZ) stem cell niche of the senescence-accelerated mouse prone-8 (SAM-P8) aging model. Bromodeoxyuridine (BrdU) assays with longtime survival revealed a lower number of label-retaining stem cells in the SAM-P8 SVZ compared with the SAM-Resistant 1 (SAM-R1) control strain. We also found that in SAM-P8 niche signaling is attenuated and the stem cell pool is less responsive to the self-renewal niche factor pigmented epithelium-derived factor (PEDF). Protein analysis demonstrated stable amounts of the PEDF ligand in the SAM-P8 SVZ niche; however, SAM-P8 stem cells present a significant expression decrease of patatin-like phospholipase domain containing 2, a receptor for PEDF (PNPLA2-PEDF) receptor, but not of laminin receptor (LR), a receptor for PEDF (LR-PEDF) receptor. We observed changes in self-renewal related genes (hairy and enhancer of split 1 (Hes1), hairy and enhancer of split 1 (Hes5), Sox2] and report that although these genes are down-regulated in SAM-P8, differentiation genes (Pax6) are up-regulated and neurogenesis is increased. Finally, sheltering mammalian telomere complexes might be also involved given a down-regulation of telomeric repeat binding factor 1 (Terf1) expression was observed in SAM-P8 at young age periods. Differences between these 2 models, SAM-P8 and SAM-R1 controls, have been previously detected at more advanced ages. We now describe alterations in the PEDF signaling pathway and stem cell self-renewal at a very young age, which could be involved in the premature senescence observed in the SAM-P8 model. © FASEB.

Inhibition of angiogenesis by S-adenosylmethionine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahin, Mehmet, E-mail: msahin@akdeniz.edu.tr; Sahin, Emel; Guemueslue, Saadet

2011-04-29

Highlights: {yields} Effects of S-adenosylmethionine (SAM) were investigated in endothelial cells. {yields} Our results showed that SAM decreased proliferation of endothelial cells. {yields} SAM influentially inhibited the percentage of cell migration. {yields} SAM probably stopped migration as independent from its effects on proliferation. {yields} SAM was shown to suppress in vitro angiogenesis. -- Abstract: Metastasis is a leading cause of mortality and morbidity in cancer. One of the steps in metastasis process is the formation of new blood vessels. Aberrant DNA methylation patterns are common in cancer cells. In recent studies, S-adenosylmethionine (SAM), which is a DNA methylating agent, hasmore » been found to have inhibitory effects on some carcinoma cells in vivo and in vitro. In the present study, we have used SAM to investigate whether it is effective against angiogenesis in vitro. Our results have shown that SAM can reduce the formation and organization of capillary-like structures of endothelial cells in tumoral environment. Besides, we have found SAM can block endothelial cell proliferation and the migration of cells towards growth factors-rich media. In conclusion, our study suggests that SAM may be used against angiogenesis as a natural bio-product.« less

Integrated Space Asset Management Database and Modeling

NASA Technical Reports Server (NTRS)

MacLeod, Todd; Gagliano, Larry; Percy, Thomas; Mason, Shane

2015-01-01

Effective Space Asset Management is one key to addressing the ever-growing issue of space congestion. It is imperative that agencies around the world have access to data regarding the numerous active assets and pieces of space junk currently tracked in orbit around the Earth. At the center of this issues is the effective management of data of many types related to orbiting objects. As the population of tracked objects grows, so too should the data management structure used to catalog technical specifications, orbital information, and metadata related to those populations. Marshall Space Flight Center's Space Asset Management Database (SAM-D) was implemented in order to effectively catalog a broad set of data related to known objects in space by ingesting information from a variety of database and processing that data into useful technical information. Using the universal NORAD number as a unique identifier, the SAM-D processes two-line element data into orbital characteristics and cross-references this technical data with metadata related to functional status, country of ownership, and application category. The SAM-D began as an Excel spreadsheet and was later upgraded to an Access database. While SAM-D performs its task very well, it is limited by its current platform and is not available outside of the local user base. Further, while modeling and simulation can be powerful tools to exploit the information contained in SAM-D, the current system does not allow proper integration options for combining the data with both legacy and new M&S tools. This paper provides a summary of SAM-D development efforts to date and outlines a proposed data management infrastructure that extends SAM-D to support the larger data sets to be generated. A service-oriented architecture model using an information sharing platform named SIMON will allow it to easily expand to incorporate new capabilities, including advanced analytics, M&S tools, fusion techniques and user interface for visualizations. In addition, tight control of information sharing policy will increase confidence in the system, which would encourage industry partners to provide commercial data. Combined with the integration of new and legacy M&S tools, a SIMON-based architecture will provide a robust environment that can be extended and expanded indefinitely.

Hydrodynamical simulations and semi-analytic models of galaxy formation: two sides of the same coin

NASA Astrophysics Data System (ADS)

Neistein, Eyal; Khochfar, Sadegh; Dalla Vecchia, Claudio; Schaye, Joop

2012-04-01

In this work we develop a new method to turn a state-of-the-art hydrodynamical cosmological simulation of galaxy formation (HYD) into a simple semi-analytic model (SAM). This is achieved by summarizing the efficiencies of accretion, cooling, star formation and feedback given by the HYD, as functions of the halo mass and redshift. The SAM then uses these functions to evolve galaxies within merger trees that are extracted from the same HYD. Surprisingly, by turning the HYD into a SAM, we conserve the mass of individual galaxies, with deviations at the level of 0.1 dex, on an object-by-object basis, with no significant systematics. This is true for all redshifts, and for the mass of stars and gas components, although the agreement reaches 0.2 dex for satellite galaxies at low redshift. We show that the same level of accuracy is obtained even in case the SAM uses only one phase of gas within each galaxy. Moreover, we demonstrate that the formation history of one massive galaxy provides sufficient information for the SAM to reproduce the population of galaxies within the entire cosmological box. The reasons for the small scatter between the HYD and SAM galaxies are as follows. (i) The efficiencies are matched as functions of the halo mass and redshift, meaning that the evolution within merger trees agrees on average. (ii) For a given galaxy, efficiencies fluctuate around the mean value on time-scales of 0.2-2 Gyr. (iii) The various mass components of galaxies are obtained by integrating the efficiencies over time, averaging out these fluctuations. We compare the efficiencies found here to standard SAM recipes and find that they often deviate significantly. For example, here the HYD shows smooth accretion that is less effective for low-mass haloes, and is always composed of hot or dilute gas; cooling is less effective at high redshift, and star formation changes only mildly with cosmic time. The method developed here can be applied in general to any HYD, and can thus serve as a common language for both HYDs and SAMs.

Reference Manual for the System Advisor Model's Wind Power Performance Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, J.; Jorgenson, J.; Gilman, P.

2014-08-01

This manual describes the National Renewable Energy Laboratory's System Advisor Model (SAM) wind power performance model. The model calculates the hourly electrical output of a single wind turbine or of a wind farm. The wind power performance model requires information about the wind resource, wind turbine specifications, wind farm layout (if applicable), and costs. In SAM, the performance model can be coupled to one of the financial models to calculate economic metrics for residential, commercial, or utility-scale wind projects. This manual describes the algorithms used by the wind power performance model, which is available in the SAM user interface andmore » as part of the SAM Simulation Core (SSC) library, and is intended to supplement the user documentation that comes with the software.« less

Effect of S-adenosyl-L-methionine (SAM), an allosteric activator of cystathionine-β-synthase (CBS) on colorectal cancer cell proliferation and bioenergetics in vitro.

PubMed

Módis, Katalin; Coletta, Ciro; Asimakopoulou, Antonia; Szczesny, Bartosz; Chao, Celia; Papapetropoulos, Andreas; Hellmich, Mark R; Szabo, Csaba

2014-09-15

Recent data show that colon cancer cells selectively overexpress cystathionine-β-synthase (CBS), which produces hydrogen sulfide (H2S), to maintain cellular bioenergetics, support tumor growth and stimulate angiogenesis and vasorelaxation in the tumor microenvironment. The purpose of the current study was to investigate the effect of the allosteric CBS activator S-adenosyl-L-methionine (SAM) on the proliferation and bioenergetics of the CBS-expressing colon cancer cell line HCT116. The non-transformed, non-tumorigenic colon epithelial cell line NCM356 was used as control. For assessment of cell proliferation, the xCELLigence system was used. Bioenergetic function was measured by Extracellular Flux Analysis. Experiments using human recombinant CBS or HCT116 homogenates complemented the cell-based studies. SAM markedly enhanced CBS-mediated H2S production in vitro, especially when a combination of cysteine and homocysteine was used as substrates. Addition of SAM (0.1-3 mM) to HCT116 cells induced a concentration-dependent increase H2S production. SAM exerted time- and concentration-dependent modulatory effects on cell proliferation. At 0.1-1 mM SAM increased HCT116 proliferation between 0 and 12 h, while the highest SAM concentration (3 mM) inhibited proliferation. Over a longer time period (12-24 h), only the lowest concentration of SAM used (0.1 mM) stimulated cell proliferation; higher SAM concentrations produced a concentration-dependent inhibition. The short-term stimulatory effects of SAM were attenuated by the CBS inhibitor aminooxyacetic acid (AOAA) or by stable silencing of CBS. In contrast, the inhibitory effects of SAM on cell proliferation was unaffected by CBS inhibition or CBS silencing. In contrast to HCT116 cells, the lower rate of proliferation of the low-CBS expressor NCM356 cells was unaffected by SAM. Short-term (1 h) exposure of HCT116 cells to SAM induced a concentration-dependent increase in oxygen consumption and bioenergetic function at 0.1-1 mM, while 3 mM was inhibitory. Longer-term (72 h) exposure of HCT116 cells to all concentrations of SAM tested suppressed mitochondrial oxygen consumption rate, cellular ATP content and cell viability. The stimulatory effect of SAM on bioenergetics was attenuated in cells with stable CBS silencing, while the inhibitory effects were unaffected. In NCM356 cells SAM exerted smaller effects on cellular bioenergetics than in HCT116 cells. We have also observed a downregulation of CBS in response to prolonged exposure of SAM both in HCT116 and NCM356 cells. Taken together, the results demonstrate that H2S production in HCT116 cells is stimulated by the allosteric CBS activator, SAM. At low-to intermediate levels and early time periods the resulting H2S serves as an endogenous cancer cell growth and bioenergetic factor. In contrast, the inhibition of cell proliferation and bioenergetic function by SAM does not appear to relate to adverse autocrine effects of H2S resulting from CBS over-stimulation but, rather to CBS-independent pharmacological effects. Copyright © 2014 Elsevier Inc. All rights reserved.

Study of gain and photoresponse characteristics for back-illuminated separate absorption and multiplication GaN avalanche photodiodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiaodong; Pan, Ming; Hou, Liwei

2014-01-07

The gain and photoresponse characteristics have been numerically studied for back-illuminated separate absorption and multiplication (SAM) GaN avalanche photodiodes (APDs). The parameters of fundamental models are calibrated by simultaneously comparing the simulated dark and light current characteristics with the experimental results. Effects of environmental temperatures and device dimensions on gain characteristics have been investigated, and a method to achieve the optimum thickness of charge layer is obtained. The dependence of gain characteristics and breakdown voltage on the doping concentration of the charge layer is also studied in detail to get the optimal charge layer. The bias-dependent spectral responsivity and quantummore » efficiency are then presented to study the photoresponse mechanisms inside SAM GaN APDs. It is found the responsivity peak red-shifts at first due to the Franz-Keldysh effect and then blue-shifts due to the reach-through effect of the absorption layer. Finally, a new SAM GaN/AlGaN heterojunction APD structure is proposed for optimizing SAM GaN APDs.« less

Is a top-heavy initial mass function needed to reproduce the submillimetre galaxy number counts?

NASA Astrophysics Data System (ADS)

Safarzadeh, Mohammadtaher; Lu, Yu; Hayward, Christopher C.

2017-12-01

Matching the number counts and redshift distribution of submillimetre galaxies (SMGs) without invoking modifications to the initial mass ffunction (IMF) has proved challenging for semi-analytic models (SAMs) of galaxy formation. We adopt a previously developed SAM that is constrained to match the z = 0 galaxy stellar mass function and makes various predictions which agree well with observational constraints; we do not recalibrate the SAM for this work. We implement three prescriptions to predict the submillimetre flux densities of the model galaxies; two depend solely on star formation rate, whereas the other also depends on the dust mass. By comparing the predictions of the models, we find that taking into account the dust mass, which affects the dust temperature and thus influences the far-infrared spectral energy distribution, is crucial for matching the number counts and redshift distribution of SMGs. Moreover, despite using a standard IMF, our model can match the observed SMG number counts and redshift distribution reasonably well, which contradicts the conclusions of some previous studies that a top-heavy IMF, in addition to taking into account the effect of dust mass, is needed to match these observations. Although we have not identified the key ingredient that is responsible for our model matching the observed SMG number counts and redshift distribution without IMF variation - which is challenging given the different prescriptions for physical processes employed in the SAMs of interest - our results demonstrate that in SAMs, IMF variation is degenerate with other physical processes, such as stellar feedback.

Structural insights into SAM domain-mediated tankyrase oligomerization.

PubMed

DaRosa, Paul A; Ovchinnikov, Sergey; Xu, Wenqing; Klevit, Rachel E

2016-09-01

Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP-ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain-mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head-to-tail polymer that facilitates TNKS self-association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM-TNKS2 SAM) hetero-oligomeric structures mediated by their SAM domains. Though wild-type tankyrase proteins have very low solubility, model-based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP-ribosyl)ation (PARylation) and PARylation-dependent ubiquitylation. © 2016 The Protein Society.

Integration, Validation, and Application of a PV Snow Coverage Model in SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryberg, David; Freeman, Janine

2015-09-01

Due to the increasing deployment of PV systems in snowy climates, there is significant interest in a method capable of estimating PV losses resulting from snow coverage that has been verified for a wide variety of system designs and locations. A scattering of independent snow coverage models have been developed over the last 15 years; however, there has been very little effort spent on verifying these models beyond the system design and location on which they were based. Moreover, none of the major PV modeling software products have incorporated any of these models into their workflow. In response to thismore » deficiency, we have integrated the methodology of the snow model developed in the paper by Marion et al. [1] into the National Renewable Energy Laboratory's (NREL) System Advisor Model (SAM). In this work we describe how the snow model is implemented in SAM and discuss our demonstration of the model's effectiveness at reducing error in annual estimations for two PV arrays. Following this, we use this new functionality in conjunction with a long term historical dataset to estimate average snow losses across the United States for a typical PV system design. The open availability of the snow loss estimation capability in SAM to the PV modeling community, coupled with our results of the nation-wide study, will better equip the industry to accurately estimate PV energy production in areas affected by snowfall.« less

The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors.

PubMed

Mercurio, Flavia Anna; Di Natale, Concetta; Pirone, Luciano; Iannitti, Roberta; Marasco, Daniela; Pedone, Emilia Maria; Palumbo, Rosanna; Leone, Marilisa

2017-12-12

The lipid phosphatase Ship2 represents a drug discovery target for the treatment of different diseases, including cancer. Its C-terminal sterile alpha motif domain (Ship2-Sam) associates with the Sam domain from the EphA2 receptor (EphA2-Sam). This interaction is expected to mainly induce pro-oncogenic effects in cells therefore, inhibition of the Ship2-Sam/EphA2-Sam complex may represent an innovative route to discover anti-cancer therapeutics. In the present work, we designed and analyzed several peptide sequences encompassing the interaction interface of EphA2-Sam for Ship2-Sam. Peptide conformational analyses and interaction assays with Ship2-Sam conducted through diverse techniques (CD, NMR, SPR and MST), identified a positively charged penta-amino acid native motif in EphA2-Sam, that once repeated three times in tandem, binds Ship2-Sam. NMR experiments show that the peptide targets the negatively charged binding site of Ship2-Sam for EphA2-Sam. Preliminary in vitro cell-based assays indicate that -at 50 µM concentration- it induces necrosis of PC-3 prostate cancer cells with more cytotoxic effect on cancer cells than on normal dermal fibroblasts. This work represents a pioneering study that opens further opportunities for the development of inhibitors of the Ship2-Sam/EphA2-Sam complex for therapeutic applications.

Fast and slow responses of Southern Ocean sea surface temperature to SAM in coupled climate models

NASA Astrophysics Data System (ADS)

Kostov, Yavor; Marshall, John; Hausmann, Ute; Armour, Kyle C.; Ferreira, David; Holland, Marika M.

2017-03-01

We investigate how sea surface temperatures (SSTs) around Antarctica respond to the Southern Annular Mode (SAM) on multiple timescales. To that end we examine the relationship between SAM and SST within unperturbed preindustrial control simulations of coupled general circulation models (GCMs) included in the Climate Modeling Intercomparison Project phase 5 (CMIP5). We develop a technique to extract the response of the Southern Ocean SST (55°S-70°S) to a hypothetical step increase in the SAM index. We demonstrate that in many GCMs, the expected SST step response function is nonmonotonic in time. Following a shift to a positive SAM anomaly, an initial cooling regime can transition into surface warming around Antarctica. However, there are large differences across the CMIP5 ensemble. In some models the step response function never changes sign and cooling persists, while in other GCMs the SST anomaly crosses over from negative to positive values only 3 years after a step increase in the SAM. This intermodel diversity can be related to differences in the models' climatological thermal ocean stratification in the region of seasonal sea ice around Antarctica. Exploiting this relationship, we use observational data for the time-mean meridional and vertical temperature gradients to constrain the real Southern Ocean response to SAM on fast and slow timescales.

S-adenosyl methionine (SAM) attenuates the development of tolerance to analgesic activity of morphine in rats.

PubMed

Katyal, Jatinder; Kumar, Hemant; Joshi, Dinesh; Gupta, Yogendra Kumar

2017-04-03

Development of tolerance to analgesic effect, on chronic administration of morphine, limits its clinical usefulness in pain management. S-adenosyl methionine (SAM) used for arthritis and approved as a supplement in many countries including United States was evaluated for reducing morphine tolerance. Male 'Wistar' rats were used. The analgesic activity was determined using tail flick analgesiometer (Columbus Instruments, USA). Rats given morphine (7mg/kg), intraperitoneally (i.p.), once daily for 5days developed tolerance to analgesic effect. To evaluate the effect of SAM on morphine tolerance, SAM 800mg/kg was administered orally (p.o.), 45min prior to each dose of morphine. The analgesic activity of SAM and opioidergic component in its activity was also evaluated. Co-administration of morphine and SAM reversed morphine tolerance. SAM exhibited analgesic effect after repeated administration which was reversed by naloxone administration. Since safety of SAM on chronic use is documented it can be a good option in morphine tolerance. Role in drug addiction and withdrawal should also be evaluated. Copyright © 2017 Elsevier B.V. All rights reserved.

Folic acid supplementation does not reduce intracellular homocysteine, and may disturb intracellular one-carbon metabolism.

PubMed

Smith, Desirée E C; Hornstra, Jacqueline M; Kok, Robert M; Blom, Henk J; Smulders, Yvo M

2013-08-01

In randomized trails, folic acid (FA) lowered plasma homocysteine, but failed to reduce cardiovascular risk. We hypothesize this is due to a discrepancy between plasma and intracellular effects of FA. In a double-blind trial, 50 volunteers were randomized to received 500 µg FA daily for 8 weeks, or placebo. Plasma and peripheral blood mononuclear cell (PBMC) concentrations of homocysteine, S-adenosylmethionine (SAM), S-adenosylhomocysteine, methionine, cystathionine and 5-methyltetrahydrofolate (bioactive folate) were measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS). PBMCs were used as a cellular model since they display the full spectrum of one-carbon (1C) enzymes and reactions. At baseline, plasma concentrations were a poor reflection of intracellular concentrations for most 1C metabolites, except 5-methyltetrahydrofolate (R=0.33, p=0.02), homocysteine (Hcy) (R=0.35, p=0.01), and cystathionine (R=0.45, p=0.001). FA significantly lowered plasma homocysteine (p=0.00), but failed to lower intracellular homocysteine or change the concentrations of any of the other PBMC 1C metabolites. At baseline, PBMC homocysteine concentrations correlated to PBMC SAM. After FA supplementation, PBMC homocysteine no longer correlated with PBMC SAM, suggesting a loss of SAM's regulatory function. In vitro experiments in lymphoblasts confirmed that at higher folate substrate concentrations, physiological concentrations of SAM no longer effectively inhibit the key regulatory enzyme methylenetetrahydrofolate reductase (MTHFR). FA supplementation does not reduce intracellular concentrations of Hcy or any of its closely related substances. Rather, FA may disturb physiological regulation of intracellular 1C metabolism by interfering with SAM's inhibitory effect on MTHFR activity.

The vesicle protein SAM-4 regulates the processivity of synaptic vesicle transport.

PubMed

Zheng, Qun; Ahlawat, Shikha; Schaefer, Anneliese; Mahoney, Tim; Koushika, Sandhya P; Nonet, Michael L

2014-10-01

Axonal transport of synaptic vesicles (SVs) is a KIF1A/UNC-104 mediated process critical for synapse development and maintenance yet little is known of how SV transport is regulated. Using C. elegans as an in vivo model, we identified SAM-4 as a novel conserved vesicular component regulating SV transport. Processivity, but not velocity, of SV transport was reduced in sam-4 mutants. sam-4 displayed strong genetic interactions with mutations in the cargo binding but not the motor domain of unc-104. Gain-of-function mutations in the unc-104 motor domain, identified in this study, suppress the sam-4 defects by increasing processivity of the SV transport. Genetic analyses suggest that SAM-4, SYD-2/liprin-α and the KIF1A/UNC-104 motor function in the same pathway to regulate SV transport. Our data support a model in which the SV protein SAM-4 regulates the processivity of SV transport.

The Vesicle Protein SAM-4 Regulates the Processivity of Synaptic Vesicle Transport

PubMed Central

Zheng, Qun; Ahlawat, Shikha; Schaefer, Anneliese; Mahoney, Tim; Koushika, Sandhya P.; Nonet, Michael L.

2014-01-01

Axonal transport of synaptic vesicles (SVs) is a KIF1A/UNC-104 mediated process critical for synapse development and maintenance yet little is known of how SV transport is regulated. Using C. elegans as an in vivo model, we identified SAM-4 as a novel conserved vesicular component regulating SV transport. Processivity, but not velocity, of SV transport was reduced in sam-4 mutants. sam-4 displayed strong genetic interactions with mutations in the cargo binding but not the motor domain of unc-104. Gain-of-function mutations in the unc-104 motor domain, identified in this study, suppress the sam-4 defects by increasing processivity of the SV transport. Genetic analyses suggest that SAM-4, SYD-2/liprin-α and the KIF1A/UNC-104 motor function in the same pathway to regulate SV transport. Our data support a model in which the SV protein SAM-4 regulates the processivity of SV transport. PMID:25329901

Evaluating the effectiveness of self-administration of medication (SAM) schemes in the hospital setting: a systematic review of the literature.

PubMed

Richardson, Suzanna J; Brooks, Hannah L; Bramley, George; Coleman, Jamie J

2014-01-01

Self-administration of medicines is believed to increase patients' understanding about their medication and to promote their independence and autonomy in the hospital setting. The effect of inpatient self-administration of medication (SAM) schemes on patients, staff and institutions is currently unclear. To systematically review the literature relating to the effect of SAM schemes on the following outcomes: patient knowledge, patient compliance/medication errors, success in self-administration, patient satisfaction, staff satisfaction, staff workload, and costs. Keyword and text word searches of online databases were performed between January and March 2013. Included articles described and evaluated inpatient SAM schemes. Case studies and anecdotal studies were excluded. 43 papers were included for final analysis. Due to the heterogeneity of results and unclear findings it was not possible to perform a quantitative synthesis of results. Participation in SAM schemes often led to increased knowledge about drugs and drug regimens, but not side effects. However, the effect of SAM schemes on patient compliance/medication errors was inconclusive. Patients and staff were highly satisfied with their involvement in SAM schemes. SAM schemes appear to provide some benefits (e.g. increased patient knowledge), but their effect on other outcomes (e.g. compliance) is unclear. Few studies of high methodological quality using validated outcome measures exist. Inconsistencies in both measuring and reporting outcomes across studies make it challenging to compare results and draw substantive conclusions about the effectiveness of SAM schemes.

SAM Theory Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Rui

The System Analysis Module (SAM) is an advanced and modern system analysis tool being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM development aims for advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability for reactor transient analyses. To facilitate the code development, SAM utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage modern advanced software environments and numerical methods. SAM focuses on modeling advanced reactormore » concepts such as SFRs (sodium fast reactors), LFRs (lead-cooled fast reactors), and FHRs (fluoride-salt-cooled high temperature reactors) or MSRs (molten salt reactors). These advanced concepts are distinguished from light-water reactors in their use of single-phase, low-pressure, high-temperature, and low Prandtl number (sodium and lead) coolants. As a new code development, the initial effort has been focused on modeling and simulation capabilities of heat transfer and single-phase fluid dynamics responses in Sodium-cooled Fast Reactor (SFR) systems. The system-level simulation capabilities of fluid flow and heat transfer in general engineering systems and typical SFRs have been verified and validated. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As the code is still under ongoing development, this SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.« less

Status Report on NEAMS System Analysis Module Development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, R.; Fanning, T. H.; Sumner, T.

2015-12-01

Under the Reactor Product Line (RPL) of DOE-NE’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, an advanced SFR System Analysis Module (SAM) is being developed at Argonne National Laboratory. The goal of the SAM development is to provide fast-running, improved-fidelity, whole-plant transient analyses capabilities. SAM utilizes an object-oriented application framework MOOSE), and its underlying meshing and finite-element library libMesh, as well as linear and non-linear solvers PETSc, to leverage modern advanced software environments and numerical methods. It also incorporates advances in physical and empirical models and seeks closure models based on information from high-fidelity simulations and experiments. This reportmore » provides an update on the SAM development, and summarizes the activities performed in FY15 and the first quarter of FY16. The tasks include: (1) implement the support of 2nd-order finite elements in SAM components for improved accuracy and computational efficiency; (2) improve the conjugate heat transfer modeling and develop pseudo 3-D full-core reactor heat transfer capabilities; (3) perform verification and validation tests as well as demonstration simulations; (4) develop the coupling requirements for SAS4A/SASSYS-1 and SAM integration.« less

Wind Technology Modeling Within the System Advisor Model (SAM) (Poster)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blair, N.; Dobos, A.; Ferguson, T.

This poster provides detail for implementation and the underlying methodology for modeling wind power generation performance in the National Renewable Energy Laboratory's (NREL's) System Advisor Model (SAM). SAM's wind power model allows users to assess projects involving one or more large or small wind turbines with any of the detailed options for residential, commercial, or utility financing. The model requires information about the wind resource, wind turbine specifications, wind farm layout (if applicable), and costs, and provides analysis to compare the absolute or relative impact of these inputs. SAM is a system performance and economic model designed to facilitate analysismore » and decision-making for project developers, financers, policymakers, and energy researchers. The user pairs a generation technology with a financing option (residential, commercial, or utility) to calculate the cost of energy over the multi-year project period. Specifically, SAM calculates the value of projects which buy and sell power at retail rates for residential and commercial systems, and also for larger-scale projects which operate through a power purchase agreement (PPA) with a utility. The financial model captures complex financing and rate structures, taxes, and incentives.« less

Peptide Fragments of Odin-Sam1: Conformational Analysis and Interaction Studies with EphA2-Sam.

PubMed

Mercurio, Flavia A; Di Natale, Concetta; Pirone, Luciano; Scognamiglio, Pasqualina L; Marasco, Daniela; Pedone, Emilia M; Saviano, Michele; Leone, Marilisa

2015-07-27

Odin is a protein belonging to the ANKS family, and has two tandem Sam domains. The first, Odin-Sam1, binds to the Sam domain of the EphA2 receptor (EphA2-Sam); this interaction could be crucial for the regulation of receptor endocytosis and might have an impact on cancer. Odin-Sam1 associates with EphA2-Sam by adopting a "mid-loop/end-helix" model. In this study three peptide sequences, encompassing the mid-loop interacting portion of Odin-Sam1 and its C-terminal α5 helix, were designed. Their conformational properties were analyzed by CD and NMR. In addition, their abilities to interact with EphA2-Sam were investigated by SPR studies. The peptides adopt a predominantly disordered state in aqueous buffer, but a higher helical content is evident in the presence of the cosolvent trifluoroethanol. Dissociation constants towards EphA2-Sam were in the high micromolar range. The structural findings suggest further routes for the design of potential anti-cancer therapeutics as inhibitors of EphA2-Sam heterotypic interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anti-inflammatory activity and molecular mechanism of delphinidin 3-sambubioside, a Hibiscus anthocyanin.

PubMed

Sogo, Takayuki; Terahara, Norihiko; Hisanaga, Ayami; Kumamoto, Takuma; Yamashiro, Takaaki; Wu, Shusong; Sakao, Kozue; Hou, De-Xing

2015-01-01

Delphinidin 3-sambubioside (Dp3-Sam), a Hibiscus anthocyanin, was isolated from the dried calices of Hibiscus sabdariffa L, which has been used for folk beverages and herbal medicine although the molecular mechanisms are poorly defined. Based on the properties of Dp3-Sam and the information of inflammatory processes, we investigated the anti-inflammatory activity and molecular mechanisms in both cell and animal models in the present study. In the cell model, Dp3-Sam and Delphinidin (Dp) reduced the levels of inflammatory mediators including iNOS, NO, IL-6, MCP-1, and TNF-α induced by LPS. Cellular signaling analysis revealed that Dp3-Sam and Dp downregulated NF-κB pathway and MEK1/2-ERK1/2 signaling. In animal model, Dp3-Sam and Dp reduced the production of IL-6, MCP-1 and TNF-α and attenuated mouse paw edema induced by LPS. Our in vitro and in vivo data demonstrated that Hibiscus Dp3-Sam possessed potential anti-inflammatory properties. © 2015 International Union of Biochemistry and Molecular Biology.

Descriptive Analysis of a Baseline Concussion Battery Among U.S. Service Academy Members: Results from the Concussion Assessment, Research, and Education (CARE) Consortium.

PubMed

O'Connor, Kathryn L; Dain Allred, C; Cameron, Kenneth L; Campbell, Darren E; D'Lauro, Christopher J; Houston, Megan N; Johnson, Brian R; Kelly, Tim F; McGinty, Gerald; O'Donnell, Patrick G; Peck, Karen Y; Svoboda, Steven J; Pasquina, Paul; McAllister, Thomas; McCrea, Michael; Broglio, Steven P

2018-03-28

The prevalence and possible long-term consequences of concussion remain an increasing concern to the U.S. military, particularly as it pertains to maintaining a medically ready force. Baseline testing is being used both in the civilian and military domains to assess concussion injury and recovery. Accurate interpretation of these baseline assessments requires one to consider other influencing factors not related to concussion. To date, there is limited understanding, especially within the military, of what factors influence normative test performance. Given the significant physical and mental demands placed on service academy members (SAM), and their relatively high risk for concussion, it is important to describe demographics and normative profile of SAMs. Furthermore, the absence of available baseline normative data on female and non-varsity SAMs makes interpretation of post-injury assessments challenging. Understanding how individuals perform at baseline, given their unique individual characteristics (e.g., concussion history, sex, competition level), will inform post-concussion assessment and management. Thus, the primary aim of this manuscript is to characterize the SAM population and determine normative values on a concussion baseline testing battery. All data were collected as part of the Concussion Assessment, Research and Education (CARE) Consortium. The baseline test battery included a post-concussion symptom checklist (Sport Concussion Assessment Tool (SCAT), psychological health screening inventory (Brief Symptom Inventory (BSI-18) and neurocognitive evaluation (ImPACT), Balance Error Scoring System (BESS), and Standardized Assessment of Concussion (SAC). Linear regression models were used to examine differences across sexes, competition levels, and varsity contact levels while controlling for academy, freshman status, race, and previous concussion. Zero inflated negative binomial models estimated symptom scores due to the high frequency of zero scores. Significant, but small, sex effects were observed on the ImPACT visual memory task. While, females performed worse than males (p < 0.0001, pη2 = 0.01), these differences were small and not larger than the effects of the covariates. A similar pattern was observed for competition level on the SAC. There was a small, but significant difference across competition level. SAMs participating in varsity athletics did significantly worse on the SAC compared to SAMs participating in club or intramural athletics (all p's < 0.001, η2 = 0.01). When examining symptom reporting, males were more than two times as likely to report zero symptoms on the SCAT or BSI-18. Intramural SAMs had the highest number of symptoms and severity compared to varsity SAMs (p < 0.0001, Cohen's d < 0.2). Contact level was not associated with SCAT or BSI-18 symptoms among varsity SAMs. Notably, the significant differences across competition level on SCAT and BSI-18 were sub-clinical and had small effect sizes. The current analyses provide the first baseline concussion battery normative data among SAMs. While statistically significant differences may be observed on baseline tests, the effect sizes for competition and contact levels are very small, indicating that differences are likely not clinically meaningful at baseline. Identifying baseline differences and significant covariates is important for future concussion-related analyses to inform concussion evaluations for all athlete levels.

Bioadhesion to model thermally responsive surfaces

NASA Astrophysics Data System (ADS)

Andrzejewski, Brett Paul

This dissertation focuses on the characterization of two surfaces: mixed self-assembled monolayers (SAMs) of hexa(ethylene glycol) and alkyl thiolates (mixed SAM) and poly(N-isopropylacrylamide) (PNIPAAm). The synthesis of hexa(ethylene gylcol) alkyl thiol (C11EG 6OH) is presented along with the mass spectrometry and nuclear magnetic resonance results. The gold substrates were imaged prior to SAM formation with atomic force micrscopy (AFM). Average surface roughness of the gold substrate was 0.44 nm, 0.67 nm, 1.65 nm for 15, 25 and 60 nm gold thickness, respectively. The height of the mixed SAM was measured by ellipsometry and varied from 13 to 28°A depending on surface mole fraction of C11EG6OH. The surface mole fraction of C11EG6OH for the mixed SAM was determined by X-ray photoelectron spectroscopy (XPS) with optimal thermal responsive behavior in the range of 0.4 to 0.6. The mixed SAM surface was confirmed to be thermally responsive by contact angle goniometry, 35° at 28°C and ˜55° at 40°C. In addition, the mixed SAM surfaces were confirmed to be thermally responsive for various aqueous mediums by tensiometry. Factors such as oxygen, age, and surface mole fraction and how they affect the thermal responsive of the mixed SAM are discussed. Lastly, rat fibroblasts were grown on the mixed SAM and imaged by phase contrast microscopy to show inhibition of attachment at temperatures below the molecular transition. Qualitative and quantitative measurements of the fibroblast adhesion data are provided that support the hypothesis of the mixed SAM exhibits a dominantly non-fouling molecular conformation at 25°C whereas it exhibits a dominantly fouling molecular conformation at 40°C. The adhesion of six model proteins: bovine serum albumin, collagen, pyruvate kinase, cholera toxin subunit B, ribonuclease, and lysozyme to the model thermally responsive mixed SAM were examined using AFM. All six proteins possessed adhesion to the pure component alkyl thiol, in contrast possessed no adhesion to the pure component C11EG6OH SAM at both temperatures examined, 25 and 40°C. The protein adhesion data to the mixed SAM also supports the hypothesis that the mixed SAM displays a non-fouling molecular conformation at 25°C whereas it displays a dominantly fouling molecular conformation at 40°C. Advancing contact angles obtained through tensiometry were used to find the surface free energy of the mixed SAM before and after the thermal response using the van Oss-Good-Chaudhury method. The surface tension values obtained, 42 and 38 mN/m for 22 and 40°C, respectively, are not dissimilar enough with regard to error to make conclusions. In a similar manner, the surface free energy of another mixed SAM composed of alkyl and trimethylamine thiolates was also calculated. PNIPAAm brushes grown on a silicon substrate by atom-transfer radical polymerization (ATRP) were imaged by AFM and characterized by XPS. The height of the resulting brushes could be controlled from ˜5 to 55 nm by reaction time. A thermal response was observed for polymer brushes with a length greater than 20 nm. For polymer brush lengths greater than 20 nm, the static contact angle at 22°C was 35° and varied from 60 to 80° at 40°C. The thermal response was also observed using the captive bubble method. Force-distance curves of the PNIPAAm brushes were taken with an unmodified silicon nitride AFM cantilever at incremental temperature steps. At room temperature the force-distance data was fit to the Alexander-de Gennes model resulting in a hydrated polymer length of 235 nm. The Young's modulus was calculated using the Hertz model and changed from ˜80 MPa at 26°C to ˜350 MPa at 40°C. The solvent condition of the Alexander-de Gennes model was set to the case of good solvent and showed close match to the force-distance data at 26°C. The match was not as close when the solvent condition was set to theta solvent condition and compared to the force-distance data at 40°C. Finally, the effective diffusion coefficients of a dye were obtained for the uptake, encapsulation, and release from a lipid bilayer coated mesoporous particle using a mathematical solution to the experimental system. The resulting effective diffusion coefficients are: 1*10-12 m2/s, 0.4*10-12 m2/s, and 0.7*10-12 m2/s for uptake, encapsulation, and release, respectively. The particles are characterized by scanning electron microscopy and nitrogen adsorption measurements. In contrast to our hypothesis, the lipid bilayer did not completely inhibit diffusion of the rhodamine dye from the particles when encapsulated.

The SAM-responsive SMK box is a reversible riboswitch

PubMed Central

Smith, Angela M.; Fuchs, Ryan T.; Grundy, Frank J.; Henkin, Tina M.

2010-01-01

The SMK (SAM-III) box is an S-adenosylmethionine (SAM)-responsive riboswitch found in the 5′ untranslated region of metK genes, encoding SAM synthetase, in many members of the Lactobacillales. SAM binding causes a structural rearrangement in the RNA that sequesters the Shine-Dalgarno (SD) sequence by pairing with a complementary anti-SD (ASD) sequence; sequestration of the SD sequence inhibits binding of the 30S ribosomal subunit and prevents translation initiation. We observed a slight increase in the half-life of the metK transcript in vivo when Enterococcus faecalis cells were depleted for SAM, but no significant change in overall transcript abundance, consistent with the model that this riboswitch regulates at the level of translation initiation. The half-life of the SAM-SMK box RNA complex in vitro is shorter than that of the metK transcript in vivo, raising the possibility of reversible binding of SAM. We used a fluorescence assay to directly visualize reversible switching between the SAM-free and SAM-bound conformations. We propose that the SMK box riboswitch can make multiple SAM-dependent regulatory decisions during the lifetime of the transcript in vivo, acting as a reversible switch that allows the cell to respond rapidly to fluctuations in SAM pools by modulating expression of the SAM synthetase gene. PMID:21143313

Molten Salt Power Tower Cost Model for the System Advisor Model (SAM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turchi, C. S.; Heath, G. A.

2013-02-01

This report describes a component-based cost model developed for molten-salt power tower solar power plants. The cost model was developed by the National Renewable Energy Laboratory (NREL), using data from several prior studies, including a contracted analysis from WorleyParsons Group, which is included herein as an Appendix. The WorleyParsons' analysis also estimated material composition and mass for the plant to facilitate a life cycle analysis of the molten salt power tower technology. Details of the life cycle assessment have been published elsewhere. The cost model provides a reference plant that interfaces with NREL's System Advisor Model or SAM. The referencemore » plant assumes a nominal 100-MWe (net) power tower running with a nitrate salt heat transfer fluid (HTF). Thermal energy storage is provided by direct storage of the HTF in a two-tank system. The design assumes dry-cooling. The model includes a spreadsheet that interfaces with SAM via the Excel Exchange option in SAM. The spreadsheet allows users to estimate the costs of different-size plants and to take into account changes in commodity prices. This report and the accompanying Excel spreadsheet can be downloaded at https://sam.nrel.gov/cost.« less

Intensity and duration of activity bouts decreases in healthy children between 7 and 13 years of age: a new, higher resolution method to analyze StepWatch Activity Monitor data.

PubMed

Tulchin-Francis, Kirsten; Stevens, Wilshaw; Jeans, Kelly A

2014-11-01

Assessment of physical, ambulatory, activity using accelerometer-based devices has been reported in healthy individuals across a wide range of ages, as well as in multiple patient populations. Many researchers who utilize the StepWatch Activity Monitor (SAM) rely on the default settings for data collection and analysis. A comparison was made between the standard output from the SAM software, and a novel method to evaluate all walking bouts using an Intensity-Duration-Volume (I-D-V) model in healthy children aged 7-13. 105 children without impairment wore the SAM for a total of 1691 d. Statistically significant differences were seen between 7-8-9 year olds and 10-11-12 year olds using the I-D-V model that were not seen using the standard SAM software default output. The increased sensitivity of this technique could be critical for observing the effect of various interventions on patients who experience physical limitations. This new analytical model also allows researchers to monitor activity and exercise-type behavior in a way which coincides with exercise prescription by assessing intensity, duration and volume of activity bouts.

Simulation of different types of ENSO impacts on South Asian Monsoon in CCSM4

NASA Astrophysics Data System (ADS)

Islam, Siraj ul; Tang, Youmin

2017-02-01

It has been found in observation that there are different types of influences of El Nino Southern Oscillation (ENSO) on the South Asian Monsoon (SAM). A correct description and representation of these teleconnections is critical for climate models to simulate and predict SAM. In this study, we examine these teleconnections in NCAR CAM4 and CCSM4 models, including the strength and weakness of these models in preserving different types of ENSO-SAM relationships. By using observational and simulation dataset, the composite analysis, based on specific selection criteria, is performed for both SAM rainfall and the eastern equatorial Pacific sea surface temperature (SST) anomalies. Anomalous SAM rainfall is characterized in three different types i.e. the indirect influence of the SST anomalies of preceding winter (DJF-only), direct influence of the SST anomalies of concurrent summer (JJAS-only) and the combined influence of both preceding winter and concurrent summer (DJF&JJAS). The analysis reveals that CAM4 uncoupled simulation can reasonably well reproduce the anomalous SAM rainfall in DJF-only and DJF&JJAS types whereas the model fails to simulate the anomalous rainfall in the JJAS-only type. The better performance of CAM4, particularly in DJF&JJAS type, comes from its realistic simulation of moisture content and thermal contrast. Its failure to preserve the ENSO-SAM relationship of JJAS-only type is due to the absence of ENSO induced warming in Northern Indian Ocean via atmospheric circulation which is indirectly linked to the lack of air-sea coupling. The role of Indian Ocean in controlling the ENSO-SAM teleconnections of the DJF&JJAS type is further investigated using CAM4 sensitivity experiments. It is found that in absence of Indian Ocean SST, the anomalous SAM summer rainfall suppresses in the DJF&JJAS type, suggesting the important modulation by Indian Ocean SST probably through the preceding winter equatorial Pacific SST forcing and the atmospheric circulations. On the other hand, CCSM4 shows large systematical errors in DJF-only and DJF&JJAS types and reproduce weak anomalous SAM rainfall. The failure of CCSM4 in simulating DJF-only and DJF&JJAS types is found mainly due to the errors in its SST simulation. The JJAS-only type is better reproduced in the CCSM4 simulation as compared to CAM4 and observation composites. Strong convergence over the SAM region which intensifies the anomalous SAM is seen to be responsible for its better simulation in this type. It is found that the atmospheric circulations in CCSM4 contribute more than the thermal contrast in modulating the intensity of anomalous rainfall in JJAS-only type. This study suggests that, although air-sea coupling is important for better SAM simulation and its relationship with ENSO, the SST bias in coupled model can significantly degrade ENSO-SAM relationship.

Annular mode changes in the CMIP5 simulations

NASA Astrophysics Data System (ADS)

Gillett, N. P.; Fyfe, J. C.

2013-03-01

We investigate simulated changes in the annular modes in historical and RCP 4.5 scenario simulations of 37 models from the fifth Coupled Model Intercomparison Project (CMIP5), a much larger ensemble of models than has previously been used to investigate annular mode trends, with improved resolution and forcings. The CMIP5 models on average simulate increases in the Northern Annular Mode (NAM) and Southern Annular Mode (SAM) in every season by 2100, and no CMIP5 model simulates a significant decrease in either the NAM or SAM in any season. No significant increase in the NAM or North Atlantic Oscillation (NAO) is simulated in response to volcanic aerosol, and no significant NAM or NAO response to solar irradiance variations is simulated. The CMIP5 models simulate a significant negative SAM response to volcanic aerosol in MAM and JJA, and a significant positive SAM response to solar irradiance variations in MAM, JJA and DJF.

Influence of Superparameterization and a Higher-Order Turbulence Closure on Rainfall Bias Over Amazonia in Community Atmosphere Model Version 5: How Parameterization Changes Rainfall

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Kai; Fu, Rong; Shaikh, Muhammad J.

We evaluate the Community Atmosphere Model Version 5 (CAM5) with a higher-order turbulence closure scheme, named Cloud Layers Unified By Binomials (CLUBB), and a Multiscale Modeling Framework (MMF) with two different microphysics configurations to investigate their influences on rainfall simulations over Southern Amazonia. The two different microphysics configurations in MMF are the one-moment cloud microphysics without aerosol treatment (SAM1MOM) and two-moment cloud microphysics coupled with aerosol treatment (SAM2MOM). Results show that both MMF-SAM2MOM and CLUBB effectively reduce the low biases of rainfall, mainly during the wet season. The CLUBB reduces low biases of humidity in the lower troposphere with furthermore » reduced shallow clouds. The latter enables more surface solar flux, leading to stronger convection and more rainfall. MMF, especially MMF-SAM2MOM, unstablizes the atmosphere with more moisture and higher atmospheric temperatures in the atmospheric boundary layer, allowing the growth of more extreme convection and further generating more deep convection. MMF-SAM2MOM significantly increases rainfall in the afternoon, but it does not reduce the early bias of the diurnal rainfall peak; LUBB, on the other hand, delays the afternoon peak time and produces more precipitation in the early morning, due to more realistic gradual transition between shallow and deep convection. MMF appears to be able to realistically capture the observed increase of relative humidity prior to deep convection, especially with its two-moment configuration. In contrast, in CAM5 and CAM5 with CLUBB, occurrence of deep convection in these models appears to be a result of stronger heating rather than higher relative humidity.« less

The Sam Domain of EphA2 Receptor and its Relevance to Cancer: A Novel Challenge for Drug Discovery?

PubMed

Mercurio, Flavia A; Leone, Marilisa

2016-01-01

Eph receptors play important functions in developmental processes and diseases and among them EphA2 is well known for its controversial role in cancer. Drug discovery strategies are mainly centered on EphA2 extracellular ligand-binding domain however, the receptor also contains a largely unexplored cytosolic Sam (Sterile alpha motif) domain at the C-terminus. EphA2-Sam binds the Sam domain from the lipid phosphatase Ship2 and the first Sam domain of Odin. Sam-Sam interactions may be important to regulate ligand-induced receptor endocytosis and degradation i.e., processes that could be engaged against tumor malignancy. We critically analyzed literature related to a) Eph receptors with particular emphasis on EphA2 and its role in cancer, b) Sam domains, c) heterotypic Sam-Sam interactions involving EphA2-Sam. While literature data indicate that binding of EphA2-Sam to Ship2-Sam should largely generate pro-oncogenic effects in cancer cells, the correlation between EphA2- Sam/Odin-Sam1 complex and the disease is unclear. Recently a few linear peptides encompassing binding interfaces from either Ship2-Sam and Odin-Sam1 have been characterized but failed to efficiently block heterotypic Sam-Sam interactions involving EphA2-Sam due to the lack of a native like fold. Molecule antagonists of heterotypic EphA2-Sam associations could work as potential anticancer agents or be implemented as tools to further clarify receptor functions and eventually validate its role as a novel target in the field of anti-cancer drug discovery. Due to the failure of linear peptides there is a crucial need for novel approaches, based on cyclic or helical molecules, to target Sam-Sam interfaces.

Benchmark Simulation of Natural Circulation Cooling System with Salt Working Fluid Using SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, K. K.; Scarlat, R. O.; Hu, R.

Liquid salt-cooled reactors, such as the Fluoride Salt-Cooled High-Temperature Reactor (FHR), offer passive decay heat removal through natural circulation using Direct Reactor Auxiliary Cooling System (DRACS) loops. The behavior of such systems should be well-understood through performance analysis. The advanced system thermal-hydraulics tool System Analysis Module (SAM) from Argonne National Laboratory has been selected for this purpose. The work presented here is part of a larger study in which SAM modeling capabilities are being enhanced for the system analyses of FHR or Molten Salt Reactors (MSR). Liquid salt thermophysical properties have been implemented in SAM, as well as properties ofmore » Dowtherm A, which is used as a simulant fluid for scaled experiments, for future code validation studies. Additional physics modules to represent phenomena specific to salt-cooled reactors, such as freezing of coolant, are being implemented in SAM. This study presents a useful first benchmark for the applicability of SAM to liquid salt-cooled reactors: it provides steady-state and transient comparisons for a salt reactor system. A RELAP5-3D model of the Mark-1 Pebble-Bed FHR (Mk1 PB-FHR), and in particular its DRACS loop for emergency heat removal, provides steady state and transient results for flow rates and temperatures in the system that are used here for code-to-code comparison with SAM. The transient studied is a loss of forced circulation with SCRAM event. To the knowledge of the authors, this is the first application of SAM to FHR or any other molten salt reactors. While building these models in SAM, any gaps in the code’s capability to simulate such systems are identified and addressed immediately, or listed as future improvements to the code.« less

Evaluating SAMS in Hong Kong Schools.

ERIC Educational Resources Information Center

Kwok, Lam-for; Lau, Chi-kuen; Fung, Sun-wai

1999-01-01

Describes the School Administration and Management Systems (SAMS) that was developed to support elementary and secondary schools in Hong Kong in administrative and managerial tasks. Reports results of a survey that investigated the impact of SAMS, evaluated its effectiveness, and identified possible areas of improvement to SAMS operation.…

Systems Operation Studies for Automated Guideway Transit Systems : System Availability Model User's Manual

DOT National Transportation Integrated Search

1981-01-01

The System Availability Model (SAM) is a system-level model which provides measures of vehicle and passenger availability. The SAM operates in conjunction with the AGT discrete Event Simulation Model (DESM). The DESM output is the normal source of th...

SAM in a Nutshell.

ERIC Educational Resources Information Center

Givens, Larry R.

2000-01-01

Explains what the Association of Higher Education Facilities Officers' Strategic Assessment Model (SAM) is and how to use it to achieve organizational excellence through continuous improvement. Showing features of both the Malcolm Baldrige programs and the Balanced Scorecard, the SAM components are described along with an explanation of the four…

Treatment of severe and moderate acute malnutrition in low- and middle-income settings: a systematic review, meta-analysis and Delphi process

PubMed Central

2013-01-01

Background Globally, moderate acute malnutrition (MAM) and severe acute malnutrition (SAM) affect approximately 52 million children under five. This systematic review evaluates the effectiveness of interventions for SAM including the World Health Organization (WHO) protocol for inpatient management and community-based management with ready-to-use-therapeutic food (RUTF), as well as interventions for MAM in children under five years in low- and middle-income countries. Methods We systematically searched the literature and included 14 studies in the meta-analysis. Study quality was assessed using CHERG adaptation of GRADE criteria. A Delphi process was undertaken to complement the systematic review in estimating case fatality and recovery rates that were necessary for modelling in the Lives Saved Tool (LiST). Results Case fatality rates for inpatient treatment of SAM using the WHO protocol ranged from 3.4% to 35%. For community-based treatment of SAM, children given RUTF were 51% more likely to achieve nutritional recovery than the standard care group. For the treatment of MAM, children in the RUSF group were significantly more likely to recover and less likely to be non-responders than in the CSB group. In both meta-analyses, weight gain in the intervention group was higher, and although statistically significant, these differences were small. Overall limitations in our analysis include considerable heterogeneity in many outcomes and an inability to evaluate intervention effects separate from commodity effect. The Delphi process indicated that adherence to standardized protocols for the treatment of SAM and MAM should have a marked positive impact on mortality and recovery rates; yet, true consensus was not achieved. Conclusions Gaps in our ability to estimate effectiveness of overall treatment approaches for SAM and MAM persist. In addition to further impact studies conducted in a wider range of settings, more high quality program evaluations need to be conducted and the results disseminated. PMID:24564235

On LAM's and SAM's for Halley's rotation

NASA Technical Reports Server (NTRS)

Peale, Stanton J.

1992-01-01

Non principal axis rotation for comet Halley is inferred from dual periodicities evident in the observations. The modes where the spin axis precesses around the axis of minimum moment of inertia (long axis mode or LAM) and where it precesses around the axis of maximum moment of inertia (short axis mode or SAM) are described from an inertial point of view. The currently favored LAM model for Halley's rotation state satisfies observational and dynamical constraints that apparently no SAM can satisfy. But it cannot reproduce the observed post perihelion brightening through seasonal illumination of localized sources on the nucleus, whereas a SAM can easily produce post or pre perihelion brightening by this mechanism. However, the likelihood of a LAM rotation for elongated nuclei of periodic comets such as Halley together with Halley's extreme post perihelion behavior far from the Sun suggest that Halley's post perihelion brightening may be due to effects other than seasonal illumination of localized sources, and therefore such brightening may not constrain its rotation state.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

PubMed

Reimers, Jeffrey R; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J J; Hendriksen, Bas L M; Elemans, Johannes A A W; Hush, Noel S; Crossley, Maxwell J

2015-11-10

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Utilizing self-assembled-monolayer-based gate dielectrics to fabricate molybdenum disulfide field-effect transistors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawanago, Takamasa, E-mail: kawanago.t.ab@m.titech.ac.jp; Oda, Shunri

In this study, we apply self-assembled-monolayer (SAM)-based gate dielectrics to the fabrication of molybdenum disulfide (MoS{sub 2}) field-effect transistors. A simple fabrication process involving the selective formation of a SAM on metal oxides in conjunction with the dry transfer of MoS{sub 2} flakes was established. A subthreshold slope (SS) of 69 mV/dec and no hysteresis were demonstrated with the ultrathin SAM-based gate dielectrics accompanied by a low gate leakage current. The small SS and no hysteresis indicate the superior interfacial properties of the MoS{sub 2}/SAM structure. Cross-sectional transmission electron microscopy revealed a sharp and abrupt interface of the MoS{sub 2}/SAM structure.more » The SAM-based gate dielectrics are found to be applicable to the fabrication of low-voltage MoS{sub 2} field-effect transistors and can also be extended to various layered semiconductor materials. This study opens up intriguing possibilities of SAM-based gate dielectrics in functional electronic devices.« less

Systems Operation Studies for Automated Guideway Transit Systems : Availability Model Functional Specification

DOT National Transportation Integrated Search

1981-01-01

The System Availability Model (SAM) is a system-level model which provides measures of vehicle and passenger availability. The SAM will be used to evaluate the system-level influence of availability concepts employed in AGT systems. This functional s...

Non-invasive SFG spectroscopy: a tool to reveal the conformational change of grafted chains due to bacterial adhesion

NASA Astrophysics Data System (ADS)

Bulard, Emilie; Dubost, Henri; Fontaine-Aupart, Marie-Pierre; Zheng, Wanquan; Herry, Jean-Marie; Bellon-Fontaine, Marie-No"lle; Briandet, Romain; Bourguignon, Bernard

2011-07-01

In many fields such as biomedical or food industry, surface colonization by micro-organisms leads to biofilms formation that are tridimentional biostructures highly resistant to the action of antimicrobials, by mechanisms still unclear. In order to deepen our understanding of the initial interaction of bacteria cells with a solid surface, we analyze by in situ vibrational Sum Frequency Generation (SFG) spectroscopy the effect of the adhesion of hydrophilic Lactoccocus lactis bacteria and its hydrophobic mutants in distilled water on a self-assembled monolayer (SAM) of octadecanethiol (ODT) on a gold film. When a homogeneous bacterial monolayer is deposited on this ordered surface, SFG spectrum of the ODT SAM shows significant intensity changes from that in air or in water. Its modelling as a function of conformation allows to distinguish optical effects due to the water solution surrounding bacteria from conformational changes of the ODT SAM due to the presence of the bacteria cells. Futhermore, bacterial adhesion induces different measurable effects on the ODT SAM conformation, depending on the hydrophobic / hydrophilic character of the bacterial surface. Such a result deserves to be taken into account for the design of new materials with improved properties or to control biofilm formation.

Preparation for Analytical Measurements on Mars

NASA Image and Video Library

2015-03-31

A Sample Analysis at Mars (SAM) team member at NASA's Goddard Space Flight Center, Greenbelt, Maryland, prepares the SAM testbed for an experiment. This test copy of the SAM suite of instruments is inside a chamber that, when closed, can model the pressure and temperature environment that SAM sees inside NASA's Curiosity rover on Mars. Many weeks of testing are often needed to develop and refine sequences of operations that SAM uses for making specific measurements on Mars. This was the case with preparation to pull a volume of gas from the atmosphere and extract the heavy noble gas xenon. SAM's measurements of different types of xenon in the Martian atmosphere provide clues about the planet's history. http://photojournal.jpl.nasa.gov/catalog/PIA19149

Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch.

PubMed

Doshi, Urmi; Kelley, Jennifer M; Hamelberg, Donald

2012-02-01

Although S-adenosylhomocysteine (SAH), a metabolic by-product of S-adenosylmethionine (SAM), differs from SAM only by a single methyl group and an overall positive charge, SAH binds the SAM-II riboswitch with more than 1000-fold less affinity than SAM. Using atomistic molecular dynamics simulations, we investigated the molecular basis of such high selectivity in ligand recognition by SAM-II riboswitch. The biosynthesis of SAM exclusively generates the (S,S) stereoisomer, and (S,S)-SAM can spontaneously convert to the (R,S) form. We, therefore, also examined the effects of (R,S)-SAM binding to SAM-II and its potential biological function. We find that the unfavorable loss in entropy in SAM-II binding is greater for (S,S)- and (R,S)-SAM than SAH, which is compensated by stabilizing electrostatic interactions with the riboswitch. The positively charged sulfonium moiety on SAM acts as the crucial anchor point responsible for the formation of key ionic interactions as it fits favorably in the negatively charged binding pocket. In contrast, SAH, with its lone pair of electrons on the sulfur, experiences repulsion in the binding pocket of SAM-II and is enthalpically destabilized. In the presence of SAH, similar to the unbound riboswitch, the pseudoknot structure of SAM-II is not completely formed, thus exposing the Shine-Dalgarno sequence. Unlike SAM, this may further facilitate ribosomal assembly and translation initiation. Our analysis of the conformational ensemble sampled by SAM-II in the absence of ligands and when bound to SAM or SAH reveals that ligand binding follows a combination of conformational selection and induced-fit mechanisms.

Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.

PubMed

Manz, Christoph; Kobitski, Andrei Yu; Samanta, Ayan; Keller, Bettina G; Jäschke, Andres; Nienhaus, G Ulrich

2017-11-01

S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg 2+ and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis. We resolved four conformational states both in the presence and the absence of SAM and determined their Mg 2+ -dependent fractional populations and conformational dynamics, including state lifetimes, interconversion rate coefficients and equilibration timescales. Riboswitches with terminator and antiterminator folds coexist, and SAM binding only gradually shifts the populations toward terminator states. We observed a pronounced acceleration of conformational transitions upon SAM binding, which may be crucial for off-switching during the brief decision window before expression of the downstream gene.

SAP Minutes No.2015-03 for FIFRA meeting held 9/15-17/2015. A set of scientific issues being considered by the Environmental Protection Agency regarding development of a spatial aquatic model(SAM)for pesticide risk assessment

USDA-ARS?s Scientific Manuscript database

On September 15-17th, 2014, the US Environmental Protection Agency convened a public meeting of the FIFRA Scientific Advisory Panel (SAP) to address scientific issues associated with the agency’s “Development of a Spatial Aquatic Model (SAM) for Pesticide Risk Assessment”. The goal of SAM is to impr...

Learning to Construct Meaning from Text: A Case Study of the Relationship between a Tutor and an English Learner within a Response to Intervention Setting

ERIC Educational Resources Information Center

Jaeger, Elizabeth L.

2015-01-01

This case study describes the ways in which Sam, an English learner with weak comprehension, grew as a reader, student, and friend during his fourth grade year. Using the Interactive Model of Reading (Dis)ability and the RAND model of comprehension as a frame, Sam's experience in a Tier 2/3 tutorial program is examined. Over time, Sam (1) engaged…

Modulation-Frequency-Specific Adaptation in Awake Auditory Cortex

PubMed Central

Beitel, Ralph E.; Vollmer, Maike; Heiser, Marc A.; Schreiner, Christoph E.

2015-01-01

Amplitude modulations are fundamental features of natural signals, including human speech and nonhuman primate vocalizations. Because natural signals frequently occur in the context of other competing signals, we used a forward-masking paradigm to investigate how the modulation context of a prior signal affects cortical responses to subsequent modulated sounds. Psychophysical “modulation masking,” in which the presentation of a modulated “masker” signal elevates the threshold for detecting the modulation of a subsequent stimulus, has been interpreted as evidence of a central modulation filterbank and modeled accordingly. Whether cortical modulation tuning is compatible with such models remains unknown. By recording responses to pairs of sinusoidally amplitude modulated (SAM) tones in the auditory cortex of awake squirrel monkeys, we show that the prior presentation of the SAM masker elicited persistent and tuned suppression of the firing rate to subsequent SAM signals. Population averages of these effects are compatible with adaptation in broadly tuned modulation channels. In contrast, modulation context had little effect on the synchrony of the cortical representation of the second SAM stimuli and the tuning of such effects did not match that observed for firing rate. Our results suggest that, although the temporal representation of modulated signals is more robust to changes in stimulus context than representations based on average firing rate, this representation is not fully exploited and psychophysical modulation masking more closely mirrors physiological rate suppression and that rate tuning for a given stimulus feature in a given neuron's signal pathway appears sufficient to engender context-sensitive cortical adaptation. PMID:25878263

Methodology for the in vitro evaluation of the delivery efficiency from valved holding chambers with facemasks.

PubMed

Xu, Zhen; Hsu, Wenchi; von Hollen, Dirk; Viswanath, Ashwin; Nikander, Kurt; Dalby, Richard

2014-08-01

In vitro performance studies of valved holding chamber (VHC)-facemask systems are a cost-effective means of circumventing potentially confounding clinical variables. This article reports results of an in vitro investigation into VHC-facemask performance, using three age-specific soft anatomical model (SAM) faces, under clinically relevant conditions. A potentially standardized method was developed to assess VHC-facemask seal leakage, and evaluate the in vitro delivery efficiency of conventional and antistatic VHC-facemask systems. A custom-built test rig and VHC cradles were used to position the VHC-facemask systems against the SAM faces, with a constant, reproducible force. A standardized simulated pediatric breathing pattern (tidal volume = 155 mL; inhalation:exhalation ratio = 40:60; 25 breaths/min) was utilized. Percent facemask seal leakage, percent delivered dose, and the effect of different numbers of simulated breaths (2 to 8) were investigated. Of the VHC-facemask systems tested, the OptiChamber Diamond VHC with LiteTouch facemask (Diamond) system had the lowest percent seal leakage with each SAM face. Percent seal leakage from the other VHC-facemask systems was similar with SAM0 and SAM2 faces; the AeroChamber Plus Z-Stat VHC with ComfortSeal facemask (AC Z-Stat) system had a substantially greater percent seal leakage with the SAM1 face. Regardless of the number of simulated breaths, the Diamond system delivered the greatest mean percent delivered dose, with the lowest coefficient of variation, with each SAM face. Percent delivered dose did not correlate well with seal leakage, particularly for VHC-facemask systems with high seal leakage. The electrostatic properties of the VHCs appeared to influence drug delivery. This study describes a potentially standardized method for the evaluation of VHC-facemask systems. Use of this method enabled a comprehensive investigation into the influence of clinically relevant variables, including age-specific facial anatomy, number of simulated breaths, and seal leakage, on the delivery efficiency of several commercially available VHC-facemask systems.

43 CFR 3186.1-2 - Model Exhibit “B”.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Pen 50% Max Pen 1% Frost Oil Co. 100%. Sec. 28: All Sam Small 50% Sam Small 1% 4 Sec. 27: All 1,280.00... T.J. Cook: 100% W.W. Smith 100% Sam Spade 1% W.W. Smith 100%. 10 Sec. 34: All 640.00 6-30-82 A.A...

43 CFR 3186.1-2 - Model Exhibit “B”.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Pen 50% Max Pen 1% Frost Oil Co. 100%. Sec. 28: All Sam Small 50% Sam Small 1% 4 Sec. 27: All 1,280.00... T.J. Cook: 100% W.W. Smith 100% Sam Spade 1% W.W. Smith 100%. 10 Sec. 34: All 640.00 6-30-82 A.A...

43 CFR 3186.1-2 - Model Exhibit “B”.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Pen 50% Max Pen 1% Frost Oil Co. 100%. Sec. 28: All Sam Small 50% Sam Small 1% 4 Sec. 27: All 1,280.00... T.J. Cook: 100% W.W. Smith 100% Sam Spade 1% W.W. Smith 100%. 10 Sec. 34: All 640.00 6-30-82 A.A...

43 CFR 3186.1-2 - Model Exhibit “B”.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Pen 50% Max Pen 1% Frost Oil Co. 100%. Sec. 28: All Sam Small 50% Sam Small 1% 4 Sec. 27: All 1,280.00... T.J. Cook: 100% W.W. Smith 100% Sam Spade 1% W.W. Smith 100%. 10 Sec. 34: All 640.00 6-30-82 A.A...

Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch

PubMed Central

Doshi, Urmi; Kelley, Jennifer M.; Hamelberg, Donald

2012-01-01

Although S-adenosylhomocysteine (SAH), a metabolic by-product of S-adenosylmethionine (SAM), differs from SAM only by a single methyl group and an overall positive charge, SAH binds the SAM-II riboswitch with more than 1000-fold less affinity than SAM. Using atomistic molecular dynamics simulations, we investigated the molecular basis of such high selectivity in ligand recognition by SAM-II riboswitch. The biosynthesis of SAM exclusively generates the (S,S) stereoisomer, and (S,S)-SAM can spontaneously convert to the (R,S) form. We, therefore, also examined the effects of (R,S)-SAM binding to SAM-II and its potential biological function. We find that the unfavorable loss in entropy in SAM-II binding is greater for (S,S)- and (R,S)-SAM than SAH, which is compensated by stabilizing electrostatic interactions with the riboswitch. The positively charged sulfonium moiety on SAM acts as the crucial anchor point responsible for the formation of key ionic interactions as it fits favorably in the negatively charged binding pocket. In contrast, SAH, with its lone pair of electrons on the sulfur, experiences repulsion in the binding pocket of SAM-II and is enthalpically destabilized. In the presence of SAH, similar to the unbound riboswitch, the pseudoknot structure of SAM-II is not completely formed, thus exposing the Shine-Dalgarno sequence. Unlike SAM, this may further facilitate ribosomal assembly and translation initiation. Our analysis of the conformational ensemble sampled by SAM-II in the absence of ligands and when bound to SAM or SAH reveals that ligand binding follows a combination of conformational selection and induced-fit mechanisms. PMID:22194311

Functionalization and Characterization of Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Techane, Sirnegeda D.

2011-12-01

Surface characterization of gold nanoparticles (AuNPs) is necessary to obtain a thorough understanding of the AuNP properties and ultimately realize their full potential in applications. The work described in this dissertation strives to the structure and composition of AuNPs using highly surface sensitive techniques such as X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) in addition to the more widely used characterization techniques such as transmission electron microscopy (TEM), fourier transform infrared spectroscopy (FTIR) and UV-VIS spectroscopy. Self-assembled monolayers (SAMs) of alkanethiols were used to modify AuNPs surfaces to create positively and negatively charged surfaces. Functionalization with carboxylic acid terminated alkanethiol SAMs (COON-SAMs) was first optimized to produce clean and stable negatively charged AuNPs. Using 14nm and 40nm diameter AuNPs in combination with C11 and C16 chain length COOH-SAMs, it was found that addition of NH4OH during functionalization coupled with dialysis purification produced AuNPs that did not aggregate and did not have unbound thiols. Effects of AuNP size and COOH-SAM chain lengths were studied using 14, 25 and 40nm average diameter AuNPs functionalized with C6, C8, C11 and C16 COOH-SAMs. Flat Au surfaces were also functionalized with the COOH-SAMs for comparison. It was shown that the 14nm AuNPs with C16 COOH-SAMs were the most stable and had crystalline-like, well-ordered SAM structures. The SAMs on the 40nm AuNPs had similar surface chemistry as the SAMs on the flat Au surfaces. The effective photoelectron take-off angle of the C16 COOH-SAM decreased when the size of the AuNP increased. It was also shown that when using Kratos AxisUltra DLD XPS instrument in the hybrid mode, it was important to consider effects of both the hybrid mode and the AuNPs curvature when calculating overlayer thickness of the SAMs on AuNPs. Using the Kratos in the electrostatic mode, the overlayer thickness of C16 COON-SAM was 21A on a flat Au surface, which was comparable with previously reported values. However, the apparent thickness of the same SAM on the 14nm AuNPs was 31A, indicating the curvature of the AuNPs had an effect on the XPS measurements. To produce the positively charged AuNP surfaces, amine terminated alkanethiols (NH2 -thiols) with a C2 chain length were used in one-step AuNP synthesis and functionalization process followed by a ligand-exchange reaction with C11 chain length NH2-thiols. It was found that 14 days were needed for the ligand-exchange to be complete. After the ligand-exchange, it was found that the AuNPs with C11 NH2-SAMs were stable and could be purified, unlike AuNPs with C2 NH2-SAMs which aggregated upon purification. The C11 NH2-SAMs had both unbound and oxidized sulfur, which could be removed/converted after hydrochloric acid treatment. SESSA (simulation of electron spectra for surface analysis) allowed better interpretation of the XPS data of SAMs on AuNPs and flat Au. Comparing SESSA and experimental XPS data, it was found that C16 COON-SAM on a flat Au surface was 20A thick with a 1.5A hydrocarbon contamination overlayer and 1.05 relative surface roughness. After geometric weighing of angle-resolved XPS and SESSA data, it was found that C16 COOH-SAMs on 14nm AuNPs were 17A thick with a 1.5A hydrocarbon contamination. The decreased SAM thickness on the AuNPs is likely due to an increased tilt angle of the alkane chains or increased disorder in the SAM.

Using Latent Class Modeling to Detect Bimodality in Spacing Effect Data

ERIC Educational Resources Information Center

Verkoeijen, Peter P. J. L.; Bouwmeester, Samantha

2008-01-01

A recently proposed theory of the spacing effect [Raaijmakers, J. G. W. (2003). Spacing and repetition effects in human memory: application of the SAM model. "Cognitive Science," 27, 431-452.] suggests that the spacing effect is conditional on study-phase retrieval leading to two groups of students showing different magnitudes of the spacing…

Structural insights into SAM domain‐mediated tankyrase oligomerization

PubMed Central

DaRosa, Paul A.; Ovchinnikov, Sergey

2016-01-01

Abstract Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP‐ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain‐mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head‐to‐tail polymer that facilitates TNKS self‐association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM‐TNKS2 SAM) hetero‐oligomeric structures mediated by their SAM domains. Though wild‐type tankyrase proteins have very low solubility, model‐based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP‐ribosyl)ation (PARylation) and PARylation‐dependent ubiquitylation. PMID:27328430

Efficient surface enhanced Raman scattering on confeito-like gold nanoparticle-adsorbed self-assembled monolayers.

PubMed

Chang, Chia-Chi; Imae, Toyoko; Chen, Liang-Yih; Ujihara, Masaki

2015-12-28

Confeito-like gold nanoparticles (AuNPs; average diameter = 80 nm) exhibiting a plasmon absorption band at 590 nm were adsorbed through immersion-adsorption on two self-assembled monolayers (SAMs) of 3-aminopropyltriethoxysilane (APTES-SAM) and polystyrene spheres coated with amine-terminated poly(amido amine) dendrimers (DEN/PS-SAM). The surface enhanced Raman scattering (SERS) effect on the SAM substrates was examined using the molecules of a probe dye, rhodamine 6G (R6G). The Raman scattering was strongly intensified on both substrates, but the enhancement factor (>10,000) of the AuNP/DEN/PS-SAM hierarchy substrate was 5-10 times higher than that of the AuNP/APTES-SAM substrate. This strong enhancement is attributed to the large surface area of the substrate and the presence of hot spots. Furthermore, analyzing the R6G concentration dependence of SERS suggested that the enhancement mechanism effectively excited the R6G molecules in the first layer on the hot spots and invoked the strong SERS effect. These results indicate that the SERS activity of confeito-like AuNPs on SAM substrates has high potential in molecular electronic devices and ultrasensitive analyses.

Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3.

PubMed

Leettola, Catherine N; Knight, Mary Jane; Cascio, Duilio; Hoffman, Sigrid; Bowie, James U

2014-07-07

Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic disorder leading to end-stage renal failure in humans. In the PKD/Mhm(cy/+) rat model of ADPKD, the point mutation R823W in the sterile alpha motif (SAM) domain of the protein ANKS6 is responsible for disease. SAM domains are known protein-protein interaction domains, capable of binding each other to form polymers and heterodimers. Despite its physiological importance, little is known about the function of ANKS6 and how the R823W point mutation leads to PKD. Recent work has revealed that ANKS6 interacts with a related protein called ANKS3. Both ANKS6 and ANKS3 have a similar domain structure, with ankyrin repeats at the N-terminus and a SAM domain at the C-terminus. The SAM domain of ANKS3 is identified as a direct binding partner of the ANKS6 SAM domain. We find that ANKS3-SAM polymerizes and ANKS6-SAM can bind to one end of the polymer. We present crystal structures of both the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex, revealing the molecular details of their association. We also learn how the R823W mutation disrupts ANKS6 function by dramatically destabilizing the SAM domain such that the interaction with ANKS3-SAM is lost. ANKS3 is a direct interacting partner of ANKS6. By structurally and biochemically characterizing the interaction between the ANKS3 and ANKS6 SAM domains, our work provides a basis for future investigation of how the interaction between these proteins mediates kidney function.

Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3

PubMed Central

2014-01-01

Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic disorder leading to end-stage renal failure in humans. In the PKD/Mhm(cy/+) rat model of ADPKD, the point mutation R823W in the sterile alpha motif (SAM) domain of the protein ANKS6 is responsible for disease. SAM domains are known protein-protein interaction domains, capable of binding each other to form polymers and heterodimers. Despite its physiological importance, little is known about the function of ANKS6 and how the R823W point mutation leads to PKD. Recent work has revealed that ANKS6 interacts with a related protein called ANKS3. Both ANKS6 and ANKS3 have a similar domain structure, with ankyrin repeats at the N-terminus and a SAM domain at the C-terminus. Results The SAM domain of ANKS3 is identified as a direct binding partner of the ANKS6 SAM domain. We find that ANKS3-SAM polymerizes and ANKS6-SAM can bind to one end of the polymer. We present crystal structures of both the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex, revealing the molecular details of their association. We also learn how the R823W mutation disrupts ANKS6 function by dramatically destabilizing the SAM domain such that the interaction with ANKS3-SAM is lost. Conclusions ANKS3 is a direct interacting partner of ANKS6. By structurally and biochemically characterizing the interaction between the ANKS3 and ANKS6 SAM domains, our work provides a basis for future investigation of how the interaction between these proteins mediates kidney function. PMID:24998259

Edge-to-edge repair for prevention and treatment of mitral valve systolic anterior motion.

PubMed

Myers, Patrick O; Khalpey, Zain; Maloney, Ann M; Brinster, Derek R; D'Ambra, Michael N; Cohn, Lawrence H

2013-10-01

The edge-to-edge technique has been proposed to prevent systolic anterior motion (SAM) of the mitral valve. There is limited clinical data available on outcomes of this technique for this indication. We reviewed the midterm results of this technique for SAM prevention and treatment. A total of 2226 patients had mitral valve repair between 2000 and 2011, 1148 of which were for myxomatous mitral regurgitation. Beginning in 2000, predictability of postrepair SAM based on the prebypass, intraoperative transesophageal echocardiogram arose in our program. The edge-to-edge technique was used in 65 patients (5.7%) for SAM management, in 53 patients preemptively for transesophageal echocardiogram-based SAM prediction, and in 12 patients for postrepair SAM treatment. There was no operative mortality. Postoperative mitral regurgitation was significantly improved in all patients compared with the preoperative grade (P < .001). SAM was completely eliminated, the mean mitral regurgitation grade in the postoperative period was 0.7 ± 0.9, and the mean transmitral gradient was 1.3 ± 2.2 mm Hg. During a mean follow-up of 26 months, 1 patient in the SAM treatment group presented late recurrence of SAM and no patients developed mitral stenosis (mean transmitral gradient, 2.0 ± 2.6 mm Hg; P = .12). Without SAM prediction and preemptive edge-to-edge technique, the expected rate of SAM would have been 5.7%; however, the observed rate was 1% (12 of 1148 patients). Initiating an expectation for prebypass SAM prediction, combined with a surgical SAM prevention strategy, resulted in a reduced prevalence of SAM compared with our model of observed to-expected-ratios and to published norms. Copyright © 2013 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

Effect of Time and Deposition Method on Quality of Phosphonic Acid Modifier Self-Assembled Monolayers on Indium Zinc Oxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sang, Lingzi; Knesting, Kristina M.; Bulusu, Anuradha

Phosphonic acid (PA) self-assembled monolayers (SAMs) are utilized at critical interfaces between transparent conductive oxides (TCO) and organic active layers in organic photovoltaic devices (OPVs). The effects of PA deposition method and time on the formation of close-packed, high-quality monolayers is investigated here for SAMs fabricated by solution deposition, micro-contact printing, and spray coating. The solution deposition isotherm for pentafluorinated benzylphosphonic acid (F5BnPA) on indium-doped zinc oxide (IZO) is studied using polarization modulation-infrared reflection-absorption spectroscopy (PM-IRRAS) at room temperature as a model PA/IZO system. Fast surface adsorption occurs within the first min; however, well-oriented high-quality SAMs are reached only aftermore » -48 h, presumably through a continual process of molecular adsorption/desorption and monolayer filling accompanied by molecular reorientation. Two other rapid, soak-free deposition techniques, micro-contact printing and spray coating, are also explored. SAM quality is compared for deposition of phenyl phosphonic acid (PPA), F13-octylphosphonic acid (F13OPA), and pentafluorinated benzyl phosphonic acid (F5BnPA) by solution deposition, micro-contact printing and spray coating using PM-IRRAS. In contrast to micro-contact printing and spray coating techniques, 48-168 h solution deposition at both room temperature and 70 degrees C result in contamination- and surface etch-free close-packed monolayers with good reproducibility. SAMs fabricated by micro-contact printing and spray coating are much less well ordered.« less

Development of a comprehensive urban commodity/freight movement model for Texas.

DOT National Transportation Integrated Search

2006-01-01

The Texas Department of Transportation (TxDOT) developed the Texas Statewide Analysis Model (SAM) to provide analysis and : forecasting capabilities of passenger and commodity/freight movements in Texas. The SAM provides data and results at a level :...

SAM Technical Review Committee Final Report: Summary and Key Recommendations from the Onsite TRC Meeting Held April 22-23, 2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blair, N.; Dobos, S.; Janzou, S.

2013-08-01

The System Advisor Model (SAM) is a broad and robust set of models and frameworks for analyzing both system performance and system financing. It does this across a range of technologies dominated by solar technologies including photovoltaics (PV) and concentrated solar power (CSP). The U.S. Department of Energy (DOE) Solar Energy Technology Program requested the SAM development team to review the photovoltaic performance modeling with the development community and specifically, with the independent engineering community. The report summarizes the major effort for this technical review committee (TRC).

Technoeconomic Modeling of Battery Energy Storage in SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiOrio, Nicholas; Dobos, Aron; Janzou, Steven

Detailed comprehensive lead-acid and lithium-ion battery models have been integrated with photovoltaic models in an effort to allow System Advisor Model (SAM) to offer the ability to predict the performance and economic benefit of behind the meter storage. In a system with storage, excess PV energy can be saved until later in the day when PV production has fallen, or until times of peak demand when it is more valuable. Complex dispatch strategies can be developed to leverage storage to reduce energy consumption or power demand based on the utility rate structure. This document describes the details of the batterymore » performance and economic models in SAM.« less

Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance.

PubMed

Hutchins, Daniel Orrin; Weidner, Tobias; Baio, Joe; Polishak, Brent; Acton, Orb; Cernetic, Nathan; Ma, Hong; Jen, Alex K-Y

2013-01-04

A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH 2 ) 12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm 2 V -1 s -1 . It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm 2 V -1 s -1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed.

Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance

PubMed Central

Hutchins, Daniel Orrin; Weidner, Tobias; Baio, Joe; Polishak, Brent; Acton, Orb; Cernetic, Nathan; Ma, Hong; Jen, Alex K.-Y.

2013-01-01

A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH2)12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm2 V−1 s−1. It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm2 V−1 s−1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed. PMID:24086795

Improving the productivity of S-adenosyl-l-methionine by metabolic engineering in an industrial Saccharomyces cerevisiae strain.

PubMed

Zhao, Weijun; Hang, Baojian; Zhu, Xiangcheng; Wang, Ri; Shen, Minjie; Huang, Lei; Xu, Zhinan

2016-10-20

S-Adenosyl-l-methionine (SAM) is an important metabolite having prominent roles in treating various diseases. In order to improve the production of SAM, the regulation of three metabolic pathways involved in SAM biosynthesis were investigated in an industrial yeast strain ZJU001. GLC3 encoded glycogen-branching enzyme (GBE), SPE2 encoded SAM decarboxylase, as well as ERG4 and ERG6 encoded key enzymes in ergosterol biosynthesis, were knocked out in ZJU001 accordingly. The results indicated that blocking of either glycogen pathway or SAM decarboxylation pathway could improve the SAM accumulation significantly in ZJU001, while single disruption of either ERG4 or ERG6 gene had no obvious effect on SAM production. Moreover, the double mutant ZJU001-GS with deletion of both GLC3 and SPE2 genes was also constructed, which showed further improvement of SAM accumulation. Finally, SAM2 was overexpressed in ZJU001-GS to give the best SAM-producing recombinant strain ZJU001-GS-SAM2, in which 12.47g/L SAM was produced by following our developed pseudo-exponential fed-batch cultivation strategy, about 81.0% increase comparing to its parent strain ZJU001. The present work laid a solid base for large-scale SAM production with the industrial Saccharomyces cerevisiae strain. Copyright © 2016 Elsevier B.V. All rights reserved.

Infrared spectroscopy of large scale single layer graphene on self assembled organic monolayer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woo Kim, Nak; Youn Kim, Joo; Lee, Chul

2014-01-27

We study the effect of self-assembled monolayer (SAM) organic molecule substrate on large scale single layer graphene using infrared transmission measurement on Graphene/SAM/SiO{sub 2}/Si composite samples. From the Drude weight of the chemically inert CH{sub 3}-SAM, the electron-donating NH{sub 2}-SAM, and the SAM-less graphene, we determine the carrier density doped into graphene by the three sources—the SiO{sub 2} substrate, the gas-adsorption, and the functional group of the SAM's—separately. The SAM-treatment leads to the low carrier density N ∼ 4 × 10{sup 11} cm{sup −2} by blocking the dominant SiO{sub 2}- driven doping. The carrier scattering increases by the SAM-treatment rather than decreases. However, the transportmore » mobility is nevertheless improved due to the reduced carrier doping.« less

SAM-2 ground-truth plan: Correlative measurements for the Stratospheric Aerosol Measurement-2 (SAM 2) sensor on the Nimbus G satellite

NASA Technical Reports Server (NTRS)

Russell, P. B.; Mccormick, M. P.; Mcmaster, L. R.; Pepin, T. J.; Chu, W. P.; Swissler, T. J.

1978-01-01

The SAM-2 will fly aboard the Nimbus-G satellite for launch in the fall of 1978 and measure stratospheric vertical profiles of aerosol extinction in high latitude bands. The plan gives details of the location and times for the simultaneous satellite/correlative measurements for the nominal launch time, the rationale and choice of the correlative sensors, their characteristics and expected accuracies, and the conversion of their data to extinction profiles. The SAM-2 expected instrument performance and data inversion results are presented. Various atmospheric models representative of polar stratospheric aerosols are used in the SAM-2 and correlative sensor analyses.

Stabilization of S-adenosyl-L-methionine promoted by trehalose.

PubMed

Morana, Alessandra; Stiuso, Paola; Colonna, Giovanni; Lamberti, Monica; Cartenì, Maria; De Rosa, Mario

2002-11-14

S-adenosyl-L-methionine (SAM), an important metabolic intermediate of mammals, is a well-known therapeutic agent. The molecule is chemically unstable, both in solution and in dry state, and forms different degradation products. Because the chemical instability represents a real problem during the preparation of therapeutic formulations, we investigated the capacity of some sugars to improve the SAM stability over time. In the present work, we demonstrated that the disaccharide trehalose exercises a protective effect towards the lyophilized SAM slackening its degradation (65% of SAM was detected after 50 days at 37 degrees C). A parallel study, performed to stabilize the SAM into lyophilized yeast cells enriched in the sulfonium compound, assessed the positive effect of trehalose also in whole cells, but in lesser measure.

The Use of Explosion Aftershock Probabilities for Planning and Deployment of Seismic Aftershock Monitoring System for an On-site Inspection

NASA Astrophysics Data System (ADS)

Labak, P.; Ford, S. R.; Sweeney, J. J.; Smith, A. T.; Spivak, A.

2011-12-01

One of four elements of CTBT verification regime is On-site inspection (OSI). Since the sole purpose of an OSI shall be to clarify whether a nuclear weapon test explosion or any other nuclear explosion has been carried out, inspection activities can be conducted and techniques used in order to collect facts to support findings provided in inspection reports. Passive seismological monitoring, realized by the seismic aftershock monitoring (SAMS) is one of the treaty allowed techniques during an OSI. Effective planning and deployment of SAMS during the early stages of an OSI is required due to the nature of possible events recorded and due to the treaty related constrains on size of inspection area, size of inspection team and length of an inspection. A method, which may help in planning the SAMS deployment is presented. An estimate of aftershock activity due to a theoretical underground nuclear explosion is produced using a simple aftershock rate model (Ford and Walter, 2010). The model is developed with data from the Nevada Test Site and Semipalatinsk Test Site, which we take to represent soft- and hard-rock testing environments, respectively. Estimates of expected magnitude and number of aftershocks are calculated using the models for different testing and inspection scenarios. These estimates can help to plan the SAMS deployment for an OSI by giving a probabilistic assessment of potential aftershocks in the Inspection Area (IA). The aftershock assessment combined with an estimate of the background seismicity in the IA and an empirically-derived map of threshold magnitude for the SAMS network could aid the OSI team in reporting. We tested the hard-rock model to a scenario similar to the 2008 Integrated Field Exercise 2008 deployment in Kazakhstan and produce an estimate of possible recorded aftershock activity.

The effectiveness of treatment for Severe Acute Malnutrition (SAM) delivered by community health workers compared to a traditional facility based model.

PubMed

Alvarez Morán, J L; Alé, G B Franck; Charle, P; Sessions, N; Doumbia, S; Guerrero, S

2018-03-27

In most health systems, Community Health Workers (CHWs) identify and screen for severe acute malnutrition (SAM) in the community. This study aimed to investigate the potential of integrating SAM identification and treatment delivered by CHWs, in order to improve the coverage of SAM treatment services. This multicentre, randomised intervention study was conducted in Kita, Southwest Mali between February 2015 and February 2016. Treatment for uncomplicated SAM was provided in health facilities in the control area, and by Community Health Workers and health facilities in the intervention area. Clinical outcomes (cure, death and defaulter ratios), treatment coverage and quality of care were examined in both the control and intervention group. Six hundred ninety nine children were admitted to the intervention group and 235 children to the control group. The intervention group reported cure ratios of 94.2% compared to 88.6% in the control group (risk ratio 1.07 [95% CI 1.01; 1.13]). Defaulter ratios were twice as high in the control group compared to the intervention group (10.8% vs 4.5%; RR 0.42 [95% CI 0.25; 0.71]). Differences in mortality ratios were not statistically significant (0.9% in the intervention group compared to 0.8% in the control group). Coverage rates in December 2015 were 86.7% in intervention group compared to 41.6% in the control (p < 0.0001). With minimal training, CHWs are able to appropriately treat SAM in the community. Allowing CHWs to treat SAM reduces defaulter ratios without compromising treatment outcomes and can lead to improved access to treatment. Retrospectively registered in ISRCTN Register with ISRCTN33578874 on March 7th 2018.

Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montange, R.; Mondragon, E; van Tyne, D

2010-01-01

The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-{angstrom} X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-{angstrom} improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity ofmore » SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.« less

Analysis of the liver mitochondrial proteome in response to ethanol and S-adenosylmethionine treatments: novel molecular targets of disease and hepatoprotection.

PubMed

Andringa, Kelly K; King, Adrienne L; Eccleston, Heather B; Mantena, Sudheer K; Landar, Aimee; Jhala, Nirag C; Dickinson, Dale A; Squadrito, Giuseppe L; Bailey, Shannon M

2010-05-01

S-adenosylmethionine (SAM) minimizes alcohol hepatotoxicity; however, the molecular mechanisms responsible for SAM hepatoprotection remain unknown. Herein, we use proteomics to determine whether the hepatoprotective action of SAM against early-stage alcoholic liver disease is linked to alterations in the mitochondrial proteome. For this, male rats were fed control or ethanol-containing liquid diets +/- SAM and liver mitochondria were prepared for proteomic analysis. Two-dimensional isoelectric focusing (2D IEF/SDS-PAGE) and blue native gel electrophoresis (BN-PAGE) were used to determine changes in matrix and oxidative phosphorylation (OxPhos) proteins, respectively. SAM coadministration minimized alcohol-dependent inflammation and preserved mitochondrial respiration. SAM supplementation preserved liver SAM levels in ethanol-fed rats; however, mitochondrial SAM levels were increased by ethanol and SAM treatments. With use of 2D IEF/SDS-PAGE, 30 proteins showed significant changes in abundance in response to ethanol, SAM, or both. Classes of proteins affected by ethanol and SAM treatments were chaperones, beta oxidation proteins, sulfur metabolism proteins, and dehydrogenase enzymes involved in methionine, glycine, and choline metabolism. BN-PAGE revealed novel changes in the levels of 19 OxPhos proteins in response to ethanol, SAM, or both. Ethanol- and SAM-dependent alterations in the proteome were not linked to corresponding changes in gene expression. In conclusion, ethanol and SAM treatment led to multiple changes in the liver mitochondrial proteome. The protective effects of SAM against alcohol toxicity are mediated, in part, through maintenance of proteins involved in key mitochondrial energy conserving and biosynthetic pathways. This study demonstrates that SAM may be a promising candidate for treatment of alcoholic liver disease.

Sam68 promotes Schwann cell proliferation by enhancing the PI3K/Akt pathway and acts on regeneration after sciatic nerve crush

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Weijie, E-mail: 459586768@qq.com; Liu, Yuxi, E-mail: 924013616@qq.com; Wang, Youhua, E-mail: wyouhua1516@163.com

Sam68 (Src-associated in mitosis of 68 kD), a KH domain RNA-binding protein, is not only important in signaling transduction cascades, but crucial in a variety of cellular processes. Sam68 is reported to be involved in the phospoinositide3-kinase (PI3K) and nuclear factor-kappa B (NF-κB) signaling pathways, and it is closely associated with cell proliferation, RNA metabolism, and tumor progression. However, we know little about the role of Sam68 during peripheral nervous system injury and regeneration. In this study, we investigated the expression of Sam68 and its biological significances in sciatic nerve crush. Interestingly, we found Sam68 had a co-localization with S100 (Schwannmore » cell marker). Moreover, after crush, Sam68 had a spatiotemporal protein expression, which was in parallel with proliferation cell nuclear antigen (PCNA). In vitro, we also observed increased expression of Sam68 during the process of TNF-α-induced Schwann cell proliferation model. Besides, flow cytometry analyses, CCK-8, and EDU were all performed with the purpose of investigating the role of Sam68 in the regulation of Schwann cell proliferation. Even more importantly, we discovered that Sam68 could enhance the phosphorylation of Akt while LY294002 (a PI3K inhibitor) obviously reversed Sam68-induced cell proliferation. Finally, we detected the variance during regeneration progress through the rat walk footprint test. In summary, all these evidences demonstrated that Sam68 might participate in Schwann cell proliferation partially via PI3K/Akt pathway and also regulate regeneration after sciatic nerve crush. -- Highlights: •The dynamic changes and location of Sam68 after sciatic nerve crush. •Sam68 promoted Schwann cell proliferation via PI3K/Akt pathway. •Sam68 modulated functional recovery after sciatic nerve crush.« less

Giant Shoot Apical Meristems in Cacti Have Ordinary Leaf Primordia but Altered Phyllotaxy and Shoot Diameter

PubMed Central

MAUSETH, JAMES D.

2004-01-01

• Background and Aims Shoot apical meristems (SAMs) in most seed plants are quite uniform in size and zonation, and molecular genetic studies of Arabidopsis and other model plants are revealing details of SAM morphogenesis. Some cacti have SAMs much larger than those of A. thaliana and other seed plants. This study examined how SAM size affects leaf primordium (LP) size, phyllotaxy and shoot diameter. • Methods. Apices from 183 species of cacti were fixed, microtomed and studied by light microscopy. • Key Results Cactus SAM diameter varies from 93 to 2565 µm, the latter being 36 times wider than SAMs of A. thaliana and having a volume 45 thousand times larger. Phyllotaxy ranges from distichous to having 56 rows of leaves and is not restricted to Fibonacci numbers. Leaf primordium diameter ranges from 44 to 402 µm, each encompassing many more cells than do LP of other plants. Species with high phyllotaxy have smaller LP, although the correlation is weak. There is almost no correlation between SAM diameter and LP size, but SAM diameter is strongly correlated with shoot diameter, with shoots being about 189·5 times wider than SAMs. • Conclusions Presumably, genes such as SHOOT‐MERISTEMLESS, WUSCHEL and CLAVATA must control much larger volumes of SAM tissue in cacti than they do in A. thaliana, and genes such as PERIANTHIA might establish much more extensive fields of inhibition around LP. These giant SAMs should make it possible to more accurately map gene expression patterns relative to SAM zonation and LP sites. PMID:15145794

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

PubMed Central

Reimers, Jeffrey R.; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J.; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J. J.; Hendriksen, Bas L. M.; Elemans, Johannes A. A. W.; Hush, Noel S.; Crossley, Maxwell J.

2015-01-01

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate−molecule interactions (e.g., −100 kcal mol−1 to −150 kcal mol−1 for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70–110 kcal mol−1) and entropy effects (25–40 kcal mol−1 at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations. PMID:26512115

Electroactive Self-Assembled Monolayers Detect Micelle Formation.

PubMed

Dionne, Eric R; Badia, Antonella

2017-02-15

The interfacial electrochemistry of self-assembled monolayers (SAMs) of ferrocenyldodecanethiolate on gold (FcC 12 SAu) electrodes is applied to detect the micellization of some common anionic surfactants, sodium n-alkyl sulfates, sodium n-alkyl sulfonates, sodium diamyl sulfosuccinate, and sodium dodecanoate, in aqueous solution by cyclic voltammetry. The apparent formal redox potential (E°' SAM ) of the FcC 12 SAu SAM is used to track changes in the concentration of the unaggregated surfactant anions and determine the critical micelle concentration (cmc). The effect of added salt (NaF) on the sodium alkyl sulfate concentration dependence of E°' SAM is also investigated. Weakly hydrated anions, such as ClO 4 - , pair with the electrogenerated SAM-bound ferroceniums to neutralize the excess positive charge created at the SAM/electrolyte solution interface and stabilize the oxidized cations. E°' SAM exhibits a Nernstian-type dependence on the anion activity in solution. Aggregation of the surfactant anions into micelles above the cmc causes the free surfactant anion activity to deviate from the molar concentration of added surfactant, resulting in a break in the plot of E°' SAM versus the logarithm of the concentration of anionic surfactant. The concentration at which this deviation occurs is in good agreement with literature or experimentally determined values of the cmc. The effects of Ohmic potential drop, liquid junction potential, and surfactant adsorption behavior on E°' SAM are addressed. Ultimately, the E°' SAM response as a function of the anionic surfactant concentration exhibits the same features reported using potentiometry and surfactant ion-selective electrodes, which provide a direct measure of the free surfactant anion activity, thus making FcC 12 SAu SAM electrodes useful for the detection of surfactant aggregation and micelle formation.

Contributions of Greenhouse Gas Forcing and the Southern Annular Mode to Historical Southern Ocean Surface Temperature Trends

NASA Astrophysics Data System (ADS)

Kostov, Yavor; Ferreira, David; Armour, Kyle C.; Marshall, John

2018-01-01

We examine the 1979-2014 Southern Ocean (SO) sea surface temperature (SST) trends simulated in an ensemble of coupled general circulation models and evaluate possible causes of the models' inability to reproduce the observed 1979-2014 SO cooling. For each model we estimate the response of SO SST to step changes in greenhouse gas (GHG) forcing and in the seasonal indices of the Southern Annular Mode (SAM). Using these step-response functions, we skillfully reconstruct the models' 1979-2014 SO SST trends. Consistent with the seasonal signature of the Antarctic ozone hole and the seasonality of SO stratification, the summer and fall SAM exert a large impact on the simulated SO SST trends. We further identify conditions that favor multidecadal SO cooling: (1) a weak SO warming response to GHG forcing, (2) a strong multidecadal SO cooling response to a positive SAM trend, and (3) a historical SAM trend as strong as in observations.

The "ComPAS Trial" combined treatment model for acute malnutrition: study protocol for the economic evaluation.

PubMed

Lelijveld, Natasha; Bailey, Jeanette; Mayberry, Amy; Trenouth, Lani; N'Diaye, Dieynaba S; Haghparast-Bidgoli, Hassan; Puett, Chloe

2018-04-24

Acute malnutrition is currently divided into severe (SAM) and moderate (MAM) based on level of wasting. SAM and MAM currently have separate treatment protocols and products, managed by separate international agencies. For SAM, the dose of treatment is allocated by the child's weight. A combined and simplified protocol for SAM and MAM, with a standardised dose of ready-to-use therapeutic food (RUTF), is being trialled for non-inferior recovery rates and may be more cost-effective than the current standard protocols for treating SAM and MAM. This is the protocol for the economic evaluation of the ComPAS trial, a cluster-randomised controlled, non-inferiority trial that compares a novel combined protocol for treating uncomplicated acute malnutrition compared to the current standard protocol in South Sudan and Kenya. We will calculate the total economic costs of both protocols from a societal perspective, using accounting data, interviews and survey questionnaires. The incremental cost of implementing the combined protocol will be estimated, and all costs and outcomes will be presented as a cost-consequence analysis. Incremental cost-effectiveness ratio will be calculated for primary and secondary outcome, if statistically significant. We hypothesise that implementing the combined protocol will be cost-effective due to streamlined logistics at clinic level, reduced length of treatment, especially for MAM, and reduced dosages of RUTF. The findings of this economic evaluation will be important for policymakers, especially given the hypothesised non-inferiority of the main health outcomes. The publication of this protocol aims to improve rigour of conduct and transparency of data collection and analysis. It is also intended to promote inclusion of economic evaluation in other nutrition intervention studies, especially for MAM, and improve comparability with other studies. ISRCTN 30393230 , date: 16/03/2017.

In situ analysis of martian regolith with the SAM experiment during the first mars year of the MSL mission: Identification of organic molecules by gas chromatography from laboratory measurements

NASA Astrophysics Data System (ADS)

Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; François, P.; Coscia, D.; Bonnet, J. Y.; Teinturier, S.; Cabane, M.; Mahaffy, P. R.

2016-09-01

The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

In Situ Analysis of Martian Regolith with the SAM Experiment During the First Mars Year of the MSL Mission: Identification of Organic Molecules by Gas Chromatography from Laboratory Measurements

NASA Technical Reports Server (NTRS)

Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; Francois, P.; Coscia, D.; Bonnet, J. Y.;

The methyl donor S-adenosylmethionine prevents liver hypoxia and dysregulation of mitochondrial bioenergetic function in a rat model of alcohol-induced fatty liver disease.

PubMed

King, Adrienne L; Mantena, Sudheer K; Andringa, Kelly K; Millender-Swain, Telisha; Dunham-Snary, Kimberly J; Oliva, Claudia R; Griguer, Corinne E; Bailey, Shannon M

2016-10-01

Mitochondrial dysfunction and bioenergetic stress play an important role in the etiology of alcoholic liver disease. Previous studies from our laboratory show that the primary methyl donor S-Adenosylmethionine (SAM) minimizes alcohol-induced disruptions in several mitochondrial functions in the liver. Herein, we expand on these earlier observations to determine whether the beneficial actions of SAM against alcohol toxicity extend to changes in the responsiveness of mitochondrial respiration to inhibition by nitric oxide (NO), induction of the mitochondrial permeability transition (MPT) pore, and the hypoxic state of the liver. For this, male Sprague-Dawley rats were pair-fed control and alcohol-containing liquid diets with and without SAM for 5 weeks and liver hypoxia, mitochondrial respiration, MPT pore induction, and NO-dependent control of respiration were examined. Chronic alcohol feeding significantly enhanced liver hypoxia, whereas SAM supplementation attenuated hypoxia in livers of alcohol-fed rats. SAM supplementation prevented alcohol-mediated decreases in mitochondrial state 3 respiration and cytochrome c oxidase activity. Mitochondria isolated from livers of alcohol-fed rats were more sensitive to calcium-mediated MPT pore induction (i.e., mitochondrial swelling) than mitochondria from pair-fed controls, whereas SAM treatment normalized sensitivity for calcium-induced swelling in mitochondria from alcohol-fed rats. Liver mitochondria from alcohol-fed rats showed increased sensitivity to NO-dependent inhibition of respiration compared with pair-fed controls. In contrast, mitochondria isolated from the livers of SAM treated alcohol-fed rats showed no change in the sensitivity to NO-mediated inhibition of respiration. Collectively, these findings indicate that the hepato-protective effects of SAM against alcohol toxicity are mediated, in part, through a mitochondrial mechanism involving preservation of key mitochondrial bioenergetic parameters and the attenuation of hypoxic stress. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

The influence of ozone forcing on blocking in the Southern Hemisphere

NASA Astrophysics Data System (ADS)

Dennison, Fraser W.; McDonald, Adrian; Morgenstern, Olaf

2016-12-01

We investigate the influence of ozone depletion and recovery on tropospheric blocking in the Southern Hemisphere. Blocking events are identified using a persistent positive anomaly method applied to 500 hPa geopotential height. Using the National Institute for Water and Atmospheric Research-United Kingdom Chemistry and Aerosols chemistry-climate model, we compare reference runs that include forcing due to greenhouse gases (GHGs) and ozone-depleting substances to sensitivity simulations in which ozone-depleting substances are fixed at their 1960 abundances and other sensitivity simulations with GHGs fixed at their 1960 abundances. Blocking events in the South Atlantic are shown to follow stratospheric positive anomalies in the Southern Annular Mode (SAM) index; this is not the case for South Pacific blocking events. This relationship means that summer ozone depletion, and corresponding positive SAM anomalies, leads to an increased frequency of blocking in the South Atlantic while having little effect in the South Pacific. Similarly, ozone recovery, having the opposite effect on the SAM, leads to a decline in blocking frequency in the South Atlantic, although this may be somewhat counteracted by the effect of increasing GHGs.

The SAM, not the electrodes, dominates charge transport in metal-monolayer//Ga2O3/gallium-indium eutectic junctions.

PubMed

Reus, William F; Thuo, Martin M; Shapiro, Nathan D; Nijhuis, Christian A; Whitesides, George M

2012-06-26

The liquid-metal eutectic of gallium and indium (EGaIn) is a useful electrode for making soft electrical contacts to self-assembled monolayers (SAMs). This electrode has, however, one feature whose effect on charge transport has been incompletely understood: a thin (approximately 0.7 nm) film-consisting primarily of Ga(2)O(3)-that covers its surface when in contact with air. SAMs that rectify current have been measured using this electrode in Ag(TS)-SAM//Ga(2)O(3)/EGaIn (where Ag(TS) = template-stripped Ag surface) junctions. This paper organizes evidence, both published and unpublished, showing that the molecular structure of the SAM (specifically, the presence of an accessible molecular orbital asymmetrically located within the SAM), not the difference between the electrodes or the characteristics of the Ga(2)O(3) film, causes the observed rectification. By examining and ruling out potential mechanisms of rectification that rely either on the Ga(2)O(3) film or on the asymmetry of the electrodes, this paper demonstrates that the structure of the SAM dominates charge transport through Ag(TS)-SAM//Ga(2)O(3)/EGaIn junctions, and that the electrical characteristics of the Ga(2)O(3) film have a negligible effect on these measurements.

Gene switching in Amoeba proteus caused by endosymbiotic bacteria.

PubMed

Jeon, Taeck J; Jeon, Kwang W

2004-02-01

The expression of genes for S-adenosylmethionine synthetase (SAMS), which catalyzes the synthesis of S-adenosylmethionine (AdoMet), a major methyl donor in cells, was studied in symbiont-free (D) and symbiont-bearing (xD) amoeba strains to determine the effect of bacterial endosymbionts. The symbionts suppressed the expression of the gene in host xD amoebae, but amoebae still exhibited about half the enzyme activity found in symbiont-free D amoebae. The study was aimed at elucidating mechanisms of the suppression of the amoeba's gene and determining the alternative source for the gene product. Unexpectedly, we found a second sams (sams2) gene in amoebae, which encoded 390 amino acids. Results of experiments measuring SAMS activities and amounts of AdoMet in D and xD amoebae showed that the half SAMS activity found in xD amoebae came from the amoeba's SAMS2 and not from their endosymbionts. The expression of amoeba sams genes was switched from sams1 to sams2 as a result of infection with X-bacteria, raising the possibility that the switch in the expression of sams genes by bacteria plays a role in the development of symbiosis and the host-pathogen interactions. This is the first report showing such a switch in the expression of host sams genes by infecting bacteria.

Improving Learning for All Students through Equity-Based Inclusive Reform Practices: Effectiveness of a Fully Integrated Schoolwide Model on Student Reading and Math Achievement

ERIC Educational Resources Information Center

Choi, Jeong Hoon; Meisenheimer, Jessica M.; McCart, Amy B.; Sailor, Wayne

2017-01-01

The present investigation examines the schoolwide applications model (SAM) as a potentially effective school reform model for increasing equity-based inclusive education practices while enhancing student reading and math achievement for all students. A 3-year quasi-experimental comparison group analysis using latent growth modeling (LGM) was used…

Alzheimer Abeta(1-42) monomer adsorbed on the self-assembled monolayers.

PubMed

Wang, Qiuming; Zhao, Jun; Yu, Xiang; Zhao, Chao; Li, Lingyan; Zheng, Jie

2010-08-03

Amyloid-beta (Abeta) peptide aggregation on the cell membranes is a key pathological event responsible for neuron cell death in Alzheimer's disease (AD). We present a collection of molecular docking and molecular dynamics simulations to study the conformational dynamics and adsorption behavior of Abeta monomer on the self-assembled monolayer (SAM), in comparison to Abeta structure in bulk solution. Two distinct Abeta conformations (i.e., alpha-helix and beta-hairpin) are selected as initial structures to mimic different adsorption states, whereas four SAM surfaces with different end groups in hydrophobicity and charge distribution are used to examine the effect of surface chemistry on Abeta structure and adsorption. Simulation results show that alpha-helical monomer displays higher structural stability than beta-hairpin monomer on all SAMs, suggesting that the preferential conformation of Abeta monomer could be alpha-helical or random structure when bound to surfaces. Structural stability and adsorption behavior of Abeta monomer on the SAMs originates from competitive interactions between Abeta and SAM and between SAM and interfacial water, which involve the conformation of Abeta, the surface chemistry of SAM, and the structure and dynamics of interfacial waters. The relative net binding affinity of Abeta with the SAMs is in the favorable order of COOH-SAM > NH(2)-SAM > CH(3)-SAM > OH-SAM, highlighting the importance of electrostatic and hydrophobic interactions for driving Abeta adsorption at the SAMs, but both interactions contribute differently to each Abeta-SAM complex. This work provides parallel insights into the understanding of Abeta structure and aggregation on cell membrane.

EFFECTS OF POLYCYCLIC AROMATIC HYDROCARBON OF SAM-COATED ELECTRODES USING FERRYICYANIDE AS THE REDOX INDICATOR

EPA Science Inventory

Electrochemical responses on self-assembled monolayer (SAM)-coated polycrystalline gold electrodes were investigated using cyclic voltammetry and square wave voltammetry with a three electrode system. Experimental results show potential in the application of pyrene-imprinted SAM...

Adsorption of hydrophobin on different self-assembled monolayers: the role of the hydrophobic dipole and the electric dipole.

PubMed

Peng, Chunwang; Liu, Jie; Zhao, Daohui; Zhou, Jian

2014-09-30

In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.

The Improvement of SAM Accumulation by Integrating the Endogenous Methionine Adenosyltransferase Gene SAM2 in Genome of the Industrial Saccharomyces cerevisiae Strain.

PubMed

Zhao, Weijun; Shi, Feng; Hang, Baojian; Huang, Lei; Cai, Jin; Xu, Zhinan

2016-03-01

S-Adenosyl-L-methionine (SAM) plays important roles in trans-methylation, trans-sulfuration, and polyamine synthesis in all living cells, and it is also an effective cure for liver disease, depressive syndromes, and osteoarthritis. The increased demands of SAM in pharmaceuticals industry have aroused lots of attempts to improve its production. In this study, a multiple-copy integrative plasmid pYMIKP-SAM2 was introduced into the chromosome of wild-type Saccharomyces cerevisiae strain ZJU001 to construct the recombined strain R1-ZJU001. Further studies showed that the recombinant yeast exhibited higher enzymatic activity of methionine adenosyltransferase and improved its SAM biosynthesis. With a three-phase fed-batch strategy in 15-liter bench-top fermentor, 8.81 g/L SAM was achieved after 52 h cultivation of R1-ZJU001, about 27.1 % increase over its parent strain ZJU001, whereas the SAM content was also improved from 64.6 mg/g DCW to 91.0 mg/g DCW. Our results shall provide insights into the metabolic engineering of SAM pathway in yeast for improved productivity of SAM and subsequent industrial applications.

Atmospheric modeling of Mars CH4 subsurface clathrates releases mimicking SAM and 2003 Earth-based detections

NASA Astrophysics Data System (ADS)

Pla-Garcia, Jorge

2017-10-01

The aim of this work is to establish the amount of mixing during all martian seasons to test whether CH4 releases inside or outside of Gale crater are consistent with MSL-SAM observations. Several modeling scenarios were configured, including instantaneous and steady releases, both inside and outside the crater. A simulation to mimic the 2003 Earth-based detections (Mumma et al. 2009 or M09) was also performed. In the instantaneous release inside Gale experiments, Ls270 was shown to be the faster mixing season when air within and outside the crater was well mixed: all tracer mass inside the crater is diluted after just 8 hours. The mixing of near surface crater air with the external environment in the rest of the year is potentially rapid but slower than Ls270. In the instantaneous release outside Gale (NW) experiment, in just 12 hours the CH4 that makes it to the MSL landing location is diluted by six orders of magnitude. The timescale of mixing in the model is on the order of 1 sol regardless of season. The duration of the CH4 peak observed by SAM is 100 sols. Therefore there is a steady release inside the crater, or there is a large magnitude steady release outside the crater. In the steady release Gale experiments, CH4 flux rate from ground is 1.8 kg m-2 s-1 (Gloesener et al. 2017) and it is not predictive. In these experiments, ~200 times lower CH4 values detected by SAM are modeled around MSL location. There are CH4 concentration variations of orders of magnitude depending on the hour, so timing of SAM measurements is important. With a larger (but further away) outside crater release area compared to inside, similar CH4 values around MSL are modeled, so distance to source is important. In the steady experiments mimicking M09 detection release area, only 12 times lower CH4 values detected by SAM are modeled around MSL. The highest value in the M09 modeled scenario (0.6 ppbv) is reached in Ls270. This value is the highest of all modeled experiments. With our initial conditions, SAM should not be able to detect CH4, but if we multiply flux by 12, increase the release area or move it closer to MSL (or all of above), it may be possible to get CH4 values that SAM could detect regardless where it comes from.

Construct Validation of the Louisiana School Analysis Model (SAM) Instructional Staff Questionnaire

ERIC Educational Resources Information Center

Bray-Clark, Nikki; Bates, Reid

2005-01-01

The purpose of this study was to validate the Louisiana SAM Instructional Staff Questionnaire, a key component of the Louisiana School Analysis Model. The model was designed as a comprehensive evaluation tool for schools. Principle axis factoring with oblique rotation was used to uncover the underlying structure of the SISQ. (Contains 1 table.)

Severe acute malnutrition.

PubMed

Nel, E D

2016-05-01

The mortality and morbidity associated with severe acute malnutrition (SAM) remain high. A summary of recent studies that are of interest to clinicians treating children with SAM is provided. Three important themes emerged in 2015: the use of anthropometry in the diagnosis of SAM and its correlation with body composition; the composition of ready-to-use therapeutic feeds (RUTF); and an improved understanding of the pathophysiology of SAM. Standard anthropometry does not accurately predict body composition and mid-upper arm circumference more accurately reflects fat mass in children. As single measure, mid-upper arm circumference identifies those children who are most likely to die from SAM and is not influenced by dehydration. However, a significant proportion of SAM children requiring treatment will not be detected. Present RUTF formulations are deficient in long chain polyunsaturated fatty acids. Current evidence suggests that preformed docosahexaenoic acid should be added and/or the content of linoleic acid reduced in RUTF. In contrast to an animal model, stabile children with SAM have the same cardiac index as children without SAM. The situation in haemodynamically unstable children is unknown, continued conservative use of intravenous fluids seems advisable. A reduction in variability of the faecal DNA virome may account for increased susceptibility to malnutrition in vulnerable children.

Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

PubMed

Zhang, Yue; Barnes, George L; Yan, Tianying; Hase, William L

2010-05-07

Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Science, 2007, 317, 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface, and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly, much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM, perpendicular to the interface, results in nearly identical temperatures for the CH(2) and CH(3) groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate, the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM, there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.

Optical imaging beyond the diffraction limit by SNEM: effects of AFM tip modifications with thiol monolayers on imaging quality.

PubMed

Cumurcu, Aysegul; Diaz, Jordi; Lindsay, Ian D; de Beer, Sissi; Duvigneau, Joost; Schön, Peter; Julius Vancso, G

2015-03-01

Tip-enhanced nanoscale optical imaging techniques such as apertureless scanning near-field optical microscopy (a-SNOM) and scanning near-field ellipsometric microscopy (SNEM) applications can suffer from a steady degradation in performance due to adhesion of atmospheric contaminants to the metal coated tip. Here, we demonstrate that a self-assembled monolayer (SAM) of ethanethiol (EtSH) is an effective means of protecting gold-coated atomic force microscopy (AFM) probe tips from accumulation of surface contaminants during prolonged exposure to ambient air. The period over which they yield consistent and reproducible results for scanning near-field ellipsometric microscopy (SNEM) imaging is thus extended. SNEM optical images of a microphase separated polystyrene-block-poly (methylmethacrylate) (PS-b-PMMA) diblock copolymer film, which were captured with bare and SAM-protected gold-coated AFM probes, both immediately after coating and following five days of storage in ambient air, were compared. During this period the intensity of the optical signals from the untreated gold tip fell by 66%, while those from the SAM protected tip fell by 14%. Additionally, gold coated AFM probe tips were modified with various lengths of alkanethiols to measure the change in intensity variation in the optical images with SAM layer thickness. The experimental results were compared to point dipole model calculations. While a SAM of 1-dodecanethiol (DoSH) was found to strongly suppress field enhancement we find that it can be locally removed from the tip apex by deforming the molecules under load, restoring SNEM image contrast. Copyright © 2014 Elsevier B.V. All rights reserved.

Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch

PubMed Central

Boyapati, Vamsi Krishna; Huang, Wei; Spedale, Jessica; Aboul-ela, Fareed

2012-01-01

Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming “hybrid” structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding. PMID:22543867

Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch.

PubMed

Boyapati, Vamsi Krishna; Huang, Wei; Spedale, Jessica; Aboul-Ela, Fareed

2012-06-01

Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming "hybrid" structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.

A unifying view of the broad-spectrum antiviral activity of RSAD2 (viperin) based on its radical-SAM chemistry.

PubMed

Honarmand Ebrahimi, Kourosh

2018-04-25

RSAD2 (cig-5), also known as viperin (virus inhibitory protein, endoplasmic reticulum associated, interferon inducible), is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes. Since the discovery of this enzyme more than a decade ago, numerous studies have shown that it exhibits antiviral activity against a wide range of viruses. However, there is no clear picture demonstrating the mechanism by which RSAD2 restricts the replication process of different viruses, largely because there is no direct evidence describing its in vivo enzymatic activity. As a result, a multifunctionality model has emerged. According to this model the mechanism by which RSAD2 restricts replication of different viruses varies and in many cases is not dependent on the radical-SAM chemistry of RSAD2. If the radical-SAM activity of RSAD2 is not required for its antiviral function, the question worth asking is: why does the cellular defence mechanism induce the expression of the radical-SAM enzyme RSAD2, which is metabolically expensive due to the requirement for a [4Fe-4S] cluster and usage of SAM? Here, in contrast to the multifunctionality view, I put forward a unifying model. I postulate that the radical-SAM activity of RSAD2 modulates cellular metabolic pathways essential for viral replication and/or cell proliferation and survival. As a result, its catalytic activity restricts the replication of a wide range of viruses via a common cellular function. This view is based on recent discoveries hinting towards possible substrates of RSAD2, re-evaluation of previous studies regarding the antiviral activity of RSAD2, and accumulating evidence suggesting a role of human RSAD2 in the metabolic reprogramming of cells.

Predictions of psychophysical measurements for sinusoidal amplitude modulated (SAM) pulse-train stimuli from a stochastic model.

PubMed

Xu, Yifang; Collins, Leslie M

2007-08-01

Two approaches have been proposed to reduce the synchrony of the neural response to electrical stimuli in cochlear implants. One approach involves adding noise to the pulse-train stimulus, and the other is based on using a high-rate pulse-train carrier. Hypotheses regarding the efficacy of the two approaches can be tested using computational models of neural responsiveness prior to time-intensive psychophysical studies. In our previous work, we have used such models to examine the effects of noise on several psychophysical measures important to speech recognition. However, to date there has been no parallel analytic solution investigating the neural response to the high-rate pulse-train stimuli and their effect on psychophysical measures. This work investigates the properties of the neural response to high-rate pulse-train stimuli with amplitude modulated envelopes using a stochastic auditory nerve model. The statistics governing the neural response to each pulse are derived using a recursive method. The agreement between the theoretical predictions and model simulations is demonstrated for sinusoidal amplitude modulated (SAM) high rate pulse-train stimuli. With our approach, predicting the neural response in modern implant devices becomes tractable. Psychophysical measurements are also predicted using the stochastic auditory nerve model for SAM high-rate pulse-train stimuli. Changes in dynamic range (DR) and intensity discrimination are compared with that observed for noise-modulated pulse-train stimuli. Modulation frequency discrimination is also studied as a function of stimulus level and pulse rate. Results suggest that high rate carriers may positively impact such psychophysical measures.

The Growth-Suppressive Function of the Polycomb Group Protein Polyhomeotic Is Mediated by Polymerization of Its Sterile Alpha Motif (SAM) Domain*

PubMed Central

Robinson, Angela K.; Leal, Belinda Z.; Chadwell, Linda V.; Wang, Renjing; Ilangovan, Udayar; Kaur, Yogeet; Junco, Sarah E.; Schirf, Virgil; Osmulski, Pawel A.; Gaczynska, Maria; Hinck, Andrew P.; Demeler, Borries; McEwen, Donald G.; Kim, Chongwoo A.

2012-01-01

Polyhomeotic (Ph), a member of the Polycomb Group (PcG), is a gene silencer critical for proper development. We present a previously unrecognized way of controlling Ph function through modulation of its sterile alpha motif (SAM) polymerization leading to the identification of a novel target for tuning the activities of proteins. SAM domain containing proteins have been shown to require SAM polymerization for proper function. However, the role of the Ph SAM polymer in PcG-mediated gene silencing was uncertain. Here, we first show that Ph SAM polymerization is indeed required for its gene silencing function. Interestingly, the unstructured linker sequence N-terminal to Ph SAM can shorten the length of polymers compared with when Ph SAM is individually isolated. Substituting the native linker with a random, unstructured sequence (RLink) can still limit polymerization, but not as well as the native linker. Consequently, the increased polymeric Ph RLink exhibits better gene silencing ability. In the Drosophila wing disc, Ph RLink expression suppresses growth compared with no effect for wild-type Ph, and opposite to the overgrowth phenotype observed for polymer-deficient Ph mutants. These data provide the first demonstration that the inherent activity of a protein containing a polymeric SAM can be enhanced by increasing SAM polymerization. Because the SAM linker had not been previously considered important for the function of SAM-containing proteins, our finding opens numerous opportunities to manipulate linker sequences of hundreds of polymeric SAM proteins to regulate a diverse array of intracellular functions. PMID:22275371

Self assembled monolayers on silicon for molecular electronics.

PubMed

Aswal, D K; Lenfant, S; Guerin, D; Yakhmi, J V; Vuillaume, D

2006-05-24

We present an overview of various aspects of the self-assembly of organic monolayers on silicon substrates for molecular electronics applications. Different chemical strategies employed for grafting the self-assembled monolayers (SAMs) of alkanes having different chain lengths on native oxide of Si or on bare Si have been reviewed. The utility of different characterization techniques in determination of the thickness, molecular ordering and orientation, surface coverage, growth kinetics and chemical composition of the SAMs has been discussed by choosing appropriate examples. The metal counterelectrodes are an integral part of SAMs for measuring their electrical properties as well as using them for molecular electronic devices. A brief discussion on the variety of options available for the deposition of metal counterelectrodes, that is, soft metal contacts, vapor deposition and soft lithography, has been presented. Various theoretical models, namely, tunneling (direct and Fowler-Nordheim), thermionic emission, Poole-Frenkel emission and hopping conduction, used for explaining the electronic transport in dielectric SAMs have been outlined and, some experimental data on alkane SAMs have been analyzed using these models. It has been found that short alkyl chains show excellent agreement with tunneling models; while more experimental data on long alkyl chains are required to understand their transport mechanism(s). Finally, the concepts and realization of various molecular electronic components, that is, diodes, resonant tunnel diodes, memories and transistors, based on appropriate architecture of SAMs comprising of alkyl chains (sigma- molecule) and conjugated molecules (pi-molecule) have been presented.

Self-organizing map (SOM) of space acceleration measurement system (SAMS) data.

PubMed

Sinha, A; Smith, A D

1999-01-01

In this paper, space acceleration measurement system (SAMS) data have been classified using self-organizing map (SOM) networks without any supervision; i.e., no a priori knowledge is assumed regarding input patterns belonging to a certain class. Input patterns are created on the basis of power spectral densities of SAMS data. Results for SAMS data from STS-50 and STS-57 missions are presented. Following issues are discussed in details: impact of number of neurons, global ordering of SOM weight vectors, effectiveness of a SOM in data classification, and effects of shifting time windows in the generation of input patterns. The concept of 'cascade of SOM networks' is also developed and tested. It has been found that a SOM network can successfully classify SAMS data obtained during STS-50 and STS-57 missions.

Self-organizing map (SOM) of space acceleration measurement system (SAMS) data

NASA Technical Reports Server (NTRS)

Sinha, A.; Smith, A. D.

1999-01-01

In this paper, space acceleration measurement system (SAMS) data have been classified using self-organizing map (SOM) networks without any supervision; i.e., no a priori knowledge is assumed regarding input patterns belonging to a certain class. Input patterns are created on the basis of power spectral densities of SAMS data. Results for SAMS data from STS-50 and STS-57 missions are presented. Following issues are discussed in details: impact of number of neurons, global ordering of SOM weight vectors, effectiveness of a SOM in data classification, and effects of shifting time windows in the generation of input patterns. The concept of 'cascade of SOM networks' is also developed and tested. It has been found that a SOM network can successfully classify SAMS data obtained during STS-50 and STS-57 missions.

Spatial Analysis and Modeling Systems (SAMS)

NASA Technical Reports Server (NTRS)

Vermillion, Charles; Chan, Paul; Hill, John; Jaske, Robert; Rochon, Gilbert; Stetina, Fran

1991-01-01

The objective is to develop a uniform environmental data gathering and distribution system to support (1) emergency management for environmental disasters, and (2) the calibration and validation of remotely sensed data. Initial activities will be to select a data test site and to demonstrate multi-discipline applications using simulated or satellite data in a non real-time mode. Rainfall and flooding are chosen as the testbeds for the SAMS concept because of the abundance of data and the availability of models. The capability to display and process GOES data and analyze GOES generated rain-rate maps will be integrated into SAMS.

The SAM domain of ANKS6 has different interacting partners and mutations can induce different cystic phenotypes.

PubMed

Bakey, Zeineb; Bihoreau, Marie-Thérèse; Piedagnel, Rémi; Delestré, Laure; Arnould, Catherine; de Villiers, Alexandre d'Hotman; Devuyst, Olivier; Hoffmann, Sigrid; Ronco, Pierre; Gauguier, Dominique; Lelongt, Brigitte

2015-08-01

The ankyrin repeat and sterile α motif (SAM) domain-containing six gene (Anks6) is a candidate for polycystic kidney disease (PKD). Originally identified in the PKD/Mhm(cy/+) rat model of PKD, the disease is caused by a mutation (R823W) in the SAM domain of the encoded protein. Recent studies support the etiological role of the ANKS6 SAM domain in human cystic diseases, but its function in kidney remains unknown. To investigate the role of ANKS6 in cyst formation, we screened an archive of N-ethyl-N-nitrosourea-treated mice and derived a strain carrying a missense mutation (I747N) within the SAM domain of ANKS6. This mutation is only six amino acids away from the PKD-causing mutation (R823W) in cy/+ rats. Evidence of renal cysts in these mice confirmed the crucial role of the SAM domain of ANKS6 in kidney function. Comparative phenotype analysis in cy/+ rats and our Anks6(I747N) mice further showed that the two models display noticeably different PKD phenotypes and that there is a defective interaction between ANKS6 with ANKS3 in the rat and between ANKS6 and BICC1 (bicaudal C homolog 1) in the mouse. Thus, our data demonstrate the importance of ANKS6 for kidney structure integrity and the essential mediating role of its SAM domain in the formation of protein complexes.

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

PubMed Central

Huang, Wei; Kim, Joohyun; Jha, Shantenu; Aboul-ela, Fareed

2013-01-01

Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites. Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression. Previous structural studies of riboswitches largely focused on aptamers, truncating the expression domain to suppress conformational switching. To link ligand/aptamer binding to conformational switching, we constructed models of an S-adenosyl methionine (SAM)-I riboswitch RNA segment incorporating elements of the expression platform, allowing formation of an antiterminator (AT) helix. Using Anton, a computer specially developed for long timescale Molecular Dynamics (MD), we simulated an extended (three microseconds) MD trajectory with SAM bound to a modeled riboswitch RNA segment. Remarkably, we observed a strand migration, converting three base pairs from an antiterminator (AT) helix, characteristic of the transcription ON state, to a P1 helix, characteristic of the OFF state. This conformational switching towards the OFF state is observed only in the presence of SAM. Among seven extended trajectories with three starting structures, the presence of SAM enhances the trend towards the OFF state for two out of three starting structures tested. Our simulation provides a visual demonstration of how a small molecule (<500 MW) binding to a limited surface can trigger a large scale conformational rearrangement in a 40 kDa RNA by perturbing the Free Energy Landscape. Such a mechanism can explain minimal requirements for SAM binding and transcription termination for SAM-I riboswitches previously reported experimentally. PMID:23704854

48 CFR 9.405 - Effect of listing.

Code of Federal Regulations, 2014 CFR

2014-10-01

... contractors. (b) Contractors included in the SAM Exclusions as having been declared ineligible on the basis of... proposals, the contracting officer shall review the SAM Exclusions. (2) Bids received from any listed... to award, the contracting officer shall again review the SAM Exclusions to ensure that no award is...

48 CFR 9.405 - Effect of listing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... contractors. (b) Contractors included in the SAM Exclusions as having been declared ineligible on the basis of... proposals, the contracting officer shall review the SAM Exclusions. (2) Bids received from any listed... to award, the contracting officer shall again review the SAM Exclusions to ensure that no award is...

A Retrieval Model for Both Recognition and Recall.

ERIC Educational Resources Information Center

Gillund, Gary; Shiffrin, Richard M.

1984-01-01

The Search of Associative Memory (SAM) model for recall is extended by assuming that a familiarity process is used for recognition. The model, formalized in a computer simulation program, correctly predicts a number of findings in the literature as well as results from an experiment on the word-frequency effect. (Author/BW)

17 CFR Appendix to Subpart B of... - Model Forms

Code of Federal Regulations, 2013 CFR

2013-04-01

...) REGULATIONS S-P AND S-AM Regulation S-AM: Limitations on Affiliate Marketing Pt. 248, Subpt. B, App. Appendix...—Model Form for Initial Opt Out Notice (Single-Affiliate Notice)—[Your Choice to Limit Marketing]/[Marketing Opt Out] • [Name of Affiliate] is providing this notice. • [Optional: Federal law gives you the...

17 CFR Appendix to Subpart B of... - Model Forms

Code of Federal Regulations, 2012 CFR

2012-04-01

...) REGULATIONS S-P AND S-AM Regulation S-AM: Limitations on Affiliate Marketing Pt. 248, Subpt. B, App. Appendix...—Model Form for Initial Opt Out Notice (Single-Affiliate Notice)—[Your Choice to Limit Marketing]/[Marketing Opt Out] • [Name of Affiliate] is providing this notice. • [Optional: Federal law gives you the...

17 CFR Appendix to Subpart B of... - Model Forms

Code of Federal Regulations, 2011 CFR

2011-04-01

...) REGULATIONS S-P AND S-AM Regulation S-AM: Limitations on Affiliate Marketing Pt. 248, Subpt. B, App. Appendix...—Model Form for Initial Opt Out Notice (Single-Affiliate Notice)—[Your Choice to Limit Marketing]/[Marketing Opt Out] • [Name of Affiliate] is providing this notice. • [Optional: Federal law gives you the...

The nuclear protein Sam68 is cleaved by the FMDV 3C protease redistributing Sam68 to the cytoplasm during FMDV infection of host cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawrence, Paul; Schafer, Elizabeth A.; Rieder, Elizabeth, E-mail: elizabeth.rieder@ars.usda.gov

2012-03-30

Picornavirus infection can lead to disruption of nuclear pore traffic, shut-off of cell translation machinery, and cleavage of proteins involved in cellular signal transduction and the innate response to infection. Here, we demonstrated that the FMDV 3C{sup pro} induced the cleavage of nuclear RNA-binding protein Sam68 C-terminus containing the nuclear localization sequence (NLS). Consequently, it stimulated the redistribution of Sam68 to the cytoplasm. The siRNA knockdown of Sam68 resulted in a 1000-fold reduction in viral titers, which prompted us to study the effect of Sam68 on FMDV post-entry events. Interestingly, Sam68 interacts with the internal ribosomal entry site within themore » 5 Prime non-translated region of the FMDV genome, and Sam68 knockdown decreased FMDV IRES-driven activity in vitro suggesting that it could modulate translation of the viral genome. The results uncover a novel role for Sam68 in the context of picornaviruses and the proteolysis of a new cellular target of the FMDV 3C{sup pro}.« less

Future's operation areas: new-generation suppression enemy air defence (SEAD) elements

NASA Astrophysics Data System (ADS)

Hazinedar, Ä.°lker

2015-05-01

Since air vehicles took place in the theater of operations, they have become the indispensable elements and the strongest attack power of armed forces. In the following period, with technological development, supersonic aircrafts took place in the operation area and this increased effectiveness of air vehicles much more. Air forces have used these aircrafts during important missions like strategic attack and air defense operations. On the other hand, decision makers understood that it was not feasible to intercept fighter aircrafts by executing combat air patrol flight missions. Since there is not enough reaction time to intercept the high speed aircrafts, ground stationed Surface to Air Missiles (SAM) system requirement has emerged. Therefore, SAM systems took place in the operation scene as well. Due to the fact that SAM systems emerged against the attack power, the attack aircrafts are to keep away from the fire of the ground stationed SAM systems. Hence, the requirement of Suppression Enemy Air Defense (SEAD) arose. SEAD elements take under suppression the radar of the SAM systems. In this way, attack aircrafts are able to attack without the risk of SAM systems. The purpose of this study is to find new methods or concepts in order to protect friendly attack aircrafts against ground based surface to air missiles' fires. Modernization of SAM systems and new generation SAM system producing activities have proceeded with positive acceleration. So, current SEAD elements and concepts are not able to cover the requirements due to the increased SAM system ranges. According to the concepts, SEAD weapons` ranges must be longer than the SAM weapons' ranges to protect friendly aircrafts. In this study, new concept was offered to overcome the deficiencies of current SEAD concept. The elements of new concepts were put forward. Classic SEAD concept and new generation concepts were assessed by using SWOT analysis technique. As a result, this study has revealed that, air forces' effectiveness can be enhanced by using new generation SEAD concepts against enemy SAM systems.

Structural investigation of a C-terminal EphA2 receptor mutant: Does mutation affect the structure and interaction properties of the Sam domain?

PubMed

Mercurio, Flavia A; Costantini, Susan; Di Natale, Concetta; Pirone, Luciano; Guariniello, Stefano; Scognamiglio, Pasqualina L; Marasco, Daniela; Pedone, Emilia M; Leone, Marilisa

2017-09-01

Ephrin A2 receptor (EphA2) plays a key role in cancer, it is up-regulated in several types of tumors and the process of ligand-induced receptor endocytosis, followed by degradation, is considered as a potential path to diminish tumor malignancy. Protein modulators of this mechanism are recruited at the cytosolic Sterile alpha motif (Sam) domain of EphA2 (EphA2-Sam) through heterotypic Sam-Sam associations. These interactions engage the C-terminal helix of EphA2 and close loop regions (the so called End Helix side). In addition, several studies report on destabilizing mutations in EphA2 related to cataract formation and located in/or close to the Sam domain. Herein, we analyzed from a structural point of view, one of these mutants characterized by the insertion of a novel 39 residue long polypeptide at the C-terminus of EphA2-Sam. A 3D structural model was built by computational methods and revealed partial disorder in the acquired C-terminal tail and a few residues participating in an α-helix and two short β-strands. We investigated by CD and NMR studies the conformational properties in solution of two peptides encompassing the whole C-terminal tail and its predicted helical region, respectively. NMR binding experiments demonstrated that these peptides do not interact relevantly with either EphA2-Sam or its interactor Ship2-Sam. Molecular dynamics (MD) simulations further indicated that the EphA2 mutant could be represented only through a conformational ensemble and that the C-terminal tail should not largely wrap the EphA2-Sam End-Helix interface and affect binding to other Sam domains. Copyright © 2017 Elsevier B.V. All rights reserved.

Regulation of C. elegans presynaptic differentiation and neurite branching via a novel signaling pathway initiated by SAM-10

PubMed Central

Zheng, Qun; Schaefer, Anneliese M.; Nonet, Michael L.

2011-01-01

Little is known about transcriptional control of neurite branching or presynaptic differentiation, events that occur relatively late in neuronal development. Using the Caenorhabditis elegans mechanosensory circuit as an in vivo model, we show that SAM-10, an ortholog of mammalian single-stranded DNA-binding protein (SSDP), functions cell-autonomously in the nucleus to regulate synaptic differentiation, as well as positioning of, a single neurite branch. PLM mechanosensory neurons in sam-10 mutants exhibit abnormal placement of the neurite branch point, and defective synaptogenesis, characterized by an overextended synaptic varicosity, underdeveloped synaptic morphology and disrupted colocalization of active zone and synaptic vesicles. SAM-10 functions coordinately with Lim domain-binding protein 1 (LDB-1), demonstrated by our observations that: (1) mutations in either gene show similar defects in PLM neurons; and (2) LDB-1 is required for SAM-10 nuclear localization. SAM-10 regulates PLM synaptic differentiation by suppressing transcription of prk-2, which encodes an ortholog of the mammalian Pim kinase family. PRK-2-mediated activities of SAM-10 are specifically involved in PLM synaptic differentiation, but not other sam-10 phenotypes such as neurite branching. Thus, these data reveal a novel transcriptional signaling pathway that regulates neuronal specification of neurite branching and presynaptic differentiation. PMID:21115607

Regulation of C. elegans presynaptic differentiation and neurite branching via a novel signaling pathway initiated by SAM-10.

PubMed

Zheng, Qun; Schaefer, Anneliese M; Nonet, Michael L

2011-01-01

Little is known about transcriptional control of neurite branching or presynaptic differentiation, events that occur relatively late in neuronal development. Using the Caenorhabditis elegans mechanosensory circuit as an in vivo model, we show that SAM-10, an ortholog of mammalian single-stranded DNA-binding protein (SSDP), functions cell-autonomously in the nucleus to regulate synaptic differentiation, as well as positioning of, a single neurite branch. PLM mechanosensory neurons in sam-10 mutants exhibit abnormal placement of the neurite branch point, and defective synaptogenesis, characterized by an overextended synaptic varicosity, underdeveloped synaptic morphology and disrupted colocalization of active zone and synaptic vesicles. SAM-10 functions coordinately with Lim domain-binding protein 1 (LDB-1), demonstrated by our observations that: (1) mutations in either gene show similar defects in PLM neurons; and (2) LDB-1 is required for SAM-10 nuclear localization. SAM-10 regulates PLM synaptic differentiation by suppressing transcription of prk-2, which encodes an ortholog of the mammalian Pim kinase family. PRK-2-mediated activities of SAM-10 are specifically involved in PLM synaptic differentiation, but not other sam-10 phenotypes such as neurite branching. Thus, these data reveal a novel transcriptional signaling pathway that regulates neuronal specification of neurite branching and presynaptic differentiation.

Laparoscopic transgastric circumferential stapler-assisted versus endoscopic esophageal mucosectomy in a porcine model

PubMed Central

Steinemann, Daniel C.; Zerz, Andreas; Müller, Philip C.; Sauer, Peter; Schaible, Anja; Lasitschka, Felix; Schwarz, Anne-Catherine; Müller-Stich, Beat P.; Linke, Georg R.

2018-01-01

Background and study aims Extensive endoscopic mucosal resection (EMR) for Barrett’s esophagus (BE) may lead to stenosis. Laparoscopic, transgastric, stapler-assisted mucosectomy (SAM) retrieving circumferential specimens is proposed. Methods SAM was evaluated in two phases. The feasibility of SAM and the quality of specimens was assessed in eight animals. The mucosal healing was evaluated in a 6-weeks survival experiment comparing SAM (n=6) and EMR (n=6). The ratio of the esophageal lumen width (REL) at the resection level measured in fluoroscopy after 6-weeks divided by the width immediately after resection was compared. Results In all animals a circular mucosectomy specimen was successfully obtained with an area of 492(426-573)mm2 and 941(813-1209)mm2 using a 21-mm and 25-mm stapler, respectively. In the survival experiments two animals developed symptomatic stenosis after EMR and none after SAM. The REL was 0.27[0.18-0.39] and 0.96[0.9-1.04] (p<0.0001) for EMR and SAM, respectively. Conclusions SAM provides a novel technique for en-bloc mucosectomy in BE. In contrast to EMR mucosal healing in SAM was not associated with stenosis up to six weeks after intervention. PMID:28301879

Electron Processing at 50 eV of Terphenylthiol Self-Assembled Monolayers: Contributions of Primary and Secondary Electrons.

PubMed

Houplin, Justine; Dablemont, Céline; Sala, Leo; Lafosse, Anne; Amiaud, Lionel

2015-12-22

Aromatic self-assembled monolayers (SAMs) can serve as platforms for development of supramolecular assemblies driven by surface templates. For many applications, electron processing is used to locally reinforce the layer. To achieve better control of the irradiation step, chemical transformations induced by electron impact at 50 eV of terphenylthiol SAMs are studied, with these SAMs serving as model aromatic SAMs. High-resolution electron energy loss spectroscopy (HREELS) and electron-stimulated desorption (ESD) of neutral fragment measurements are combined to investigate electron-induced chemical transformation of the layer. The decrease of the CH stretching HREELS signature is mainly attributed to dehydrogenation, without a noticeable hybridization change of the hydrogenated carbon centers. Its evolution as a function of the irradiation dose gives an estimate of the effective hydrogen content loss cross-section, σ = 2.7-4.7 × 10(-17) cm(2). Electron impact ionization is the major primary mechanism involved, with the impact electronic excitation contributing only marginally. Therefore, special attention is given to the contribution of the low-energy secondary electrons to the induced chemistry. The effective cross-section related to dissociative secondary electron attachment at 6 eV is estimated to be 1 order of magnitude smaller. The 1 eV electrons do not induce significant chemical modification for a 2.5 mC cm(-2) dose, excluding their contribution.

Electrochemistry of redox-active self-assembled monolayers

PubMed Central

Eckermann, Amanda L.; Feld, Daniel J.; Shaw, Justine A.; Meade, Thomas J.

2010-01-01

Redox-active self-assembled monolayers (SAMs) provide an excellent platform for investigating electron transfer kinetics. Using a well-defined bridge, a redox center can be positioned at a fixed distance from the electrode and electron transfer kinetics probed using a variety of electrochemical techniques. Cyclic voltammetry, AC voltammetry, electrochemical impedance spectroscopy, and chronoamperometry are most commonly used to determine the rate of electron transfer of redox-activated SAMs. A variety of redox species have been attached to SAMs, and include transition metal complexes (e.g., ferrocene, ruthenium pentaammine, osmium bisbipyridine, metal clusters) and organic molecules (e.g., galvinol, C60). SAMs offer an ideal environment to study the outer-sphere interactions of redox species. The composition and integrity of the monolayer and the electrode material influence the electron transfer kinetics and can be investigated using electrochemical methods. Theoretical models have been developed for investigating SAM structure. This review discusses methods and monolayer compositions for electrochemical measurements of redox-active SAMs. PMID:20563297

Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

PubMed

Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

2016-09-19

Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, characterization, and relative stabilities of self-assembled monolayers on gold generated from bidentate n-alkyl xanthic acids.

PubMed

Moore, H Justin; Colorado, Ramon; Lee, Han Ju; Jamison, Andrew C; Lee, T Randall

2013-08-27

A series of self-assembled monolayers (SAMs) on gold were generated by the adsorption of n-alkyl xanthic acids (NAXAs) having the general formula CH3(CH2)nOCS2H (n = 12-15). The structural features of these SAMs were characterized by optical ellipsometry, contact angle goniometry, polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and X-ray photoelectron spectroscopy (XPS). This series of xanthate SAMs were compared to SAMs generated from the corresponding n-alkanethiols and aliphatic dithiocarboxylic acids (ADTCAs). The collected data indicate that the NAXAs generate densely packed and well-ordered monolayers. The contact angles of hexadecane on the xanthate monolayers exhibited a large "odd-even" effect similar to that produced by the ADTCA SAMs. The relative stability of these bidentate xanthate SAMs was evaluated by monitoring the changes in ellipsometric thicknesses and wettability as a function of time under various conditions. The results demonstrate that SAMs formed from NAXAs are much less stable than analogous n-alkanethiolate and ADTCA SAMs.

Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer

PubMed Central

Luan, Binquan; Afzali, Ali; Harrer, Stefan; Peng, Hongbo; Waggoner, Philip; Polonsky, Stas; Stolovitzky, Gustavo; Martyna, Glenn

2010-01-01

A biomimetic nanochannel coated with a self-assembled monolayer (SAM) can be used for sensing and analyzing biomolecules. The interaction between a transported biomolecule and a SAM governs the mechanically or electrically driven motion of the molecule. To investigate the translocation dynamics of a biomolecule, we performed all-atom molecular dynamics simulations on a single-stranded DNA in a solid-state nanochannel coated with a SAM that consists of octane or octanol polymers. Simulation results demonstrate that the interaction between DNA and a hydrophobic or a hydrophilic SAM is effectively repulsive or adhesive, respectively, resulting in different translocation dynamics of DNA. Therefore, with proper designs of SAMs coated on a channel surface, it is possible to control the translocation dynamics of a biomolecule. This work also demonstrates that traditional tribology methods can be deployed to study a biological or bio-mimetic transport process. PMID:21128651

Surface adhesion and confinement variation of Staphylococcus aurius on SAM surfaces

NASA Astrophysics Data System (ADS)

Amroski, Alicia; Olsen, Morgan; Calabrese, Joseph; Senevirathne, Reshani; Senevirathne, Indrajith

2012-02-01

Controlled surface adhesion of non - pathogenic gram positive strain, Staphylococcus aureus is interesting as a model system due to possible development of respective biosensors for prevention and detection of the pathogenic strain methicillin resistant Staphylococcus aureus (MRSA) and further as a study for bio-machine interfacing. Self Assembled Monolayers (SAM) with engineered surfaces of linear thiols on Au(111) were used as the substrate. Sub cultured S. aureus were used for the analysis. The SAM layered surfaces were dipped in 2 -- 4 Log/ml S. aureus solution. Subsequent surface adhesion at different bacterial dilutions on surfaces will be discussed, and correlated with quantitative and qualitative adhesion properties of bacteria on the engineered SAM surfaces. The bacteria adhered SAM surfaces were investigated using intermittent contact, noncontact, lateral force and contact modes of Atomic Force Microscopy (AFM).

Properties of Self-Assembled Monolayers Revealed via Inverse Tensiometry.

PubMed

Chen, Jiahao; Wang, Zhengjia; Oyola-Reynoso, Stephanie; Thuo, Martin M

2017-11-28

Self-assembled monolayers (SAMs) have emerged as a simple platform technology and hence have been broadly studied. With advances in state-of-the-art fabrication and characterization methods, new insights into SAM structure and related properties have been delineated, albeit with some discrepancies and/or incoherencies. Some discrepancies, especially between experimental and theoretical work, are in part due to the misunderstanding of subtle structural features such as phase evolution and SAM quality. Recent work has, however, shown that simple techniques, such as the measurement of static contact angles, can be used to delineate otherwise complex properties of the SAM, especially when complemented by other more advanced techniques. In this article, we highlight the effect of nanoscale substrate asperities and molecular chain length on the SAM structure and associated properties. First, surfaces with tunable roughness are prepared on both Au and Ag, and their corresponding n-alkanethiolate SAMs are characterized through wetting and spectroscopy. From these data, chain-length- and substrate-morphology-dependent limits to the odd-even effect (structure and properties vary with the number of carbons in the molecules and the nature of the substrate), parametrization of gauche defect densities, and structural phase evolution (liquidlike, waxy, crystalline interfaces) are deduced. An evaluation of the correlation between the effect of roughness and the components of surface tension (polar-γ p and dispersive-γ d ) reveals that wetting, at nanoscale rough surfaces, evolves proportionally with the ratio of the two components of surface tension. The evolution of conformational order is captured over a range of molecular lengths and parametrized through a dimensionless number, χ c . By deploying a well-known tensiometry technique (herein the liquid is used to characterize the solid, hence the term inverse tensiometry) to characterize SAMs, we demonstrate that complex molecular-level phenomena in SAMs can be understood through simplicity.

Perceptions of usage and unintended consequences of provision of ready-to-use therapeutic food for management of severe acute child malnutrition. A qualitative study in Southern Ethiopia.

PubMed

Tadesse, Elazar; Berhane, Yemane; Hjern, Anders; Olsson, Pia; Ekström, Eva-Charlotte

2015-12-01

Severe acute child malnutrition (SAM) is associated with high risk of mortality. To increase programme effectiveness in management of SAM, community-based management of acute malnutrition (CMAM) programme that treats SAM using ready-to-use-therapeutic foods (RUTF) has been scaled-up and integrated into existing government health systems. The study aimed to examine caregivers' and health workers perceptions of usages of RUTF in a chronically food insecure area in South Ethiopia. This qualitative study recorded, transcribed and translated focus group discussions and individual interviews with caregivers of SAM children and community health workers (CHWs). Data were complemented with field notes before qualitative content analysis was applied. RUTF was perceived and used as an effective treatment of SAM; however, caregivers also see it as food to be shared and when necessary a commodity to be sold for collective benefits for the household. Caregivers expected prolonged provision of RUTF to contribute to household resources, while the programme guidelines prescribed RUTF as a short-term treatment to an acute condition in a child. To get prolonged access to RUTF caregivers altered the identities of SAM children and sought multiple admissions to CMAM programme at different health posts that lead to various control measures by the CHWs. Even though health workers provide RUTF as a treatment for SAM children, their caregivers use it also for meeting broader food and economic needs of the household endangering the effectiveness of CMAM programme. In chronically food insecure contexts, interventions that also address economic and food needs of entire household are essential to ensure successful treatment of SAM children. This may need a shift to view SAM as a symptom of broader problems affecting a family rather than a disease in an individual child. © The Author 2015. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Perceptions of usage and unintended consequences of provision of ready-to-use therapeutic food for management of severe acute child malnutrition. A qualitative study in Southern Ethiopia

PubMed Central

Tadesse, Elazar; Berhane, Yemane; Hjern, Anders; Olsson, Pia; Ekström, Eva-Charlotte

2015-01-01

Background: Severe acute child malnutrition (SAM) is associated with high risk of mortality. To increase programme effectiveness in management of SAM, community-based management of acute malnutrition (CMAM) programme that treats SAM using ready-to-use-therapeutic foods (RUTF) has been scaled-up and integrated into existing government health systems. The study aimed to examine caregivers’ and health workers perceptions of usages of RUTF in a chronically food insecure area in South Ethiopia. Methods: This qualitative study recorded, transcribed and translated focus group discussions and individual interviews with caregivers of SAM children and community health workers (CHWs). Data were complemented with field notes before qualitative content analysis was applied. Results: RUTF was perceived and used as an effective treatment of SAM; however, caregivers also see it as food to be shared and when necessary a commodity to be sold for collective benefits for the household. Caregivers expected prolonged provision of RUTF to contribute to household resources, while the programme guidelines prescribed RUTF as a short-term treatment to an acute condition in a child. To get prolonged access to RUTF caregivers altered the identities of SAM children and sought multiple admissions to CMAM programme at different health posts that lead to various control measures by the CHWs. Conclusion: Even though health workers provide RUTF as a treatment for SAM children, their caregivers use it also for meeting broader food and economic needs of the household endangering the effectiveness of CMAM programme. In chronically food insecure contexts, interventions that also address economic and food needs of entire household are essential to ensure successful treatment of SAM children. This may need a shift to view SAM as a symptom of broader problems affecting a family rather than a disease in an individual child. PMID:25749873

17 CFR Appendix to Subpart B of... - Model Forms

Code of Federal Regulations, 2014 CFR

2014-04-01

...) REGULATIONS S-P, S-AM, AND S-ID Regulation S-AM: Limitations on Affiliate Marketing Pt. 248, Subpt. B, App...—Model Form for Initial Opt Out Notice (Single-Affiliate Notice)—[Your Choice to Limit Marketing]/[Marketing Opt Out] • [Name of Affiliate] is providing this notice. • [Optional: Federal law gives you the...

A Confirmatory Factor Analysis of the Structure of Statistics Anxiety Measure: An examination of four alternative models

PubMed Central

Vahedi, Shahram; Farrokhi, Farahman

2011-01-01

Objective The aim of this study is to explore the confirmatory factor analysis results of the Persian adaptation of Statistics Anxiety Measure (SAM), proposed by Earp. Method The validity and reliability assessments of the scale were performed on 298 college students chosen randomly from Tabriz University in Iran. Confirmatory factor analysis (CFA) was carried out to determine the factor structures of the Persian adaptation of SAM. Results As expected, the second order model provided a better fit to the data than the three alternative models. Conclusions Hence, SAM provides an equally valid measure for use among college students. The study both expands and adds support to the existing body of math anxiety literature. PMID:22952530

[German translation and validation of the Stress Appraisal Measure (SAM)].

PubMed

Delahaye, M; Stieglitz, R D; Graf, M; Keppler, C; Maes, J; Pflueger, M

2015-05-01

In the present study, the German-language version of the Stress Appraisal Measure (SAM) by Peacock and Wong was validated in a student population. SAM is a relatively short questionnaire (28 items) that evaluates a current, stress-triggering event. The theoretical background is provided by the stress model of Lazarus and Folkman. 85 students (age: 23; 59 female, 26 male) were exposed to two stress scenarios in order to test whether they were suited to provoke stress. A factor analysis was performed and the internal consistency of the seven SAM scales was determined. In addition, the convergent validity of SAM with State and Trait Anxiety Inventory (STAI), Coping Inventory for Stressful Situations (CISS) and specific emotion scales was investigated via Pearson's product-moment correlation. The two stress scenarios were suited to evoke stress. The factor structure and the internal consistency of the individual scales, as well as the convergent validity of SAM were replicated with minor limitations in the present German version. Some items (especially from the fifth factor) were only replicated partially. SAM can also be employed in the German language version. © Georg Thieme Verlag KG Stuttgart · New York.

The Social Accuracy Model of Interpersonal Perception: Assessing Individual Differences in Perceptive and Expressive Accuracy

ERIC Educational Resources Information Center

Biesanz, Jeremy C.

2010-01-01

The social accuracy model of interpersonal perception (SAM) is a componential model that estimates perceiver and target effects of different components of accuracy across traits simultaneously. For instance, Jane may be generally accurate in her perceptions of others and thus high in "perceptive accuracy"--the extent to which a particular…

Query Monitoring and Analysis for Database Privacy - A Security Automata Model Approach

PubMed Central

Kumar, Anand; Ligatti, Jay; Tu, Yi-Cheng

2015-01-01

Privacy and usage restriction issues are important when valuable data are exchanged or acquired by different organizations. Standard access control mechanisms either restrict or completely grant access to valuable data. On the other hand, data obfuscation limits the overall usability and may result in loss of total value. There are no standard policy enforcement mechanisms for data acquired through mutual and copyright agreements. In practice, many different types of policies can be enforced in protecting data privacy. Hence there is the need for an unified framework that encapsulates multiple suites of policies to protect the data. We present our vision of an architecture named security automata model (SAM) to enforce privacy-preserving policies and usage restrictions. SAM analyzes the input queries and their outputs to enforce various policies, liberating data owners from the burden of monitoring data access. SAM allows administrators to specify various policies and enforces them to monitor queries and control the data access. Our goal is to address the problems of data usage control and protection through privacy policies that can be defined, enforced, and integrated with the existing access control mechanisms using SAM. In this paper, we lay out the theoretical foundation of SAM, which is based on an automata named Mandatory Result Automata. We also discuss the major challenges of implementing SAM in a real-world database environment as well as ideas to meet such challenges. PMID:26997936

Query Monitoring and Analysis for Database Privacy - A Security Automata Model Approach.

PubMed

Kumar, Anand; Ligatti, Jay; Tu, Yi-Cheng

2015-11-01

Privacy and usage restriction issues are important when valuable data are exchanged or acquired by different organizations. Standard access control mechanisms either restrict or completely grant access to valuable data. On the other hand, data obfuscation limits the overall usability and may result in loss of total value. There are no standard policy enforcement mechanisms for data acquired through mutual and copyright agreements. In practice, many different types of policies can be enforced in protecting data privacy. Hence there is the need for an unified framework that encapsulates multiple suites of policies to protect the data. We present our vision of an architecture named security automata model (SAM) to enforce privacy-preserving policies and usage restrictions. SAM analyzes the input queries and their outputs to enforce various policies, liberating data owners from the burden of monitoring data access. SAM allows administrators to specify various policies and enforces them to monitor queries and control the data access. Our goal is to address the problems of data usage control and protection through privacy policies that can be defined, enforced, and integrated with the existing access control mechanisms using SAM. In this paper, we lay out the theoretical foundation of SAM, which is based on an automata named Mandatory Result Automata. We also discuss the major challenges of implementing SAM in a real-world database environment as well as ideas to meet such challenges.

Atmospheric modeling of Mars CH4 subsurface clathrates releases mimicking SAM and 2003 Earth-based detections

NASA Astrophysics Data System (ADS)

Pla-García, J.; Rafkin, S. C.

2017-12-01

The aim of this work is to establish the amount of mixing during all martian seasons to test whether CH4 releases inside or outside of Gale crater are consistent with MSL-SAM observations. Several modeling scenarios were configured, including instantaneous and steady releases, both inside and outside the crater. A simulation to mimic the 2003 Earth-based detections (Mumma et al. 2009 or M09) was also performed. In the instantaneous release inside Gale experiments, Ls270 was shown to be the faster mixing season when air within and outside the crater was well mixed: all tracer mass inside the crater is diluted after just 8 hours. The mixing of near surface crater air with the external environment in the rest of the year is potentially rapid but slower than Ls270.In the instantaneous release outside Gale (NW) experiment, in just 12 hours the CH4 that makes it to the MSL landing location is diluted by six orders of magnitude. The timescale of mixing in MRAMS experiments is on the order of 1 sol regardless of season. The duration of the CH4 peak observed by SAM is 100 sols. Therefore there is a steady release inside the crater, or there is a very large magnitude steady release outside the crater. In the steady release Gale experiments, CH4 flux rate from ground is 1.8 kg m-2 s-1 (derived from Gloesener et al. 2017 clathrates fluxes) and it is not predictive. In these experiments, 200 times lower CH4 values detected by SAM are modeled around MSL location. There are CH4 concentration variations of orders of magnitude depending on the hour, so timing of SAM measurements is important. With a larger (but further away) outside crater release area compared to inside, similar CH4 values around MSL are modeled, so distance to source is important. In the steady experiments mimicking M09 detection release area, only 12 times lower CH4 values detected by SAM are modeled around MSL. The highest value in the M09 modeled scenario (0.6 ppbv) is reached in Ls270. This value is the highest of all modeled experiments. With our initial conditions (flux rates, release area size and distance to MSL), SAM should not be able (or very difficult) to detect CH4, but if we multiply flux by 12, increase the release area or move it closer to MSL (or all of above), it may be possible to get CH4 values that SAM could detect regardless where it comes from: inside, outside (close to) or far away from Gale.

Self-assembled monolayers from biphenyldithiol derivatives: optimization of the deprotection procedure and effect of the molecular conformation.

PubMed

Shaporenko, Andrey; Elbing, Mark; Błaszczyk, Alfred; von Hänisch, Carsten; Mayor, Marcel; Zharnikov, Michael

2006-03-09

A series of biphenyl-derived dithiol (BDDT) compounds with terminal acetyl-protected sulfur groups and different structural arrangements of both phenyl rings have been synthesized and fully characterized. The different arrangements were achieved by introducing hydrocarbon substituents in the 2 and 2' positions of the biphenyl backbone. The presented model compounds enable the investigation of the correlation between the intramolecular conformation and other physical properties of interest, like, e.g., molecular assembly or electronic transport properties. Here, the ability of these model compounds to form self-assembled monolayers (SAMs) on Au(111) and Ag(111) is investigated in details. The deprotection of the target molecules was performed in situ using either NH4OH or triethylamine (TEA) deprotection agent. The fabricated films were characterized by synchrotron-based high-resolution photoelectron spectroscopy and near-edge absorption fine structure spectroscopy. Whereas the deprotection by NH4OH was found to result in the formation of multilayer films, the deprotection by TEA allowed the preparation of densely packed BDDT SAMs with a noticeably higher orientational order and smaller molecular inclination on Ag than on Au. Introduction of the alkyl bridge between the individual rings of the biphenyl backbone did not lead to a noticeable change in the structure and packing density of the BDDT SAMs as long as the molecule had a planar conformation in the respective SAM. The deviation from this conformation resulted in the deterioration of the film quality and a decrease of the orientational order.

Protective Effects of Hericium erinaceus Mycelium and Its Isolated Erinacine A against Ischemia-Injury-Induced Neuronal Cell Death via the Inhibition of iNOS/p38 MAPK and Nitrotyrosine

PubMed Central

Lee, Kam-Fai; Chen, Jiann-Hwa; Teng, Chih-Chuan; Shen, Chien-Heng; Hsieh, Meng-Chiao; Lu, Chien-Chang; Lee, Ko-Chao; Lee, Li-Ya; Chen, Wan-Ping; Chen, Chin-Chu; Huang, Wen-Shih; Kuo, Hsing-Chun

2014-01-01

Hericium erinaceus, an edible mushroom, has been demonstrated to potentiate the effects of numerous biological activities. The aim of this study was to investigate whether H. erinaceus mycelium could act as an anti-inflammatory agent to bring about neuroprotection using a model of global ischemic stroke and the mechanisms involved. Rats were treated with H. erinaceus mycelium and its isolated diterpenoid derivative, erinacine A, after ischemia reperfusion brain injuries caused by the occlusion of the two common carotid arteries. The production of inflammatory cytokines in serum and the infracted volume of the brain were measured. The proteins from the stroke animal model (SAM) were evaluated to determine the effect of H. erinaceus mycelium. H. erinaceus mycelium reduced the total infarcted volumes by 22% and 44% at a concentration of 50 and 300 mg/kg, respectively, compared to the SAM group. The levels of acute inflammatory cytokines, including interleukin-1β, interleukin-6 and tumor necrosis factor á, were all reduced by erinacine A. Levels of nitrotyrosine-containing proteins, phosphorylation of p38 MAPK and CCAAT enhancer-binding protein (C/EBP) and homologous protein (CHOP) expression were attenuated by erinacine A. Moreover, the modulation of ischemia injury factors present in the SAM model by erinacine A seemed to result in the suppression of reactive nitrogen species and the downregulation of inducible NO synthase (iNOS), p38 MAPK and CHOP. These findings confirm the nerve-growth properties of Hericium erinaceus mycelium, which include the prevention of ischemic injury to neurons; this protective effect seems to be involved in the in vivo activity of iNOS, p38 MAPK and CHOP. PMID:25167134

Protective effects of Hericium erinaceus mycelium and its isolated erinacine A against ischemia-injury-induced neuronal cell death via the inhibition of iNOS/p38 MAPK and nitrotyrosine.

PubMed

Lee, Kam-Fai; Chen, Jiann-Hwa; Teng, Chih-Chuan; Shen, Chien-Heng; Hsieh, Meng-Chiao; Lu, Chien-Chang; Lee, Ko-Chao; Lee, Li-Ya; Chen, Wan-Ping; Chen, Chin-Chu; Huang, Wen-Shih; Kuo, Hsing-Chun

2014-08-27

Hericium erinaceus, an edible mushroom, has been demonstrated to potentiate the effects of numerous biological activities. The aim of this study was to investigate whether H. erinaceus mycelium could act as an anti-inflammatory agent to bring about neuroprotection using a model of global ischemic stroke and the mechanisms involved. Rats were treated with H. erinaceus mycelium and its isolated diterpenoid derivative, erinacine A, after ischemia reperfusion brain injuries caused by the occlusion of the two common carotid arteries. The production of inflammatory cytokines in serum and the infracted volume of the brain were measured. The proteins from the stroke animal model (SAM) were evaluated to determine the effect of H. erinaceus mycelium. H. erinaceus mycelium reduced the total infarcted volumes by 22% and 44% at a concentration of 50 and 300 mg/kg, respectively, compared to the SAM group. The levels of acute inflammatory cytokines, including interleukin-1β, interleukin-6 and tumor necrosis factor á, were all reduced by erinacine A. Levels of nitrotyrosine-containing proteins, phosphorylation of p38 MAPK and CCAAT enhancer-binding protein (C/EBP) and homologous protein (CHOP) expression were attenuated by erinacine A. Moreover, the modulation of ischemia injury factors present in the SAM model by erinacine A seemed to result in the suppression of reactive nitrogen species and the downregulation of inducible NO synthase (iNOS), p38 MAPK and CHOP. These findings confirm the nerve-growth properties of Hericium erinaceus mycelium, which include the prevention of ischemic injury to neurons; this protective effect seems to be involved in the in vivo activity of iNOS, p38 MAPK and CHOP.

Increasing faculty participation in resident education and providing cost-effective self-assessment module credit to faculty through resident-generated didactics.

PubMed

Kim, Hyun; Malatesta, Theresa M; Anné, Pramila R; McAna, John; Bar-Ad, Voichita; Dicker, Adam P; Den, Robert B

Board certified radiation oncologists and medical physicists are required to earn self-assessment module (SAM) continuing medical education (CME) credit, which may require travel costs or usage fees. Data indicate that faculty participation in resident teaching activities is beneficial to resident education. Our hypothesis was that providing the opportunity to earn SAM credit in resident didactics would increase faculty participation in and improve resident education. SAM applications, comprising CME certified category 1 resident didactic lectures and faculty-generated questions with respective answers, rationales, and references, were submitted to the American Board of Radiology for formal review. Surveys were distributed to assess main academic campus physician, affiliate campus physician, physicist, and radiation oncology resident impressions regarding the quality of the lectures. Survey responses were designed in Likert-scale format. Sign-test was performed with P < .05 considered statistically different from neutral. First submission SAM approval was obtained for 9 of 9 lectures to date. A total of 52 SAM credits have been awarded to 4 physicists and 7 attending physicians. Main academic campus physician and affiliate campus physician attendance increased from 20% and 0%, respectively, over the 12 months preceding CME/SAM lectures, to 55.6% and 20%, respectively. Survey results indicated that the change to SAM lectures increased the quality of resident lectures (P = .001), attending physician participation in resident education (P < .0001), physicist involvement in medical resident education (P = .0006), and faculty motivation to attend resident didactics (P = .004). Residents reported an increased amount of time required to prepare lectures (P = .008). We are the first department, to our knowledge, to offer SAM credit to clinical faculty for participation in resident-generated didactics. Offering SAM credit at resident lectures is a cost-effective alternative to purchasing SAM resources, increases faculty attendance, and may improve the quality of radiation oncology resident education. Copyright © 2016 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

Response of Antarctic ice shelf melt to SAM trend and possible feedbacks with the ice-dynamics

NASA Astrophysics Data System (ADS)

Donat-Magnin, Marion; Jourdain, Nicolas C.; Gallée, Hubert; Spence, Paul; Cornford, Stephen L.; Le Sommer, Julien; Durand, Gaël

2017-04-01

The observed positive trend in the Southern Annular Mode (SAM) may warm the Southern Ocean sub-surface through decreased Ekman downward pumping. Subsequent change in ice-shelves melt has been suggested to trigger glacier acceleration in West Antarctica. Here we use a regional ocean model configuration of the Amundsen Sea that includes interactive ice-shelf cavities. Our results show that the inclusion of ice-shelves changes the ocean response to the projected SAM trend, i.e. it typically inhibits a part of the SAM-induced subsurface warming. Heat budget analysis has been used to propose responsible mechanisms. Regarding Thwaites and Pine Island, sub ice-shelf melt increases above 400m by approximately 40% for Thwaites and 10% for Pine Island and decreases by up to 10% below in response to ocean temperature changes driven by the projected SAM trend. The melt sensitivity to poleward shifting winds is nonetheless small compared to the sensitivity to an ice-sheet instability, i.e. to a projected change in the shape of ice-shelf cavities. For instance, the sub ice-shelf melt are doubled near the grounding line of some glaciers in response to the largest grounding line retreat projected for 2100. Large increase in basal melt close to the grounding line could largely impact instability and glacier acceleration. Our work suggests the need for including ice shelves into ocean models, and to couple ocean models to ice-sheet models in climate projections.

Electro-optic investigation of the n-alkanethiol GaAs(001) interface: Surface phenomena and applications to photoluminescence-based biosensing

NASA Astrophysics Data System (ADS)

Marshall, Gregory M.

Semiconductor surfaces coupled to molecular structures derived from organic chemistry form the basis of an emerging class of field-effect devices. In addition to molecular electronics research, these interfaces are developed for a variety of sensor applications in the electronic and optical domains. Of practical interest are self-assembled monolayers (SAMs) comprised of n-alkanethiols [HS(CH2)n], which couple to the GaAs(001) surface through S-GaAs covalent bond formation. These SAMs offer potential functionality in terms of the requisite sensor chemistry and the passivation effect such coupling is known to afford. In this thesis, the SAM-GaAs interface is investigated in the context of a photonic biosensor based on photoluminescence (PL) variation. The scope of the work is categorized into three parts: i) the structural and compositional analysis of the surface using X-ray photoelectron spectroscopy (XPS), ii) the investigation of electronic properties at the interface under equilibrium conditions using infrared (IR) spectroscopy, the Kelvin probe method, and XPS, and iii) the analysis of the electro-optic response under steady-state photonic excitation, specifically, the surface photovoltage (SPV) and PL intensity. Using a partial overlayer model of angle-resolved XPS spectra in which the component assignments are shown to be quantitatively valid, the coverage fraction of methyl-terminated SAMs is shown to exceed 90%. Notable among the findings are a low-oxide, Ga-rich surface with elemental As present in sub-monolayer quantities consistent with theoretical surface morphologies. Modal analysis of transmission IR spectra show that the SAM molecular order is sufficient to support a Beer-Lambert determination of the IR optical constants, which yields the observation of a SAM-specific absorbance enhancement. By correlation of the IR absorbance with the SAM dipole layer potential, the enhancement mechanism is attributed to the vibrational moments added by the electronic polarizability in the static field of the SAM. Lastly, the surface Fermi level position is determined by XPS and is used to interpret SPV results in terms of a thiol-induced reduction of the surface cross-section for minority carrier-capture. Numerical analysis confirms this result based on the carrier transport theory of PL intensity by means of a reduction of the surface recombination velocity. Keywords: photonics, biosensor, GaAs, self-assembled monolayers, X-ray photoelectron spectroscopy, IR spectroscopy, photoluminescence, surface Fermi level, surface photovoltage.

Empirical Evidence for Roughness-Dependent Limit in Observation of Odd-Even Effect in Wetting Properties of Polar Liquids on n-Alkanethiolate Self-Assembled Monolayers.

PubMed

Wang, Zhengjia; Chen, Jiahao; Oyola-Reynoso, Stephanie; Thuo, Martin

2016-08-16

Substrate roughness influences the wetting properties of self-assembled monolayers (SAMs), but details on this dependency at the sub-nanometer level are still lacking. This study investigates the effect of surface roughness on interfacial properties of n-alkanethiolate SAMs, specifically wetting, and confirms the predicted limit to the observation of the odd-even effect in hydrophobicity. This article studies static contact angles of polar and nonpolar probe liquids on a series of n-alkanethiolate SAMs on surfaces with tunable roughness. We prepared Ag surfaces with root-mean-square roughness (Rrms) of ∼0.6-2.2 nm and compared the wetting properties of n-alkanethiolate SAMs fabricated on these surfaces. We measured the static contact angles, θs, formed between SAM and probe liquids [water, glycerol, and hexadecane]. Hexadecane showed an odd-even effect on all surfaces irrespective of the degree of roughness. Polar liquids (water and glycerol), however, showed a dependency on the roughness of the substrate with an odd-even effect observable only on smooth, but not rougher (Rrms ≥ 1.15 nm), surfaces. These results confirm that the previously predicted limit to observation of the odd-even effect in hydrophobicity (here extended to polar liquids) is real. From the results with glycerol, we infer that this limit is not limited just to hydrophobicity but may extend to other polar liquids. Results from hexadecane, however, suggest that this limit may not be a universal property of the SAM.

Bicc1 Polymerization Regulates the Localization and Silencing of Bound mRNA

PubMed Central

Rothé, Benjamin; Leal-Esteban, Lucia; Bernet, Florian; Urfer, Séverine; Doerr, Nicholas; Weimbs, Thomas; Iwaszkiewicz, Justyna

2015-01-01

Loss of the RNA-binding protein Bicaudal-C (Bicc1) provokes renal and pancreatic cysts as well as ectopic Wnt/β-catenin signaling during visceral left-right patterning. Renal cysts are linked to defective silencing of Bicc1 target mRNAs, including adenylate cyclase 6 (AC6). RNA binding of Bicc1 is mediated by N-terminal KH domains, whereas a C-terminal sterile alpha motif (SAM) self-polymerizes in vitro and localizes Bicc1 in cytoplasmic foci in vivo. To assess a role for multimerization in silencing, we conducted structure modeling and then mutated the SAM domain residues which in this model were predicted to polymerize Bicc1 in a left-handed helix. We show that a SAM-SAM interface concentrates Bicc1 in cytoplasmic clusters to specifically localize and silence bound mRNA. In addition, defective polymerization decreases Bicc1 stability and thus indirectly attenuates inhibition of Dishevelled 2 in the Wnt/β-catenin pathway. Importantly, aberrant C-terminal extension of the SAM domain in bpk mutant Bicc1 phenocopied these defects. We conclude that polymerization is a novel disease-relevant mechanism both to stabilize Bicc1 and to present associated mRNAs in specific silencing platforms. PMID:26217012

Electrochemical applications. How click chemistry brought biomimetic models to the next level: electrocatalysis under controlled rate of electron transfer.

PubMed

Decréau, Richard A; Collman, James P; Hosseini, Ali

2010-04-01

This tutorial review discusses the immobilization of alkyne-terminated cytochrome c oxidase models on azide-functionalized self-assembled monolayers (SAM) coated gold electrodes that was made possible by click chemistry. The rate of electron delivery from the electrode to the model could be tuned by changing the nature of the SAM. Biologically relevant electron transfer rates (2-4 s(-1)) were obtained on slow SAMs allowing the model to turn over catalytically under steady-state conditions. Hence, click chemistry was a crucial tool to demonstrate, through electrocatalytic studies: (1) the role played by several features present in the distal side of the model, such as the Cu(B)-Tyr244 pair, the distal pocket, and the stabilizing role of a distal water cluster; (2) the reversible inhibition of O(2) reduction by H(2)S.

Molecular Level Understanding of Interfaces and Excited State Electronic Structure in Organic Solar Cells Using Soft X-ray Techniques

NASA Astrophysics Data System (ADS)

Gliboff, Matthew

Transparent conductive oxides like indium tin oxide (ITO) are common substrates for optoelectronic devices, including organic light emitting diodes and organic solar cells. Tailoring the interface between the oxide and the active layer by adjusting the work function or wettability of the oxide can improve the performance of these devices in both emissive and photovoltaic applications. Molecular design of self-assembled monolayers (SAMs) allows for a range of surface properties using the same oxide material. The molecular ordering and conformation adopted by the SAMs determine properties such as work function and wettability at these critical interfaces. I use angle-dependent near edge x-ray absorption fine structure (NEXAFS) spectroscopy, to determine the molecular orientations of a variety of dipolar phosphonic acid surface modifiers. For a model system, phenylphosphonic acid on indium zinc oxide, the SAMs prove to be surprisingly well-oriented, with the phenyl ring adopting a well-defined tilt angle of 12-16° from the surface normal. The NEXAFS results agree with polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) results and orientations calculated from density functional theory (DFT). These results not only provide a detailed picture of the molecular structure of a technologically important class of SAMs, but they also resolve a long-standing ambiguity regarding the vibrational-mode assignments for phosphonic acids on oxide surfaces, thus improving the utility of PM-IRRAS for future studies. The effect of fluorination on the orientation of these phosponic-acid SAMs is non-trivial, due to the combined effects of the fluorination on binding mode and steric packing. The latter effects are found to be more dominant in aliphatic SAMs, leading to a more upright orientation in the fluorinated SAM. In the aromatic case, the fluorinated SAM adopted a less upright orientation which I attribute to changes in binding mode. The relationship between structure and performance in active layer polymers for organic electronics is not yet well understood. To gain insight into the effect of the excited state electronic structure on device performance, we examine two similar donor-acceptor polymers: PCPDTBT and PCDTBT, which produce devices with internal quantum efficiency (IQE) of 70% and 100% respectively. We use time-dependent density functional theory (TD-DFT) in combination with near edge x-ray absorption fine structure (NEXAFS) and resonant Auger spectroscopy to predict the electronic structure of the lowest unoccupied molecular orbital (LUMO). The resonant Auger results are found to be independent of film morphology and likely dominated by monomer structure. We show that the degree of LUMO localization onto the benzothiadiazole acceptor group in each polymer is similar, indicating that that the differences in IQE between these two polymers are driven by larger-scale morphology and not explained by the electronic structure of the excited state.

Threshold-Voltage Shifts in Organic Transistors Due to Self-Assembled Monolayers at the Dielectric: Evidence for Electronic Coupling and Dipolar Effects.

PubMed

Aghamohammadi, Mahdieh; Rödel, Reinhold; Zschieschang, Ute; Ocal, Carmen; Boschker, Hans; Weitz, R Thomas; Barrena, Esther; Klauk, Hagen

2015-10-21

The mechanisms behind the threshold-voltage shift in organic transistors due to functionalizing of the gate dielectric with self-assembled monolayers (SAMs) are still under debate. We address the mechanisms by which SAMs determine the threshold voltage, by analyzing whether the threshold voltage depends on the gate-dielectric capacitance. We have investigated transistors based on five oxide thicknesses and two SAMs with rather diverse chemical properties, using the benchmark organic semiconductor dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene. Unlike several previous studies, we have found that the dependence of the threshold voltage on the gate-dielectric capacitance is completely different for the two SAMs. In transistors with an alkyl SAM, the threshold voltage does not depend on the gate-dielectric capacitance and is determined mainly by the dipolar character of the SAM, whereas in transistors with a fluoroalkyl SAM the threshold voltages exhibit a linear dependence on the inverse of the gate-dielectric capacitance. Kelvin probe force microscopy measurements indicate this behavior is attributed to an electronic coupling between the fluoroalkyl SAM and the organic semiconductor.

Immunoassay of S-adenosylmethionine and S-adenosylhomocysteine: the methylation index as a biomarker for disease and health status.

PubMed

Hao, Xiujuan; Huang, Yan; Qiu, Ming; Yin, Chunlin; Ren, Huiming; Gan, Hongjie; Li, Huijun; Zhou, Yaxia; Xia, Jiazhi; Li, Wenting; Guo, Lijuan; Angres, Isaac A

2016-11-28

S-Adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are relevant to a variety of diseases. Previous reports that quantified SAM and SAH were based on HPLC or LC-MS/MS. No antibody against SAM has been generated, and the antibody against SAH cannot be used with blood samples. Immunoassays have not been used to measure SAM and SAH. In this study, ELISA was used to measure blood SAM and SAH levels. Specific antibodies against SAM were produced for the first time using a stable analog as the antigen. The monoclonal antibodies against SAM and SAH were characterized. No cross-reactivity was detected for the analyzed analogs. For the anti-SAM antibodies, the ELISA sensitivity was ~2 nM, and the affinity was 7.29 × 10 10 L/mol. For the anti-SAH antibodies, the sensitivity was ~15 nM, and the affinity was 2.79 × 10 8 L/mol. Using high-quality antibodies against SAM and SAH, immunoassays for the detection of SAM and SAH levels in blood and tissue samples were developed. Clinical investigations using immunoassays to measure SAM, SAH and the methylation index (MI) in normal and diseased samples indicated that (1) the SAM level is age and gender dependent; (2) the SAM level is associated with the severity of liver diseases, inflammatory reactions and other diseases; and (3) the methylation index (MI) is significantly reduced in many diseases and may serve as a screening biomarker to identify potentially unfavorable health conditions. It is possible to generate antibodies against active small biomolecules with weak immunogenicity, such as SAM and SAH, using traditional hybridoma technology. The antigens and antibodies described here will contribute to the development of immunoassays to measure SAM, SAH and related molecules. These assays enable the MI to be measured specifically, accurately, easily and quickly without costly equipment. This preliminary study indicates that the MI could be an effective indicator of general health, except under conditions that may alter the value of the MI, such as special diets and medications.

Case Studies Comparing System Advisor Model (SAM) Results to Real Performance Data: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blair, N.; Dobos, A.; Sather, N.

2012-06-01

NREL has completed a series of detailed case studies comparing the simulations of the System Advisor Model (SAM) and measured performance data or published performance expectations. These case studies compare PV measured performance data with simulated performance data using appropriate weather data. The measured data sets were primarily taken from NREL onsite PV systems and weather monitoring stations.

Standardized added metabolic activity (SAM): a partial volume independent marker of total lesion glycolysis in liver metastases.

PubMed

Mertens, Jeroen; Dobbeleir, André; Ham, Hamphrey; D'Asseler, Yves; Goethals, Ingeborg; Van de Wiele, Christophe

2012-09-01

The standardized added metabolic activity (SAM) is a new marker of total lesion glycolysis that avoids partial volume effect (PVE) and thresholding. SAM is calculated by drawing a volume of interest (VOI(1)) around the tumour and a larger VOI (VOI(2)) around VOI(1). Subtracting the background activity in VOI(2)-VOI(1) from VOI(1) yields SAM. If VOI(1) is set at a reasonable distance from the tumour, PVE are avoided. Phantom and initial clinical validation data are presented. Spheres of a Jaszczak phantom were filled with a 5.4, 3.64 and 2.0 times higher concentration relative to background activity and positron emission tomography (PET) data were acquired during 10 min. SAM of all spheres was expressed as a percentage of the expected value (the actual activity ratio minus 1). In 15 patients a 10-min list-mode acquisition PET study centred on their primary squamous cell carcinoma (PSCC) was performed and images of 1-10 min reconstructed. SAM1-9min values of PSCC were expressed as a percentage of SAM10min. Nineteen patients suffering from liver metastases treated with chemotherapy underwent PET/CT prior to (scan 1) and after 3-6 cycles of chemotherapy (scan 2). SAM and maximum standardized uptake values (SUV(max)) of the liver lesions on scan 1 (SAM1 and SUV(max)1) and the percentage reduction between both ΔSAM and ΔSUV(max) were related to Response Evaluation Criteria in Solid Tumors (RECIST) response. For the phantom acquisitions, the mean normalized SAM/sphere volume calculated was 94.9 % (SD 5.9 %) of the expected value. In the PSCC patients, the mean difference between SAM1min and SAM10min was only 4 % (SD 5 %). SUV(max)1min and SUV(max)10min proved to be not significantly different, but the variability was slightly larger than that of SAM (SD 6.4 %). SAM1 and ΔSAM values for responders versus non-responders were, respectively, 57 (SD 119) versus 297 (SD 625) for SAM1 (p = 0.2) and 99 % (SD 3 %) versus 32 % (SD 44 %) for ΔSAM (p = 0.001). SUV(max)1 and ΔSUV(max) values in responders versus non-responders were, respectively, 3.9 (SD 2.4) versus 6.3 (SD 3.1) for SUV(max)1 (p = 0.08) and 94 % (SD 17) versus 7 % (SD 40 %) for ΔSUV(max) (p = 0.0001). The AUC of ΔSAM and ΔSUV(max) were not significantly different on receiver-operating characteristic (ROC) analysis (AUC 1.0 and 0.99, respectively, p = 0.6). SAM is a promising parameter for tumour response assessment of liver metastases by means of (18)F-fluorodeoxyglucose PET.

Effects of polyamine biosynthesis inhibitors on S-adenosylmethionine synthetase and S-adenosylmethionine decarboxylase activities in carrot cell cultures

Treesearch

S.C. Minocha; R. Minocha; A. Komamine

1991-01-01

Changes in the activites of S-adcnosylmethionine (SAM) synthetase (methionine adenosyltransferase, EC 2.5.1.6.) and SAM decarboxylase (EC 4.1.1.50) were studied in carrot (Daucus carota) cell cultures in response to 2,4-dichlorophenoxyacetic acid (2,4-D) and several inhibitors of polyamine biosynthesis. Activity of SAM synthetase increased...

Centennial-scale solar forcing of the South American Monsoon System recorded in stalagmites.

PubMed

Novello, Valdir F; Vuille, Mathias; Cruz, Francisco W; Stríkis, Nicolás M; de Paula, Marcos Saito; Edwards, R Lawrence; Cheng, Hai; Karmann, Ivo; Jaqueto, Plínio F; Trindade, Ricardo I F; Hartmann, Gelvam A; Moquet, Jean S

2016-04-21

The South American Monsoon System (SAMS) is generally considered to be highly sensitive to Northern Hemisphere (NH) temperature variations on multi-centennial timescales. The direct influence of solar forcing on moisture convergence in global monsoon systems on the other hand, while well explored in modeling studies, has hitherto not been documented in proxy data from the SAMS region. Hence little is known about the sensitivity of the SAMS to solar forcing over the past millennium and how it might compete or constructively interfere with NH temperature variations that occurred primarily in response to volcanic forcing. Here we present a new annually-resolved oxygen isotope record from a 1500-year long stalagmite recording past changes in precipitation in the hitherto unsampled core region of the SAMS. This record details how solar variability consistently modulated the strength of the SAMS on centennial time scales during the past 1500 years. Solar forcing, besides the previously recognized influence from NH temperature changes and associated Intertropical Convergence Zone (ITCZ) shifts, appears as a major driver affecting SAMS intensity at centennial time scales.

Competition of bovine serum albumin adsorption and bacterial adhesion onto surface-grafted ODT: in situ study by vibrational SFG and fluorescence confocal microscopy.

PubMed

Bulard, Emilie; Fontaine-Aupart, Marie-Pierre; Dubost, Henri; Zheng, Wanquan; Bellon-Fontaine, Marie-Noëlle; Herry, Jean-Marie; Bourguignon, Bernard

2012-12-11

The interaction of hydrophilic and hydrophobic ovococcoid bacteria and bovine serum albumin (BSA) proteins with a well ordered surface of octadecanethiol (ODT) self assembled monolayer (SAM) has been studied in different situations where proteins were either preadsorbed on ODT or adsorbed simultaneously with bacterial adhesion as in life conditions. The two situations lead to very different antimicrobial behavior. Bacterial adhesion on preadsorbed BSA is very limited, while the simultaneous exposure of ODT SAM to proteins and bacteria lead to a markedly weaker antimicrobial effect. The combination of sum frequency generation spectroscopy and fluorescence confocal microscopy experiments allow one to draw conclusions on the factors that govern the ODT SAM or BSA film interaction with bacteria at the molecular level. On the hydrophobic ODT surface, interaction with hydrophobic or hydrophilic biomolecules results in opposite effects on the SAM, namely, a flattening or a raise of the terminal methyl groups of ODT. On an amphiphilic BSA layer, the bacterial adhesion strength is weakened by the negative charges carried by both BSA and bacteria. Surprisingly, preadsorbed BSA that cover part of the bacteria cell walls increase the adhesion strength to the BSA film and reduce hydrophobic interactions with the ODT SAM. Finally, bacterial adhesion on a BSA film is shown to modify the BSA proteins in some way that change their interaction with the ODT SAM. The antimicrobial effect is much stronger in the case of a preadsorbed BSA layer than when BSA and bacteria are in competition to colonize the ODT SAM surface.

Injection-modulated polarity conversion by charge carrier density control via a self-assembled monolayer for all-solution-processed organic field-effect transistors

NASA Astrophysics Data System (ADS)

Roh, Jeongkyun; Lee, Taesoo; Kang, Chan-Mo; Kwak, Jeonghun; Lang, Philippe; Horowitz, Gilles; Kim, Hyeok; Lee, Changhee

2017-04-01

We demonstrated modulation of charge carrier densities in all-solution-processed organic field-effect transistors (OFETs) by modifying the injection properties with self-assembled monolayers (SAMs). The all-solution-processed OFETs based on an n-type polymer with inkjet-printed Ag electrodes were fabricated as a test platform, and the injection properties were modified by the SAMs. Two types of SAMs with different dipole direction, thiophenol (TP) and pentafluorobenzene thiol (PFBT) were employed, modifying the work function of the inkjet-printed Ag (4.9 eV) to 4.66 eV and 5.24 eV with TP and PFBT treatments, respectively. The charge carrier densities were controlled by the SAM treatment in both dominant and non-dominant carrier-channel regimes. This work demonstrates that control of the charge carrier densities can be efficiently achieved by modifying the injection property with SAM treatment; thus, this approach can achieve polarity conversion of the OFETs.

Supra-physiological folic acid concentrations induce aberrant DNA methylation in normal human cells in vitro.

PubMed

Charles, Michelle A; Johnson, Ian T; Belshaw, Nigel J

2012-07-01

The micronutrients folate and selenium may modulate DNA methylation patterns by affecting intracellular levels of the methyl donor S-adenosylmethionine (SAM) and/or the product of methylation reactions S-adenosylhomocysteine (SAH). WI-38 fibroblasts and FHC colon epithelial cells were cultured in the presence of two forms of folate or four forms of selenium at physiologically-relevant doses, and their effects on LINE-1 methylation, gene-specific CpG island (CGI) methylation and intracellular SAM:SAH were determined. At physiologically-relevant doses the forms of folate or selenium had no effect on LINE-1 or CGI methylation, nor on intracellular SAM:SAH. However the commercial cell culture media used for the selenium studies, containing supra-physiological concentrations of folic acid, induced LINE-1 hypomethylation, CGI hypermethylation and decreased intracellular SAM:SAH in both cell lines. We conclude that the exposure of normal human cells to supra-physiological folic acid concentrations present in commercial cell culture media perturbs the intracellular SAM:SAH ratio and induces aberrant DNA methylation.

Coupling the System Analysis Module with SAS4A/SASSYS-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fanning, T. H.; Hu, R.

2016-09-30

SAS4A/SASSYS-1 is a simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced reactors, with an emphasis on sodium fast reactors. SAS4A/SASSYS-1 has been under development and in active use for nearly forty-five years, and is currently maintained by the U.S. Department of Energy under the Office of Advanced Reactor Technology. Although SAS4A/SASSYS-1 contains a very capable primary and intermediate system modeling component, PRIMAR-4, it also has some shortcomings: outdated data management and code structure makes extension of the PRIMAR-4 module somewhat difficult. The user input format formore » PRIMAR-4 also limits the number of volumes and segments that can be used to describe a given system. The System Analysis Module (SAM) is a fairly new code development effort being carried out under the U.S. DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM is being developed with advanced physical models, numerical methods, and software engineering practices; however, it is currently somewhat limited in the system components and phenomena that can be represented. For example, component models for electromagnetic pumps and multi-layer stratified volumes have not yet been developed. Nor is there support for a balance of plant model. Similarly, system-level phenomena such as control-rod driveline expansion and vessel elongation are not represented. This report documents fiscal year 2016 work that was carried out to couple the transient safety analysis capabilities of SAS4A/SASSYS-1 with the system modeling capabilities of SAM under the joint support of the ART and NEAMS programs. The coupling effort was successful and is demonstrated by evaluating an unprotected loss of flow transient for the Advanced Burner Test Reactor (ABTR) design. There are differences between the stand-alone SAS4A/SASSYS-1 simulations and the coupled SAS/SAM simulations, but these are mainly attributed to the limited maturity of the SAM development effort. The severe accident modeling capabilities in SAS4A/SASSYS-1 (sodium boiling, fuel melting and relocation) will continue to play a vital role for a long time. Therefore, the SAS4A/SASSYS-1 modernization effort should remain a high priority task under the ART program to ensure continued participation in domestic and international SFR safety collaborations and design optimizations. On the other hand, SAM provides an advanced system analysis tool, with improved numerical solution schemes, data management, code flexibility, and accuracy. SAM is still in early stages of development and will require continued support from NEAMS to fulfill its potential and to mature into a production tool for advanced reactor safety analysis. The effort to couple SAS4A/SASSYS-1 and SAM is the first step on the integration of these modeling capabilities.« less

Targeted knockout of a chemokine-like gene increases anxiety and fear responses.

PubMed

Choi, Jung-Hwa; Jeong, Yun-Mi; Kim, Sujin; Lee, Boyoung; Ariyasiri, Krishan; Kim, Hyun-Taek; Jung, Seung-Hyun; Hwang, Kyu-Seok; Choi, Tae-Ik; Park, Chul O; Huh, Won-Ki; Carl, Matthias; Rosenfeld, Jill A; Raskin, Salmo; Ma, Alan; Gecz, Jozef; Kim, Hyung-Goo; Kim, Jin-Soo; Shin, Ho-Chul; Park, Doo-Sang; Gerlai, Robert; Jamieson, Bradley B; Kim, Joon S; Iremonger, Karl J; Lee, Sang H; Shin, Hee-Sup; Kim, Cheol-Hee

2018-01-30

Emotional responses, such as fear and anxiety, are fundamentally important behavioral phenomena with strong fitness components in most animal species. Anxiety-related disorders continue to represent a major unmet medical need in our society, mostly because we still do not fully understand the mechanisms of these diseases. Animal models may speed up discovery of these mechanisms. The zebrafish is a highly promising model organism in this field. Here, we report the identification of a chemokine-like gene family, samdori ( sam ), and present functional characterization of one of its members, sam2 We show exclusive mRNA expression of s am2 in the CNS, predominantly in the dorsal habenula, telencephalon, and hypothalamus. We found knockout (KO) zebrafish to exhibit altered anxiety-related responses in the tank, scototaxis and shoaling assays, and increased crh mRNA expression in their hypothalamus compared with wild-type fish. To investigate generalizability of our findings to mammals, we developed a Sam2 KO mouse and compared it to wild-type littermates. Consistent with zebrafish findings, homozygous KO mice exhibited signs of elevated anxiety. We also found bath application of purified SAM2 protein to increase inhibitory postsynaptic transmission onto CRH neurons of the paraventricular nucleus. Finally, we identified a human homolog of SAM2 , and were able to refine a candidate gene region encompassing SAM2 , among 21 annotated genes, which is associated with intellectual disability and autism spectrum disorder in the 12q14.1 deletion syndrome. Taken together, these results suggest a crucial and evolutionarily conserved role of sam2 in regulating mechanisms associated with anxiety. Copyright © 2018 the Author(s). Published by PNAS.

Mice heterozygous for the Mdr2 gene demonstrate decreased PEMT activity and diminished steatohepatitis on the MCD diet.

PubMed

Igolnikov, Alexander C; Green, Richard M

2006-03-01

The administration of a methionine and choline deficient (MCD) diet to mice serves as an animal model of NASH. The multidrug resistant 2 (Mdr2) P-glycoprotein encodes for the canalicular phospholipid transporter, and Mdr2 (+/-) mice secrete 40% less phosphatidylcholine than wild-type mice. We have hypothesized that phosphatidylethanolamine-N-methyl transferase (PEMT) up-regulation is a consequence of MCD diet administration, and is important for the pathogenesis of steatohepatitis in this model. However, the effect of decreased phosphatidylcholine secretion and modulation of PEMT on the development of diet-induced steatohepatitis in Mdr2 (+/-) mice has not been explored. Thus, the purpose of the study is to examine the effects of the MCD diet on Mdr2 (+/-) mice. Mdr2 (+/-) and Mdr2 (+/+) mice were treated with an MCD or control diet for up to 30 days, and the severity of steatohepatitis, PEMT activity and hepatic S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH) levels were measured. Serum ALT levels, hepatic inflammation, and PEMT activity were significantly lower, and hepatic SAM:SAH ratios were significantly higher in Mdr2 (+/-) mice at 7 and 30 days on the MCD diet. Mdr2 (+/-) mice have diminished susceptibility to MCD diet-induced NASH, which is associated with a relative decrease in PEMT activity and increased SAM:SAH ratios.

Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

PubMed

Roy, Susmita; Onuchic, José N; Sanbonmatsu, Karissa Y

2017-07-25

The S-adenosylmethionine (SAM)-I riboswitch is a noncoding RNA that regulates the transcription termination process in response to metabolite (SAM) binding. The aptamer portion of the riboswitch may adopt an open or closed state depending on the presence of metabolite. Although the transition between the open and closed states is critical for the switching process, its atomistic details are not well understood. Using atomistic simulations, we calculate the effect of SAM and magnesium ions on the folding free energy landscape of the SAM-I riboswitch. These molecular simulation results are consistent with our previous wetlab experiments and aid in interpreting the SHAPE probing measurements. Here, molecular dynamics simulations explicitly identify target RNA motifs sensitive to magnesium ions and SAM. In the simulations, we observe that, whereas the metabolite mostly stabilizes the P1 and P3 helices, magnesium serves an important role in stabilizing a pseudoknot interaction between the P2 and P4 helices, even at high metabolite concentrations. The pseudoknot stabilization by magnesium, in combination with P1 stabilization by SAM, explains the requirement of both SAM and magnesium to form the fully collapsed metabolite-bound closed state of the SAM-I riboswitch. In the absence of SAM, frequent open-to-closed conformational transitions of the pseudoknot occur, akin to breathing. These pseudoknot fluctuations disrupt the binding site by facilitating fluctuations in the 5'-end of helix P1. Magnesium biases the landscape toward a collapsed state (preorganization) by coordinating pseudoknot and 5'-P1 fluctuations. The cooperation between SAM and magnesium in stabilizing important tertiary interactions elucidates their functional significance in transcription regulation. Published by Elsevier Inc.

Allosteric monofunctional aspartate kinases from Arabidopsis.

PubMed

Curien, Gilles; Laurencin, Mathieu; Robert-Genthon, Mylène; Dumas, Renaud

2007-01-01

Plant monofunctional aspartate kinase is unique among all aspartate kinases, showing synergistic inhibition by lysine and S-adenosyl-l-methionine (SAM). The Arabidopsis genome contains three genes for monofunctional aspartate kinases. We show that aspartate kinase 2 and aspartate kinase 3 are inhibited only by lysine, and that aspartate kinase 1 is inhibited in a synergistic manner by lysine and SAM. In the absence of SAM, aspartate kinase 1 displayed low apparent affinity for lysine compared to aspartate kinase 2 and aspartate kinase 3. In the presence of SAM, the apparent affinity of aspartate kinase 1 for lysine increased considerably, with K(0.5) values for lysine inhibition similar to those of aspartate kinase 2 and aspartate kinase 3. For all three enzymes, the inhibition resulted from an increase in the apparent K(m) values for the substrates ATP and aspartate. The mechanism of aspartate kinase 1 synergistic inhibition was characterized. Inhibition by lysine alone was fast, whereas synergistic inhibition by lysine plus SAM was very slow. SAM by itself had no effect on the enzyme activity, in accordance with equilibrium binding analyses indicating that SAM binding to aspartate kinase 1 requires prior binding of lysine. The three-dimensional structure of the aspartate kinase 1-Lys-SAM complex has been solved [Mas-Droux C, Curien G, Robert-Genthon M, Laurencin M, Ferrer JL & Dumas R (2006) Plant Cell18, 1681-1692]. Taken together, the data suggest that, upon binding to the inactive aspartate kinase 1-Lys complex, SAM promotes a slow conformational transition leading to formation of a stable aspartate kinase 1-Lys-SAM complex. The increase in aspartate kinase 1 apparent affinity for lysine in the presence of SAM thus results from the displacement of the unfavorable equilibrium between aspartate kinase 1 and aspartate kinase 1-Lys towards the inactive form.

S-Adenosylmethionine attenuates bile duct early warm ischemia reperfusion injury after rat liver transplantation.

PubMed

Tang, Yong; Chu, Hongpeng; Cao, Guojun; Du, Xiaolong; Min, Xiaobo; Wan, Chidan

2018-03-01

Warm ischemia reperfusion injury (IRI) plays a key role in biliary complication, which is a substantial vulnerability of liver transplantation. The early pathophysiological changes of IRI are characterized by an excessive inflammatory response. S-Adenosylmethionine (SAM) is an important metabolic intermediate that modulates inflammatory reactions; however, its role in bile duct warm IRI is not known. In this study, male rats were treated with or without SAM (170 μmol/kg body weight) after orthotopic autologous liver transplantation. The histopathological observations showed that bile duct injury in the IRI group was more serious than in the SAM group. The alanine aminotransferase (ALT), alkaline phosphatase (ALP) and direct bilirubin (DBIL) levels in the serum of the IRI group were significantly increased compared to the SAM group (P < .05). Simultaneously, SAM effectively improved the survival of the transplant recipients. Furthermore, the H 2 O 2 and malondialdehyde (MDA) of the IRI group were much higher compared to the SAM group (P < .05). The GSH/GSSG ratio in the SAM group was significantly increased by SAM treatment compared to the IRI group (P < .05). SAM administration significantly inhibited macrophage infiltration in liver and bile duct tissues, down-regulated TNF-α levels and up-regulated IL-10 expression in bile duct tissues compared to the IRI group (P < .05). The number of apoptotic biliary epithelial cells and caspase-3-positive cells in IRI rat livers were much higher compared to those in SAM-treated rats at 24 h after liver transplantation (P < .05). These data suggested that SAM protected bile ducts against warm IRI by suppressing oxidative stress, inflammatory reactions and apoptosis of biliary epithelial cells after liver transplantation.α. Copyright © 2018 Elsevier Ltd. All rights reserved.

Expression of SHOOT MERISTEMLESS, WUSCHEL, and ASYMMETRIC LEAVES1 Homologs in the Shoots of Podostemaceae: Implications for the Evolution of Novel Shoot Organogenesis[W

PubMed Central

Katayama, Natsu; Koi, Satoshi; Kato, Masahiro

2010-01-01

Podostemaceae (the river weeds) are ecologically and morphologically unusual angiosperms. The subfamily Tristichoideae has typical shoot apical meristems (SAMs) that produce leaves, but Podostemoideae is devoid of SAMs and new leaves arise below the base of older leaves. To reveal the genetic basis for the evolution of novel shoot organogenesis in Podostemaceae, we examined the expression patterns of key regulatory genes for shoot development (i.e., SHOOT MERISTEMLESS (STM), WUSCHEL (WUS), and ASYMMETRIC LEAVES1/ROUGH SHEATH2/PHANTASTICA (ARP) orthologs) in Tristichoideae and Podostemoideae. In the SAM-mediated shoots of Tristichoideae, like in model plants, STM and WUS orthologs were expressed in the SAM. In the SAM-less shoots of Podostemoideae, STM and WUS orthologs were expressed in the initiating leaf/bract primordium. In older leaf/bract primordia, WUS expression disappeared and STM expression became restricted to the basal part, whereas ARP was expressed in the distal part in a complementary pattern to STM expression. In the reproductive shoots of Podostemoideae with a normal mode of flower development, STM and WUS were expressed in the floral meristem, but not in the floral organs, similar to the pattern in model plants. These results suggest that the leaf/bract of Podostemoideae is initiated as a SAM and differentiates into a single apical leaf/bract, resulting in the evolution of novel shoot-leaf mixed organs in Podostemaceae. PMID:20647344

The [4Fe-4S](2+) cluster in reconstituted biotin synthase binds S-adenosyl-L-methionine.

PubMed

Cosper, Michele Mader; Jameson, Guy N L; Davydov, Roman; Eidsness, Marly K; Hoffman, Brian M; Huynh, Boi Hanh; Johnson, Michael K

2002-11-27

The combination of resonance Raman, electron paramagnetic resonance and Mössbauer spectroscopies has been used to investigate the effect of S-adenosyl-l-methionine (SAM) on the spectroscopic properties of the [4Fe-4S]2+ cluster in biotin synthase. The results indicate that SAM interacts directly at a unique iron site of the [4Fe-4S]2+ cluster in BioB and support the hypothesis of a common inner-sphere mechanism for the reductive cleavage of SAM in the radical SAM family of Fe-S enzymes.

Ionic Strength, Surface Charge, and Packing Density Effects on the Properties of Peptide Self-Assembled Monolayers.

PubMed

Leo, Norman; Liu, Juan; Archbold, Ian; Tang, Yongan; Zeng, Xiangqun

2017-02-28

The various environmental parameters of packing density, ionic strength, and solution charge were examined for their effects on the properties of the immobilized peptide mimotope CH19 (CGSGSGSQLGPYELWELSH) that binds with the therapeutic antibody Trastuzumab (Herceptin) on a gold substrate. The immobilization of CH19 onto gold was examined with a quartz crystal microbalance (QCM). The QCM data showed the presence of intermolecular interactions resulting in the increase of viscoelastic properties of the peptide self-assembled monolayer (SAM). The CH19 SAM was diluted with CS7 (CGSGSGS) to decrease the packing density as CH19/CS7. The packing density and ionic strength parameters were evaluated by atomic force microscopy (AFM), ellipsometry, and QCM. AFM and ellipsometry showed a distinct conformational difference between CH19 and CH19/CS7, indicating a relationship between packing density and conformational state of the immobilized peptide. The CH19 SAM thickness was 40 Å with a rough topology, while the CH19/CS7 SAM thickness was 20 Å with a smooth topology. The affinity studies showed that the affinity of CH19 and CH19/CS7 to Trastuzumab were both on the order of 10 7 M -1 in undiluted PBS buffer, while the dilution of the buffer by 1000× increased both SAMs affinities to Trastuzumab to the order of 10 15 M -2 and changed the binding behavior from noncooperative to cooperative binding. This indicated that ionic strength had a more pronounced effect on binding properties of the CH19 SAM than packing density. Electrochemical impedance spectroscopy (EIS) was conducted on the CH19/CS7 SAM, which showed an increase in impedance after each EIS measurement cycle. Cyclic voltammetry on the CH19/CS7 SAM decreased impedance to near initial values. The impact of the packing density, buffer ionic strength, and local charge perturbation of the peptide SAM properties was interpreted based on the titratable sites in CH19 that could participate in the proton transfer and water equilibrium.

Review and standardization of cell phone exposure calculations using the SAM phantom and anatomically correct head models.

PubMed

Beard, Brian B; Kainz, Wolfgang

2004-10-13

We reviewed articles using computational RF dosimetry to compare the Specific Anthropomorphic Mannequin (SAM) to anatomically correct models of the human head. Published conclusions based on such comparisons have varied widely. We looked for reasons that might cause apparently similar comparisons to produce dissimilar results. We also looked at the information needed to adequately compare the results of computational RF dosimetry studies. We concluded studies were not comparable because of differences in definitions, models, and methodology. Therefore we propose a protocol, developed by an IEEE standards group, as an initial step in alleviating this problem. The protocol calls for a benchmark validation study comparing the SAM phantom to two anatomically correct models of the human head. It also establishes common definitions and reporting requirements that will increase the comparability of all computational RF dosimetry studies of the human head.

Review and standardization of cell phone exposure calculations using the SAM phantom and anatomically correct head models

PubMed Central

Beard, Brian B; Kainz, Wolfgang

2004-01-01

We reviewed articles using computational RF dosimetry to compare the Specific Anthropomorphic Mannequin (SAM) to anatomically correct models of the human head. Published conclusions based on such comparisons have varied widely. We looked for reasons that might cause apparently similar comparisons to produce dissimilar results. We also looked at the information needed to adequately compare the results of computational RF dosimetry studies. We concluded studies were not comparable because of differences in definitions, models, and methodology. Therefore we propose a protocol, developed by an IEEE standards group, as an initial step in alleviating this problem. The protocol calls for a benchmark validation study comparing the SAM phantom to two anatomically correct models of the human head. It also establishes common definitions and reporting requirements that will increase the comparability of all computational RF dosimetry studies of the human head. PMID:15482601

Validation of PV-RPM Code in the System Advisor Model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klise, Geoffrey Taylor; Lavrova, Olga; Freeman, Janine

2017-04-01

This paper describes efforts made by Sandia National Laboratories (SNL) and the National Renewable Energy Laboratory (NREL) to validate the SNL developed PV Reliability Performance Model (PV - RPM) algorithm as implemented in the NREL System Advisor Model (SAM). The PV - RPM model is a library of functions that estimates component failure and repair in a photovoltaic system over a desired simulation period. The failure and repair distributions in this paper are probabilistic representations of component failure and repair based on data collected by SNL for a PV power plant operating in Arizona. The validation effort focuses on whethermore » the failure and repair dist ributions used in the SAM implementation result in estimated failures that match the expected failures developed in the proof - of - concept implementation. Results indicate that the SAM implementation of PV - RPM provides the same results as the proof - of - concep t implementation, indicating the algorithms were reproduced successfully.« less

Comparisons of Computed Mobile Phone Induced SAR in the SAM Phantom to That in Anatomically Correct Models of the Human Head.

PubMed

Beard, Brian B; Kainz, Wolfgang; Onishi, Teruo; Iyama, Takahiro; Watanabe, Soichi; Fujiwara, Osamu; Wang, Jianqing; Bit-Babik, Giorgi; Faraone, Antonio; Wiart, Joe; Christ, Andreas; Kuster, Niels; Lee, Ae-Kyoung; Kroeze, Hugo; Siegbahn, Martin; Keshvari, Jafar; Abrishamkar, Houman; Simon, Winfried; Manteuffel, Dirk; Nikoloski, Neviana

2006-06-05

The specific absorption rates (SAR) determined computationally in the specific anthropomorphic mannequin (SAM) and anatomically correct models of the human head when exposed to a mobile phone model are compared as part of a study organized by IEEE Standards Coordinating Committee 34, SubCommittee 2, and Working Group 2, and carried out by an international task force comprising 14 government, academic, and industrial research institutions. The detailed study protocol defined the computational head and mobile phone models. The participants used different finite-difference time-domain software and independently positioned the mobile phone and head models in accordance with the protocol. The results show that when the pinna SAR is calculated separately from the head SAR, SAM produced a higher SAR in the head than the anatomically correct head models. Also the larger (adult) head produced a statistically significant higher peak SAR for both the 1- and 10-g averages than did the smaller (child) head for all conditions of frequency and position.

The SAM domain inhibits EphA2 interactions in the plasma membrane.

PubMed

Singh, Deo R; Ahmed, Fozia; Paul, Michael D; Gedam, Manasee; Pasquale, Elena B; Hristova, Kalina

2017-01-01

All members of the Eph receptor family of tyrosine kinases contain a SAM domain near the C terminus, which has been proposed to play a role in receptor homotypic interactions and/or interactions with binding partners. The SAM domain of EphA2 is known to be important for receptor function, but its contribution to EphA2 lateral interactions in the plasma membrane has not been determined. Here we use a FRET-based approach to directly measure the effect of the SAM domain on the stability of EphA2 dimers on the cell surface in the absence of ligand binding. We also investigate the functional consequences of EphA2 SAM domain deletion. Surprisingly, we find that the EphA2 SAM domain inhibits receptor dimerization and decreases EphA2 tyrosine phosphorylation. This role is dramatically different from the role of the SAM domain of the related EphA3 receptor, which we previously found to stabilize EphA3 dimers and increase EphA3 tyrosine phosphorylation in cells in the absence of ligand. Thus, the EphA2 SAM domain likely contributes to a unique mode of EphA2 interaction that leads to distinct signaling outputs. Copyright © 2016 Elsevier B.V. All rights reserved.

Methylene blue not ferrocene: Optimal reporters for electrochemical detection of protease activity.

PubMed

González-Fernández, Eva; Avlonitis, Nicolaos; Murray, Alan F; Mount, Andrew R; Bradley, Mark

2016-10-15

Electrochemical peptide-based biosensors are attracting significant attention for the detection and analysis of proteins. Here we report the optimisation and evaluation of an electrochemical biosensor for the detection of protease activity using self-assembled monolayers (SAMs) on gold surfaces, using trypsin as a model protease. The principle of detection was the specific proteolytic cleavage of redox-tagged peptides by trypsin, which causes the release of the redox reporter, resulting in a decrease of the peak current as measured by square wave voltammetry. A systematic enhancement of detection was achieved through optimisation of the properties of the redox-tagged peptide; this included for the first time a side-by-side study of the applicability of two of the most commonly applied redox reporters used for developing electrochemical biosensors, ferrocene and methylene blue, along with the effect of changing both the nature of the spacer and the composition of the SAM. Methylene blue-tagged peptides combined with a polyethylene-glycol (PEG) based spacer were shown to be the best platform for trypsin detection, leading to the highest fidelity signals (characterised by the highest sensitivity (signal gain) and a much more stable background than that registered when using ferrocene as a reporter). A ternary SAM (T-SAM) configuration, which included a PEG-based dithiol, minimised the non-specific adsorption of other proteins and was sensitive towards trypsin in the clinically relevant range, with a Limit of Detection (LoD) of 250pM. Kinetic analysis of the electrochemical response with time showed a good fit to a Michaelis-Menten surface cleavage model, enabling the extraction of values for kcat and KM. Fitting to this model enabled quantitative determination of the solution concentration of trypsin across the entire measurement range. Studies using an enzyme inhibitor and a range of real world possible interferents demonstrated a selective response to trypsin cleavage. This indicates that a PEG-based peptide, employing methylene blue as redox reporter, and deposited on an electrode as a ternary SAM configuration, is a suitable platform to develop clinically-relevant and quantitative electrochemical peptide-based protease biosensing. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

An analytical approach to air defense: cost, effectiveness and SWOT analysis of employing fighter aircraft and modern SAM systems

NASA Astrophysics Data System (ADS)

Kus, Orcun; Kocaman, Ibrahim; Topcu, Yucel; Karaca, Volkan

2012-05-01

The problem of defending a specific airspace is among the main issues a military commander to solve. Proper protection of own airspace is crucial for mission success at the battlefield. The military doctrines of most world armed forces involve two main options of defending the airspace. One of them is utilizing formations of fighter aircraft, which is a flexible choice. The second option is deploying modern SAM (Surface to Air Missile) systems, which is more expansive. On the other hand the decision makers are to cope with miscellaneous restrictions such as the budgeting problems. This study defines air defense concept according to modern air warfare doctrine. It considers an air defense scenario over an arbitrary airspace and compares the performance and cost-effectiveness of employing fighter aircraft and SAM systems. It also presents SWOT (Strenghts - Weakness - Opportunities - Threats) analyses of air defense by fighter aircraft and by modern SAMs and tries to point out whichever option is better. We conclude that deploying SAMs has important advantages over using fighter aircraft by means of interception capacity within a given time period and is cost-effective.

Effects of different self-assembled monolayers on thin-film morphology: a combined DFT/MD simulation protocol.

PubMed

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Motta, Alessandro; Nicolotti, Orazio; Lattanzi, Gianluca

2015-10-06

Organic thin film transistors (OTFTs) are multilayer field-effect transistors that employ an organic conjugated material as semiconductor. Several experimental groups have recently demonstrated that the insertion of an organic self-assembled monolayer (SAM) between the dielectric and the semiconductive layer is responsible for a sensible improvement of the OTFT performances in terms of an increased charge carrier mobility caused by a higher degree of order in the organic semiconductor layer. Here, we describe a combined periodic density functional theory (DFT) and classical molecular dynamics (MD) protocol applied to four different SAMs and a pentacene monolayer deposited onto their surfaces. In particular, we investigate the morphology and the surface of the four SAMs and the translational, orientational, and nematic order of the monolayer through the calculation of several distribution functions and order parameters pointing out the differences among the systems and relating them to known experimental results. Our calculations also suggest that small differences in the SAM molecular design will produce remarkable differences in the SAM surface and monolayer order. In particular, our simulations explain how a SAM with a bulky terminal group results in an irregular and rough surface that determines the deposition of a disordered semiconductive monolayer. On the contrary, SAMs with a small terminal group generate smooth surfaces with uninterrupted periodicity, thus favoring the formation of an ordered pentacene monolayer that increases the mobility of charge carriers and improves the overall performances of the OTFT devices. Our results clearly point out that the in silico procedure presented here might be of help in tuning the design of SAMs in order to improve the quality of OTFT devices.

Simulation and Modeling of Self-Assembled Monolayers of Carboxylic Acid Thiols on Flat and Nanoparticle Gold Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Techane, Sirnegeda D.; Baer, Donald R.; Castner, David G.

2011-09-01

Quantitative analysis of the 16-mercaptohexadecanoic acid self-assembled monolayer (C16 COOH-SAM) layer thickness on gold nanoparticles (AuNPs) was performed using simulation of electron spectra for surface analysis (SESSA) and x-ray photoelectron spectroscopy (XPS). XPS measurements of C16 COOH SAMs on flat gold surfaces were made at 9 different photoelectron take-off angles (5o to 85o in 5o increments), corrected using geometric weighting factors and then summed together to approximate spherical AuNPs. The SAM thickness and relative surface roughness (RSA) in SESSA were optimized to determine the best agreement between simulated and experimental surface composition. Based on the glancing angle results, it wasmore » found that inclusion of a hydrocarbon contamination layer on top the C16 COOH-SAM was necessary to improve the agreement between the SESSA and XPS results. For the 16 COOH-SAMs on flat Au surfaces, using a SAM thickness of 1.1Å/CH2 group, an RSA of 1.05 and a 1.5Å CH2-contamination overlayer (total film thickness = 21.5Å) for the SESSA calculations provided the best agreement with the experimental XPS data. After applying the appropriate geometric corrections and summing the SESSA flat surface compositions, the best fit results for the 16 COOH-SAM thickness and surface roughness on the AuNPs were determined to be 0.9Å/CH2 group and 1.06 RSA with a 1.5Å CH2-contamination overlayer (total film thickness = 18.5Å). The three angstrom difference in SAM thickness between the flat Au and AuNP surfaces suggests the alkyl chains of the SAM are slightly more tilted or disordered on the AuNP surfaces.« less

Comparative metabolomics reveals the mechanism of avermectin production enhancement by S-adenosylmethionine.

PubMed

Tian, Pingping; Cao, Peng; Hu, Dong; Wang, Depei; Zhang, Jian; Wang, Lin; Zhu, Yan; Gao, Qiang

2017-05-01

It was found that S-adenosylmethionine (SAM) could effectively improve avermectin titer with 30-60 μg/mL addition to FH medium. To clearly elucidate the mechanism of SAM on intracellular metabolites of Streptomyces avermitilis, a GC-MS-based comparative metabolomics approach was carried out. First, 230 intracellular metabolites were identified and 14 of them remarkably influenced avermectin biosynthesis were discriminative biomarkers between non-SAM groups and SAM-treated groups by principal components analysis (PCA) and partial least squares (PLS). Based on further key metabolic pathway analyses, these biomarkers, such as glucose, oxaloacetic acid, fatty acids (in soybean oil), threonine, valine, and leucine, were identified as potentially beneficial precursors and added in medium. Compared with single-precursor feeding, the combined feeding of the precursors and SAM markedly increased the avermectin titer. The co-feeding approach not only directly verified our hypothesis on the mechanism of SAM by comparative metabolomics, but also provided a novel strategy to increase avermectin production.

Modulation of the Seasonal Cycle of Antarctic Sea Ice Extent Related to the Southern Annular Mode

NASA Astrophysics Data System (ADS)

Doddridge, Edward W.; Marshall, John

2017-10-01

Through analysis of remotely sensed sea surface temperature (SST) and sea ice concentration data, we investigate the impact of winds related to the Southern Annular Mode (SAM) on sea ice extent around Antarctica. We show that positive SAM anomalies in the austral summer are associated with anomalously cold SSTs that persist and lead to anomalous ice growth in the following autumn, while negative SAM anomalies precede warm SSTs and a reduction in sea ice extent during autumn. The largest effect occurs in April, when a unit change in the detrended summertime SAM is followed by a 1.8±0.6 ×105 km2 change in detrended sea ice extent. We find no evidence that sea ice extent anomalies related to the summertime SAM affect the wintertime sea ice extent maximum. Our analysis shows that the wind anomalies related to the negative SAM during the 2016/2017 austral summer contributed to the record minimum Antarctic sea ice extent observed in March 2017.

Heterotypic Sam-Sam association between Odin-Sam1 and Arap3-Sam: binding affinity and structural insights.

PubMed

Mercurio, Flavia A; Marasco, Daniela; Pirone, Luciano; Scognamiglio, Pasqualina L; Pedone, Emilia M; Pellecchia, Maurizio; Leone, Marilisa

2013-01-02

Arap3 is a phosphatidylinositol 3 kinase effector protein that plays a role as GTPase activator (GAP) for Arf6 and RhoA. Arap3 contains a sterile alpha motif (Sam) domain that has high sequence homology with the Sam domain of the EphA2-receptor (EphA2-Sam). Both Arap3-Sam and EphA2-Sam are able to associate with the Sam domain of the lipid phosphatase Ship2 (Ship2-Sam). Recently, we reported a novel interaction between the first Sam domain of Odin (Odin-Sam1), a protein belonging to the ANKS (ANKyrin repeat and Sam domain containing) family, and EphA2-Sam. In our latest work, we applied NMR spectroscopy, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to characterize the association between Arap3-Sam and Odin-Sam1. We show that these two Sam domains interact with low micromolar affinity. Moreover, by means of molecular docking techniques, supported by NMR data, we demonstrate that Odin-Sam1 and Arap3-Sam might bind with a topology that is common to several Sam-Sam complexes. The revealed structural details form the basis for the design of potential peptide antagonists that could be used as chemical tools to investigate functional aspects related to heterotypic Arap3-Sam associations. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient degradation of sulfamethazine in simulated and real wastewater at slightly basic pH values using Co-SAM-SCS /H2O2 Fenton-like system.

PubMed

Cheng, Min; Zeng, Guangming; Huang, Danlian; Lai, Cui; Liu, Yang; Zhang, Chen; Wan, Jia; Hu, Liang; Zhou, Chengyun; Xiong, Weiping

2018-07-01

The presence of antibiotics in aquatic environments has attracted global concern. Fenton process is an attractive yet challenging method for antibiotics degradation, especially when such a reaction can be conducted at neutral pH values. In this study, a novel composite Fe/Co catalyst was synthesized via the modification of steel converter slag (SCS) by salicylic acid-methanol (SAM) and cobalt nitrate (Co(NO 3 ) 2 ). The catalysts were characterized by N 2 -Brunauer-Emmett-Teller (BET), X-ray diffraction (XRD), Fourier transform infrared (FT-IR), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results indicated that the Co-SAM-SCS/H 2 O 2 Fenton-like system was very effective for sulfamethazine (SMZ) degradation at a wide pH range. At initial pH of 7.0, the degradation rate of SMZ in Co-SAM-SCS/H 2 O 2 system was 2.48, 3.20, 6.18, and 16.21 times of that in Fe-SAM-SCS/H 2 O 2 , SAM-SCS/H 2 O 2 , Co(NO 3 ) 2 /H 2 O 2 and SCS/H 2 O 2 system, respectively. The preliminary analysis suggested that high surface area of Co-SAM-SCS sample and synergistic effect between introduced Co and SAM-SCS are responsible for the efficient catalytic activity. During the degradation, three main intermediates were identified by high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. Based on this, a possible degradation pathway was proposed. The SEM images, XRD patterns and XPS spectra before and after the reactions demonstrate that the crystal and chemical structure of Co-SAM-SCS after five cycles are almost unchanged. Besides, the Co-SAM-SCS presented low iron and cobalt leaching (0.17 mg/L and 2.36 mg/L, respectively). The studied Fenton-like process also showed high degradation of SMZ in river water and municipal wastewater. The progress will bring valuable insights to develop high-performance heterogeneous Fenton-like catalysts for environmental remediation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fibrinogen adsorption, platelet adhesion and activation on mixed hydroxyl-/methyl-terminated self-assembled monolayers.

PubMed

Rodrigues, Sofia N; Gonçalves, Inês C; Martins, M C L; Barbosa, Mário A; Ratner, Buddy D

2006-11-01

The effect of surface wettability on fibrinogen adsorption, platelet adhesion and platelet activation was investigated using self-assembled monolayers (SAMs) containing different ratios of longer chain methyl- and shorter chain hydroxyl-terminated alkanethiols (C15CH3 vs. C11OH) on gold. Protein adsorption studies were performed using radiolabeled human fibrinogen (HFG). Platelet adhesion and activation studies with and without pre-adsorbed fibrinogen, albumin and plasma were assessed using scanning electron microscopy (SEM) and a glutaraldehyde-induced fluorescence technique (GIFT). Results demonstrated a linear decrease of HFG adsorption with the increase of OH groups on the monolayer (increase of the hydrophilicity). Platelet adhesion and activation also decrease with increase of hydrophilicity of surface. Concerning SAMs pre-immersed in proteins, fibrinogen adsorption was related with high platelet adhesion and activation. The passivant effect of albumin on platelet adhesion and activation was only demonstrated on SAMs contained C11OH. When all the blood proteins are present (plasma) platelet adhesion was almost absent on SAMs with 65% and 100% C11OH. This could be explained by the higher albumin affinity of the SAMs with 65% C11OH and the lower total protein adsorption associated with SAMs with 100% C11OH.

A role of the SAM domain in EphA2 receptor activation.

PubMed

Shi, Xiaojun; Hapiak, Vera; Zheng, Ji; Muller-Greven, Jeannine; Bowman, Deanna; Lingerak, Ryan; Buck, Matthias; Wang, Bing-Cheng; Smith, Adam W

2017-03-24

Among the 20 subfamilies of protein receptor tyrosine kinases (RTKs), Eph receptors are unique in possessing a sterile alpha motif (SAM domain) at their C-terminal ends. However, the functions of SAM domains in Eph receptors remain elusive. Here we report on a combined cell biology and quantitative fluorescence study to investigate the role of the SAM domain in EphA2 function. We observed elevated tyrosine autophosphorylation levels upon deletion of the EphA2 SAM domain (EphA2ΔS) in DU145 and PC3 prostate cancer cells and a skin tumor cell line derived from EphA1/A2 knockout mice. These results suggest that SAM domain deletion induced constitutive activation of EphA2 kinase activity. In order to explain these effects, we applied fluorescence correlation spectroscopy to investigate the lateral molecular organization of EphA2. Our results indicate that SAM domain deletion (EphA2ΔS-GFP) increases oligomerization compared to the full length receptor (EphA2FL-GFP). Stimulation with ephrinA1, a ligand for EphA2, induced further oligomerization and activation of EphA2FL-GFP. The SAM domain deletion mutant, EphA2ΔS-GFP, also underwent further oligomerization upon ephrinA1 stimulation, but the oligomers were larger than those observed for EphA2FL-GFP. Based on these results, we conclude that the EphA2 SAM domain inhibits kinase activity by reducing receptor oligomerization.

NREL's System Advisor Model Simplifies Complex Energy Analysis (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2015-01-01

NREL has developed a tool -- the System Advisor Model (SAM) -- that can help decision makers analyze cost, performance, and financing of any size grid-connected solar, wind, or geothermal power project. Manufacturers, engineering and consulting firms, research and development firms, utilities, developers, venture capital firms, and international organizations use SAM for end-to-end analysis that helps determine whether and how to make investments in renewable energy projects.

Operational Maneuver: Function or Fiction?

DTIC Science & Technology

1996-02-12

characteristics of Vego’s operational functions. Although Schroedel’s model was constructed for the art and science of operational maneuver, his model...Schroedel, Joseph. "The Art and Science of operational Maneuver. " Fort Leavenworth, Kansas, SAMS Monograph, 1988, p. 5. 3 U.S. Joint Chiefs of Staff...Important Than Others? Ft. Leavenworth, Kansas: Study, 1986. Schroedel, Joseph. "The Art and Science of Operational Maneuver." Ft. Leavenworth, Kansas: SAMS

Inelastic electron tunneling process for alkanethiol self-assembled monolayers

NASA Astrophysics Data System (ADS)

Okabayashi, Norio; Paulsson, Magnus; Komeda, Tadahiro

2013-02-01

Recent investigations of inelastic electron tunneling spectroscopy (IETS) for alkanethiol self-assembled monolayers (SAMs) are reviewed. Alkanethiol SAMs are usually prepared by immersing a gold substrate into a solution of alkanethiol molecules, and they are very stable, even under ambient conditions. Thus, alkanethiol SAMs have been used as typical molecules for research into molecular electronics. Infrared spectroscopy and electron energy loss spectroscopy (EELS) have frequently been employed to characterize SAMs on the macroscopic scale. For characterization of alkanethiol SAMs on the nanometer scale region, or for single alkanethiol molecules through which electrons actually tunnel, IETS has proven to be an effective method. However, IETS experiments for alkanethiol SAMs employing different methods have shown large differences, i.e., there is a lack of standard data for alkanethiol SAMs with which to understand the IET process or to satisfactorily compare with theoretical investigations. An effective means of acquiring standard data is the formation of a tunneling junction with scanning tunneling microscopy (STM). After explanation of the STM experimental techniques, standard IETS data are presented whereby a contact condition between the tip and SAM is tuned. We have found that many vibrational modes are detected by STM-IETS, as is also the case for EELS. These results are compared with IET spectra measured with different tunneling junctions. In order to precisely investigate which vibrational modes are active in IETS, isotope labeling of alkanethiols with specifically synthesized isotopically substituted molecule has been examined. This method provides unambiguous assignments of IET spectra peaks and site selectivity for alkanethiol SAMs such that all parts of the alkanethiol molecules almost equally contribute to the IET process. The IET process is also discussed based on density functional theory and nonequilibrium Green’s function calculations. These results quantitatively reproduce many the experimentally observed features, whereas Fermi’s golden rule for IETS qualitatively explains the propensity rule and site selectivity observed in the experiments. However, comparison between experiment and theory reveals a large difference in IETS intensity for the C-H stretching mode that originates from the side chains of the alkanethiol molecules. In order to explain this difference, we discuss the importance of an intermolecular tunneling process in the SAM. Application of STM-IETS to identify a hydrogenated alkanethiol molecule inserted into a deuterated alkanethiol SAM matrix is also demonstrated.

Starting Small for Big School Improvement

ERIC Educational Resources Information Center

Scharff, Helen A.; DeAngelis, Deirdre A.; Talbert, Joan E.

2010-01-01

In the Scaffolded Apprenticeship Model (SAM), a school improvement strategy in place in New York City; Boston, Massachusetts; and Oakland, California, teacher teams improve their schools by studying and closing high-leverage learning gaps for small groups of struggling students as a strategy for systemic change. SAM's goal is for each school to…

Facilities Performance Indicators Report, 2006-07

ERIC Educational Resources Information Center

Glazner, Steve, Ed.

2008-01-01

The "Facilities Performance Indicators Survey" ("FPI") supersedes and builds upon the two major surveys APPA conducted in the past: the Comparative Costs and Staffing (CCAS) survey and the Strategic Assessment Model (SAM). The "FPI" covers all the materials collected in CCAS and SAM, along with some select new data points and improved survey…

Sam37 is crucial for formation of the mitochondrial TOM-SAM supercomplex, thereby promoting β-barrel biogenesis.

PubMed

Wenz, Lena-Sophie; Ellenrieder, Lars; Qiu, Jian; Bohnert, Maria; Zufall, Nicole; van der Laan, Martin; Pfanner, Nikolaus; Wiedemann, Nils; Becker, Thomas

2015-09-28

Biogenesis of mitochondrial β-barrel proteins requires two preprotein translocases, the general translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). TOM and SAM form a supercomplex that promotes transfer of β-barrel precursors. The SAM core complex contains the channel protein Sam50, which cooperates with Sam35 in precursor recognition, and the peripheral membrane protein Sam37. The molecular function of Sam37 has been unknown. We report that Sam37 is crucial for formation of the TOM-SAM supercomplex. Sam37 interacts with the receptor domain of Tom22 on the cytosolic side of the mitochondrial outer membrane and links TOM and SAM complexes. Sam37 thus promotes efficient transfer of β-barrel precursors to the SAM complex. We conclude that Sam37 functions as a coupling factor of the translocase supercomplex of the mitochondrial outer membrane. © 2015 Wenz et al.

Substratum interfacial energetic effects on the attachment of marine bacteria

NASA Astrophysics Data System (ADS)

Ista, Linnea Kathryn

Biofilms represent an ancient, ubiquitous and influential form of life on earth. Biofilm formation is initiated by attachment of bacterial cells from an aqueous suspension onto a suitable attachment substratum. While in certain, well studied cases initial attachment and subsequent biofilm formation is mediated by specific ligand-receptor pairs on the bacteria and attachment substratum, in the open environment, including the ocean, it is assumed to be non-specific and mediated by processes similar to those that drive adsorption of colloids at the water-solid interface. Colloidal principles are studied to determine the molecular and physicochemical interactions involved in the attachment of the model marine bacterium, Cobetia marina to model self-assembled monolayer surfaces. In the simplest application of colloidal principles the wettability of attachment substrata, as measured by the advancing contact angle of water (theta AW) on the surface, is frequently used as an approximation for the surface tension. We demonstrate the applicability of this approach for attachment of C. marina and algal zoospores and extend it to the development of a means to control attachment and release of microorganisms by altering and tuning surface thetaAW. In many cases, however, thetaAW does not capture all the information necessary to model attachment of bacteria to attachment substrata; SAMs with similar thetaAW attach different number of bacteria. More advanced colloidal models of initial bacterial attachment have evolved over the last several decades, with the emergence of the model proposed by van Oss, Chaudhury and Good (VCG) as preeminent. The VCG model enables calculation of interfacial tensions by dividing these into two major interactions thought to be important at biointerfaces: apolar, Lifshitz-van der Waals and polar, Lewis acid-base (including hydrogen bonding) interactions. These interfacial tensions are combined to yield DeltaGadh, the free energy associated with attachment of bacteria to a substratum. We use VCG to model DeltaGadh and interfacial tensions as they relate to model bacterial attachment on SAMs that accumulate cells to different degrees. Even with the more complex interactions measured by VCG, surface energy of the attachment substratum alone was insufficient to predict attachment. VCG was then employed to model attachment of C. marina to a series of SAMs varying systematically in the number of ethylene glycol residues present in the molecule; an identical series has been previously shown to vary dramatically in the number of cells attached as a function of ethylene glycols present. Our results indicate that while VCG adequately models the interfacial tension between water and ethylene glycol SAMs in a manner that predicts bacterial attachment, DeltaGadh as calculated by VCG neither qualitatively nor quantitatively reflects the attachment data. The VCG model, thus, fails to capture specific information regarding the interactions between the attaching bacteria, water, and the SAM. We show that while hydrogen-bond accepting interactions are very well captured by this model, the ability for SAMs and bacteria to donate hydrogen bonds is not adequately described as the VCG model is currently applied. We also describe ways in which VCG fails to capture two specific biological aspects that may be important in bacterial attachment to surfaces:1.) specific interactions between molecules on the surface and bacteria and 2.) bacterial cell surface heterogeneities that may be important in differential attachment to different substrata.

Mapping the Impact of Aerosol-Cloud Interactions on Cloud Formation and Warm-season Rainfall in Mountainous Regions Using Observations and Models

NASA Astrophysics Data System (ADS)

Duan, Yajuan

Light rainfall (< 3 mm/hr) amounts to 30-70% of the annual water budget in the Southern Appalachian Mountains (SAM), a mid-latitude mid-mountain system in the SE CONUS. Topographic complexity favors the diurnal development of regional-scale convergence patterns that provide the moisture source for low-level clouds and fog (LLCF). Low-level moisture and cloud condensation nuclei (CCN) are distributed by ridge-valley circulations favoring LLCF formation that modulate the diurnal cycle of rainfall especially the mid-day peak. The overarching objective of this dissertation is to advance the quantitative understanding of the indirect effect of aerosols on the diurnal cycle of LLCF and warm-season precipitation in mountainous regions generally, and in the SAM in particular, for the purpose of improving the representation of orographic precipitation processes in remote sensing retrievals and physically-based models. The research approach consists of integrating analysis of in situ observations from long-term observation networks and an intensive field campaign, multi-sensor satellite data, and modeling studies. In the first part of this dissertation, long-term satellite observations are analyzed to characterize the spatial and temporal variability of LLCF and to elucidate the physical basis of the space-time error structure in precipitation retrievals. Significantly underestimated precipitation errors are attributed to variations in low-level rainfall microstructure undetected by satellites. Column model simulations including observed LLCF microphysics demonstrate that seeder-feeder interactions (SFI) among upper-level precipitation and LLCF contribute to an three-fold increase in observed rainfall accumulation and can enhance surface rainfall by up to ten-fold. The second part of this dissertation examines the indirect effect of aerosols on cloud formation and warm-season daytime precipitation in the SAM. A new entraining spectral cloud parcel model was developed and applied to provide the first assessment of aerosol-cloud interactions in the early development of mid-day cumulus congestus over the inner SAM. Leveraging comprehensive measurements from the Integrated Precipitation and Hydrology Experiment (IPHEx) in 2014, model results indicate that simulated spectra with a low value of condensation coefficient (0.01) are in good agreement with IPHEx aircraft observations. Further, to explore sensitivity of warm-season precipitation processes to CCN characteristics, detailed intercomparisons of Weather Research and Forecasting (WRF) model simulations using IPHEx and standard continental CCN spectra were conducted. The simulated CDNC using the local spectrum show better agreement with IPHEx airborne observations and better replicate the widespread low-level cloudiness around mid-day over the inner region. The local spectrum simulation also indicate suppressed early precipitation, enhanced ice processes tied to more vigorous vertical development of individual storm cells. The studied processes here are representative of dominant moist atmospheric processes in complex terrain and cloud forests in the humid tropics and extra-tropics, thus findings from this research in the SAM are transferable to mountainous areas elsewhere.

The production and verification of pristine semi-fluorinated thiol monolayers on gold.

PubMed

Ford, Kym; Battersby, Bronwyn J; Wood, Barry J; Gentle, Ian R

2012-03-15

The presence of adventitious contamination of self-assembled monolayers (SAMs) is a well-known phenomenon that is often overlooked or underestimated in the literature. Herein, we demonstrate that it is possible to produce pristine self-assembled monolayers (SAMs) on gold surfaces that are devoid of adventitious species. The chemical purity or the pristine quality of the SAM was verified by the experimental relative atomic ratios measured by X-ray photoelectron spectroscopy (XPS) of all elements including carbon and corresponded to within 5% of the stoichiometric ratios. Perfluoro-octyl-thiolate (F8) was used as a model compound in this study, where monolayers were assembled from solutions of an acetylated F8 precursor. Quantitative elemental characterization of the acetylated F8 precursor by cold-stage XPS provided valuable reference data for the analysis of the subsequent SAMs. Comprehensive analysis of high-resolution XPS C 1s spectra proved to be essential for establishing the purity of the SAMs, since the peaks of the adventitious species were easily distinguished from those of the F8. Analyses of deliberately contaminated F8 SAMs showed that the adventitious species persisted during the process of self-assembly and therefore co-existed with the SAM in the interfacial region. The work also established that even a lengthy deposition time of 18 h was incapable of displacing the adventitious species present at the interface. Copyright © 2011 Elsevier Inc. All rights reserved.

Field Calibration of the Saltation-Abrasion Model Using Measurements of the Energy Delivered to the Channel Bed

NASA Astrophysics Data System (ADS)

Turowski, J. M.; Wyss, C. R.; Beer, A. R.

2014-12-01

The saltation-abrasion model (SAM) is one of the highest-developed process models for fluvial bedrock erosion, describing bedrock erosion due to the impact of saltating bedload particles. The fundamental assumption in the model is a proportionality of the erosion rate and the energy delivered to the channel bed by these impacts. So far, the SAM has been calibrated on laboratory data, but field tests are rare. Here, we exploit the availability of high-quality field data at the Erlenbach bedload observatory to test and calibrate the SAM. The Erlenbach is a small, steep stream in the Swiss Prealps that hosts a well-instrumented observatory for bedload transport and erosion. Bedload samples can be taken during floods with automatic basket samplers and bedload transport rates are measured continuously with Swiss plate geophones, a surrogate method for bedload monitoring. The geophone plates can also be used to measure the energy transferred to the bed by passingbedload. Thus, we can calibrate the SAM by exploiting independent data on particle impacts, the energy they transfer to the bed, and bedload samples including grain size distributions. We find that the dimensionless pre-factor to the model is dependent on grain size. Predictions of bedrock erosion can be compared to spatial erosion data obtained from successive scans of bedrock slabs installed in the channel bed immediately upstream of the plate geophones.

An online replanning method using warm start optimization and aperture morphing for flattening-filter-free beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahunbay, Ergun E., E-mail: eahunbay@mcw.edu; Ates,

Purpose: In a situation where a couch shift for patient positioning is not preferred or prohibited (e.g., MR-linac), segment aperture morphing (SAM) can address target dislocation and deformation. For IMRT/VMAT with flattening-filter-free (FFF) beams, however, SAM method would lead to an adverse translational dose effect due to the beam unflattening. Here the authors propose a new two-step process to address both the translational effect of FFF beams and the target deformation. Methods: The replanning method consists of an offline and an online step. The offline step is to create a series of preshifted-plans (PSPs) obtained by a so-called “warm start”more » optimization (starting optimization from the original plan, rather than from scratch) at a series of isocenter shifts. The PSPs all have the same number of segments with very similar shapes, since the warm start optimization only adjusts the MLC positions instead of regenerating them. In the online step, a new plan is obtained by picking the closest PSP or linearly interpolating the MLC positions and the monitor units of the closest PSPs for the shift determined from the image of the day. This two-step process is completely automated and almost instantaneous (no optimization or dose calculation needed). The previously developed SAM algorithm is then applied for daily deformation. The authors tested the method on sample prostate and pancreas cases. Results: The two-step interpolation method can account for the adverse dose effects from FFF beams, while SAM corrects for the target deformation. Plan interpolation method is effective in diminishing the unflat beam effect and may allow reducing the required number of PSPs. The whole process takes the same time as the previously reported SAM process (5–10 min). Conclusions: The new two-step method plus SAM can address both the translation effects of FFF beams and target deformation, and can be executed in full automation except the delineation of target contour required by the SAM process.« less

Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance

PubMed Central

Wong, Chui E; Bhalla, Prem L; Ottenhof, Harald; Singh, Mohan B

2008-01-01

Background Despite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity. Results In order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag). Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation. Conclusion The presented data provide a picture of the transcriptional profile of the pea SAM, and reveal possible roles of differentially expressed transcripts in meristem function and maintenance. PMID:18590528

A critical appraisal of guidelines used for management of severe acute malnutrition in South Africa's referral system.

PubMed

Mambulu-Chikankheni, Faith Nankasa; Eyles, John; Eboreime, Ejemai Amaize; Ditlopo, Prudence

2017-10-18

Focusing on healthcare referral processes for children with severe acute malnutrition (SAM) in South Africa, this paper discusses the comprehensiveness of documents (global and national) that guide the country's SAM healthcare. This research is relevant because South African studies on SAM mostly examine the implementation of WHO guidelines in hospitals, making their technical relevance to the country's lower level and referral healthcare system under-explored. To add to both literature and methods for studying SAM healthcare, we critically appraised four child healthcare guidelines (global and national) and conducted complementary expert interviews (n = 5). Combining both methods enabled us to examine the comprehensiveness of the documents as related to guiding SAM healthcare within the country's referral system as well as the credibility (rigour and stakeholder representation) of the guideline documents' development process. None of the guidelines appraised covered all steps of SAM referrals; however, each addressed certain steps thoroughly, apart from transit care. Our study also revealed that national documents were mostly modelled after WHO guidelines but were not explicitly adapted to local context. Furthermore, we found most guidelines' formulation processes to be unclear and stakeholder involvement in the process to be minimal. In adapting guidelines for management of SAM in South Africa, it is important that local context applicability is taken into consideration. In doing this, wider stakeholder involvement is essential; this is important because factors that affect SAM management go beyond in-hospital care. Community, civil society, medical and administrative involvement during guideline formulation processes will enhance acceptability and adherence to the guidelines.

The effect of changing wind forcing on Antarctic ice shelf melting in high-resolution, global sea ice-ocean simulations with the Accelerated Climate Model for Energy (ACME)

NASA Astrophysics Data System (ADS)

Asay-Davis, Xylar; Price, Stephen; Petersen, Mark; Wolfe, Jonathan

2017-04-01

The capability for simulating sub-ice shelf circulation and submarine melting and freezing has recently been added to the U.S. Department of Energy's Accelerated Climate Model for Energy (ACME). With this new capability, we use an eddy permitting ocean model to conduct two sets of simulations in the spirit of Spence et al. (GRL, 41, 2014), who demonstrate increased warm water upwelling along the Antarctic coast in response to poleward shifting and strengthening of Southern Ocean westerly winds. These characteristics, symptomatic of a positive Southern Annular Mode (SAM), are projected to continue into the 21st century under anthropogenic climate change (Fyfe et al., J. Clim., 20, 2007). In our first simulation, we force the climate model using the standard CORE interannual forcing dataset (Large and Yeager; Clim. Dyn., 33, 2009). In our second simulation, we force our climate model using an altered version of CORE interannual forcing, based on the latter half of the full time series, which we take as a proxy for a future climate state biased towards a positive SAM. We compare ocean model states and sub-ice shelf melt rates with observations, exploring sources of model biases as well as the effects of the two forcing scenarios.

Geotectonic setting of the Suwałki Anorthosite Massif (NE-Poland) - constraints for 3D geological modelling

NASA Astrophysics Data System (ADS)

Wiszniewska, Janina; Petecki, Zdzislaw; Rosowiecka, Olga; Krzemińska, Ewa

2017-04-01

Suwałki Anorthosite Massif (SAM) is located within 200 km long Mesoproterozoic magmatic terrane called Mazury Complex (NE Poland) (Wiszniewska et al. 2002). This is a belt of granitoids and associated mafic and intermediate igneous rocks followed an E-W trending lineament extending from the Baltic Sea through northern Poland and southern Lithuania to western Belarus. Crystalline basement of the Suwałki region is covered by a thick pile (550-1300m) of Phanerozoic sedimentary rocks, which are dipping towards the SW East European Craton`s border. SAM is a complex structure composed primarily of magmatic massif type anorthosites, surrounded by a rim of norite-gabbronorite and diorite rocks. SAM is characterized by magnetic and gravimetric negative anomalies. The gravimetric one is related to anorthosite massif. It is surrounded by a few positive anomalies, which reflect occurrences of denser rocks such as granite, monzodiorite and granodiorite. The large magnetic anomaly is supposed to reflect an effect of an negative inclination of remanent magnetization of anorthosite rocks. This hypothesis was confirmed by magnetic modelling along DSS POLONAISE'97 profile P4 (Petecki, 2006). Existing measurements however do not show prevailing negative inclinations, even though they prove very high remanent magnetization of anorthosites. A pronounced residual magnetic anomalies of Udryń and Krzemianka are related to Fe-Ti-(V) ore deposits recognized by deep boreholes. Based on potential field data it was suggested that anorthosite bottom reaches 2,5-4,5 km depth. Thus it is evident that the geological architecture of SAM and its surrounding area is not fully recognized. The problem is supposed to be resolved using modern methods of geophysical transformations and 3D modelling using GeoModeller software. The final result of the research will be to recognize spatial structure of the SAM and its surrounding. Petrological, mineralogical, geochronological (U-Pb SHRIMP method on zircons and titanite) and tectonic testing from SAM were carried out. Structural analysis were also performed on a basis of the identified tectonic structures on selected cores. Recognition of possible connections of tectonic structures with magmatic processes and pegmatite, aplite, quartz veins including their mineral composition have been checked. For pegmatite, aplite, hydrothermal and quartz veins age determinations, U-Pb SHRIMP IIe method on zircon, monazite and titanite have been done. The primary age measurements of zircons from microgranite veins within anorthosite have shown consistent Paleoproterozoic ages of protolith ( 1844±11 Ma for Krzemianka 73) with Mezoproterozoic ages ( 1.5 Ga) of metamorphic rims, similar to monazite ages ( 1469±16 Ma). The microgranite veins are probably derived from the older Paleoproterozoic crust, carrying a relic zircons of 1.84 Ga ages but also some inherited older ages as 2.0 to 2.3 Ga. The future planned works will concern the genesis and evolution of igneous AMCG rocks suite and related ore mineralization of the SAM. Petecki Z., 2006: Integrated gravity and magnetic modelling along P4 seismic profile (in Polish). Pr. Państw. Inst. Geol. CLXI., 193p. Wiszniewska J., Claesson S., Stein H., Vander Auwera J., Duchense J-C., 2002: The north-eastern Polish anorthosite massifs: petrological, geochemical and isotopic evidence for a crustal derivation. Terra Nova 14, p.451-460 This is a contribution to the project " Determination of architecture and geological evolution of the Suwałki Anothosite Massif by 3D geological and geophysical data modelling method" NCN grant 51.2115.1601.09.0

Motivation towards dual career of European student-athletes.

PubMed

Lupo, Corrado; Guidotti, Flavia; Goncalves, Carlos E; Moreira, Liliana; Doupona Topic, Mojca; Bellardini, Helena; Tonkonogi, Michail; Colin, Allen; Capranica, Laura

2015-01-01

The present study aimed to investigate motivations for the dual career of European student-athletes living in countries providing different educational services for elite athletes: State-centric regulation-State as sponsor/facilitator (State), National Sporting Federations/Institutes as intermediary (Federation) and Laisser Faire, no formal structures (No Structure). Therefore, the European Student-athletes' Motivation towards Sports and Academics Questionnaire (SAMSAQ-EU) was administered to 524 European student-athletes. Exploratory Factor Analysis, and Confirmatory Factor Analysis were applied to test the factor structure, and the reliability and validity of the SAMSAQ-EU, respectively. A multivariate approach was applied to verify subgroup effects (P ≤ 0.05) according to gender (i.e., female and male), age (i.e., ≤ 24 years, > 24 years), type of sport (i.e., individual sport and team sport) and competition level (i.e., national and international). Insufficient confirmatory indexes were reported for the whole European student-athlete group, whereas distinct three factor models [i.e., Student Athletic Motivation (SAM); Academic Motivation (AM); Career Athletic Motivation (CAM)] emerged, with acceptable reliability estimates, for State (SAM = 0.82; AM = 0.75; and CAM = 0.75), Federation (SAM = 0.82; AM = 0.66; and CAM = 0.87) and No Structure (SAM = 0.78; AM = 0.74; and CAM = 0.79) subgroups. Differences between subgroups were found only for competition level (P < 0.001) in relation to SAM (P = 0.001) and CAM (P < 0.001). For SAM, the highest and lowest values emerged for Federation (national, 5.1 ± 0.5; international, 5.4 ± 0.5) and State (national, 4.5 ± 0.9; international, 4.8 ± 0.7). The opposite picture emerged for CAM (Federation: national, 3.3 ± 0.7; international, 3.5 ± 0.9; State: national, 5.0 ± 0.8; international, 5.0 ± 0.9). Therefore, despite SAMSAQ-EU demonstrated to be a useful tool, results showed that European student-athletes' motivation for dual career has to be specifically investigated according to social contexts.

Southern Hemisphere extratropical circulation: Recent trends and natural variability

NASA Astrophysics Data System (ADS)

Thomas, Jordan L.; Waugh, Darryn W.; Gnanadesikan, Anand

2015-07-01

Changes in the Southern Annular Mode (SAM), Southern Hemisphere (SH) westerly jet location, and magnitude are linked with changes in ocean circulation along with ocean heat and carbon uptake. Recent trends have been observed in these fields but not much is known about the natural variability. Here we aim to quantify the natural variability of the SH extratropical circulation by using Coupled Model Intercomparison Project Phase 5 (CMIP5) preindustrial control model runs and compare with the observed trends in SAM, jet magnitude, and jet location. We show that trends in SAM are due partly to external forcing but are not outside the natural variability as described by these models. Trends in jet location and magnitude, however, lie outside the unforced natural variability but can be explained by a combination of natural variability and the ensemble mean forced trend. These results indicate that trends in these three diagnostics cannot be used interchangeably.

Multiple polymer architectures of human Polyhomeotic homolog 3 (PHC3) SAM

PubMed Central

Nanyes, David R.; Junco, Sarah E.; Taylor, Alexander B.; Robinson, Angela K.; Patterson, Nicolle L.; Shivarajpur, Ambika; Halloran, Jonathan; Hale, Seth M.; Kaur, Yogeet; Hart, P. John; Kim, Chongwoo A.

2014-01-01

The self-association of sterile alpha motifs (SAMs) into a helical polymer architecture is a critical functional component of many different and diverse array of proteins. For the Drosophila Polycomb group (PcG) protein Polyhomeotic (Ph), its SAM polymerization serves as the structural foundation to cluster multiple PcG complexes, helping to maintain a silenced chromatin state. Ph SAM shares 64% sequence identity with its human ortholog, PHC3 SAM, and both SAMs polymerize. However, in the context of their larger protein regions, PHC3 SAM forms longer polymers compared to Ph SAM. Motivated to establish the precise structural basis for the differences, if any, between Ph and PHC3 SAM, we determined the crystal structure of the PHC3 SAM polymer. PHC3 SAM utilizes the same SAM-SAM interaction as the Ph SAM six-fold repeat polymer. Yet, PHC3 SAM polymerizes utilizing just five SAMs per turn of the helical polymer rather than the typical six per turn observed for all SAM polymers reported to date. Structural analysis suggested that malleability of the PHC3 SAM would allow formation of not just the five-fold repeat structure but possibly others. Indeed, a second PHC3 SAM polymer in a different crystal form forms a six-fold repeat polymer. These results suggest that the polymers formed by PHC3 SAM, and likely others, are quite dynamic. The functional consequence of the variable PHC3 SAM polymers may be to create different chromatin architectures. PMID:25044168

Process-level improvements in CMIP5 models and their impact on tropical variability, the Southern Ocean, and monsoons

NASA Astrophysics Data System (ADS)

Lauer, Axel; Jones, Colin; Eyring, Veronika; Evaldsson, Martin; Hagemann, Stefan; Mäkelä, Jarmo; Martin, Gill; Roehrig, Romain; Wang, Shiyu

2018-01-01

The performance of updated versions of the four earth system models (ESMs) CNRM, EC-Earth, HadGEM, and MPI-ESM is assessed in comparison to their predecessor versions used in Phase 5 of the Coupled Model Intercomparison Project. The Earth System Model Evaluation Tool (ESMValTool) is applied to evaluate selected climate phenomena in the models against observations. This is the first systematic application of the ESMValTool to assess and document the progress made during an extensive model development and improvement project. This study focuses on the South Asian monsoon (SAM) and the West African monsoon (WAM), the coupled equatorial climate, and Southern Ocean clouds and radiation, which are known to exhibit systematic biases in present-day ESMs. The analysis shows that the tropical precipitation in three out of four models is clearly improved. Two of three updated coupled models show an improved representation of tropical sea surface temperatures with one coupled model not exhibiting a double Intertropical Convergence Zone (ITCZ). Simulated cloud amounts and cloud-radiation interactions are improved over the Southern Ocean. Improvements are also seen in the simulation of the SAM and WAM, although systematic biases remain in regional details and the timing of monsoon rainfall. Analysis of simulations with EC-Earth at different horizontal resolutions from T159 up to T1279 shows that the synoptic-scale variability in precipitation over the SAM and WAM regions improves with higher model resolution. The results suggest that the reasonably good agreement of modeled and observed mean WAM and SAM rainfall in lower-resolution models may be a result of unrealistic intensity distributions.

Intercomparison between CMIP5 model and MODIS satellite-retrieved data of aerosol optical depth, cloud fraction, and cloud-aerosol interactions

NASA Astrophysics Data System (ADS)

Sockol, Alyssa; Small Griswold, Jennifer D.

2017-08-01

Aerosols are a critical component of the Earth's atmosphere and can affect the climate of the Earth through their interactions with solar radiation and clouds. Cloud fraction (CF) and aerosol optical depth (AOD) at 550 nm from the Moderate Resolution Imaging Spectroradiometer (MODIS) are used with analogous cloud and aerosol properties from Historical Phase 5 of the Coupled Model Intercomparison Project (CMIP5) model runs that explicitly include anthropogenic aerosols and parameterized cloud-aerosol interactions. The models underestimate AOD by approximately 15% and underestimate CF by approximately 10% overall on a global scale. A regional analysis is then used to evaluate model performance in two regions with known biomass burning activity and absorbing aerosol (South America (SAM) and South Africa (SAF)). In SAM, the models overestimate AOD by 4.8% and underestimate CF by 14%. In SAF, the models underestimate AOD by 35% and overestimate CF by 13.4%. Average annual cycles show that the monthly timing of AOD peaks closely match satellite data in both SAM and SAF for all except the Community Atmosphere Model 5 and Geophysical Fluid Dynamics Laboratory (GFDL) models. Monthly timing of CF peaks closely match for all models (except GFDL) for SAM and SAF. Sorting monthly averaged 2° × 2.5° model or MODIS CF as a function of AOD does not result in the previously observed "boomerang"-shaped CF versus AOD relationship characteristic of regions with absorbing aerosols from biomass burning. Cloud-aerosol interactions, as observed using daily (or higher) temporal resolution data, are not reproducible at the spatial or temporal resolution provided by the CMIP5 models.

Practical aspects in the management of statin-associated muscle symptoms (SAMS).

PubMed

Laufs, Ulrich; Filipiak, Krysztof J; Gouni-Berthold, Ioanna; Catapano, Alberico L

2017-04-01

Statin-associated muscle symptoms (SAMS) frequently cause statin non-adherence, switching and discontinuation, contributing to adverse cardiovascular (CV) outcomes. Therefore, the management of SAMS is key in the effective treatment of patients with cardiovascular disease (CVD), through achievement of maximum-tolerated statin dosing and other practical aspects. The aim of this article is to provide practical, focused advice for healthcare professionals on the management of patients with SAMS. An expert working group combined current evidence, published guidelines and experiences surrounding a number of topics concerning SAMS to provide recommendations on how to best assess and manage this condition and reach the highest tolerated dose of statin for each individual patient. The group collaborated to provide guidance on definitions in the SAMS field, psychological issues, re-challenging and switching treatments, as well as interpretation of current guidelines and optimal treatment of SAMS in different patient populations. An algorithm was developed to guide the management of patients with SAMS. In addition, the expert working group considered some of the more complex scenarios in a series of frequently asked questions and suggested answers. The expert working group gave recommendations for healthcare professionals on the management of SAMS but highlighted the importance of tailoring the treatment approach to each individual patient. Evidence supporting the role of nutraceuticals and complementary therapies, such as vitamin D, was lacking, however the majority of the group favoured combination therapy with ezetimibe and the addition of PCSK9 inhibitors in high-risk patients. Copyright © 2017 Elsevier B.V. All rights reserved.

The Vod Couple

ERIC Educational Resources Information Center

Schaffhauser, Dian

2009-01-01

This article features two high school chemistry teachers, Aaron Sams and Jonathan Bergmann, who have overturned conventional classroom instruction by using video podcasts to form the root of a new learning model. Thumbing through an issue of "MacWorld" a few years ago, Aaron Sams was struck by an article about an application called ProfCast that…

Rhesus Monkey - Miss Sam - Fiberglass Couch - Little Joe (LJ)-1B Flight - Prep

NASA Image and Video Library

1959-12-04

B59-00828 (21 Jan. 1959) --- The test subject, a rhesus monkey named Miss Sam, is seen encased in a model of the Mercury fiberglass contour couch. She is being placed in a container for the Little Joe 1B suborbital test flight of the Mercury Capsule. Photo credit: NASA

BRIGHTEST SATELLITE GALAXY ALIGNMENT OF SLOAN DIGITAL SKY SURVEY GALAXY GROUPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Zhigang; Wang Yougang; Chen Xuelei

2013-05-01

We study the alignment signal between the distribution of the brightest satellite galaxies (BSGs) and the major axes of their host groups using the Sloan Digital Sky Survey group catalog constructed by Yang et al. After correcting for the effect of group ellipticity, a statistically significant ({approx}5{sigma}) major-axis alignment is detected and the alignment angle is found to be 43. Degree-Sign 0 {+-} 0. Degree-Sign 4. More massive and richer groups show a stronger BSG alignment. The BSG alignment around blue brightest central galaxies (BCGs) is slightly stronger than that around red BCGs. Red BSGs have a much stronger major-axismore » alignment than blue BSGs. Unlike BSGs, other satellites do not show very significant alignment with their group's major axis. We further explore BSG alignment using the semi-analytic model (SAM) constructed by Guo et al. In general, we found good agreement of the model with observations: BSGs in the SAM show a strong major-axis alignment that depends on group mass and richness in the same way as in observations and none of the other satellites exhibit prominent alignment. However, a discrepancy also exists in that the SAM shows a BSG color dependence opposite of that in observations, which is most probably induced by a missing large-scale environment ingredient in the SAM. The combination of two popular scenarios can explain the BSG alignment we detected. First, satellites merged into the group along the surrounding filaments, which are strongly aligned with the major axis of the group. Second, BSGs entered their host group more recently than other satellites, so they have preserved more information about their assembling history and major-axis alignment. In the SAM, we found positive evidence for the second scenario in the fact that BSGs merged into groups statistically more recently than other satellites. We also found that most of the BSGs (80%) were BCGs before they merged into groups and earlier merging BSGs tend to be closer to their BCGs than other BSGs. On the other hand, although the BSG color dependence in observations is the opposite of that in the SAM, it might also indicate that the first scenario is a good explanation.« less

Does Coenzyme Q10 Supplementation Mitigate Statin-Associated Muscle Symptoms? Pharmacological and Methodological Considerations.

PubMed

Taylor, Beth A

2018-04-01

Statin drugs markedly reduce low-density lipoprotein cholesterol and consequently the incidence of cardiac events. In approximately 5-10% of adults, these drugs are associated with a range of muscle side effects such as muscle pain, cramping and weakness. Reduction in mitochondrial coenzyme Q10 (CoQ10), or ubiquinone, has been proposed as a mechanism for these statin-associated muscle symptoms (SAMS), and thus various formulations of CoQ10 are marketed and consumed for the prevention and treatment of SAMS. However, data supporting the efficacy of CoQ10 are equivocal, with some studies showing that CoQ10 supplementation reduces the incidence and severity of SAMS and others finding no beneficial effects of supplementation. Methodological and pharmacological issues may confound interpretation of data on this topic. For example, many patients who report SAMS, such as those who have been enrolled in previous CoQ10 studies, may be experiencing non-specific (non-statin-associated) muscle pain. In addition, the effectiveness of oral CoQ10 supplementation to increase mitochondrial CoQ10 in human skeletal muscle is not well established. This manuscript will critically evaluate the published data on the efficacy of CoQ10 supplements in the prevention and treatment of SAMS.

Molecular Self-Assembly and Interfacial Engineering for Highly Efficient Organic Field Effect Transistors and Solar Cells

DTIC Science & Technology

2012-09-23

balance between disordered SAMs to promote large pentacene grains and thick SAMs to aid in physically buffering the charge carriers in pentacene from...to 0.76 µF/cm2), and enhanced pentacene OFET device performance such as higher charge carrier mobility, current on/off ratio, and lower threshold...surface charge trap • Tuning of surface energy • Control of surface group orientation SAM/MO ultrathin dielectric: • Low-voltage operation

Morphology of self assembled monolayers using liquid phase reaction on silica and their effect on the morphology of adsorbed insulin

NASA Astrophysics Data System (ADS)

Sharma, Indu; Pattanayek, Sudip K.; Aggarwal, Varsha; Ghosh, Subhasis

2017-05-01

The effect of roughness of two different categories of self-assembled monolayers (SAMs) with propyl amine and propyl groups respectively on the morphology of adsorbed insulin is observed. SAMs are obtained by liquid phase reaction of silica with organo silane coupling agents (SCA). The influence of the morphology and physical characteristics of the SAMs on the reaction time and concentration of the modifiers are explored. We have tested three SCA containing propyl amine with varying groups linked to Si present on it. In addition, we have used a silane coupling agent to prepare SAM of methyl head group. The approach of these molecules towards the surface depends on the head group and the groups linked to Si of the SCA. The morphology of the surfaces is analysed using power spectral density distribution (PSD), skewness, ellipsometry thickness and surface energy. Both chemical nature and physical morphology of the adsorbent influence the morphology of the adsorbed insulin. In general, a low number of aggregates of big size are formed on the surfaces obtained from low concentration of SAMs, while a higher number but of smaller size of aggregates are formed over surfaces obtained from 1% concentration of SAMs modifiers. The peak to valley ratio of the aggregates of insulin is strongly influenced by the size of grains of SCA over the adsorbent.

Comparisons of Computed Mobile Phone Induced SAR in the SAM Phantom to That in Anatomically Correct Models of the Human Head

PubMed Central

Beard, Brian B.; Kainz, Wolfgang; Onishi, Teruo; Iyama, Takahiro; Watanabe, Soichi; Fujiwara, Osamu; Wang, Jianqing; Bit-Babik, Giorgi; Faraone, Antonio; Wiart, Joe; Christ, Andreas; Kuster, Niels; Lee, Ae-Kyoung; Kroeze, Hugo; Siegbahn, Martin; Keshvari, Jafar; Abrishamkar, Houman; Simon, Winfried; Manteuffel, Dirk; Nikoloski, Neviana

2018-01-01

The specific absorption rates (SAR) determined computationally in the specific anthropomorphic mannequin (SAM) and anatomically correct models of the human head when exposed to a mobile phone model are compared as part of a study organized by IEEE Standards Coordinating Committee 34, SubCommittee 2, and Working Group 2, and carried out by an international task force comprising 14 government, academic, and industrial research institutions. The detailed study protocol defined the computational head and mobile phone models. The participants used different finite-difference time-domain software and independently positioned the mobile phone and head models in accordance with the protocol. The results show that when the pinna SAR is calculated separately from the head SAR, SAM produced a higher SAR in the head than the anatomically correct head models. Also the larger (adult) head produced a statistically significant higher peak SAR for both the 1- and 10-g averages than did the smaller (child) head for all conditions of frequency and position. PMID:29515260

Reactive Landing of Gramicidin S and Ubiquitin Ions onto Activated Self-Assembled Monolayer Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laskin, Julia; Hu, Qichi

2017-03-13

Using mass-selected ion deposition combined with in situ infrared reflection absorption spectroscopy (IRRAS), we examined the reactive landing of gramicidin S and ubiquitin ions onto activated self-assembled monolayer (SAM) surfaces terminated with N-hydroxysuccinimidyl ester (NHS-SAM) and acyl fluoride (COF-SAM) groups. Doubly protonated gramicidin S, [GS+2H]2+, and two charge states of ubiquitin, [U+5H]5+ and [U+13H]13+, were used as model systems, allowing us to explore the effect of the number of free amino groups and the secondary structure on the efficiency of covalent bond formation between the projectile ion and the surface. For all projectile ions, ion deposition resulted in the depletionmore » of IRRAS bands corresponding to the terminal groups on the SAM and the appearance of several new bands not associated with the deposited species. These new bands were assigned to the C=O stretching vibrations of COOH and COO- groups formed on the surface as a result of ion deposition. The presence of these bands was attributed to an alternative reactive landing pathway that competes with covalent bond formation. This pathway with similar yields for both gramicidin S and ubiquitin ions is analogous to the hydrolysis of the NHS ester bond in solution. The covalent bond formation efficiency increased linearly with the number of free amino groups and was found to be lower for the more compact conformation of ubiquitin compared with the fully unfolded conformation. This observation was attributed to the limited availability of amino groups on the surface of the folded conformation. Our results have provided new insights on the efficiency and mechanism of reactive landing of peptides and proteins onto activated SAMs« less

Reactive Landing of Gramicidin S and Ubiquitin Ions onto Activated Self-Assembled Monolayer Surfaces

NASA Astrophysics Data System (ADS)

Laskin, Julia; Hu, Qichi

2017-07-01

Using mass-selected ion deposition combined with in situ infrared reflection absorption spectroscopy (IRRAS), we examined the reactive landing of gramicidin S and ubiquitin ions onto activated self-assembled monolayer (SAM) surfaces terminated with N-hydroxysuccinimidyl ester (NHS-SAM) and acyl fluoride (COF-SAM) groups. Doubly protonated gramicidin S, [GS + 2H]2+, and two charge states of ubiquitin, [U + 5H]5+ and [U + 13H]13+, were used as model systems, allowing us to explore the effect of the number of free amino groups and the secondary structure on the efficiency of covalent bond formation between the projectile ion and the surface. For all projectile ions, ion deposition resulted in the depletion of IRRAS bands corresponding to the terminal groups on the SAM and the appearance of several new bands not associated with the deposited species. These new bands were assigned to the C=O stretching vibrations of COOH and COO- groups formed on the surface as a result of ion deposition. The presence of these bands was attributed to an alternative reactive landing pathway that competes with covalent bond formation. This pathway with similar yields for both gramicidin S and ubiquitin ions is analogous to the hydrolysis of the NHS ester bond in solution. The covalent bond formation efficiency increased linearly with the number of free amino groups and was found to be lower for the more compact conformation of ubiquitin compared with the fully unfolded conformation. This observation was attributed to the limited availability of amino groups on the surface of the folded conformation. Our results have provided new insights on the efficiency and mechanism of reactive landing of peptides and proteins onto activated SAMs.

Microwave-Accelerated Surface Modification of Plasmonic Gold Thin Films with Self-Assembled Monolayers of Alkanethiols

PubMed Central

Grell, Tsehai A.J.; Alabanza, Anginelle M.; Gaskell, Karen; Aslan, Kadir

2013-01-01

A rapid surface modification technique for the formation of self-assembled monolayers (SAMs) of alkanethiols on gold thin films using microwave heating in less than 10 min is reported. In this regard, SAMs of two model alkanethiols, 11-mercaptoundecanoic acid (11-MUDA, to generate a hydrophilic surface) and undecanethiol (UDET, a hydrophobic surface), were successfully formed on gold thin films using selective microwave heating in 1) a semi-continuous and 2) a continuous fashion and at room temperature (24 hours, control experiment, no microwave heating). The formation of SAMs of 11-MUDA and UDET were confirmed by contact angle measurements, Fourier–transform infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The contact angles for water on SAMs formed by the selective microwave heating and conventional room temperature incubation technique (24 hours) were measured to be similar for 11-MUDA and UDET. FT-IR spectroscopy results confirmed that the internal structure of SAMs prepared using both microwave heating and at room temperature were similar. XPS results revealed that the organic and sulfate contaminants found on bare gold thin films were replaced by SAMs after the surface modification process was carried out using both microwave heating and at room temperature. PMID:24083414

Southern Annular Mode drives multicentury wildfire activity in southern South America.

PubMed

Holz, Andrés; Paritsis, Juan; Mundo, Ignacio A; Veblen, Thomas T; Kitzberger, Thomas; Williamson, Grant J; Aráoz, Ezequiel; Bustos-Schindler, Carlos; González, Mauro E; Grau, H Ricardo; Quezada, Juan M

2017-09-05

The Southern Annular Mode (SAM) is the main driver of climate variability at mid to high latitudes in the Southern Hemisphere, affecting wildfire activity, which in turn pollutes the air and contributes to human health problems and mortality, and potentially provides strong feedback to the climate system through emissions and land cover changes. Here we report the largest Southern Hemisphere network of annually resolved tree ring fire histories, consisting of 1,767 fire-scarred trees from 97 sites (from 22 °S to 54 °S) in southern South America (SAS), to quantify the coupling of SAM and regional wildfire variability using recently created multicentury proxy indices of SAM for the years 1531-2010 AD. We show that at interannual time scales, as well as at multidecadal time scales across 37-54 °S, latitudinal gradient elevated wildfire activity is synchronous with positive phases of the SAM over the years 1665-1995. Positive phases of the SAM are associated primarily with warm conditions in these biomass-rich forests, in which widespread fire activity depends on fuel desiccation. Climate modeling studies indicate that greenhouse gases will force SAM into its positive phase even if stratospheric ozone returns to normal levels, so that climate conditions conducive to widespread fire activity in SAS will continue throughout the 21st century.

Standardized added metabolic activity (SAM) IN ¹⁸F-FDG PET assessment of treatment response in colorectal liver metastases.

PubMed

Mertens, Jeroen; De Bruyne, S; Van Damme, N; Smeets, P; Ceelen, W; Troisi, R; Laurent, S; Geboes, K; Peeters, M; Goethals, I; Van de Wiele, C

2013-08-01

Standardized added metabolic activity (SAM) is a PET parameter for assessing the total metabolic load of malignant processes, avoiding partial volume effects and lesion segmentation. The potential role of this parameter in the assessment of response to chemotherapy and bevacizumab was tested in patients with metastatic colorectal cancer with potentially resectable liver metastases (mCRC). (18)F-FDG PET/CT was performed in 18 mCRC patients with liver metastases before treatment and after five cycles of FOLFOX/FOLFIRI and bevacizumab. Of the 18 patients, 16 subsequently underwent resection of liver metastases. Baseline and follow-up SUVmax, and SAM as well as reduction in SUVmax (∆SUVmax) and SAM (∆SAM) of all liver metastases were correlated with morphological response, and progression-free and overall survival (PFS and OS). A significant reduction in metabolic activity of the liver metastases was seen after chemotherapy with a median ∆SUVmax of 25.3% and ∆SAM of 94.5% (p = 0.033 and 0.003). Median baseline SUVmax and SAM values were significantly different between morphological responders and nonresponders (3.8 vs. 7.2, p = 0.021; and 34 vs. 211, p = 0.002, respectively), but neither baseline PET parameters nor morphological response was correlated with PFS or OS. Follow-up SUVmax and SAM as well as ∆SAM were found to be prognostic factors. The median PFS and OS in the patient group with a high follow-up SUVmax were 10.4 months and 32 months, compared to a median PFS of 14.7 months and a median OS which had not been reached in the group with a low follow-up SUVmax (p = 0.01 and 0.003, respectively). The patient group with a high follow-up SAM and a low ∆SAM had a median PFS and OS of 9.4 months and 32 months, whereas the other group had a median PFS of 14.7 months and a median OS which had not been reached (p = 0.002 for both PFS and OS). (18)F-FDG PET imaging is a useful tool to assess treatment response and predict clinical outcome in patients with mCRC who undergo chemotherapy before liver metastasectomy. Follow-up SUVmax, follow-up SAM and ∆SAM were found to be significant prognostic factors for PFS and OS.

S-adenosyl methionine prevents ASD like behaviors triggered by early postnatal valproic acid exposure in very young mice.

PubMed

Ornoy, Asher; Weinstein-Fudim, Liza; Tfilin, Matanel; Ergaz, Zivanit; Yanai, Joseph; Szyf, Moshe; Turgeman, Gadi

2018-01-16

A common animal model of ASD is the one induced by valproic acid (VPA), inducing epigenetic changes and oxidative stress. We studied the possible preventive effect of the methyl donor for epigenetic enzymatic reactions, S-adenosine methionine (SAM), on ASD like behavioral changes and on redox potential in the brain and liver in this model. ICR albino mice were injected on postnatal day 4 with one dose of 300 mg/kg of VPA, with normal saline (controls) or with VPA and SAM that was given orally for 3 days at the dose of 30 mg/kg body weight. From day 50, we carried out neurobehavioral tests and assessment of the antioxidant status of the prefrontal cerebral cortex, liver assessing SOD and CAT activity, lipid peroxidation and the expression of antioxidant genes. Mice injected with VPA exhibited neurobehavioral deficits typical of ASD that were more prominent in males. Changes in the activity of SOD and CAT increased lipid peroxidation and changes in the expression of antioxidant genes were observed in the prefrontal cortex of VPA treated mice, more prominent in females, while ASD like behavior was more prominent in males. There were no changes in the redox potential of the liver. The co-administration of VPA and SAM alleviated most ASD like neurobehavioral symptoms and normalized the redox potential in the prefrontal cortex. Early postnatal VPA administration induces ASD like behavior that is more severe in males, while the redox status changes are more severe in females; SAM corrects both. VPA-induced ASD seems to result from epigenetic changes, while the redox status changes may be secondary. Copyright © 2018. Published by Elsevier Inc.

Selective Absorption Mechanism for the Maintenance of Blocking

NASA Astrophysics Data System (ADS)

Yamazaki, Akira; Itoh, Hisanori

2010-05-01

Atmospheric blocking is one of the most influential phenomena in global atmospheric environments. The understanding of its dynamical processes is important to clarify weather extremes and the stratosphere-troposphere coupling and to extend forecast periods. In the dynamics of blocking, especially, its maintenance mechanism has been a stimulating topic for many meteorologists. About the maintenance mechanism of blocking, Shutts (1983) evaluated the effect of synoptic eddies in his numerical model and proposed the Eddy Straining Mechanism (hereafter, referred to as ESM). Using simple numerical models, he demonstrated that synoptic eddies strained in the north-south direction by blocking provide negative/positive vorticity to a blocking high/low and this vorticity forcing, i.e., the second-order flow maintains the blocking dipole structure against dissipation. Some pieces of evidence, however have shown that the ESM does not work well in several real cases of the block maintenance. For example, Arai and Mukougawa (2002) performed a similar experiment to Shutts (1983) and indicated the strong sensitivity of the ESM against a small meridional shift of the stormtrack (strictly speaking, wavemaker), or a small change of the size of high-frequency eddies. This is a very adverse constraint in the real atmosphere because the relative positions of blocking to the stormtrack tend to fluctuate from case to case so that they do not necessarily exist in the same latitude band. Thus, we propose a more realistic mechanism of the block maintenance named as the Selective Absorption Mechanism (hereafter referred to as SAM), in which a blocking anticyclone selectively and exclusively absorbs synoptic anticyclones. This mechanism is essentially the same mechanism as the Fujiwhara effect, which qualitatively explains that binary eddies with the same polarity merge and eddies with the opposite polarity separate. In this study, we verify the effectiveness of the SAM by observational analyses and simple numerical experiments. Ten episodes of blocking that occurred in the mid-North Pacific and the eastern North Atlantic between 1990 and 2005 are investigated. Trajectories of synoptic anticyclones and cyclones during blocking persistent periods are analyzed and show the selective absorption of anticyclonic eddies by the blocking highs. We also perform numerical experiments using the nonlinear barotropic vorticity equation on a beta-plane channel. The maintenance rate of blocking is quantitatively evaluated by using an areal averaged method. The result supports the block maintenance by the SAM. From the above two results, we can conclude that the SAM is more adaptive as the block maintenance mechanism than the ESM, because the essence of the SAM is absorption of eddies, not but eddy straining.

Human polyhomeotic homolog 3 (PHC3) sterile alpha motif (SAM) linker allows open-ended polymerization of PHC3 SAM.

PubMed

Robinson, Angela K; Leal, Belinda Z; Nanyes, David R; Kaur, Yogeet; Ilangovan, Udayar; Schirf, Virgil; Hinck, Andrew P; Demeler, Borries; Kim, Chongwoo A

2012-07-10

Sterile alpha motifs (SAMs) are frequently found in eukaryotic genomes. An intriguing property of many SAMs is their ability to self-associate, forming an open-ended polymer structure whose formation has been shown to be essential for the function of the protein. What remains largely unresolved is how polymerization is controlled. Previously, we had determined that the stretch of unstructured residues N-terminal to the SAM of a Drosophila protein called polyhomeotic (Ph), a member of the polycomb group (PcG) of gene silencers, plays a key role in controlling Ph SAM polymerization. Ph SAM with its native linker created shorter polymers compared to Ph SAM attached to either a random linker or no linker. Here, we show that the SAM linker for the human Ph ortholog, polyhomeotic homolog 3 (PHC3), also controls PHC3 SAM polymerization but does so in the opposite fashion. PHC3 SAM with its native linker allows longer polymers to form compared to when attached to a random linker. Attaching the PHC3 SAM linker to Ph SAM also resulted in extending Ph SAM polymerization. Moreover, in the context of full-length Ph protein, replacing the SAM linker with PHC3 SAM linker, intended to create longer polymers, resulted in greater repressive ability for the chimera compared to wild-type Ph. These findings show that polymeric SAM linkers evolved to modulate a wide dynamic range of SAM polymerization abilities and suggest that rationally manipulating the function of SAM containing proteins through controlling their SAM polymerization may be possible.

Even the Odd Numbers Help: Failure Modes of SAM-Based Tunnel Junctions Probed via Odd-Even Effects Revealed in Synchrotrons and Supercomputers.

PubMed

Thompson, Damien; Nijhuis, Christian A

2016-10-18

This Account describes a body of research in atomic level design, synthesis, physicochemical characterization, and macroscopic electrical testing of molecular devices made from ferrocene-functionalized alkanethiol molecules, which are molecular diodes, with the aim to identify, and resolve, the failure modes that cause leakage currents. The mismatch in size between the ferrocene headgroup and alkane rod makes waxlike highly dynamic self-assembled monolayers (SAMs) on coinage metals that show remarkable atomic-scale sensitivity in their electrical properties. Our results make clear that molecular tunnel junction devices provide an excellent testbed to probe the electronic and supramolecular structures of SAMs on inorganic substrates. Contacting these SAMs to a eutectic "EGaIn" alloy top-electrode, we designed highly stable long-lived molecular switches of the form electrode-SAM-electrode with robust rectification ratios of up to 3 orders of magnitude. The graphic that accompanies this conspectus displays a computed SAM packing structure, illustrating the lollipop shape of the molecules that gives dynamic SAM supramolecular structures and also the molecule-electrode van der Waals (vdW) contacts that must be controlled to form good SAM-based devices. In this Account, we first trace the evolution of SAM-based electronic devices and rationalize their operation using energy level diagrams. We describe the measurement of device properties using near edge X-ray absorption fine structure spectroscopy, cyclic voltammetry, and X-ray photoelectron spectroscopy complemented by molecular dynamics and electronic structure calculations together with large numbers of electrical measurements. We discuss how data obtained from these combined experimental/simulation codesign studies demonstrate control over the supramolecular and electronic structure of the devices, tuning odd-even effects to optimize inherent packing tendencies of the molecules in order to minimize leakage currents in the junctions. It is now possible, but still very costly to create atomically smooth electrodes and we discuss progress toward masking electrode imperfections using cooperative molecule-electrode contacts that are only accessible by dynamic SAM structures. Finally, the unique ability of SAM devices to achieve simultaneously high and atom-sensitive electrical switching is summarized and discussed. While putting these structures to work as real world electronic devices remains very challenging, we speculate on the scientific and technological advances that are required to further improve electronic and supramolecular structure, toward the creation of high yields of long-lived molecular devices with (very) large, reproducible rectification ratios.

Malnutrition in HIV-Infected Children Is an Indicator of Severe Disease with an Impaired Response to Antiretroviral Therapy.

PubMed

Muenchhoff, Maximilian; Healy, Michael; Singh, Ravesh; Roider, Julia; Groll, Andreas; Kindra, Chirjeev; Sibaya, Thobekile; Moonsamy, Angeline; McGregor, Callum; Phan, Michelle Q; Palma, Alejandro; Kloverpris, Henrik; Leslie, Alasdair; Bobat, Raziya; LaRussa, Philip; Ndung'u, Thumbi; Goulder, Philip; Sobieszczyk, Magdalena E; Archary, Mohendran

2018-01-01

This observational study aimed to describe immunopathogenesis and treatment outcomes in children with and without severe acute malnutrition (SAM) and HIV-infection. We studied markers of microbial translocation (16sDNA), intestinal damage (iFABP), monocyte activation (sCD14), T-cell activation (CD38, HLA-DR) and immune exhaustion (PD1) in 32 HIV-infected children with and 41 HIV-infected children without SAM prior to initiation of antiretroviral therapy (ART) and cross-sectionally compared these children to 15 HIV-uninfected children with and 19 HIV-uninfected children without SAM. We then prospectively measured these markers and correlated them to treatment outcomes in the HIV-infected children at 48 weeks following initiation of ART. Plasma levels of 16sDNA, iFABP and sCD14 were measured by quantitative real time PCR, ELISA and Luminex, respectively. T cell phenotype markers were measured by flow cytometry. Multiple regression analysis was performed using generalized linear models (GLMs) and the least absolute shrinkage and selection operator (LASSO) approach for variable selection. Microbial translocation, T cell activation and exhaustion were increased in HIV-uninfected children with SAM compared to HIV-uninfected children without SAM. In HIV-infected children microbial translocation, immune activation, and exhaustion was strongly increased but did not differ by SAM-status. SAM was associated with increased mortality rates early after ART initiation. Malnutrition, age, microbial translocation, monocyte, and CD8 T cell activation were independently associated with decreased rates of CD4% immune recovery after 48 weeks of ART. SAM is associated with increased microbial translocation, immune activation, and immune exhaustion in HIV-uninfected children and with worse prognosis and impaired immune recovery in HIV-infected children on ART.

Malnutrition in HIV-Infected Children Is an Indicator of Severe Disease with an Impaired Response to Antiretroviral Therapy

PubMed Central

Healy, Michael; Singh, Ravesh; Roider, Julia; Groll, Andreas; Kindra, Chirjeev; Sibaya, Thobekile; Moonsamy, Angeline; McGregor, Callum; Phan, Michelle Q.; Palma, Alejandro; Kloverpris, Henrik; Leslie, Alasdair; Bobat, Raziya; LaRussa, Philip; Ndung'u, Thumbi; Goulder, Philip; Sobieszczyk, Magdalena E.; Archary, Mohendran

2018-01-01

Abstract This observational study aimed to describe immunopathogenesis and treatment outcomes in children with and without severe acute malnutrition (SAM) and HIV-infection. We studied markers of microbial translocation (16sDNA), intestinal damage (iFABP), monocyte activation (sCD14), T-cell activation (CD38, HLA-DR) and immune exhaustion (PD1) in 32 HIV-infected children with and 41 HIV-infected children without SAM prior to initiation of antiretroviral therapy (ART) and cross-sectionally compared these children to 15 HIV-uninfected children with and 19 HIV-uninfected children without SAM. We then prospectively measured these markers and correlated them to treatment outcomes in the HIV-infected children at 48 weeks following initiation of ART. Plasma levels of 16sDNA, iFABP and sCD14 were measured by quantitative real time PCR, ELISA and Luminex, respectively. T cell phenotype markers were measured by flow cytometry. Multiple regression analysis was performed using generalized linear models (GLMs) and the least absolute shrinkage and selection operator (LASSO) approach for variable selection. Microbial translocation, T cell activation and exhaustion were increased in HIV-uninfected children with SAM compared to HIV-uninfected children without SAM. In HIV-infected children microbial translocation, immune activation, and exhaustion was strongly increased but did not differ by SAM-status. SAM was associated with increased mortality rates early after ART initiation. Malnutrition, age, microbial translocation, monocyte, and CD8 T cell activation were independently associated with decreased rates of CD4% immune recovery after 48 weeks of ART. SAM is associated with increased microbial translocation, immune activation, and immune exhaustion in HIV-uninfected children and with worse prognosis and impaired immune recovery in HIV-infected children on ART. PMID:28670966

Quality of care of treatment for uncomplicated severe acute malnutrition provided by lady health workers in Pakistan.

PubMed

Rogers, Eleanor; Ali, Muhammad; Fazal, Shahid; Kumar, Deepak; Guerrero, Saul; Hussain, Imtiaz; Soofi, Sajid; Alvarez Morán, Jose Luis

2018-02-01

To assess the quality of care provided by lady health workers (LHW) managing cases of uncomplicated severe acute malnutrition (SAM) in the community. Cross-sectional quality-of-care study. The feasibility of the implementation of screening and treatment for uncomplicated SAM in the community by LHW was tested in Sindh Province, Pakistan. An observational, clinical prospective multicentre cohort study compared the LHW-delivered care with the existing outpatient health facility model. LHW implementing treatment for uncomplicated SAM in the community. Oedema was diagnosed conducted correctly for 87·5 % of children; weight and mid upper-arm circumference were measured correctly for 60·0 % and 57·4 % of children, respectively. The appetite test was conducted correctly for 42·0 % of cases. Of all cases of SAM without complications assessed during the study, 68·0 % received the correct medical and nutrition treatment. The proportion of cases that received the correct medical and nutrition treatment and key counselling messages was 4·0 %. This quality-of-care study supports existing evidence that LHW are able to identify uncomplicated SAM, and a majority can provide appropriate nutrition and medical treatment in the community. However, the findings also show that their ability to provide the complete package with an acceptable level of care is not assured. Additional evidence on the impact of supervision and training on the quality of SAM treatment and counselling provided by LHW to children with SAM is required. The study has also shown that, as in other sectors, it is essential that operational challenges are addressed in a timely manner and that implementers receive appropriate levels of support, if SAM is to be treated successfully in the community.

Large scale study on the variation of RF energy absorption in the head & brain regions of adults and children and evaluation of the SAM phantom conservativeness.

PubMed

Keshvari, J; Kivento, M; Christ, A; Bit-Babik, G

2016-04-21

This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases.

Large scale study on the variation of RF energy absorption in the head & brain regions of adults and children and evaluation of the SAM phantom conservativeness

NASA Astrophysics Data System (ADS)

Keshvari, J.; Kivento, M.; Christ, A.; Bit-Babik, G.

2016-04-01

This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases.

Mesospheric effects of solar ultraviolet variations - Further analysis of SME IR ozone and Nimbus 7 SAMS temperature data

NASA Astrophysics Data System (ADS)

Hood, L. L.; Huang, Z.; Bougher, S. W.

1991-07-01

In order to improve the constraints on models of the mesospheric response to solar UV variations, an analysis is conducted of the Solar Mesosphere Explorer (SME) IR ozone data and Nimbus 7 stratosphere and mesosphere sounder (SAMS) temperature data. Maximum low-altitude ozone and temperature-response amplitudes occur at about the same altitude, where a strong coupling between photochemical and thermal components of the mesospheric response is suggested by the simultaneous positive temperature and negative ozone response maxima. Increased Lyman-alpha dissociation of water vapor and temperature feedback are theorized to account for the negative ozone response. HO(x) chemical heating can increase as ozone destruction increases, and can therefore account for the positive temperature response.

Mesospheric effects of solar ultraviolet variations - Further analysis of SME IR ozone and Nimbus 7 SAMS temperature data

NASA Technical Reports Server (NTRS)

Hood, L. L.; Huang, Z.; Bougher, S. W.

1991-01-01

In order to improve the constraints on models of the mesospheric response to solar UV variations, an analysis is conducted of the Solar Mesosphere Explorer (SME) IR ozone data and Nimbus 7 stratosphere and mesosphere sounder (SAMS) temperature data. Maximum low-altitude ozone and temperature-response amplitudes occur at about the same altitude, where a strong coupling between photochemical and thermal components of the mesospheric response is suggested by the simultaneous positive temperature and negative ozone response maxima. Increased Lyman-alpha dissociation of water vapor and temperature feedback are theorized to account for the negative ozone response. HO(x) chemical heating can increase as ozone destruction increases, and can therefore account for the positive temperature response.

SAM68 is a physiological regulator of SMN2 splicing in spinal muscular atrophy

PubMed Central

Pagliarini, Vittoria; Pelosi, Laura; Bustamante, Maria Blaire; Nobili, Annalisa; Berardinelli, Maria Grazia; D’Amelio, Marcello; Musarò, Antonio

2015-01-01

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. The almost identical SMN2 gene is unable to compensate for this deficiency because of the skipping of exon 7 during pre–messenger RNA (mRNA) processing. Although several splicing factors can modulate SMN2 splicing in vitro, the physiological regulators of this disease-causing event are unknown. We found that knockout of the splicing factor SAM68 partially rescued body weight and viability of SMAΔ7 mice. Ablation of SAM68 function promoted SMN2 splicing and expression in SMAΔ7 mice, correlating with amelioration of SMA-related defects in motor neurons and skeletal muscles. Mechanistically, SAM68 binds to SMN2 pre-mRNA, favoring recruitment of the splicing repressor hnRNP A1 and interfering with that of U2AF65 at the 3′ splice site of exon 7. These findings identify SAM68 as the first physiological regulator of SMN2 splicing in an SMA mouse model. PMID:26438828

Combined Mössbauer spectroscopic, multi-edge X-ray absorption spectroscopic, and density functional theoretical study of the radical SAM enzyme spore photoproduct lyase.

PubMed

Silver, Sunshine C; Gardenghi, David J; Naik, Sunil G; Shepard, Eric M; Huynh, Boi Hanh; Szilagyi, Robert K; Broderick, Joan B

2014-03-01

Spore photoproduct lyase (SPL), a member of the radical S-adenosyl-L-methionine (SAM) superfamily, catalyzes the direct reversal of the spore photoproduct, a thymine dimer specific to bacterial spores, to two thymines. SPL requires SAM and a redox-active [4Fe-4S] cluster for catalysis. Mössbauer analysis of anaerobically purified SPL indicates the presence of a mixture of cluster states with the majority (40 %) as [2Fe-2S](2+) clusters and a smaller amount (15 %) as [4Fe-4S](2+) clusters. On reduction, the cluster content changes to primarily (60 %) [4Fe-4S](+). The speciation information from Mössbauer data allowed us to deconvolute iron and sulfur K-edge X-ray absorption spectra to uncover electronic (X-ray absorption near-edge structure, XANES) and geometric (extended X-ray absorption fine structure, EXAFS) structural features of the Fe-S clusters, and their interactions with SAM. The iron K-edge EXAFS data provide evidence for elongation of a [2Fe-2S] rhomb of the [4Fe-4S] cluster on binding SAM on the basis of an Fe···Fe scatterer at 3.0 Å. The XANES spectra of reduced SPL in the absence and presence of SAM overlay one another, indicating that SAM is not undergoing reductive cleavage. The X-ray absorption spectroscopy data for SPL samples and data for model complexes from the literature allowed the deconvolution of contributions from [2Fe-2S] and [4Fe-4S] clusters to the sulfur K-edge XANES spectra. The analysis of pre-edge features revealed electronic changes in the Fe-S clusters as a function of the presence of SAM. The spectroscopic findings were further corroborated by density functional theory calculations that provided insights into structural and electronic perturbations that can be correlated by considering the role of SAM as a catalyst or substrate.

Human Viperin Causes Radical SAM-Dependent Elongation of Escherichia coli, Hinting at Its Physiological Role.

PubMed

Nelp, Micah T; Young, Anthony P; Stepanski, Branden M; Bandarian, Vahe

2017-08-01

Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible) is a widely distributed protein that is expressed in response to infection and causes antiviral effects against a broad spectrum of viruses. Viperin is a member of the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes, which typically employ a 4Fe-4S cluster to reductively cleave SAM to initiate chemistry. Though the specific reaction catalyzed by viperin remains unknown, it has been shown that expression of viperin causes an increase in the fluidity of lipid membranes, which impedes the budding of nascent viral particles from the membrane inhibiting propagation of the infection. Herein, we show that expression of the human viperin homologue induces a dramatically elongated morphology of the host Escherichia coli cells. Mutation of an essential cysteine that coordinates the radical SAM cluster abrogates this effect. Thus, the native radical SAM activity of viperin is likely occurring in the host bacteria, indicating the elusive substrate is shared between both bacteria and humans, significantly narrowing the range of potential candidate substrates and providing a convenient bacterial platform from which future studies can occur.

Organizing for Effective Joint Warfare: A Deductive Analysis of U.S. Armed Forces Joint Doctrine

DTIC Science & Technology

1993-06-18

8217, Unpublished SAMS Monogram , (U.S. Army Command and General Staff College, Fort Leavenworth, KS: i988) p. 25. 3. Frank 0. Hough, et al, History of...SAMS Monogram , (U.S. Army Command and General Staff College, Fort Leavenworth, KS: 1988) , p, 16 and p. 29; and William 0. Pierce, ’Span of Control and...The Operational Commandetr: Is it More Than Just a Nun:ber?", Unpublished SAMS Monogram , (U.S. Army Command and Ueneral Staff College, Fort Leavenworth

Effects of Immersion Solvent on Photovoltaic and Photophysical Properties of Porphyrin-Sensitized Solar Cells.

PubMed

Hayashi, Hironobu; Higashino, Tomohiro; Kinjo, Yuriko; Fujimori, Yamato; Kurotobi, Kei; Chabera, Pavel; Sundström, Villy; Isoda, Seiji; Imahori, Hiroshi

2015-08-26

Memory effects in self-assembled monolayers (SAMs) of zinc porphyrin carboxylic acid on TiO2 electrodes have been demonstrated for the first time by evaluating the photovoltaic and electron transfer properties of porphyrin-sensitized solar cells prepared by using different immersion solvents sequentially. The structure of the SAM of the porphyrin on the TiO2 was maintained even after treating the porphyrin monolayer with different neat immersion solvents (memory effect), whereas it was altered by treatment with solutions containing different porphyrins (inverse memory effect). Infrared spectroscopy shows that the porphyrins in the SAM on the TiO2 could be exchanged with the same or analogous porphyrin, leading to a change in the structure of the porphyrin SAM. The memory and inverse memory effects are well correlated with a change in porphyrin geometry, mainly the tilt angle of the porphyrin along the long molecular axis from the surface normal on the TiO2, as well as with kinetics of electron transfer between the porphyrin and TiO2. Such a new structure-function relationship for DSSCs will be very useful for the rational design and optimization of photoelectrochemical and photovoltaic properties of molecular assemblies on semiconductor surfaces.

Magnolol protects neurons against ischemia injury via the downregulation of p38/MAPK, CHOP and nitrotyrosine.

PubMed

Chen, Jiann-Hwa; Kuo, Hsing-Chun; Lee, Kam-Fai; Tsai, Tung-Hu

2014-09-15

Magnolol is isolated from the herb Magnolia officinalis, which has been demonstrated to exert pharmacological effects. Our aim was to investigate whether magnolol is able to act as an anti-inflammatory agent that brings about neuroprotection using a global ischemic stroke model and to determine the mechanisms involved. Rats were treated with and without magnolol after ischemia reperfusion brain injury by occlusion of the two common carotid arteries. The inflammatory cytokine production in serum and the volume of infarction in the brain were measured. The proteins present in the brains obtained from the stroke animal model (SAM) and control animal groups with and without magnolol treatment were compared. Magnolol reduces the total infarcted volume by 15% and 30% at dosages of 10 and 30mg/kg, respectively, compared to the untreated SAM group. The levels of acute inflammatory cytokines, including interleukin-1 beta, tumor necrosis factor alpha, and interleukin-6 were attenuated by magnolol. Magnolol was also able to suppress the production of nitrotyrosine, 4-hydroxy-2-nonenal (4-HNE), inducible NO synthase (iNOS), various phosphorylated p38 mitogen-activated protein kinases and various C/EBP homologues. Furthermore, this modulation of ischemia injury factors in the SAM model group treated with magnolol seems to result from a suppression of reactive oxygen species production and the upregulation of p-Akt and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). These findings confirm the anti-oxidative properties of magnolol, including the inhibition of ischemic injury to neurons; this protective effect seems to involve changes in the in vivo activity of Akt, GSK3β and NF-κB. Copyright © 2014 Elsevier Inc. All rights reserved.

Alcohol-induced S-adenosylhomocysteine accumulation in the liver sensitizes to TNF hepatotoxicity: possible involvement of mitochondrial S-adenosylmethionine transport.

PubMed

Song, Zhenyuan; Zhou, Zhanxiang; Song, Ming; Uriarte, Silvia; Chen, Theresa; Deaciuc, Ion; McClain, Craig J

2007-08-01

Hepatocytes are resistant to tumor necrosis factor-alpha- (TNF) induced killing/apoptosis under normal circumstances, but primary hepatocytes from rats chronically fed alcohol have increased TNF cytotoxicity. Therefore, there must be mechanism(s) by which alcohol exposure "sensitizes" to TNF hepatotoxicity. Abnormal metabolism of methionine and S-adenosylmethionine (SAM) are well-documented acquired metabolic abnormalities in ALD. S-adenosylhomocysteine (SAH) is the product of SAM in hepatic transmethylation reactions, and SAH hydrolase (SAHH) is the only enzyme to metabolize SAH to homocysteine and adenosine. Our previous studies demonstrated that chronic intracellular accumulation of SAH sensitized hepatocytes to TNF cytotoxicity in vitro. In the current study, we extended our previous observations by further characterizing the effects of chronic alcohol intake on mitochondrial SAM levels in liver and examining its possible involvement in SAH sensitization to TNF hepatotoxicity. Chronic alcohol consumption in mice not only increased cytosolic SAH levels, but also decreased mitochondrial SAM concentration, leading to decreased mitochondrial SAM to SAH ratio. Moreover, accumulation of hepatic SAH induced by administration of 3-deaza-adenosine (DZA-a potent inhibitor of SAHH) enhanced lipopolysaccharide (LPS)/TNF hepatotoxicity in mice in vivo. Inhibition of SAHH by DZA resulted not only in accumulation of cytoplasmic SAH, but also in depletion of the mitochondrial SAM pool. Further studies using mitochondrial SAM transporter inhibitors showed that inhibition of SAM transport into mitochondria sensitized HepG2 cells to TNF cytotoxicity. In conclusion, our results demonstrate that depletion of the mitochondrial SAM pool by SAH, which is elevated during chronic alcohol consumption, plays a critical role in SAH induced sensitization to TNF hepatotoxicity.

A computationally efficient method for full-core conjugate heat transfer modeling of sodium fast reactors

DOE PAGES

Hu, Rui; Yu, Yiqi

2016-09-08

For efficient and accurate temperature predictions of sodium fast reactor structures, a 3-D full-core conjugate heat transfer modeling capability is developed for an advanced system analysis tool, SAM. The hexagon lattice core is modeled with 1-D parallel channels representing the subassembly flow, and 2-D duct walls and inter-assembly gaps. The six sides of the hexagon duct wall and near-wall coolant region are modeled separately to account for different temperatures and heat transfer between coolant flow and each side of the duct wall. The Jacobian Free Newton Krylov (JFNK) solution method is applied to solve the fluid and solid field simultaneouslymore » in a fully coupled fashion. The 3-D full-core conjugate heat transfer modeling capability in SAM has been demonstrated by a verification test problem with 7 fuel assemblies in a hexagon lattice layout. In addition, the SAM simulation results are compared with RANS-based CFD simulations. Very good agreements have been achieved between the results of the two approaches.« less

DNA adenine methylation of sams1 gene in symbiont-bearing Amoeba proteus.

PubMed

Jeon, Taeck J

2008-10-01

The expression of amoeba sams genes is switched from sams1 to sams2 when amoebae are infected with Legionella jeonii. To elucidate the mechanism for the inactivation of host sams1 gene by endosymbiotic bacteria, methylation states of the sams1 gene of D and xD amoebae was compared in this study. The sams1 gene of amoebae was methylated at an internal adenine residue of GATC site in symbiont-bearing xD amoebae but not in symbiont-free D amoebae, suggesting that the modification might have caused the inactivation of sams1 in xD amoebae. The sams1 gene of xD amoebae was inactivated at the transcriptional level. Analysis of DNA showed that adenine residues in L. jeonii sams were also methylated, implying that L. jeonii bacteria belong to a Dam methylase-positive strain. In addition, both SAM and Met appeared to act as negative regulators for the expression of sams1 whereas the expression of sams2 was not affected in amoebae.

SU-E-J-126: An Online Replanning Method for FFF Beams Without Couch Shift

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahunbay, E; Ates, O; Li, X

2015-06-15

Purpose: In a situation that couch shift for patient positioning is not preferred or prohibited (e.g., MR-Linac), segment aperture morphing (SAM) can address target dislocation and deformation. For IMRT/VMAT with flattening filter free (FFF) beams, however, SAM method would lead to an adverse translational dose effect due to the beam unflattening. Here we propose a new 2-step process to address both the translational effect of FFF beams and the target deformation. Methods: The replanning method consists of an offline and an online steps. The offline step is to create a series of pre-shifted plans (PSP) obtained by a so calledmore » “warm start” optimization (starting optimization from the original plan, rather from scratch) at a series of isocenter shifts with fixed distance (e.g. 2 cm, at x,y,z = 2,0,0 ; 2,2,0 ; 0,2,0; …;− 2,0,0). The PSPs all have the same number of segments with very similar shapes, since the warm-start optimization only adjusts the MLC positions instead of regenerating them. In the online step, a new plan is obtained by linearly interpolating the MLC positions and the monitor units of the closest PSPs for the shift determined from the image of the day. This two-step process is completely automated, and instantaneously fast (no optimization or dose calculation needed). The previously-developed SAM algorithm is then applied for daily deformation. We tested the method on sample prostate and pancreas cases. Results: The two-step interpolation method can account for the adverse dose effects from FFF beams, while SAM corrects for the target deformation. The whole process takes the same time as the previously reported SAM process (5–10 min). Conclusion: The new two-step method plus SAM can address both the translation effects of FFF beams and target deformation, and can be executed in full automation requiring no additional time from the SAM process. This research was supported by Elekta inc. (Crawley, UK)« less

The effects of dietary supplementation of methionine on genomic stability and p53 gene promoter methylation in rats.

PubMed

Amaral, Cátia Lira Do; Bueno, Rafaela de Barros E Lima; Burim, Regislaine Valéria; Queiroz, Regina Helena Costa; Bianchi, Maria de Lourdes Pires; Antunes, Lusânia Maria Greggi

2011-05-18

Methionine is a component of one-carbon metabolism and a precursor of S-adenosylmethionine (SAM), the methyl donor for DNA methylation. When methionine intake is high, an increase of S-adenosylmethionine (SAM) is expected. DNA methyltransferases convert SAM to S-adenosylhomocysteine (SAH). A high intracellular SAH concentration could inhibit the activity of DNA methyltransferases. Therefore, high methionine ingestion could induce DNA damage and change the methylation pattern of tumor suppressor genes. This study investigated the genotoxicity of a methionine-supplemented diet. It also investigated the diet's effects on glutathione levels, SAM and SAH concentrations and the gene methylation pattern of p53. Wistar rats received either a methionine-supplemented diet (2% methionine) or a control diet (0.3% methionine) for six weeks. The methionine-supplemented diet was neither genotoxic nor antigenotoxic to kidney cells, as assessed by the comet assay. However, the methionine-supplemented diet restored the renal glutathione depletion induced by doxorubicin. This fact may be explained by the transsulfuration pathway, which converts methionine to glutathione in the kidney. Methionine supplementation increased the renal concentration of SAH without changing the SAM/SAH ratio. This unchanged profile was also observed for DNA methylation at the promoter region of the p53 gene. Further studies are necessary to elucidate this diet's effects on genomic stability and DNA methylation. 2011 Elsevier B.V. All rights reserved.

Renormalizing a viscous fluid model for large scale structure formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Führer, Florian; Rigopoulos, Gerasimos, E-mail: fuhrer@thphys.uni-heidelberg.de, E-mail: gerasimos.rigopoulos@ncl.ac.uk

2016-02-01

Using the Stochastic Adhesion Model (SAM) as a simple toy model for cosmic structure formation, we study renormalization and the removal of the cutoff dependence from loop integrals in perturbative calculations. SAM shares the same symmetry with the full system of continuity+Euler equations and includes a viscosity term and a stochastic noise term, similar to the effective theories recently put forward to model CDM clustering. We show in this context that if the viscosity and noise terms are treated as perturbative corrections to the standard eulerian perturbation theory, they are necessarily non-local in time. To ensure Galilean Invariance higher ordermore » vertices related to the viscosity and the noise must then be added and we explicitly show at one-loop that these terms act as counter terms for vertex diagrams. The Ward Identities ensure that the non-local-in-time theory can be renormalized consistently. Another possibility is to include the viscosity in the linear propagator, resulting in exponential damping at high wavenumber. The resulting local-in-time theory is then renormalizable to one loop, requiring less free parameters for its renormalization.« less

Expanding the Chemistry of the Class C Radical SAM Methyltransferase NosN by Using an Allyl Analogue of SAM.

PubMed

Ji, Xinjian; Mandalapu, Dhanaraju; Cheng, Jinduo; Ding, Wei; Zhang, Qi

2018-03-30

The radical S-adenosylmethionine (SAM) superfamily enzymes cleave SAM reductively to generate a highly reactive 5'-deoxyadenosyl (dAdo) radical, which initiates remarkably diverse reactions. Unlike most radical SAM enzymes, the class C radical SAM methyltransferase NosN binds two SAMs in the active site, using one SAM to produce a dAdo radical and the second as a methyl donor. Here, we report a mechanistic investigation of NosN in which an allyl analogue of SAM (allyl-SAM) was used. We show that NosN cleaves allyl-SAM efficiently and the resulting dAdo radical can be captured by the olefin moieties of allyl-SAM or 5'-allylthioadenosine (ATA), the latter being a derivative of allyl-SAM. Remarkably, we found that NosN produced two distinct sets of products in the presence and absence of the methyl acceptor substrate, thus suggesting substrate-triggered production of ATA from allyl-SAM. We also show that NosN produces S-adenosylhomocysteine from 5'-thioadenosine and homoserine lactone. These results support the idea that 5'-methylthioadenosine is the direct methyl donor in NosN reactions, and demonstrate great potential to modulate radical SAM enzymes for novel catalytic activities. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parabolic Trough Collector Cost Update for the System Advisor Model (SAM)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurup, Parthiv; Turchi, Craig S.

2015-11-01

This report updates the baseline cost for parabolic trough solar fields in the United States within NREL's System Advisor Model (SAM). SAM, available at no cost at https://sam.nrel.gov/, is a performance and financial model designed to facilitate decision making for people involved in the renewable energy industry. SAM is the primary tool used by NREL and the U.S. Department of Energy (DOE) for estimating the performance and cost of concentrating solar power (CSP) technologies and projects. The study performed a bottom-up build and cost estimate for two state-of-the-art parabolic trough designs -- the SkyTrough and the Ultimate Trough. The SkyTroughmore » analysis estimated the potential installed cost for a solar field of 1500 SCAs as $170/m 2 +/- $6/m 2. The investigation found that SkyTrough installed costs were sensitive to factors such as raw aluminum alloy cost and production volume. For example, in the case of the SkyTrough, the installed cost would rise to nearly $210/m 2 if the aluminum alloy cost was $1.70/lb instead of $1.03/lb. Accordingly, one must be aware of fluctuations in the relevant commodities markets to track system cost over time. The estimated installed cost for the Ultimate Trough was only slightly higher at $178/m 2, which includes an assembly facility of $11.6 million amortized over the required production volume. Considering the size and overall cost of a 700 SCA Ultimate Trough solar field, two parallel production lines in a fully covered assembly facility, each with the specific torque box, module and mirror jigs, would be justified for a full CSP plant.« less

Activation of amino-based monolayers for electroless metallization of high-aspect-ratio through-silicon vias by using a simple ultrasonic-assisted plating solution

NASA Astrophysics Data System (ADS)

Chen, Sung-Te; Cheng, Yu-Syun; Chang, Yiu-Hsiang; Yang, Tzu-Ming; Lee, Jyun-Ting; Chen, Giin-Shan

2018-05-01

In this paper, we present the method and results of electroless plating of through-silicon via (TSV) contacts using Ni nanoparticle seeds on self-assembled monolayers (SAMs). This approach where the nanoparticles are evenly distributed and stabilized on the SAM allows the successive electroless metallization schemes such as Co-alloy barrier and Cu plug used typically in TSV as interconnects. The seeding was tested on SiO2 layers with surfaces functionalized by an amino-based aminopropyltrimethoxysilane (APTMS) SAM. APTMS-SAM after a suitable SC-1 treatment yielded a remarkably good barrier layer, with high adhesion strength (70 MPa) and low electrical resistivity (28 μΩ-cm). Moreover, the SAM assisted seeding protocol was followed by an ultrasonic-assisted (or mechanically agitated) electroless-plating stage together with a relatively simple plating solution. Conformal plating of Co-alloy barrier and seem/void-free Cu-plug filling into high-aspect-ratio TSVs (>10) was only achieved by using an ultrasonic-assisted plating process. The SAM layers were characterized by X-ray photoelectron spectroscopy to elucidate the surface functionalization effect.

Molecular Photovoltaics in Nanoscale Dimension

PubMed Central

Burtman, Vladimir; Zelichonok, Alexander; Pakoulev, Andrei V.

2011-01-01

This review focuses on the intrinsic charge transport in organic photovoltaic (PVC) devices and field-effect transistors (SAM-OFETs) fabricated by vapor phase molecular self-assembly (VP-SAM) method. The dynamics of charge transport are determined and used to clarify a transport mechanism. The 1,4,5,8-naphthalene-tetracarboxylic diphenylimide (NTCDI) SAM devices provide a useful tool to study the fundamentals of polaronic transport at organic surfaces and to discuss the performance of organic photovoltaic devices in nanoscale. Time-resolved photovoltaic studies allow us to separate the charge annihilation kinetics in the conductive NTCDI channel from the overall charge kinetic in a SAM-OFET device. It has been demonstrated that tuning of the type of conductivity in NTCDI SAM-OFET devices is possible by changing Si substrate doping. Our study of the polaron charge transfer in organic materials proposes that a cation-radical exchange (redox) mechanism is the major transport mechanism in the studied SAM-PVC devices. The role and contribution of the transport through delocalized states of redox active surface molecular aggregates of NTCDI are exposed and investigated. This example of technological development is used to highlight the significance of future technological development of nanotechnologies and to appreciate a structure-property paradigm in organic nanostructures. PMID:21339983

Protein adsorption and cell adhesion controlled by the surface chemistry of binary perfluoroalkyl/oligo(ethylene glycol) self-assembled monolayers.

PubMed

Li, Shanshan; Yang, Dingyun; Tu, Haiyang; Deng, Hongtao; Du, Dan; Zhang, Aidong

2013-07-15

This work reports a study of protein adsorption and cell adhesion on binary self-assembled monolayers (SAMs) of alkanethiols with terminal perfluoroalkyl (PFA) and oligo(ethylene glycol) (OEG) chains in varying ratios. The surface chemistry of the SAMs was characterized by contact angle measurement, grazing angle infrared spectroscopy (GIR), X-ray photoelectron spectroscopy, and the effect on protein adsorption was investigated by surface plasmon resonance, GIR, and immunosorbent assay. Hela cell adhesion on these surfaces was also studied by fluorescence microscopy. Results reveal that, compared to OEG, PFA tended to be a higher fraction of the composition in SAM than in the assembly solution. More interestingly, the nearly 38% PFA SAM had a strong antifouling property whereas the 74% PFA SAM showed a high adsorption capacity to protein and cell. The binary PFA/OEG SAMs were favorable for maintaining the fibrinogen conformation, hence its high activity. The findings may have important implications for constructing PFA-containing surfaces with the distinct properties that is highly resistant or highly favorable toward protein adsorption and cell adhesion. Copyright © 2013 Elsevier Inc. All rights reserved.

The epigenetic effects of a high prenatal folate intake in male mouse fetuses exposed in utero to arsenic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsang, Verne; Fry, Rebecca C.; Niculescu, Mihai D.

Inorganic arsenic (iAs) is a complete transplacental carcinogen in mice. Previous studies have demonstrated that in utero exposure to iAs promotes cancer in adult mouse offspring, possibly acting through epigenetic mechanisms. Humans and rodents enzymatically convert iAs to its methylated metabolites. This reaction requires S-adenosylmethionine (SAM) as methyl group donor. SAM is also required for DNA methylation. Supplementation with folate, a major dietary source of methyl groups for SAM synthesis, has been shown to modify iAs metabolism and the adverse effects of iAs exposure. However, effects of gestational folate supplementation on iAs metabolism and fetal DNA methylation have never beenmore » thoroughly examined. In the present study, pregnant CD1 mice were fed control (i.e. normal folate, or 2.2 mg/kg) or high folate diet (11 mg/kg) from gestational day (GD) 5 to 18 and drank water with 0 or 85 ppm of As (as arsenite) from GD8 to 18. The exposure to iAs significantly decreased body weight of GD18 fetuses and increased both SAM and S-adenosylhomocysteine (SAH) concentrations in fetal livers. High folate intake lowered the burden of total arsenic in maternal livers but did not prevent the effects of iAs exposure on fetal weight or hepatic SAM and SAH concentrations. In fact, combined folate-iAs exposure caused further significant body weight reduction. Notably, iAs exposure alone had little effect on DNA methylation in fetal livers. In contrast, the combined folate-iAs exposure changed the CpG island methylation in 2,931 genes, including genes known to be imprinted. Most of these genes were associated with neurodevelopment, cancer, cell cycle, and signaling networks. The canonical Wnt-signaling pathway, which regulates fetal development, was among the most affected biological pathways. Taken together, our results suggest that a combined in utero exposure to iAs and a high folate intake may adversely influence DNA methylation profiles and weight of fetuses, compromising fetal development and possibly increasing the risk for early-onset of disease in offspring. Highlights: ► We used transplacental CD1 mice model for inorganic arsenic (iAs) carcinogenesis. ► We examined the effects of gestational iAs and high folate exposure on DNA methylation. ► iAs–folate interaction resulted in low fetal weights and changes in DNA methylation. ► Epigenetically altered genes were associated with cancer and neurodevelopment. ► We showed that in utero iAs–folate interaction negatively affects fetal development.« less

A Sophomore-to-Junior Mentoring Program that Works: The SAM Program at the University of Texas Pan American

ERIC Educational Resources Information Center

Reyes, Maria Elena

2012-01-01

In an effort to increase the retention rates of college sophomores in a Hispanic Serving Institution in south Texas, university administrators created and implemented a successful peer mentoring model, the Sophomore Academic Mentoring (SAM) Program. Results suggest that the program has contributed to an increase in retention for second year,…

75 FR 56147 - Notice of Permits Issued Under the Antarctic Conservation Act of 1978

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

... received. Permits were issued on September 9, 2010 to: Sam Feola Permit No. 2011-009. Sam Feola Permit No. 2011-010. Sam Feola Permit No. 2011-011. Sam Feola Permit No. 2011-012. Sam Feola Permit No. 2011-013. Sam Feola Permit No. 2011-014. Sam Feola Permit No. 2011-015. Nadene G. Kennedy, Permit Officer. [FR...

SAMS Acceleration Measurements on Mir from June to November 1995

NASA Technical Reports Server (NTRS)

DeLombard, Richard; Hrovat, Ken; Moskowitz, Milton; McPherson, Kevin

1996-01-01

The NASA Microgravity Science and Applications Division (MSAD) sponsors science experiments on a variety of microgravity carriers, including sounding rockets, drop towers, parabolic aircraft, and Orbiter missions. The MSAD sponsors the Space Acceleration Measurement System (SAMS) to support microgravity science experiments with acceleration measurements to characterize the microgravity environment to which the experiments were exposed. The Principal Investigator Microgravity Services project at the NASA Lewis Research Center supports principal investigators of microgravity experiments as they evaluate the effects of varying acceleration levels on their experiments. In 1993, a cooperative effort was started between the United States and Russia involving science utilization of the Russian Mir space station by scientists from the United States and Russia. MSAD is currently sponsoring science experiments participating in the Shuttle-Mir Science Program in cooperation with the Russians on the Mir space station. Included in the complement of MSAD experiments and equipment is a SAMS unit In a manner similar to Orbiter mission support, the SAMS unit supports science experiments from the U.S. and Russia by measuring the microgravity environment during experiment operations. The initial SAMS supported experiment was a Protein Crystal Growth (PCG) experiment from June to November 1995. SAMS data were obtained during the PCG operations on Mir in accordance with the PCG Principal Investigator's requirements. This report presents an overview of the SAMS data recorded to support this PCG experiment. The report contains plots of the SAMS 100 Hz sensor head data as an overview of the microgravity environment, including the STS-74 Shuttle-Mir docking.

The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis.

PubMed

Bielli, Pamela; Busà, Roberta; Di Stasi, Savino M; Munoz, Manuel J; Botti, Flavia; Kornblihtt, Alberto R; Sette, Claudio

2014-04-01

Alternative splicing (AS) is tightly coupled to transcription for the majority of human genes. However, how these two processes are linked is not well understood. Here, we unveil a direct role for the transcription factor FBI-1 in the regulation of AS. FBI-1 interacts with the splicing factor SAM68 and reduces its binding to BCL-X mRNA. This, in turn, results in the selection of the proximal 5' splice site in BCL-X exon 2, thereby favoring the anti-apoptotic BCL-XL variant and counteracting SAM68-mediated apoptosis. Conversely, depletion of FBI-1, or expression of a SAM68 mutant lacking the FBI-1 binding region, restores the ability of SAM68 to induce BCL-XS splicing and apoptosis. FBI-1's role in splicing requires the activity of histone deacetylases, whose pharmacological inhibition recapitulates the effects of FBI-1 knockdown. Our study reveals an unexpected function for FBI-1 in splicing modulation with a direct impact on cell survival.

The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis

PubMed Central

Bielli, Pamela; Busà, Roberta; Di Stasi, Savino M; Munoz, Manuel J; Botti, Flavia; Kornblihtt, Alberto R; Sette, Claudio

2014-01-01

Alternative splicing (AS) is tightly coupled to transcription for the majority of human genes. However, how these two processes are linked is not well understood. Here, we unveil a direct role for the transcription factor FBI-1 in the regulation of AS. FBI-1 interacts with the splicing factor SAM68 and reduces its binding to BCL-X mRNA. This, in turn, results in the selection of the proximal 5′ splice site in BCL-X exon 2, thereby favoring the anti-apoptotic BCL-XL variant and counteracting SAM68-mediated apoptosis. Conversely, depletion of FBI-1, or expression of a SAM68 mutant lacking the FBI-1 binding region, restores the ability of SAM68 to induce BCL-XS splicing and apoptosis. FBI-1's role in splicing requires the activity of histone deacetylases, whose pharmacological inhibition recapitulates the effects of FBI-1 knockdown. Our study reveals an unexpected function for FBI-1 in splicing modulation with a direct impact on cell survival. PMID:24514149

Amazon Basin climate under global warming: the role of the sea surface temperature.

PubMed

Harris, Phil P; Huntingford, Chris; Cox, Peter M

2008-05-27

The Hadley Centre coupled climate-carbon cycle model (HadCM3LC) predicts loss of the Amazon rainforest in response to future anthropogenic greenhouse gas emissions. In this study, the atmospheric component of HadCM3LC is used to assess the role of simulated changes in mid-twenty-first century sea surface temperature (SST) in Amazon Basin climate change. When the full HadCM3LC SST anomalies (SSTAs) are used, the atmosphere model reproduces the Amazon Basin climate change exhibited by HadCM3LC, including much of the reduction in Amazon Basin rainfall. This rainfall change is shown to be the combined effect of SSTAs in both the tropical Atlantic and the Pacific, with roughly equal contributions from each basin. The greatest rainfall reduction occurs from May to October, outside of the mature South American monsoon (SAM) season. This dry season response is the combined effect of a more rapid warming of the tropical North Atlantic relative to the south, and warm SSTAs in the tropical east Pacific. Conversely, a weak enhancement of mature SAM season rainfall in response to Atlantic SST change is suppressed by the atmospheric response to Pacific SST. This net wet season response is sufficient to prevent dry season soil moisture deficits from being recharged through the SAM season, leading to a perennial soil moisture reduction and an associated 30% reduction in annual Amazon Basin net primary productivity (NPP). A further 23% NPP reduction occurs in response to a 3.5 degrees C warmer air temperature associated with a global mean SST warming.

Southern Annular Mode drives multicentury wildfire activity in southern South America

PubMed Central

Paritsis, Juan; Mundo, Ignacio A.; Veblen, Thomas T.; Kitzberger, Thomas; Williamson, Grant J.; Aráoz, Ezequiel; Bustos-Schindler, Carlos; González, Mauro E.; Grau, H. Ricardo; Quezada, Juan M.

2017-01-01

The Southern Annular Mode (SAM) is the main driver of climate variability at mid to high latitudes in the Southern Hemisphere, affecting wildfire activity, which in turn pollutes the air and contributes to human health problems and mortality, and potentially provides strong feedback to the climate system through emissions and land cover changes. Here we report the largest Southern Hemisphere network of annually resolved tree ring fire histories, consisting of 1,767 fire-scarred trees from 97 sites (from 22 °S to 54 °S) in southern South America (SAS), to quantify the coupling of SAM and regional wildfire variability using recently created multicentury proxy indices of SAM for the years 1531–2010 AD. We show that at interannual time scales, as well as at multidecadal time scales across 37–54 °S, latitudinal gradient elevated wildfire activity is synchronous with positive phases of the SAM over the years 1665–1995. Positive phases of the SAM are associated primarily with warm conditions in these biomass-rich forests, in which widespread fire activity depends on fuel desiccation. Climate modeling studies indicate that greenhouse gases will force SAM into its positive phase even if stratospheric ozone returns to normal levels, so that climate conditions conducive to widespread fire activity in SAS will continue throughout the 21st century. PMID:28827329

AhR and SHP regulate phosphatidylcholine and S-adenosylmethionine levels in the one-carbon cycle.

PubMed

Kim, Young-Chae; Seok, Sunmi; Byun, Sangwon; Kong, Bo; Zhang, Yang; Guo, Grace; Xie, Wen; Ma, Jian; Kemper, Byron; Kemper, Jongsook Kim

2018-02-07

Phosphatidylcholines (PC) and S-adenosylmethionine (SAM) are critical determinants of hepatic lipid levels, but how their levels are regulated is unclear. Here, we show that Pemt and Gnmt, key one-carbon cycle genes regulating PC/SAM levels, are downregulated after feeding, leading to decreased PC and increased SAM levels, but these effects are blunted in small heterodimer partner (SHP)-null or FGF15-null mice. Further, aryl hydrocarbon receptor (AhR) is translocated into the nucleus by insulin/PKB signaling in the early fed state and induces Pemt and Gnmt expression. This induction is blocked by FGF15 signaling-activated SHP in the late fed state. Adenoviral-mediated expression of AhR in obese mice increases PC levels and exacerbates steatosis, effects that are blunted by SHP co-expression or Pemt downregulation. PEMT, AHR, and PC levels are elevated in simple steatosis patients, but PC levels are robustly reduced in steatohepatitis-fibrosis patients. This study identifies AhR and SHP as new physiological regulators of PC/SAM levels.

Characterization of sams genes of Amoeba proteus and the endosymbiotic X-bacteria.

PubMed

Jeon, Taeck J; Jeon, Kwang W

2003-01-01

As a result of harboring obligatory bacterial endosymbionts, the xD strain of Amoeba proteus no longer produces its own S-adenosylmethionine synthetase (SAMS). When symbiont-free D amoebae are infected with symbionts (X-bacteria), the amount of amoeba SAMS decreases to a negligible level within four weeks, but about 47% of the SAMS activity, which apparently comes from another source, is still detected. Complete nucleotide sequences of sams genes of D and xD amoebae are presented and show that there are no differences between the two. Long-established xD amoebae contain an intact sams gene and thus the loss of xD amoeba's SAMS is not due to the loss of the gene itself. The open reading frame of the amoeba's sams gene has 1,281 nucleotides, encoding SAMS of 426 amino acids with a mass of 48 kDa and pI of 6.5. The amino acid sequence of amoeba SAMS is longer than the SAMS of other organisms by having an extra internal stretch of 28 amino acids. The 5'-flanking region of amoeba sams contains consensus-binding sites for several transcription factors that are related to the regulation of sams genes in E. coli and yeast. The complete nucleotide sequence of the symbiont's sams gene is also presented. The open reading frame of X-bacteria sams is 1,146 nucleotides long, encoding SAMS of 381 amino acids with a mass of 41 kDa and pI of 6.0. The X-bacteria SAMS has 45% sequence identity with that of A. proteus.

Technology choice and development in Brazil: An assessment of Brazil's alternative fuel program and the agriculture, manufacturing, energy, and service sectors

NASA Astrophysics Data System (ADS)

Nolan, Lucy A.

Technology choice profoundly affects a country's development process because capital-intensive and labor-intensive technologies have different socioeconomic linkages within the economy. This research examines the impacts of technology choice through the use of a social accounting matrix (SAM) framework. SAM-based modeling determines the direct and indirect effects of technology choice on development, particularly poverty alleviation in Brazil. Brazil's alternative fuel program was analyzed as a special example of technology choice. Two ethanol production technologies and the gasoline sector were compared; to make the study more robust, labor and capital intensive technologies were evaluated in the production of agriculture, manufacturing, energy, and services. Growth in these economic sectors was examined to assess the effects on employment, factor and household income, energy intensity, and carbon dioxide costs. Poverty alleviation was a focus, so income to unskilled agriculture labor, unskilled non-agriculture labor, and income to rural and urban households in poverty was also analyzed. The major research finding is that overall, labor-intensive technologies generate more employment, factor and household income, environmental and energy benefits to Brazil's economy than capital-intensive technologies. In addition, labor-intensive technologies make a particular contribution to poverty alleviation. The results suggest that policies to encourage the adoption of these technologies, especially in the agriculture and renewable energy sectors, are important because of their intersectoral linkages within the economy. Many studies have shown that Brazil's fuel ethanol program has helped to realize multiple macroeconomic objectives. However, this is the first empirical study to quantify its household income effects. The ethanol industry generated the most household income of the energy sectors. The research confirms a key finding of the appropriate technology literature, namely that government policies are important to the implementation of labor-intensive technologies. Finally, this research makes two important contributions to the SAM methodology. It is one of the first SAM modeling exercises to quantify the costs of carbon dioxide emissions and the impact of alternative fuels on regional and human development. The addition of an environmental sector enables the planner to determine carbon dioxide effects resulting from growth in different socioeconomic sectors. This will have implications for greenhouse gas mitigation strategies.

Interaction between caspofungin or voriconazole and cefoperazone-sulbactam or piperacillin-tazobactam by in vitro and in vivo methods.

PubMed

Keçeli, Sema Aşkin; Willke, Ayse; Tamer, Gulden Sonmez; Boral, Ozden Buyukbaba; Sonmez, Nese; Cağatay, Penbe

2014-05-01

Immunosuppressive patients are at risk of fungal and bacterial infections. Therefore, these patients receive prophylactic, preemptive, empirical or target antifungal and concomitant antibiotic therapy. To this end, caspofungin (CAS) or voriconazole (VRC) antifungals and cefoperazone-sulbactam (CPZ/SAM) or piperacillin-tazobactam (PIP/TAZ) antibiotics may be used. Here, we aimed to investigate the interaction between these antifungals and antibiotics by in vitro and in vivo methods. The interaction was tested by chequerboard analysis and fractional inhibitory concentration index (FICI). It was also tested in a neutropenic mice-invasive candidiasis model and evaluated by fungal burden in kidney tissue of infected animals from the first day to the fifth day of treatment with 24 h intervals. A synergism was detected between CAS and CPZ/SAM (FICI = 0.1) and PIP/TAZ (FICI = 0.3). Fungal burden in tissues of drug-treated mice was reduced compared with controls in a time-dependent manner. In comparison with CAS-alone treated group, there were 1.32 log10 reductions of fungal burden in CAS + CPZ/SAM (p = 0.002) and in CAS + PIP/TAZ group (p = 0.14). The same interactions were not found with VRC and antibiotics. CPZ/SAM had stronger synergistic interaction with CAS than PIP/TAZ. The mechanism of synergism is not well understood. This is most likely due to an increase in the anticandidal effect of CAS plus antibiotics. © 2013 APMIS. Published by John Wiley & Sons Ltd.

Dual sensitivity of inferior colliculus neurons to ITD in the envelopes of high-frequency sounds: experimental and modeling study

PubMed Central

Wang, Le; Devore, Sasha; Delgutte, Bertrand

2013-01-01

Human listeners are sensitive to interaural time differences (ITDs) in the envelopes of sounds, which can serve as a cue for sound localization. Many high-frequency neurons in the mammalian inferior colliculus (IC) are sensitive to envelope-ITDs of sinusoidally amplitude-modulated (SAM) sounds. Typically, envelope-ITD-sensitive IC neurons exhibit either peak-type sensitivity, discharging maximally at the same delay across frequencies, or trough-type sensitivity, discharging minimally at the same delay across frequencies, consistent with responses observed at the primary site of binaural interaction in the medial and lateral superior olives (MSO and LSO), respectively. However, some high-frequency IC neurons exhibit dual types of envelope-ITD sensitivity in their responses to SAM tones, that is, they exhibit peak-type sensitivity at some modulation frequencies and trough-type sensitivity at other frequencies. Here we show that high-frequency IC neurons in the unanesthetized rabbit can also exhibit dual types of envelope-ITD sensitivity in their responses to SAM noise. Such complex responses to SAM stimuli could be achieved by convergent inputs from MSO and LSO onto single IC neurons. We test this hypothesis by implementing a physiologically explicit, computational model of the binaural pathway. Specifically, we examined envelope-ITD sensitivity of a simple model IC neuron that receives convergent inputs from MSO and LSO model neurons. We show that dual envelope-ITD sensitivity emerges in the IC when convergent MSO and LSO inputs are differentially tuned for modulation frequency. PMID:24155013

AFM Study of Surface Nanobubbles on Binary Self-Assembled Monolayers on Ultraflat Gold with Identical Macroscopic Static Water Contact Angles and Different Terminal Functional Groups.

PubMed

Song, Bo; Chen, Kun; Schmittel, Michael; Schönherr, Holger

2016-11-01

All experimental findings related to surface nanobubbles, such as their pronounced stability and the striking differences of macroscopic and apparent nanoscopic contact angles, need to be addressed in any theory or model of surface nanobubbles. In this work we critically test a recent explanation of surface nanobubble stability and their consequences and contrast this with previously proposed models. In particular, we elucidated the effect of surface chemical composition of well-controlled solid-aqueous interfaces of identical roughness and defect density on the apparent nanoscopic contact angles. Expanding on a previous atomic force microscopy (AFM) study on the systematic variation of the macroscopic wettability using binary self-assembled monolayers (SAMs) on ultraflat template stripped gold (TSG), we assessed here the effect of different surface chemical composition for macroscopically identical static water contact angles. SAMs on TSG with a constant macroscopic water contact angle of 81 ± 2° were obtained by coadsorption of a methyl-terminated thiol and a second thiol with different terminal functional groups, including hydroxy, amino, and carboxylic acid groups. In addition, surface nanobubbles formed by entrainment of air on SAMs of a bromoisobutyrate-terminated thiol were analyzed by AFM. Despite the widely differing surface potentials and different functionality, such as hydrogen bond acceptor or donor, and different dipole moments and polarizability, the nanoscopic contact angles (measured through the condensed phase and corrected for AFM tip broadening effects) were found to be 145 ± 10° for all surfaces. Hence, different chemical functionalities at identical macroscopic static water contact angle do not noticeably influence the apparent nanoscopic contact angle of surface nanobubbles. This universal contact angle is in agreement with recent models that rely on contact line pinning and the equilibrium of gas outflux due to the Laplace pressure and gas influx due to gas oversaturation in the aqueous medium.

Exposure limits: the underestimation of absorbed cell phone radiation, especially in children.

PubMed

Gandhi, Om P; Morgan, L Lloyd; de Salles, Alvaro Augusto; Han, Yueh-Ying; Herberman, Ronald B; Davis, Devra Lee

2012-03-01

The existing cell phone certification process uses a plastic model of the head called the Specific Anthropomorphic Mannequin (SAM), representing the top 10% of U.S. military recruits in 1989 and greatly underestimating the Specific Absorption Rate (SAR) for typical mobile phone users, especially children. A superior computer simulation certification process has been approved by the Federal Communications Commission (FCC) but is not employed to certify cell phones. In the United States, the FCC determines maximum allowed exposures. Many countries, especially European Union members, use the "guidelines" of International Commission on Non-Ionizing Radiation Protection (ICNIRP), a non governmental agency. Radiofrequency (RF) exposure to a head smaller than SAM will absorb a relatively higher SAR. Also, SAM uses a fluid having the average electrical properties of the head that cannot indicate differential absorption of specific brain tissue, nor absorption in children or smaller adults. The SAR for a 10-year old is up to 153% higher than the SAR for the SAM model. When electrical properties are considered, a child's head's absorption can be over two times greater, and absorption of the skull's bone marrow can be ten times greater than adults. Therefore, a new certification process is needed that incorporates different modes of use, head sizes, and tissue properties. Anatomically based models should be employed in revising safety standards for these ubiquitous modern devices and standards should be set by accountable, independent groups.

An Investigation of the Effects of Self-Assembled Monolayers on Protein Crystallisation

PubMed Central

Zhang, Chen-Yan; Shen, He-Fang; Wang, Qian-Jin; Guo, Yun-Zhu; He, Jin; Cao, Hui-Ling; Liu, Yong-Ming; Shang, Peng; Yin, Da-Chuan

2013-01-01

Most protein crystallisation begins from heterogeneous nucleation; in practice, crystallisation typically occurs in the presence of a solid surface in the solution. The solid surface provides a nucleation site such that the energy barrier for nucleation is lower on the surface than in the bulk solution. Different types of solid surfaces exhibit different surface energies, and the nucleation barriers depend on the characteristics of the solid surfaces. Therefore, treatment of the solid surface may alter the surface properties to increase the chance to obtain protein crystals. In this paper, we propose a method to modify the glass cover slip using a self-assembled monolayer (SAM) of functional groups (methyl, sulfydryl and amino), and we investigated the effect of each SAM on protein crystallisation. The results indicated that both crystallisation success rate in a reproducibility study, and crystallisation hits in a crystallisation screening study, were increased using the SAMs, among which, the methyl-modified SAM demonstrated the most significant improvement. These results illustrated that directly modifying the crystallisation plates or glass cover slips to create surfaces that favour heterogeneous nucleation can be potentially useful in practical protein crystallisation, and the utilisation of a SAM containing a functional group can be considered a promising technique for the treatment of the surfaces that will directly contact the crystallisation solution. PMID:23749116

Control of hydroxyapatite coating by self-assembled monolayers on titanium and improvement of osteoblast adhesion.

PubMed

Shen, Juan; Qi, Yongcheng; Jin, Bo; Wang, Xiaoyan; Hu, Yamin; Jiang, Qiying

2017-01-01

Self-assembly technique was applied to introduce functional groups and form hydroxyl-, amine-, and carboxyl-terminal self-assembled monolayers (SAMs). The SAMs were grafted onto titanium substrates to obtain a molecularly smooth functional surface. Subsequent hydrothermal crystal growth formed homogeneous and crack-free crystalline hydroxyapatite (HA) coatings on these substrates. AFM and XPS were used to characterize the SAM surfaces, and XRD, SEM, and TEM were used to characterize the HA coatings. Results show that highly crystalline, dense, and oriented HA coatings can be formed on the OH-, NH 2 -, and COOH-SAM surfaces. The SAM surface with -COOH exhibited stronger nucleating ability than that with -OH and -NH 2 . The nucleation and growth processes of HA coatings were effectively controlled by varying reaction time, pH, and temperature. By using this method, highly crystalline, dense, and adherent HA coatings were obtained. In addition, in vitro cell evaluation demonstrated that HA coatings improved cell adhesion as compared with pristine titanium substrate. The proposed method is considerably effective in introducing the HA coatings on titanium surfaces for various biomedical applications and further usage in other industries. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 124-135, 2017. © 2015 Wiley Periodicals, Inc.

Fostering the Development of Critical Thinking Skills, and Reading Comprehension of Undergraduates Using a Web 2.0 Tool Coupled with a Learning System

ERIC Educational Resources Information Center

Mendenhall, Anne; Johnson, Tristan E.

2010-01-01

A social annotation model learning system (SAM-LS) was created using multiple instructional strategies thereby supporting the student in improving in critical thinking, critical writing and related literacy. There are four mechanisms in which the SAM-LS methodology is believed to improve learning and performance. These mechanisms include providing…

Mutational analysis of residues in human arsenic (III) methyltransferase (hAS3MT) belonging to 5 Å around S-adenosylmethionine (SAM).

PubMed

Li, Xiangli; Geng, Zhirong; Chang, Jiayin; Song, Xiaoli; Wang, Zhilin

2014-12-01

The functions of residues 57-RY-58, G60, L77, 80-GSGR-83, I101, T104, 134-GY-135, N155, V157 and 160-LV-161 in human arsenic (III) methyltransferase (hAS3MT) 5 Å around S-adenosylmethionine (SAM) have not been studied. Herein, sixteen mutants were designed by substituting these residues with Ala. Mutants G60A, G80A, I101A, N155A and L160A were completely inactive. Only MMA was detected when mutants R57A, Y58A, G82A and T104A were used as the enzymes, which suggested that their catalytic activities were seriously impaired compared with that of wild type (WT). The catalytic capacities of other mutants were also lower than that of WT-hAS3MT. The KM(SAM) values of mutants were 1.9–8.7 times that of WT, suggesting their affinities to SAM were weakened. As evidenced by the experimental data herein, earlier literature and the model of hAS3MT-SAM, 57-RYYG-60, G78, G80, G82 and 155-NCV-157 interacted with the methionine of SAM, and 101-IDMT-104 and 135-YIE-137 were associated with the nucleotide adenosine of SAM. Since C156 and L160 were the common residues between 5 Å around SAM and 5 Å around As, and C156S and L160A were inactive, we proposed that C156 and L160 functioned in the methyl transfer process. G78, G80 and G82 belonging to the consensus GxGxG were located in a loop connecting the first β-strand and α-helix in the Rossmann fold core. Y59, N155, C156 and L160 oriented S(+)-CH(3) during its approach to the arsenic lone pair, and further activated methyl transfer. G78, D102, M103, T104, I136 and N155 formed hydrogen bonds with SAM.

In situ analysis of Mars soil sample with the sam gcms instrumentation onboard Curiosity : interpretation and comparison of measurements done at Rocknest and Yelloknife bay sites

NASA Astrophysics Data System (ADS)

Szopa, Cyril; Coll, Patrice; Cabane, Michel; Coscia, David; Buch, Arnaud; Francois, Pascaline; Millan, Maeva; Teinturier, Sammy; Navarro-Gonzales, Rafael; Glavin, Daniel; Freissinet, Caro; Steele, Andrew; Eigenbrode, Jen; Mahaffy, Paul

2014-05-01

The characterisation of the chemical and mineralogical composition of regolith samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Amongst the SAM suite of instruments [1], SAM-GC (Gas Chromatograph) is devoted to identify and quantify volatiles evolved from the thermal (heating up to about 900°C)/chemical (derivatization procedure) treatment of any soil sample collected by the Curiosity rover. With the aim to search for potential organic molecules outgassed from the samples, a SAM-GC analytical channel composed of thermal-desorption injector and a MXT-CLP chromatographic column was chosen to achieve all the measurements done up today, as it was designed for the separation of a wide range of volatile organic molecules. Three solid samples have been analyzed with GCMS, one sand sample collected at the Rocknest site, and two rock samples (John Klein and Cumberland respectively) collected at the Yellowknife Bay site using the Curiosity driller. All the measurements were successful and they produced complex chromatograms with both detectors used for SAM GC, i.e. a thermal conductivity detector and the SAM quandrupole mass spectrometer. Their interpretation already revealed the presence of an oxychlorine phase present in the sample which is at the origin of chlorohydrocarbons clearly identified [2] but this represents only a fraction of the GCMS signal recorded [3,4]. This work presents a systematic comparison of the GCMS measurements done for the different samples collected, supported by reference data obtained in laboratory with different spare models of the gas chromatograph, with the aim to bring new elements of interpretation of the SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013), Science, [4] Ming D. et al. (2013), Science, 32, 64-67. Acknowledgements: SAM-GC team acknowledges support from the French Space Agency (CNES), French National Programme of Planetology (PNP), National French Council (CNRS), Pierre Simon Laplace Institute, Institut Universitaire de France (IUF) and ESEP Labex.

Probing the nature and resistance of the molecule-electrode contact in SAM-based junctions.

PubMed

Sangeeth, C S Suchand; Wan, Albert; Nijhuis, Christian A

2015-07-28

It is challenging to quantify the contact resistance and to determine the nature of the molecule-electrode contacts in molecular two-terminal junctions. Here we show that potentiodynamic and temperature dependent impedance measurements give insights into the nature of the SAM-electrode interface and other bottlenecks of charge transport (the capacitance of the SAM (C(SAM)) and the resistance of the SAM (R(SAM))), unlike DC methods, independently of each other. We found that the resistance of the top-electrode-SAM contact for junctions with the form of Ag(TS)-SC(n)//GaO(x)/EGaIn with n = 10, 12, 14, 16 or 18 is bias and temperature independent and hence Ohmic (non-rectifying) in nature, and is orders of magnitude smaller than R(SAM). The C(SAM) and R(SAM) are independent of the temperature, indicating that the mechanism of charge transport in these SAM-based junctions is coherent tunneling and the charge carrier trapping at the interfaces is negligible.

Structural basis for diversity in the SAM clan of riboswitches.

PubMed

Trausch, Jeremiah J; Xu, Zhenjiang; Edwards, Andrea L; Reyes, Francis E; Ross, Phillip E; Knight, Rob; Batey, Robert T

2014-05-06

In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.

Roles of Salmonella typhimurium umuDC and samAB in UV mutagenesis and UV sensitivity.

PubMed Central

Nohmi, T; Yamada, M; Watanabe, M; Murayama, S Y; Sofuni, T

1992-01-01

Expression of the umuDC operon is required for UV mutagenesis and most chemical mutagenesis in Escherichia coli. The closely related species Salmonella typhimurium has two sets of umuDC-like operons; the samAB operon is located in a 60-MDa cryptic plasmid, while the S. typhimurium umuDC (umuDCST) operon resides in a chromosome. The roles of these two umuDC-like operons in UV mutagenesis and UV sensitivity of S. typhimurium were investigated. A pBR322-derived plasmid carrying the samAB operon more efficiently restored UV mutability to a umuD44 strain and a umuC122::Tn5 strain of E. coli than a plasmid carrying the umuDCST operon did. When the umuDCST operon was specifically deleted from the chromosome of S. typhimurium TA2659, the resulting strain was not UV mutable and was more sensitive to the killing effect of UV irradiation than the parent strain was. Curing of the 60-MDa cryptic plasmid carrying the samAB operon did not influence the UV mutability of strain TA2659 but did increase its resistance to UV killing. A pSC101-derived plasmid carrying the samAB operon did not restore UV mutability to a umuD44 strain of E. coli, whereas pBR322- or pBluescript-derived plasmids carrying the samAB operon efficiently did restore UV mutability. We concluded that the umuDCST operon plays a major role in UV mutagenesis in S. typhimurium and that the ability of the samAB operon to promote UV mutagenesis is strongly affected by gene dosage. Possible reasons for the poor ability of samAB to promote UV mutagenesis when it is present on low-copy-number plasmids are discussed. Images PMID:1400244

Multitechnique characterization of oligo(ethylene glycol) functionalized gold nanoparticles.

PubMed

Rafati, Ali; Shard, Alexander G; Castner, David G

2016-11-09

Gold nanoparticles (AuNPs) with average diameters of ∼14 and ∼40 nm, as well as flat gold coated silicon wafers, were functionalized with oligo ethylene glycol (OEG) terminated 1-undecanethiol (HS-CH 2 ) 11 self-assembled monolayers (SAMs). Both hydroxyl [(OEG) 4 OH] and methoxy [(OEG) 4 OMe] terminated SAMs were prepared. The AuNPs were characterized with transmission electron microscopy (TEM), time of flight secondary ion mass spectrometry (ToF-SIMS), x-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier infrared spectroscopy (ATR-FTIR), and low-energy ion scattering (LEIS). These studies provided quantitative information about the OEG functionalized AuNPs. TEM showed the 14 nm AuNPs were more spherical and had a narrower size distribution than the 40 nm AuNPs. ToF-SIMS clearly differentiated between the two OEG SAMs based on the C 3 H 7 O + peak attributed to the methoxy group in the OMe terminated SAMs as well as the different masses of the [Au + M] - ion (M = mass of the thiol molecule) from each type of SAM. Overlayer/substrate ratios quantitatively determined with XPS show a greater proportion of OEG units at the surface of 40 nm AuNPs compared to the 14 nm AuNPs. ATR-FTIR suggested the C11 backbone of the two SAMs on both AuNPs are similar and crystalline, but the OEG head groups are more crystalline on the 40 nm AuNPs compared to the 14 nm AuNPs. This indicated a better ordered SAM present at the surface of the larger, more irregular particles due to greater ordering of the OEG groups. This was consistent with the XPS and LEIS results, which showed a 30% thicker SAM was formed on the 40 nm AuNPs compared to the 14 nm AuNPs. The OH or OMe functionality did not have a significant effect on the ordering and thickness of the OEG SAMs.

Do Children with Uncomplicated Severe Acute Malnutrition Need Antibiotics? A Systematic Review and Meta-Analysis

PubMed Central

Alcoba, Gabriel; Kerac, Marko; Breysse, Serge; Salpeteur, Cécile; Galetto-Lacour, Annick; Briend, André; Gervaix, Alain

2013-01-01

Background Current (1999) World Health Organization guidelines recommend giving routine antibiotics (AB) for all children with severe acute malnutrition (SAM), even if they have uncomplicated disease with no clinically obvious infections. We examined the evidence behind this recommendation. Methods and Findings OVID-MEDLINE, EMBASE, COCHRANE, GLOBAL-HEALTH, CINAHL, POPLINE, AFRICA-WIDE-NiPAD, and LILACS were searched for AB efficacy, bacterial resistance, and infection rates in SAM. Following PRISMA guidelines, a systematic review and meta-analysis were performed. Three randomised controlled trials (RCT), five Cochrane reviews, and 37 observational studies were identified. One cohort-study showed no increase in nutritional-cure and mortality in uncomplicated SAM where no AB were used. (p>0.05). However, an unpublished RCT in this setting did show mortality benefits. Another RCT did not show superiority of ceftriaxone over amoxicilllin for these same outcomes, but adressed SAM children with and without complications (p = 0.27). Another RCT showed no difference between amoxicillin and cotrimoxazole efficacies for pneumonia in underweight, but not SAM. Our meta-analysis of 12 pooled susceptibility-studies for all types of bacterial isolates, including 2767 stricly SAM children, favoured amoxicillin over cotrimoxazole for susceptibility medians: 42% (IQR 27–55%) vs 22% (IQR 17–23%) and population-weighted-means 52.9% (range 23–57%) vs 35.4% (range 6.7–42%). Susceptibilities to second-line AB were better, above 80%. Prevalence of serious infections in SAM, pooled from 24 studies, ranged from 17% to 35.2%. No study infered any association of infection prevalence with AB regimens in SAM. Conclusions The evidence underlying current antibiotic recommendations for uncomplicated SAM is weak. Susceptibility-studies favour amoxicillin over cotrimoxazole. However, given that these antibiotics have side-effects, costs, and risks as well as benefits, their routine use needs urgent testing. With reliable monitoring, we believe that there is sufficient equipoise for placebo controlled RCTs, the only robust way to demonstrate true efficacy. PMID:23326395

The Value of Using an E-Text in a Flipped Course

ERIC Educational Resources Information Center

Enfield, Jacob

2016-01-01

The flipped, or inverted, classroom model of instruction has been an effective pedagogical strategy for over a decade (Baker 2000; Lage et al. in "Journal of Economic Education," 31(1), 30-43, 2000; Bergmann and Sams 2011; Wright 2011; Pearson in "Education Canada," 52(5), 2012; Butt 2012; Bates and Galloway 2012). Arguably, to…

A multi-center, open-label trial to compare the efficacy and pharmacokinetics of Artemether-Lumefantrine in children with severe acute malnutrition versus children without severe acute malnutrition: study protocol for the MAL-NUT study.

PubMed

Denoeud-Ndam, Lise; Dicko, Alassane; Baudin, Elisabeth; Guindo, Ousmane; Grandesso, Francesco; Sagara, Issaka; Lasry, Estrella; Palma, Pedro Pablo; Parra, Angeles M Lima; Stepniewska, Kasia; Djimde, Abdoulaye A; Barnes, Karen I; Doumbo, Ogobara K; Etard, Jean-François

2015-06-12

Malnutrition and malaria frequently coexist in sub-Saharan African countries. Studies on efficacy of antimalarial treatments usually follow the WHO standardized protocol in which severely malnourished children are systematically excluded. Few studies have assessed the efficacy of chloroquine, sulfadoxine-pyrimethamine and quinine in severe acute malnourished children. Overall, efficacy of these treatments appeared to be reduced, attributed to lower immunity and for some antimalarials altered pharmacokinetic profiles and lower drug concentrations. However, similar research on the efficacy and pharmacokinetic profiles of artemisinin-combination therapies (ACTs) and especially artemether-lumefantrine in malnourished children is currently lacking. The main objective of this study is to assess whether artemether-lumefantrine is less efficacious in children suffering from severe acute malnutrition (SAM) compared to non-SAM children, and if so, to what extent this can be attributed to a sub-optimal pharmacokinetic profile. In two sites, Ouelessebougou, Mali and Maradi, Niger, children with uncomplicated microscopically-confirmed P. falciparum malaria aged between 6 and 59 months will be enrolled. Two non-SAM children will be enrolled after the enrolment of each SAM case. Children with severe manifestations of malaria or complications of acute malnutrition needing intensive treatment will be excluded. Treatment intakes will be supervised and children will be followed-up for 42 days, according to WHO guidance for surveillance of antimalarial drug efficacy. Polymerase Chain Reaction genotyping will be used to distinguish recrudescence from re-infection. SAM children will also benefit from the national nutritional rehabilitation program. Outcomes will be compared between the SAM and non-SAM populations. The primary outcome will be adequate clinical and parasitological response at day 28 after PCR correction, estimated by Kaplan-Meier analysis. To assess the pharmacokinetic profile of lumefantrine, a sparse sampling approach will be used with randomized allocation of sampling times (5 per child). A total of 180 SAM children and 360 non-SAM children will be recruited during the 2013 and 2014 malaria seasons. This study will provide important information that is currently lacking on the effect of SAM on therapeutic efficacy and pharmacokinetic profile of artemether-lumefantrine. If it shows lower therapeutic efficacy and decreased lumefantrine concentrations, it would inform dose optimization studies in SAM children. ClinicalTrials.gov: NCT01958905.

Low ratio of S-adenosylmethionine to S-adenosylhomocysteine is associated with vitamin deficiency in Brazilian pregnant women and newborns.

PubMed

Guerra-Shinohara, Elvira M; Morita, Olga E; Peres, Sabrina; Pagliusi, Regina A; Sampaio Neto, Luiz F; D'Almeida, Vânia; Irazusta, Silvia P; Allen, Robert H; Stabler, Sally P

2004-11-01

Pregnant women with low cobalamin concentrations are unable to provide the necessary amount of cobalamin to their fetuses. The effect of low maternal cobalamin concentrations on transmethylation metabolism in pregnant women and their newborns is unknown. We investigated the relation between maternal and neonatal cobalamin concentrations and changes in total homocysteine (tHcy), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH). Hematologic data and concentrations of cobalamin, red blood cell folate, serum folate, tHcy, methylmalonic acid, SAM, SAH, and other metabolites were measured in 119 serum specimens from pregnant Brazilian women (gestational age: 37-42 wk) and their newborns' placental veins at the time of delivery. The tHcy concentrations were higher in placental vein serum from newborns whose mothers had low cobalamin. Serum SAH concentrations were elevated and serum SAM and methionine concentrations were decreased in pregnant women with lower cobalamin concentrations. SAM:SAH was significantly decreased in both cobalamin-deficient pregnant women and their newborns. Lower maternal cobalamin concentrations are associated with higher tHcy and lower SAM:SAH in newborns. Because SAM:SAH is closely linked with the activity of numerous enzymatic methylation reactions, these results suggest that methylation could be impaired in cobalamin-deficient pregnant women and their newborns.

Electrostatic Repulsion-Induced Desorption of Dendritic Viologen-Arranged Molecules Anchored on a Gold Surface through a Gold-Thiolate Bond Leading to a Tunable Molecular Template.

PubMed

Kawauchi, Takehiro; Kojima, Takahiro; Sakaguchi, Hiroshi; Iyoda, Tomokazu

2018-06-05

We investigated the adsorption and desorption behavior of self-assembled monolayers (SAMs) on gold derived from dendritic viologen-arranged molecules with an ω-mercaptodecyl group (A n, n (dendritic generation) = 0-3) at the apex of the dendritic structure in polar solvents. The adsorption of the dendritic molecules occurred quickly and saturated within a few minutes in an acetonitrile/ethanol (1/1, v/v) mixture at a concentration of 2 mM. Atomic force microscopy images of the SAMs showed flat surfaces regardless of the dendritic generation because the peripheral viologen units were closely packed at the surface of the molecular layer. Individual A3 molecules immobilized on the substrate were observed by scanning tunneling microscopy measurements of a mixed SAM with decanethiol. The desorption behaviors of dendritic molecules from the A n-SAMs in several solvents such as water were also investigated. The spontaneous desorption of the A n-SAM occurred more rapidly than that of a conventional n-alkanethiol SAM. However, the desorption was inhibited by adding electrolytes such as NaNO 3 due to the shielding effect on the electrostatic repulsion between the dendritic molecules. These results indicate that the surface density of the dendritic molecules can be controlled through the desorption.

Gold cleaning methods for preparation of cell culture surfaces for self-assembled monolayers of zwitterionic oligopeptides.

PubMed

Enomoto, Junko; Kageyama, Tatsuto; Myasnikova, Dina; Onishi, Kisaki; Kobayashi, Yuka; Taruno, Yoko; Kanai, Takahiro; Fukuda, Junji

2018-05-01

Self-assembled monolayers (SAMs) have been used to elucidate interactions between cells and material surface chemistry. Gold surfaces modified with oligopeptide SAMs exhibit several unique characteristics, such as cell-repulsive surfaces, micropatterns of cell adhesion and non-adhesion regions for control over cell microenvironments, and dynamic release of cells upon external stimuli under culture conditions. However, basic procedures for the preparation of oligopeptide SAMs, including appropriate cleaning methods of the gold surface before modification, have not been fully established. Because gold surfaces are readily contaminated with organic compounds in the air, cleaning methods may be critical for SAM formation. In this study, we examined the effects of four gold cleaning methods: dilute aqua regia, an ozone water, atmospheric plasma, and UV irradiation. Among the methods, UV irradiation most significantly improved the formation of oligopeptide SAMs in terms of repulsion of cells on the surfaces. We fabricated an apparatus with a UV light source, a rotation table, and HEPA filter, to treat a number of gold substrates simultaneously. Furthermore, UV-cleaned gold substrates were capable of detaching cell sheets without serious cell injury. This may potentially provide a stable and robust approach to oligopeptide SAM-based experiments for biomedical studies. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Nuclear Protein Sam68 Interacts with the Enterovirus 71 Internal Ribosome Entry Site and Positively Regulates Viral Protein Translation.

PubMed

Zhang, Hua; Song, Lei; Cong, Haolong; Tien, Po

2015-10-01

Enterovirus 71 (EV71) recruits various cellular factors to assist in the replication and translation of its genome. Identification of the host factors involved in the EV71 life cycle not only will enable a better understanding of the infection mechanism but also has the potential to be of use in the development of antiviral therapeutics. In this study, we demonstrated that the cellular factor 68-kDa Src-associated protein in mitosis (Sam68) acts as an internal ribosome entry site (IRES) trans-acting factor (ITAF) that binds specifically to the EV71 5' untranslated region (5'UTR). Interaction sites in both the viral IRES (stem-loops IV and V) and the heterogeneous nuclear ribonucleoprotein K homology (KH) domain of Sam68 protein were further mapped using an electrophoretic mobility shift assay (EMSA) and biotin RNA pulldown assay. More importantly, dual-luciferase (firefly) reporter analysis suggested that overexpression of Sam68 positively regulated IRES-dependent translation of virus proteins. In contrast, both IRES activity and viral protein translation significantly decreased in Sam68 knockdown cells compared with the negative-control cells treated with short hairpin RNA (shRNA). However, downregulation of Sam68 did not have a significant inhibitory effect on the accumulation of the EV71 genome. Moreover, Sam68 was redistributed from the nucleus to the cytoplasm and interacts with cellular factors, such as poly(rC)-binding protein 2 (PCBP2) and poly(A)-binding protein (PABP), during EV71 infection. The cytoplasmic relocalization of Sam68 in EV71-infected cells may be involved in the enhancement of EV71 IRES-mediated translation. Since Sam68 is known to be a RNA-binding protein, these results provide direct evidence that Sam68 is a novel ITAF that interacts with EV71 IRES and positively regulates viral protein translation. The nuclear protein Sam68 is found as an additional new host factor that interacts with the EV71 IRES during infection and could potentially enhance the translation of virus protein. To our knowledge, this is the first report that describes Sam68 actively participating in the life cycle of EV71 at a molecular level. These studies will not only improve our understanding of the replication of EV71 but also have the potential for aiding in developing a therapeutic strategy against EV71 infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Improving methionine and ATP availability by MET6 and SAM2 co-expression combined with sodium citrate feeding enhanced SAM accumulation in Saccharomyces cerevisiae.

PubMed

Chen, Hailong; Wang, Zhou; Wang, Zhilai; Dou, Jie; Zhou, Changlin

2016-04-01

S-adenosyl-L-methionine (SAM), biosynthesized from methionine and ATP, exhibited diverse pharmaceutical applications. To enhance SAM accumulation in S. cerevisiae CGMCC 2842 (wild type), improvement of methionine and ATP availability through MET6 and SAM2 co-expression combined with sodium citrate feeding was investigated here. Feeding 6 g/L methionine at 12 h into medium was found to increase SAM accumulation by 38 % in wild type strain. Based on this result, MET6, encoding methionine synthase, was overexpressed, which caused a 59 % increase of SAM. To redirect intracellular methionine into SAM, MET6 and SAM2 (encoding methionine adenosyltransferase) were co-expressed to obtain the recombinant strain YGSPM in which the SAM accumulation was 2.34-fold of wild type strain. The data obtained showed that co-expression of MET6 and SAM2 improved intracellular methionine availability and redirected the methionine to SAM biosynthesis. To elevate intracellular ATP levels, 6 g/L sodium citrate, used as an auxiliary energy substrate, was fed into the batch fermentation medium, and an additional 19 % increase of SAM was observed after sodium citrate addition. Meanwhile, it was found that addition of sodium citrate improved the isocitrate dehydrogenase activity which was associated with the intracellular ATP levels. The results demonstrated that addition of sodium citrate improved intracellular ATP levels which promoted conversion of methionine into SAM. This study presented a feasible approach with considerable potential for developing highly SAM-productive strains based on improving methionine and ATP availability.

The Effectiveness of Hydrothermal Alteration Mapping based on Hyperspectral Data in Tropical Region

NASA Astrophysics Data System (ADS)

Muhammad, R. R. D.; Saepuloh, A.

2016-09-01

Hyperspectral remote sensing could be used to characterize targets at earth's surface based on their spectra. This capability is useful for mapping and characterizing the distribution of host rocks, alteration assemblages, and minerals. Contrary to the multispectral sensors, the hyperspectral identifies targets with high spectral resolution. The Wayang Windu Geothermal field in West Java, Indonesia was selected as the study area due to the existence of surface manifestation and dense vegetation environment. Therefore, the effectiveness of hyperspectral remote sensing in tropical region was targeted as the study objective. The Spectral Angle Mapper (SAM) method was used to detect the occurrence of clay minerals spatially from Hyperion data. The SAM references of reflectance spectra were obtained from field observation at altered materials. To calculate the effectiveness of hyperspectral data, we used multispectral data from Landsat-8. The comparison method was conducted by comparing the SAM's rule images from Hyperion and Landsat-8, resulting that hyperspectral was more accurate than multispectral data. Hyperion SAM's rule images showed lower value compared to Landsat-8, the significant number derived from using Hyperion was about 24% better. This inferred that the hyperspectral remote sensing is preferable for mineral mapping even though vegetation covered study area.

The evolution of biomass-burning aerosol size distributions due to coagulation: dependence on fire and meteorological details and parameterization

NASA Astrophysics Data System (ADS)

Sakamoto, Kimiko M.; Laing, James R.; Stevens, Robin G.; Jaffe, Daniel A.; Pierce, Jeffrey R.

2016-06-01

Biomass-burning aerosols have a significant effect on global and regional aerosol climate forcings. To model the magnitude of these effects accurately requires knowledge of the size distribution of the emitted and evolving aerosol particles. Current biomass-burning inventories do not include size distributions, and global and regional models generally assume a fixed size distribution from all biomass-burning emissions. However, biomass-burning size distributions evolve in the plume due to coagulation and net organic aerosol (OA) evaporation or formation, and the plume processes occur on spacial scales smaller than global/regional-model grid boxes. The extent of this size-distribution evolution is dependent on a variety of factors relating to the emission source and atmospheric conditions. Therefore, accurately accounting for biomass-burning aerosol size in global models requires an effective aerosol size distribution that accounts for this sub-grid evolution and can be derived from available emission-inventory and meteorological parameters. In this paper, we perform a detailed investigation of the effects of coagulation on the aerosol size distribution in biomass-burning plumes. We compare the effect of coagulation to that of OA evaporation and formation. We develop coagulation-only parameterizations for effective biomass-burning size distributions using the SAM-TOMAS large-eddy simulation plume model. For the most-sophisticated parameterization, we use the Gaussian Emulation Machine for Sensitivity Analysis (GEM-SA) to build a parameterization of the aged size distribution based on the SAM-TOMAS output and seven inputs: emission median dry diameter, emission distribution modal width, mass emissions flux, fire area, mean boundary-layer wind speed, plume mixing depth, and time/distance since emission. This parameterization was tested against an independent set of SAM-TOMAS simulations and yields R2 values of 0.83 and 0.89 for Dpm and modal width, respectively. The size distribution is particularly sensitive to the mass emissions flux, fire area, wind speed, and time, and we provide simplified fits of the aged size distribution to just these input variables. The simplified fits were tested against 11 aged biomass-burning size distributions observed at the Mt. Bachelor Observatory in August 2015. The simple fits captured over half of the variability in observed Dpm and modal width even though the freshly emitted Dpm and modal widths were unknown. These fits may be used in global and regional aerosol models. Finally, we show that coagulation generally leads to greater changes in the particle size distribution than OA evaporation/formation does, using estimates of OA production/loss from the literature.

Redox Behavior of the S-Adenosylmethionine (SAM)-Binding Fe-S Cluster in Methylthiotransferase RimO, toward Understanding Dual SAM Activity.

PubMed

Molle, Thibaut; Moreau, Yohann; Clemancey, Martin; Forouhar, Farhad; Ravanat, Jean-Luc; Duraffourg, Nicolas; Fourmond, Vincent; Latour, Jean-Marc; Gambarelli, Serge; Mulliez, Etienne; Atta, Mohamed

2016-10-18

RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C 3 methylthiolation of the D89 residue in the ribosomal S 12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS - ligand bound to the additional cluster. Furthermore, by using density functional theory-based methods, we provide a description of the reaction mechanism that predicts the attack of the carbon radical substrate on the methylthio group attached to the additional [4Fe-4S] cluster.

Catalytic mechanism of human N-acetylserotonin methyltransferase: a theoretical investigation

NASA Astrophysics Data System (ADS)

Wang, Li; Zhang, Ting; Li, Jieqiong; He, Chaozheng; He, Hongqing; Zhang, Jinglai

2015-11-01

The methyl-transfer mechanism of human N-acetylserotonin methyltransferase and the roles of several residues around the active sites are investigated by density function theory method. This enzyme will catalyse the conversion of N-acetylserotonin and S-adenosyl-L-methionine (SAM) into melatonin and S-asenosylhomocysteine, which is the terminal step in the melatonin (N-acetyl-5-methoxytryptamine) biosynthesis. The calculated results confirm that the methyl transfer and proton transfer will take place via a SN2 step with a concerted mechanism, which is different from the experimental estimation via a water bridge. The residues H255, D256, E311, and R252 play an important role in reducing the barrier height and inducing methyl transfer. In addition, a full SAM molecule is considered in this work, which is never explored in previous reports. We find that some residues around the SAM in the centre of active site are essential factors to influence the mechanism and barrier height. So a truncated SAM model may not be suitable for all reactions.

Potential impact of the May Southern Hemisphere annular mode on the Indian summer monsoon rainfall

NASA Astrophysics Data System (ADS)

Dou, Juan; Wu, Zhiwei; Zhou, Yefan

2017-04-01

El Niño-Southern Oscillation (ENSO) is probably a most important external forcing to Indian summer monsoon (ISM) rainfall (ISMR), yet the observed ENSO-ISMR relationship has become weak in recent years. It's essential to explore other predominant modes of variability which can contribute to the ISMR. As the leading mode of the variability in Southern Hemisphere (SH) extratropical atmospheric circulation, the SH annular mode (SAM) has potential influence both on the northern and southern hemispheric climate. The present study investigates the relationship between the SAM and ISMR. It is found that the May SAM exhibits a significant positive correlation with the monsoon precipitation over the Indian sub-continent and the adjacent areas in JunetJuly (JJ). Observational and numerical evidences indicate that the May SAM anomaly can trigger a South Indian Ocean dipole (SIOD) sea surface temperature anomaly (SSTA) through air-sea interactions. The SIOD SSTA persisting into the following months of JJ excites abnormal meridional circulation and modulates the low-level cross-equatorial flow. Accordingly, the ascending (or descending) motion and water vapor transportation are enhanced (or suppressed), which favors more (or less) precipitation over the Indian sub-continent and the adjacent areas. In fact, the SIOD SSTA plays an "ocean bridge" role to "prolong" the influence of the May SAM to the subsequent season and in turn impacts on the ISMR. Moreover, an empirical model is established to forecast the JJ ISMR strength based on the ENSO, Indian Ocean Dipole (IOD) and May SAM. The hindcast is carried out for the period 1979-2014, and performs better than the multimodel ensemble mean (MME) obtained from the Development of a European MME system for seasonal to interannual prediction (DEMETER) project. Since all these predictors can be monitored in real time before the early boreal summer, the empirical model might provide a practical real-time forecast tool for predicting ISMR variations.

Potential impact of the May Southern Hemisphere annular mode on the Indian summer monsoon rainfall

NASA Astrophysics Data System (ADS)

Dou, Juan; Wu, Zhiwei; Zhou, Yefan

2017-08-01

El Niño-Southern Oscillation (ENSO) is probably a most important external forcing to Indian summer monsoon (ISM) rainfall (ISMR), yet the observed ENSO-ISMR relationship has become weak in recent years. It's essential to explore other predominant modes of variability which can contribute to the ISMR. As the leading mode of the variability in Southern Hemisphere (SH) extratropical atmospheric circulation, the SH annular mode (SAM) has potential influence both on the northern and southern hemispheric climate. The present study investigates the relationship between the SAM and ISMR. It is found that the May SAM exhibits a significant positive correlation with the monsoon precipitation over the Indian sub-continent and the adjacent areas in June-July (JJ). Observational and numerical evidences indicate that the May SAM anomaly can trigger a South Indian Ocean dipole (SIOD) sea surface temperature anomaly (SSTA) through air-sea interactions. The SIOD SSTA persisting into the following months of JJ excites abnormal meridional circulation and modulates the low-level cross-equatorial flow. Accordingly, the ascending (or descending) motion and water vapor transportation are enhanced (or suppressed), which favors more (or less) precipitation over the Indian sub-continent and the adjacent areas. In fact, the SIOD SSTA plays an "ocean bridge" role to "prolong" the influence of the May SAM to the subsequent season and in turn impacts on the ISMR. Moreover, an empirical model is established to forecast the JJ ISMR strength based on the ENSO, Indian Ocean Dipole and May SAM. The hindcast is carried out for the period 1979-2014, and performs better than the multimodel ensemble mean (MME) obtained from the Development of a European MME system for seasonal to interannual prediction (DEMETER) project. Since all these predictors can be monitored in real time before the early boreal summer, the empirical model might provide a practical real-time forecast tool for predicting ISMR variations.

Risk factors for severe acute malnutrition in children below 5 y of age in India: a case-control study.

PubMed

Mishra, Kirtisudha; Kumar, Praveen; Basu, Srikanta; Rai, Kiran; Aneja, Satinder

2014-08-01

To determine the possible risk factors for severe acute malnutrition (SAM) in children below 5 y admitted in a hospital in north India. This case-control study was conducted in a medical college hospital in children below 5 y of age. All cases of SAM (diagnosed as per WHO definition) between 6 and 59 mo of age were compared with age-matched controls with weight for height above -2SD of WHO 2006 growth standards. Data regarding socio-demographic parameters, feeding practices and immunization were compared between the groups by univariable and multivariable logistic regression models. A total of 76 cases and 115 controls were enrolled. Among the 14 factors compared, maternal illiteracy, daily family income less than Rs. 200, large family size, lack of exclusive breast feeding in first 6 mo, bottle feeding, administration of pre-lacteals, deprivation of colostrum and incomplete immunization were significant risk factors for SAM. Regarding complementary feeding, it was the consistency, rather than the age of initiation, frequency and variety which showed a significant influence on occurrence of SAM. Multivariate analysis revealed that the risk of SAM was independently associated with 6 factors, namely, illiteracy among mothers, incomplete immunization, practice of bottle feeding, consistency of complementary feeding, deprivation of colostrum and receipt of pre-lacteals at birth. The present study identifies certain risk factors which need to be focused on during health planning and policy making related to children with SAM in India.

Unsupervised classification of Space Acceleration Measurement System (SAMS) data using ART2-A

NASA Technical Reports Server (NTRS)

Smith, A. D.; Sinha, A.

1999-01-01

The Space Acceleration Measurement System (SAMS) has been developed by NASA to monitor the microgravity acceleration environment aboard the space shuttle. The amount of data collected by a SAMS unit during a shuttle mission is in the several gigabytes range. Adaptive Resonance Theory 2-A (ART2-A), an unsupervised neural network, has been used to cluster these data and to develop cause and effect relationships among disturbances and the acceleration environment. Using input patterns formed on the basis of power spectral densities (psd), data collected from two missions, STS-050 and STS-057, have been clustered.

A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection

PubMed Central

Wu, Jianguo; Wang, Yu; Ji, Shaoyi; Zhu, Shuyi; Wei, Chunhong; Zhang, Jinsong

2017-01-01

Ethylene plays critical roles in plant development and biotic stress response, but the mechanism of ethylene in host antiviral response remains unclear. Here, we report that Rice dwarf virus (RDV) triggers ethylene production by stimulating the activity of S-adenosyl-L-methionine synthetase (SAMS), a key component of the ethylene synthesis pathway, resulting in elevated susceptibility to RDV. RDV-encoded Pns11 protein specifically interacted with OsSAMS1 to enhance its enzymatic activity, leading to higher ethylene levels in both RDV-infected and Pns11-overexpressing rice. Consistent with a counter-defense role for ethylene, Pns11-overexpressing rice, as well as those overexpressing OsSAMS1, were substantially more susceptible to RDV infection, and a similar effect was observed in rice plants treated with an ethylene precursor. Conversely, OsSAMS1-knockout mutants, as well as an osein2 mutant defective in ethylene signaling, resisted RDV infection more robustly. Our findings uncover a novel mechanism which RDV manipulates ethylene biosynthesis in the host plants to achieve efficient infection. PMID:28994391

A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection.

PubMed

Zhao, Shanshan; Hong, Wei; Wu, Jianguo; Wang, Yu; Ji, Shaoyi; Zhu, Shuyi; Wei, Chunhong; Zhang, Jinsong; Li, Yi

2017-10-10

Ethylene plays critical roles in plant development and biotic stress response, but the mechanism of ethylene in host antiviral response remains unclear. Here, we report that Rice dwarf virus (RDV) triggers ethylene production by stimulating the activity of S-adenosyl-L-methionine synthetase (SAMS), a key component of the ethylene synthesis pathway, resulting in elevated susceptibility to RDV. RDV-encoded Pns11 protein specifically interacted with OsSAMS1 to enhance its enzymatic activity, leading to higher ethylene levels in both RDV-infected and Pns11-overexpressing rice. Consistent with a counter-defense role for ethylene, Pns11-overexpressing rice, as well as those overexpressing OsSAMS1 , were substantially more susceptible to RDV infection, and a similar effect was observed in rice plants treated with an ethylene precursor. Conversely, OsSAMS1- knockout mutants, as well as an osein2 mutant defective in ethylene signaling, resisted RDV infection more robustly. Our findings uncover a novel mechanism which RDV manipulates ethylene biosynthesis in the host plants to achieve efficient infection.

Home-based management of severely acute malnutrition: feasibility of ethically designed, community-based randomised clinical trials.

PubMed

Patil, Rajan R

2015-01-01

The Indian Council of Medical Research had, on May 31, 2011, called for research proposals on severely acute malnourished (SAM) children to generate evidence for the development of practical and scalable regimens to medically rehabilitate children suffering from SAM, without serious complications, at the home/community level and/or peripheral inpatient facilities. The primary outcomes of the proposed research study are recovery from SAM in the short term, as well as sustenance of recovery (for at least six months after the initiation of treatment). The secondary outcomes are the acceptability, feasibility and safety of the regimes being tested. It was suggested that the studies be designed as individual or cluster randomised or quasi randomised controlled trials (RCTs). This paper analyses the methodological, operational, and most importantly, ethical challenges and implications of conducting community-based RCTs involving SAM children. The paper dwells in detail on why and how the RCT design is inappropriate and unsuitable for studying the effectiveness of home-based management of SAM children in the community.

CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam.

PubMed

Mercurio, Flavia A; Scognamiglio, Pasqualina L; Di Natale, Concetta; Marasco, Daniela; Pellecchia, Maurizio; Leone, Marilisa

2014-11-01

The lipid phosphatase Ship2 is a protein that intervenes in several diseases such as diabetes, cancer, neurodegeneration, and atherosclerosis. It is made up of a catalytic domain and several protein docking modules such as a C-terminal Sam (Sterile alpha motif) domain. The Sam domain of Ship2 (Ship2-Sam) binds to the Sam domains of the EphA2 receptor (EphA2-Sam) and the PI3K effector protein Arap3 (Arap3-Sam). These heterotypic Sam-Sam interactions occur through formation of dimers presenting the canonical "Mid Loop/End Helix" binding mode. The central region of Ship2-Sam, spanning the C-terminal end of α2, the α3 and α4 helices together with the α2α3 and α3α4 interhelical loops, forms the Mid Loop surface that is needed to bind partners Sam domains. A peptide encompassing most of the Ship2-Sam Mid Loop interface (Shiptide) capable of binding to both EphA2-Sam and Arap3-Sam, was previously identified. Here we investigated the conformational features of this peptide, through solution CD and NMR studies in different conditions. These studies reveal that the peptide is highly flexible in aqueous buffer, while it adopts a helical conformation in presence of 2,2,2-trifluoroethanol. The discovered structural insights and in particular the identification of a helical motif, may lead to the design of more constrained and possibly cell permeable Shiptide analogs that could work as efficient antagonists of Ship2-Sam heterotypic interactions and embrace therapeutic applications. © 2014 Wiley Periodicals, Inc.

Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.

PubMed

Huang, Wei; Kim, Joohyun; Jha, Shantenu; Aboul-Ela, Fareed

2012-05-18

Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5' riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I riboswitch RNA using constructs with different 3' truncation points experimentally. Folding was monitored through fluorescence, susceptibility to base-catalyzed cleavage, nuclear magnetic resonance, and indirectly through SAM binding. We identify key decision windows at which SAM can affect the folding pathway towards the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths is crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism. Copyright © 2012 Elsevier Ltd. All rights reserved.

Boron (B) deprivation increases plasma homocysteine and decreases liver S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) in rats

USDA-ARS?s Scientific Manuscript database

The diverse effects of B deprivation suggest that B affects a biomolecule involved in a variety of biochemical reactions. An experiment was conducted to determine whether dietary B affects the liver concentration of SAM, a frequently used enzyme substrate, especially for methylation reactions that y...

S-adenosylmethionine lowers the inflammatory response in macrophages associated with changes in DNA methylation

USDA-ARS?s Scientific Manuscript database

S-adenosylmethionine (SAM), the unique methyl donor in DNA methylation, has been shown to lower inflammation. We assessed whether epigenetic mechanisms mediate this effect. Human THP-1 cells were differentiated into macrophages and treated with 0 micromole/L, 500 micromole/L or 1000 micromole/L SAM ...

Space acceleration measurement system description and operations on the First Spacelab Life Sciences Mission

NASA Technical Reports Server (NTRS)

Delombard, Richard; Finley, Brian D.

1991-01-01

The Space Acceleration Measurement System (SAMS) project and flight units are briefly described. The SAMS operations during the STS-40 mission are summarized, and a preliminary look at some of the acceleration data from that mission are provided. The background and rationale for the SAMS project is described to better illustrate its goals. The functions and capabilities of each SAMS flight unit are first explained, then the STS-40 mission, the SAMS's function for that mission, and the preparation of the SAMS are described. Observations about the SAMS operations during the first SAMS mission are then discussed. Some sample data are presented illustrating several aspects of the mission's microgravity environment.

Binding and Function of Phosphotyrosines of the Ephrin A2 (EphA2) Receptor Using Synthetic Sterile α Motif (SAM) Domains*

PubMed Central

Borthakur, Susmita; Lee, HyeongJu; Kim, SoonJeung; Wang, Bing-Cheng; Buck, Matthias

2014-01-01

The sterile α motif (SAM) domain of the ephrin receptor tyrosine kinase, EphA2, undergoes tyrosine phosphorylation, but the effect of phosphorylation on the structure and interactions of the receptor is unknown. Studies to address these questions have been hindered by the difficulty of obtaining site-specifically phosphorylated proteins in adequate amounts. Here, we describe the use of chemically synthesized and specifically modified domain-length peptides to study the behavior of phosphorylated EphA2 SAM domains. We show that tyrosine phosphorylation of any of the three tyrosines, Tyr921, Tyr930, and Tyr960, has a surprisingly small effect on the EphA2 SAM structure and stability. However, phosphorylation at Tyr921 and Tyr930 enables differential binding to the Src homology 2 domain of the adaptor protein Grb7, which we propose will lead to distinct functional outcomes. Setting up different signaling platforms defined by selective interactions with adaptor proteins thus adds another level of regulation to EphA2 signaling. PMID:24825902

Using Measured Plane-of-Array Data Directly in Photovoltaic Modeling: Methodology and Validation: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, Janine; Freestate, David; Riley, Cameron

2016-11-01

Measured plane-of-array (POA) irradiance may provide a lower-cost alternative to standard irradiance component data for photovoltaic (PV) system performance modeling without loss of accuracy. Previous work has shown that transposition models typically used by PV models to calculate POA irradiance from horizontal data introduce error into the POA irradiance estimates, and that measured POA data can correlate better to measured performance data. However, popular PV modeling tools historically have not directly used input POA data. This paper introduces a new capability in NREL's System Advisor Model (SAM) to directly use POA data in PV modeling, and compares SAM results frommore » both POA irradiance and irradiance components inputs against measured performance data for eight operating PV systems.« less

Using Measured Plane-of-Array Data Directly in Photovoltaic Modeling: Methodology and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, Janine; Freestate, David; Hobbs, William

2016-11-21

Measured plane-of-array (POA) irradiance may provide a lower-cost alternative to standard irradiance component data for photovoltaic (PV) system performance modeling without loss of accuracy. Previous work has shown that transposition models typically used by PV models to calculate POA irradiance from horizontal data introduce error into the POA irradiance estimates, and that measured POA data can correlate better to measured performance data. However, popular PV modeling tools historically have not directly used input POA data. This paper introduces a new capability in NREL's System Advisor Model (SAM) to directly use POA data in PV modeling, and compares SAM results frommore » both POA irradiance and irradiance components inputs against measured performance data for eight operating PV systems.« less

Using Measured Plane-of-Array Data Directly in Photovoltaic Modeling: Methodology and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, Janine; Freestate, David; Hobbs, William

2016-06-05

Measured plane-of-array (POA) irradiance may provide a lower-cost alternative to standard irradiance component data for photovoltaic (PV) system performance modeling without loss of accuracy. Previous work has shown that transposition models typically used by PV models to calculate POA irradiance from horizontal data introduce error into the POA irradiance estimates, and that measured POA data can correlate better to measured performance data. However, popular PV modeling tools historically have not directly used input POA data. This paper introduces a new capability in NREL's System Advisor Model (SAM) to directly use POA data in PV modeling, and compares SAM results frommore » both POA irradiance and irradiance components inputs against measured performance data for eight operating PV systems.« less

Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions.

PubMed

Wang, Yue; Shang, Yuan; Li, Jianchao; Chen, Weidi; Li, Gang; Wan, Jun; Liu, Wei; Zhang, Mingjie

2018-05-11

The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain many Eph SAM mutations identified in patients suffering from cancers and other diseases. © 2018, Wang et al.

Combining occurrence and abundance distribution models for the conservation of the Great Bustard.

PubMed

Mi, Chunrong; Huettmann, Falk; Sun, Rui; Guo, Yumin

2017-01-01

Species distribution models (SDMs) have become important and essential tools in conservation and management. However, SDMs built with count data, referred to as species abundance models (SAMs), are still less commonly used to date, but increasingly receiving attention. Species occurrence and abundance do not frequently display similar patterns, and often they are not even well correlated. Therefore, only using information based on SDMs or SAMs leads to an insufficient or misleading conservation efforts. How to combine information from SDMs and SAMs and how to apply the combined information to achieve unified conservation remains a challenge. In this study, we introduce and propose a priority protection index (PI). The PI combines the prediction results of the occurrence and abundance models. As a case study, we used the best-available presence and count records for an endangered farmland species, the Great Bustard ( Otis tarda dybowskii ), in Bohai Bay, China. We then applied the Random Forest algorithm (Salford Systems Ltd. Implementation) with eleven predictor variables to forecast the spatial occurrence as well as the abundance distribution. The results show that the occurrence model had a decent performance (ROC: 0.77) and the abundance model had a RMSE of 26.54. It is noteworthy that environmental variables influenced bustard occurrence and abundance differently. The area of farmland, and the distance to residential areas were the top important variables influencing bustard occurrence. While the distance to national roads and to expressways were the most important influencing abundance. In addition, the occurrence and abundance models displayed different spatial distribution patterns. The regions with a high index of occurrence were concentrated in the south-central part of the study area; and the abundance distribution showed high populations occurrence in the central and northwestern parts of the study area. However, combining occurrence and abundance indices to produce a priority protection index (PI) to be used for conservation could guide the protection of the areas with high occurrence and high abundance (e.g., in Strategic Conservation Planning). Due to the widespread use of SDMs and the easy subsequent employment of SAMs, these findings have a wide relevance and applicability than just those only based on SDMs or SAMs. We promote and strongly encourage researchers to further test, apply and update the priority protection index (PI) elsewhere to explore the generality of these findings and methods that are now readily available.

Combining occurrence and abundance distribution models for the conservation of the Great Bustard

PubMed Central

Mi, Chunrong; Huettmann, Falk; Sun, Rui

2017-01-01

Species distribution models (SDMs) have become important and essential tools in conservation and management. However, SDMs built with count data, referred to as species abundance models (SAMs), are still less commonly used to date, but increasingly receiving attention. Species occurrence and abundance do not frequently display similar patterns, and often they are not even well correlated. Therefore, only using information based on SDMs or SAMs leads to an insufficient or misleading conservation efforts. How to combine information from SDMs and SAMs and how to apply the combined information to achieve unified conservation remains a challenge. In this study, we introduce and propose a priority protection index (PI). The PI combines the prediction results of the occurrence and abundance models. As a case study, we used the best-available presence and count records for an endangered farmland species, the Great Bustard (Otis tarda dybowskii), in Bohai Bay, China. We then applied the Random Forest algorithm (Salford Systems Ltd. Implementation) with eleven predictor variables to forecast the spatial occurrence as well as the abundance distribution. The results show that the occurrence model had a decent performance (ROC: 0.77) and the abundance model had a RMSE of 26.54. It is noteworthy that environmental variables influenced bustard occurrence and abundance differently. The area of farmland, and the distance to residential areas were the top important variables influencing bustard occurrence. While the distance to national roads and to expressways were the most important influencing abundance. In addition, the occurrence and abundance models displayed different spatial distribution patterns. The regions with a high index of occurrence were concentrated in the south-central part of the study area; and the abundance distribution showed high populations occurrence in the central and northwestern parts of the study area. However, combining occurrence and abundance indices to produce a priority protection index (PI) to be used for conservation could guide the protection of the areas with high occurrence and high abundance (e.g., in Strategic Conservation Planning). Due to the widespread use of SDMs and the easy subsequent employment of SAMs, these findings have a wide relevance and applicability than just those only based on SDMs or SAMs. We promote and strongly encourage researchers to further test, apply and update the priority protection index (PI) elsewhere to explore the generality of these findings and methods that are now readily available. PMID:29255652

The origin of the scatter of the star forming main sequence at z=0

NASA Astrophysics Data System (ADS)

Shanahan, Clare; Somerville, Rachel S.; Saintonge, Amelie; Huang, Mei-Ling

2016-01-01

We investigate the origin of the dispersion in the relationship between star formation rate (SFR) and stellar mass, known as the star forming main sequence (SFMS). Our study includes predictions from a state-of-the-art semi-analytic model (SAM) as well as observations from the COLDGASS, Bluedisk, and GAMA surveys. Using a simple toy model we demonstrate that, in the absence of a correlation between gas fraction and galaxy size, we would expect more compact disks to live 'high' on the SFMS, and vice versa, due to the observational Kennicutt relation. We demonstrate that this correlation is not seen in the observations, nor is it predicted by the SAM. We find in both the model and the observations that extended disks have a higher fraction of their baryonic mass in total cold gas and in HI and $H_{2}$ gas separately, offsetting the dependence of SFR on disk size. We investigate the origin of the gas fraction-size correlation in the SAMs, and find that it is connected with the rate of cosmological accretion of gas from the intergalactic medium.

Interactions of doxorubicin with self-assembled monolayer-modified electrodes: electrochemical, surface plasmon resonance (SPR), and gravimetric studies.

PubMed

Nieciecka, Dorota; Krysinski, Pawel

2011-02-01

We present the results on the partitioning of doxorubicin (DOX), a potent anticancer drug, through the model membrane system, self-assembled monolayers (SAMs) on gold electrodes. The monolayers were formed from alkanethiols of comparable length with different ω-terminal groups facing the aqueous electrolyte: the hydrophobic -CH(3) groups for the case of dodecanethiol SAMs or hydrophilic -OH groups of mercaptoundecanol SAMs. The electrochemical experiments combined with the surface plasmon resonance (SPR) and gravimetric studies show that doxorubicin is likely adsorbed onto the surface of hydrophilic monolayer, while for the case of the hydrophobic one the drug mostly penetrates the monolayer moiety. The adsorption of the drug hinders further penetration of doxorubicin into the monolayer moiety.

Ultraflat Au nanoplates as a new building block for molecular electronics.

PubMed

Jeong, Wooseok; Lee, Miyeon; Lee, Hyunsoo; Lee, Hyoban; Kim, Bongsoo; Park, Jeong Young

2016-05-27

We demonstrate the charge transport properties of a self-assembled organic monolayer on Au nanoplates with conductive probe atomic force microscopy (CP-AFM). Atomically flat Au nanoplates, a few hundred micrometers on each side, that have only (111) surfaces, were synthesized using the chemical vapor transport method; these nanoplates were employed as the substrates for hexadecanethiol (HDT) self-assembled monolayers (SAMs). Atomic-scale high-resolution images show (√3 x √3) R30° molecular periodicity, indicating a well-ordered structure of the HDT on the Au nanoplates. We observed reduced friction and adhesion forces on the HDT SAMs on Au nanoplates, compared with Si substrates, which is consistent with the lubricating nature of HDT SAMs. The electrical properties, such as I-V characteristics and current as a function of load, were measured using CP-AFM. We obtained a tunneling decay constant (β) of 0.57 Å(-1), including through-bond (βtb = 0.99 Å(-1)) and through-space (βts = 1.36 Å(-1)) decay constants for the two-pathway model. This indicates that the charge transport properties of HDT SAMs on Au nanoplates are consistent with those on a Au (111) film, suggesting that SAMs on nanoplates can provide a new building block for molecular electronics.

Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes.

PubMed

Long, Yunming; Zhao, Lifeng; Niu, Baixiao; Su, Jing; Wu, Hao; Chen, Yuanling; Zhang, Qunyu; Guo, Jingxin; Zhuang, Chuxiong; Mei, Mantong; Xia, Jixing; Wang, Lan; Wu, Haibin; Liu, Yao-Guang

2008-12-02

Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM(+)SaF(+), whereas all japonica cultivars have SaM(-)SaF(-) that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM(-). This allele-specific gamete elimination results from a selective interaction of SaF(+) with SaM(-), a truncated protein, but not with SaM(+) because of the presence of an inhibitory domain, although SaM(+) is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding.

7 CFR 1739.10 - Eligible applicant.

Code of Federal Regulations, 2014 CFR

2014-01-01

...'s number. (d) Register in the System for Award Management (SAM) (formerly Central Contractor... paper, must be registered in the SAM prior to submitting an application. Applicants may register for the SAM at https://www.sam.gov/. (2) The SAM registration must remain active, with current information, at...

Effect of SLCO1B1 gene polymorphisms and vitamin D on statin-induced myopathy.

PubMed

Alghalyini, Baraa; El Shamieh, Said; Salami, Ali; Visvikis Siest, Sophie; Fakhoury, Hana M; Fakhoury, Rajaa

2018-03-28

Background Statin therapy used to lower cholesterol levels results in a substantial reduction in cardiovascular complications. Previous observations in different ethnic populations showed that rs2306283A>G, p.Asn130Asp and rs4149056T>C, p.Val174Ala in solute carrier organic anion transporter 1B1 (SLCO1B1) gene encoding the organic transporter protein may be responsible for statin uptake, thus explaining the majority of statin-associated symptoms. In addition to the genetic component, vitamin D (vit D) deficiency is common in Saudi Arabia and worldwide and may cause muscle dysfunction and ache. The aim of the present study was first to reveal an effect of vit D, rs2306283A>G, and rs4149056T>C and related haplotypes on statin-associated myopathy (SAM) and then to investigate a possible interaction between low vit D levels and the above-mentioned variants. Methods The genomic DNA obtained from 50 individuals diagnosed with hypercholesterolemia was genotyped using light SNiP hybridization probes. Results Low vit D levels were associated with SAM (OR=3.6, p=0.03); however, CK levels, rs2306283A>G, and rs4149056T>C did not show any association. Interestingly, rs4149056T>C was interacting with vit D to influence SAM (p=0.02). Haplotype analysis showed that SLCO1B1 *1B and *15 were more prevalent in individuals with SAM (p=0.05). When stratified according to vit D levels, rs2306283A allele showed an increase in individuals having SAM along with low vit D (p=0.03). Conclusions Although preliminary, our results show an involvement of vit D and rs4149056T>C of SLCO1B1 in SAM.

Excessive S-Adenosyl-L-Methionine-Dependent Methylation Increases Levels of Methanol, Formaldehyde and Formic Acid in Rat Brain Striatal Homogenates: Possible role in S-adenosyl-L-methionine-induced Parkinson’s disease-like disorders

PubMed Central

Lee, Eun-Sook; Chen, Hongtao; Hardman, Chadwick; Simm, Anthony; Charlton, Clivel

2009-01-01

Aims Excessive methylation may be a precipitating factor for Parkinson’s disease (PD) since S-adenosylmethionine (SAM), the endogenous methyl donor, induces PD-like changes when injected into the rat brain. The hydrolysis of the methyl ester bond of the methylated proteins produces methanol. Since methanol is oxidized into formaldehyde, and formaldehyde into formic acid in the body, we investigated the effects of SAM on the production of methanol, formaldehyde and formic acid in rat brain striatal homogenates and the toxicity of these products in PC12 cells. Main methods radio-enzymatic and colorimetric assays, cell viability, Western blot. Key findings SAM increased the formation of methanol, formaldehyde and formic acid in a concentration and time-dependent manner. Concentrations of [3H-methyl]-SAM at 0.17, 0.33, 0.67 and 1.34 nM produced 3.8, 8.0, 18.3 and 34.4 fmol/mg protein/h of [3H] methanol in rat striatal homogenates, respectively. SAM also significantly generated formaldehyde and formic acid in striatal homogenates. Formaldehyde was the most toxic metabolite to differentiated PC12 pheochromocytoma cells in cell culture studies, indicating that formaldehyde formed endogenously may contribute to neuronal damage in excessive methylation conditions. Subtoxic concentration of formaldehyde decreased the expression of tyrosine hydroxylase, the limiting factor in dopamine synthesis. Formaldehyde was more toxic to catecholaminergic PC12 cells than C6 glioma cells, indicating that neurons are more vulnerable to formaldehyde than glia cells. Significance We suggest that excessive carboxylmethylation of proteins might be involved in the SAM-induced PD-like changes and in the aging process via the toxic effects of formaldehyde. PMID:18930743

Effect of TiO2 modification with amino-based self-assembled monolayer on inverted organic solar cell

NASA Astrophysics Data System (ADS)

Tozlu, Cem; Mutlu, Adem; Can, Mustafa; Havare, Ali Kemal; Demic, Serafettin; Icli, Sıddık

2017-11-01

The effects of surface modification of titanium dioxide (TiO2) on the performance of inverted type organic solar cells (i-OSCs) was investigated in this study. A series of benzoic acid derivatized self-assembled monolayer (SAM) molecules of 4‧-[(hexyloxy)phenyl]amino-3,5-biphenyl dicarboxylic acid (CT17) and 4‧-[1-naphthyl (phenyl)amino]biphenyl-4-carboxylic acid (CT19) were utilized to modify the interface between TiO2 buffer layer and poly-3 hexylthiophene (P3HT):[6,6]-phenyl C61 butyric acid methyl ester (PC61BM) active layer having the device structure of ITO/TiO2/SAM/P3HT:PC61BM/MoO3/Ag. The work function and surface wetting properties of TiO2 buffer layer served as electron transporting layer between ITO and PC61BM active layer were tuned by SAM method. The solar cell of the SAM modified devices exhibited better performance. The power conversion efficiency (PCE) of i-OSCs devices with bare TiO2 electrodes enhanced from 2.00% to 2.21% and 2.43% with CT17 and CT19 treated TiO2 electrodes, respectively. The open circuit voltage (Voc) of the SAM treated TiO2 devices reached to 0.60 V and 0.61 V, respectively, while the Voc of untreated TiO2 was 0.57 V. The water contact angle of i-OSCs with CT17 and CT19 SAMs was also higher than the value of the unmodified TiO2 electrode. These results show that inserting a monolayer at the interface between organic and inorganic layers is an useful alternative method to improve the performance of i-OSCs.

When Words were Wanted, But Woefully Wanting, We Waged War With Chess.

PubMed

Seitler, Burton Norman

2016-12-01

What do you say to a child who rarely speaks? How do you work with such a youngster? What are the sine qua nons or guiding principles upon which analysts can draw? And, how do we know if we are being helpful? Sam was 9-years when I began treating him. He was extremely withdrawn and rarely spoke more than a few words. Instead, he mainly played chess. I did not know at first whether Sam's taciturn demeanor was due to shyness, limited verbal abilities, or the stultifying effects of trauma. Fortuitously, during one of many seemingly "innocent" games of chess, Sam happened to make a bold move, to which I admiringly remarked, "What a move, you're killing me." His surprising reaction permanently altered the trajectory of treatment. Curiously, upon returning from summer vacation, not only did Sam no longer need to play chess, but he also found his voice. It was then that he began to discuss things for the first time. Initially, what he said was cloaked in symbolic and indirect referents, suggesting that there were things about which he still could not speak. I proceeded with patience and eventually Sam was able to disclose what he had been harboring inside. In this article, I will discuss the role and psychoanalytic meaning of chess in Sam's play therapy and how it served as a means of symbolically expressing an unspoken, yet ongoing trauma; how it non-verbally, and thus safely communicated Sam's desperate need for understanding and his urgent (but silent) disguised plea for help.

Structural Basis for Methyl Transfer by a Radical SAM Enzyme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boal, Amie K.; Grove, Tyler L.; McLaughlin, Monica I.

2014-10-02

The radical S-adenosyl-l-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys{sup 355}) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys{sup 355} is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfermore » binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.« less

Supporting the Distant Student: The Effect of ARCS-Based Strategies on Confidence and Performance

ERIC Educational Resources Information Center

Huett, Jason Bond; Young, Jon; Huett, Kimberly Cleaves; Moller, Leslie; Bray, Marty

2008-01-01

The purpose of this research was to manipulate the component of confidence found in Keller's ARCS Model to enhance the confidence and performance of undergraduate students enrolled in an online course at a Texas University. This experiment used SAM Office 2003 and WebCT for the delivery of the tactics, strategies, confidence-enhancing e-mails…

A Phase 2 clinical trial of PF-05212377 (SAM-760) in subjects with mild to moderate Alzheimer's disease with existing neuropsychiatric symptoms on a stable daily dose of donepezil.

PubMed

Fullerton, Terence; Binneman, Brendon; David, William; Delnomdedieu, Marielle; Kupiec, James; Lockwood, Peter; Mancuso, Jessica; Miceli, Jeffrey; Bell, Joanne

2018-04-05

Symptomatic benefits have been reported for 5-HT 6 receptor antagonists in Alzheimer's disease (AD) trials. SAM-760 is a potent and selective 5-HT 6 receptor antagonist that has demonstrated central 5-HT 6 receptor saturation in humans at a dose of 30 mg. This was a randomized, double-blind, placebo-controlled, parallel-group, multicenter trial evaluating the efficacy and safety of SAM-760 30 mg once daily (QD) for 12 weeks in subjects with AD on a stable regimen of donepezil 5 to 10 mg QD. The study included an interim analysis with stopping rules for futility or efficacy after 180 subjects completed the week 12 visit. Up to 342 subjects with AD (Mini-Mental State Examination (MMSE) score 10-24) and neuropsychiatric symptoms (Neuropsychiatric Inventory (NPI) total score ≥ 10) were to be enrolled if the study continued after the interim analysis. After a 4-week, single-blind, placebo run-in period, subjects entered the 12-week double-blind period and were randomized to either SAM-760 or placebo. The primary and key secondary efficacy endpoints were the change from baseline in Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog13) and NPI total scores. Mixed models for repeated measures were used to analyze the data. At the interim analysis, when 186 subjects had been randomized and 163 had completed the week 12 visit, the study met futility criteria and was stopped. The mean week 12 treatment difference was 0.70 points (P = 0.43) for ADAS-cog13 and 2.19 points (P = 0.20) for NPI score, both of which were numerically in favor of placebo. Other secondary endpoints did not demonstrate any significant benefit for SAM-760. In total, 46.2% of SAM-760 subjects reported adverse events (AE) versus 44.7% for placebo, and there were 5 (5.5%) serious AEs in the SAM-760 group versus 3 (3.2%) for placebo. There were two deaths, one prior to randomization and one in the SAM-760 group (due to a traffic accident during washout of active treatment). SAM-760 was safe and well tolerated, but there was no benefit of SAM-760 on measures of cognition, neuropsychiatric symptoms, or daily function. Differences in trial design, study population, region, or pharmacological profile may explain differences in outcome compared with other 5-HT 6 receptor antagonists. Clinicaltrials.gov, NCT01712074 . Registered 19 October 2012.

Mixed carboranethiol self-assembled monolayers on gold surfaces

NASA Astrophysics Data System (ADS)

Yavuz, Adem; Sohrabnia, Nima; Yilmaz, Ayşen; Danışman, M. Fatih

2017-08-01

Carboranethiol self-assembled monolayers on metal surfaces have been shown to be very convenient systems for surface engineering. Here we have studied pure and mixed self-assembled monolayers (SAMs) of three different carboranethiol (CT) isomers on gold surfaces. The isomers were chosen with dipole moments pointing parallel to (m-1-carboranethiol, M1), out of (m-9-carboranethiol, M9) and into (o-1-carboranethiol, O1) the surface plane, in order to investigate the effect of dipole moment orientation on the film properties. In addition, influence of the substrate surface morphology on the film properties was also studied by using flame annealed (FA) and template stripped (TS) gold surfaces. Contact angle measurements indicate that in M1/M9 and M1/O1 mixed SAMs, M1 is the dominant species on the surface even for low M1 ratio in the growth solution. Whereas for O1/M9 mixed SAMs no clear evidence could be observed indicating dominance of one of the species over the other one. Though contact angle values were lower and hysteresis values were higher for SAMs grown on TS gold surfaces, the trends in the behavior of the contact angles with changing mixing ratio were identical for SAMs grown on both substrates. Atomic force microscopy images of the SAMs on TS gold surfaces indicate that the films have similar morphological properties regardless of mixing ratio.

Evidence for S-adenosyl-L-methionine (SAM-e) for the treatment of major depressive disorder.

PubMed

Papakostas, George I

2009-01-01

Despite the increasingly large array of antidepressants available to treat major depressive disorder, patients continue to experience relatively modest response and remission rates. In addition, patients may experience adverse side effects from pharmacotherapy that not only hinder treatment compliance and adherence but, in some cases, may also contribute to increased disability, patient suffering, morbidity, and mortality. In order to enhance treatment efficacy and tolerability, patients and clinicians have become increasingly interested in nonpharmaceutical supplements for treating depression. One of the best-studied of these supplements is S-adenosyl-L-methionine (SAM-e), a naturally occurring molecule present in all living cells and a major methyl group donor in the human body. Controlled trials have found SAM-e to be more efficacious than placebo and equal in efficacy to the tricyclic antidepressants for treating major depressive disorder (MDD) when administered parenterally (either intravenously or intramuscularly). Less evidence supports the use of oral SAM-e, although some trials have demonstrated its efficacy as well. In addition, there is a paucity of evidence examining whether oral forms of SAM-e can be safe, well tolerated, and efficacious when used as adjunctive treatment for antidepressant nonresponders with MDD. Although preliminary data suggest SAM-e may be useful as an adjunctive therapy to antidepressants, controlled studies are needed to confirm or refute these preliminary findings. (c) Copyright 2009 Physicians Postgraduate Press, Inc.

Ablation of the Sam68 RNA Binding Protein Protects Mice from Age-Related Bone Loss

PubMed Central

Richard, Stéphane; Torabi, Nazi; Franco, Gladys Valverde; Tremblay, Guy A; Chen, Taiping; Vogel, Gillian; Morel, Mélanie; Cléroux, Patrick; Forget-Richard, Alexandre; Komarova, Svetlana; Tremblay, Michel L; Li, Wei; Li, Ailian; Gao, Yun Jing; Henderson, Janet E

2005-01-01

The Src substrate associated in mitosis of 68 kDa (Sam68) is a KH-type RNA binding protein that has been shown to regulate several aspects of RNA metabolism; however, its physiologic role has remained elusive. Herein we report the generation of Sam68-null mice by homologous recombination. Aged Sam68−/− mice preserved their bone mass, in sharp contrast with 12-month-old wild-type littermates in which bone mass was decreased up to approximately 75%. In fact, the bone volume of the 12-month-old Sam68−/− mice was virtually indistinguishable from that of 4-month-old wild-type or Sam68−/− mice. Sam68−/− bone marrow stromal cells had a differentiation advantage for the osteogenic pathway. Moreover, the knockdown of Sam68 using short hairpin RNA in the embryonic mesenchymal multipotential progenitor C3H10T1/2 cells resulted in more pronounced expression of the mature osteoblast marker osteocalcin when differentiation was induced with bone morphogenetic protein-2. Cultures of mouse embryo fibroblasts generated from Sam68+/+ and Sam68−/− littermates were induced to differentiate into adipocytes with culture medium containing pioglitazone and the Sam68−/− mouse embryo fibroblasts shown to have impaired adipocyte differentiation. Furthermore, in vivo it was shown that sections of bone from 12-month-old Sam68−/− mice had few marrow adipocytes compared with their age-matched wild-type littermate controls, which exhibited fatty bone marrow. Our findings identify endogenous Sam68 as a positive regulator of adipocyte differentiation and a negative regulator of osteoblast differentiation, which is consistent with Sam68 being a modulator of bone marrow mesenchymal cell differentiation, and hence bone metabolism, in aged mice. PMID:16362077

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers.

PubMed

Zhao, Jun; Wang, Qiuming; Liang, Guizhao; Zheng, Jie

2011-12-20

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface. © 2011 American Chemical Society

Resilience as positive coping appraisals: Testing the schematic appraisals model of suicide (SAMS).

PubMed

Johnson, J; Gooding, P A; Wood, A M; Tarrier, N

2010-03-01

The Schematic Appraisals Model of Suicide (SAMS) suggests that positive self-appraisals may be important for buffering suicidal thoughts and behaviours, potentially providing a key source of resilience. The current study aimed to explore whether positive self-appraisals buffered individuals from suicidality in the face of stressful life events. 78 participants who reported experiencing some degree of suicidality were recruited from a student population. They completed a battery of questionnaires including measures of suicidality, stressful life events and positive self-appraisals. Positive self-appraisals moderated the association between stressful life events and suicidality. For those reporting moderate or high levels of positive self-appraisals, raised incidence of stressful life events did not lead to increases in suicidality. These results support the SAMS framework, and suggest that positive self-appraisals may confer resilience to suicide. Positive self-appraisals may be a promising avenue for further resilience research, and an important area to target for suicide interventions. 2009 Elsevier Ltd. All rights reserved.

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells

PubMed Central

Wang, Yan; Sun, ZhongSheng; Szyf, Moshe

2017-01-01

S-adenosyl methionine (SAM) is a ubiquitous methyl donor that was reported to have chemo- protective activity against liver cancer, however the molecular footprint of SAM is unknown. We show here that SAM selectively inhibits growth, transformation and invasiveness of hepatocellular carcinoma cell lines but not normal primary liver cells. Analysis of the transcriptome of SAM treated and untreated liver cancer cell lines HepG2 and SKhep1 and primary liver cells reveals pathways involved in cancer and metastasis that are upregulated in cancer cells and are downregulated by SAM. Analysis of the methylome using bisulfite mapping of captured promoters and enhancers reveals that SAM hyper-methylates and downregulates genes in pathways of growth and metastasis that are upregulated in liver cancer cells. Depletion of two SAM downregulated genes STMN1 and TAF15 reduces cellular transformation and invasiveness, providing evidence that SAM targets are genes important for cancer growth and invasiveness. Taken together these data provide a molecular rationale for SAM as an anticancer agent. PMID:29340097

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells.

PubMed

Wang, Yan; Sun, ZhongSheng; Szyf, Moshe

2017-12-19

S-adenosyl methionine (SAM) is a ubiquitous methyl donor that was reported to have chemo- protective activity against liver cancer, however the molecular footprint of SAM is unknown. We show here that SAM selectively inhibits growth, transformation and invasiveness of hepatocellular carcinoma cell lines but not normal primary liver cells. Analysis of the transcriptome of SAM treated and untreated liver cancer cell lines HepG2 and SKhep1 and primary liver cells reveals pathways involved in cancer and metastasis that are upregulated in cancer cells and are downregulated by SAM. Analysis of the methylome using bisulfite mapping of captured promoters and enhancers reveals that SAM hyper-methylates and downregulates genes in pathways of growth and metastasis that are upregulated in liver cancer cells. Depletion of two SAM downregulated genes STMN1 and TAF15 reduces cellular transformation and invasiveness, providing evidence that SAM targets are genes important for cancer growth and invasiveness. Taken together these data provide a molecular rationale for SAM as an anticancer agent.

In Situ Analysis of Mars Soil and Rocks Sample with the Sam Gcms Instrumentation Onboard Curiosity : Interpretation and Comparison of Measurements Done during the First Martian Year of Curiosity on Mars

NASA Astrophysics Data System (ADS)

Szopa, C.; Coll, P. J.; Cabane, M.; Buch, A.; Coscia, D.; Millan, M.; Francois, P.; Belmahadi, I.; Teinturier, S.; Navarro-Gonzalez, R.; Glavin, D. P.; Freissinet, C.; Steele, A.; Eigenbrode, J. L.; Mahaffy, P. R.

2014-12-01

The characterisation of the chemical and mineralogical composition of solid surface samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Amongst the SAM suite of instruments [1], SAM-GC (Gas Chromatograph) is devoted to identify and quantify volatiles evolved from the thermal (heating up to about 900°C)/chemical (derivatization procedure) treatment of any soil sample collected by the Curiosity rover. With the aim to search for potential organic molecules outgassed from the samples, SAM-GC analytical channels composed of thermal-desorption injector, and a MXT-CLP or a MXT-Q chromatographic column was chosen to achieve all the measurements done up today, with the aim to separate of a wide range of volatile inorganic and organic molecules. Four solid samples have been analyzed with GCMS, one sand sample collected at the Rocknest site, two rock samples (John Klein and Cumberland respectively) collected at the Yellowknife Bay site using the Curiosity driller, and one rock sample collected at the Kimberly site. All the measurements were successful and they produced complex chromatograms with both detectors used for SAM GC, i.e. a thermal conductivity detector and the SAM quandrupole mass spectrometer. Their interpretation already revealed the presence of an oxychlorine phase present in the sample which is at the origin of chlorohydrocarbons clearly identified [2] but this represents only a fraction of the GCMS signal recorded [3,4]. This work presents a systematic comparison of the GCMS measurements done for the different samples collected, supported by reference data obtained in laboratory with different spare models of the gas chromatograph, with the aim to bring new elements of interpretation of the SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013), Science, [4] Ming D. et al. (2013), Science, 32, 64-67. Acknowledgements: SAM-GC team acknowledges support from the French Space Agency (CNES), French National Programme of Planetology (PNP), National French Council (CNRS), Pierre Simon Laplace Institute, Institut Universitaire de France (IUF) and ESEP Labex, and the great MSL team

The use of alkanethiol self-assembled monolayers on 316L stainless steel for coronary artery stent nanomedicine applications: an oxidative and in vitro stability study.

PubMed

Mahapatro, Anil; Johnson, Dave M; Patel, Devang N; Feldman, Marc D; Ayon, Arturo A; Agrawal, C Mauli

2006-09-01

The use of self-assembled monolayers (SAMs) on medical devices offers a methodology for the incorporation of nanotechnology into medicine. SAMs are highly ordered nanosized molecular coatings, adding 1 to 10 nm thickness to a surface. This work is part of an overall goal to deliver therapeutic drugs from the surface of metal coronary stents using SAMs. In this study the oxidative and in vitro stability of functional alkylthiol SAMs on 316L stainless steel (SS) has been demonstrated. SAMs of 11-mercaptoundecanoic acid (-COOH SAM) and 11-mercapto-1-undecanol (-OH SAM) were formed on 316L SS. X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and contact angle (CA) measurements collectively confirmed the formation of functional alkylthiol SAMs on 316L SS. Well-formed SAMs (CA: 82 deg +/- 9 deg) were achieved within 48 hours of immersion in ethanolic solutions, after which no significant improvement in CA was observed. The ratio of the thiolate peak (163.5 eV) to the oxidized sulfur (sulfonates) peak (166.5 eV) gives us an indication of the percentage SAMs that would bind to the metal and serve as a drug reservoir in vivo; which in turn represents the stability and viability of these SAMs, keeping in mind the cardiovascular application under consideration. Oxidative and in vitro stability studies showed that alkanethiol SAMs oxidized completely within 14 days. The SAMs tend to desorb and leave the metal surface after longer time periods (21 days) in phosphate-buffered saline (PBS) immersion, whereas for oxidative exposure the SAMs continue to remain on the metal surface in the form of sulfonates. Although the chemistry of bonding of alkylthiol with the 316L SS is not well understood, the nanosized alkylthiol SAMs demonstrate sufficient stability to justify further study on these systems for potential in vivo drug delivery in the chosen coronary artery stent applications.

78 FR 80369 - Federal Acquisition Regulation; Service Contracts Reporting Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-31

...-and- materials, and labor-hour contracts and orders above the simplified acquisition threshold (SAT... thresholds established in FAR 4.1703 (e.g., above the SAT for cost-reimbursement, time-and-materials, and... reporting will be made at www.sam.gov (See section 3.10 of the SAM User Guide at https://www.sam.gov/sam/SAM...

Unanticipated coordination of tris buffer to the Radical SAM cluster of the RimO methylthiotransferase.

PubMed

Molle, Thibaut; Clémancey, Martin; Latour, Jean-Marc; Kathirvelu, Velavan; Sicoli, Giuseppe; Forouhar, Farhad; Mulliez, Etienne; Gambarelli, Serge; Atta, Mohamed

2016-07-01

Radical SAM enzymes generally contain a [4Fe-4S](2+/1+) (RS cluster) cluster bound to the protein via the three cysteines of a canonical motif CxxxCxxC. The non-cysteinyl iron is used to coordinate SAM via its amino-carboxylate moiety. The coordination-induced proximity between the cluster acting as an electron donor and the adenosyl-sulfonium bond of SAM allows for the homolytic cleavage of the latter leading to the formation of the reactive 5'-deoxyadenosyl radical used for substrate activation. Most of the structures of Radical SAM enzymes have been obtained in the presence of SAM, and therefore, little is known about the situation when SAM is not present. In this report, we show that RimO, a methylthiotransferase belonging to the radical SAM superfamily, binds a Tris molecule in the absence of SAM leading to specific spectroscopic signatures both in Mössbauer and pulsed EPR spectroscopies. These data provide a cautionary note for researchers who work with coordinative unsaturated iron sulfur clusters.

Measuring Sulfur Isotope Ratios from Solid Samples with the Sample Analysis at Mars Instrument and the Effects of Dead Time Corrections

NASA Technical Reports Server (NTRS)

Franz, H. B.; Mahaffy, P. R.; Kasprzak, W.; Lyness, E.; Raaen, E.

2011-01-01

The Sample Analysis at Mars (SAM) instrument suite comprises the largest science payload on the Mars Science Laboratory (MSL) "Curiosity" rover. SAM will perform chemical and isotopic analysis of volatile compounds from atmospheric and solid samples to address questions pertaining to habitability and geochemical processes on Mars. Sulfur is a key element of interest in this regard, as sulfur compounds have been detected on the Martian surface by both in situ and remote sensing techniques. Their chemical and isotopic composition can belp constrain environmental conditions and mechanisms at the time of formation. A previous study examined the capability of the SAM quadrupole mass spectrometer (QMS) to determine sulfur isotope ratios of SO2 gas from a statistical perspective. Here we discuss the development of a method for determining sulfur isotope ratios with the QMS by sampling SO2 generated from heating of solid sulfate samples in SAM's pyrolysis oven. This analysis, which was performed with the SAM breadboard system, also required development of a novel treatment of the QMS dead time to accommodate the characteristics of an aging detector.

Surface force and vibrational spectroscopic analyses of interfacial water molecules in the vicinity of methoxy-tri(ethylene glycol)-terminated monolayers: mechanisms underlying the effect of lateral packing density on bioinertness.

PubMed

Sekine, Taito; Asatyas, Syifa; Sato, Chikako; Morita, Shigeaki; Tanaka, Masaru; Hayashi, Tomohiro

Unequivocal dependence of bioinertness of self-assembled monolayers of methoxy-tri(ethylene glycol)-terminated alkanethiol (EG3-OMe SAMs) on their packing density has been a mystery for more than two decades. We tackled this long-standing question by performing surface force and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements. Our surface force measurements revealed a physical barrier of interfacial water in the vicinity of the Au-supported EG3-OMe SAM (low packing density), whereas the Ag-supported one (high packing density) did not possess such interfacial water. In addition, the results of SEIRA measurements clearly exhibited that hydrogen bonding states of the interfacial water differ depending on the substrates. We also characterized the bioinertness of these SAMs by protein adsorption tests and adhesion assays of platelet and human umbilical vein endothelial cells. The hydrogen bonding states of the interfacial water and water-induced interaction clearly correlated with the bioinertness of the SAMs, suggesting that the interfacial water plays an important role determining the interaction of the SAMs with biomolecules and cells.

Self-Assembled Monolayers of Dithiophosphinic Acids on Gold

NASA Astrophysics Data System (ADS)

San Juan, Ronan Roca

This dissertation reports the synthesis of derivatives of dithiophosphinic acids (R1R2DTPAs), and the formation and characterization of DTPA SAMs on gold to build a knowledge base on their nature of binding, organization of the alkyl chains and electrochemical barrier properties. The binding of DTPA molecules on gold depends on the morphology of the gold film: They bind in a mixed monodentate and bidentate modes on standard as-deposited (As-Dep) gold, while they fully chelate on smoother template-stripped (TS) gold. Chapter 2 focuses on van der Waals interactions of various alkyl chain lengths of symmetrical R2DTPA SAMs, which increase with increasing chain lengths similar to those of the analogous n-alkanethiol SAMs, but with alkyl chains that are generally less dense than those of n-alkanethiol SAMs. Chapter 3 addresses why the DTPA compounds do not chelate on the standard As-Dep gold by comparing (C16)2DTPA SAM to (C16 )2DDP SAM. Here, side chain crystallinity stabilizes DTPA SAM structure at the expense of chelation of the DTPA molecules, which leads to a mixture of bidentate and monodentate DTPA molecules, whereas the increased flexibility of the chains in DDP due to the oxygen atoms retains chelation of the DDP molecules. Chapter 4 focuses on the SAMs formed from RlongRshort DTPAs, which shows that the length of the short chain spacer affects SAM packing density and thickness. The SAMs of these molecules also show homogeneous mixing of Rlong and Rshort chains. Chapter 5 investigates PhRDTPA SAMs in preparation for molecular junction studies. The chelation of PhRDTPA molecules on TS gold allows the PhRDTPAs to act as molecular alligator clips. The length of the alkyl chains controls the density of the phenyl group and they fill in the voids between adsorbates to prevent electrical shorting. Finally, Chapter 6 incorporates OH tail group(s) to control the wettability of DTPA SAMs. The presence of OH groups in DTPAs forms hydrophilic SAMs. The symmetrical OH-terminated DTPA forms a SAM with similar packing density to that of an analogous CH3-terminated DTPA SAM, while the OH/CH 3-terminated DTPA forms a thin SAM with low molecular packing, however, the chains of this SAM are homogeneously mixed.

Impacts of Atmosphere-Ocean Coupling on Southern Hemisphere Climate Change

NASA Technical Reports Server (NTRS)

Li, Feng; Newman, Paul; Pawson, Steven

2013-01-01

Climate in the Southern Hemisphere (SH) has undergone significant changes in recent decades. These changes are closely linked to the shift of the Southern Annular Mode (SAM) towards its positive polarity, which is driven primarily by Antarctic ozone depletion. There is growing evidence that Antarctic ozone depletion has significant impacts on Southern Ocean circulation change. However, it is poorly understood whether and how ocean feedback might impact the SAM and climate change in the SH atmosphere. This outstanding science question is investigated using the Goddard Earth Observing System Coupled Atmosphere-Ocean-Chemistry Climate Model(GEOS-AOCCM).We perform ensemble simulations of the recent past (1960-2010) with and without the interactive ocean. For simulations without the interactive ocean, we use sea surface temperatures and sea ice concentrations produced by the interactive ocean simulations. The differences between these two ensemble simulations quantify the effects of atmosphere-ocean coupling. We will investigate the impacts of atmosphere-ocean coupling on stratospheric processes such as Antarctic ozone depletion and Antarctic polar vortex breakup. We will address whether ocean feedback affects Rossby wave generation in the troposphere and wave propagation into the stratosphere. Another focuson this study is to assess how ocean feedback might affect the tropospheric SAM response to Antarctic ozone depletion

A microchip fabricated with a vapor-diffusion self-assembled-monolayer method to transport droplets across superhydrophobic to hydrophilic surfaces.

PubMed

Lai, Yu-Hsuan; Yang, Jing-Tang; Shieh, Dar-Bin

2010-02-21

A wettability gradient to transport a droplet across superhydrophobic to hydrophilic surfaces is fabricated on combining a structure gradient and a self-assembled-monolayer (SAM) gradient. The combination of these two gradients is realized with a simple but versatile SAM technique, in which the textured silicon wafer strip is placed vertically in a bottle that contains a decyltrichlorosilane solution to form concurrently a saturated SAM below the liquid surface and a wettability gradient above. The platform fabricated in this way has a water-contact angle from 151.2 degrees to 39.7 degrees; the self-transport distance is hence increased significantly to about 9 mm. A theoretical model that approximates the shape of a moving drop to a spheroidal cap is developed to predict the self-transport behavior. Satisfactory agreement is shown for most regions except where the hysteresis effect is unmeasurable and an unsymmetrical deformation occurs. A double-directional gradient surface to alter the direction of movement of a droplet is also realized. The platforms we developed serve not only to transport a fluid over a long distance but also for a broad spectrum of biomedical applications such as protein adsorption, cell adhesion and DNA-based biosensors.

Integrating Dimensional and Discrete Theories of Emotions: A New Set of Anger- and Fear-Eliciting Stimuli for Children.

PubMed

Scaini, Simona; Rancoita, Paola M V; Martoni, Riccardo M; Omero, Micol; Ogliari, Anna; Brombin, Chiara

2017-01-01

The selection of appropriate stimuli for inducing specific emotional states has become one of the most challenging topics in psychological research. In the literature there is a lack of affective picture database specifically suited to investigate emotional response in children. Here the authors present the methodology that led us to create a new database (called Anger- and Fear-Eliciting Stimuli for Children) of affective stimuli inducing experiences of 3 target emotions (neutral, anger, and fear) to use in experimental session involving children. A total of 84 children were asked to (a) indicate the perceived emotion and its intensity and (b) rate the three affective dimensions of the Self-Assessment Manikin (SAM). Based on concordance between labeled and expected target emotion, the authors decided to select 15 stimuli to be included in Multivariate modeling techniques were applied to evaluate the association between expected target emotion and SAM ratings. The authors found that the hit rate for the neutral pictures was good (greater than 81%), for fear-eliciting pictures it was greater than 64%, and for anger-eliciting pictures it was moderate (between 45% and 56%). The study results reveal also an age effect only in the arousal scale. However, the authors did not find significant gender-related differences in SAM ratings.

Impact of hydrophilic and hydrophobic functionalization of flat TiO2/Ti surfaces on proteins adsorption

NASA Astrophysics Data System (ADS)

Fabre, Héloïse; Mercier, Dimitri; Galtayries, Anouk; Portet, David; Delorme, Nicolas; Bardeau, Jean-François

2018-02-01

Controlling adsorption of proteins onto medical devices is a key issue for implant-related infections. As self-assembled monolayers (SAMs) on titanium oxide represent a good model to study the surface-protein interactions, TiO2 surface properties were modified by grafting bisphosphonate molecules terminated with hydrophilic poly(ethylene glycol) groups and hydrophobic perfluoropolyether ones, respectively. Characterisation of the surface chemistry and surface topography of the modified surfaces was performed using XPS and atomic force microscopy (AFM). Quartz-crystal microbalance with dissipation (QCM-D) was used to determine the mass of adsorbed proteins as well as its kinetics. Poly(ethylene glycol)-terminated SAMs were the most effective surfaces to limit the adsorption of both BSA and fibrinogen in comparison to perfluorinated-terminated SAMs and non-modified TiO2 surfaces, as expected. The adsorption was not reversible in the case of BSA, while a partial reversibility was observed with Fg, most probably due to multilayers of proteins. The grafted surfaces adsorbed about the same quantity of proteins in terms of molecules per surface area, most probably in monolayer or island-like groups of adsorbed proteins. The adsorption on pristine TiO2 reveals a more important, non-specific adsorption of proteins.

Serum S-adenosylmethionine, but not methionine, increases in response to overfeeding in humans.

PubMed

Elshorbagy, A K; Jernerén, F; Samocha-Bonet, D; Refsum, H; Heilbronn, L K

2016-01-25

Plasma concentration of the methyl donor S-adenosylmethionine (SAM) is linearly associated with body mass index (BMI) and fat mass. As SAM is a high-energy compound and a sensor of cellular nutrient status, we hypothesized that SAM would increase with overfeeding. Forty normal to overweight men and women were overfed by 1250 kcal per day for 28 days. Serum SAM increased from 106 to 130 nmol/l (P=0.006). In stratified analysis, only those with weight gain above the median (high-weight gainers; average weight gain 3.9±0.3 kg) had increased SAM (+42%, P=0.001), whereas low-weight gainers (weight gain 1.5±0.2 kg) did not (Pinteraction=0.018). Overfeeding did not alter serum concentrations of the SAM precursor, methionine or the products, S-adenosyl-homocysteine and homocysteine. The SAM/SAH (S-adenosylhomocysteine) ratio was unchanged in the total population, but increased in high-weight gainers (+52%, P=0.006, Pinteraction =0.005). Change in SAM correlated positively with change in weight (r=0.33, P=0.041) and fat mass (r=0.44, P=0.009), but not with change in protein intake or plasma methionine, glucose, insulin or low-density lipoprotein (LDL)-cholesterol. Overfeeding raised serum SAM in proportion to the fat mass gained. The increase in SAM may help stabilize methionine levels, and denotes a responsiveness of SAM to nutrient state in humans. The role of SAM in human energy metabolism deserves further attention.

Development of a Reduced-Order Three-Dimensional Flow Model for Thermal Mixing and Stratification Simulation during Reactor Transients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Rui

2017-09-03

Mixing, thermal-stratification, and mass transport phenomena in large pools or enclosures play major roles for the safety of reactor systems. Depending on the fidelity requirement and computational resources, various modeling methods, from the 0-D perfect mixing model to 3-D Computational Fluid Dynamics (CFD) models, are available. Each is associated with its own advantages and shortcomings. It is very desirable to develop an advanced and efficient thermal mixing and stratification modeling capability embedded in a modern system analysis code to improve the accuracy of reactor safety analyses and to reduce modeling uncertainties. An advanced system analysis tool, SAM, is being developedmore » at Argonne National Laboratory for advanced non-LWR reactor safety analysis. While SAM is being developed as a system-level modeling and simulation tool, a reduced-order three-dimensional module is under development to model the multi-dimensional flow and thermal mixing and stratification in large enclosures of reactor systems. This paper provides an overview of the three-dimensional finite element flow model in SAM, including the governing equations, stabilization scheme, and solution methods. Additionally, several verification and validation tests are presented, including lid-driven cavity flow, natural convection inside a cavity, laminar flow in a channel of parallel plates. Based on the comparisons with the analytical solutions and experimental results, it is demonstrated that the developed 3-D fluid model can perform very well for a wide range of flow problems.« less

Acceptance of the Samuel Epstein Medal and Science Innovation Award by James Farquhar

NASA Astrophysics Data System (ADS)

Farquhar, James

2015-06-01

Thank you Mark for your kind introduction. I am deeply honored to receive this award and to be here to honor the memory of Sam Epstein. If I think back to my time as a graduate student, I remember reading many articles by Sam Epstein and those who worked with him. What I saw was an incredible breadth of applications and a willingness to let the science guide and to address all sorts of questions - questions that extend from understanding animals, plants, the oceans, partitioning at high temperature, fluids in the crust, nebular chemistry, the list goes on and on and on. As a graduate student I struggled and did my best to hang on, but I had dreams of being able to do science following a model specifically like the one he saw Sam had pursued. I had one time to meet Sam and speak with him, and I saw curiosity, decency, and an interested positive outlook that I imagine was part of what led to his enormous impact on the field.

Optimized Model Surfaces for Advanced Atomic Force Microscopy Studies of Surface Nanobubbles.

PubMed

Song, Bo; Zhou, Yi; Schönherr, Holger

2016-11-01

The formation of self-assembled monolayers (SAMs) of binary mixtures of 16-mercaptohexadecanoic acid (MHDA) and 1-octadecanethiol (ODT) on ultraflat template-stripped gold (TSG) surfaces was systematically investigated to clarify the assembly behavior, composition, and degree of possible phase segregation in light of atomic force microscopy (AFM) studies of surface nanobubbles on these substrates. The data for SAMs on TSG were compared to those obtained by adsorption on rough evaporated gold, as reported in a previous study. Quartz crystal microbalance and surface plasmon resonance data acquired in situ on TSG indicate that similar to SAM formation on conventional evaporated gold substrates ODT and MHDA form monolayers and bilayers, respectively. The second layer on MHDA, whose formation is attributed to hydrogen bonding, can be easily removed by adequate rinsing with water. The favorable agreement of the grazing incidence reflection Fourier transform infrared (GIR FTIR) spectroscopy and contact angle data analyzed with the Israelachvili-Gee model suggests that the binary SAMs do not segregate laterally. This conclusion is fully validated by high-resolution friction force AFM observations down to a length scale of 8-10 nm, which is much smaller than the typical observed surface nanobubble radii. Finally, correspondingly functionalized TSG substrates are shown to be valuable supports for studying surface nanobubbles by AFM in water and for addressing the relation between surface functionality and nanobubble formation and properties.

Lipid dip-pen nanolithography on self-assembled monolayers

NASA Astrophysics Data System (ADS)

Gavutis, Martynas; Navikas, Vytautas; Rakickas, Tomas; Vaitekonis, Šarūnas; Valiokas, Ramūnas

2016-02-01

Dip-pen nanolithography (DPN) with lipids as an ink enables functional micro/nanopatterning on different substrates at high process speeds. However, only a few studies have addressed the influence of the physicochemical properties of the surface on the structure and phase behavior of DPN-printed lipid assemblies. Therefore, by combining the scanning probe and optical imaging techniques in this work we have analyzed lipid microdomain formation on the self-assembled monolayers (SAMs) on gold as well-defined model surfaces that displayed hydrophilic (protein-repellent) or hydrophobic (protein-adhesive) characteristics. We have found that on the tri(ethylene glycol)-terminated SAM the lipid ink transfer was fast (~10-1 μm3 s-1), quasi-linear and it yielded unstable, sparsely packed lipid microspots. Contrary to this, on the methyl-terminated SAM the lipid transfer was ~20 times slower, nonlinear, and the obtained stable dots of ~1 μm in diameter consisted of lipid multilayers. Our comparative analysis indicated that the measured lipid transfer was consistent with the previously reported so-called polymer transfer model (Felts et al 2012, Nanotechnology 23 215301). Further on, by employing the observed distinct contrast in the DPN ink behavior we constructed confined lipid microdomains on pre-patterned SAMs, in which the lipids assembled either into monolayer or multilamellar phases. Such microdomains can be further utilized for lipid membrane mimetics in microarray and lab-on-a-chip device formats.

Galactic conformity measured in semi-analytic models

NASA Astrophysics Data System (ADS)

Lacerna, I.; Contreras, S.; González, R. E.; Padilla, N.; Gonzalez-Perez, V.

2018-03-01

We study the correlation between the specific star formation rate of central galaxies and neighbour galaxies, also known as `galactic conformity', out to 20 h^{-1} {Mpc} using three semi-analytic models (SAMs, one from L-GALAXIES and other two from GALFORM). The aim is to establish whether SAMs are able to show galactic conformity using different models and selection criteria. In all the models, when the selection of primary galaxies is based on an isolation criterion in real space, the mean fraction of quenched (Q) galaxies around Q primary galaxies is higher than that around star-forming primary galaxies of the same stellar mass. The overall signal of conformity decreases when we remove satellites selected as primary galaxies, but the effect is much stronger in GALFORM models compared with the L-GALAXIES model. We find this difference is partially explained by the fact that in GALFORM once a galaxy becomes a satellite remains as such, whereas satellites can become centrals at a later time in L-GALAXIES. The signal of conformity decreases down to 60 per cent in the L-GALAXIES model after removing central galaxies that were ejected from their host halo in the past. Galactic conformity is also influenced by primary galaxies at fixed stellar mass that reside in dark matter haloes of different masses. Finally, we explore a proxy of conformity between distinct haloes. In this case, the conformity is weak beyond ˜3 h^{-1} {Mpc} (<3 per cent in L-GALAXIES, <1-2 per cent in GALFORM models). Therefore, it seems difficult that conformity is directly related with a long-range effect.

A nano-patterned self assembled monolayer (SAM) rutile titania cancer chip for rapid, low cost, highly sensitive, direct cancer analysis in MALDI-MS.

PubMed

Manikandan, M; Gopal, Judy; Hasan, Nazim; Wu, Hui-Fen

2014-12-01

We developed a cancer chip by nano-patterning a highly sensitive SAM titanium surface capable of capturing and sensing concentrations as low as 10 cancer cells/mL from the environment by Matrix Assisted Laser Desorption and Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS). The current approach evades any form of pretreatment and sample preparation processes; it is time saving and does not require the (expensive) conventional MALDI target plate. The home made aluminium (Al) target holder cost, on which we loaded the cancer chips for MALDI-TOF MS analysis, is about 60 USD. While the conventional stainless steel MALDI target plate is more than 700 USD. The SAM surface was an effective platform leading to on-chip direct MALDI-MS detection of cancer cells. We compared the functionality of this chip with the unmodified titanium surfaces and thermally oxidized (TO) titanium surfaces. The lowest detectable concentration of the TO chip was 10(3) cells/mL, while the lowest detectable concentration of the control or unmodified titanium chips was 10(6) cells/mL. Compared to the control surface, the SAM cancer chip showed 100,000 times of enhanced sensitivity and compared with the TO chip, 1000 times of increased sensitivity. The high sensitivity of the SAM surfaces is attributed to the presence of the rutile SAM, surface roughness and surface wettability as confirmed by AFM, XRD, contact angle microscope and FE-SEM. This study opens a new avenue for the potent application of the SAM cancer chip for direct cancer diagnosis by MALDI-TOF MS in the near future. Copyright © 2014. Published by Elsevier B.V.

Frequencies of immune hypersensitivity reaction-associated HLA class I alleles in healthy South African Indian and mixed ancestry populations determined by a novel real-time PCR assay.

PubMed

Loubser, S; Paximadis, M; Gentle, N; Puren, A; Gray, C M; Tiemessen, C T

2014-10-01

We have determined the frequencies of human leucocyte antigen (HLA)-B*57:01, HLA-B*35:05, HLA-C*04 and HLA-C*08 in healthy individuals of South African Indian (SAI) ethnicity (n = 50) and South African mixed (SAM) ancestry (n = 50) using real-time allele-specific polymerase chain reaction (AS-PCR) assay. HLA-B*57:01 associates with immune hypersensitivity reaction (IHR) in individuals exposed to abacavir (ABC), while nevirapine (NVP) IHR associates with HLA-B*35:05, HLA-C*04 and HLA-C*08. Real-time AS-PCR assays typically use less DNA, are more cost-effective and rapid compared with conventional genotyping methods, such as sequence-based typing (SBT). The assay was developed using samples of known HLA class I genotype and subsequently applied to the SAI and SAM samples. HLA-B*57:01 was detected in SAM and SAI populations at frequencies of 8.0% and 12.0%, respectively, while HLA-B*35:05 was not found in SAI individuals, but was present in 6.0% of SAM individuals. HLA-C*04 was detected in 22.0% and 24.0% of SAM and SAI individuals, respectively, while 10.0% and 8.0% of SAM and SAI individuals, respectively, were HLA-C*08 positive. This study reports the development of a novel real-time AS-PCR assay to identify HLA class I alleles associated with ABC and NVP IHR and has established the frequencies of these alleles present in healthy SAI and SAM populations. Using South African demographic data, our hypothetical analysis suggests that a substantial number of individuals would benefit from the assay. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Selection and Characteristics of Fermented Salted Seafood (jeotgal)-Originated Strains with Excellent S-adenosyl-L-methionine (SAM) Production and Probiotics Efficacy.

PubMed

Kim, Min-Jeong; Park, Sunhyun; Lee, Ran-Sook; Lim, Sang-Dong; Kim, Hyo Jin; Lee, Myung-Ki

2014-01-01

This study is executed to develop probiotics which produce S-adenosyl-L-methionine (SAM), a methyl group donor of the 5-methyltetrahydrofolate methylation reaction within the animal cell. SAM is an essential substance for the synthesis, activation, and metabolism of hormones, neurotransmitters, nucleic acids, phospholipids, and cell membranes of animals. The SAM is also known as a nutritional supplement to improve brain functions of the human. In this study, the SAM-producing strains are identified in 18 types of salted fish, and then, the strains with excellent SAM productions are being identified, with 1 strain in the Enterococcus genus and 9 strains in the Bacillus genus. Strains with a large amount of SAM production include the lactic acid bacteria such as En. faecium and En. durans, En. sanguinicola, as well as various strains in the Bacil-lus genus. The SAM-overproducing strains show antibacterial activities with certain harmful microbes in addition to the weak acid resistances and strong bile resistances, indicating characteristics of probiotics. It is possible that the jeotgal-originated beneficial strains with overproducing SAM can be commercially utilized in order to manufacture SAM enriched foods.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Zhiwei; Walker, Amy V., E-mail: amy.walker@utdallas.edu

The room temperature atomic layerlike deposition (ALLD) of ZnS on functionalized self-assembled monolayers (SAMs) was investigated, using diethyl zinc (DEZ) and in situ generated H{sub 2}S as reactants. Depositions on SAMs with three different terminal groups, –CH{sub 3,} –OH, and –COOH, were studied. It was found that the reaction of DEZ with the SAM terminal group is critical in determining the film growth rate. Little or no deposition is observed on –CH{sub 3} terminated SAMs because DEZ does not react with the methyl terminal group. ZnS does deposit on both –OH and –COOH terminated SAMs, but the grow rate onmore » –COOH terminated SAMs is ∼10% lower per cycle than on –OH terminated SAMs. DEZ reacts with the hydroxyl group on –OH terminated SAMs, while on –COOH terminated SAMs it reacts with both the hydroxyl and carbonyl bonds of the terminal groups. The carbonyl reaction is found to lead to the formation of ketones rather than deposition of ZnS, lowering the growth rate on –COOH terminated SAMs. SIMS spectra show that both –OH and –COOH terminated SAMs are covered by the deposited ZnS layer after five ALLD cycles. In contrast to ZnO ALLD where the composition of the film differs for the first few layers on –COOH and –OH terminated SAMs, the deposited film composition is the same for both –COOH and –OH terminated SAMs. The deposited film is found to be Zn-rich, suggesting that the reaction of H{sub 2}S with the Zn-surface adduct may be incomplete.« less

77 FR 60496 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-03

... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-67938; File No. SR-CBOE-2012-093] Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and Immediate Effectiveness of a Proposed Rule Change Related to AIM, SAM, FLEX AIM, FLEX SAM and FLEX Electronic RFQs September 27, 2012. Pursuant to Section 19(b)(1)...

Enhanced flux of substrates into polyamine biosynthesis but not ethylene in tomato fruit engineered with yeast S-adenosylmethionine decarboxylase gene

Treesearch

Yi Lasanajak; Rakesh Minocha; Subhash C. Minocha; Ravinder Goyal; Tahira Fatima; Avtar K. Handa; Autar K. Mattoo

2014-01-01

S-adenosylmethionine (SAM), a major substrate in 1-C metabolism is a common precursor in the biosynthetic pathways of polyamines and ethylene, two important plant growth regulators, which exhibit opposing developmental effects, especially during fruit ripening. However, the flux of various substrates including SAM into the two competing pathways in...

Effects of Chromosomal Integration of the Vitreoscilla Hemoglobin Gene (vgb) and S-Adenosylmethionine Synthetase Gene (metK) on ε-Poly-L-Lysine Synthesis in Streptomyces albulus NK660.

PubMed

Gu, Yanyan; Wang, Xiaomeng; Yang, Chao; Geng, Weitao; Feng, Jun; Wang, Yuanyuan; Wang, Shufang; Song, Cunjiang

2016-04-01

ε-Poly-L-lysine (ε-PL) is a widely used natural food preservative. To test the effects of the Vitreoscilla hemoglobin (VHb) and S-adenosylmethionine (SAM) on ε-PL synthesis in Streptomyces albulus NK660, the heterologous VHb gene (vgb) and SAM synthetase gene (metK) were inserted into the S. albulus NK660 chromosome under the control of the constitutive ermE* promoter. CO-difference spectrum analysis showed S. albulus NK660-VHb strain could express functional VHb. S. albulus NK660-VHb produced 26.67 % higher ε-PL and 14.57 % higher biomass than the wild-type control, respectively. Reversed-phase high-pressure liquid chromatography (RP-HPLC) results showed the overexpression of the metK gene resulted in increased intracellular SAM synthesis in S. albulus NK660-SAM, which caused increases of biomass as well as the transcription level of ε-PL synthetase gene (pls). Results indicated that the expression of vgb and metK gene improved on ε-PL synthesis and biomass for S. albulus NK660, respectively.

SAM-CAAM: A Concept for Acquiring Systematic Aircraft Measurements to Characterize Aerosol Air Masses.

PubMed

Kahn, Ralph A; Berkoff, Tim A; Brock, Charles; Chen, Gao; Ferrare, Richard A; Ghan, Steven; Hansico, Thomas F; Hegg, Dean A; Martins, J Vanderlei; McNaughton, Cameron S; Murphy, Daniel M; Ogren, John A; Penner, Joyce E; Pilewskie, Peter; Seinfeld, John H; Worsnop, Douglas R

2017-10-01

A modest operational program of systematic aircraft measurements can resolve key satellite-aerosol-data-record limitations. Satellite observations provide frequent, global aerosol-amount maps, but offer only loose aerosol property constraints needed for climate and air quality applications. We define and illustrate the feasibility of flying an aircraft payload to measure key aerosol optical, microphysical, and chemical properties in situ . The flight program could characterize major aerosol air-mass types statistically, at a level-of-detail unobtainable from space. It would: (1) enhance satellite aerosol retrieval products with better climatology assumptions, and (2) improve translation between satellite-retrieved optical properties and species-specific aerosol mass and size simulated in climate models to assess aerosol forcing, its anthropogenic components, and other environmental impacts. As such, Systematic Aircraft Measurements to Characterize Aerosol Air Masses (SAM-CAAM) could add value to data records representing several decades of aerosol observations from space, improve aerosol constraints on climate modeling , help interrelate remote-sensing, in situ, and modeling aerosol-type definitions , and contribute to future satellite aerosol missions. Fifteen Required Variables are identified, and four Payload Options of increasing ambition are defined, to constrain these quantities. "Option C" could meet all the SAM-CAAM objectives with about 20 instruments, most of which have flown before, but never routinely several times per week, and never as a group. Aircraft integration, and approaches to data handling, payload support, and logistical considerations for a long-term, operational mission are discussed. SAM-CAAM is feasible because, for most aerosol sources and specified seasons, particle properties tend to be repeatable , even if aerosol loading varies.

Ectopic shoot meristem generation in monocotyledonous rpk1 mutants is linked to SAM loss and altered seedling morphology.

PubMed

Fiesselmann, Birgit S; Luichtl, Miriam; Yang, Xiaomeng; Matthes, Michaela; Peis, Ottilie; Torres-Ruiz, Ramon A

2015-07-07

In dicot Arabidopsis thaliana embryos two cotyledons develop largely autonomously from the shoot apical meristem (SAM). Recessive mutations in the Arabidopsis receptor-like kinase RPK1 lead to monocotyledonous seedlings, with low (10 %) penetrance due to complex functional redundancy. In strong rpk1 alleles, about 10 % of these (i. e. 1 % of all homozygotes) did not develop a SAM. We wondered whether RPK1 might also control SAM gene expression and SAM generation in addition to its known stochastic impact on cell division and PINFORMED1 (PIN1) polarity in the epidermis. SAM-less seedlings developed a simple morphology with a straight and continuous hypocotyl-cotyledon structure lacking a recognizable epicotyl. According to rpk1's auxin-related PIN1 defect, the seedlings displayed defects in the vascular tissue. Surprisingly, SAM-less seedlings variably expressed essential SAM specific genes along the hypocotyl-cotyledon structure up into the cotyledon lamina. Few were even capable of developing an ectopic shoot meristem (eSM) on top of the cotyledon. The results highlight the developmental autonomy of the SAM vs. cotyledons and suggest that the primary rpk1 defect does not lie in the seedling's ability to express SAM genes or to develop a shoot meristem. Rather, rpk1's known defects in cell division and auxin homeostasis, by disturbed PIN1 polarity, impact on SAM and organ generation. In early embryo stages this failure generates a simplified monocotyledonous morphology. Once generated, this likely entails a loss of positional information that in turn affects the spatiotemporal development of the SAM. SAM-bearing and SAM-less monocotyledonous phenotypes show morphological similarities either to real monocots or to dicot species, which only develop one cotyledon. The specific cotyledon defect in rpk1 mutants thus sheds light upon the developmental implications of the transition from two cotyledons to one.

Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch

PubMed Central

Lu, Changrui; Smith, Angela M; Ding, Fang; Chowdhury, Anirban; Henkin, Tina M; Ke, Ailong

2012-01-01

The SMK box (SAM-III) translational riboswitches were identified in S-adenosyl-L-methionine (SAM) synthetase metK genes in members of the Lactobacillales. This riboswitch switches between two alternative conformations in response to the intracellular SAM concentration and controls metK expression at the level of translation initiation. We previously reported the crystal structure of the SAM-bound SMK box riboswitch. In this study we combined SHAPE chemical probing with mutagenesis to probe the ligand-induced conformational switching mechanism. We revealed that while the majority of the apo SMK box RNA molecules exist in an alternatively base paired (ON) conformation, a subset of them pre-organize into a SAM-bound-like (READY) conformation, which upon SAM exposure is selectively stabilized into the SAM-bound (OFF) conformation through an induced-fit mechanism. Mutagenesis showed that the ON state is only slightly more stable than the READY state, as several single-nucleotide substitutions in a hypervariable region outside the SAM-binding core can alter the folding landscape to favor the READY state. Such SMK variants display a “constitutively-OFF” behavior both in vitro and in vivo. Time-resolved and temperature-dependent SHAPE analyses revealed adaptation of the SMK box RNA to its mesothermal working environment. The latter analysis revealed that the SAM-bound SMK box RNA follows a two-step folding/unfolding process. PMID:21549712

Seasonally different carbon flux changes in the Southern Ocean in response to the southern annular mode.

PubMed

Hauck, J; Völker, C; Wang, T; Hoppema, M; Losch, M; Wolf-Gladrow, D A

2013-12-01

Stratospheric ozone depletion and emission of greenhouse gases lead to a trend of the southern annular mode (SAM) toward its high-index polarity. The positive phase of the SAM is characterized by stronger than usual westerly winds that induce changes in the physical carbon transport. Changes in the natural carbon budget of the upper 100 m of the Southern Ocean in response to a positive SAM phase are explored with a coupled ecosystem-general circulation model and regression analysis. Previously overlooked processes that are important for the upper ocean carbon budget during a positive SAM period are identified, namely, export production and downward transport of carbon north of the polar front (PF) as large as the upwelling in the south. The limiting micronutrient iron is brought into the surface layer by upwelling and stimulates phytoplankton growth and export production but only in summer. This leads to a drawdown of carbon and less summertime outgassing (or more uptake) of natural CO 2 . In winter, biological mechanisms are inactive, and the surface ocean equilibrates with the atmosphere by releasing CO 2 . In the annual mean, the upper ocean region south of the PF loses more carbon by additional export production than by the release of CO 2 into the atmosphere, highlighting the role of the biological carbon pump in response to a positive SAM event.

Summary Status of the Space Acceleration Measurement System (SAMS), September 1993

NASA Technical Reports Server (NTRS)

DeLombard, Richard

1993-01-01

The Space Acceleration Measurement System (SAMS) was developed to measure the microgravity acceleration environment to which NASA science payloads are exposed during microgravity science missions on the shuttle. Six flight units have been fabricated to date. The inaugural flight of a SAMS unit was on STS-40 in June 1991 as part of the flrst Spacelab Life Sciences mission. Since that time, SAMS has flown on six additional missions and gathered 18 gigabytes of data representing 68 days of microgravity environment. The SAMS units have been flown in the shuttle middeck and cargo bay, in the Spacelab module, and in the Spacehab module. This paper summarizes the missions and experiments which SAMS has supported. The quantity of data and the utilization of the SAMS data is described. Future activities are briefly described for the SAMS project and.the Microgravity Measurement and Analysis Project (MMAP) to support science experiments and scientists with microgravity environment measurement and analysis.

Segment Alignment Maintenance System for the Hobby-Eberly Telescope

NASA Technical Reports Server (NTRS)

Rakoczy, John; Burdine, Robert (Technical Monitor)

2001-01-01

NASA's Marshall Space Flight Center, in collaboration with Blue Line Engineering of Colorado Springs, Colorado, is developing a Segment Alignment Maintenance System (SAMS) for McDonald Observatory's Hobby-Eberly Telescope (HET). The SAMS shall sense motions of the 91 primary mirror segments and send corrections to HET's primary mirror controller as the mirror segments misalign due to thermo -elastic deformations of the mirror support structure. The SAMS consists of inductive edge sensors. All measurements are sent to the SAMS computer where mirror motion corrections are calculated. In October 2000, a prototype SAMS was installed on a seven-segment cluster of the HET. Subsequent testing has shown that the SAMS concept and architecture are a viable practical approach to maintaining HET's primary mirror figure, or the figure of any large segmented telescope. This paper gives a functional description of the SAMS sub-array components and presents test data to characterize the performance of the subarray SAMS.

Best Practice in Developing Critical Analyses: An Empirical Study of Self-Efficacy from an Interdisciplinary Perspective

ERIC Educational Resources Information Center

Sams, Coleen; Sams, Doreen

2011-01-01

Despite substantial usage of case study analyses as learning tools in diverse fields of study, business graduate students often arrive with little to no prior knowledge in how to effectively use this tool. Using the Sams efficacy model (2009) strategic to business education this study identified a dearth in the usage of case study analyses in…

Jeffries Matusita-Spectral Angle Mapper (JM-SAM) spectral matching for species level mapping at Bhitarkanika, Muthupet and Pichavaram mangroves

NASA Astrophysics Data System (ADS)

Padma, S.; Sanjeevi, S.

2014-12-01

This paper proposes a novel hyperspectral matching algorithm by integrating the stochastic Jeffries-Matusita measure (JM) and the deterministic Spectral Angle Mapper (SAM), to accurately map the species and the associated landcover types of the mangroves of east coast of India using hyperspectral satellite images. The JM-SAM algorithm signifies the combination of a qualitative distance measure (JM) and a quantitative angle measure (SAM). The spectral capabilities of both the measures are orthogonally projected using the tangent and sine functions to result in the combined algorithm. The developed JM-SAM algorithm is implemented to discriminate the mangrove species and the landcover classes of Pichavaram (Tamil Nadu), Muthupet (Tamil Nadu) and Bhitarkanika (Odisha) mangrove forests along the Eastern Indian coast using the Hyperion image dat asets that contain 242 bands. The developed algorithm is extended in a supervised framework for accurate classification of the Hyperion image. The pixel-level matching performance of the developed algorithm is assessed by the Relative Spectral Discriminatory Probability (RSDPB) and Relative Spectral Discriminatory Entropy (RSDE) measures. From the values of RSDPB and RSDE, it is inferred that hybrid JM-SAM matching measure results in improved discriminability of the mangrove species and the associated landcover types than the individual SAM and JM algorithms. This performance is reflected in the classification accuracies of species and landcover map of Pichavaram mangrove ecosystem. Thus, the JM-SAM (TAN) matching algorithm yielded an accuracy better than SAM and JM measures at an average difference of 13.49 %, 7.21 % respectively, followed by JM-SAM (SIN) at 12.06%, 5.78% respectively. Similarly, in the case of Muthupet, JM-SAM (TAN) yielded an increased accuracy than SAM and JM measures at an average difference of 12.5 %, 9.72 % respectively, followed by JM-SAM (SIN) at 8.34 %, 5.55% respectively. For Bhitarkanika, the combined JM-SAM (TAN) and (SIN) measures improved the performance of individual SAM by (16.1 %, 15%) and of JM by (10.3%, 9.2%) respectively.

Revisiting the relationship between jet position, forced response, and annular mode variability in the southern midlatitudes

NASA Astrophysics Data System (ADS)

Simpson, Isla R.; Polvani, Lorenzo M.

2016-03-01

Climate models exhibit a wide range in latitudinal position of the Southern Hemisphere westerly jet. Previous work has demonstrated, in the annual mean, that models with lower latitude jets, exhibit greater poleward jet shifts under climate forcings. It has been argued that this behavior is due to stronger eddy/mean flow feedbacks in models with lower latitude jets, as inferred from the timescale of the Southern Annular Mode (SAM). Here we revisit this question with a focus on seasonality. Using a larger set of models and forcing scenarios from the Coupled Model Intercomparison Project, phase 5, we find that the jet position/jet shift relationship is strong in winter but insignificant in summer, whereas the model spread in SAM timescales arises primarily in summer, with winter timescales similar across models. The results, therefore, question previous interpretations and motivate an improved understanding of the spread in model behavior.

SAM/SAH Analogs as Versatile Tools for SAM-Dependent Methyltransferases.

PubMed

Zhang, Jing; Zheng, Yujun George

2016-03-18

S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.

Trends in malnutrition and mortality in Darfur, Sudan, between 2004 and 2008: a meta-analysis of publicly available surveys.

PubMed

Nielsen, Jens; Prudhon, Claudine; de Radigues, Xavier

2011-08-01

The humanitarian response to the crisis in Darfur is the largest humanitarian operation in the world. To investigate the evolution of the conditions of the affected population, we analysed trends in malnutrition and mortality, the most widely accepted indicators for assessing the degree of severity of a crisis. We did a meta-analysis of 164 publicly available surveys taking into account changes in the contextual situation and humanitarian aid; type of population [residents and internally displaced persons (IDPs)]; and seasonal variations. Data on global acute malnutrition (GAM), severe acute malnutrition (SAM), crude death rate (CDR) and under-five death rate (U5DR) were analysed using a random effect model. GAM and SAM decreased by 16% and 28%, respectively, in 2004-05, whereas CDR dropped by 44-75% per year depending on state and type of population and U5DR decreased by an overall 50% yearly. Both security and the humanitarian contexts became increasingly complex after 2005, but levels of malnutrition stabilized in North and South Darfur. In West Darfur, GAM remained stable but SAM tended to increase for IDPs, although mortality rates remained constant. Mortality increased slightly for residents in South Darfur after 2005, even though nutritional status was stable. GAM, SAM, CDR and U5DR fluctuated markedly with seasons. A meta-analysis of myriads of surveys permitted us to draw an overall picture of the situation in Darfur and to identify some of its influencing factors. The large humanitarian operation, which gained momentum through 2004-05, was able to contain the crisis despite huge difficulties, but did not compensate for seasonal variations. The situation has remained fragile with some negative patterns tending to emerge. It is crucial that the humanitarian situation continues to be closely monitored.

Mutation of the Salt Bridge-forming Residues in the ETV6-SAM Domain Interface Blocks ETV6-NTRK3-induced Cellular Transformation*

PubMed Central

Cetinbas, Naniye; Huang-Hobbs, Helen; Tognon, Cristina; Leprivier, Gabriel; An, Jianghong; McKinney, Steven; Bowden, Mary; Chow, Connie; Gleave, Martin; McIntosh, Lawrence P.; Sorensen, Poul H.

2013-01-01

The ETV6-NTRK3 (EN) chimeric oncogene is expressed in diverse tumor types. EN is generated by a t(12;15) translocation, which fuses the N-terminal SAM (sterile α-motif) domain of the ETV6 (or TEL) transcription factor to the C-terminal PTK (protein-tyrosine kinase) domain of the neurotrophin-3 receptor NTRK3. SAM domain-mediated polymerization of EN leads to constitutive activation of the PTK domain and constitutive signaling of the Ras-MAPK and PI3K-Akt pathways, which are essential for EN oncogenesis. Here we show through complementary biophysical and cellular biological techniques that mutation of Lys-99, which participates in a salt bridge at the SAM polymer interface, reduces self-association of the isolated SAM domain as well as high molecular mass complex formation of EN and abrogates the transformation activity of EN. We also show that mutation of Asp-101, the intermolecular salt bridge partner of Lys-99, similarly blocks transformation of NIH3T3 cells by EN, reduces EN tyrosine phosphorylation, inhibits Akt and Mek1/2 signaling downstream of EN, and abolishes tumor formation in nude mice. In contrast, mutations of Glu-100 and Arg-103, residues in the vicinity of the interdomain Lys-99–Asp-101 salt bridge, have little or no effect on these oncogenic characteristics of EN. Our results underscore the importance of specific electrostatic interactions for SAM polymerization and EN transformation. PMID:23798677

Mutation of the salt bridge-forming residues in the ETV6-SAM domain interface blocks ETV6-NTRK3-induced cellular transformation.

PubMed

Cetinbas, Naniye; Huang-Hobbs, Helen; Tognon, Cristina; Leprivier, Gabriel; An, Jianghong; McKinney, Steven; Bowden, Mary; Chow, Connie; Gleave, Martin; McIntosh, Lawrence P; Sorensen, Poul H

2013-09-27

The ETV6-NTRK3 (EN) chimeric oncogene is expressed in diverse tumor types. EN is generated by a t(12;15) translocation, which fuses the N-terminal SAM (sterile α-motif) domain of the ETV6 (or TEL) transcription factor to the C-terminal PTK (protein-tyrosine kinase) domain of the neurotrophin-3 receptor NTRK3. SAM domain-mediated polymerization of EN leads to constitutive activation of the PTK domain and constitutive signaling of the Ras-MAPK and PI3K-Akt pathways, which are essential for EN oncogenesis. Here we show through complementary biophysical and cellular biological techniques that mutation of Lys-99, which participates in a salt bridge at the SAM polymer interface, reduces self-association of the isolated SAM domain as well as high molecular mass complex formation of EN and abrogates the transformation activity of EN. We also show that mutation of Asp-101, the intermolecular salt bridge partner of Lys-99, similarly blocks transformation of NIH3T3 cells by EN, reduces EN tyrosine phosphorylation, inhibits Akt and Mek1/2 signaling downstream of EN, and abolishes tumor formation in nude mice. In contrast, mutations of Glu-100 and Arg-103, residues in the vicinity of the interdomain Lys-99-Asp-101 salt bridge, have little or no effect on these oncogenic characteristics of EN. Our results underscore the importance of specific electrostatic interactions for SAM polymerization and EN transformation.

Experimental and computational investigation of graphene/SAMs/n-Si Schottky diodes

NASA Astrophysics Data System (ADS)

Aydin, H.; Bacaksiz, C.; Yagmurcukardes, N.; Karakaya, C.; Mermer, O.; Can, M.; Senger, R. T.; Sahin, H.; Selamet, Y.

2018-01-01

We have investigated the effect of two different self-assembled monolayers (SAMs) on electrical characteristics of bilayer graphene (BLG)/n-Si Schottky diodes. Novel 4″bis(diphenylamino)-1, 1‧:3″-terphenyl-5‧ carboxylic acids (TPA) and 4,4-di-9H-carbazol-9-yl-1,1‧:3‧1‧-terphenyl-5‧ carboxylic acid (CAR) aromatic SAMs have been used to modify n-Si surfaces. Cyclic voltammetry (CV) and Kelvin probe force microscopy (KPFM) results have been evaluated to verify the modification of n-Si surface. The current-voltage (I-V) characteristics of bare and SAMs modified devices show rectification behaviour verifying a Schottky junction at the interface. The ideality factors (n) from ln(I)-V dependences were determined as 2.13, 1.96 and 2.07 for BLG/n-Si, BLG/TPA/n-Si and BLG/CAR/n-Si Schottky diodes, respectively. In addition, Schottky barrier height (SBH) and series resistance (Rs) of SAMs modified diodes were decreased compared to bare diode due to the formation of a compatible interface between graphene and Si as well as π-π interaction between aromatic SAMs and graphene. The CAR-based device exhibits better diode characteristic compared to the TPA-based device. Computational simulations show that the BLG/CAR system exhibits smaller energy-level-differences than the BLG/TPA, which supports the experimental findings of a lower Schottky barrier and series resistance in BLG/CAR diode.

Iron-Based Amorphous Coatings Produced by HVOF Thermal Spray Processing-Coating Structure and Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beardsley, M B

2008-03-26

The feasibility to coat large SNF/HLW containers with a structurally amorphous material (SAM) was demonstrated on sub-scale models fabricated from Type 316L stainless steel. The sub-scale model were coated with SAM 1651 material using kerosene high velocity oxygen fuel (HVOF) torch to thicknesses ranging from 1 mm to 2 mm. The process parameters such as standoff distance, oxygen flow, and kerosene flow, were optimized in order to improve the corrosion properties of the coatings. Testing in an electrochemical cell and long-term exposure to a salt spray environment were used to guide the selection of process parameters.

Readability, Suitability and Health Content Assessment of Cancer Screening Announcements in Municipal Newspapers in Japan.

PubMed

Okuhara, Tsuyoshi; Ishikawa, Hirono; Okada, Hiroko; Kiuchi, Takahiro

2015-01-01

The objective of this study was to assess the readability, suitability, and health content of cancer screening information in municipal newspapers in Japan. Suitability Assessment of Materials (SAM) and the framework of Health Belief Model (HBM) were used for assessment of municipal newspapers that were published in central Tokyo (23 wards) from January to December 2013. The mean domain SAM scores of content, literacy demand, and layout/typography were considered superior. The SAM scores of interaction with readers, an indication of the models of desirable actions, and elaboration to enhance readers' self-efficacy were low. According to the HBM coding, messages of medical/clinical severity, of social severity, of social benefits, and of barriers of fear were scarce. The articles were generally well written and suitable. However, learning stimulation/motivation was scarce and the HBM constructs were not fully addressed. Articles can be improved to motivate readers to obtain cancer screening by increasing interaction with readers, introducing models of desirable actions and devices to raise readers' self-efficacy, and providing statements of perceived barriers of fear for pain and time constraints, perceived severity, and social benefits and losses.

Noncanonical Radical SAM Enzyme Chemistry Learned from Diphthamide Biosynthesis.

PubMed

Dong, Min; Zhang, Yugang; Lin, Hening

2018-05-10

Radical S-adenosylmethionine (SAM) enzymes are a superfamily of enzymes that use SAM and reduced [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical to catalyze numerous challenging reactions. We have reported a type of noncanonical radical SAM enzymes in the diphthamide biosynthesis pathway. These enzymes also use SAM and reduced [4Fe-4S] clusters, but generate a 3-amino-3-carboxypropyl (ACP) radical to modify the substrate protein, translation elongation factor 2. The regioselective cleavage of a different C-S bond of the sulfonium center of SAM in these enzymes comparing to canonical radical SAM enzymes is intriguing. Here, we highlight some recent findings in the mechanism of these types of enzymes, showing that the diphthamide biosynthetic radial SAM enzymes bound SAM with a distinct geometry. In this way, the unique iron of the [4Fe-4S] cluster in the enzyme can only attack the carbon on the ACP group to form an organometallic intermediate. The homolysis of the organometallic intermediate releases the ACP radical and generates the EF2 radial.

Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism

PubMed Central

Lu, Changrui; Smith, Angela M; Fuchs, Ryan T; Ding, Fang; Rajashankar, Kanagalaghatta; Henkin, Tina M; Ke, Ailong

2011-01-01

Three distinct classes of S-adenosyl-l-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-Å crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti–Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-l-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions. PMID:18806797

Crystal structures of the SAM-III/S[subscript MK] riboswitch reveal the SAM-dependent translation inhibition mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, C.; Smith, A.M.; Fuchs, R.T.

2010-01-07

Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-{angstrom} crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti-Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions withmore » the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.« less

Transverse spin in the scattering of focused radially and azimuthally polarized vector beams

NASA Astrophysics Data System (ADS)

Singh, Ankit Kumar; Saha, Sudipta; Gupta, Subhasish Dutta; Ghosh, Nirmalya

2018-04-01

We study the effect of focusing of the radially and azimuthally polarized vector beams on the spin angular momentum (SAM) density and Poynting vector of scattered waves from a Mie particle. Remarkably, the study reveals that the SAM density of the scattered field is solely transverse in nature for radially and azimuthally polarized incident vector beams; however, the Poynting vector shows the usual longitudinal character. We also demonstrate that the transverse SAM density can further be tuned with wavelength and focusing of the incident beam by exploiting the interference of different scattering modes. These results may stimulate further experimental techniques to detect the transverse spin and Belinfante's spin-momentum densities.

Successful microscopic renal autotransplantation for left renal aneurysm associated with segmental arterial mediolysis.

PubMed

Yoshioka, Takashi; Araki, Motoo; Ariyoshi, Yuichi; Wada, Koichiro; Tanaka, Noriyuki; Nasu, Yasutomo

2017-07-01

Segmental arterial mediolysis (SAM) is an uncommon, nonarteriosclerotic vascular disease. SAM is characterized by lysis of arterial media and can lead to aneurysm formation. The renal arteries are the third most common arteries associated with SAM. We report the case of a 32-year-old man with left renal artery aneurysm associated with SAM. We successfully performed left renal autotransplantation using microscopic vascular reconstruction. SAM is characterized by vascular fragility; therefore, microscopic surgery is favorable for treating aneurysms associated with SAM. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

ER residency of the ceramide phosphoethanolamine synthase SMSr relies on homotypic oligomerization mediated by its SAM domain.

PubMed

Cabukusta, Birol; Kol, Matthijs; Kneller, Laura; Hilderink, Angelika; Bickert, Andreas; Mina, John G M; Korneev, Sergei; Holthuis, Joost C M

2017-01-25

SMSr/SAMD8 is an ER-resident ceramide phosphoethanolamine synthase with a critical role in controlling ER ceramides and suppressing ceramide-induced apoptosis in cultured cells. SMSr-mediated ceramide homeostasis relies on the enzyme's catalytic activity as well as on its N-terminal sterile α-motif or SAM domain. Here we report that SMSr-SAM is structurally and functionally related to the SAM domain of diacylglycerol kinase DGKδ, a central regulator of lipid signaling at the plasma membrane. Native gel electrophoresis indicates that both SAM domains form homotypic oligomers. Chemical crosslinking studies show that SMSr self-associates into ER-resident trimers and hexamers that resemble the helical oligomers formed by DGKδ-SAM. Residues critical for DGKδ-SAM oligomerization are conserved in SMSr-SAM and their substitution causes a dissociation of SMSr oligomers as well as a partial redistribution of the enzyme to the Golgi. Conversely, treatment of cells with curcumin, a drug disrupting ceramide and Ca 2+ homeostasis in the ER, stabilizes SMSr oligomers and promotes retention of the enzyme in the ER. Our data provide first demonstration of a multi-pass membrane protein that undergoes homotypic oligomerization via its SAM domain and indicate that SAM-mediated self-assembly of SMSr is required for efficient retention of the enzyme in the ER.

Experiments with a Regional Vector-Vorticity Model, and Comparison with Other Models

NASA Astrophysics Data System (ADS)

Konor, C. S.; Dazlich, D. A.; Jung, J.; Randall, D. A.

2017-12-01

The Vector-Vorticity Model (VVM) is an anelastic model with a unique dynamical core that predicts the three-dimensional vorticity instead of the three-dimensional momentum. The VVM is used in the CRMs of the Global Quasi-3D Multiscale Modeling Framework, which is discussed by Joon-Hee Jung and collaborators elsewhere in this session. We are updating the physics package of the VVM, replacing it with the physics package of the System for Atmosphere Modeling (SAM). The new physics package includes a double-moment microphysics, Mellor-Yamada turbulence, Monin-Obukov surface fluxes, and the RRTMG radiation parameterization. We briefly describe the VVM and show results from standard test cases, including TWP-ICE. We compare the results with those obtained using the earlier physics. We also show results from experiments on convection aggregation in radiative-convective equilibrium, and compare with those obtained using both SAM and the Regional Atmospheric Modeling System (RAMS).

Vapor-phase-processed fluorinated self-assembled monolayer for organic thin-film transistors

NASA Astrophysics Data System (ADS)

Roh, Jeongkyun; Lee, Changhee; Kwak, Jeonghun; Jung, Byung Jun; Kim, Hyeok

2015-09-01

A vapor-phase-processed fluorinated silazane self-assembled monolayer (SAM), 1,3-bis(trifluoropropyl)-1,1,3,3-tetramethyldisilazane (FPDS), was introduced as a surface modifier for pentacene-based organic thin-film transistors (OTFTs). A remarkable improvement in the field effect mobility from 0.25 cm2/Vs (without SAM-treatment) to 0.42 cm2/Vs (with FPDS-treatment) was observed, which was attributed to the better pentacene growth on a hydrophobic surface. A significant reduction in the contact resistance was also observed by FPDS treatment due to the improved bulk conductivity and diminished charge trapping at the gate dielectric surface by the SAM treatment. In addition, FPDS treatment efficiently improved the bias stability of the OTFTs; the drain-to-source current degradation by the bias stress was greatly reduced from 80% to 50% by FPDS treatment, and the characteristic time for charge trapping of the FPDS treated OTFTs was approximately one order of magnitude larger than that of the OTFTs without SAM treatment.

Systematic biochemical characterization of the SAM domains in Eph receptor family from Mus Musculus.

PubMed

Wang, Yue; Li, Qingxia; Zheng, Yunhua; Li, Gang; Liu, Wei

2016-05-13

The Eph receptor family is the largest subfamily of receptor tyrosine kinases and well-known for their pivotal roles in axon guidance, synaptogenesis, artery/venous differentiation and tumorigenesis, etc. Activation of the Eph receptor needs multimerization of the receptors. The intracellular C-terminal SAM domain of Eph receptor was reported to mediate self-association of Eph receptors via the homo SAM-SAM interaction. In this study, we systematically expressed and purified the SAM domain proteins of all fourteen Eph receptors of Mus musculus in Escherichia coli. The FPLC (fast protein liquid chromatography) results showed the recombinant SAM domains were highly homogeneous. Using CD (circular dichroism) spectrometry, we found that the secondary structure of all the SAM domains was typically alpha helical folded and remarkably similar. The thermo-stability tests showed that they were quite stable in solution. SEC-MALS (size exclusion chromatography coupled with multiple angle light scattering) results illustrated 200 μM Eph SAM domains behaved as good monomers in the size-exclusion chromatography. More importantly, DLS (dynamic light scattering) results revealed the overwhelming majority of SAM domains was not multimerized in solution either at 200 μM or 2000 μM protein concentration, which indicating the SAM domain alone was not sufficient to mediate the polymerization of Eph receptor. In summary, our studies provided the systematic biochemical characterizations of the Eph receptor SAM domains and implied their roles in Eph receptor mediated signaling pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.

PubMed

Kim, Jungwook; Xiao, Hui; Bonanno, Jeffrey B; Kalyanaraman, Chakrapani; Brown, Shoshana; Tang, Xiangying; Al-Obaidi, Nawar F; Patskovsky, Yury; Babbitt, Patricia C; Jacobson, Matthew P; Lee, Young-Sam; Almo, Steven C

2013-06-06

The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and regulatory mechanisms. We describe a new metabolite, carboxy-S-adenosyl-l-methionine (Cx-SAM), its biosynthetic pathway and its role in transfer RNA modification. The structure of CmoA, a member of the SAM-dependent methyltransferase superfamily, revealed a ligand consistent with Cx-SAM in the catalytic site. Mechanistic analyses showed an unprecedented role for prephenate as the carboxyl donor and the involvement of a unique ylide intermediate as the carboxyl acceptor in the CmoA-mediated conversion of SAM to Cx-SAM. A second member of the SAM-dependent methyltransferase superfamily, CmoB, recognizes Cx-SAM and acts as a carboxymethyltransferase to convert 5-hydroxyuridine into 5-oxyacetyl uridine at the wobble position of multiple tRNAs in Gram-negative bacteria, resulting in expanded codon-recognition properties. CmoA and CmoB represent the first documented synthase and transferase for Cx-SAM. These findings reveal new functional diversity in the SAM-dependent methyltransferase superfamily and expand the metabolic and biological contributions of SAM-based biochemistry. These discoveries highlight the value of structural genomics approaches in identifying ligands within the context of their physiologically relevant macromolecular binding partners, and in revealing their functions.

Progress & Frontiers in PV Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deline, Chris; DiOrio, Nick; Jordan, Dirk

2016-09-12

PowerPoint slides for a presentation given at Solar Power International 2016. Presentation includes System Advisor Model (SAM) introduction and battery modeling, bifacial PV modules and modeling, shade modeling and module level power electronics (MLPE), degradation rates, and PVWatts updates and validation.

Microdissection of Shoot Meristem Functional Domains

USDA-ARS?s Scientific Manuscript database

The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection–microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes th...

Benchmark Simulations of the Thermal-Hydraulic Responses during EBR-II Inherent Safety Tests using SAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Rui; Sumner, Tyler S.

2016-04-17

An advanced system analysis tool SAM is being developed for fast-running, improved-fidelity, and whole-plant transient analyses at Argonne National Laboratory under DOE-NE’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. As an important part of code development, companion validation activities are being conducted to ensure the performance and validity of the SAM code. This paper presents the benchmark simulations of two EBR-II tests, SHRT-45R and BOP-302R, whose data are available through the support of DOE-NE’s Advanced Reactor Technology (ART) program. The code predictions of major primary coolant system parameter are compared with the test results. Additionally, the SAS4A/SASSYS-1 code simulationmore » results are also included for a code-to-code comparison.« less

Fluorocarbon Contamination from the Drill on the Mars Science Laboratory: Potential Science Impact on Detecting Martian Organics by Sample Analysis at Mars (SAM)

NASA Technical Reports Server (NTRS)

Eigenbrode, J. L.; McAdam, A.; Franz, H.; Freissinet, C.; Bower, H.; Floyd, M.; Conrad, P.; Mahaffy, P.; Feldman, J.; Hurowitz, J.;

Synergistic Effects of SAM and Selenium Compounds on Proliferation, Migration and Adhesion of HeLa Cells.

PubMed

Sun, Licui; Zhang, Jianxin; Yang, Qiu; Si, Yang; Liu, Yiqun; Wang, Qin; Han, Feng; Huang, Zhenwu

2017-08-01

To determine the antitumor activities and molecular mechanism of selenium compounds in HeLa cells. Western blotting was used to detect ERK and AKT activation in HeLa cells induced by selenium compounds selenomethionine (SeMet), methylselenocysteine (MeSeCys) and methylseleninic acids (MeSeA). Using MTT, wound-healing and Matrigel adhesion assays, the antitumor effects of SAM and selenium compounds were evaluated in HeLa cells. MeSeA inhibited ERK and AKT signaling pathways and suppressed the proliferation (p<0.05 vs. HeLa control), migration (p<0.05 vs. HeLa control) and adhesion (p<0.01 vs. HeLa control) of HeLa cells. MeSeCys and SeMet inhibited AKT signaling pathways and the migration (p<0.05 vs. HeLa control) and adhesion (p<0.01 vs. HeLa control) of HeLa cells. The synergistic action of MeSeA with SAM led to a statistically significant inhibition of proliferation, migration and adhesion of HeLa cells. MeSeA, MeSeCys and SeMet exert different antitumor activities by inhibiting ERK and AKT signaling pathways. The combination of MeSeA and SAM exhibited better antitumor effects compared to the other treatments. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Summary Status of the Space Acceleration Measurement System (SAMS), September 1993

NASA Technical Reports Server (NTRS)

DeLombard, Richard

1994-01-01

The Space Acceleration Measurement System (SAMS) was developed to measure the microgravity acceleration environment to which NASA science payloads are exposed during microgravity science missions on the shuttle. Six flight units have been fabricated to date. The inaugural flight of a SAMS unit was on STS-40 in June 1991 as part of the First Spacelab Life Sciences mission. Since that time, SAMS has flown on six additional missions and gathered eighteen gigabytes of data representing sixty-eight days of microgravity environment. The SAMS units have been flown in the shuttle middeck and cargo bay, in the Spacelab module, and in the Spacehab module. This paper summarizes the missions and experiments which SAMS has supported. The quantity of data and the utilization of the SAMS data is described. Future activities are briefly described for the SAMS project and the Microgravity Measurement and Analysis project (MMAP) to support science experiments and scientists with microgravity environment measurement and analysis.

Structure-guided design of fluorescent S-adenosylmethionine analogs for a high-throughput screen to target SAM-I riboswitch RNAs.

PubMed

Hickey, Scott F; Hammond, Ming C

2014-03-20

Many classes of S-adenosylmethionine (SAM)-binding RNAs and proteins are of interest as potential drug targets in diverse therapeutic areas, from infectious diseases to cancer. In the former case, the SAM-I riboswitch is an attractive target because this structured RNA element is found only in bacterial mRNAs and regulates multiple genes in several human pathogens. Here, we describe the synthesis of stable and fluorescent analogs of SAM in which the fluorophore is introduced through a functionalizable linker to the ribose. A Cy5-labeled SAM analog was shown to bind several SAM-I riboswitches via in-line probing and fluorescence polarization assays, including one from Staphylococcus aureus that controls the expression of SAM synthetase in this organism. A fluorescent ligand displacement assay was developed and validated for high-throughput screening of compounds to target the SAM-I riboswitch class. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural analysis of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis.

PubMed

Park, Sun Cheol; Song, Wan Seok; Yoon, Sung-il

2014-04-18

S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) methylate diverse biological molecules using a SAM cofactor. The ytqB gene of Bacillus subtilis encodes a putative MTase and its biological function has never been characterized. To reveal the structural features and the cofactor binding mode of YtqB, we have determined the crystal structures of YtqB alone and in complex with its cofactor, SAM, at 1.9 Å and 2.2 Å resolutions, respectively. YtqB folds into a β-sheet sandwiched by two α-helical layers, and assembles into a dimeric form. Each YtqB monomer contains one SAM binding site, which shapes SAM into a slightly curved conformation and exposes the reactive methyl group of SAM potentially to a substrate. Our comparative structural analysis of YtqB and its homologues indicates that YtqB is a SAM-dependent class I MTase, and provides insights into the substrate binding site of YtqB. Copyright © 2014 Elsevier Inc. All rights reserved.

Demonstration of a Segment Alignment Maintenance System on a Seven-Segment Sub-Array of the Hobby-Eberly Telescope

NASA Technical Reports Server (NTRS)

Rakoczy, John; Whitaker, Ann F. (Technical Monitor)

2001-01-01

NASA's Marshall Space Flight Center, in collaboration with Blue Line Engineering of Colorado Springs, Colorado, is developing a Segment Alignment Maintenance System (SAMS) for McDonald Observatory's Hobby-Eberly Telescope (HET). The SAMS shall sense motions of the 91 primary mirror segments and send corrections to HET's primary mirror controller as the mirror segments misalign due to thermo-elastic deformations of the mirror support structure. The SAMS consists of inductive edge sensors supplemented by inclinometers for global radius of curvature sensing. All measurements are sent to the SAMS computer where mirror motion corrections are calculated. In October 2000, a prototype SAMS was installed on a seven-segment cluster of the HET. Subsequent testing has shown that the SAMS concept and architecture are a viable practical approach to maintaining HET's primary mirror figure, or the figure of any large segmented telescope. This paper gives a functional description of the SAMS sub-array components and presents test data to characterize the performance of the sub-array SAMS.

Sample Analysis at Mars Instrument Simulator

NASA Technical Reports Server (NTRS)

Benna, Mehdi; Nolan, Tom

2013-01-01

The Sample Analysis at Mars Instrument Simulator (SAMSIM) is a numerical model dedicated to plan and validate operations of the Sample Analysis at Mars (SAM) instrument on the surface of Mars. The SAM instrument suite, currently operating on the Mars Science Laboratory (MSL), is an analytical laboratory designed to investigate the chemical and isotopic composition of the atmosphere and volatiles extracted from solid samples. SAMSIM was developed using Matlab and Simulink libraries of MathWorks Inc. to provide MSL mission planners with accurate predictions of the instrument electrical, thermal, mechanical, and fluid responses to scripted commands. This tool is a first example of a multi-purpose, full-scale numerical modeling of a flight instrument with the purpose of supplementing or even eliminating entirely the need for a hardware engineer model during instrument development and operation. SAMSIM simulates the complex interactions that occur between the instrument Command and Data Handling unit (C&DH) and all subsystems during the execution of experiment sequences. A typical SAM experiment takes many hours to complete and involves hundreds of components. During the simulation, the electrical, mechanical, thermal, and gas dynamics states of each hardware component are accurately modeled and propagated within the simulation environment at faster than real time. This allows the simulation, in just a few minutes, of experiment sequences that takes many hours to execute on the real instrument. The SAMSIM model is divided into five distinct but interacting modules: software, mechanical, thermal, gas flow, and electrical modules. The software module simulates the instrument C&DH by executing a customized version of the instrument flight software in a Matlab environment. The inputs and outputs to this synthetic C&DH are mapped to virtual sensors and command lines that mimic in their structure and connectivity the layout of the instrument harnesses. This module executes, and thus validates, complex command scripts prior to their up-linking to the SAM instrument. As an output, this module generates synthetic data and message logs at a rate that is similar to the actual instrument.

Sensitivity analysis of gene ranking methods in phenotype prediction.

PubMed

deAndrés-Galiana, Enrique J; Fernández-Martínez, Juan L; Sonis, Stephen T

2016-12-01

It has become clear that noise generated during the assay and analytical processes has the ability to disrupt accurate interpretation of genomic studies. Not only does such noise impact the scientific validity and costs of studies, but when assessed in the context of clinically translatable indications such as phenotype prediction, it can lead to inaccurate conclusions that could ultimately impact patients. We applied a sequence of ranking methods to damp noise associated with microarray outputs, and then tested the utility of the approach in three disease indications using publically available datasets. This study was performed in three phases. We first theoretically analyzed the effect of noise in phenotype prediction problems showing that it can be expressed as a modeling error that partially falsifies the pathways. Secondly, via synthetic modeling, we performed the sensitivity analysis for the main gene ranking methods to different types of noise. Finally, we studied the predictive accuracy of the gene lists provided by these ranking methods in synthetic data and in three different datasets related to cancer, rare and neurodegenerative diseases to better understand the translational aspects of our findings. In the case of synthetic modeling, we showed that Fisher's Ratio (FR) was the most robust gene ranking method in terms of precision for all the types of noise at different levels. Significance Analysis of Microarrays (SAM) provided slightly lower performance and the rest of the methods (fold change, entropy and maximum percentile distance) were much less precise and accurate. The predictive accuracy of the smallest set of high discriminatory probes was similar for all the methods in the case of Gaussian and Log-Gaussian noise. In the case of class assignment noise, the predictive accuracy of SAM and FR is higher. Finally, for real datasets (Chronic Lymphocytic Leukemia, Inclusion Body Myositis and Amyotrophic Lateral Sclerosis) we found that FR and SAM provided the highest predictive accuracies with the smallest number of genes. Biological pathways were found with an expanded list of genes whose discriminatory power has been established via FR. We have shown that noise in expression data and class assignment partially falsifies the sets of discriminatory probes in phenotype prediction problems. FR and SAM better exploit the principle of parsimony and are able to find subsets with less number of high discriminatory genes. The predictive accuracy and the precision are two different metrics to select the important genes, since in the presence of noise the most predictive genes do not completely coincide with those that are related to the phenotype. Based on the synthetic results, FR and SAM are recommended to unravel the biological pathways that are involved in the disease development. Copyright © 2016 Elsevier Inc. All rights reserved.

Lay-screeners and use of WHO growth standards increase case finding of hospitalized Malawian children with severe acute malnutrition.

PubMed

LaCourse, Sylvia M; Chester, Frances M; Preidis, Geoffrey; McCrary, Leah M; Maliwichi, Madalitso; McCollum, Eric D; Hosseinipour, Mina C

2015-02-01

Strategies to effectively identify and refer children with severe acute malnutrition (SAM) to Nutritional Rehabilitation units (NRU) can reduce morbidity and mortality. From December 2011 to May 2012, we conducted a prospective study task-shifting inpatient malnutrition screening of Malawian children 6-60 months to lay-screeners and evaluated World Health Organization (WHO) criteria vs. the National Center for Health Statistics (NCHS) guidelines for SAM. Lay-screeners evaluated 3116 children, identifying 368 (11.8%) with SAM by WHO criteria, including 210 (6.7%) who met NCHS criteria initially missed by standard clinician NRU referrals. Overall case finding increased by 56.7%. Mid-upper arm circumference (MUAC) and bipedal edema captured 86% (181/210) NCHS/NRU-eligible children and 89% of those who died (17/19) meeting WHO criteria. Mortality of NCHS/NRU-eligible children was 10 times greater than those without SAM (odds ratio 10.5, 95% confidence interval 5.4-20.6). Ward-based lay-screeners and WHO guidelines identified high-risk children with SAM missed by standard NRU referral. MUAC and edema detected the majority of NRU-eligible children. © The Author [2014]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Striped gold nanoparticles: New insights from molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Velachi, Vasumathi, E-mail: vasuphy@gmail.com; Cordeiro, M. Natália D. S., E-mail: ncordeir@fc.up.pt; Bhandary, Debdip

Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199–3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols’ arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper,more » we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl’s chain length, the length difference between the thiol mixtures, and solvent properties.« less

Common themes and differences in SAM recognition among SAM riboswitches

PubMed Central

Price, Ian R.; Grigg, Jason C.; Ke, Ailong

2014-01-01

The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-L-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. PMID:24863160

Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues.

PubMed

Mercurio, Flavia A; Marasco, Daniela; Di Natale, Concetta; Pirone, Luciano; Costantini, Susan; Pedone, Emilia M; Leone, Marilisa

2016-11-17

The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues. Several peptide sequences with high predicted helical propensities were designed, and detailed conformational analyses were conducted by diverse techniques including NMR, CD, and molecular dynamics (MD) simulations. Interaction studies were also performed by NMR, surface plasmon resonance (SPR), and microscale thermophoresis (MST) and led to the identification of two peptides capable of binding to the first Sam domain of Odin. These molecules represent early candidates for the generation of efficient Sam domain binders and antagonists of Sam-Sam interactions involving EphA2. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

ER residency of the ceramide phosphoethanolamine synthase SMSr relies on homotypic oligomerization mediated by its SAM domain

PubMed Central

Cabukusta, Birol; Kol, Matthijs; Kneller, Laura; Hilderink, Angelika; Bickert, Andreas; Mina, John G. M.; Korneev, Sergei; Holthuis, Joost C. M.

2017-01-01

SMSr/SAMD8 is an ER-resident ceramide phosphoethanolamine synthase with a critical role in controlling ER ceramides and suppressing ceramide-induced apoptosis in cultured cells. SMSr-mediated ceramide homeostasis relies on the enzyme’s catalytic activity as well as on its N-terminal sterile α-motif or SAM domain. Here we report that SMSr-SAM is structurally and functionally related to the SAM domain of diacylglycerol kinase DGKδ, a central regulator of lipid signaling at the plasma membrane. Native gel electrophoresis indicates that both SAM domains form homotypic oligomers. Chemical crosslinking studies show that SMSr self-associates into ER-resident trimers and hexamers that resemble the helical oligomers formed by DGKδ-SAM. Residues critical for DGKδ-SAM oligomerization are conserved in SMSr-SAM and their substitution causes a dissociation of SMSr oligomers as well as a partial redistribution of the enzyme to the Golgi. Conversely, treatment of cells with curcumin, a drug disrupting ceramide and Ca2+ homeostasis in the ER, stabilizes SMSr oligomers and promotes retention of the enzyme in the ER. Our data provide first demonstration of a multi-pass membrane protein that undergoes homotypic oligomerization via its SAM domain and indicate that SAM-mediated self-assembly of SMSr is required for efficient retention of the enzyme in the ER. PMID:28120887

48 CFR 4.1102 - Policy.

Code of Federal Regulations, 2014 CFR

2014-10-01

... SAM database prior to award of a contract or agreement, except for— (1) Purchases under the micro... registration in the SAM database, or use of SAM data, could compromise the safeguarding of classified... (a)(3) of this section to require SAM registration. (c)(1)(i) If a contractor has legally changed its...

78 FR 62627 - Sam Rayburn Dam Rate

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-22

..., Wholesale Rates for Hydro Power and Energy Sold to Sam Rayburn Dam Electric Cooperative, Inc. (Contract No... Schedule SRD-08, Wholesale Rates for Hydro Power and Energy Sold to Sam Rayburn Dam Electric Cooperative... ADMINISTRATION RATE SCHEDULE SRD-13 \\1\\ WHOLESALE RATES FOR HYDRO POWER AND ENERGY SOLD TO SAM RAYBURN DAM...

Projections of Southern Hemisphere atmospheric circulation interannual variability

NASA Astrophysics Data System (ADS)

Grainger, Simon; Frederiksen, Carsten S.; Zheng, Xiaogu

2017-02-01

An analysis is made of the coherent patterns, or modes, of interannual variability of Southern Hemisphere 500 hPa geopotential height field under current and projected climate change scenarios. Using three separate multi-model ensembles (MMEs) of coupled model intercomparison project phase 5 (CMIP5) models, the interannual variability of the seasonal mean is separated into components related to (1) intraseasonal processes; (2) slowly-varying internal dynamics; and (3) the slowly-varying response to external changes in radiative forcing. In the CMIP5 RCP8.5 and RCP4.5 experiments, there is very little change in the twenty-first century in the intraseasonal component modes, related to the Southern annular mode (SAM) and mid-latitude wave processes. The leading three slowly-varying internal component modes are related to SAM, the El Niño-Southern oscillation (ENSO), and the South Pacific wave (SPW). Structural changes in the slow-internal SAM and ENSO modes do not exceed a qualitative estimate of the spatial sampling error, but there is a consistent increase in the ENSO-related variance. Changes in the SPW mode exceed the sampling error threshold, but cannot be further attributed. Changes in the dominant slowly-varying external mode are related to projected changes in radiative forcing. They reflect thermal expansion of the tropical troposphere and associated changes in the Hadley Cell circulation. Changes in the externally-forced associated variance in the RCP8.5 experiment are an order of magnitude greater than for the internal components, indicating that the SH seasonal mean circulation will be even more dominated by a SAM-like annular structure. Across the three MMEs, there is convergence in the projected response in the slow-external component.

SAM-CAAM: A Concept for Acquiring Systematic Aircraft Measurements to Characterize Aerosol Air Masses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kahn, Ralph A.; Berkoff, Tim A.; Brock, Charles

A modest operational program of systematic aircraft measurements can resolve key satellite aerosol data record limitations. Satellite observations provide frequent global aerosol amount maps but offer only loose aerosol property constraints needed for climate and air quality applications. In this paper, we define and illustrate the feasibility of flying an aircraft payload to measure key aerosol optical, microphysical, and chemical properties in situ. The flight program could characterize major aerosol airmass types statistically, at a level of detail unobtainable from space. It would 1) enhance satellite aerosol retrieval products with better climatology assumptions and 2) improve translation between satellite-retrieved opticalmore » properties and species-specific aerosol mass and size simulated in climate models to assess aerosol forcing, its anthropogenic components, and other environmental impacts. As such, Systematic Aircraft Measurements to Characterize Aerosol Air Masses (SAM-CAAM) could add value to data records representing several decades of aerosol observations from space; improve aerosol constraints on climate modeling; help interrelate remote sensing, in situ, and modeling aerosol-type definitions; and contribute to future satellite aerosol missions. Fifteen required variables are identified and four payload options of increasing ambition are defined to constrain these quantities. “Option C” could meet all the SAM-CAAM objectives with about 20 instruments, most of which have flown before, but never routinely several times per week, and never as a group. Aircraft integration and approaches to data handling, payload support, and logistical considerations for a long-term, operational mission are discussed. Finally, SAM-CAAM is feasible because, for most aerosol sources and specified seasons, particle properties tend to be repeatable, even if aerosol loading varies.« less

SAM-CAAM: A Concept for Acquiring Systematic Aircraft Measurements to Characterize Aerosol Air Masses

DOE PAGES

Kahn, Ralph A.; Berkoff, Tim A.; Brock, Charles; ...

2017-10-30

A modest operational program of systematic aircraft measurements can resolve key satellite aerosol data record limitations. Satellite observations provide frequent global aerosol amount maps but offer only loose aerosol property constraints needed for climate and air quality applications. In this paper, we define and illustrate the feasibility of flying an aircraft payload to measure key aerosol optical, microphysical, and chemical properties in situ. The flight program could characterize major aerosol airmass types statistically, at a level of detail unobtainable from space. It would 1) enhance satellite aerosol retrieval products with better climatology assumptions and 2) improve translation between satellite-retrieved opticalmore » properties and species-specific aerosol mass and size simulated in climate models to assess aerosol forcing, its anthropogenic components, and other environmental impacts. As such, Systematic Aircraft Measurements to Characterize Aerosol Air Masses (SAM-CAAM) could add value to data records representing several decades of aerosol observations from space; improve aerosol constraints on climate modeling; help interrelate remote sensing, in situ, and modeling aerosol-type definitions; and contribute to future satellite aerosol missions. Fifteen required variables are identified and four payload options of increasing ambition are defined to constrain these quantities. “Option C” could meet all the SAM-CAAM objectives with about 20 instruments, most of which have flown before, but never routinely several times per week, and never as a group. Aircraft integration and approaches to data handling, payload support, and logistical considerations for a long-term, operational mission are discussed. Finally, SAM-CAAM is feasible because, for most aerosol sources and specified seasons, particle properties tend to be repeatable, even if aerosol loading varies.« less

Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quinlan, Casey L.; Kaiser, Stephen E.; Bolaños, Ben

S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzymemore » turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.« less

Delocalized versus localized excitations in the photoisomerization of azobenzene-functionalized alkanethiolate SAMs

NASA Astrophysics Data System (ADS)

Bronsch, Wibke; Moldt, Thomas; Boie, Larissa; Gahl, Cornelius; Weinelt, Martin

2017-12-01

Self-assembled monolayers of azobenzene-functionalized alkanethiolates form molecular ensembles with preferential orientation and significant excitonic coupling among the azobenzene chromophores. We have studied their optical switching with differential reflectance and two-photon-photoemission spectroscopy tuning the excitation wavelength through the excitonically broadened S2 absorption band. While the effective isomerization cross-section increases towards shorter wavelengths, the fraction of cis molecules in the photostationary state decreases. We attribute this observation to the absorption of the cis isomer in the SAM. The photoisomerization in the SAM thereby follows the behavior of non-interacting chromophores in solution, despite the formation of H-aggregates. Our study thus reveals that photoswitching occurs via localized excitations while strongly excitonically coupled, delocalized states do not contribute significantly.

Charge carrier transport and optical properties of SAM-induced conducting channel in organic semiconductors.

NASA Astrophysics Data System (ADS)

Podzorov, Vitaly

2009-03-01

Certain types of self-assembled monolayers (SAM) grown directly at the surface of organic semiconductors can induce a high surface conductivity in these materials [1]. For example, the conductivity induced by perfluorinated alkyl silanes in organic molecular crystals approaches 10 to -5 Siemens per square. The observed large electronic effect opens new opportunities for nanoscale surface functionalization of organic semiconductors and provides experimental access to the regime of high carrier density. Here, we will discuss temperature variable measurements of SAM-induced conductivity in several types of organic semiconductors. [1]. M. F. Calhoun, J. Sanchez, D. Olaya, M. E. Gershenson and V. Podzorov, ``Electronic functionalization of the surface of organic semiconductors with self-assembled monolayers'', Nature Mat. 7, 84 (2008).

The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch

PubMed Central

Hennelly, Scott P.; Novikova, Irina V.; Sanbonmatsu, Karissa Y.

2013-01-01

Riboswitch operation involves the complex interplay between the aptamer domain and the expression platform. During transcription, these two domains compete against each other for shared sequence. In this study, we explore the cooperative effects of ligand binding and Magnesium interactions in the SAM-I riboswitch in the context of aptamer collapse and anti-terminator formation. Overall, our studies show the apo-aptamer acts as (i) a pre-organized aptamer competent to bind ligand and undergo structural collapse and (ii) a conformation that is more accessible to anti-terminator formation. We show that both Mg2+ ions and SAM are required for a collapse transition to occur. We then use competition between the aptamer and expression platform for shared sequence to characterize the stability of the collapsed aptamer. We find that SAM and Mg2+ interactions in the aptamer are highly cooperative in maintaining switch polarity (i.e. aptamer ‘off-state’ versus anti-terminator ‘on-state’). We further show that the aptamer off-state is preferentially stabilized by Mg2+ and similar divalent ions. Furthermore, the functional switching assay was used to select for phosphorothioate interference, and identifies potential magnesium chelation sites while characterizing their coordinated role with SAM in aptamer stabilization. In addition, we find that Mg2+ interactions with the apo-aptamer are required for the full formation of the anti-terminator structure, and that higher concentrations of Mg2+ (>4 mM) shift the equilibrium toward the anti-terminator on-state even in the presence of SAM. PMID:23258703

Shock Wave Response of Iron-based In Situ Metallic Glass Matrix Composites

PubMed Central

Khanolkar, Gauri R.; Rauls, Michael B.; Kelly, James P.; Graeve, Olivia A.; Hodge, Andrea M.; Eliasson, Veronica

2016-01-01

The response of amorphous steels to shock wave compression has been explored for the first time. Further, the effect of partial devitrification on the shock response of bulk metallic glasses is examined by conducting experiments on two iron-based in situ metallic glass matrix composites, containing varying amounts of crystalline precipitates, both with initial composition Fe49.7Cr17.7Mn1.9Mo7.4W1.6B15.2C3.8Si2.4. The samples, designated SAM2X5-600 and SAM2X5-630, are X-ray amorphous and partially crystalline, respectively, due to differences in sintering parameters during sample preparation. Shock response is determined by making velocity measurements using interferometry techniques at the rear free surface of the samples, which have been subjected to impact from a high-velocity projectile launched from a powder gun. Experiments have yielded results indicating a Hugoniot Elastic Limit (HEL) to be 8.58 ± 0.53 GPa for SAM2X5-600 and 11.76 ± 1.26 GPa for SAM2X5-630. The latter HEL result is higher than elastic limits for any BMG reported in the literature thus far. SAM2X5-600 catastrophically loses post-yield strength whereas SAM2X5-630, while showing some strain-softening, retains strength beyond the HEL. The presence of crystallinity within the amorphous matrix is thus seen to significantly aid in strengthening the material as well as preserving material strength beyond yielding. PMID:26932846

Shock Wave Response of Iron-based In Situ Metallic Glass Matrix Composites.

PubMed

Khanolkar, Gauri R; Rauls, Michael B; Kelly, James P; Graeve, Olivia A; Hodge, Andrea M; Eliasson, Veronica

2016-03-02

The response of amorphous steels to shock wave compression has been explored for the first time. Further, the effect of partial devitrification on the shock response of bulk metallic glasses is examined by conducting experiments on two iron-based in situ metallic glass matrix composites, containing varying amounts of crystalline precipitates, both with initial composition Fe49.7Cr17.7Mn1.9Mo7.4W1.6B15.2C3.8Si2.4. The samples, designated SAM2X5-600 and SAM2X5-630, are X-ray amorphous and partially crystalline, respectively, due to differences in sintering parameters during sample preparation. Shock response is determined by making velocity measurements using interferometry techniques at the rear free surface of the samples, which have been subjected to impact from a high-velocity projectile launched from a powder gun. Experiments have yielded results indicating a Hugoniot Elastic Limit (HEL) to be 8.58 ± 0.53 GPa for SAM2X5-600 and 11.76 ± 1.26 GPa for SAM2X5-630. The latter HEL result is higher than elastic limits for any BMG reported in the literature thus far. SAM2X5-600 catastrophically loses post-yield strength whereas SAM2X5-630, while showing some strain-softening, retains strength beyond the HEL. The presence of crystallinity within the amorphous matrix is thus seen to significantly aid in strengthening the material as well as preserving material strength beyond yielding.

The mthA mutation conferring low-level resistance to streptomycin enhances antibiotic production in Bacillus subtilis by increasing the S-adenosylmethionine pool size.

PubMed

Tojo, Shigeo; Kim, Ji-Yun; Tanaka, Yukinori; Inaoka, Takashi; Hiraga, Yoshikazu; Ochi, Kozo

2014-04-01

Certain Str(r) mutations that confer low-level streptomycin resistance result in the overproduction of antibiotics by Bacillus subtilis. Using comparative genome-sequencing analysis, we successfully identified this novel mutation in B. subtilis as being located in the mthA gene, which encodes S-adenosylhomocysteine/methylthioadenosine nucleosidase, an enzyme involved in the S-adenosylmethionine (SAM)-recycling pathways. Transformation experiments showed that this mthA mutation was responsible for the acquisition of low-level streptomycin resistance and overproduction of bacilysin. The mthA mutant had an elevated level of intracellular SAM, apparently acquired by arresting SAM-recycling pathways. This increase in the SAM level was directly responsible for bacilysin overproduction, as confirmed by forced expression of the metK gene encoding SAM synthetase. The mthA mutation fully exerted its effect on antibiotic overproduction in the genetic background of rel(+) but not the rel mutant, as demonstrated using an mthA relA double mutant. Strikingly, the mthA mutation activated, at the transcription level, even the dormant ability to produce another antibiotic, neotrehalosadiamine, at concentrations of 150 to 200 μg/ml, an antibiotic not produced (<1 μg/ml) by the wild-type strain. These findings establish the significance of SAM in initiating bacterial secondary metabolism. They also suggest a feasible methodology to enhance or activate antibiotic production, by introducing either the rsmG mutation to Streptomyces or the mthA mutation to eubacteria, since many eubacteria have mthA homologues.

The mthA Mutation Conferring Low-Level Resistance to Streptomycin Enhances Antibiotic Production in Bacillus subtilis by Increasing the S-Adenosylmethionine Pool Size

PubMed Central

Tojo, Shigeo; Kim, Ji-Yun; Tanaka, Yukinori; Inaoka, Takashi; Hiraga, Yoshikazu

2014-01-01

Certain Strr mutations that confer low-level streptomycin resistance result in the overproduction of antibiotics by Bacillus subtilis. Using comparative genome-sequencing analysis, we successfully identified this novel mutation in B. subtilis as being located in the mthA gene, which encodes S-adenosylhomocysteine/methylthioadenosine nucleosidase, an enzyme involved in the S-adenosylmethionine (SAM)-recycling pathways. Transformation experiments showed that this mthA mutation was responsible for the acquisition of low-level streptomycin resistance and overproduction of bacilysin. The mthA mutant had an elevated level of intracellular SAM, apparently acquired by arresting SAM-recycling pathways. This increase in the SAM level was directly responsible for bacilysin overproduction, as confirmed by forced expression of the metK gene encoding SAM synthetase. The mthA mutation fully exerted its effect on antibiotic overproduction in the genetic background of rel+ but not the rel mutant, as demonstrated using an mthA relA double mutant. Strikingly, the mthA mutation activated, at the transcription level, even the dormant ability to produce another antibiotic, neotrehalosadiamine, at concentrations of 150 to 200 μg/ml, an antibiotic not produced (<1 μg/ml) by the wild-type strain. These findings establish the significance of SAM in initiating bacterial secondary metabolism. They also suggest a feasible methodology to enhance or activate antibiotic production, by introducing either the rsmG mutation to Streptomyces or the mthA mutation to eubacteria, since many eubacteria have mthA homologues. PMID:24509311

A surprising way to control the charge transport in molecular electronics: the subtle impact of the coverage of self-assembled monolayers of floppy molecules adsorbed on metallic electrodes.

PubMed

Bâldea, Ioan

2017-10-26

Inspired by earlier attempts in organic electronics aiming at controlling charge injection from metals into organic materials by manipulating the Schottky energy barrier using self-assembled monolayers (SAMs), recent experimental and theoretical work in molecular electronics showed that metal-organic interfaces can be controlled via changes in the metal work function that are induced by SAMs. In this paper we indicate a different route to achieve interface-driven control over the charge transfer/transport at the molecular scale. It is based on the fact that, in floppy molecule based SAMs, the molecular conformation can be tuned by varying the coverage of the adsorbate. We demonstrate this effect with the aid of benchmark molecules that are often used to fabricate nanojunctions and consist of two rings that can easily rotate relative to each other. We show that, by varying the coverage of the SAM, the twisting angle φ of the considered molecular species can be modified by a factor of two. Given the fact that the low bias conductance G scales as cos 2  φ, this results in a change in G of over one order of magnitude for the considered molecular species. Tuning the twisting angle by controlling the SAM coverage may be significant, e.g., for current efforts to fabricate molecular switches. Conversely, the lack of control over the local SAM coverage may be problematic for the reproducibility and interpretation of the STM (scanning tunneling microscope) measurements on repeatedly forming single molecule break junctions.

Screening for trauma‐related symptoms via a smartphone app: The validity of Smart Assessment on your Mobile in referred police officers

PubMed Central

Bakker, Anne; Schrieken, Bart A.L.; Hoofwijk, Marthe C.; Olff, Miranda

2017-01-01

Abstract To facilitate easily accessible screening for trauma‐related symptoms, a web‐based application called Smart Assessment on your Mobile (SAM) was developed. In this study, we examined whether SAM was able to accurately identify posttraumatic stress disorder (PTSD) and depression in adults. Eighty‐nine referred police officers completed SAM, containing the PTSD Checklist for Diagnostic and Statistical Manual of Mental Disorders (DSM)‐5 (PCL‐5) and the Depression Anxiety and Stress Scale (DASS‐21), on their own device prior to a diagnostic interview where the Clinician‐Administered PTSD Scale for DSM‐5 (CAPS‐5) and Structured Clinical Interview for DSM‐IV (SCID‐I/P) were administered. Results showed a substantial agreement between SAM and the diagnostic interview in the assessment of PTSD and depression. An optimal trade‐off between sensitivity (89%) and specificity (68%) levels was found at a cut‐off score of 31 on the PTSD Checklist for DSM‐5 (area under the curve = 0.845, 95% CI [0.765, 0.925], diagnostic odds ratio = 15.97). This is one of the first studies to support the validity and reliability of a mobile screener following trauma. SAM may facilitate screening for trauma‐related symptoms on a large scale and could be a first step in a stepped‐care model for trauma survivors to help identify individuals who need further diagnostics and care. PMID:28948699

Surface sealing using self-assembled monolayers and its effect on metal diffusion in porous low-k dielectrics studied using monoenergetic positron beams

NASA Astrophysics Data System (ADS)

Uedono, Akira; Armini, Silvia; Zhang, Yu; Kakizaki, Takeaki; Krause-Rehberg, Reinhard; Anwand, Wolfgang; Wagner, Andreas

2016-04-01

Surface sealing effects on the diffusion of metal atoms in porous organosilicate glass (OSG) films were studied by monoenergetic positron beams. For a Cu(5 nm)/MnN(3 nm)/OSG(130 nm) sample fabricated with pore stuffing, C4F8 plasma etch, unstuffing, and a self-assembled monolayer (SAM) sealing process, it was found that pores with cubic pore side lengths of 1.1 and 3.1 nm coexisted in the OSG film. For the sample without the SAM sealing process, metal (Cu and Mn) atoms diffused from the top Cu/MnN layer into the OSG film and were trapped by the pores. As a result, almost all pore interiors were covered with those metals. For the sample damaged by an Ar/C4F8 plasma etch treatment before the SAM sealing process, SAMs diffused into the OSG film, and they were preferentially trapped by larger pores. The cubic pore side length in these pores containing self-assembled molecules was estimated to be 0.7 nm. Through this work, we have demonstrated that monoenergetic positron beams are a powerful tool for characterizing capped porous films and the trapping of atoms and molecules by pores.

Magnolol protects neurons against ischemia injury via the downregulation of p38/MAPK, CHOP and nitrotyrosine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jiann-Hwa; School of Medicine, Fu-Jen Catholic University, Taipei, Taiwan; Department of Emergency Medicine, Cathay General Hospital, Taipei, Taiwan

Magnolol is isolated from the herb Magnolia officinalis, which has been demonstrated to exert pharmacological effects. Our aim was to investigate whether magnolol is able to act as an anti-inflammatory agent that brings about neuroprotection using a global ischemic stroke model and to determine the mechanisms involved. Rats were treated with and without magnolol after ischemia reperfusion brain injury by occlusion of the two common carotid arteries. The inflammatory cytokine production in serum and the volume of infarction in the brain were measured. The proteins present in the brains obtained from the stroke animal model (SAM) and control animal groupsmore » with and without magnolol treatment were compared. Magnolol reduces the total infarcted volume by 15% and 30% at dosages of 10 and 30 mg/kg, respectively, compared to the untreated SAM group. The levels of acute inflammatory cytokines, including interleukin-1 beta, tumor necrosis factor alpha, and interleukin-6 were attenuated by magnolol. Magnolol was also able to suppress the production of nitrotyrosine, 4-hydroxy-2-nonenal (4-HNE), inducible NO synthase (iNOS), various phosphorylated p38 mitogen-activated protein kinases and various C/EBP homologues. Furthermore, this modulation of ischemia injury factors in the SAM model group treated with magnolol seems to result from a suppression of reactive oxygen species production and the upregulation of p-Akt and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). These findings confirm the anti-oxidative properties of magnolol, including the inhibition of ischemic injury to neurons; this protective effect seems to involve changes in the in vivo activity of Akt, GSK3β and NF-κB. - Graphical abstract: Schematic presentation of the signaling pathways involved in magnolol inhibited transient global ischemia brain apoptosis and inflammation in rats. The effect of magnolol on the scavenger of ROS, which inhibits p38 MAPK and CHOP protein inactivation. These results suggest that another role for the iNOS/Akt pathway may be involved in neuronal survival or plasticity by magnolol after ischemic injury. - Highlights: • Magnolol attenuates brain damage in ischemic rats. • Effects of magnolol on stroke animals in ROS and acute inflammation cytokines. • Oxidants and Akt/NF-κB signaling are involved in the neuroprotection of magnolol.« less

Crystal structure of SAM-dependent methyltransferase from Pyrococcus horikoshii.

PubMed

Pampa, K J; Madan Kumar, S; Hema, M K; Kumara, Karthik; Naveen, S; Kunishima, Naoki; Lokanath, N K

2017-12-01

Methyltransferases (MTs) are enzymes involved in methylation that are needed to perform cellular processes such as biosynthesis, metabolism, gene expression, protein trafficking and signal transduction. The cofactor S-adenosyl-L-methionine (SAM) is used for catalysis by SAM-dependent methyltransferases (SAM-MTs). The crystal structure of Pyrococcus horikoshii SAM-MT was determined to a resolution of 2.1 Å using X-ray diffraction. The monomeric structure consists of a Rossmann-like fold (domain I) and a substrate-binding domain (domain II). The cofactor (SAM) molecule binds at the interface between adjacent subunits, presumably near to the active site(s) of the enzyme. The observed dimeric state might be important for the catalytic function of the enzyme.

SAMS-II Requirements and Operations

NASA Technical Reports Server (NTRS)

Wald, Lawrence W.

1998-01-01

The Space Acceleration Measurements System (SAMS) II is the primary instrument for the measurement, storage, and communication of the microgravity environment aboard the International Space Station (ISS). SAMS-II is being developed by the NASA Lewis Research Center Microgravity Science Division to primarily support the Office of Life and Microgravity Science and Applications (OLMSA) Microgravity Science and Applications Division (MSAD) payloads aboard the ISS. The SAMS-II is currently in the test and verification phase at NASA LeRC, prior to its first hardware delivery scheduled for July 1998. This paper will provide an overview of the SAMS-II instrument, including the system requirements and topology, physical and electrical characteristics, and the Concept of Operations for SAMS-II aboard the ISS.

C 90 temperature effects on relative stabilities of the IPR isomers

NASA Astrophysics Data System (ADS)

Slanina, Zdeněk; Zhao, Xiang; Lee, Shyi-Long; Ōsawa, Eiji

1997-07-01

The complete set of 46 isolated-pentagon-rule (IPR) isomers of C 90 is treated by the SAMI quantum-chemical method (Semi-Ab-Initio Model 1), and their energetics is also checked by ab initio SCF computations (HF/3-21G, HF/4-31G) and the AM1 and PM3 semiempirical methods. All the methods point out a C2 species as the system state (with an exception at the HF/3-21G level). However, the energetics itself is not able to produce a good agreement with recent observations (one C2 v, three C2, and one C1, separeted into three HPLC fractions). The symmetries of the five SAM1 lowest-energy structures are: C2, C2 v, Cs, D5 h, C1. In order to respect temperature effects on relative stabilities, entropy contributions are also computed and significant changes are found. The symmetries of the five structures most populated in a high-temperature region are according to the SAM1 computations: two times C2, Cs, C2 v, C1. One of the recently reported HPLC fractions shows 70 lines in the 13C NMR spectrum, assigned to a C2 species (45 lines) and C2 v species (25 lines, 5 weaker). There is however an alternative interpretation of the spectrum: a Cs (46 lines, 2 weaker) and a C2 v species (24 lines, 3 weaker). The last two structures are indeed present in the SAM1 high-temperature stability set so that agreement between observations and calculations can be achieved.

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

PubMed

Fenwick, Michael K; Mehta, Angad P; Zhang, Yang; Abdelwahed, Sameh H; Begley, Tadhg P; Ealick, Steven E

2015-03-27

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

Influences of spring-to-summer sea surface temperatures over different Indian Ocean domains on the Asian summer monsoon

NASA Astrophysics Data System (ADS)

Li, Zhenning; Yang, Song

2017-11-01

The influences of spring-to-summer sea surface temperature (SST) anomalies in different domains of the Indian Ocean (IO) on the Asian summer monsoon are investigated by conducting a series of numerical experiments using the NCAR CAM4 model. It is found that, to a certain extent, the springtime IO SST anomalies can persist to the summer season. The spring-to-summer IO SST anomalies associated with the IO basin warming mode are strongly linked to the summer climate over Asia, especially the South Asian monsoon (SAM) and the East Asian monsoon. Among this connection, the warming of tropical IO plays the most critical role, and the warming of southern IO is important for monsoon variation and prediction prior to the full development of the monsoon. The atmospheric response to IO basin wide warming is similar with that to tropical IO warming. The influence of northern IO warming on the SAM, however, is opposite to the effect of southern IO warming. Meanwhile, the discrepancies between the results from idealized SST forcing simulations and observations, especially for the southern IO, reveal that the dominant role of air-sea interaction in the monsoon-IO coupled system cannot be ignored. Moreover, the springtime northern IO warming seems to favor an early onset or a stronger persistence of the SAM.

Arabidopsis thaliana gonidialess A/Zuotin related factors (GlsA/ZRF) are essential for maintenance of meristem integrity.

PubMed

Guzmán-López, José Alfredo; Abraham-Juárez, María Jazmín; Lozano-Sotomayor, Paulina; de Folter, Stefan; Simpson, June

2016-05-01

Observation of a differential expression pattern, including strong expression in meristematic tissue of an Agave tequilana GlsA/ZRF ortholog suggested an important role for this gene during bulbil formation and developmental changes in this species. In order to better understand this role, the two GlsA/ZFR orthologs present in the genome of Arabidopsis thaliana were functionally characterized by analyzing expression patterns, double mutant phenotypes, promoter-GUS fusions and expression of hormone related or meristem marker genes. Patterns of expression for A. thaliana show that GlsA/ZFR genes are strongly expressed in SAMs and RAMs in mature plants and developing embryos and double mutants showed multiple changes in morphology related to both SAM and RAM tissues. Typical double mutants showed stunted growth of aerial and root tissue, formation of multiple ectopic meristems and effects on cotyledons, leaves and flowers. The KNOX genes STM and BP were overexpressed in double mutants whereas CLV3, WUSCHEL and AS1 were repressed and lack of AtGlsA expression was also associated with changes in localization of auxin and cytokinin. These results suggest that GlsA/ZFR is an essential component of the machinery that maintains the integrity of SAM and RAM tissue and underline the potential to identify new genes or gene functions based on observations in non-model plants.

SAM Companion Documents

EPA Pesticide Factsheets

SAM Companion Documents and Sample Collection Procedures provide information intended to complement the analytical methods listed in Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.

PubMed

Rothé, Benjamin; Leettola, Catherine N; Leal-Esteban, Lucia; Cascio, Duilio; Fortier, Simon; Isenschmid, Manuela; Bowie, James U; Constam, Daniel B

2018-02-06

Head-to-tail polymers of sterile alpha motifs (SAM) can scaffold large macromolecular complexes. Several SAM-domain proteins that bind each other are mutated in patients with cystic kidneys or laterality defects, including the Ankyrin (ANK) and SAM domain-containing proteins ANKS6 and ANKS3, and the RNA-binding protein Bicc1. To address how their interactions are regulated, we first determined a high-resolution crystal structure of a Bicc1-SAM polymer, revealing a canonical SAM polymer with a high degree of flexibility in the subunit interface orientations. We further mapped interactions between full-length and distinct domains of Bicc1, ANKS3, and ANKS6. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. However, ANKS3 recruited ANKS6 to Bicc1, and the three proteins together cooperatively generated giant macromolecular complexes. Thus, the giant assemblies are shaped by SAM domains, their flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impact of submerged aquatic macrophytes on 3-dim current systems and hydrodynamic transport processes in Lake Constance

NASA Astrophysics Data System (ADS)

Wolf, Thomas; Lüddeke, Frauke; Thiange, Christophe

2015-04-01

According to the assessment criteria of the European water framework directive Lake Constance is having a good water quality. Nevertheless upcoming criteria using environmental quality measures show that there are still problems with respect to micropollutants. In fact, we observe significantly enhanced concentrations of micropollutants close to river mouths and in the areas of shallow water zones within Lake Constance compared to deep water concentrations. These findings are caused by river water plumes which can flow over distances of kilometers in the lake without being diluted or mixed only weakly with the surrounding lake water body. Besides, in the area of interest exist large populations of submerged aquatic macrophytes (SAM). There is only little knowledge, how these influence the distribution and transport processes of micropollutants. In order to assess the impact and distribution of river water plumes in different areas of the lake we implemented a 3-dim hydrodynamic model using DELFT3D-FLOW on a locally refined numerical grid which enables to cover different process scales of the distribution of river water bodies ranging from a few meters up to basin wide scales in the order of a few kilometers. We used numerical tracers (conservative and non-conservative) in order to quantify the impact of different abstract substance classes which are distinguished by their decay rates. In order to asses the influence of SAM populations on current field and transport processes we used a special simulation technique - the trachytope concept. The results of our 3-dim hydrodynamic model showed significantly changed current velocities, residence times and age of water parameters within the SAM areas compared to the control simulation without SAM. By simulating the propagation of coliform bacteria using numerical tracers with spatially and temporarily variable decay rates, we found complex impact pattern of the SAM on the distribution of these potentially harmful microorganisms.

Square Wave Voltammetry of TNT at Gold Electrodes Modified with Self-Assembled Monolayers Containing Aromatic Structures

PubMed Central

Trammell, Scott A.; Zabetakis, Dan; Moore, Martin; Verbarg, Jasenka; Stenger, David A.

2014-01-01

Square wave voltammetry for the reduction of 2,4,6-trinitrotoluene (TNT) was measured in 100 mM potassium phosphate buffer (pH 8) at gold electrodes modified with self-assembled monolayers (SAMs) containing either an alkane thiol or aromatic ring thiol structures. At 15 Hz, the electrochemical sensitivity (µA/ppm) was similar for all SAMs tested. However, at 60 Hz, the SAMs containing aromatic structures had a greater sensitivity than the alkane thiol SAM. In fact, the alkane thiol SAM had a decrease in sensitivity at the higher frequency. When comparing the electrochemical response between simulations and experimental data, a general trend was observed in which most of the SAMs had similar heterogeneous rate constants within experimental error for the reduction of TNT. This most likely describes a rate limiting step for the reduction of TNT. However, in the case of the alkane SAM at higher frequency, the decrease in sensitivity suggests that the rate limiting step in this case may be electron tunneling through the SAM. Our results show that SAMs containing aromatic rings increased the sensitivity for the reduction of TNT when higher frequencies were employed and at the same time suppressed the electrochemical reduction of dissolved oxygen. PMID:25549081

Motor coordination defects in mice deficient for the Sam68 RNA-binding protein.

PubMed

Lukong, Kiven E; Richard, Stéphane

2008-06-03

The role of RNA-binding proteins in the central nervous system and more specifically their role in motor coordination and learning are poorly understood. We previously reported that ablation of RNA-binding protein Sam68 in mice results in male sterility and delayed mammary gland development and protection against osteoporosis in females. Sam68 however is highly expressed in most regions of the brain especially the cerebellum and thus we investigated the cerebellar-related manifestations in Sam68-null mice. We analyzed the mice for motor function, sensory function, and learning and memory abilities. Herein, we report that Sam68-null mice have motor coordination defects as assessed by beam walking and rotorod performance. Forty-week-old Sam68-null mice (n=12) were compared to their wild-type littermates (n=12). The Sam68-null mice exhibited more hindpaw faults in beam walking tests and fell from the rotating drum at lower speeds and prematurely compared to the wild-type controls. The Sam68-null mice were, however, normal for forelimb strength, tail-hang reflex, balance test, grid walking, the Morris water task, recognition memory, visual discrimination, auditory stimulation and conditional taste aversion. Our findings support a role for Sam68 in the central nervous system in the regulation of motor coordination.

Exploring the Cognitive Foundations of the Shared Attention Mechanism: Evidence for a Relationship Between Self-Categorization and Shared Attention Across the Autism Spectrum.

PubMed

Skorich, Daniel P; Gash, Tahlia B; Stalker, Katie L; Zheng, Lidan; Haslam, S Alexander

2017-05-01

The social difficulties of autism spectrum disorder (ASD) are typically explained as a disruption in the Shared Attention Mechanism (SAM) sub-component of the theory of mind (ToM) system. In the current paper, we explore the hypothesis that SAM's capacity to construct the self-other-object relations necessary for shared-attention arises from a self-categorization process, which is weaker among those with more autistic-like traits. We present participants with self-categorization and shared-attention tasks, and measure their autism-spectrum quotient (AQ). Results reveal a negative relationship between AQ and shared-attention, via self-categorization, suggesting a role for self-categorization in the disruption in SAM seen in ASD. Implications for intervention, and for a ToM model in which weak central coherence plays a role are discussed.

Pleiotropic effects of methionine adenosyltransferases deregulation as determinants of liver cancer progression and prognosis.

PubMed

Frau, Maddalena; Feo, Francesco; Pascale, Rosa M

2013-10-01

Downregulation of liver-specific MAT1A gene, encoding S-adenosylmethionine (SAM) synthesizing isozymes MATI/III, and upregulation of widely expressed MAT2A, encoding MATII isozyme, known as MAT1A:MAT2A switch, occurs in hepatocellular carcinoma (HCC). Being inhibited by its reaction product, MATII isoform upregulation cannot compensate for MATI/III decrease. Therefore, MAT1A:MAT2A switch contributes to decrease in SAM level in rodent and human hepatocarcinogenesis. SAM administration to carcinogen-treated rats prevents hepatocarcinogenesis, whereas MAT1A-KO mice, characterized by chronic SAM deficiency, exhibit macrovesicular steatosis, mononuclear cell infiltration in periportal areas, and HCC development. This review focuses upon the pleiotropic changes, induced by MAT1A/MAT2A switch, associated with HCC development. Epigenetic control of MATs expression occurs at transcriptional and post-transcriptional levels. In HCC cells, MAT1A/MAT2A switch is associated with global DNA hypomethylation, decrease in DNA repair, genomic instability, and signaling deregulation including c-MYC overexpression, rise in polyamine synthesis, upregulation of RAS/ERK, IKK/NF-kB, PI3K/AKT, and LKB1/AMPK axis. Furthermore, decrease in MAT1A expression and SAM levels results in increased HCC cell proliferation, cell survival, and microvascularization. All of these changes are reversed by SAM treatment in vivo or forced MAT1A overexpression or MAT2A inhibition in cultured HCC cells. In human HCC, MAT1A:MAT2A and MATI/III:MATII ratios correlate negatively with cell proliferation and genomic instability, and positively with apoptosis and global DNA methylation. This suggests that SAM decrease and MATs deregulation represent potential therapeutic targets for HCC. Finally, MATI/III:MATII ratio strongly predicts patients' survival length suggesting that MAT1A:MAT2A expression ratio is a putative prognostic marker for human HCC. Copyright © 2013 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Fragmentation and reactivity in collisions of protonated diglycine with chemically modified perfluorinated alkylthiolate-self-assembled monolayer surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnes, George L.; Yang Li; Hase, William L.

2011-03-07

Direct dynamics simulations are reported for quantum mechanical (QM)/molecular mechanical (MM) trajectories of N-protonated diglycine (gly{sub 2}-H{sup +}) colliding with chemically modified perfluorinated octanethiolate self-assembled monolayer (SAM) surfaces. The RM1 semiempirical theory is used for the QM component of the trajectories. RM1 activation and reaction energies were compared with those determined from higher-level ab initio theories. Two chemical modifications are considered in which a head group (-COCl or -CHO) is substituted on the terminal carbon of a single chain of the SAM. These surfaces are designated as the COCl-SAM and CHO-SAM, respectively. Fragmentation, peptide reaction with the SAM, and covalentmore » linkage of the peptide or its fragments with the SAM surface are observed. Peptide fragmentation via concerted CH{sub 2}-CO bond breakage is the dominant pathway for both surfaces. HCl formation is the dominant species produced by reaction with the COCl-SAM, while for the CHO-SAM a concerted H-atom transfer from the CHO-SAM to the peptide combined with either a H-atom or radical transfer from the peptide to the surface to form singlet reaction products is the dominant pathway. A strong collision energy dependence is found for the probability of peptide fragmentation, its reactivity, and linkage with the SAM. Surface deposition, i.e., covalent linkage between the surface and the peptide, is compared to recent experimental observations of such bonding by Laskin and co-workers [Phys. Chem. Chem. Phys. 10, 1512 (2008)]. Qualitative differences in reactivity are seen between the COCl-SAM and CHO-SAM showing that chemical identity is important for surface reactivity. The probability of reactive surface deposition, which is most closely analogous to experimental observables, peaks at a value of around 20% for a collision energy of 50 eV.« less

Testing the validity, reliability and utility of the Self-Administration of Medication (SAM) tool in patients undergoing rehabilitation.

PubMed

Anderson, Jessica; Manias, Elizabeth; Kusljic, Snezana; Finch, Sue

2014-01-01

Determination of patients' ability to self-administer medications in the hospital has largely been determined using the subjective judgment of health professionals. To examine the validity, reliability and utility of the Self-Administration of Medication (SAM) tool as an objective means to determine patients' ability to self-administer in a rehabilitation unit of a public teaching hospital in Melbourne, Australia. To assess validity of the SAM tool, associations were examined between the total SAM tool score and of the patients' competence to self-administer from the perceptions of the tool administrator, patients and nurses. Validity also was determined from a principal component analysis. Pearson correlations were calculated for how SAM scores related to scores obtained from the Functional Independence Measure (FIM) and Barthel Score Index (BSI). To assess the SAM tool's reliability, a Cronbach's alpha coefficient was calculated. Utility of the SAM tool was evidenced by documenting its administration time. One hundred patients participated in this study. The SAM tool had a Cronbach's alpha coefficient of 0.75 and took a mean time of 5.36 min to complete. The capability to self-medicate section of the SAM tool had strong correlations with the FIM (r = 0.485) and BSI (r = 0.472) data, respectively, and the total SAM tool had moderate and strong correlations with the nurses' (r = 0.315) and tool administrator's (r = 0.632) perceptions of patients' ability to self-administer, respectively. Bland-Altman and ROC curve analyses showed poor agreement between the total SAM tool score and the nurses' perceptions. The SAM tool demonstrated acceptable overall internal consistency. It only requires a short time to be completed and is more objective than seeking out health professionals' perceptions. Additional research is needed to further validate this approach to determining patients' ability to self-medicate. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Review of the safety and efficacy of vitamin A supplementation in the treatment of children with severe acute malnutrition.

PubMed

Iannotti, Lora L; Trehan, Indi; Manary, Mark J

2013-09-12

World Health Organization (WHO) guidelines recommend for children with severe acute malnutrition (SAM), high-dose vitamin A (VA) supplements be given on day 1 of admission, and on days 2 and 14 in the case of clinical signs of vitamin A deficiency (VAD). Daily low-dose VA follows, delivered in a premix added to F-75 and F-100. This study aimed to systematically review the evidence for safety and effectiveness of high-dose VA supplementation (VAS) in treatment of children with SAM. A comprehensive literature review was undertaken for all relevant randomized controlled trials (RCT) and observational studies from 1950 to 2012. Studies identified for full review were evaluated using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology using a set of pre-defined criteria: indirectness; inconsistency; imprecision; and study limitations. A quality rating of high, moderate, or low was then assigned to each study, and only those attaining moderate to high were considered in making recommendations. Of the 2072 abstracts screened, 38 met criteria for full review, and 20 were rated moderate to high quality. Only one study replicated the WHO VA protocol in children with SAM. Indirectness was a critical limitation, as studies were not exclusive to children with SAM. There was inconsistency across trials for definitions of malnutrition, morbidities, and ages studied; and imprecision arising from sub-group analyses and small sample sizes. Evidence showed improved outcomes associated with low-dose compared to high-dose VAS, except in cases presenting with signs of VAD, measles, and severe diarrhea or shigellosis. Adverse outcomes related to respiratory infection, diarrhea, and growth were associated with high-dose VAS in children who were predominantly adequately nourished. No adverse effects of the high dose were found in children with SAM in the trial that replicated the WHO VA guideline. This is the first systematic review of the safety and efficacy of high-dose VAS in treatment of SAM. We recommend a low-dose VAS regimen for children with SAM, except in cases presenting with measles, severe diarrhea (shigellosis), and any indication of VAD. Further research is needed in exclusively malnourished children and to explore alternate delivery strategies.

The Effect of Hydrophobic Pockets in Human Serum Albumin Adsorption to Self-Assembled Monolayers

NASA Astrophysics Data System (ADS)

Choi, Eugene J.; Jia, Shijin; Petrash, Stanislaw; Foster, Mark D.

2001-04-01

Molecular properties of proteins and their interactions with surfaces have an effect on protein adsorption, which is one of the first and most important events that occurs when a biological fluid contacts a surface. For biomaterials applications, blood reaction to foreign objects can cause thrombosis. To understand thrombosis, it is necessary to understand the mechanism of adsorption of blood proteins onto artificial surfaces. Such interactions as hydrophobicity^1,2, electrostatics^3 and specific binding^4 have been found to be driving forces for protein adsorption. Self-assembled monolayers (SAMs) provide an ideal surface for which protein adsorption behavior can be studied.^1 SAMs provide chemical homogeneity, robustness, and variable surface functionality. The hydrophobicity of SAMs has been of great interest in studying surface interactions with proteins.^1, 2 The packing density of alkyl chains of SAMs can also be varied in order to obtain different surface properties. The most abundant protein in the blood is human serum albumin (HSA). Because HSA acts as a fatty acid transporter, it has six binding sites for fatty acids. Pitt and Cooper^4 have shown that alkylation of surfaces increases the initial adsorption rate of delipidized (fatty acid free) HSA. Petrash et al.^5 have shown that delipidized HSA binds more tenaciously to less densely packed alkyl SAMs than to densely packed alkyl SAMs when desorbed by sodium dodecyl sulfate. Using X-ray reflectivity to study the adsorbed protein layer thickness, lipidized HSA (fatty acid bound) adsorption and desorption studies showed that specific binding of HSA is one of the main factors in binding tenacity between HSA and less densely packed alkyl SAMs. Atomic force microscopy was used as a complementary technique to confirm these results, and neutron reflectivity and spectroscopy techniques will also be used to study the adsorption behaviors of HSA and other blood proteins in future work. 1. Prime, K. L.; Whitesides, G. M. Science 1991, 252, 1164. 2. Lu, J. R.; Su, T. J.; Thirtle, P. N.; Thomas, R. K.; Rennie, A. R.; Cubitt, R. J. Colloid Interface Sci. 1998, 206, 212. 3. Su, T. J.; Lu, J.R.; Thomas, R. K.; Cui, Z. F. J. Phys. Chem. B. 1999, 103, 3727. 4. Pitt, W. G.; Cooper, S. L. J. Biomed. Mater. Res. 1988, 22, 359. 5. Petrash, S.; Sheller, N. B.; Dando, W.; Foster, M. D. Langmuir 1997, 13, 1881.

Effects of unconditional cash transfers on the outcome of treatment for severe acute malnutrition (SAM): a cluster-randomised trial in the Democratic Republic of the Congo.

PubMed

Grellety, Emmanuel; Babakazo, Pélagie; Bangana, Amina; Mwamba, Gustave; Lezama, Ines; Zagre, Noël Marie; Ategbo, Eric-Alain

2017-04-26

Cash transfer programs (CTPs) aim to strengthen financial security for vulnerable households. This potentially enables improvements in diet, hygiene, health service access and investment in food production or income generation. The effect of CTPs on the outcome of children already severely malnourished is not well delineated. The objective of this study was to test whether CTPs will improve the outcome of children treated for severe acute malnutrition (SAM) in the Democratic Republic of the Congo over 6 months. We conducted a cluster-randomised controlled trial in children with uncomplicated SAM who received treatment according to the national protocol and counselling with or without a cash supplement of US$40 monthly for 6 months. Analyses were by intention to treat. The hazard ratio of reaching full recovery from SAM was 35% higher in the intervention group than the control group (adjusted hazard ratio, 1.35, 95% confidence interval (CI) = 1.10 to 1.69, P = 0.007). The adjusted hazard ratios in the intervention group for relapse to moderate acute malnutrition (MAM) and SAM were 0.21 (95% CI = 0.11 to 0.41, P = 0.001) and 0.30 (95% CI = 0.16 to 0.58, P = 0.001) respectively. Non-response and defaulting were lower when the households received cash. All the nutritional outcomes in the intervention group were significantly better than those in the control group. After 6 months, 80% of cash-intervened children had re-gained their mid-upper arm circumference measurements and weight-for-height/length Z-scores and showed evidence of catch-up. Less than 40% of the control group had a fully successful outcome, with many deteriorating after discharge. There was a significant increase in diet diversity and food consumption scores for both groups from baseline; the increase was significantly greater in the intervention group than the control group. CTPs can increase recovery from SAM and decrease default, non-response and relapse rates during and following treatment. Household developmental support is critical in food insecure areas to maximise the efficiency of SAM treatment programs. ClinicalTrials.gov, NCT02460848 . Registered on 27 May 2015.

Fatty Acid Detection in Mars-Analogous Rock Samples with the TMAH Wet Chemistry Experiment on the Sample Analysis at Mars (SAM) Instrument

NASA Astrophysics Data System (ADS)

Williams, A. J.; Eigenbrode, J. L.; Wilhelm, M. B.; Johnson, S. S.; Craft, K.; O'Reilly, S.; Lewis, J. M. T.; Williams, R.; Summons, R. E.; Benison, K. C.; Mahaffy, P. R.

2017-12-01

The Curiosity rover is exploring sedimentary rock sequences in Gale Crater for evidence of habitability and searching for organic compounds using the Sample Analysis at Mars (SAM) instrument suite. SAM includes a gas chromatograph mass spectrometer (GC-MS) and pyrolysis ovens. SAM has the ability to perform wet chemistry experiments, one of which uses tetramethylammonium hydroxide (TMAH) thermochemolysis to liberate bound lipids, making them sufficiently volatile for detection by GC-MS. To determine the effectiveness of the SAM-like TMAH experiment on fatty acid methyl ester (FAME) biomarker identification, rock and sediment samples were collected from a variety of Mars analog environments including iron oxides from a modern mineral precipitate and older surface gossan at Iron Mountain, CA, as well as modern acid salt and neutral lake sediments with mixed iron oxides and clays from Western Australia; siliceous sinter from recently inactive and modern near-vent Icelandic hot springs deposits; modern carbonate ooids from The Bahamas, and organic-rich shale from Germany. Samples underwent pyrolysis with TMAH. Fatty acids were analyzed by pyro-GC-MS using a SAM-like heating ramp (35°C/min) as well as a 500°C flash on a Frontier pyrolyzer and Agilent GC-MS instrument. Results reveal that FAMEs were detectable with the TMAH experiment in nearly all samples. Low molecular weight (MW) C6:0-C10:0 FAMEs were present in all samples, medium MW C11:0-C18:2 FAMEs were present in select samples, and high MW (HMW) C20:0-C30:0 FAMEs were present in the shale sample. Many of these samples exhibited an even-over-odd carbon number preference, indicating biological production. These experiments demonstrate that TMAH thermochemolysis with SAM-like pyro-GC-MS is effective in fatty acid analysis from natural Mars-analog samples that vary in mineralogy, age, and microbial community input. HMW FAMEs are not detected in iron-dominated samples, and may not be detectable at low concentrations. Although mineralogies such as sinter, carbonates, and shales are not likely in Gale Crater, iron oxides mixed with clays are known to be present in the path of the Curiosity rover. Environments with these mineralogies may provide the optimal opportunity to detect fatty acids, if present in Gale Crater.

Physics based performance model of a UV missile seeker

NASA Astrophysics Data System (ADS)

James, I.

2017-10-01

Electro-optically (EO) guided surface to air missiles (SAM) have developed to use Ultraviolet (UV) wavebands supplementary to the more common Infrared (IR) wavebands. Missiles such as the US Stinger have been around for some time, these have been joined recently by Chinese FN-16 and Russian SA-29 (Verba) and there is a much higher potential proliferation risk. The purpose of this paper is to introduce a first-principles, physics based, model of a typical seeker arrangement. The model is constructed from various calculations that aim to characterise the physical effects that will affect the performance of the system. Data has been gathered from a number of sources to provide realism to the variables within the model. It will be demonstrated that many of the variables have the power to dramatically alter the performance of the system as a whole. Further, data will be shown to illustrate the expected performance of a typical UV detector within a SAM in detection range against a variety of target sizes. The trend for the detection range against aircraft size and skin reflectivity will be shown to be non-linear, this should have been expected owing to the exponential decay of a signal through atmosphere. Future work will validate the performance of the model against real world performance data for cameras (when this is available) to ensure that it is operates within acceptable errors.

Efficacy of artemether-lumefantrine in relation to drug exposure in children with and without severe acute malnutrition: an open comparative intervention study in Mali and Niger.

PubMed

Denoeud-Ndam, Lise; Dicko, Alassane; Baudin, Elisabeth; Guindo, Ousmane; Grandesso, Francesco; Diawara, Halimatou; Sissoko, Sibiri; Sanogo, Koualy; Traoré, Seydou; Keita, Sekouba; Barry, Amadou; de Smet, Martin; Lasry, Estrella; Smit, Michiel; Wiesner, Lubbe; Barnes, Karen I; Djimde, Abdoulaye A; Guerin, Philippe J; Grais, Rebecca F; Doumbo, Ogobara K; Etard, Jean-François

2016-10-24

Severe acute malnutrition (SAM) affects almost all organs and has been associated with reduced intestinal absorption of medicines. However, very limited information is available on the pharmacokinetic properties of antimalarial drugs in this vulnerable population. We assessed artemether-lumefantrine (AL) clinical efficacy in children with SAM compared to those without. Children under 5 years of age with uncomplicated P. falciparum malaria were enrolled between November 2013 and January 2015 in Mali and Niger, one third with uncomplicated SAM and two thirds without. AL was administered under direct observation with a fat intake consisting of ready-to-use therapeutic food (RUTF - Plumpy'Nut®) in SAM children, twice daily during 3 days. Children were followed for 42 days, with PCR-corrected adequate clinical and parasitological response (ACPR) at day 28 as the primary outcome. Lumefantrine concentrations were assessed in a subset of participants at different time points, including systematic measurements on day 7. A total of 399 children (360 in Mali and 39 in Niger) were enrolled. Children with SAM were younger than their non-SAM counterparts (mean 17 vs. 28 months, P < 0.0001). PCR-corrected ACPR was 100 % (95 % CI, 96.8-100 %) in SAM at both day 28 and 42, versus 98.8 % (96.4-99.7 %) at day 28 and 98.3 % (95.6-99.4 %) at day 42 in non-SAM (P = 0.236 and 0.168, respectively). Compared to younger children, children older than 21 months experienced more reinfections and SAM was associated with a greater risk of reinfection until day 28 (adjusted hazard ratio = 2.10 (1.04-4.22), P = 0.038). Day 7 lumefantrine concentrations were significantly lower in SAM than non-SAM (median 251 vs. 365 ng/mL, P = 0.049). This study shows comparable therapeutic efficacy of AL in children without SAM and in those with SAM when given in combination with RUTF, but a higher risk of reinfection in older children suffering from SAM. This could be associated with poorer exposure to the antimalarials as documented by a lower lumefantrine concentration on day 7. ClinicalTrials.gov: NCT01958905 , registration date: October 7, 2013.

Prognostic value of mid-regional pro-adrenomedullin levels taken on admission and discharge in non-ST-elevation myocardial infarction: the LAMP (Leicester Acute Myocardial Infarction Peptide) II study.

PubMed

Dhillon, Onkar S; Khan, Sohail Q; Narayan, Hafid K; Ng, Kelvin H; Struck, Joachim; Quinn, Paulene A; Morgenthaler, Nils G; Squire, Iain B; Davies, Joan E; Bergmann, Andreas; Ng, Leong L

2010-07-06

The purpose of this study was to assess the prognostic value of admission and discharge mid-regional pro-adrenomedullin (sAM) levels in non-ST-elevation myocardial infarction (MI) and identify values to aid clinical decision making. N-terminal pro-B-type natriuretic peptide and GRACE (Global Registry of Acute Coronary Events) score were used as comparators. sAM is a stable precursor of adrenomedullin. We measured plasma sAM on admission and discharge in 745 non-ST-elevation MI patients (514 men, median age 70.0 +/- 12.7 years). The primary end point was a composite of death, heart failure, hospitalization, and recurrent acute MI over mean follow-up of 760 days (range 150 to 2,837 days), with each event assessed individually as secondary end points. During follow-up, 120 (16.1%) patients died, and there were 65 (8.7%) hospitalizations for heart failure and 77 (10.3%) recurrent acute MIs. Both admission and discharge levels were increased (median 0.81 nmol/l [range 0.06 to 5.75 nmol/l] and 0.76 nmol/l [range 0.25 to 6.95 nmol/l], respectively) compared with established normal ranges. Multivariate adjusted Cox regression models revealed that both were associated with the primary end point (hazard ratio: 9.75 on admission and 7.54 on discharge; both p < 0.001). Admission sAM was particularly associated with early (<30 days) mortality (c-statistic = 0.90, p < 0.001), and when compared with N-terminal pro-B-type natriuretic peptide and GRACE score, it was the only independent predictor of this end point. Admission sAM >1.11 nmol/l identified those at highest risk of death (p < 0.001). Patients with above-median admission sAM may benefit from revascularization. sAM level is prognostic for death or heart failure. Admission levels are a strong predictor of early mortality and, when >1.11 nmol/l, complements the GRACE score to improve risk stratification. Copyright 2010 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Calibration and Sequence Development Status for the Sample Analysis at Mars Investigation on the Mars Science Laboratory

NASA Technical Reports Server (NTRS)

Mahaffy, Paul R.

2012-01-01

The measurement goals of the Sample Analysis at Mars (SAM) instrument suite on the "Curiosity" Rover of the Mars Science Laboratory (MSL) include chemical and isotopic analysis of organic and inorganic volatiles for both atmospheric and solid samples [1,2]. SAM directly supports the ambitious goals of the MSL mission to provide a quantitative assessment of habitability and preservation in Gale crater by means of a range of chemical and geological measurements [3]. The SAM FM combined calibration and environmental testing took place primarily in 2010 with a limited set of tests implemented after integration into the rover in January 2011. The scope of SAM FM testing was limited both to preserve SAM consumables such as life time of its electromechanical elements and to minimize the level of terrestrial contamination in the SAM instrument. A more comprehensive calibration of a SAM-like suite of instruments will be implemented in 2012 with calibration runs planned for the SAM testbed. The SAM Testbed is nearly identical to the SAM FM and operates in a ambient pressure chamber. The SAM Instrument Suite: SAM's instruments are a Quadrupole Mass Spectrometer (QMS), a 6-column Gas Chromatograph (GC), and a 2-channel Tunable Laser Spectrometer (TLS). Gas Chromatography Mass Spectrometry is designed for identification of even trace organic compounds. The TLS [5] secures the C, H, and O isotopic composition in carbon dioxide, water, and methane. Sieved materials are delivered from the MSL sample acquisition and processing system to one of68 cups of the Sample Manipulation System (SMS). 59 of these cups are fabricated from inert quartz. After sample delivery, a cup is inserted into one of 2 ovens for evolved gas analysis (EGA ambient to >9500C) by the QMS and TLS. A portion of the gas released can be trapped and subsequently analyzed by GCMS. Nine sealed cups contain liquid solvents and chemical derivatization or thermochemolysis agents to extract and transform polar molecules such as amino acids, nucleobases, and carboxylic acids into compounds that are sufficiently volatile to transmit through the GC columns. The remaining 6 cups contain calibrants. SAM FM Calibration Overview: The SAM FM calibration in the Mars chamber employed a variety of pure gases, gas mixtures, and solid materials. Isotope calibration runs for the TLS utilized 13C enriched C02 standards and 0 enriched CH4. A variety of fluorocarbon compounds that spanned the entire mass range of the QMS as well as C3-C6 hydrocarbons were utilized for calibration of the GCMS. Solid samples consisting of a mixture of calcite, melanterite, and inert silica glass either doped or not with fluorocarbons were introduced into the SAM FM cups through the SAM inlet funnel/tube system.

Formulation of additional observables for ENTREE

NASA Technical Reports Server (NTRS)

Findlay, J. T.; Heck, M. L.

1980-01-01

The S-band X and Y angles, SAMS, and TACAN range and bearing were incorporated into the ENTREE software for use by experimenters at LaRC for entry trajectory reconstruction purposes. Background discussions present the need for this added capability. Formulations for the various observables are presented. Both north-south and east-west antenna mounts were provided for in the S-band angle computations. Sub-vehicle terrain height variations are included in the SAMS model. Local magnetic variations were incorporated for the TACAN bearing computations. Observable formulations are discussed in detail along with the partial computations.

75 FR 4579 - Certificate of Alternative Compliance for the Tugboat MR SAM

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-28

... Compliance for the Tugboat MR SAM AGENCY: Coast Guard, DHS. ACTION: Notice. SUMMARY: The Coast Guard announces that a Certificate of Alternative Compliance was issued for the tugboat MR SAM as required by 33 U... Title 33, Code of Federal Regulations, Parts 81 and 89, has been issued for the tugboat MR SAM, O.N...

The Epigenetic Effects of a High Prenatal Folate Intake in Male Mouse Fetuses Exposed In Utero to Arsenic

PubMed Central

Tsang, Verne; Fry, Rebecca C.; Niculescu, Mihai D.; Rager, Julia E.; Saunders, Jesse; Paul, David S.; Zeisel, Steven H.; Waalkes, Michael P.; Stýblo, Miroslav; Drobná, Zuzana

2012-01-01

Inorganic arsenic (iAs) is a complete transplacental carcinogen in mice. Previous studies have demonstrated that in utero exposure to iAs promotes cancer in adult mouse offspring, possibly acting through epigenetic mechanisms. Humans and rodents enzymatically convert iAs to its methylated metabolites. This reaction requires S-adenosylmethionine (SAM) as methyl group donor. SAM is also required for DNA methylation. Supplementation with folate, a major dietary source of methyl groups for SAM synthesis, has been shown to modify iAs metabolism and the adverse effects of iAs exposure. However, effects of gestational folate supplementation on iAs metabolism and fetal DNA methylation have never been thoroughly examined. In the present study, pregnant CD1 mice were fed control (i.e. normal folate, or 2.2 mg/kg) or high folate diet (11 mg/kg) from gestational day (GD) 5 to 18 and drank water with 0 or 85 ppm of As (as arsenite) from GD8 to 18. The exposure to iAs significantly decreased body weight of GD18 fetuses and increased both SAM and S-adenosylhomocysteine (SAH) concentrations in fetal livers. High folate intake lowered the burden of total arsenic in maternal livers but did not prevent the effects of iAs exposure on fetal weight or hepatic SAM and SAH concentrations. In fact, combined folate-iAs exposure caused further significant body weight reduction. Notably, iAs exposure alone had little effect on DNA methylation in fetal livers. In contrast, the combined folate-iAs exposure changed the CpG island methylation in 2,931 genes, including genes known to be imprinted. Most of these genes were associated with neurodevelopment, cancer, cell cycle, and signaling networks. The canonical Wnt-signaling pathway, which regulates fetal development, was among the most affected biological pathways. Taken together, our results suggest that a combined in utero exposure to iAs and a high folate intake may adversely influence DNA methylation profiles and weight of fetuses, compromising fetal development and possibly increasing the risk for early-onset of disease in offspring. PMID:22959928

The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study

NASA Astrophysics Data System (ADS)

Manz, Christoph; Kobitski, Andrei Yu.; Samanta, Ayan; Jäschke, Andres; Nienhaus, G. Ulrich

2018-03-01

RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase. We have measured smFRET histograms over wide ranges of Mg2+ concentration for three RS variants that were specifically labeled with fluorescent dyes on different sites. In the analysis, different conformations are associated with discrete Gaussian model distributions, which are typically fairly broad on the FRET efficiency scale and thus can be extremely challenging to unravel due to their mutual overlap. Our earlier work on two SAM-I RS variants revealed four major conformations. By introducing a global fitting procedure which models both the Mg2+ concentration dependencies of the fractional populations and the average FRET efficiencies of the individual FRET distributions according to Mg2+ binding isotherms, we were able to consistently describe the histogram data of both variants at all studied Mg2+ concentrations. With the third FRET-labeled variant, however, we found significant deviations when applying the four-state model to the data. This can arise because the different FRET labeling of the new variant allows two states to be distinguished that were previously not separable due to overlap. Indeed, the resulting five-state model presented here consistently describes the smFRET histograms of all three variants as well as their variations with Mg2+ concentration. We also performed a triangulation of the donor position for two of the constructs to explore how the expression platform is oriented with respect to the aptamer.

Controlled Synthesis of Pd/Pt Core Shell Nanoparticles Using Area-selective Atomic Layer Deposition

PubMed Central

Cao, Kun; Zhu, Qianqian; Shan, Bin; Chen, Rong

2015-01-01

We report an atomic scale controllable synthesis of Pd/Pt core shell nanoparticles (NPs) via area-selective atomic layer deposition (ALD) on a modified surface. The method involves utilizing octadecyltrichlorosilane (ODTS) self-assembled monolayers (SAMs) to modify the surface. Take the usage of pinholes on SAMs as active sites for the initial core nucleation, and subsequent selective deposition of the second metal as the shell layer. Since new nucleation sites can be effectively blocked by surface ODTS SAMs in the second deposition stage, we demonstrate the successful growth of Pd/Pt and Pt/Pd NPs with uniform core shell structures and narrow size distribution. The size, shell thickness and composition of the NPs can be controlled precisely by varying the ALD cycles. Such core shell structures can be realized by using regular ALD recipes without special adjustment. This SAMs assisted area-selective ALD method of core shell structure fabrication greatly expands the applicability of ALD in fabricating novel structures and can be readily applied to the growth of NPs with other compositions. PMID:25683469

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

PubMed Central

Roy, Susmita; Lammert, Heiko; Dayie, T. Kwaku; Sanbonmatsu, Karissa Y.

2017-01-01

Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function. PMID:28248966

Multifunctional Self-Assembled Monolayers for Organic Field-Effect Transistors

NASA Astrophysics Data System (ADS)

Cernetic, Nathan

Organic field effect transistors (OFETs) have the potential to reach commercialization for a wide variety of applications such as active matrix display circuitry, chemical and biological sensing, radio-frequency identification devices and flexible electronics. In order to be commercially competitive with already at-market amorphous silicon devices, OFETs need to approach similar performance levels. Significant progress has been made in developing high performance organic semiconductors and dielectric materials. Additionally, a common route to improve the performance metric of OFETs is via interface modification at the critical dielectric/semiconductor and electrode/semiconductor interface which often play a significant role in charge transport properties. These metal oxide interfaces are typically modified with rationally designed multifunctional self-assembled monolayers. As means toward improving the performance metrics of OFETs, rationally designed multifunctional self-assembled monolayers are used to explore the relationship between surface energy, SAM order, and SAM dipole on OFET performance. The studies presented within are (1) development of a multifunctional SAM capable of simultaneously modifying dielectric and metal surface while maintaining compatibility with solution processed techniques (2) exploration of the relationship between SAM dipole and anchor group on graphene transistors, and (3) development of self-assembled monolayer field-effect transistor in which the traditional thick organic semiconductor is replaced by a rationally designed self-assembled monolayer semiconductor. The findings presented within represent advancement in the understanding of the influence of self-assembled monolayers on OFETs as well as progress towards rationally designed monolayer transistors.

Overexpression of S-adenosylmethionine decarboxylase (SAMDC) in early Xenopus embryos induces cell dissociation and inhibits transition from the blastula to gastrula stage.

PubMed

Shibata, M; Shinga, J; Yasuhiko, Y; Kai, M; Miura, K; Shimogori, T; Kashiwagi, K; Igarashi, K; Shiokawa, K

1998-07-01

Xenopus early embryos contain relatively low levels of S-adenosyl-methionine decarboxylase (SAMDC) and its mRNA. When SAMDC mRNA was injected into Xenopus embryos, it was preserved until the blastula stage and induced a large increase in SAMDC activity. The SAMDC-overexpressed embryos developed normally until the blastula stage but at the early gastrula stage cells which received the mRNA, dissociated autonomously and stopped synthesizing protein. In a hypotonic medium, the dissociated cells, and hence whole embryos, autolyzed. However, in isotonic media dissociated cells did not autolyze, although they did not divide and their DNA and RNA synthesis activity was greatly inhibited. The effects of SAMDC overexpression were abolished by coinjection of ethylglyoxal-bis(guanylhydrazone) (EGBG), a specific inhibitor of SAMDC. In SAMDC-overexpressed embryos the level of putrescine decreased and that of spermidine increased, though to limited extents, resulting in a considerable decrease in the putrescine/spermidine ratio. However, direct injection of spermidine did not mimic the effect of SAMDC overexpression, and putrescine coinjected with SAMDC mRNA to maintain the normal putrescine/spermidine ratio did not rescue the embryos. Conversely, the level of S-adenosylmethionine (SAM) greatly decreased and coinjection of SAM, which restored the level of SAM, rescued the embryos. We concluded that in SAMDC-overexpressed embryos a SAM-deficient state was induced and this caused cell dissociation and inhibition of transition from the blastula to gastrula stage. We suggest that the SAM-deficient embryos obtained in the present study provide a unique system for studying the cellular control mechanism underlying the blastula-gastrula transition.

The Investigation of Chlorates as a Possible Source of Oxygen and Chlorine Detected by the Sample Analysis at Mars (SAM) Instrument in Gale Crater, Mars

NASA Technical Reports Server (NTRS)

Sutter, B.; Archer, D. P.; Ming, D. W.; Niles, P. B.; Eigenbrode, J. L.; Franz, H.; Glavin, D. P.; McAdam, A. C.; Mahaffy, P; Stern, J. C.;

Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs.

PubMed

Putkinen, Anuliina; Larmola, Tuula; Tuomivirta, Tero; Siljanen, Henri M P; Bodrossy, Levente; Tuittila, Eeva-Stiina; Fritze, Hannu

2014-06-01

Sphagnum-associated methanotrophs (SAM) are an important sink for the methane (CH4) formed in boreal peatlands. We aimed to reveal how peatland succession, which entails a directional change in several environmental variables, affects SAM and their activity. Based on the pmoA microarray results, SAM community structure changes when a peatland develops from a minerotrophic fen to an ombrotrophic bog. Methanotroph subtypes Ia, Ib, and II showed slightly contrasting patterns during succession, suggesting differences in their ecological niche adaptation. Although the direct DNA-based analysis revealed a high diversity of type Ib and II methanotrophs throughout the studied peatland chronosequence, stable isotope probing (SIP) of the pmoA gene indicated they were active mainly during the later stages of succession. In contrast, type Ia methanotrophs showed active CH4 consumption in all analyzed samples. SIP-derived (13)C-labeled 16S rRNA gene clone libraries revealed a high diversity of SAM in every succession stage including some putative Methylocella/Methyloferula methanotrophs that are not detectable with the pmoA-based approach. In addition, a high diversity of 16S rRNA gene sequences likely representing cross-labeled nonmethanotrophs was discovered, including a significant proportion of Verrucomicrobia-related sequences. These results help to predict the effects of changing environmental conditions on SAM communities and activity. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

A pilot study investigating the feasibility of symptom assessment manager (SAM), a Web-based real-time tool for monitoring challenging behaviors.

PubMed

Loi, Samantha M; Wanasinghage, Sangeeth; Goh, Anita; Lautenschlager, Nicola T; Darby, David G; Velakoulis, Dennis

2018-04-01

Improving and minimizing challenging behaviors seen in psychiatric conditions, including behavioral and psychological symptoms of dementia are important in the care of people with these conditions. Yet there is a lack of systematic evaluation of these as a part of routine clinical care. The Neuropsychiatric Inventory is a validated and reliable tool for rating the severity and disruptiveness of challenging behaviors. We report on the evaluation of a Web-based symptom assessment manager (SAM), designed to address the limitation of previous tools using some of the Neuropsychiatric Inventory functions, to monitor behaviors by staff caring for people with dementia and other psychiatric conditions in inpatient and residential care settings. The SAM was piloted in an 8-bed inpatient neuropsychiatry unit over 5 months. Eleven nurses and 4 clinicians were trained in usage of SAM. Primary outcomes were usage of SAM and perceived usability, utility, and acceptance of SAM. Secondary outcomes were the frequencies of documented behavior. Usage data were analyzed using chi-square and logistic regression analyses. The SAM was used for all admitted patients regardless of diagnosis, with a usage rate of 64% for nurses regularly employed in the unit. Staff provided positive feedback regarding the utility of SAM. The SAM appeared to offer individualized behavior assessment by providing a quick, structured, and standardized platform for assessing behavior in a real-world setting. Further research would involve trialing SAM with more staff in alternative settings such as in home or residential care settings. Copyright © 2017 John Wiley & Sons, Ltd.

Predicting the synergy of multiple stress effects

NASA Astrophysics Data System (ADS)

Liess, Matthias; Foit, Kaarina; Knillmann, Saskia; Schäfer, Ralf B.; Liess, Hans-Dieter

2016-09-01

Toxicants and other, non-chemical environmental stressors contribute to the global biodiversity crisis. Examples include the loss of bees and the reduction of aquatic biodiversity. Although non-compliance with regulations might be contributing, the widespread existence of these impacts suggests that for example the current approach of pesticide risk assessment fails to protect biodiversity when multiple stressors concurrently affect organisms. To quantify such multiple stress effects, we analysed all applicable aquatic studies and found that the presence of environmental stressors increases individual sensitivity to toxicants (pesticides, trace metals) by a factor of up to 100. To predict this dependence, we developed the “Stress Addition Model” (SAM). With the SAM, we assume that each individual has a general stress capacity towards all types of specific stress that should not be exhausted. Experimental stress levels are transferred into general stress levels of the SAM using the stress-related mortality as a common link. These general stress levels of independent stressors are additive, with the sum determining the total stress exerted on a population. With this approach, we provide a tool that quantitatively predicts the highly synergistic direct effects of independent stressor combinations.

A Response to Sam McKegney's "Strategies for Ethical Engagement: An Open Letter Concerning Non-Native Scholars of Native Literatures"

ERIC Educational Resources Information Center

Appleford, Rob

2009-01-01

This article presents the author's response to Sam McKegney's "Strategies for Ethical Engagement: An Open Letter Concerning Non-Native Scholars of Native Literatures." In his response to Sam's diagnosis of the malaise currently afflicting non-Aboriginal critics of this literature, the author attempts to consider the "cure" Sam offers (albeit…

Walking with a Slower Friend

ERIC Educational Resources Information Center

Bailey, Herb; Kalman, Dan

2011-01-01

Fay and Sam go for a walk. Sam walks along the left side of the street while Fay, who walks faster, starts with Sam but walks to a point on the right side of the street and then returns to meet Sam to complete one segment of their journey. We determine Fay's optimal path minimizing segment length, and thus maximizing the number of times they meet…

An adaptor role for cytoplasmic Sam68 in modulating Src activity during cell polarization.

PubMed

Huot, Marc-Etienne; Brown, Claire M; Lamarche-Vane, Nathalie; Richard, Stéphane

2009-04-01

The Src-associated substrate during mitosis with a molecular mass of 68 kDa (Sam68) is predominantly nuclear and is known to associate with proteins containing the Src homology 3 (SH3) and SH2 domains. Although Sam68 is a Src substrate, little is known about the signaling pathway that link them. Src is known to be activated transiently after cell spreading, where it modulates the activity of small Rho GTPases. Herein we report that Sam68-deficient cells exhibit loss of cell polarity and cell migration. Interestingly, Sam68-deficient cells exhibited sustained Src activity after cell attachment, resulting in the constitutive tyrosine phosphorylation and activation of p190RhoGAP and its association with p120rasGAP. Consistently, we observed that Sam68-deficient cells exhibited deregulated RhoA and Rac1 activity. By using total internal reflection fluorescence microscopy, we observed Sam68 near the plasma membrane after cell attachment coinciding with phosphorylation of its C-terminal tyrosines and association with Csk. These findings show that Sam68 localizes near the plasma membrane during cell attachment and serves as an adaptor protein to modulate Src activity for proper signaling to small Rho GTPases.

Ontogeny of the Maize Shoot Apical Meristem[W][OA

PubMed Central

Takacs, Elizabeth M.; Li, Jie; Du, Chuanlong; Ponnala, Lalit; Janick-Buckner, Diane; Yu, Jianming; Muehlbauer, Gary J.; Schnable, Patrick S.; Timmermans, Marja C.P.; Sun, Qi; Nettleton, Dan; Scanlon, Michael J.

2012-01-01

The maize (Zea mays) shoot apical meristem (SAM) arises early in embryogenesis and functions during stem cell maintenance and organogenesis to generate all the aboveground organs of the plant. Despite its integral role in maize shoot development, little is known about the molecular mechanisms of SAM initiation. Laser microdissection of apical domains from developing maize embryos and seedlings was combined with RNA sequencing for transcriptomic analyses of SAM ontogeny. Molecular markers of key events during maize embryogenesis are described, and comprehensive transcriptional data from six stages in maize shoot development are generated. Transcriptomic profiling before and after SAM initiation indicates that organogenesis precedes stem cell maintenance in maize; analyses of the first three lateral organs elaborated from maize embryos provides insight into their homology and to the identity of the single maize cotyledon. Compared with the newly initiated SAM, the mature SAM is enriched for transcripts that function in transcriptional regulation, hormonal signaling, and transport. Comparisons of shoot meristems initiating juvenile leaves, adult leaves, and husk leaves illustrate differences in phase-specific (juvenile versus adult) and meristem-specific (SAM versus lateral meristem) transcript accumulation during maize shoot development. This study provides insight into the molecular genetics of SAM initiation and function in maize. PMID:22911570

(13)C-metabolic flux analysis in S-adenosyl-L-methionine production by Saccharomyces cerevisiae.

PubMed

Hayakawa, Kenshi; Kajihata, Shuichi; Matsuda, Fumio; Shimizu, Hiroshi

2015-11-01

S-Adenosyl-L-methionine (SAM) is a major biological methyl group donor, and is used as a nutritional supplement and prescription drug. Yeast is used for the industrial production of SAM owing to its high intracellular SAM concentrations. To determine the regulation mechanisms responsible for such high SAM production, (13)C-metabolic flux analysis ((13)C-MFA) was conducted to compare the flux distributions in the central metabolism between Kyokai no. 6 (high SAM-producing) and S288C (control) strains. (13)C-MFA showed that the levels of tricarboxylic acid (TCA) cycle flux in SAM-overproducing strain were considerably increased compared to those in the S228C strain. Analysis of ATP balance also showed that a larger amount of excess ATP was produced in the Kyokai 6 strain because of increased oxidative phosphorylation. These results suggest that high SAM production in Kyokai 6 strains could be attributed to enhanced ATP regeneration with high TCA cycle fluxes and respiration activity. Thus, maintaining high respiration efficiency during cultivation is important for improving SAM production. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Quasielastic charged-current neutrino scattering in the scaling model with relativistic effective mass

NASA Astrophysics Data System (ADS)

Ruiz Simo, I.; Martinez-Consentino, V. L.; Amaro, J. E.; Ruiz Arriola, E.

2018-06-01

We use a recent scaling analysis of the quasielastic electron scattering data from C 12 to predict the quasielastic charge-changing neutrino scattering cross sections within an uncertainty band. We use a scaling function extracted from a selection of the (e ,e') cross section data, and an effective nucleon mass inspired by the relativistic mean-field model of nuclear matter. The corresponding superscaling analysis with relativistic effective mass (SuSAM*) describes a large amount of the electron data lying inside a phenomenological quasielastic band. The effective mass incorporates the enhancement of the transverse current produced by the relativistic mean field. The scaling function incorporates nuclear effects beyond the impulse approximation, in particular meson-exchange currents and short-range correlations producing tails in the scaling function. Besides its simplicity, this model describes the neutrino data as reasonably well as other more sophisticated nuclear models.

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

DOE PAGES

Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; ...

2015-03-27

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active sitemore » metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.« less

Selective Plasma Deposition of Fluorocarbon Films on SAMs

NASA Technical Reports Server (NTRS)

Crain, Mark M., III; Walsh, Kevin M.; Cohn, Robert W.

2006-01-01

A dry plasma process has been demonstrated to be useful for the selective modification of self-assembled monolayers (SAMs) of alkanethiolates. These SAMs are used, during the fabrication of semiconductor electronic devices, as etch masks on gold layers that are destined to be patterned and incorporated into the devices. The selective modification involves the formation of fluorocarbon films that render the SAMs more effective in protecting the masked areas of the gold against etching by a potassium iodide (KI) solution. This modification can be utilized, not only in the fabrication of single electronic devices but also in the fabrication of integrated circuits, microelectromechanical systems, and circuit boards. In the steps that precede the dry plasma process, a silicon mold in the desired pattern is fabricated by standard photolithographic techniques. A stamp is then made by casting polydimethylsiloxane (commonly known as silicone rubber) in the mold. The stamp is coated with an alkanethiol solution, then the stamp is pressed on the gold layer of a device to be fabricated in order to deposit the alkanethiol to form an alkanethiolate SAM in the desired pattern (see figure). Next, the workpiece is exposed to a radio-frequency plasma generated from a mixture of CF4 and H2 gases. After this plasma treatment, the SAM is found to be modified, while the exposed areas of gold remain unchanged. This dry plasma process offers the potential for forming masks superior to those formed in a prior wet etching process. Among the advantages over the wet etching process are greater selectivity, fewer pin holes in the masks, and less nonuniformity of the masks. The fluorocarbon films formed in this way may also be useful as intermediate layers for subsequent fabrication steps and as dielectric layers to be incorporated into finished products.

Functional relationship between CABIT, SAM and 14-3-3 binding domains of GAREM1 that play a role in its subcellular localization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishino, Tasuku; Matsunaga, Ryota; Konishi, Hiroaki, E-mail: hkonishi@pu-hiroshima.ac.jp

2015-08-21

GAREM1 (Grb2-associated regulator of Erk/MAPK1) is an adaptor protein that is involved in the epidermal growth factor (EGF) pathway. The nuclear localization of GAREM1 depends on the nuclear localization sequence (NLS), which is located at the N-terminal CABIT (cysteine-containing, all in Themis) domain. Here, we identified 14-3-3ε as a GAREM-binding protein, and its binding site is closely located to the NLS. This 14-3-3 binding site was of the atypical type and independent of GAREM phosphorylation. Moreover, the binding of 14-3-3 had an effect on the nuclear localization of GAREM1. Unexpectedly, we observed that the CABIT domain had intramolecular association withmore » the C-terminal SAM (sterile alpha motif) domain. This association might be inhibited by binding of 14-3-3 at the CABIT domain. Our results demonstrate that the mechanism underlying the nuclear localization of GAREM1 depends on its NLS in the CABIT domain, which is controlled by the binding of 14-3-3 and the C-terminal SAM domain. We suggest that the interplay between 14-3-3, SAM domain and CABIT domain might be responsible for the distribution of GAREM1 in mammalian cells. - Highlights: • 14-3-3ε regulated the nuclear localization of GAREM1 as its binding partner. • The atypical 14-3-3 binding site of GAREM1 is located near the NLS in CABIT domain. • The CABIT domain had intramolecular association with the SAM domain in GAREM1. • Subcellular localization of GAREM1 is affected with its CABIT-SAM interaction.« less

A comprehensive study of extended tetrathiafulvalene cruciform molecules for molecular electronics: synthesis and electrical transport measurements.

PubMed

Parker, Christian R; Leary, Edmund; Frisenda, Riccardo; Wei, Zhongming; Jennum, Karsten S; Glibstrup, Emil; Abrahamsen, Peter Bæch; Santella, Marco; Christensen, Mikkel A; Della Pia, Eduardo Antonio; Li, Tao; Gonzalez, Maria Teresa; Jiang, Xingbin; Morsing, Thorbjørn J; Rubio-Bollinger, Gabino; Laursen, Bo W; Nørgaard, Kasper; van der Zant, Herre; Agrait, Nicolas; Nielsen, Mogens Brøndsted

2014-11-26

Cruciform-like molecules with two orthogonally placed π-conjugated systems have in recent years attracted significant interest for their potential use as molecular wires in molecular electronics. Here we present synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene) (OPE) and tetrathiafulvalene (TTF) scaffolds, end-capped with acetyl-protected thiolates as electrode anchoring groups. The molecules were subjected to a comprehensive study of their conducting properties as well as their photophysical and electrochemical properties in solution. The complex nature of the molecules and their possible binding in different configurations in junctions called for different techniques of conductance measurements: (1) conducting-probe atomic force microscopy (CP-AFM) measurements on self-assembled monolayers (SAMs), (2) mechanically controlled break-junction (MCBJ) measurements, and (3) scanning tunneling microscopy break-junction (STM-BJ) measurements. The CP-AFM measurements showed structure-property relationships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increased with the number of dithiafulvene (DTF) units (0, 1, 2) along the wire, and it increased when substituting two arylethynyl end groups of the OPE3 backbone with two DTF units. The MCBJ and STM-BJ studies on single molecules both showed that DTFs decreased the junction formation probability, but, in contrast, no significant influence on the single-molecule conductance was observed. We suggest that the origins of the difference between SAM and single-molecule measurements lie in the nature of the molecule-electrode interface as well as in effects arising from molecular packing in the SAMs. This comprehensive study shows that for complex molecules care should be taken when directly comparing single-molecule measurements and measurements of SAMs and solid-state devices thereof.

The SAM Suite

NASA Image and Video Library

2013-04-08

This illustration shows the instruments and subsystems of the Sample Analysis at Mars SAM suite on the Curiosity Rover of NASA Mars Science Laboratory Project. SAM analyzes the gases in the Martian atmosphere.

Common themes and differences in SAM recognition among SAM riboswitches.

PubMed

Price, Ian R; Grigg, Jason C; Ke, Ailong

2014-10-01

The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-l-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. This article is part of a Special Issue entitled: Riboswitches. Copyright © 2014 Elsevier B.V. All rights reserved.

Evolved Gas Analyses of Sedimentary Materials in Gale Crater, Mars: Results of the Curiosity Rover's Sample Analysis at Mars (SAM) Instrument from Yellowknife Bay to the Stimson Formation

NASA Technical Reports Server (NTRS)

Sutter, B.; McAdam, A. C.; Rampe, E. B.; Ming, D. W.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Stern, J. C.; Eigenbrode, J. L.; Archer, P. D.

2016-01-01

The Sample Analysis at Mars (SAM) instrument aboard the Mars Science Laboratory rover has analyzed 10 samples from Gale Crater. All SAM evolved gas analyses have yielded a multitude of volatiles (e.g, H2O, SO2, H2S, CO2, CO, NO, O2, HC1). The objectives of this work are to 1) Characterize the evolved H2O, SO2, CO2, and O2 gas traces of sediments analyzed by SAM through sol 1178, 2) Constrain sediment mineralogy/composition based on SAM evolved gas analysis (SAM-EGA), and 3) Discuss the implications of these results releative to understanding the geochemical history of Gale Crater.

Better Organic Ternary Memory Performance through Self-Assembled Alkyltrichlorosilane Monolayers on Indium Tin Oxide (ITO) Surfaces.

PubMed

Hou, Xiang; Cheng, Xue-Feng; Zhou, Jin; He, Jing-Hui; Xu, Qing-Feng; Li, Hua; Li, Na-Jun; Chen, Dong-Yun; Lu, Jian-Mei

2017-11-16

Recently, surface engineering of the indium tin oxide (ITO) electrode of sandwich-like organic electric memory devices was found to effectively improve their memory performances. However, there are few methods to modify the ITO substrates. In this paper, we have successfully prepared alkyltrichlorosilane self-assembled monolayers (SAMs) on ITO substrates, and resistive random access memory devices are fabricated on these surfaces. Compared to the unmodified ITO substrates, organic molecules (i.e., 2-((4-butylphenyl)amino)-4-((4-butylphenyl)iminio)-3-oxocyclobut-1-en-1-olate, SA-Bu) grown on these SAM-modified ITO substrates have rougher surface morphologies but a smaller mosaicity. The organic layer on the SAM-modified ITO further aged to eliminate the crystalline phase diversity. In consequence, the ternary memory yields are effectively improved to approximately 40-47 %. Our results suggest that the insertion of alkyltrichlorosilane self-assembled monolayers could be an efficient method to improve the performance of organic memory devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding the effects of packing and chemical terminations on the optical excitations of azobenzene-functionalized self-assembled monolayers

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Draxl, Claudia

2017-10-01

In a first-principles study based on many-body perturbation theory, we analyze the optical excitations of azobenzene-functionalized self-assembled monolayers (SAMs) with increasing packing density and different terminations, considering for comparison the corresponding gas-phase molecules and dimers. Intermolecular coupling increases with the density of the chromophores independently of the functional groups. The intense π → π* resonance that triggers photo-isomerization is present in the spectra of isolated dimers and diluted SAMs, but it is almost completely washed out in tightly packed architectures. Intermolecular coupling is partially inhibited by mixing differently functionalized azobenzene derivatives, in particular when large groups are involved. In this way, the excitation band inducing the photo-isomerization process is partially preserved and the effects of dense packing partly counterbalanced. Our results suggest that a tailored design of azobenzene-functionalized SAMs which optimizes the interplay between the packing density of the chromophores and their termination can lead to significant improvements in the photo-switching efficiency of these systems.

Real-Time Observation of Atomic Layer Deposition Inhibition: Metal Oxide Growth on Self-Assembled Alkanethiols

DOE PAGES

Avila, Jason R.; DeMarco, Erica J.; Emery, Jonathan D.; ...

2014-07-21

Through in-situ quartz crystal microbalance (QCM) monitoring we resolve the growth of a self-assembled monolayer (SAM) and subsequent metal oxide deposition with high resolution. Here, we introduce the fitting of mass deposited during each atomic layer deposition (ALD) cycle to an analytical island-growth model that enables quantification of growth inhibition, nucleation density, and the uninhibited ALD growth rate. A long-chain alkanethiol was self-assembled as a monolayer on gold-coated quartz crystals in order to investigate its effectiveness as a barrier to ALD. Compared to solution-loading, vapor-loading is observed to produce a SAM with equal or greater inhibition-ability in minutes vs. days.more » The metal oxide growth temperature and the choice of precursor also significantly affect the nucleation density, which ranges from 0.001 to 1 sites/nm 2. Finally, we observe a minimum 100 cycle inhibition of an oxide ALD process, ZnO, under moderately optimized conditions.« less

Observing the On-going Formation of Planets and its Effects on Their Parent Discs

NASA Astrophysics Data System (ADS)

Willson, Matthew Alexander

2017-06-01

As the number of known exoplanetary systems has grown, it has become increasing apparent that our current understanding of planet formation is insufficient to explain the broad but distinct distributions of planets and planetary systems we observe. In particular, constructing a coherent model of planetary formation and migration within a circumstellar disc which is capable of producing both hot Jupiters or Solar System-like planetary system is high challenging. Resolved observations of where planets form and how they influence their parent discs provides essential information for tackling this important question. A promising technique for detecting close-in companions is Sparse Aperture Masking (SAM). The technique uses a mask to transform a single aperture telescope into a compact interferometric array capable of reliably detecting point sources at the diffraction limit or closer to a bright star with superior contrasts than extreme AO systems at the cost of smaller fields of view. Applying image reconstruction techniques to the interferometric information allows an observer to recover detailed structure in the circumstellar material. In this thesis I present work on the interpretation of SAM interferometry data on protoplanetary discs through the simulation of a number of scenarios expected to be commonly seen, and the application of this technique to a number of objects. Analysing data taken as part of a SAM survey of transitional and pre-transitional discs using the Keck-II/NIRC2 instrument, I detected three companion candidates within the discs of DM Tau, LkHα 330, and TW Hya, and resolved a gap in the disc around FP Tau as indicated by flux from the disc rim. The location of all three of the companions detected as part of the survey are positioned in interesting regions of their parent discs. The candidate, LkHα 330 b is a potentially cavity opening companion due to its close radial proximity to the inner rim of the outer disc. DM Tau b is located immediately outside of a ring of dusty material largely responsible for the NIR comment of the disc SED, similar to TW Hya b located in a shallow gap in the dust disc outside another ring of over-dense dusty material which bounds a deep but narrow gap. Both of these companion candidates maybe migrating cores which are feeding from the enriched ring of material. I conducted a more extensive study of the pre-transitional disc, V1247 Ori, covering three epochs and the H-, K- and L-wavebands. Complementary observations with VLT/SPHERE in Hα and continuum plus SMA observations in CO (2-1) and continuum were performed. The orientation and geometry of the outer disc was recovered with the SMA data and determine the direction of rotation. We image the inner rim of the outer disc in L-band SAM data, recovering the rim in all three epochs. Combining all three data sets together we form a detailed image of the rim. In H- and K-band SAM data we observe the motion of a close-in companion candidate. This motion was found to be too large to be adequately explained through a near-circular Keplerian orbit within the plane of the disc around the central star. Hence an alternate hypothesis had to be developed. I postulated that the fitted position of the companion maybe influenced by the emission from the disc rim seen in the L-band SAM data. I constructed a suite of model SAM data sets of a companion and a disc rim and found that under the right conditions the fitted separation of a companion will be larger than the true separation. Under these conditions we find the motion of the companion candidate to be consistent with a near-circular Keplerian orbit within the plane of the disc at a semi-major axis of ˜6 au. The Hα data lack the necessary resolution to confirm the companion as an accreting body, but through the high contrast sensitivities enabled by the state of the art SPHERE instrument I was able to rule out any other accreting body within the gap, unless deeply embedded by the sparse population of MIR emitting dust grains previously inferred to reside within the gap. Through the combination of SAM and SMA data we constrain the 3-D orientation of the disc, and through multi-wavelength SAM observation identify a close-in companion potentially responsible for the gap clearing and asymmetric arm structures seen in previous observations of this target. During my PhD I have contributed to the field of planet formation through the identification of four new candidate protoplanets observed in the discs of pre-main sequence stars. To do so I have quantified the confidence levels of companion fits to SAM data sets and formed synthetic data from models of asymmetric structures seen in these discs. I have described for the first time the effects of extended sources of emission on the fitted results of companion searches within interferometric data sets. I have combined SAM data sets from two separate telescopes with different apertures and masks to produce reconstructed image of an illuminated disc rim with superior uv-cover! age. I have used the expertise I have developed in this field to contribute to a number of other studies, including the study of the young star TYC 8241 2652 1, resulting in the rejection of a sub-stellar companion as the cause of the rapid dispersal of the star`s disc. The companion candidates I have identified here should be followed up to confirm their presence and nature as accreting protoplanets. Objects such as these will provide the opportunity for more detailed study of the process of planet formation in the near future with the next generation of instruments in the JWST and E-ELT.

Effect of the presence of chlorates and perchlorates on the pyrolysis of organic compounds: implications for measurements done with the SAM experiment onboard the Curiosity rover

NASA Astrophysics Data System (ADS)

Millan, Maeva; Szopa, Cyril; Buch, Arnaud; Belmahdi, Imène; Coll, Patrice; Glavin, Daniel P.; Freissinet, Caroline; Archer, Doug; Sutter, Brad; Summons, Roger E.; Navarro-Gonzalez, Rafael; Cabane, Michel; Mahaffy, Paul

2016-04-01

The Sample Analysis at Mars (SAM) experiment onboard the Curiosity rover of the Mars Science Laboratory mission is partly devoted to the in situ molecular analysis of gases evolving from solid samples collected on Mars surface/sub-surface. SAM has a gas-chromatograph coupled to a quadrupole mass spectrometer (GC-QMS) devoted to the separation and identification of organic and inorganic material [1]. Before proceeding to the GC-QMS analysis, the solid sample collected by Curiosity is subjected to a thermal treatment thanks to the pyrolysis oven to release the volatiles into the gas processing system. As the Viking landers in 1976 [2], SAM detected chlorohydrocarbons with the pyrolysis GC-QMS experiment [3,4]. The detection of perchlorates salts in soil at the Phoenix Landing site [6] suggests that these chlorohydrocarbons could come from the reaction of organics with oxychlorines. Oxychlorines indeed decomposed into molecular oxygen and volatile chlorine when heated and react with the organic matter in the samples by oxidation and/or chlorination processes. [3,5,7,8]. During SAM pyrolysis, samples are heated to 850°C. SAM detected C1 to C3 chloroalkanes, entirely attributed to reaction products occurring during the pyrolysis experiment between oxychlorines and organic carbon from instrument background [3] and chlorobenzene and C2 to C4 dichloroalkanes produced by reaction between Mars endogenous organics with oxychlorines [4]. To help understanding the influence of perchlorate and chlorate salts on organic matter during SAM pyrolysis, we systemically study the reaction products formed during pyrolysis of various organic compounds mixed with various perchlorates and chlorates. We selected organics from simple molecule forms as for instance PAHs and amino acids to complex material (>30 carbon atoms) such as kerogen. The perchlorate and chlorate salts are prepared at 1 wt % concentration in silica and mixed with the organics to study the potential qualitative and/or quantitative effects. The experiments are performed on a laboratory GC-QMS with a Restek Rxi-5 column (30m x 0.25mm x 0.25μm) and an Intersciences pyrolyser. The mixture is pyrolyzed at different temperatures up to 900°C to cover the SAM temperature range. Different experiments are done to discriminate the pyrolysis products directly coming from the organics, and those produced from the reaction with oxychlorine. These experiments are under progress and should bring key information on the potential to identify Martian organics when pyrolyzing solid samples. Depending on the organic families studied, we may find recurring molecules, which are potentially present in Mars' surface samples. This work could thus highlight some organic precursors of the chlorinated compounds found on Mars, and support the interpretation of SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Biemann, K. et al (1977) JGR, 82, 4641-4658. [3] Glavin, D. et al. (2013), JGR 118, 1955-1973. [4] Freissinet, C. et al. (2015) JGR. [5] Leshin L. et al. (2013), Science. [6] Hecht, (2009), Science, 325 64-67. [7] Navarro-Gonzalez et al. (2010) JGR 115, EI12010. [8] Steninger, H. et al (2012) Planet. Space Sci. 71, 9-17. Acknowledgments: French Space Agency (CNES) support for SAM-GC development and exploitation.

The nature of massive transition galaxies in CANDELS, GAMA and cosmological simulations

NASA Astrophysics Data System (ADS)

Pandya, Viraj; Brennan, Ryan; Somerville, Rachel S.; Choi, Ena; Barro, Guillermo; Wuyts, Stijn; Taylor, Edward N.; Behroozi, Peter; Kirkpatrick, Allison; Faber, Sandra M.; Primack, Joel; Koo, David C.; McIntosh, Daniel H.; Kocevski, Dale; Bell, Eric F.; Dekel, Avishai; Fang, Jerome J.; Ferguson, Henry C.; Grogin, Norman; Koekemoer, Anton M.; Lu, Yu; Mantha, Kameswara; Mobasher, Bahram; Newman, Jeffrey; Pacifici, Camilla; Papovich, Casey; van der Wel, Arjen; Yesuf, Hassen M.

2017-12-01

We explore observational and theoretical constraints on how galaxies might transition between the 'star-forming main sequence' (SFMS) and varying 'degrees of quiescence' out to z = 3. Our analysis is focused on galaxies with stellar mass M* > 1010 M⊙, and is enabled by GAMA and CANDELS observations, a semi-analytic model (SAM) of galaxy formation, and a cosmological hydrodynamical 'zoom in' simulation with momentum-driven AGN feedback. In both the observations and the SAM, transition galaxies tend to have intermediate Sérsic indices, half-light radii, and surface stellar mass densities compared to star-forming and quiescent galaxies out to z = 3. We place an observational upper limit on the average population transition time-scale as a function of redshift, finding that the average high-redshift galaxy is on a 'fast track' for quenching whereas the average low-redshift galaxy is on a 'slow track' for quenching. We qualitatively identify four physical origin scenarios for transition galaxies in the SAM: oscillations on the SFMS, slow quenching, fast quenching, and rejuvenation. Quenching time-scales in both the SAM and the hydrodynamical simulation are not fast enough to reproduce the quiescent population that we observe at z ∼ 3. In the SAM, we do not find a clear-cut morphological dependence of quenching time-scales, but we do predict that the mean stellar ages, cold gas fractions, SMBH (supermassive black hole) masses and halo masses of transition galaxies tend to be intermediate relative to those of star-forming and quiescent galaxies at z < 3.

The influence of mesoscale porosity on cortical bone anisotropy. Investigations via asymptotic homogenization

PubMed Central

Parnell, William J; Grimal, Quentin

2008-01-01

Recently, the mesoscale of cortical bone has been given particular attention in association with novel experimental techniques such as nanoindentation, micro-computed X-ray tomography and quantitative scanning acoustic microscopy (SAM). A need has emerged for reliable mathematical models to interpret the related microscopic and mesoscopic data in terms of effective elastic properties. In this work, a new model of cortical bone elasticity is developed and used to assess the influence of mesoscale porosity on the induced anisotropy of the material. Only the largest pores (Haversian canals and resorption cavities), characteristic of the mesoscale, are considered. The input parameters of the model are derived from typical mesoscale experimental data (e.g. SAM data). We use the method of asymptotic homogenization to determine the local effective elastic properties by modelling the propagation of low-frequency elastic waves through an idealized material that models the local mesostructure. We use a novel solution of the cell problem developed by Parnell & Abrahams. This solution is stable for the physiological range of variation of mesoscopic porosity and elasticity found in bone. Results are computed efficiently (in seconds) and the solutions can be implemented easily by other workers. Parametric studies are performed in order to assess the influence of mesoscopic porosity, the assumptions regarding the material inside the mesoscale pores (drained or undrained bone) and the shape of pores. Results are shown to be in good qualitative agreement with existing schemes and we describe the potential of the scheme for future use in modelling more complex microstructures for cortical bone. In particular, the scheme is shown to be a useful tool with which to predict the qualitative changes in anisotropy due to variations in the structure at the mesoscale. PMID:18628200

Low vitamin D does not predict statin associated muscle symptoms but is associated with transient increases in muscle damage and pain.

PubMed

Taylor, Beth A; Lorson, Lindsay; White, C Michael; Thompson, Paul D

2017-01-01

Low vitamin D (VITD) may contribute to statin-associated muscle symptoms (SAMS). We examined the influence of baseline and change in VITD in patients with verified SAMS. SAMS was verified in 120 patients with prior statin muscle complaints using 8-week randomized, double-blind crossover trials of simvastatin (SIMVA) 20 mg/d and placebo. 25 (OH)vitamin D was measured at each phase of the trial. Forty-three patients (35.8%) experienced muscle pain on SIMVA but not placebo, exhibiting confirmed SAMS. VITD (mean ± standard deviation) prior to SIMVA treatment was not different between patients who did (31.7 ± 12.1 ng/mL, n = 43) or did not (31.6 ± 10.3 ng/mL, n = 77) develop SAMS and did not predict SAMS (p = 0.96). The change in VITD with SIMVA treatment was not different between patients with and without SAMS (0.3 ± 5.9 vs. 0.2 ± 8.3 ng/mL, respectively) and did not predict SAMS (p = 0.96). The proportion of patients classified as VITD deficient (<20 ng/mL) did not differ between patients with (n = 16) and without (n = 10) SAMS (χ 2  = 1.45; p = 0.23), nor did the proportion of patients classified as VITD insufficient (<30 ng/mL) (n = 42 vs. 48; χ 2  < 0.01 and p = 0.94). Both baseline and on-statin VITD were inversely related to the change in creatine kinase (CK) with statin therapy (p = 0.01 and 0.02, respectively), independent of SAMS (p = 0.36 and 0.35). Baseline VITD, VITD deficiency/insufficiency and changes in VITD with statin therapy do not predict SAMS in patients with rigorously verified SAMS. However, low VITD may exacerbate statin-induced muscle injury and could contribute to SAMS development with a longer duration of statin treatment. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Amplitude-dependent relationship between the Southern Annular Mode and the El Niño Southern Oscillation in austral summer

NASA Astrophysics Data System (ADS)

Kim, Baek-Min; Choi, Hyesun; Kim, Seong-Joong; Choi, Wookap

2017-02-01

Co-variability between the Southern Annular Mode (SAM) and the El Niño Southern Oscillation (ENSO) during the austral summer is examined, and it is found that there exists an apparent co-variability of a negative (positive) SAM during the mature period of El Niño (La Niña). However, this co-variability is largely controlled by the small number of strong ENSO cases. When strong ENSO cases are excluded, the correlation becomes non-significant. This behavior in the relationship between SAM and ENSO is supported by a series of general circulation model experiments with prescribed sea surface temperature boundary conditions that represent the incremental strengthening of El Niño (La Niña) conditions. The modeled Antarctic sub-polar jet exhibits similar behavior to that identified through observational analysis. Marked changes in both the magnitude and position of the sub-polar jet are largely controlled by particularly strong transient eddy forcing. Planetary wave forcing plays only a minor role in the co-variability, but it can explain in part the asymmetric response of the sub-polar jet between El Niño and La Niña.

Informing Mexico's Distributed Generation Policy with System Advisor Model (SAM) Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aznar, Alexandra Y; Zinaman, Owen R; McCall, James D

The Government of Mexico recognizes the potential for clean distributed generation (DG) to meaningfully contribute to Mexico's clean energy and emissions reduction goals. However, important questions remain about how to fairly value DG and foster inclusive and equitable market growth that is beneficial to investors, electricity ratepayers, electricity distributors, and society. The U.S. National Renewable Energy Laboratory (NREL) has partnered with power sector institutions and stakeholders in Mexico to provide timely analytical support and expertise to help inform policymaking processes on clean DG. This document describes two technical assistance interventions that used the System Advisor Model (SAM) to inform Mexico'smore » DG policymaking processes with a focus on rooftop solar regulation and policy.« less

Metabolism of a 5HT6 antagonist, 2-methyl-1-(phenylsulfonyl)-4-(piperazin-1-yl)-1H-benzo[d]imidazole (SAM-760): impact of sulfonamide metabolism on diminution of a ketoconazole mediated clinical drug-drug interaction.

PubMed

Sawant-Basak, Aarti; Obach, R Scott; Doran, Angela C; Lockwood, Peter; Schildknegt, Klaas; Gao, Hongying; Mancuso, Jessica; Tse, Susanna; Comery, Tom

2018-04-25

SAM-760, (2-methyl-1-(phenylsulfonyl)-4-(piperazin-1-yl)-1H-benzo[d]imidazole), a 5HT 6 antagonist, was investigated in humans for the treatment of Alzheimer's dementia. In liver microsomes and recombinant CYP450 isozymes, SAM-760 was predominantly metabolized by CYP3A (~85%). Based on these observations and an expectation of 5-fold magnitude of interaction with moderate to strong CYP3A inhibitors, a clinical DDI study was performed. In presence of ketoconazole, mean C max and AUC 0-inf of SAM-760 showed only a modest increase by 30% and 38%, respectively. In vitro investigation of this unexpectedly low interaction was undertaken using [ 14 C]SAM-760. Radiometric profiling in human hepatocytes, confirmed all oxidative metabolites observed previously with unlabeled SAM-760; however the pre-dominant radiometric peak was an unexpected polar metabolite which was insensitive to pan-CYP inhibitor, 1-aminobenzotriazole. In human hepatocytes, radiometric integration attributed 43% of total metabolism of SAM-760 to this non-CYP pathway. Using an authentic standard, this predominant metabolite was confirmed as benzenesulfinic acid. Additional investigation revealed that the benzenesulfinic acid metabolite may be a novel, non-enzymatic, thiol mediated reductive cleavage of aryl sulfonamide group of SAM-760. We also determined the relative contribution of P450 to metabolism of SAM-760 in human hepatocytes, by following the rate of formation of oxidative metabolites in presence and absence of P450 isoform specific inhibitors. P450 mediated oxidative metabolism of SAM-760 was still primarily attributed to CYP3A (33%), with minor contributions from CYP isoforms 2C19 and 2D6. Thus, disposition of [ 14 C]SAM-760 in human hepatocytes via novel sulfonamide metabolism and CYP3A verified the lower than expected clinical DDI when SAM-760 was co-administered with ketoconazole. The American Society for Pharmacology and Experimental Therapeutics.

Membrane protein resistance of oligo(ethylene oxide) self-assembled monolayers.

PubMed

Vaish, Amit; Vanderah, David J; Vierling, Ryan; Crawshaw, Fay; Gallagher, D Travis; Walker, Marlon L

2014-10-01

As part of an effort to develop biointerfaces for structure-function studies of integral membrane proteins (IMPs) a series of oligo(ethylene oxide) self-assembled monolayers (OEO-SAMs) were evaluated for their resistance to protein adsorption (RPA) of IMPs on Au and Pt. Spectroscopic ellipsometry (SE) was used to determine SAM thicknesses and compare the RPA of HS(CH2)3O(CH2CH2O)6CH3 (1), HS(CH2)3O(CH2CH2O)6H (2), [HS(CH2)3]2CHO(CH2CH2O)6CH3 (3) and [HS(CH2)3]2CHO(CH2CH2O)6H (4), assembled from water. For both substrates, SAM thicknesses for 1 to 4 were found to be comparable indicating SAMs with similar surface coverages and OEO chain order and packing densities. Fibrinogen (Fb), a soluble plasma protein, and rhodopsin (Rd), an integral membrane G-protein coupled receptor, adsorbed to the SAMs of 1, as expected from previous reports, but not to the hydroxy-terminated SAMs of 2 and 4. The methoxy-terminated SAMs of 3 were resistant to Fb but, surprisingly, not to Rd. The stark difference between the adsorption of Rd to the SAMs of 3 and 4 clearly indicate that a hydroxy-terminus of the OEO chain is essential for high RPA of IMPs. The similar thicknesses and high RPA of the SAMs of 2 and 4 show the conditions of protein resistance (screening the underlying substrate, packing densities, SAM order, and conformational mobility of the OEO chains) defined from previous studies on Au are applicable to Pt. In addition, the SAMs of 4, exhibiting the highest resistance to Fb and Rd, were placed in contact with undiluted fetal bovine serum for 2h. Low protein adsorption (≈12.4ng/cm(2)), obtained under these more challenging conditions, denote a high potential of the SAMs of 4 for various applications requiring the suppression of non-specific protein adsorption. Published by Elsevier B.V.

The word-frequency paradox for recall/recognition occurs for pictures.

PubMed

Karlsen, Paul Johan; Snodgrass, Joan Gay

2004-08-01

A yes-no recognition task and two recall tasks were conducted using pictures of high and low familiarity ratings. Picture familiarity had analogous effects to word frequency, and replicated the word-frequency paradox in recall and recognition. Low-familiarity pictures were more recognizable than high-familiarity pictures, pure lists of high-familiarity pictures were more recallable than pure lists of low-familiarity pictures, and there was no effect of familiarity for mixed lists. These results are consistent with the predictions of the Search of Associative Memory (SAM) model.

Mechanism for Prevention of Alcohol-Induced Liver Injury by Dietary Methyl Donors

PubMed Central

Powell, Christine L.; Bradford, Blair U.; Craig, Christopher Patrick; Tsuchiya, Masato; Uehara, Takeki; O’Connell, Thomas M.; Pogribny, Igor P.; Melnyk, Stepan; Koop, Dennis R.; Bleyle, Lisa; Threadgill, David W.; Rusyn, Ivan

2010-01-01

Alcohol-induced liver injury (ALI) has been associated with, among other molecular changes, abnormal hepatic methionine metabolism, resulting in decreased levels of S-adenosylmethionine (SAM). Dietary methyl donor supplements such as SAM and betaine mitigate ALI in animal models; however, the mechanisms of protection remain elusive. It has been suggested that methyl donors may act via attenuation of alcohol-induced oxidative stress. We hypothesized that the protective action of methyl donors is mediated by an effect on the oxidative metabolism of alcohol in the liver. Male C57BL/6J mice were administered a control high-fat diet or diet enriched in methyl donors with or without alcohol for 4 weeks using the enteral alcohol feeding model. As expected, attenuation of ALI and an increase in reduced glutathione:oxidized glutathione ratio were achieved with methyl donor supplementation. Interestingly, methyl donors led to a 35% increase in blood alcohol elimination rate, and while there was no effect on alcohol metabolism in the stomach, a profound effect on liver alcohol metabolism was observed. The catalase-dependent pathway of alcohol metabolism was induced, yet the increase in CYP2E1 activity by alcohol was blunted, which may be mitigating production of oxidants. Additional factors contributing to the protective effects of methyl donors in ALI were increased activity of low- and high-Km aldehyde dehydrogenases leading to lower hepatic acetaldehyde, maintenance of the efficient mitochondrial energy metabolism, and promotion of peroxisomal β-oxidation. Profound changes in alcohol metabolism represent additional important mechanism of the protective effect of methyl donors in ALI. PMID:20118189